Concerted actions of DnaA complexes with DNA-unwinding sequences within and flanking replication origin oriC promote DnaB helicase loading

Unwinding of the replication origin and loading of DNA helicases underlie the initiation of chromosomal replication. In Escherichia coli, the minimal origin oriC contains a duplex unwinding element (DUE) region and three (Left, Middle, and Right) regions that bind the initiator protein DnaA. The Left/Right regions bear a set of DnaA-binding sequences, constituting the Left/Right-DnaA subcomplexes, while the Middle region has a single DnaA-binding site, which stimulates formation of the Left/Right-DnaA subcomplexes. In addition, a DUE-flanking AT-cluster element (TATTAAAAAGAA) is located just outside of the minimal oriC region. The Left-DnaA subcomplex promotes unwinding of the flanking DUE exposing TT[A/G]T(T) sequences that then bind to the Left-DnaA subcomplex, stabilizing the unwound state required for DnaB helicase loading. However, the role of the Right-DnaA subcomplex is largely unclear. Here, we show that DUE unwinding by both the Left/Right-DnaA subcomplexes, but not the Left-DnaA subcomplex only, was stimulated by a DUE-terminal subregion flanking the AT-cluster. Consistently, we found the Right-DnaA subcomplex–bound single-stranded DUE and AT-cluster regions. In addition, the Left/Right-DnaA subcomplexes bound DnaB helicase independently. For only the Left-DnaA subcomplex, we show the AT-cluster was crucial for DnaB loading. The role of unwound DNA binding of the Right-DnaA subcomplex was further supported by in vivo data. Taken together, we propose a model in which the Right-DnaA subcomplex dynamically interacts with the unwound DUE, assisting in DUE unwinding and efficient loading of DnaB helicases, while in the absence of the Right-DnaA subcomplex, the AT-cluster assists in those processes, supporting robustness of replication initiation.

The initiation of bacterial DNA replication requires local duplex unwinding of the chromosomal replication origin oriC, which is regulated by highly ordered initiation complexes. In Escherichia coli, the initiation complex contains oriC, the ATP-bound form of the DnaA initiator protein (ATP–DnaA), and the DNA-bending protein IHF (Fig. 1, A and B), which promotes local unwinding of oriC (1, 2, 3, 4). Upon this oriC unwinding, two hexamers of DnaB helicases are bidirectionally loaded onto the resultant single-stranded (ss) region with the help of the DnaC helicase loader (Fig. 1B), leading to bidirectional chromosomal replication (5, 6, 7, 8). However, the fundamental mechanism underlying oriC-dependent bidirectional DnaB loading remains elusive.Open in a separate windowFigure 1Schematic structures of oriC, DnaA, and the initiation complexes. A, the overall structure of oriC. The minimal oriC region and the AT-cluster region are indicated. The sequence of the AT-cluster−DUE (duplex-unwinding element) region is also shown below. The DUE region (DUE; pale orange bars) contains three 13-mer repeats: L-DUE, M-DUE, and R-DUE. DnaA-binding motifs in M/R-DUE, TT(A/G)T(T), are indicated by red characters. The AT-cluster region (AT cluster; brown bars) is flanked by DUE outside of the minimal oriC. The DnaA-oligomerization region (DOR) consists of three subregions called Left-, Middle-, and Right-DOR. B, model for replication initiation. DnaA is shown as light brown (for domain I–III) and darkbrown (for domain IV) polygons (right panel). ATP–DnaA forms head-to-tail oligomers on the Left- and Right-DORs (left panel). The Middle-DOR (R2 box)-bound DnaA interacts with DnaA bound to the Left/Right-DORs using domain I, but not domain III, stimulating DnaA assembly. IHF, shown as purple hexagons, bends DNA >160° and supports DUE unwinding by the DnaA complexes. M/R-DUE regions are efficiently unwound. Unwound DUE is recruited to the Left-DnaA subcomplex and mainly binds to R1/R5M-bound DnaA molecules. The sites of ssDUE-binding B/H-motifs V211 and R245 of R1/R5M-bound DnaA molecules are indicated (pink). Two DnaB homohexamer helicases (light green) are recruited and loaded onto the ssDUE regions with the help of the DnaC helicase loader (cyan). ss, single stranded.The minimal oriC region consists of the duplex unwinding element (DUE) and the DnaA oligomerization region (DOR), which contains specific arrays of 9-mer DnaA-binding sites (DnaA boxes) with the consensus sequence TTA[T/A]NCACA (Fig. 1A) (3, 4). The DUE underlies the local unwinding and contains 13-mer AT-rich sequence repeats named L-, M-, and R-DUE (9). The M/R-DUE region includes TT[A/G]T(A) sequences with specific affinity for DnaA (10). In addition, a DUE-flanking AT-cluster (TATTAAAAAGAA) region resides just outside of the minimal oriC (Fig. 1A) (11). The DOR is divided into three subregions, the Left-, Middle-, and Right-DORs, where DnaA forms structurally distinct subcomplexes (Fig. 1A) (8, 12, 13, 14, 15, 16, 17). The Left-DOR contains high-affinity DnaA box R1, low-affinity boxes R5M, τ1−2, and I1-2, and an IHF-binding region (17, 18, 19, 20). The τ1 and IHF-binding regions partly overlap (17).In the presence of IHF, ATP–DnaA molecules cooperatively bind to R1, R5M, τ2, and I1-2 boxes in the Left-DOR, generating the Left-DnaA subcomplex (Fig. 1B) (8, 17). Along with IHF causing sharp DNA bending, the Left-DnaA subcomplex plays a leading role in DUE unwinding and subsequent DnaB loading. The Middle-DOR contains moderate-affinity DnaA box R2. Binding of DnaA to this box stimulates DnaA assembly in the Left- and Right-DORs using interaction by DnaA N-terminal domain (Fig. 1B; also see below) (8, 12, 14, 16, 21). The Right-DOR contains five boxes (C3-R4 boxes) and cooperative binding of ATP–DnaA molecules to these generates the Right-DnaA subcomplex (Fig. 1B) (12, 18). This subcomplex is not essential for DUE unwinding and plays a supportive role in DnaB loading (8, 15, 17). The Left-DnaA subcomplex interacts with DnaB helicase, and the Right-DnaA subcomplex has been suggested to play a similar role (Fig. 1B) (8, 13, 16).In the presence of ATP–DnaA, M- and R-DUE adjacent to the Left-DOR are predominant sites for in vitro DUE unwinding: unwinding of L-DUE is less efficient than unwinding of the other two (Fig. 1B) (9, 22, 23). Deletion of L-DUE or the whole DUE inhibits replication of oriC in vitro moderately or completely, respectively (23). A chromosomal oriC Δ(AT-cluster−L-DUE) mutant with an intact DOR, as well as deletion of Right-DOR, exhibits limited inhibition of replication initiation, whereas the synthetic mutant combining the two deletions exhibits severe inhibition of cell growth (24). These studies suggest that AT-cluster−L-DUE regions stimulate replication initiation in a manner concerted with Right-DOR, although the underlying mechanisms remain elusive.DnaA consists of four functional domains (Fig. 1B) (4, 25). Domain I supports weak domain I–domain I interaction and serves as a hub for interaction with various proteins such as DnaB helicase and DiaA, which stimulates ATP–DnaA assembly at oriC (26, 27, 28, 29, 30). Two or three domain I molecules of the oriC–DnaA subcomplex bind a single DnaB hexamer, forming a stable higher-order complex (7). Domain II is a flexible linker (28, 31). Domain III contains AAA+ (ATPase associated with various cellular activities) motifs essential for ATP/ADP binding, ATP hydrolysis, and DnaA–DnaA interactions in addition to specific sites for ssDUE binding and a second, weak interaction with DnaB helicase (1, 4, 8, 10, 19, 25, 32, 33, 34, 35). Domain IV bears a helix-turn-helix motif with specific affinity for the DnaA box (36).As in typical AAA+ proteins, a head-to-tail interaction underlies formation of ATP–DnaA pentamers on the DOR, where the AAA+ arginine-finger motif Arg285 recognizes ATP bound to the adjacent DnaA protomer, promoting cooperative ATP–DnaA binding (Fig. 1B) (19, 32). DnaA ssDUE-binding H/B-motifs (Val211 and Arg245) in domain III sustain stable unwinding by directly binding to the T-rich (upper) strand sequences TT[A/G]T(A) within the unwound M/R-DUE (Fig. 1B) (8, 10). Val211 residue is included in the initiator-specific motif of the AAA+ protein family (10). For DUE unwinding, ssDUE is recruited to the Left-DnaA subcomplex via DNA bending by IHF and directly interacts with H/B-motifs of DnaA assembled on Left-DOR, resulting in stable DUE unwinding competent for DnaB helicase loading; in particular, DnaA protomers bound to R1 and R5M boxes play a crucial role in the interaction with M/R-ssDUE (Fig. 1B) (8, 10, 17). Collectively, these mechanisms are termed ssDUE recruitment (4, 17, 37).Two DnaB helicases are thought to be loaded onto the upper and lower strands of the region including the AT-cluster and DUE, with the aid of interactions with DnaC and DnaA (Fig. 1B) (25, 38, 39). DnaC binding modulates the closed ring structure of DnaB hexamer into an open spiral form for entry of ssDNA (40, 41, 42, 43). Upon ssDUE loading of DnaB, DnaC is released from DnaB in a manner stimulated by interactions with ssDNA and DnaG primase (44, 45). Also, the Left- and Right-DnaA subcomplexes, which are oriented opposite to each other, could regulate bidirectional loading of DnaB helicases onto the ssDUE (Fig. 1B) (7, 8, 35). Similarly, recent works suggest that the origin complex structure is bidirectionally organized in both archaea and eukaryotes (1, 46). In Saccharomyces cerevisiae, two origin recognition complexes containing AAA+ proteins bind to the replication origin region in opposite orientations; this, in turn, results in efficient loading of two replicative helicases, leading to head-to-head interactions in vitro (46). Consistent with this, origin recognition complex dimerization occurs in the origin region during the late M-G1 phase (47). The fundamental mechanism of bidirectional origin complexes might be widely conserved among species.In this study, we analyzed various mutants of oriC and DnaA in reconstituted systems to reveal the regulatory mechanisms underlying DUE unwinding and DnaB loading. The Right-DnaA subcomplex assisted in the unwinding of oriC, dependent upon an interaction with L-DUE, which is important for efficient loading of DnaB helicases. The AT-cluster region adjacent to the DUE promoted loading of DnaB helicase in the absence of the Right-DnaA subcomplex. Consistently, the ssDNA-binding activity of the Right-DnaA subcomplex sustained timely initiation of growing cells. These results indicate that DUE unwinding and efficient loading of DnaB helicases are sustained by concerted actions of the Left- and Right-DnaA subcomplexes. In addition, loading of DnaB helicases are sustained by multiple mechanisms that ensure robust replication initiation, although the complete mechanisms are required for precise timing of initiation during the cell cycle.     

The tubulin code: Molecular components,readout mechanisms,and functions

Microtubules are cytoskeletal filaments that are dynamically assembled from α/β-tubulin heterodimers. The primary sequence and structure of the tubulin proteins and, consequently, the properties and architecture of microtubules are highly conserved in eukaryotes. Despite this conservation, tubulin is subject to heterogeneity that is generated in two ways: by the expression of different tubulin isotypes and by posttranslational modifications (PTMs). Identifying the mechanisms that generate and control tubulin heterogeneity and how this heterogeneity affects microtubule function are long-standing goals in the field. Recent work on tubulin PTMs has shed light on how these modifications could contribute to a “tubulin code” that coordinates the complex functions of microtubules in cells.

Introduction

Microtubules are key elements of the eukaryotic cytoskeleton that dynamically assemble from heterodimers of α- and β-tubulin. The structure of microtubules, as well as the protein sequences of α- and β-tubulin, is highly conserved in evolution, and consequently, microtubules look alike in almost all species. Despite the high level of conservation, microtubules adapt to a large variety of cellular functions. This adaptation can be mediated by a large panel of microtubule-associated proteins (MAPs), including molecular motors, as well as by mechanisms that directly modify the microtubules, thus either changing their biophysical properties or attracting subsets of MAPs that convey specific functions to the modified microtubules. Two different mechanism can generate microtubule diversity: the expression of different α- and β-tubulin genes, referred to as tubulin isotypes, and the generation of posttranslational modifications (PTMs) on α- and β-tubulin (Figs. 1 and ​and2).2). Although known for several decades, deciphering how tubulin heterogeneity controls microtubule functions is still largely unchartered. This review summarizes the current advances in the field and discusses new concepts arising.Open in a separate windowFigure 1.Tubulin heterogeneity generated by PTMs. (A) Schematic representation of the distribution of different PTMs of tubulin on the α/β-tubulin dimer with respect to their position in the microtubule lattice. Acetylation (Ac), phosphorylation (P), and polyamination (Am) are found within the tubulin bodies that assemble into the microtubule lattice, whereas polyglutamylation, polyglycylation, detyrosination, and C-terminal deglutamylation take place within the C-terminal tubulin tails that project away from the lattice surface. The tubulin dimer represents TubA1A and TubB2B (Fig. 2), and modification sites for polyglutamylation and polyglycylation have been randomly chosen. (B) Chemical structure of the branched peptide formed by polyglutamylation and polyglycylation, using the γ-carboxyl groups of the modified glutamate residues as acceptor sites for the isopeptide bonds. Note that in the case of polyglutamylation, the elongation of the side chains generates classical peptide bonds (Redeker et al., 1991).Open in a separate windowFigure 2.Heterogeneity of C-terminal tails of tubulin isotypes and their PTMs. The amino acid sequences of all tubulin genes found in the human genome are indicated, starting at the last amino acid of the folded tubulin bodies. Amino acids are represented in single-letter codes and color coded according to their biochemical properties. Known sites for polyglutamylation are indicated (Eddé et al., 1990; Alexander et al., 1991; Rüdiger et al., 1992). Potential modification sites (all glutamate residues) are indicated. Known C-terminal truncation reactions of α/β-tubulin (tub) are indicated. The C-terminal tails of the yeast Saccharomyces cerevisiae are shown to illustrate the phylogenetic diversity of these domains.

Tubulin isotypes

The cloning of the first tubulin genes in the late 1970’s (Cleveland et al., 1978) revealed the existence of multiple genes coding for α- or β-tubulin (Ludueña and Banerjee, 2008) that generate subtle differences in their amino acid sequences, particularly in the C-terminal tails (Fig. 2). It was assumed that tubulin isotypes, as they were named, assemble into discrete microtubule species that carry out unique functions. This conclusion was reinforced by the observation that some isotypes are specifically expressed in specialized cells and tissues and that isotype expression changes during development (Lewis et al., 1985; Denoulet et al., 1986). These high expectations were mitigated by a subsequent study showing that all tubulin isotypes freely copolymerize into heterogeneous microtubules (Lewis et al., 1987). To date, only highly specialized microtubules, such as ciliary axonemes (Renthal et al., 1993; Raff et al., 2008), neuronal microtubules (Denoulet et al., 1986; Joshi and Cleveland, 1989), and microtubules of the marginal band of platelets (Wang et al., 1986; Schwer et al., 2001) are known to depend on some specific (β) tubulin isotypes, whereas the function of most other microtubules appears to be independent of their isotype composition.More recently, a large number of mutations in single tubulin isotypes have been linked to deleterious neurodevelopmental disorders (Keays et al., 2007; Fallet-Bianco et al., 2008; Tischfield et al., 2010; Cederquist et al., 2012; Niwa et al., 2013). Mutations of a single tubulin isotype could lead to an imbalance in the levels of tubulins as a result of a lack of incorporation of mutant isoforms into the microtubule lattice or to incorporation that perturbs the architecture or dynamics of the microtubules. The analysis of tubulin disease mutations is starting to reveal how subtle alterations of the microtubule cytoskeleton can lead to functional aberrations in cells and organisms and might provide novel insights into the roles of tubulin isotypes that have so far been considered redundant.

Tubulin PTMs

Tubulin is subject to a large range of PTMs (Fig. 1), from well-known ones, such as acetylation or phosphorylation, to others that have so far mostly been found on tubulin. Detyrosination/tyrosination, polyglutamylation, and polyglycylation, for instance, might have evolved to specifically regulate tubulin and microtubule functions, in particular in cilia and flagella, as their evolution is closely linked to these organelles. The strong link between those modifications and tubulin evolution has led to the perception that they are tubulin PTMs; however, apart from detyrosination/tyrosination, most of them have other substrates (Regnard et al., 2000; Xie et al., 2007; van Dijk et al., 2008; Rogowski et al., 2009).

Tubulin acetylation.

Tubulin acetylation was discovered on lysine 40 (K40; Fig. 1 A) of flagellar α-tubulin in Chlamydomonas reinhardtii (L’Hernault and Rosenbaum, 1985) and is generally enriched on stable microtubules in cells. Considering that K40 acetylation per se has no effect on the ultrastructure of microtubules (Howes et al., 2014), it is rather unlikely that it directly stabilizes microtubules. As a result of its localization at the inner face of microtubules (Soppina et al., 2012), K40 acetylation might rather affect the binding of microtubule inner proteins, a poorly characterized family of proteins (Nicastro et al., 2011; Linck et al., 2014). Functional experiments in cells have further suggested that K40 acetylation regulates intracellular transport by regulating the traffic of kinesin motors (Reed et al., 2006; Dompierre et al., 2007). These observations could so far not be confirmed by biophysical measurements in vitro (Walter et al., 2012; Kaul et al., 2014), suggesting that in cells, K40 acetylation might affect intracellular traffic by indirect mechanisms.Enzymes involved in K40 acetylation are HDAC6 (histone deacetylase family member 6; Hubbert et al., 2002) and Sirt2 (sirtuin type 2; North et al., 2003). Initial functional studies used overexpression, depletion, or chemical inhibition of these enzymes. These studies should be discussed with care, as both HDAC6 and Sirt2 deacetylate other substrates and have deacetylase-independent functions and chemical inhibition of HDAC6 is not entirely selective for this enzyme (Valenzuela-Fernández et al., 2008). In contrast, acetyl transferase α-Tat1 (or Mec-17; Akella et al., 2010; Shida et al., 2010) specifically acetylates α-tubulin K40 (Fig. 3), thus providing a more specific tool to investigate the functions of K40 acetylation. Knockout mice of α-Tat1 are completely void of K40-acetylated tubulin; however, they show only slight phenotypic aberrations, for instance, in their sperm flagellum (Kalebic et al., 2013). A more detailed analysis of α-Tat1 knockout mice demonstrated that absence of K40 acetylation leads to reduced contact inhibition in proliferating cells (Aguilar et al., 2014). In migrating cells, α-Tat1 is targeted to microtubules at the leading edge by clathrin-coated pits, resulting in locally restricted acetylation of those microtubules (Montagnac et al., 2013). A recent structural study of α-Tat1 demonstrated that the low catalytic rate of this enzyme, together with its localization inside the microtubules, caused acetylation to accumulate selectively in stable, long-lived microtubules (Szyk et al., 2014), thus explaining the link between this PTM and stable microtubules in cells. However, the direct cellular function of K40 acetylation on microtubules is still unclear.Open in a separate windowFigure 3.Enzymes involved in PTM of tubulin. Schematic representation of known enzymes (mammalian enzymes are shown) involved in the generation and removal of PTMs shown in Fig. 1. Note that some enzymes still remain unknown, and some modifications are irreversible. (*CCP5 preferentially removes branching points [Rogowski et al., 2010]; however, the enzyme can also hydrolyze linear glutamate chains [Berezniuk et al., 2013]).Recent discoveries have brought up the possibility that tubulin could be subject to multiple acetylation events. A whole-acetylome study identified >10 novel sites on α- and β-tubulin (Choudhary et al., 2009); however, none of these sites have been confirmed. Another acetylation event has been described at lysine 252 (K252) of β-tubulin. This modification is catalyzed by the acetyltransferase San (Fig. 3) and might regulate the assembly efficiency of microtubules as a result of its localization at the polymerization interface (Chu et al., 2011).

Tubulin detyrosination.

Most α-tubulin genes in different species encode a C-terminal tyrosine residue (Fig. 2; Valenzuela et al., 1981). This tyrosine can be enzymatically removed (Hallak et al., 1977) and religated (Fig. 3; Arce et al., 1975). Mapping of tyrosinated and detyrosinated microtubules in cells using specific antibodies (Gundersen et al., 1984; Geuens et al., 1986; Cambray-Deakin and Burgoyne, 1987a) revealed that subsets of interphase and mitotic spindle microtubules are detyrosinated (Gundersen and Bulinski, 1986). As detyrosination was mostly found on stable and long-lived microtubules, especially in neurons (Cambray-Deakin and Burgoyne, 1987b; Robson and Burgoyne, 1989; Brown et al., 1993), it was assumed that this modification promotes microtubule stability (Gundersen et al., 1987; Sherwin et al., 1987). Although a direct stabilization of the microtubule lattice was considered unlikely (Khawaja et al., 1988), it was found more recently that detyrosination protects cellular microtubules from the depolymerizing activity of kinesin-13–type motor proteins, such as KIF2 or MCAK, thus increasing their longevity (Peris et al., 2009; Sirajuddin et al., 2014).Besides kinesin-13 motors, plus end–tracking proteins with cytoskeleton-associated protein glycine-rich (CAP-Gly) domains, such as CLIP170 or p150/glued, specifically interact with tyrosinated microtubules (Peris et al., 2006; Bieling et al., 2008) via this domain (Honnappa et al., 2006). In contrast, kinesin-1 moves preferentially on detyrosinated microtubules tracks in cells (Liao and Gundersen, 1998; Kreitzer et al., 1999; Konishi and Setou, 2009). The effect of detyrosination on kinesin-1 motor behavior was recently measured in vitro, and a small but significant increase in the landing rate and processivity of the motor has been found (Kaul et al., 2014). Such subtle changes in the motor behavior could, in conjunction with other factors, such as regulatory MAPs associated with cargo transport complexes (Barlan et al., 2013), lead to a preferential use of detyrosinated microtubules by kinesin-1 in cells.Despite the early biochemical characterization of a detyrosinating activity, the carboxypeptidase catalyzing detyrosination of α-tubulin has yet to be identified (Hallak et al., 1977; Argaraña et al., 1978, 1980). In contrast, the reverse enzyme, tubulin tyrosine ligase (TTL; Fig. 3; Raybin and Flavin, 1975; Deanin and Gordon, 1976; Argaraña et al., 1980), has been purified (Schröder et al., 1985) and cloned (Ersfeld et al., 1993). TTL modifies nonpolymerized tubulin dimers exclusively. This selectivity is determined by the binding interface between the TTL and tubulin dimers (Szyk et al., 2011, 2013; Prota et al., 2013). In contrast, the so far unidentified detyrosinase acts preferentially on polymerized microtubules (Kumar and Flavin, 1981; Arce and Barra, 1983), thus modifying a select population of microtubules within cells (Gundersen et al., 1987).In most organisms, only one unique gene for TTL exists. Consequently, TTL knockout mice show a huge accumulation of detyrosinated and particularly Δ2-tubulin (see next section). TTL knockout mice die before birth (Erck et al., 2005) with major developmental defects in the nervous system that might be related to aberrant neuronal differentiation (Marcos et al., 2009). TTL is strictly tubulin specific (Prota et al., 2013), indicating that all observed defects in TTL knockout mice are directly related to the deregulation of the microtubule cytoskeleton.

Δ2-tubulin and further C-terminal modification.

A biochemical study of brain tubulin revealed that ∼35% of α-tubulin cannot be retyrosinated (Paturle et al., 1989) because of the lack of the penultimate C-terminal glutamate residue of the primary protein sequence (Fig. 2; Paturle-Lafanechère et al., 1991). This so-called Δ2-tubulin (for two C-terminal amino acids missing) cannot undergo retyrosination as a result of structural constraints within TTL (Prota et al., 2013) and thus is considered an irreversible PTM.Δ2-tubulin accumulates in long-lived microtubules of differentiated neurons, axonemes of cilia and flagella, and also in cellular microtubules that have been artificially stabilized, for instance, with taxol (Paturle-Lafanechère et al., 1994). The generation of Δ2-tubulin requires previous detyrosination of α-tubulin; thus, the levels of this PTM are indirectly regulated by the detyrosination/retyrosination cycle. This mechanistic link is particularly apparent in the TTL knockout mice, which show massive accumulation of Δ2-tubulin in all tested tissues (Erck et al., 2005). Loss of TTL and the subsequent increase of Δ2-tubulin levels were also linked to tumor growth and might contribute to the aggressiveness of the tumors by an as-yet-unknown mechanism (Lafanechère et al., 1998; Mialhe et al., 2001). To date, no specific biochemical role of Δ2-tubulin has been determined; thus, one possibility is that the modification simply locks tubulin in the detyrosinated state.The enzymes responsible for Δ2-tubulin generation are members of a family of cytosolic carboxypeptidases (CCPs; Fig. 3; Kalinina et al., 2007; Rodriguez de la Vega et al., 2007), and most of them also remove polyglutamylation from tubulin (see next section; Rogowski et al., 2010). These enzymes are also able to generate Δ3-tubulin (Fig. 1 A; Berezniuk et al., 2012), indicating that further degradation of the tubulin C-terminal tails are possible; however, the functional significance of this event is unknown.

Polyglutamylation.

Polyglutamylation is a PTM that occurs when secondary glutamate side chains are formed on γ-carboxyl groups of glutamate residues in a protein (Fig. 1, A and B). The modification was first discovered on α- and β-tubulin from the brain (Eddé et al., 1990; Alexander et al., 1991; Rüdiger et al., 1992; Mary et al., 1994) as well as on axonemal tubulin from different species (Mary et al., 1996, 1997); however, it is not restricted to tubulin (Regnard et al., 2000; van Dijk et al., 2008). Using a glutamylation-specific antibody, GT335 (Wolff et al., 1992), it was observed that tubulin glutamylation increases during neuronal differentiation (Audebert et al., 1993, 1994) and that axonemes of cilia and flagella (Fouquet et al., 1994), as well as centrioles of mammalian centrosomes (Bobinnec et al., 1998), are extensively glutamylated.Enzymes catalyzing polyglutamylation belong to the TTL-like (TTLL) family (Regnard et al., 2003; Janke et al., 2005). In mammals, nine glutamylases exist, each of them showing intrinsic preferences for modifying either α- or β-tubulin as well as for initiating or elongating glutamate chains (Fig. 3; van Dijk et al., 2007). Two of the six well-characterized TTLL glutamylases also modify nontubulin substrates (van Dijk et al., 2008).Knockout or depletion of glutamylating enzymes in different model organisms revealed an evolutionarily conserved role of glutamylation in cilia and flagella. In motile cilia, glutamylation regulates beating behavior (Janke et al., 2005; Pathak et al., 2007; Ikegami et al., 2010) via the regulation of flagellar dynein motors (Kubo et al., 2010; Suryavanshi et al., 2010). Despite the expression of multiple glutamylases in ciliated cells and tissues, depletion or knockout of single enzymes often lead to ciliary defects, particularly in motile cilia (Ikegami et al., 2010; Vogel et al., 2010; Bosch Grau et al., 2013; Lee et al., 2013), suggesting essential and nonredundant regulatory functions of these enzymes in cilia.Despite the enrichment of polyglutamylation in neuronal microtubules (Audebert et al., 1993, 1994), knockout of TTLL1, the major polyglutamylase in brain (Janke et al., 2005), did not show obvious neuronal defects in mice (Ikegami et al., 2010; Vogel et al., 2010). This suggests a tolerance of neuronal microtubules to variations in polyglutamylation.Deglutamylases, the enzymes that reverse polyglutamylation, were identified within a novel family of CCPs (Kimura et al., 2010; Rogowski et al., 2010). So far, three out of six mammalian CCPs have been shown to cleave C-terminal glutamate residues, thus catalyzing both the reversal of polyglutamylation and the removal of gene-encoded glutamates from the C termini of proteins (Fig. 3). The hydrolysis of gene-encoded glutamate residues is not restricted to tubulin, in which it generates Δ2- and Δ3-tubulin, but has also been reported for other proteins such as myosin light chain kinase (Rusconi et al., 1997; Rogowski et al., 2010). One enzyme of the CCP family, CCP5, preferentially removes branching points generated by glutamylation, thus allowing the complete reversal of the polyglutamylation modification (Kimura et al., 2010; Rogowski et al., 2010). However, CCP5 can also hydrolyze C-terminal glutamate residues from linear peptide chains similar to other members of the CCP family (Berezniuk et al., 2013).CCP1 is mutated in a well-established mouse model for neurodegeneration, the pcd (Purkinje cell degeneration) mouse (Mullen et al., 1976; Greer and Shepherd, 1982; Fernandez-Gonzalez et al., 2002). The absence of a key deglutamylase leads to strong hyperglutamylation in brain regions that undergo degeneration, such as the cerebellum and the olfactory bulb (Rogowski et al., 2010). When glutamylation levels were rebalanced by depletion or knockout of the major brain polyglutamylase TTLL1 (Rogowski et al., 2010; Berezniuk et al., 2012), Purkinje cells survived. Although the molecular mechanisms of hyperglutamylation-induced degeneration remain to be elucidated, perturbation of neuronal transport, as well as changes in the dynamics and stability of microtubules, is expected to be induced by hyperglutamylation. Increased polyglutamylation levels have been shown to affect kinesin-1–mediated transport in cultured neurons (Maas et al., 2009), and the turnover of microtubules can also be regulated by polyglutamylation via the activation of microtubule-severing enzymes such as spastin (Lacroix et al., 2010).Subtle differences in polyglutamylation can be seen on diverse microtubules in different cell types. The functions of these modifications remain to be studied; however, its wide distribution strengthens the idea that it could be involved in fine-tuning a range of microtubule functions.

Polyglycylation.

Tubulin polyglycylation or glycylation, like polyglutamylation, generates side chains of glycine residues within the C-terminal tails of α- and β-tubulin (Fig. 1, A and B). The modification sites of glycylation are considered to be principally the same as for glutamylation, and indeed, both PTMs have been shown to be interdependent in cells (Rogowski et al., 2009; Wloga et al., 2009). Initially discovered on Paramecium tetraurelia tubulin (Redeker et al., 1994), glycylation has been extensively studied using two antibodies, TAP952 and AXO49 (Bressac et al., 1995; Levilliers et al., 1995; Bré et al., 1996). In contrast to polyglutamylation, glycylation is restricted to cilia and flagella in most organisms analyzed so far.Glycylating enzymes are also members of the TTLL family, and homologues of these enzymes have so far been found in all organisms with proven glycylation of ciliary axonemes (Rogowski et al., 2009; Wloga et al., 2009). In mammals, initiating (TTLL3 and TTLL8) and elongating (TTLL10) glycylases work together to generate polyglycylation (Fig. 3). In contrast, the two TTLL3 orthologues from Drosophila melanogaster can both initiate and elongate glycine side chains (Rogowski et al., 2009).In mice, motile ependymal cilia in brain ventricles acquire monoglycylation upon maturation, whereas polyglycylation is observed only after several weeks (Bosch Grau et al., 2013). Sperm flagella, in contrast, acquire long glycine chains much faster, suggesting that the extent of polyglycylation could correlate with the length of the axonemes (Rogowski et al., 2009). Depletion of glycylases in mice (ependymal cilia; Bosch Grau et al., 2013), zebrafish (Wloga et al., 2009; Pathak et al., 2011), Tetrahymena thermophila (Wloga et al., 2009), and D. melanogaster (Rogowski et al., 2009) consistently led to ciliary disassembly or severe ciliary defects. How glycylation regulates microtubule functions remains unknown; however, the observation that glycylation-depleted axonemes disassemble after initial assembly (Rogowski et al., 2009; Bosch Grau et al., 2013) suggests a role of this PTM in stabilizing axonemal microtubules. Strikingly, human TTLL10 is enzymatically inactive; thus, humans have lost the ability to elongate glycine side chains (Rogowski et al., 2009). This suggests that the elongation of the glycine side chains is not an essential aspect of the function of this otherwise critical tubulin PTM.

Other tubulin PTMs.

Several other PTMs have been found on tubulin. Early studies identified tubulin phosphorylation (Eipper, 1974; Gard and Kirschner, 1985; Díaz-Nido et al., 1990); however, no specific functions were found. The perhaps best-studied phosphorylation event on tubulin takes place at serine S172 of β-tubulin (Fig. 1 A), is catalyzed by the Cdk1 (Fig. 3), and might regulate microtubule dynamics during cell division (Fourest-Lieuvin et al., 2006; Caudron et al., 2010). Tubulin can be also modified by the spleen tyrosine kinase Syk (Fig. 3; Peters et al., 1996), which might play a role in immune cells (Faruki et al., 2000; Sulimenko et al., 2006) and cell division (Zyss et al., 2005; Sulimenko et al., 2006).Polyamination has recently been discovered on brain tubulin (Song et al., 2013), after having been overlooked for many years as a result of the low solubility of polyaminated tubulin. Among several glutamine residues of α- and β-tubulin that can be polyaminated, Q15 of β-tubulin is considered the primary modification site (Fig. 1 A). Polyamination is catalyzed by transglutaminases (Fig. 3), which modify free tubulin as well as microtubules in an irreversible manner, and most likely contribute to the stabilization of microtubules (Song et al., 2013).Tubulin was also reported to be palmitoylated (Caron, 1997; Ozols and Caron, 1997; Caron et al., 2001), ubiquitinated (Ren et al., 2003; Huang et al., 2009; Xu et al., 2010), glycosylated (Walgren et al., 2003; Ji et al., 2011), arginylated (Wong et al., 2007), methylated (Xiao et al., 2010), and sumoylated (Rosas-Acosta et al., 2005). These PTMs have mostly been reported without follow-up studies, and some of them are only found in specific cell types or organisms and/or under specific metabolic conditions. Further studies will be necessary to gain insights into their potential roles for the regulation of the microtubule cytoskeleton.

Current advances and future perspectives

The molecular heterogeneity of microtubules, generated by the expression of different tubulin isotypes and by the PTM of tubulin has fascinated the scientific community for ∼40 years. Although many important advances have been made in the past decade, the dissection of the molecular mechanisms and a comprehensive understanding of the biological functions of tubulin isotypes and PTMs will be a challenging field of research in the near future.

Direct measurements of the impact of tubulin heterogeneity.

The most direct and reliable type of experiments to determine the impact of tubulin heterogeneity on microtubule behavior are in vitro measurements with purified proteins. However, most biophysical work on microtubules has been performed with tubulin purified from bovine, ovine, or porcine brains, which can be obtained in large quantities and with a high degree of purity and activity (Vallee, 1986; Castoldi and Popov, 2003). Brain tubulin is a mixture of different tubulin isotypes and is heavily posttranslationally modified and thus inept for investigating the functions of tubulin heterogeneity (Denoulet et al., 1986; Cambray-Deakin and Burgoyne, 1987b; Paturle et al., 1989; Eddé et al., 1990). Thus, pure, recombinant tubulin will be essential to dissect the roles of different tubulin isoforms and PTMs.Attempts to produce recombinant, functional α- and β-tubulin in bacteria have failed so far (Yaffe et al., 1988), most likely because of the absence of the extensive tubulin-specific folding machinery (Yaffe et al., 1992; Gao et al., 1993; Tian et al., 1996; Vainberg et al., 1998) in prokaryotes. An alternative source of tubulin with less isotype heterogeneity and with almost no PTMs is endogenous tubulin from cell lines such as HeLa, which in the past has been purified using a range of biochemical procedures (Bulinski and Borisy, 1979; Weatherbee et al., 1980; Farrell, 1982; Newton et al., 2002; Fourest-Lieuvin, 2006). Such tubulin can be further modified with tubulin-modifying enzymes, such as polyglutamylases, either by expressing those enzymes in the cells before tubulin purification (Lacroix and Janke, 2011) or in vitro with purified enzymes (Vemu et al., 2014). Despite some technical limitations of these methods, HeLa tubulin modified in cells has been successfully used in an in vitro study on the role of polyglutamylation in microtubule severing (Lacroix et al., 2010).Naturally occurring variants of tubulin isotypes and PTMs can be purified from different organisms, organs, or cell types, but obviously, only some combinations of tubulin isotypes and PTMs can be obtained by this approach. The recent development of an affinity purification method using the microtubule-binding TOG (tumor overexpressed gene) domain of yeast Stu2p has brought a new twist to this approach, as it allows purifying small amounts of tubulin from any cell type or tissue (Widlund et al., 2012).The absence of tubulin heterogeneity in yeast has made budding and fission yeast potential expression systems for recombinant, PTM-free tubulin (Katsuki et al., 2009; Drummond et al., 2011; Johnson et al., 2011). However, the expression of mammalian tubulin in this system has remained impossible. This problem was then partially circumvented by expressing tubulin chimeras that consist of a yeast tubulin body fused to mammalian C-terminal tubulin tails, thus mimicking different tubulin isotypes (Sirajuddin et al., 2014). Moreover, detyrosination can be generated by deleting the key C-terminal residue from endogenous or chimeric α-tubulin (Badin-Larçon et al., 2004), and polyglutamylation is generated by chemically coupling glutamate side chains to specifically engineered tubulin chimeras (Sirajuddin et al., 2014). These approaches allowed the first direct measurements of the impact of tubulin isotypes and PTMs on the behavior of molecular motors in vitro (Sirajuddin et al., 2014) and the analysis of the effects of tubulin heterogeneity on microtubule behavior and interactions inside the yeast cell (Badin-Larçon et al., 2004; Aiken et al., 2014).Currently, the most promising development has been the successful purification of fully functional recombinant tubulin from the baculovirus expression system (Minoura et al., 2013). Using this system, defined α/β-tubulin dimers can be obtained using two different epitope tags on α- and β-tubulin, respectively. Although these epitope tags are essential for separating recombinant from the endogenous tubulin, they could also affect tubulin assembly or microtubule–MAP interactions. Thus, future developments should focus on eliminating these tags.Current efforts have brought the possibility of producing recombinant tubulin into reach. Further improvement and standardization of these methods will certainly provide a breakthrough in understanding the mechanisms by which tubulin heterogeneity contributes to microtubule functions.

Complexity of tubulin—understanding the regulatory principles.

The diversity of tubulin genes (isotypes) and the complexity of tubulin PTMs have led to the proposal of the term “tubulin code” (Verhey and Gaertig, 2007; Wehenkel and Janke, 2014), in analogy to the previously coined histone code (Jenuwein and Allis, 2001). Tubulin molecules consist of a highly structured and thus evolutionarily conserved tubulin body and the unstructured and less conserved C-terminal tails (Nogales et al., 1998). As PTMs and sequence variations within the tubulin body are expected to affect the conserved tubulin fold and therefore the properties of the microtubule lattice, they are not likely to be involved in generating the tubulin code. In contrast, modulations of the C-terminal tails could encode signals on the microtubule surface without perturbing basic microtubule functions and properties (Figs. 1 A and ​and4).4). Indeed, the highest degree of gene-encoded diversity (Fig. 2) and the highest density and complexity of PTMs (Fig. 1) are found within these tail domains.Open in a separate windowFigure 4.Molecular components of the tubulin code. Schematic representation of potential coding elements that could generate specific signals for the tubulin code. (A) The length of the C-terminal tails of different tubulin isotypes differ significantly (Fig. 2) and could have an impact on the interactions between microtubules and MAPs. (B) Tubulin C-terminal tails are rich in charged amino acid residues. The distribution of these residues and local densities of charges could influence the electrostatic interactions with the tails and the readers. (C) Although each glutamate residue within the C-terminal tails could be considered a potential modification site, only some sites have been found highly occupied in tubulin purifications from native sources. This indicates selectivity of the modification reactions, which can participate in the generation of specific modification patterns (see D). Modification sites might be distinguished by their neighboring amino acid residues, which could create specific modification epitopes. (D) As a result of the large number of modification sites and the variability of side chains, a large variety of modification patterns could be generated within a single C-terminal tail of tubulin. (E) Modification patterns as shown in D can be distinct between α- and β-tubulin. These modification patterns could be differentially distributed at the surface of the microtubule lattice, thus generating a higher-order patterning. Tub, tubulin. For color coding, see Fig. 2.Considering the number of tubulin isotypes plus all potential combinations of PTMs (e.g., each glutamate residue within the C-terminal tubulin tail could be modified by either polyglutamylation or polyglycylation, each of them generating side chains of different lengths; Fig. 4), the number of distinct signals generated by the potential tubulin code would be huge. However, as many of these potential signals represent chemical structures that are similar and might not be reliably distinguished by readout mechanisms, it is possible that the tubulin code generates probabilistic signals. In this scenario, biochemically similar modifications would have similar functional readouts, and marginal differences between those signals would only bias biological processes but not determine them. This stands in contrast to the concept of the histone code, in which precise patterns of different PTMs on the histone proteins encode distinct biological signals.The concept of probabilistic signaling is already inscribed in the machinery that generates the tubulin code. Polyglutamylases and polyglycylases from the TTLL family have preferential activities for either α- or β-tubulin and for generating different lengths of the branched glutamate or glycine chains. Although under conditions of low enzyme concentrations, as found in most cells and tissues, the enzymes seem to selectively generate their preferential type of PTM, higher enzyme concentrations induce a more promiscuous behavior, leading, for instance, to a loss of selectivity for α- or β-tubulin (van Dijk et al., 2007). Similarly, the modifying enzymes might prefer certain modification sites within the C-terminal tails of tubulin but might be equally able to modify other sites, which could be locally regulated in cells. For example, β-tubulin isotypes isolated from mammalian brain were initially found to be glutamylated on single residues (Alexander et al., 1991; Rüdiger et al., 1992), which in the light of the comparably low sensitivity of mass spectrometry at the time might rather indicate a preferential than a unique modification of these sites. Nevertheless, the neuron-specific polyglutamylase for β-tubulin TTLL7 (Ikegami et al., 2006) can incorporate glutamate onto many more modification sites of β-tubulin in vitro (Mukai et al., 2009), which clearly indicates that not all of the possible modification events take place under physiological conditions.Several examples supporting a probabilistic signaling mode of the tubulin code are found in the recent literature. In T. thermophila, a ciliate without tubulin isotype diversity (Gaertig et al., 1993) but with a huge repertoire of tubulin PTMs and tubulin-modifying enzymes (Janke et al., 2005), tubulin can be easily mutagenized to experimentally eliminate sites for PTMs. Mutagenesis of the most commonly occupied glutamylation/glycylation sites within the β-tubulin tails did not generate a clear decrease of glycylation levels nor did it cause obvious phenotypic alterations. This indicates that the modifying enzymes can deviate toward alternative modification sites and that similar PTMs on different sites can compensate the functions of the mutated site. However, when all of the key modification sites were mutated, glycylation became prominently decreased, which led to severe phenotypes, including lethality (Xia et al., 2000). Most strikingly, these phenotypes could be recovered by replacing the C-terminal tail of α-tubulin with the nonmutated β-tubulin tail. This α–β-tubulin chimera became overglycylated and functionally compensated for the absence of modification sites on β-tubulin. The conclusion of this study is that PTM- and isotype-generated signals can fulfill a biological function within a certain range of tolerance.But how efficient is such compensation? The answer can be found in a variety of already described deletion mutants for tubulin-modifying enzymes in different model organisms. Most single-gene knockouts for TTLL genes (glutamylases or glycylases) did not result in prominent phenotypic alterations in mice, even for enzymes that are ubiquitously expressed. Only some highly specialized microtubule structures show functional aberrations upon the deletion of a single enzyme. These “tips of the iceberg” are usually the motile cilia and sperm flagella, which carry very high levels of polyglutamylation and polyglycylation (Bré et al., 1996; Kann et al., 1998; Rogowski et al., 2009). It thus appears that some microtubules are essentially dependent on the generation of specific PTM patterns, whereas others can tolerate changes and appear to function normally. How “normal” these functions are remains to be investigated in future studies. It is possible that defects are subtle and thus overlooked but could become functionally important under specific conditions.A tubulin code also requires readout mechanisms. The most likely “readers” of the tubulin code are MAPs and molecular motors. Considering the probabilistic signaling hypothesis, the expected effects of the signals would be in most cases rather gradual changes, for instance, to fine-tune molecular motor traffic and/or to bias motors toward defined microtubule tracks but not to obliterate motor activity or MAP binding to microtubules. An in vitro study using recombinant tubulin chimeras purified from yeast confirmed this notion (Sirajuddin et al., 2014). By analyzing which elements of the tubulin code can regulate the velocity and processivity of the molecular motors kinesin and dynein, these researchers found that the C-terminal tails of α- and β-tubulin differentially influence the kinetic parameters of the tested motors; however, the modulation was rather modest. One of their striking observations was that a single lysine residue, present in the C-terminal tails of two β-tubulin isotypes (Figs. 2 and ​and4),4), significantly affected motor traffic and that this effect can be counterbalanced by polyglutamylation. These observations are the first in vitro evidence for the interdependence of different elements of the tubulin code and provide another indication for its probabilistic mode of signaling.

Future directions.

One of the greatest technological challenges to understanding the function of the tubulin code is to detect and interpret subtle and complex regulatory events generated by this code. It will thus be instrumental to further develop tools to better distinguish graded changes in PTM levels on microtubules in cells and tissues (Magiera and Janke, 2013) and to reliably measure subtle modulations of microtubule behavior in reconstituted systems.The current advances in the field and especially the availability of whole-organism models, as well as first insights into the pathological role of tubulin mutations (Tischfield et al., 2011), are about to transform our way of thinking about the regulation of microtubule cytoskeleton. Tubulin heterogeneity generates complex probabilistic signals that cannot be clearly attributed to single biological functions in most cases and that are not essential for most cellular processes. Nevertheless, it has been conserved throughout evolution of eukaryotes and can hardly be dismissed as not important. To understand the functional implications of these processes, we might be forced to reconsider how we define biologically important events and how we measure events that might encode probabilistic signals. The answers to these questions could provide novel insights into how complex systems, such as cells and organisms, are sustained throughout difficult and challenging life cycles, resist to environmental stress and diseases, and have the flexibility needed to succeed in evolution.     

Interplay between Velocity and Travel Distance of Kinesin-based Transport in the Presence of Tau

Although the disease-relevant microtubule-associated protein tau is known to severely inhibit kinesin-based transport in vitro, the potential mechanisms for reversing this detrimental effect to maintain healthy transport in cells remain unknown. Here we report the unambiguous upregulation of multiple-kinesin travel distance despite the presence of tau, via decreased single-kinesin velocity. Interestingly, the presence of tau also modestly reduced cargo velocity in multiple-kinesin transport, and our stochastic simulations indicate that the tau-mediated reduction in single-kinesin travel underlies this observation. Taken together, our observations highlight a nontrivial interplay between velocity and travel distance for kinesin transport, and suggest that single-kinesin velocity is a promising experimental handle for tuning the effect of tau on multiple-kinesin travel distance.Conventional kinesin is a major microtubule-based molecular motor that enables long-range transport in living cells. Although traditionally investigated in the context of single-motor experiments, two or more kinesin motors are often linked together to transport the same cargo in vivo (1–4). Understanding the control and regulation of the group function of multiple kinesins has important implications for reversing failure modes of transport in a variety of human diseases, particularly neurodegenerative diseases. Tau is a disease-relevant protein enriched in neurons (5,6). The decoration of microtubules with tau is known to strongly inhibit kinesin transport in vitro (7–9), but how kinesin-based transport is maintained in the presence of high levels of tau, particularly in healthy neurons, remains an important open question. To date, no mechanism has been directly demonstrated to reverse the inhibitory effect of tau on kinesin-based transport. Here we present a simple in vitro study that demonstrates the significant upregulation of multiple-kinesin travel distance with decreasing ATP concentration, despite the presence of tau.This investigation was motivated by our recent finding that single-kinesin velocity is a key controller for multiple-kinesin travel distance along bare microtubules (10). The active stepping of each kinesin motor is stimulated by ATP (11), and each kinesin motor remains strongly bound to the microtubule between successive steps (10,11). As demonstrated for bare microtubules (10), with decreasing ATP concentrations, each microtubule-bound kinesin experiences a decreased stepping rate per unit time and spends an increased fraction of time in the strongly bound state; additional unbound kinesins on the same cargo have more time to bind to the microtubule before cargo travel terminates. Thus, reductions in single-kinesin velocity increase the probability that at least one kinesin motor will remain bound to the microtubule per unit time, thereby increasing the travel distance of each cargo (10). Because this effect only pertains to the stepping rate of each individual kinesin and does not address the potential presence of roadblocks such as tau on the microtubules, we hypothesized in this study that single-kinesin velocity may be exploited to relieve the impact of tau on multiple-kinesin travel distance.We focused our in vitro investigation on human tau 23 (htau23, or 3RS tau), an isoform of tau that exhibits the strongest inhibitory effect on kinesin-based transport (7–9). Importantly, htau23 does not alter the stepping rate of individual kinesins (7,9), supporting our hypothesis and enabling us to decouple single-kinesin velocity from the potential effects of tau. We carried out multiple-kinesin motility experiments using polystyrene beads as in vitro cargos (8,10), ATP concentration as an in vitro handle to controllably tune single-kinesin velocity (10,11), and three input kinesin concentrations to test the generality of potential findings for multiple-kinesin transport. Combined with previous two-kinesin studies (10,12), our measurements of travel distance (Fig. 1 A) indicate that the lowest kinesin concentration employed (0.8 nM) corresponds to an average of ∼2–3 kinesins per cargo. Note that in the absence of tau, the observed decrease in bead velocity at the higher kinesin concentrations (Fig. 1 A) is consistent with a recent in vitro finding (13). At 1 mM ATP, htau23 reduced kinesin-based travel distance by a factor of two or more (Fig. 1, A and B). This observation is in good agreement with previous reports (7,8).Open in a separate windowFigure 1Distributions of multiple-kinesin travel distances measured at three experimental conditions, to verify the effect of tau (A and B) and to investigate the impact of single-kinesin velocity on the tau effect (B and C). Shaded bars at 8.7 μm indicate counts of travel exceeding the field of view. The mean travel distance (d; ± standard error of mean, SEM), sample size (n), and corresponding mean velocity (v; ± SEM) are indicated. MT denotes microtubule. Mean travel distance increased substantially at 20 μM ATP (C), despite the presence of htau23. This effect persisted across all three kinesin concentrations tested (left to right).Consistent with our hypothesis, reducing the available ATP concentration to 20 μM increased the multiple-kinesin travel distance by >1.4-fold for all three input kinesin concentrations (Fig. 1, B and C), despite the presence of htau23. The corresponding reduction in single-kinesin velocity with decreasing ATP concentration (10,11) is reflected in the ∼3.4-fold reduction in the measured bead velocities (Fig. 1, B and C). Therefore, the strong negative relationship between single-kinesin velocity and multiple-kinesin travel distance occurs not only for bare microtubules (10), but also for tau-decorated microtubules.What causes the observed increase in travel distance at the lower ATP concentration (Fig. 1, B and C)? In addition to the mechanism discussed above for the case of bare microtubules (10), an intriguing mechanism was suggested by recent studies of tau-microtubule interactions in which htau23 was observed to dynamically diffuse along microtubule lattices (14,15): reducing the stepping rate of a microtubule-bound kinesin may effectively increase the probability that a tau roadblock can diffuse away before the kinesin takes its next step.Perhaps surprisingly, although htau23 does not impact single-kinesin velocity (7,9), we observed a modest reduction in the average velocity of multiple-kinesin transport in experiments using tau-decorated microtubules (Fig. 1, A and B). This decreased velocity reflects a substantially larger variance in the instantaneous velocity for bead trajectories in the presence of htau23 (see Fig. S1 in the Supporting Material), as quantified by parsing each bead trajectory into a series of constant-velocity segments using a previously developed automatic software incorporating Bayesian statistics (16).To test the possibility that single-kinesin travel distance impacts multiple-kinesin velocity, we performed stochastic simulations (see the Supporting Material) that assumed N identical kinesin motors available for transport and included kinesin’s detachment kinetics (17). Previously, this model successfully captured multiple-dynein travel distances in vivo using single-dynein characteristics measured in vitro (18). In this study, we introduced one (and only one) free parameter to reflect the probability of each bound kinesin encountering tau at each step. When encountering tau, each kinesin has a 54% probability of detaching from the microtubule (interpolated from Fig. 2A of Dixit et al. (7)); the undetached kinesin is assumed to remain engaged in transport and completes its step along the microtubule despite the presence of tau.Remarkably, our simple simulation suggested that the tau-mediated reduction in single-kinesin travel is sufficient to reduce multiple-kinesin velocity (Fig. 2 A). The majority of the velocity decrease is predicted to occur at the transition from single-kinesin to two-kinesin transport (Fig. 2). Further decreases in cargo velocity with increasing motor number are predicted to be modest and largely independent of tau (Fig. 2 B). The results of our simulation remain qualitatively the same when evaluated at two bounds (40 and 65%) encompassing the interpolated 54% probability of kinesin detaching at tau (see Fig. S2).Open in a separate windowFigure 2Stochastic simulations predict a tau-dependent reduction in multiple-kinesin velocity, assuming that the only effect of tau protein is to prematurely detach kinesin from the microtubule (or, to reduce single-kinesin travel distance). (A) Average velocity of cargos carried by the indicated number of kinesins was evaluated at 1 mM ATP, and for four probabilities that a kinesin may encounter tau at each step. Mean velocity was evaluated using 600 simulated trajectories for all simulation conditions. Error bars indicate SEM. (B) Change in cargo velocity with each additional kinesin (ΔVel/kinesin) as a function of tau-encounter probability. These values were calculated from cargo velocities shown in panel A. Error bars indicate SEM.We note that our simple simulations do not consider the possibility that kinesin may pause in front of a tau roadblock, as previously reported in Dixit et al. (7). We omitted this consideration because the interaction strength between kinesin and the microtubule in such a paused state is unknown. In a multiple-motor geometry, could a paused kinesin be dragged along by the other motors bound to the same cargo? Could a tau roadblock be forcefully swept off the microtubule surface by the collective motion of the cargo-motor complex? Significant experimental innovations are necessary to specifically address these questions in future multiple-motor assays and to guide modeling efforts. Nonetheless, our simple simulation demonstrates that reducing single-kinesin travel distance is sufficient to decrease multiple-kinesin travel distance.Taken together, our observations highlight a nontrivial interplay between velocity and travel distance for kinesin-based transport in the presence of tau. We uncover a previously unexplored dual inhibition of tau on kinesin-transport: in addition to limiting cargo travel distance, the tau-mediated reduction in single-kinesin travel distance also leads to a modest reduction in multiple-kinesin velocity. We provide what we believe to be the first demonstration of the unambiguous upregulation of multiple-kinesin travel distance despite the presence of tau, via reducing single-kinesin velocity, suggesting a mechanism that could be harnessed for future therapeutic interventions in diseases that result from aberrant kinesin-based transport.     

Maturation Stress Generation in Poplar Tension Wood Studied by Synchrotron Radiation Microdiffraction

Tension wood is widespread in the organs of woody plants. During its formation, it generates a large tensile mechanical stress, called maturation stress. Maturation stress performs essential biomechanical functions such as optimizing the mechanical resistance of the stem, performing adaptive movements, and ensuring long-term stability of growing plants. Although various hypotheses have recently been proposed, the mechanism generating maturation stress is not yet fully understood. In order to discriminate between these hypotheses, we investigated structural changes in cellulose microfibrils along sequences of xylem cell differentiation in tension and normal wood of poplar (Populus deltoides × Populus trichocarpa ‘I45-51’). Synchrotron radiation microdiffraction was used to measure the evolution of the angle and lattice spacing of crystalline cellulose associated with the deposition of successive cell wall layers. Profiles of normal and tension wood were very similar in early development stages corresponding to the formation of the S1 and the outer part of the S2 layer. The microfibril angle in the S2 layer was found to be lower in its inner part than in its outer part, especially in tension wood. In tension wood only, this decrease occurred together with an increase in cellulose lattice spacing, and this happened before the G-layer was visible. The relative increase in lattice spacing was found close to the usual value of maturation strains, strongly suggesting that microfibrils of this layer are put into tension and contribute to the generation of maturation stress.Wood cells are produced in the cambium at the periphery of the stem. The formation of the secondary wall occurs at the end of cell elongation by the deposition of successive layers made of cellulose microfibrils bounded by an amorphous polymeric matrix. Each layer has a specific chemical composition and is characterized by a particular orientation of the microfibrils relative to the cell axis (Mellerowicz and Sundberg, 2008). Microfibrils are made of crystalline cellulose and are by far the stiffest constituent of the cell wall. The microfibril angle (MFA) in each layer is determinant for cell wall architecture and wood mechanical properties.During the formation of wood cells, a mechanical stress of a large magnitude, known as “maturation stress” or “growth stress” (Archer, 1986; Fournier et al., 1991), occurs in the cell walls. This stress fulfills essential biomechanical functions for the tree. It compensates for the comparatively low compressive strength of wood and thus improves the stem resistance against bending loads. It also provides the tree with a motor system (Moulia et al., 2006), necessary to maintain the stem at a constant angle during growth (Alméras and Fournier, 2009) or to achieve adaptive reorientations. In angiosperms, a large tensile maturation stress is generated by a specialized tissue called “tension wood.” In poplar (Populus deltoides × Populus trichocarpa), as in most temperate tree species, tension wood fibers are characterized by the presence of a specific layer, called the G-layer (Jourez et al., 2001; Fang et al., 2008), where the matrix is almost devoid of lignin (Pilate et al., 2004) and the microfibrils are oriented parallel to the fiber axis (Fujita et al., 1974). This type of reaction cell is common in plant organs whose function involves the bending or contraction of axes, such as tendrils, twining vines (Bowling and Vaughn, 2009), or roots (Fisher, 2008).The mechanism at the origin of tensile maturation stress has been the subject of a lot of controversy and is still not fully understood. However, several recent publications have greatly improved our knowledge about the ultrastructure, chemical composition, molecular activity, mechanical state, and behavior of tension wood. Different models have been proposed and discussed to explain the origin of maturation stress (Boyd, 1972; Bamber, 1987, 2001; Okuyama et al., 1994, 1995; Yamamoto, 1998, 2004; Alméras et al., 2005, 2006; Bowling and Vaughn, 2008; Goswami et al., 2008; Mellerowicz et al., 2008). The specific organization of the G-layer suggests a tensile force induced in the microfibrils during the maturation process. Different hypotheses have been proposed to explain this mechanism, such as the contraction of amorphous zones within the cellulose microfibrils (Yamamoto, 2004), the action of xyloglucans during the formation of microfibril aggregates (Nishikubo et al., 2007; Mellerowicz et al., 2008), and the effect of changes in moisture content stimulated by pectin-like substances (Bowling and Vaughn, 2008). A recent work (Goswami et al., 2008) argued an alternative model, initially proposed by Münch (1938), which proposed that the maturation stress originates in the swelling of the G-layer during cell maturation and is transmitted to the adjacent secondary layers, where the larger MFAs allow an efficient conversion of lateral stress into axial tensile stress. Although the proposed mechanism is not consistent with the known hygroscopic behavior of tension wood, which shrinks when it dries and not when it takes up water (Clair and Thibaut, 2001; Fang et al., 2007; Clair et al., 2008), this hypothesis focused attention on the possible role of cell wall layers other than the G-layer. As a matter of fact, many types of wood fibers lacking a G-layer are known to produce axial tensile stress, such as normal wood of angiosperms and conifers (Archer, 1986) and the tension wood of many tropical species (Onaka, 1949; Clair et al., 2006b; Ruelle et al., 2007), so that mechanisms strictly based on an action of the G-layer cannot provide a general explanation for the origin of tensile maturation stress in wood.In order to further understanding, direct observations of the mechanical state of the different cell wall layers and their evolution during the formation of the tension wood fibers are needed. X-ray diffraction can be used to investigate the orientation of microfibrils (Cave, 1966, 1997a, 1997b; Peura et al., 2007, 2008a, 2008b) and the lattice spacing of crystalline cellulose. The axial lattice spacing d₀₀₄ is the distance between successive monomers along a cellulose microfibril and reflects its state of mechanical stress (Clair et al., 2006a; Peura et al., 2007). If cellulose microfibrils indeed support a tensile stress, they should be found in an extended state of deformation. Under this assumption, the progressive development of maturation stress during the cell wall formation should be accompanied by an increase in cellulose lattice spacing. Synchrotron radiation allows a reduction in the size of the x-ray beam to some micrometers while retaining a strong signal, whereby diffraction analysis can be performed at a very local scale (Riekel, 2000). This technique has been used to study sequences of wood cell development (Hori et al., 2000; Müller et al., 2002). In this study, we report an experiment where a microbeam was used to analyze the structural changes of cellulose in the cell wall layers of tension wood and normal wood fibers along the sequence of xylem cell differentiation extending from the cambium to mature wood (Fig. 1). The experiment was designed to make this measurement in planta, in order to minimize sources of mechanical disturbance and be as close as possible to the native mechanical state (Clair et al., 2006a). The 200 and 004 diffraction patterns of cellulose were analyzed to investigate the process of maturation stress generation in tension wood.Open in a separate windowFigure 1.Schematic of the experimental setup, showing the x-ray beam passing perpendicular to the longitudinal-radial plane of wood and the contribution of the 004 and 200 crystal planes to the diffraction pattern recorded by the camera. [See online article for color version of this figure.]     

Structural basis of the super- and hyper-relaxed states of myosin II

Super-relaxation is a state of muscle thick filaments in which ATP turnover by myosin is much slower than that of myosin II in solution. This inhibited state, in equilibrium with a faster (relaxed) state, is ubiquitous and thought to be fundamental to muscle function, acting as a mechanism for switching off energy-consuming myosin motors when they are not being used. The structural basis of super-relaxation is usually taken to be a motif formed by myosin in which the two heads interact with each other and with the proximal tail forming an interacting-heads motif, which switches the heads off. However, recent studies show that even isolated myosin heads can exhibit this slow rate. Here, we review the role of head interactions in creating the super-relaxed state and show how increased numbers of interactions in thick filaments underlie the high levels of super-relaxation found in intact muscle. We suggest how a third, even more inhibited, state of myosin (a hyper-relaxed state) seen in certain species results from additional interactions involving the heads. We speculate on the relationship between animal lifestyle and level of super-relaxation in different species and on the mechanism of formation of the super-relaxed state. We also review how super-relaxed thick filaments are activated and how the super-relaxed state is modulated in healthy and diseased muscles.

The super-relaxed state of myosinAnimal life is characterized by the constant need for food, which provides the raw materials for making ATP used in the body’s energy-requiring processes. A substantial amount of energy is expended by skeletal muscle, which in humans amounts to 30–40% of body mass (Janssen et al., 2000). During contraction, ATP is rapidly consumed by the molecular motor, myosin II, as it pulls on actin filaments to produce force and movement. But ATP is also used at a significant basal rate even in the resting state. Producing ATP is costly for the cell, so there is a substantial evolutionary advantage to minimizing its waste. Animals have adapted to this requirement by evolving a mechanism that reduces the consumption of ATP to minimal levels in relaxed (RX) muscle. This mechanism is known as super-relaxation or the super-relaxed state (SRX).SRX is a biochemical state in which ATP turnover by a portion of the myosin heads in the RX state of muscle thick filaments is much slower (∼10 times) than that of myosin II molecules in solution (Stewart et al., 2010; Cooke, 2011; Nag and Trivedi, 2021). This inhibited state, in equilibrium with a faster (RX) state, was suggested by early studies showing that the metabolic rate of live, resting muscle was much less than that expected from the ATP turnover rate of purified myosin (Ferenczi et al., 1978) and similarly that ATPase activity of RX myofibrils was also lower than expected from isolated myosin (Myburgh et al., 1995). A slow rate of ATP turnover was later directly demonstrated in studies of skinned muscle fibers (Stewart et al., 2010). The single ATP turnover rate is typically measured as the rate of binding of fluorescent ATP (mantATP) to, or release from, myosin heads in solution or in skinned fiber bundles (Hooijman et al., 2011; McNamara et al., 2015); conceptually, because P_i release is rate limiting, the apparent rates of ATP binding and ADP release effectively reveal the overall ATP turnover rate. Experimental curves are generally interpreted in terms of two exponentials, one with a slow rate (SRX) and the other with a faster but still slow (RX) rate of ATP use (Cooke, 2011), although additional exponentials can sometimes be resolved (Hooijman et al., 2011; Naber et al., 2011).The SRX state is ubiquitous and thought to be fundamental to muscle function, acting as a mechanism for parking and switching off—like a car—energy-consuming myosin motors when they are not being used. It has been detected in all muscles where it has been studied: vertebrate (including human) and invertebrate, fast and slow skeletal, and cardiac muscle (Stewart et al., 2010; Cooke, 2011; Hooijman et al., 2011; Naber et al., 2011; McNamara et al., 2015; Phung et al., 2020). A highly inhibited rate of ATP turnover also characterizes the switched-off state of vertebrate smooth muscle and nonmuscle myosin II molecules (Cross et al., 1988). SRX plays a critical role in muscle energetics, conserving ATP in resting as well as contracting muscles and providing a reserve of myosin heads for enhanced contractility in cardiac muscles (Cooke, 2011; Hooijman et al., 2011; Brunello et al., 2020; Ma et al., 2021b).What are the key features of the SRX state?The SRX state has two main parameters: (1) the rate of ATP use (i.e., ATP turnover rate, often expressed as its inverse, the ATP turnover time) and (2) the fraction of molecules exhibiting this rate. Both parameters are essential to understanding the significance of SRX in the energy balance of muscle: myosin heads with a very slow rate would be of little consequence if not present in substantial numbers. The rate of ATP use has been attributed to the specific conformation of the myosin head, which can impede, or not, the release of the products of ATP hydrolysis (ADP and P_i; Anderson et al., 2018), and the fraction of heads with this rate in muscle appears to be related to the intra- and intermolecular interactions that the heads undergo in thick filaments, as discussed below.ATP turnover by myosin heads can vary by six orders of magnitude, depending on the muscle and its state of activity (Cooke, 2011; Naber et al., 2011). These fall into four main groups, which, on a logarithmic scale, differ internally by small amounts, but by an order of magnitude or more between groups (Fig. 1 A). The fastest use of ATP is in contracting muscle (rate ≈ 10 s⁻¹), where actin activates the release of hydrolysis products in a process coupled to the power stroke of the myosin head. The advantages of force and movement are paid for by a rapid consumption of ATP. RX heads use ATP at least 100 times more slowly: some at the RX rate, similar to that of purified myosin in solution (<0.1 s⁻¹), and others at an SRX rate, 10 times slower (Fig. 1, A and B). As might be predicted from the two parameters of the SRX, nature has evolved different ways of saving energy in this state: decreasing the ATP turnover rate, increasing the fraction with the low rate, or a combination of the two. These strategies appear adapted to the different systems in which they are found. The SRX rate typically occurs in 50% or more of the heads in a thick filament, the balance being RX heads (Cooke, 2011). In certain muscles, there is an even slower rate (10 times slower than SRX), which we refer to as “hyper-relaxed” (HRX), present together with SRX and RX heads (Naber et al., 2011).Open in a separate windowFigure 1.ATP turnover rates of myosin and proposed relation to head organization. (A) Logarithmic plot of rates, varying from very slow (hyper-relaxed), to slow (super-relaxed), to fast (disordered-relaxed), to very fast (actin-activated). (B) Expanded plot of relaxed rates and proposed relation to head configuration and interactions. The cartoons show the IHM as found in single molecules (upper) and thick filaments (lower); in filaments, only molecules in a single crown are shown. The colored ellipses are the interacting motor domains. The smaller, gray domains are the ELCs and RLCs, and the gray lines are the proximal region of the myosin tail (S2). Molecules with a sufficient length of S2 (25 heptads [25 hep]; ∼250 Å) form an IHM, while single heads and two-headed molecules with only two heptads of tail show no interactions. Molecules in filaments have SRX and DRX turnover rates similar to those of isolated molecules (25-heptad IHM; cf. vertebrate IHM) or more inhibited (HRX) rates. Heads turn over ATP at fast (F; noninteracting), slow (S; interacting), or very slow (VS; more interactions) rates. Slow (attached) FHs of the IHM can detach and sway out (red, double-headed arrows) and, while detached, can equilibrate between the slow and fast conformations, similar to S1 (blue, reversible arrows). The “tail” in tarantula and the uncolored IHM in scallop provide additional, intermolecular interactions leading to the very slow rate; this rate is also seen in 10S myosin through intramolecular interactions with segment 2 of its own tail. The different lengths of the bars in A correspond to the lengths in B, which are drawn to include the range of rates for HRX, SRX, and DRX; the key point is the close clustering of rates within these groups and the large gaps between them.What is the structural basis of the SRX state?The early finding that myosin filaments in muscle had a slower ATP turnover rate than myosin II molecules in solution led to the idea that interactions of heads possible in the polymer (e.g., with the thick filament backbone), but not in the monomer, inhibited their activity (Myburgh et al., 1995; Stewart et al., 2010; Cooke, 2011). The first study to unequivocally show head organization in a thick filament indeed revealed such interactions—of heads with the backbone, with each other within a molecule, and with each other between molecules (Woodhead et al., 2005). Of particular note was a folding back of the two heads onto the proximal part of the tail (subfragment 2 [S2]), with which they interacted, and intramolecular interaction between the heads through their motor domains. This structure became known as the “interacting-heads motif” (IHM; Fig. 1 B, dotted box; Fig. 2 B; Woodhead et al., 2005; Alamo et al., 2008). Such interaction between heads had first been seen in isolated myosin molecules (Wendt et al., 2001; Burgess et al., 2007) and was thought to inhibit their activity. The two heads were called “blocked” and “free” (BH and FH, respectively), referring to their actin-binding capability (Wendt et al., 2001). In this model, actin binding by the BH would be blocked by interaction of its actin-binding site with the FH. While the FH actin-binding site was exposed, movement of its converter domain, needed for ATP product release, would be inhibited by binding to the BH (Wendt et al., 2001). The overall result would be inhibition of activity of both heads, but by different mechanisms. Interaction of the folded-back heads with S2 would further inhibit the motions required for ATPase activity (Woodhead et al., 2005).Open in a separate windowFigure 2.Structural basis of SRX. (A) Proposed conformations of myosin heads (S1), in equilibrium with each other, underlying SRX (left, bent) and DRX (right, straight) ATP turnover rates (Anderson et al., 2018). MD, motor domain. (B) IHM of cardiac HMM showing BH and FH (based on Protein Data Bank accession no. 5TBY). Ellipses show regions of interaction between BH and FH motor domains (black ellipse), FH and S2 (black circle), and BH and S2 (white ellipse; interaction occurs on rear side of BH). (C) Thick filament (tarantula; EM Data Bank accession no. 1950) showing IHMs lying along four coaxial helices (three on front marked with arrows) creating intermolecular interactions (ellipses) between FH of one IHM and regulatory domain of IHM above. M-line would be at the top of the image. The reconstruction shows the average positions of the heads in the filament; however, the FHs are thought to be dynamic, leaving and returning to the IHM (Fig. 1 B; see text). Models in this figure were created with UCSF Chimera (Pettersen et al, 2004).The IHMs in RX thick filaments are organized in helical arrays, with intermolecular interactions of IHMs with each other along the helices as well as with the filament backbone (Woodhead et al., 2005; Zoghbi et al., 2008; Zhao et al., 2009; Pinto et al., 2012; Woodhead et al., 2013; Sulbarán et al., 2015). Helical ordering requires the closed conformation of the myosin heads (Xu et al., 2003; Zoghbi et al., 2004; Xu et al., 2009) and is thought to be a signature of the IHM. It can be disrupted in multiple ways (increased salt level, phosphorylation of the myosin regulatory light chains [RLCs], substitution of GTP or ADP for ATP, lowering of temperature), and this is accompanied by reduction of the SRX state in each case (Stewart et al., 2010; Cooke, 2011). Conversely, conditions that enhance the IHM, such as treatment with the myosin inhibitor blebbistatin (Zhao et al., 2008; Xu et al., 2009; Fusi et al., 2015), enhance the SRX (Wilson et al., 2014; Fusi et al., 2015). These correlations led to the view that IHMs in the ADP.Pi prepowerstroke state (Xu et al., 1999), organized in helices and bound to the core of the thick filament, may be the structural basis of the SRX state (Stewart et al., 2010; Cooke, 2011; Wilson et al., 2014; Fusi et al., 2015; Alamo et al., 2016).Despite this suggestive evidence, however, recent single ATP turnover measurements of myosin constructs have shown that slow turnover of ATP occurs not only in thick filaments but also, to a small extent (∼10–20% of molecules), in isolated myosin heads (S1; Anderson et al., 2018; Rohde et al., 2018; Gollapudi et al., 2021b; the earlier, steady-state solution ATPase observations were not capable of revealing these low rates). Thus, neither the filamentous form of myosin nor the IHM is required for the SRX rate of ATP turnover, as originally thought. It has been suggested, instead, that myosin heads in solution exist in an equilibrium between a strongly bent (“closed”) conformation (in which the lever arm is tilted more toward the prestroke direction similar to that in the IHM structure; 10–20% of molecules) and a more extended (“open”) structure (Anderson et al., 2018) and that inhibition of phosphate release and thus ATP turnover by the closed structure could account for the observation of a small level of SRX in S1 (Figs. 1 B and 2 A). If this is the case, what is the role of the IHM in SRX?Different degrees of SRX correlate with different levels of head organizationMyosin heads can exist in several structural forms: single heads, two-headed myosin molecules or constructs, and the polymeric myosin filaments found in muscle. Studies show that SRX increases (greater inhibition or greater number of inhibited molecules) as myosin heads are incorporated into more complex structures. As mentioned, ∼10–20% of isolated myosin heads in solution have a slow rate (SRX) and are thought to be in equilibrium with the balance of heads having a turnover rate similar to the conventionally measured ATPase (RX heads; Anderson et al., 2018; Rohde et al., 2018; Gollapudi et al., 2021b). When myosin heads are present in two-headed constructs containing 25 heptads of tail (∼250 Å; Figs. 1 B and 2 B) or full-length S2, similar SRX and RX rates are observed, but the fraction of SRX heads increases to ∼25–30% (at physiological ionic strength; Anderson et al., 2018; Rohde et al., 2018; Gollapudi et al., 2021b), suggesting that the presence of two heads and/or the tail stabilizes the SRX head structure. Importantly, if the tail is short (only two heptads; Fig. 1 B), the rates and fractions are similar to those of S1 (Anderson et al., 2018), demonstrating the importance of the tail in creating the SRX. Modeling and experiments show that 25 heptads (or more) of tail is long enough for molecules to form an IHM with folded-back, interacting FHs and BHs (Figs. 1 B and 2 B; Anderson et al., 2018). Head–head and head–tail interactions would stabilize the heads in their inhibited conformations (Fig. 2 B), consistent with the increase in SRX fraction. The two-heptad-long tail is too short for these interactions (Fig. 1 B), and the molecule does not show evidence of head interactions (Nag et al., 2017): the heads behave like isolated S1 in solution, with only ∼10% having the SRX rate (Fig. 1 B; Anderson et al., 2018). We conclude that the stabilizing interactions in the IHM involving the tail and the two heads increase the number of heads in the SRX conformation.Studies of whole muscle fibers (vertebrate fast skeletal) show that when myosin molecules are in native thick filaments in their helically ordered IHM conformations (Zoghbi et al., 2008; AL-Khayat et al., 2013), the RX and SRX rates are again similar to those of S1 (Fig. 1 B), but the fraction of SRX now reaches 60–75% (Stewart et al., 2010; Cooke, 2011). A similar, greatly increased fraction of SRX heads is found in slow skeletal and cardiac muscle fibers and myofibrils (Stewart et al., 2010; Hooijman et al., 2011; McNamara et al., 2017; Nelson et al., 2020; Gollapudi et al., 2021a). In filaments, IHMs undergo intermolecular interactions that cannot occur with single molecules (Zoghbi et al., 2008; AL-Khayat et al., 2013). These include interactions between heads of different IHMs along the myosin helices (Fig. 2 C), interaction of heads with tails in the filament backbone, and interaction with myosin-binding protein C (MyBP-C) and titin, lying on the filament surface (Nag et al., 2017). We suggest that these interactions further stabilize the FHs and BHs of the IHMs, without significantly affecting their conformation, leading to the high percentage of SRX in filaments (Anderson et al., 2018).These observations are consistent with the concept suggested earlier that the SRX rate is a consequence of a specific conformation of myosin heads, which inhibits ATP turnover, and with stabilization of this conformation by intra- and intermolecular interactions of the heads (Anderson et al., 2018). When heads are attached to each other in myosin constructs with a sufficient length of tail, forming the IHM, the inhibited conformation is stabilized by intramolecular interactions of the two heads with each other and with the myosin tail, approximately doubling (25–30%) the SRX fraction found in single heads (10–20%). When IHMs are incorporated into thick filaments, the inhibited heads are further stabilized by intermolecular interactions, with a further doubling of the SRX fraction to 60–75%. Thus, while the IHM is not a requirement for the SRX state, in real muscle, it strongly enhances it.Are the RX and SRX rates associated with specific heads in the IHM? It is known experimentally that the BH is more stably associated with the IHM than the FH. EM images of smooth muscle heavy meromyosin (HMM; a soluble, proteolytic fragment of myosin containing the two heads and the proximal third of the tail) show molecules where the BH is attached to S2 but the FH has dissociated (Burgess et al., 2007). This and studies of tarantula thick filaments (Brito et al., 2011; Sulbarán et al., 2013) suggest that the FH can dissociate from the IHM and become mobile (“swaying”; Fig. 1 B, red double-headed arrows), with a duty ratio that defines the fraction of time spent in the dissociated state (Alamo et al., 2017). When unconstrained in this way, the FH presumably acts essentially like S1 in solution, equilibrating between its minor SRX (bent) and its predominant RX (straight) rate of ATP turnover (Fig. 1 B, reversible blue arrows). Thus, the more stable BH would account for most of the SRX rate and the dissociated FH for the faster, RX rate. When the FH is docked in the IHM, stabilized in its inhibited form by interactions with the BH and S2 in the IHM, it may slow to approximately the BH SRX rate (Fig. 1 B; Alamo et al., 2016). The BH and docked FH may have similar enough rates that they are not resolved by the two-exponential analysis; there is in fact some evidence that additional exponentials give an improved fit (Hooijman et al., 2011), but this has not been explored in detail. The idea that some heads can move freely for a portion of the time, leading to their disordering in thick filaments, and the correlation of disorder with the RX rate, has led to the concept of the “disordered relaxed state” (DRX; Wilson et al., 2014). Thus, heads in thick filaments are typically referred to as SRX or DRX.What is the structural basis of the HRX state?Studies of invertebrate (tarantula) striated muscle show that the SRX state in some species can be enhanced by a further (10 times) slowing of the ATP turnover rate compared with the SRX (Fig. 1) and that this occurs in up to 50% of the heads (Naber et al., 2011). We refer to this as the HRX state. The HRX state has not been observed in vertebrate striated muscle thick filaments or myosin molecules. Is there a structural explanation for the greater inhibition of ATP turnover in tarantula muscle? The cryo-EM reconstruction of tarantula filaments shows that the IHMs in this species are arranged in four coaxial helices, with crowns of four IHMs spaced 145 Å apart axially (Woodhead et al., 2005). Each IHM shows the conventional structure of two heads interacting with each other through their motor domains and with the proximal portion of the myosin tail. Importantly, the reconstruction also suggests an additional key interaction that is apparently absent in vertebrate thick filaments (see below). S2, after leaving its IHM, travels along the filament toward the bare zone, passing near the next IHM along the filament axis, through a groove formed by the BH SRC homology 3 (SH3) and converter domains (Fig. 3 A; and Fig. 4, A and B; Woodhead et al., 2005). This location suggests that S2 could sterically interfere with movement of the BH converter region of this IHM that is required for product release. It could thus act as an additional constraint on the already inhibited conformation of the BH that further inhibits ATP turnover (each BH would thus interact with two S2s, its own and that from the axially adjacent IHM). In this case, we suggest that intermolecular interaction does not simply stabilize the inhibited head conformation but creates a new and additional physical barrier to motions of the BH required for ATPase activity, leading to the highly inhibited HRX turnover rate. The reconstruction shows that only the BHs are affected in this way, which could directly explain the finding that 50% of heads are in the HRX state (Naber et al., 2011).Open in a separate windowFigure 3.Comparison of intermolecular interactions in 3-D reconstructions of different thick filaments. Reconstructions are fitted with IHM atomic models (Protein Data Bank accession nos. 3JBH or 5TBY) in each case. All thick filaments (except insect flight muscle; Hu et al., 2016) show interactions between IHMs along the helical tracks (arrows), involving the FH motor domain at one level and the BH lever arm at the next. These interactions are the same at every level in tarantula and scallop (true helical structures) but different at different levels in vertebrates, which are quasi-helical. Additional interactions vary between species. (A) Tarantula shows interaction of S2 from one crown of heads with SH3 and converter domains of the next level (circles; see Fig. 4, A and B). IHM (Protein Data Bank accession no. 3JBH) was fitted to four levels of heads in cryo-EM reconstruction (EMD accession no. 1950; gray). (B) Similar fitting of IHM (Protein Data Bank accession no. 5TBY) to vertebrate (human) cardiac negative stain reconstruction of C-zone (EMD accession no. 2240) shows well-ordered IHMs at two of every three levels of heads (strong map density for pink and cyan IHMs), while the third level (yellow) is poorly ordered (weak map density, suggesting substantial IHM mobility; Zoghbi et al., 2008; AL-Khayat et al., 2013). S2 cannot be fitted unambiguously due to low resolution of map and lack of internal detail with negative stain; within these limitations, there is no obvious S2–head interaction between crowns (circles; see Video 1; cf. Video 2 for 3-D view). (C) In scallop cryo-EM reconstruction, S2 is not resolved, but the tight azimuthal crowding of IHMs around the circumference at each crown suggests potential intermolecular interaction between the SH3 domain of a BH and the motor domain of the neighboring FH (circles). Filaments are oriented with M-line at top; their different symmetries (fourfold, threefold, and sevenfold rotational symmetry, respectively) cause the varying views of the IHMs in the different filaments. All reconstructions are at the same scale. The human has a smaller diameter due to radial shrinkage occurring during negative staining and to the smaller number of molecules (n = 3) at each level. The scallop and tarantula cryo-reconstructions also have different diameters: scallop has seven molecules at each level forming a shell above the filament backbone (Woodhead et al., 2013), while tarantula has four molecules at each level, closer to the backbone (Woodhead et al., 2005), leading to a smaller diameter. Models in this figure were created with UCSF Chimera (Pettersen et al, 2004).Open in a separate windowFigure 4.Comparison of tail interactions with the SH3 and converter domains in atomic models of tarantula thick filaments and 10S smooth muscle myosin. (A and B) Tarantula thick filament (Protein Data Bank accession no. 3JBH). (C and D) 10S myosin (Protein Data Bank accession no. 6XE9). (A and C) Front views at same scale. (B and D) End views (same scale) obtained by rotating A and C 90° around the x axis so that pink IHM in A is closest to viewer (i.e., looking toward M-line). S2 in tarantula filament and segment 2 (Seg2) in 10S myosin both pass through a groove formed by the SH3 and converter (Cnv) domains of the BH motor domain (MD). The looser fit to the groove in tarantula may be due to the lower resolution of the reconstruction used to obtain the atomic model (20 Å resolution; cf. 4.3 Å for 10S myosin). Models in this figure were created with UCSF Chimera (Pettersen et al, 2004).Several observations support this structural interpretation of the HRX state. Vertebrate thick filaments have a symmetry and organization of myosin heads that is different from those in tarantula. Although no cryo-EM reconstruction of vertebrate filaments is available, two negative stain reconstructions of the C-zone (the middle section of each filament half, containing MyBP-C) clearly show the well-known quasi-helical arrangement of myosin heads characteristic of vertebrates (Zoghbi et al., 2008; AL-Khayat et al., 2013). Fitting of the IHM into the density map reveals well-ordered IHMs at two of every three levels of heads, while the third level is relatively disordered (Zoghbi et al., 2008; AL-Khayat et al., 2013). S2 cannot be fitted with certainty due to the low resolution of the map and ambiguities of negative stain; however, there is no obvious interaction of S2 from one crown with heads in the next (Fig. 3 B; Video 1; cf. Video 2). Correspondingly, vertebrate filaments do not exhibit an HRX state. There is also no HRX state in isolated S1- or S2-headed myosin constructs forming the IHM (Anderson et al., 2018; Rohde et al., 2018). These observations are consistent with the conclusion that in tarantula, intermolecular interaction with S2 from the neighboring crown is responsible for the HRX state. Note that the “ultra-relaxed” state induced in myosin by the inhibitor blebbistatin (Gollapudi et al., 2021a) has a very different origin from the HRX—the former due to internal stabilization of switch 2 in the myosin head in the closed state, inhibiting phosphate release (Zhao et al., 2008), the latter to the external structural constraints on head movements that we have described here.Video 1.Human cardiac thick filament reconstruction (EMD accession no. 2240) fitted with human cardiac atomic model (Protein Data Bank accession no. 5TBY) to show apparent absence of interaction between S2 from one level of heads and the SH3 and converter domains (red) of the next level. M-line at top. See also Fig. 3 B. Compare with Video 2.Video 2.Tarantula thick filament reconstruction (EMD accession no. 1950) fitted with tarantula IHM atomic model (Protein Data Bank accession no. 3JBH) to show 3-D view of interaction between S2 from one level of heads and the SH3 and converter domains (red) of the next level. M-line at top. See also Fig. 3 A and Fig. 4, A and B.Additional evidence comes from smooth muscle and nonmuscle myosin molecules, which can exist in a switched-off state in which the ATP turnover rate is similar to that in tarantula—also an HRX state (Cross et al., 1988). Strikingly, these myosins have a folded conformation, in which the two heads form an IHM, and the tail folds into three segments, the middle segment wrapping around the BH (Fig. 1 B; Suzuki et al., 1982; Trybus et al., 1982; Craig et al., 1983; Burgess et al., 2007; Yang et al., 2019). Cryo-EM analysis of this conformation shows intimate contact of the tail with the BH motor as it runs through the groove formed by the BH SH3 and converter domains (Fig. 4, C and D; Scarff et al., 2020; Yang et al., 2020). The regions of tail contact with the BH in these single molecules are very similar to those in the tarantula filament and would sterically impede BH converter movement, contributing to the HRX turnover rate of this inhibited form of the myosin molecule (Fig. 4). Although the inhibitory regions of the tail (S2 in tarantula, the middle segment of the tail in smooth muscle and nonmuscle myosin) and the nature of the interaction (intermolecular in one, intramolecular in the other) are both different, the likely inhibitory effects on BH converter movement and ATPase activity appear to be similar, supporting the importance of this interaction in generating the HRX state. HMM from these myosins lacks the distal two-thirds of the tail and therefore the interaction of the middle segment with the BH. Correspondingly, HMM exhibits an SRX but not an HRX rate (Cross et al., 1988). Together these observations provide strong support for the notion that interaction of the myosin tail with the SH3/converter region of the BH is the structural basis of hyper-relaxation.Another invertebrate muscle in which a putative HRX state has been observed is the scallop striated adductor. When thick filaments lose their ATP, helical ordering of the heads is lost (we would suggest by straightening of the heads in the apo state, so that the IHM can no longer form). EM shows that this process takes up to 30 min in scallop (Vibert and Craig, 1985), consistent with an HRX turnover rate. Scallop thick filaments differ from tarantula in having sevenfold rather than fourfold rotational symmetry (Vibert and Craig, 1983). Cryo-EM shows that this tightly packs the IHMs around the circumference of each crown, creating intermolecular interactions within crowns involving the SH3 domain of the BH and the motor domain of its neighbor FH (Figs. 1 B and 3 C; Woodhead et al., 2013; the heads in tarantula crowns are more widely spaced and do not show these interactions). While the reconstruction does not provide detail on possible tail interactions between crowns (as in tarantula), these additional intermolecular interactions may constrain the heads within a crown, impeding structural changes of the BH and FH and accounting for the hyper-slow release of products from scallop thick filaments through a mechanism quite different from that in tarantula.How is the IHM formed?Formation of the IHM depends on several key properties of myosin II: flexing of the heads and the head–tail junction and interaction of the motor domains with each other and with the proximal region of S2. BH–S2 interaction (where S2 runs over the bent BH) appears to be the primary binding interaction of the IHM (Alamo et al., 2016), as it is observed in smooth muscle HMM even when the FH is not bound to the BH (Burgess et al., 2007); FH–S2 interaction without interaction of the BH and BH–FH interaction without S2 are not observed. Interaction of S2 with the BH can only occur when the BH folds back onto the tail, and then only when the BH is in the strongly bent (Rosenfeld et al., 1994; Alamo et al., 2008, 2016; Scarff et al., 2020; Yang et al., 2020), nucleotide-trapping state, putatively with the SRX rate (Anderson et al., 2018). Thus, we picture the myosin molecule as having flexible heads (in a bent–straight equilibrium biased 90% toward the straight [DRX] conformation), which are flexibly attached to the tail, with the following sequence for formation of the IHM. If a transiently bent head comes in contact with S2, it binds and is stabilized in its bent (SRX) state, thereby becoming a BH (i.e., a precursor IHM; Alamo et al., 2016). The other head, flexing around its head–tail junction and in a similar bent–straight equilibrium, can now be caught (becoming an FH) when its converter region contacts the captured BH motor domain, stabilizing the FH bent conformation (Liu et al., 2003; Alamo et al., 2016; Scarff et al., 2020; Yang et al., 2020). This interaction is strengthened by contact of loops on the FH with S2 (Alamo et al., 2008; Scarff et al., 2020; Yang et al., 2020).Structural observations show that both heads of the IHM are strongly bent (Wendt et al., 2001; Woodhead et al., 2005; Scarff et al., 2020; Yang et al., 2020), while the bent structure in isolated heads may be uncommon. The sequence proposed above suggests how the IHM can be formed despite these constraints. If the bent structure occurs only rarely (e.g., 10% of the time), the likelihood of two bent heads coming together will be low: this likelihood is greatly increased by initial stabilization of one bent head (the BH) binding to S2 (forming the precursor IHM) and then binding of the second head (the FH) to the already bent BH of the precursor. This kinetic argument would explain why head–head interaction without involvement of the tail has not been observed, consistent with mutational studies (Adhikari et al., 2019). The final IHM is a tripartite structure with multiple weak interactions (BH–FH, BH–S2, and FH–S2) that inhibit ATPase activity as well as actin-binding capability (Scarff et al., 2020; Yang et al., 2020). These interactions are easily broken and in equilibrium with the noninteracting form. The result in isolated sarcomeric myosin soluble fragments at physiological ionic strength is an overall 25% SRX and 75% DRX rate (Anderson et al., 2018; Rohde et al., 2018; Gollapudi et al., 2021b). In filaments, individual IHMs (with the inhibited, bent structure of the individual heads) are stabilized by intermolecular interactions occurring in the polymer (as described earlier), increasing the fraction of SRX heads above 50%.Is there a relationship of the SRX state with animal lifestyle?We have suggested that nature uses two ways to enhance the SRX state: increase in fraction of inhibited heads and increase in degree of inhibition. The particular mechanism may be adapted to the lifestyle of the animal (Naber et al., 2011). Tarantulas spend long periods of time immobile and can survive many months without food. Minimizing ATP use during this time by hyper-relaxation of their BHs and SRX of most of their FHs would be an evolutionary advantage (Naber et al., 2011). They would nevertheless be ready for a rapid switch to the active state through the small numbers of swaying FHs that sense thin filament activation when muscle is stimulated (Brito et al., 2011). Scallops can swim quickly for short bursts by jet propulsion, using their striated adductor muscles to rapidly close their shell (e.g., to escape predators), but they remain stationary during extended periods of filter feeding (Speiser and Wilkens, 2016). In this low-activity state, the shell is held partially closed through contraction of the tonic smooth adductor muscle, which enters a catch state, maintaining force with little energy expenditure (Chantler, 2016). The striated adductor is 10 times more massive than its smooth counterpart (Naidu, 1987) and a potential metabolic drain during the long periods when the muscle is not in use: minimizing ATP use during these nonswimming periods through hyper-relaxation of their heads would be advantageous. The folded form of vertebrate smooth muscle and nonmuscle myosin is thought to serve as a storage molecule, which can be activated to form functional filaments as required through phosphorylation of their RLCs (Cross et al., 1988). The complete switching off of ATPase activity through hyper-relaxation when the molecule is not in use would again provide an evolutionary advantage.Vertebrate striated muscle thick filaments exhibit SRX but not hyper-relaxation. Interaction of IHMs with each other or with the filament backbone, MyBP-C, or titin enhances the fraction of heads in the SRX state but does not significantly increase the level of inhibition of the heads. SRX appears to be developed most strongly in the C-zone (probably in the two crowns of heads showing IHMs in each three-crown repeat), implicating MyBP-C in this inhibition (McNamara et al., 2016, 2019; Nelson et al., 2020). Myosin heads in the D-zone and in the non-IHM crown in the C-zone are less ordered (Zoghbi et al., 2008; AL-Khayat et al., 2013; Brunello et al., 2020) and may be the main source of DRX heads detected by single turnover experiments (Nelson et al., 2020). Vertebrates may make a trade-off of greater (though still low) ATP use in the RX state (SRX with some DRX heads) for the ability to switch on instantly as needed and for fine-tuning of the contractile response through interactions with other proteins such as MyBP-C.How are thick filaments activated from the SRX state?We have painted a picture in which most myosin heads in the thick filaments of resting muscle are tacked down on the filament surface in helices of IHMs in an SRX (or HRX) state. However, muscles must be ready for immediate activation from this energy-saving state. The other part of the picture therefore includes a small fraction of heads dissociated from the IHM at any particular moment. These relatively few, mobile, constitutively on (“sentinel”) heads are presumed to constantly explore the interfilament space, able to instantly sense thin filament activation and bind to actin when myosin-binding sites are exposed (by Ca²⁺-induced tropomyosin movement; Gordon et al., 2000), leading to initial tension development (Linari et al., 2015; Irving, 2017). We suggest that these are the transiently dissociated (swaying) FHs of the IHMs. In vertebrates, the sentinel heads could also include the less well-ordered heads at every third crown of the C-zone (Zoghbi et al., 2008; AL-Khayat et al., 2013) or the disordered heads in the D-zone (Brunello et al., 2020; Nelson et al., 2020). This essential role for a small number of mobile heads as the trigger for thick filament activity, when thin filaments are switched on, is paid for by the increase in ATP consumption over that used by SRX heads. What happens next depends on the type of muscle.In tarantula, the small amount of thick filament activity in an initial twitch appears to be enhanced in additional twitches by Ca²⁺-induced activation of myosin light chain kinase, which phosphorylates the FH RLCs, leading to increased release of the FHs from the IHMs, reduction in the HRX fraction and increase in the DRX fraction (Naber et al., 2011), and increased force production (Padrón et al., 2020). Prolonged high Ca²⁺ (e.g., in a tetanus) subsequently phosphorylates the BHs, resulting in their release and further enhancement of force (Padrón et al., 2020).Vertebrates have a finely tuned, graded response to activation. X-ray studies show that low-force isotonic contractions use only a small fraction of available heads (Linari et al., 2015). The majority remain helically ordered in their IHM configurations, continuing to save energy—even during contraction—representing a highly efficient use of ATP. As force increases, stress on the thick filaments rises, resulting in release of more heads, which produce greater force, in a positive feedback loop (Linari et al., 2015; Irving, 2017). In this mechanosensing model for thick filament activation, the filament is stretched by ∼1%, which may be sufficient to weaken intermolecular contacts between heads along the helical tracks that help to maintain the IHM conformations (Irving, 2017). Destabilization of the IHMs by stress could thus release the additional heads needed for strong force production. When contraction is switched off by removal of Ca²⁺ from the cytosol, IHMs rapidly go back to their helically ordered arrangement (Linari et al., 2015; cf. Ma et al., 2019), quickly returning the muscle to its energy-saving SRX state.In scallop, the thick filaments are directly activated by Ca²⁺ binding to the essential light chains (ELCs) on the myosin heads rather than through Ca²⁺ activation of the thin filaments (Szent-Györgyi et al., 1999; Chantler, 2016). Ca²⁺ binding causes breakage of the IHM intra- and intermolecular interactions, cooperatively releasing heads from their SRX/HRX state (Szent-Györgyi et al., 1999; Zhao and Craig, 2003; Jung et al., 2008; Chantler, 2016). Released Ca²⁺-activated heads can move freely, similarly to phosphorylated heads of tarantula, interacting with actin to generate force. As this process involves binding of Ca²⁺ to the myosin heads and not the slower, enzymatic phosphorylation of the light chains, full activation can occur rapidly (Zhao and Craig, 2003), making all heads immediately available for the powerful twitches that produce the strong swimming motions of this species. In the absence of a thin filament switch in scallops, sentinel heads may not be required as the heads directly sense Ca²⁺ activation.Interactions between IHMs along their helical tracks are common to all thick filaments in the SRX/HRX state. Reconstructions of tarantula, scallop, and vertebrate thick filaments, representing three distinct mechanisms of activation, all show such interactions, typically between the FH motor domain of one IHM and the BH regulatory domain of its neighbor in the next crown closer to the filament center (Figs. 2 C and ​and3;3; Woodhead et al., 2005; Zoghbi et al., 2008; AL-Khayat et al., 2013; Woodhead et al., 2013). As described earlier, these intermolecular interactions appear to stabilize the IHM conformation, enhancing the fraction of SRX heads in filaments. Concomitantly, they may also underlie rapid thick filament activation, as they provide a direct physical path for cooperative disruption of the IHM and thus exit from the SRX state (Stewart et al., 2010; McNamara et al., 2015). Cooperative exit from the SRX state has been experimentally demonstrated in skeletal and cardiac muscle incubated with mantATP chased by ADP (Stewart et al., 2010; Cooke, 2011; Gollapudi et al., 2021b). Cooperative activation is especially well developed in scallop thick filaments (Szent-Györgyi et al., 1999; Chantler, 2016), where it may underlie the rapid Ca²⁺ activation leading to the strong swimming motions of this species. The intermolecular interactions along helices and around each crown in scallops (Fig. 3 C; Woodhead et al., 2013) connect all heads in an extensive network that could be rapidly disrupted by Ca²⁺ binding.How is SRX modulated?The stability of the IHM and the level of SRX can be modulated in several ways, including myosin RLC phosphorylation and, in vertebrates, phosphorylation of MyBP-C (Stewart et al., 2010; Nag and Trivedi, 2021). RLC phosphorylation in tarantula greatly reduces the fraction of SRX and HRX heads and their ATP turnover times (Naber et al., 2011) while increasing DRX heads. This correlates with a decrease in helical ordering and extension of heads from the filament backbone (suggesting disruption of the IHM), as demonstrated by x-ray diffraction (Padrón et al., 2020) and EM (Craig et al., 1987). Phosphorylation not only activates heads but also maintains a memory of activation following the extensive phosphorylation that occurs in a tetanus; this can greatly potentiate subsequent contraction (Padrón et al., 2020). Disruption of the IHM and extension of heads toward neighboring actin filaments in the RX period following a tetanus presumably enables the stronger and more rapid interaction with actin of a post-tetanic contraction (Padrón et al., 2020). While the phosphorylated RX state that follows a tetanus would temporarily consume more ATP, it could provide a survival benefit by enabling stronger contractions when escaping predators or capturing prey. Following such periods of activity, the RLCs again become dephosphorylated, and the energy-saving SRX/HRX state, with ordered, interconnected IHMs lying along the filament surface, returns (Padrón et al., 2020), characterizing the long periods of inactivity in the life of the tarantula, when ATP savings are critical.Vertebrate skeletal muscle RLCs can also be phosphorylated, and phosphorylation correlates with post-tetanic potentiation (Sweeney et al., 1993) together with disordering of myosin helices and extension of heads from the filament surface (Levine et al., 1996; Yamaguchi et al., 2016), again suggestive of IHM disruption. As with tarantula, a corresponding reduction in the SRX state with phosphorylation (Stewart et al., 2010; Cooke, 2011; Gollapudi et al., 2021b), with a temporarily greater resting ATP consumption, pays for the greater contractility available following phosphorylation.Vertebrates have a second means of modulating the SRX state, which may provide finer control of thick filament activation/relaxation than with invertebrates. MyBP-C binds to myosin in the middle one-third of each half of the thick filament (the C-zone; Craig and Offer, 1976; Flashman et al., 2004; Luther et al., 2008), and several lines of evidence demonstrate that the SRX state is more pronounced in these regions (McNamara et al., 2016, 2019; Nelson et al., 2020; Nag and Trivedi, 2021), reaching as high as 90% (Nelson et al., 2020); this correlates with the clearest delineation of IHMs in reconstructions of the thick filament C-zone (Zoghbi et al., 2008; AL-Khayat et al., 2013). Toward the tips of the filament (the distal or D-zone), heads are less ordered (Brunello et al., 2020; R. Craig, unpublished EM data), and the SRX state is diminished (Nelson et al., 2020). In MyBP-C knockout mice, the IHM configuration is weakened or abolished (Zoghbi et al., 2008), and the SRX state is disrupted (McNamara et al., 2016). Thus MyBP-C appears to enhance the SRX state, apparently by stabilizing the IHM. This stabilization is further modulated by phosphorylation of MyBP-C, occurring in the heart in response to β-adrenergic stimulation. Enhancement of cardiac contractility by cardiac MyBP-C (cMyBP-C) phosphorylation may result in part from depression of cMyBP-C’s stabilizing effect on the SRX, which coincides with weakening of the IHM (Kensler et al., 2017; Caremani et al., 2019b; Irving and Craig, 2019; McNamara et al., 2019). These data overall imply that MyBP-C enhances energy saving by stabilizing the IHM structure and that this is modulated in the heart by cMyBP-C phosphorylation (McNamara et al., 2019).Importantly, in the healthy heart, RLC and MyBP-C phosphorylation are not zero but ∼50% (Chang et al., 2015) and ∼60% of maximum (Previs et al., 2012), respectively. This would suggest a partial weakening of the SRX state (compared with zero phosphorylation) during normal cardiac activity, which may poise myosin heads optimally between sequestration in the IHM (to save energy) and availability for interaction with actin to generate force, with fine-tuning of these levels available upon further phosphorylation. Thus, we assume that the level of SRX of a muscle (degree of IHM formation) is tuned to the physiological needs of the moment, with the goal over time of minimizing energy consumption within these limits. Strikingly, phosphorylation levels of MyBP-C and RLC can both decrease in heart failure (El-Armouche et al., 2007; Toepfer et al., 2013), which would predict a higher fraction of SRX heads. This may reduce the need for energy under these adverse circumstances but may also contribute to the compromised contractility of the failing heart.Animals can save energy when food supplies are scarce or weather conditions adverse by a reduction in body temperature. This occurs naturally in ectotherms (cold-blooded animals) when exterior temperatures drop and by hibernation in some endotherms (warm-blooded animals), where body temperature and metabolism reduce to low values. Does enhanced SRX play a role in energy conservation under these circumstances? X-ray diffraction of both mammalian and tarantula muscle at low temperatures (10°C) suggests that the number of myosin motors in the helically ordered, IHM conformation decreases substantially compared with temperatures nearer physiological levels (Malinchik et al., 1997; Xu et al., 1997; Caremani et al., 2019a, 2021; Ma et al., 2021a); modeling of tarantula suggests that it is specifically the FHs that are disordered, while the BHs remain ordered (Ma et al., 2021a). This disordering suggests that the SRX state may actually be reduced, rather than enhanced, in cold temperatures. Other factors may contribute to energy conservation by muscle under cold conditions (Caremani et al., 2021; Ma et al., 2021a): myosin heads become refractory to actin binding at low temperature (Caremani et al., 2019a), and the disordered FHs, containing ADP.Pi at the active site, may transition toward the ATP conformation, inhibiting ATP turnover (Xu et al., 1999; Ma et al., 2021a). The impact of torpor (a form of hibernation) on the SRX state has recently been explicitly studied in the 13-lined ground squirrel (Ictidomys tridecemlineatus; Toepfer et al., 2020). During torpor, core body temperature drops to 5°C, metabolic rate to 3% of basal levels, and heart rate from 311 to 6 beats per min; hummingbirds undergo a similar dramatic reduction in metabolic rate to save energy each night (Shankar et al., 2020). The fraction of SRX heads found in cardiac muscle removed from the ground squirrel during torpor was reported to increase from 65 to 75%, contrary to expectation from the low-temperature x-ray studies of mammalian muscle described above that would imply a decrease in the number of IHMs. This discrepancy could be due to performance of the SRX measurements at 21°C (Toepfer et al., 2020) rather than the low temperatures used in the x-ray experiments that revealed helical disordering. The latter would presumably reflect the thick filament structure most accurately at actual torpor temperatures. We speculate that the phenomenon of iguanas (ectotherms) falling from trees and becoming immobile when environmental temperatures are abnormally low (Stroud et al., 2020) may be caused in part by the refractory impact of temperature on the ability of their myosin heads to bind to actin; a similar effect may have contributed to extinction of the dinosaurs during the global cooling that followed the asteroid impact of 66 million years ago (Vellekoop et al., 2014).Modulation of the SRX and its putative structural correlate, the IHM, may play a critical role in a number of cardiac diseases and their treatment, summarized elsewhere (Alamo et al., 2017; Nag et al., 2017; Yotti et al., 2019; Trivedi et al., 2020; Daniels et al., 2021; Schmid and Toepfer, 2021). Hypertrophic cardiomyopathy (HCM) is an inherited disease caused by mutations in sarcomeric proteins, including myosin, and characterized by hypercontractility and the inability to fully relax during diastole (Ashrafian et al., 2011). Recent studies show that mutations in the myosin heavy chain (MYH7; accounting for ∼40% of HCM cases) strongly cluster in regions of the myosin molecule involved in the interfaces of the IHM (Alamo et al., 2017; Nag et al., 2017), and lead to a substantial decrease in SRX and increased energy use (Anderson et al., 2018; Adhikari et al., 2019; Sarkar et al., 2020). Disruption of the IHM by such mutations, at the head–head or BH–S2 interface, could release more heads for interaction with actin, accounting for the hypercontractility and impaired relaxation observed (Alamo et al., 2017; Anderson et al., 2018; Spudich, 2019; Sarkar et al., 2020). Experimental evidence for this proposal has been obtained (Adhikari et al., 2019; Sarkar et al., 2020). Mutations in MyBP-C leading to HCM also appear to partially disrupt the SRX state of the myosin heads (Toepfer et al., 2019; Nag and Trivedi, 2021), leading to an increase in the number of DRX heads, which may contribute to the observed hypercontractility (McNamara et al., 2017). Depending on the mutation, cMyBP-C may have a reduced affinity for myosin, or the amount of MyBP-C incorporated into the thick filament may be reduced. It has been proposed that either mechanism would reduce the strength of the cMyBP-C–myosin interaction, releasing heads from the filament backbone (DRX heads), which could be partially responsible for the hypercontractile phenotype observed in patients with these mutations (Colson et al., 2007; Toepfer et al., 2019; Nag and Trivedi, 2021).Impaired relaxation due to HCM mutations in myosin (and other myofibrillar proteins) can be compensated by a recently developed drug, mavacamten, which has been shown to increase the fraction of myosin heads in the SRX state (Anderson et al., 2018; Rohde et al., 2018; Spudich, 2019; Nag and Trivedi, 2021), specifically in the D-zone of thick filaments (Nelson et al., 2020), concomitant with an increased number of molecules folded into the IHM conformation (Anderson et al., 2018; Rohde et al., 2018; Gollapudi et al., 2021b). In thick filaments of intact cardiac muscle, mavacamten increases the degree of quasi-helical ordering of myosin heads, consistent with an increase in the stability or fraction of molecules in the IHM conformation (Anderson et al., 2018), supporting our overall contention that the IHM is the main basis of the SRX state in muscle. Mavacamten inhibits the ATPase activity of isolated S1, specifically by inhibiting phosphate release (Green et al., 2016), suggesting that it enhances the bent (SRX) state of the myosin head, which, based on our earlier reasoning, would lead to the observed increase in the fraction of molecules in the IHM (Anderson et al., 2018).Future directionsWe currently know the structure of the IHM at ∼15 Å resolution in tarantula (Yang et al., 2016) and insect (Hu et al., 2016) filaments and ∼4 Å resolution in single smooth muscle myosin molecules (Scarff et al., 2020; Yang et al., 2020). Improvements in resolution should enhance visualization of the side-chain interactions that stabilize the SRX state in both filament and monomer. For filaments, cryo-EM of tarantula offers the greatest potential, owing to the stability of its helices. To better understand how mutations in the IHM interfaces lead to the hypercontractility of HCM, cryo-EM of vertebrate cardiac thick filaments is required to improve the resolution beyond the current ∼40 Å (obtained with negative staining; Zoghbi et al., 2008; AL-Khayat et al., 2013), a difficult task owing to the lability and quasi-helical symmetry of the vertebrate thick filament head array. Differences in the levels of SRX in the C- and D-zones of the thick filaments (Nelson et al., 2020) suggest differences in IHM stability or interactions, which will need to be analyzed by cryo-EM, again a significant task for the reasons stated above and because of the small size of these zones. The most detailed insights into IHM intramolecular interactions should come from a high-resolution structure of the IHM in isolated cardiac myosin molecules, which is urgently needed. This could potentially be obtained by x-ray crystallography or cryo-EM of IHM constructs (e.g., 25 heptad; Fig. 1; Anderson et al., 2018), although this is likely to be hampered by the relative instability of the structure. Incubation with mavacamten may improve its stability (Anderson et al., 2018). How interaction of MyBP-C with myosin enhances the SRX state is another fertile but challenging area of investigation, which may require cryo-electron tomography of thick filaments or intact myofibrils (Burbaum et al., 2021) or single particle cryo-EM studies of MyBP-C–IHM complexes. Experiments suggest that thick filaments in muscle are in equilibrium with a pool of myosin monomer, which may play a role in thick filament assembly/disassembly during development, hypertrophy, and myosin turnover (Saad et al., 1986; Katoh et al., 1998; Ojima, 2019). Myosin monomers at physiological ionic strength form IHMs with a folded tail structure and slow ATP turnover rate, which may act as a transport form from ribosome to filament (Ankrett et al., 1991; Katoh et al., 1998; Jung et al., 2008). Whether the SRX/IHM structure in thick filaments affects the monomer–polymer equilibrium is an area for future investigation.ConclusionThe SRX state of thick filaments plays a crucial role in the energy balance of muscle and is ubiquitous across the animal kingdom. It results from a conformation of the myosin head in which ATP turnover is strongly inhibited, minimizing ATP use. This conformation is stabilized by intramolecular interactions when it is incorporated into the IHM and by additional intermolecular interactions when IHMs are assembled into thick filaments, increasing the fraction of energy-saving SRX heads. Thus, we propose that IHMs, helically organized along the thick filament surface in the relaxed state, are the major basis of SRX in living muscle. An HRX state, found in thick filaments of some invertebrates and in the folded (storage) form of smooth muscle and nonmuscle myosin molecules, is also based on the IHM but in these cases results from additional intra/intermolecular interactions. A filament in which every head was in SRX, while maximally saving ATP, would not be useful in contraction: at any time, a small fraction of heads is dissociated (DRX or sentinel heads) and available to sense thin filament activation and generate initial force. The SRX state is down-regulated in situ by RLC and MyBP-C phosphorylation in response to physiological requirements (activation), which disrupt the IHM, releasing heads for interaction with actin. Mutations in myosin or MyBP-C causing HCM disrupt the SRX state, causing hypercontractility, which can be reversed by drugs that stabilize the IHM and thus the SRX.Online supplemental materialVideo 1 shows human cardiac thick filament reconstruction fitted with a human cardiac atomic model to demonstrate an apparent absence of interaction between S2 from one level of heads and the SH3 and converter domains of the next level. Video 2 shows tarantula thick filament reconstruction fitted with a tarantula IHM atomic model to show that in this species there is an interaction between S2 from one level of heads and the SH3 and converter domains of the next level.     

Who’s in control? Principles of Rab GTPase activation in endolysosomal membrane trafficking and beyond

The eukaryotic endomembrane system consists of multiple interconnected organelles. Rab GTPases are organelle-specific markers that give identity to these membranes by recruiting transport and trafficking proteins. During transport processes or along organelle maturation, one Rab is replaced by another, a process termed Rab cascade, which requires at its center a Rab-specific guanine nucleotide exchange factor (GEF). The endolysosomal system serves here as a prime example for a Rab cascade. Along with endosomal maturation, the endosomal Rab5 recruits and activates the Rab7-specific GEF Mon1-Ccz1, resulting in Rab7 activation on endosomes and subsequent fusion of endosomes with lysosomes. In this review, we focus on the current idea of Mon1-Ccz1 recruitment and activation in the endolysosomal and autophagic pathway. We compare identified principles to other GTPase cascades on endomembranes, highlight the importance of regulation, and evaluate in this context the strength and relevance of recent developments in in vitro analyses to understand the underlying foundation of organelle biogenesis and maturation.

Membrane identity in the endomembrane systemOne key feature of eukaryotic cells is the presence of membrane-enclosed organelles, which constantly exchange proteins, lipids, or metabolites via vesicular transport or membrane contact sites (MCSs). Along the endomembrane system, vesicular trafficking requires vesicle budding from the donor membrane and directed transport toward and fusion with the acceptor compartment. The resulting trafficking routes form a regulated network that connects not only the internal organelles, but also the interior and exterior of the cell.The specific identity of organelles within the endomembrane system is defined by the lipid and protein composition of their membranes. This includes signaling lipids such as phosphoinositides (PIPs) and small GTPases of the Ras superfamily of small G proteins, namely of the Rab, Arf, and Arl families, which act as binding platforms for accessory proteins involved in multiple membrane trafficking processes (Balla, 2013).Rab GTPases, like other small GTPases, are key regulatory proteins that switch between an inactive GDP-bound (Rab-GDP) and an active GTP-bound (Rab-GTP) state (Barr, 2013; Goody et al., 2017; Hutagalung and Novick, 2011). Rabs are posttranslationally modified by the addition of geranylgeranyl moieties to C-terminal cysteine residues, which allow their reversible membrane association. Within the cytosol, Rab-GDP is kept soluble by binding to the chaperone-like GDP dissociation inhibitor (GDI). At the target membrane, an organelle-specific guanine nucleotide exchange factor (GEF) activates the Rab after its previous release from GDI, a process possibly supported by other factors (Dirac-Svejstrup et al., 1997). GTP binding stabilizes two loops in the Rab GTPase domain, which allows recruitment and binding of various so-called effector proteins to the Rab-GTP on the membrane. Rab GTPases are inefficient enzymes with a low intrinsic GTP hydrolysis rate and thus depend on a GTPase-activating protein (GAP) to hydrolyze bound GTP. GDI then extracts the Rab-GDP and keeps it soluble in the cytosol until the next activation cycle (Barr, 2013; Goody et al., 2017; Hutagalung and Novick, 2011). In addition to their conserved GTPase domain, Rabs contain a hypervariable C-terminal domain (HVD), which supports GEF recognition and therefore correct localization of the Rab (Thomas et al., 2018)Among various other functions, Rab GTPases are critical for the fusion of vesicles with the acceptor membrane by recruiting tethering proteins, which bring the two membranes into close proximity. Tethers, together with Sec1/Munc18 proteins, promote the folding of membrane-bound SNAREs at the vesicle and the target membrane into tetrameric coiled-coil complexes. This process further reduces the distance between the membranes, bypasses the hydration layer on membranes, and results in mixing of lipid bilayers and consequently membrane fusion (Wickner and Rizo, 2017; Ungermann and Kümmel, 2019).Organization and function of the endolysosomal pathwayEndocytosis allows the rapid adaptation of plasma membrane composition in response to changing environmental conditions by the uptake of membrane proteins from the plasma membrane, which are either transported to and finally degraded in the lysosome or sorted back to the plasma membrane, e.g., receptors after releasing their cargo within the endosomal lumen (Sardana and Emr, 2021). A third fate of endocytosed cargo is trafficking to the Golgi (Laidlaw and MacDonald, 2018). In addition, various kinds of endocytosis allow the uptake of very large particles such as bacteria during phagocytosis or fluids during pinocytosis (Huotari and Helenius, 2011; Babst, 2014). The endocytic pathway is also involved in the quality control system of plasma membrane proteins and allows degradation of damaged cell surface proteins as well as the down-regulation of nutrient transporters and receptors (Sardana and Emr, 2021). During endocytosis, membrane proteins marked by ubiquitination are incorporated into endocytic vesicles, which pinch off the plasma membrane and fuse with the tubular-shaped early endosome (EE) in the cell periphery (Fig. 1 A). The EE serves as a sorting station, at which membrane proteins are either sorted into tubular structures and brought to the recycling endosome (RE) or get incorporated into intraluminal vesicles (ILVs) with the help of four endosomal sorting complexes required for transport (ESCRTs; Sardana and Emr, 2021). A prerequisite for the degradation of cargo in the lysosome is the maturation of EEs into late endosomes (LEs) by changing the organelle surface composition, including specific Rab GTPases and PIPs, and organelle shape. The LE is eventually spherically shaped, containing multiple ILVs and a more acidified lumen. Therefore, it is also called Multivesicular Body (MVB). Upon fusion with the lysosome, ILVs and their content are degraded into precursor molecules, which are reused by the cell (Fig. 1 A; Sardana and Emr, 2021; Huotari and Helenius, 2011).Open in a separate windowFigure 1.Rab GTPases in the endolysosomal pathway.(A) Localization of key Rab GTPases along the endolysosomal pathway. Endocytic vesicles containing cargo (blue dot) or receptor proteins (red) are substrates of endocytosis. Endocytic vesicles (EV) fuse with the EE. Rabs are shown by numbers: Rab5 (green) on early EE is replaced by Rab7 (black) on multivesicular bodies (MVBs). GEFs are shown in blue. Positioning of lysosomes (Lys) depends on binding to motor proteins by either Arl8b (orange, 8b) or Rab7. Recycling occurs via REs involving Rab4, Rab11, and Rab14. MTOC, microtubule organizing center; Nuc, nucleus. (B) Spatiotemporal Rab5-to-Rab7 transition during endosomal maturation. Rab5 (green graph) is rapidly recruited to EE and replaced by Rab7. (C) Model of Rab7 GEF recruitment and activation on endosomes. Mon1-Ccz1 (or the trimeric complex additionally containing Rmc1/C18orf8/Bulli, as indicated by the unlabeled hexagon) requires Rab5-GTP for activation to promote Rab7 recruitment. For details, see text.Central functions of Rab5 and Rab7Along the endolysosomal system, several Rabs coordinate sorting and recycling processes at the EE and LE. Early endosomal Rab5 and late endosomal Rab7 are here the key Rabs conserved among species. Their spatiotemporal activation and therefore functions are tightly coordinated on the level of the MVB/LE (Fig. 1 B).In yeast, the Rab5-like GTPases Vps21, Ypt52, Ypt52, and Ypt10 and the Rab7-like Ypt7 structure the endocytic pathway (Singer-Krüger et al., 1994; Wichmann et al., 1992). In mammalian cells, Rab5 (with Rab5a, b, and c isoforms having nonredundant functions in the endocytic network; Chen et al., 2014, 2009) and Rab7 (with Rab7a and b isoforms, of which Rab7a is the main actor in transport processes along the endocytic pathway [Guerra and Bucci, 2016], whereas Rab7b has a role in the transport from endosome to the Golgi [Kjos et al., 2017; Progida et al., 2010]) are present (Wandinger-Ness and Zerial, 2014). While the overall organization of the endocytic pathway into EE and LE is conserved, yeast seems to have a more ancestral minimal endomembrane system, where the trans-Golgi network acts as EE and RE (Day et al., 2018). In mammalian cells, the more complex endolysosomal system depends on additional Rabs. Rab4 is involved in protein sorting at the EE, activation of Rab5, and recycling of cargo back to the plasma membrane (Kälin et al., 2015; Wandinger-Ness and Zerial, 2014; de Renzis et al., 2002), whereas Rab11 and Rab14 function at REs (Fig. 1 A; Linford et al., 2012; Takahashi et al., 2012). Furthermore, Rab9 is required for retrograde transport between LEs and the trans-Golgi network (Lombardi et al., 1993), and Rab32 and Rab38 function in the biogenesis of lysosome-related organelles (Bowman et al., 2019; Gerondopoulos et al., 2012; Wasmeier et al., 2006).During endosomal maturation, Rab5 is exchanged for Rab7 (Rink et al., 2005; Poteryaev et al., 2010). This Rab switch is highly conserved and a prime example of coordinated Rab turnover during organelle maturation. The rapid transition from Rab5 to Rab7 was explained by a so-called cutout switch, where activation of Rab5 fosters at a threshold value activation of Rab7, which in turn suppresses further Rab5 activation (Fig. 1 B; Del Conte-Zerial et al., 2008). Such a principle may apply to most Rab cascades (Barr, 2013).Rab5 has multiple functions on EEs (Wandinger-Ness and Zerial, 2014). It interacts with a number of effectors such as the lipid kinase Vps34, Rabaptin-5, which is found in complex with the Rab5-GEF Rabex5, Rabenosyn-5, and tethers such as the class C core vacuole/endosome tethering (CORVET) complex or EEA1. Therefore, Rab5 is critical for the homotypic fusion of EEs (Gorvel et al., 1991; Ohya et al., 2009; Christoforidis et al., 1999a, b; Perini et al., 2014; Marat and Haucke, 2016). Vps34 was initially identified in yeast (Schu et al., 1993) and exists in two heterotetrametric complexes, which differ by just one subunit (Kihara et al., 2001). Complex I resides on autophagosomes, whereas complex II functions on endosomes (Fig. 2 D). Both complexes generate a local pool of phosphatidylinositol-3-phosphate (PI3P), to which several effectors bind, including the early endosomal tether EEA1 and ESCRTs (Wallroth and Haucke, 2018). Recent structural insights revealed that Rab5 recruits and activates endosomal complex II, whereas Rab1 acts similarly on autophagosomal complex I (Tremel et al., 2021). This explains how Rab5-GTP promotes the formation of a local endosomal PI3P pool (Franke et al., 2019). Interestingly, Caenorhabditis elegans VPS-34 can recruit the Rab5 GAP TBC-2 to endosomal membranes, suggesting a possible link between PI3P generation and Rab5 inactivation (Law et al., 2017).Open in a separate windowFigure 2.Rab7 activation on autophagosomes.(A and B) Atg8-dependent Mon1-Ccz1 recruitment and activation. Atg8 (violet) recruits Mon1-Ccz1 (and likely also the trimeric GEF complex in higher eukaryotes, as indicated by the unlabeled hexagon) and allows fusion with lysosome. (C) Model of spatiotemporal Rab7 activation on autophagosomes. Maturation is prerequisite for successful fusion. (D) Comparison of proteins involved in maturation of LEs and autophagosomes.Rab7 is a key component in the late endocytic pathway (Langemeyer et al., 2018a). It is found on LEs, lysosomes, and autophagosomes and is required for the biogenesis and positioning of LEs and lysosomes, for MCSs of lysosomes with other organelles, and for the fusion of endosomes and autophagosomes with lysosomes (Fig. 1 A; Guerra and Bucci, 2016; McEwan et al., 2015; Ballabio and Bonifacino, 2020; Cabukusta and Neefjes, 2018). Even though both the metazoan Rab7 and yeast Ypt7 are activated by the homologous Mon1-Ccz1 GEF complex and are required for endosomal maturation, their function on LEs and lysosomes is not entirely conserved. In yeast, active Ypt7 directly binds the hexameric homotypic fusion and vacuole protein sorting (HOPS) tethering complex and mediates SNARE-dependent fusion of LEs or autophagosomes with vacuoles as well as homotypic vacuole fusion (Wickner and Rizo, 2017; Gao et al., 2018a, b). In higher eukaryotes, HOPS also promotes fusion between LEs and lysosomes, yet apparently does not directly interact with Rab7, but rather with the GTPases Rab2 and Arl8b (Gillingham et al., 2014; Fujita et al., 2017; Lőrincz et al., 2017; Khatter et al., 2015). How Rab7 contributes to fusion at the lysosome is still unclear. Rab7 interacts with several proteins on lysosomes, including the cholesterol sensor ORPL1 and the dynein-interacting lysosomal RILP (Jordens et al., 2001; Cantalupo et al., 2001; Rocha et al., 2009). Both proteins also bind HOPS (van der Kant et al., 2015, 2013), as does another multivalent adaptor protein, PLEKHM1 (McEwan et al., 2015), which binds both Arl8b and Rab7 (Marwaha et al., 2017). Interestingly, Arl8b in complex with its effector SKIP also binds TBC1D15, a Rab7 GAP, which may displace Rab7 from LEs before their fusion with lysosomes (Jongsma et al., 2020). It is thus possible that fusion of LEs and autophagosomes with lysosomes requires a complex coordination of the three GTPases, Rab7, Arl8b, and Rab2, with the HOPS complex and other effectors. Some of this complexity may be explained by a second function of Rab7 and Arl8b in binding adapters of the kinesin or dynein motor protein family, which connect LEs and lysosomes to the microtubule network. Thereby Rab7 and Arl8b control the positioning of these organelles to the periphery or perinuclear area via the microtubule network, which has functional implications (Fig. 1 A; Cabukusta and Neefjes, 2018; Bonifacino and Neefjes, 2017). Perinuclear lysosomes are the main places for degradation of cargo delivered by endosomes and autophagosomes, whereas peripheral lysosomes are involved in the regulation of mammalian target of rapamycin complex1 (mTORC1), the master regulator switching between cell growth and autophagy (Johnson et al., 2016; Korolchuk et al., 2011). This also may be connected to the role of lysosomes in lipid homeostasis, as Rab7 seems to control cholesterol export via the lysosomal NPC1 (van den Boomen et al., 2020; Shin and Zoncu, 2020; Castellano et al., 2017). How far the acidification state of perinuclear and peripheral lysosomes also affects their Rab7 and Arl8b mediated localization is still under debate (Ponsford et al., 2021). Thus, it is likely that Rab7 coordinates LE and lysosomal transport and fusion activity in coordination with endosomal biogenesis and cellular metabolism.GEF function and regulation in endosomal maturationThe heterodimeric complex Mon1-Ccz1 was identified as the GEF for Ypt7 in yeast and for Rab7 in higher eukaryotes (Nordmann et al., 2010; Gerondopoulos et al., 2012). The Mon1-Ccz1 complex is an effector of Rab5 (Kinchen and Ravichandran, 2010; Langemeyer et al., 2020; Cui et al., 2014; Li et al., 2015; Poteryaev et al., 2010; Singh et al., 2014), suggesting a direct link to endosomal maturation and Rab turnover (Fig. 1 B). Structural analyses uncovered how the two central longin domains in Mon1 and Ccz1 displace the bound nucleotide from Ypt7 (Kiontke et al., 2017). Unlike yeast, the metazoan Mon1-Ccz1 complex contains a third subunit termed RMC1 or C18orf8 in mammals and Bulli in Drosophila (Vaites et al., 2017; Dehnen et al., 2020; van den Boomen et al., 2020). Even though loss of this subunit impairs endosomal and autophagosomal biogenesis, this subunit does not affect GEF activity toward Rab7 in vitro (Dehnen et al., 2020; Langemeyer et al., 2020), indicating that the general GEF mechanism is conserved across species. As Rab7 is required on LEs, autophagosomes, and lysosomes, spatial recruitment and activity of the Rab7 GEF must be tightly regulated.Rab5 activates the Mon1-Ccz1 GEF complexDuring endosomal maturation, the Mon1-Ccz1 complex is recruited to Rab5- and PI3P-positive endosomes and activates Rab7 for subsequent fusion of endosomes with lysosomes (Nordmann et al., 2010; Poteryaev et al., 2010; Cabrera and Ungermann, 2013; Cabrera et al., 2014; Singh et al., 2014; Fig. 1 C). However, it was postulated that (but remained unclear how) Rab5 affects Rab7 GEF activity. The activity of GEFs is in the simplest way determined in solution, where the respective Rab, which has been loaded with a fluorescent- or radioactive-labeled nucleotide, is incubated with the GEF (Schoebel et al., 2009; Bergbrede et al., 2009). GDP or GTP addition then triggers displacement of the bound nucleotide, which results in a decrease of fluorescence or increase of radioactive signal in solution. Such in-solution assays can uncover the Rab specificity of GEFs yet cannot recapitulate the membrane context and potential regulating factors. Recent approaches therefore used liposomes and prenylated Rab:GDI complexes to address the role of membrane lipids and proteins in GEF activation (Thomas and Fromme, 2016; Thomas et al., 2018; Langemeyer et al., 2020, 2018b; Cezanne et al., 2020; Bezeljak et al., 2020). Details of these reconstituted systems are discussed below. In yeast, prenylated, membrane-bound, and GTP-loaded Rab5-like Vps21 was surprisingly inefficient as a single factor to recruit Mon1-Ccz1 to membranes, whereas addition of PIPs together with Vps21 enhanced recruitment (Langemeyer et al., 2020). However, activity of both the yeast and metazoan Rab7 GEF complexes showed a striking dependence on membrane-bound Rab5-GTP in the GEF assay, whereas PIPs alone were not sufficient to drive GEF activation. These observations demonstrate that the Mon1-Ccz1 complex depends on membrane-bound Rab5 for its Rab7 GEF activity, which nicely explains some of the previous in vivo observations on endosomal Rab5-to-Rab7 exchange (Poteryaev et al., 2010; Rink et al., 2005).This Rab exchange, which occurs similarly on phagosomes (Jeschke and Haas, 2016), is in vivo likely regulated in space and time. Time-lapse microscopy studies revealed that levels of fluorescently labeled Rab5 decreased, while fluorescently labeled Rab7 increased on the surface of a tracked endosome (Poteryaev et al., 2010; Yasuda et al., 2016). Analysis of the spatiotemporal Rab5-to-Rab7 transition in mammalian cells revealed that Rab5-positive endosomes can separate from Rab7-positive membranes, suggesting that a stepwise maturation process also occurs in some cells (Skjeldal et al., 2021). However, in all cases, only some insights on Mon1-Ccz1 regulation are presently available. Phosphorylation is one potential regulatory mechanism in GEF regulation (Kulasekaran et al., 2015). Indeed, yeast Mon1-Ccz1 is a substrate of the vacuolar casein kinase 1 Yck3 (Lawrence et al., 2014). When added to the Rab5-dependent GEF assay, Yck3-mediated phosphorylation inhibited Mon1-Ccz1 GEF activity, presumably by blocking the Rab5 interaction (Langemeyer et al., 2020). How the kinase is in turn regulated and whether this is the only mechanism of Mon1-Ccz1 GEF control is currently unknown.Rab7 activation and function in autophagyThe lysosome is also the destination of the autophagic catabolic pathway. During autophagy, portions of the cytosol, specific organelles, aggregates, or pathogens are engulfed into a double-layered membrane, which upon closure fuses with the lysosome for degradation and reuse of its content (Fig. 2 A; Zhao and Zhang, 2019; Nakatogawa, 2020). Autophagy is a versatile pathway required for adaptation of a cell’s organelle repertoire and quality control.Rab7 is found not just on LEs, but also on autophagosomes (Hegedűs et al., 2016; Gao et al., 2018a), although its precise function seems to differ between organisms (Kuchitsu and Fukuda, 2018). In yeast, the Rab7-homologue Ypt7 mediates HOPS-dependent fusion of autophagosomes with vacuoles (Gao et al., 2018a). In metazoan cells, Rab7 and its effectors PLEKHM1 and WDR91 are required for autolysosome/amphisome-lysosome fusion, yet Rab7 does not seem to directly bind HOPS during fusion of autophagosomes with lysosomes (Xing et al., 2021; McEwan et al., 2015; Gutierrez et al., 2004; Kuchitsu and Fukuda, 2018).Given the striking Rab5 dependence on endosomes in Mon1-Ccz1 activation, the question arises, how does Mon1-Ccz1-mediated Rab7 activation happen on autophagosomes? Some data suggest that yeast and metazoan Rab5 is directly involved in the autophagy process such as autophagosome closure (Ravikumar et al., 2008; Bridges et al., 2012; Zhou et al., 2019, 2017), whereas others do not find direct evidence, for instance in Drosophila (Hegedűs et al., 2016). Studies in yeast revealed that the LC3–like Atg8 protein directly binds and recruits Mon1-Ccz1 to the autophagosomal membrane during starvation, which results in Ypt7 activation as a prerequisite of HOPS-dependent fusion with the vacuole (Gao et al., 2018a; Fig. 2 B). Tight regulation of Mon1-Ccz1 GEF-activity is apparently mandatory to avoid fusion of premature autophagosomes with the vacuole (Fig. 2 C). How Mon1-Ccz1 localization to either endosomes or autophagosomes is coordinated (also with regard to similarities in organelle features; Fig. 2 D) and whether Atg8/LC3 also regulates the activity of the GEF complex are not yet known.Of note, an endosomal-like Rab5-to-Rab7 cascade also occurs on the mitochondrial outer membrane during mitophagy in metazoan cells, a selective pathway to degrade damaged mitochondria (Yamano et al., 2018). Here, Rab5 is activated by a mitochondrially localized Rab5 GEF, followed by Mon1-Ccz1 recruitment and Rab7A activation, which then orchestrates the subsequent mitophagy process. How this process is coupled to autophagosome maturation, and whether Rab7 is then again needed on the formed autophagosome, has not been addressed so far.These data nevertheless demonstrate the adjustable recruitment of Mon1-Ccz1 during endosomal maturation and autophagosome formation and even to the mitochondrial surface. Targeting of the Mon1-Ccz1 complex is likely coordinated between all these processes.A role for ER-endosome MCSs in endosome maturationEndosomes form MCSs with the ER. Such contact sites have multiple roles ranging from lipid transport to ion exchange (Scorrano et al., 2019; Reinisch and Prinz, 2021). The endosome-ER contact depends on Rab7 and contributes to transport and positioning of endosomes, supports endosomal fission, and facilitates endocytic cargo transport and cholesterol transfer between LEs and the ER (Rocha et al., 2009; Friedman et al., 2013; Rowland et al., 2014; Raiborg et al., 2015; Jongsma et al., 2016). Rab7 activation via the Mon1-Ccz1 complex is required for cholesterol export from the lysosome, likely in the context of MCSs. Rab7 binds to the NPC1 cholesterol transporter and may thus promote cholesterol export only at MCSs with the ER or other organelles (van den Boomen et al., 2020). The ER is also involved in endosome maturation, which requires an MCS between Reticulon-3L on the ER and endosomal Rab9. In fact, Rab9 is recruited shortly before the Rab5-to-Rab7 transition (Wu and Voeltz, 2021; Kucera et al., 2016). How Rab9 activation and MCS formation are coordinated with endosomal maturation has not yet been revealed. It is likely that the spatial positioning of endosomes (Fig. 1 A), their acidification, and TORC1 activity also contribute to this process (Bonifacino and Neefjes, 2017; Johnson et al., 2016).Retromer opposes Rab7 activationRetromer is a conserved heteropentameric complex that mediates the formation of vesicular carriers at the endosome and thus allows the transport of receptors back to the Golgi or plasma membrane. The complex consists of a trimeric core (Vps35, Vps26, and Vps29), which binds either a SNX1-SNX4 heterodimer or a SNX3 monomer (Simonetti and Cullen, 2018; Leneva et al., 2021; Kovtun et al., 2018). Retromer is an effector of Rab7, but also recruits the Rab7 GAP TBC1D5 in metazoan cells (Rojas et al., 2008; Kvainickas et al., 2019; Jimenez-Orgaz et al., 2018; Distefano et al., 2018; Seaman et al., 2009). This dual function of retromer may facilitate the formation of endosomal tubules after the Rab5-to-Rab7 transition, and these tubules eventually lose Rab7 once scission has occurred (Jongsma et al., 2020).It is not yet clear how conserved the Rab7-retromer-GAP connection is. Yeast retromer is also an effector of the Rab7-like Ypt7 and coordinates protein recycling at the endosome (Liu et al., 2012; Balderhaar et al., 2010), yet a role of a Rab7 GAP has not been described. However, yeast retromer also binds to the Rab5 GEFs Vps9 and Muk1 (Bean et al., 2015), which suggests that both Rab5 and Rab7 function contribute to efficient tubule formation at the endosome. Whether and how the Rab7 GEF Mon1-Ccz1 is functionally coordinated with retromer will be a topic of future studies.GEF regulation along the endomembrane systemIn the previous section, we focused mainly on the role of the Rab7 GEF in the context of endosome and autophagosome maturation. However, the timing of GEF activation and the subsequent recruitment of their target Rabs is critical for all membrane trafficking processes along the endomembrane system to guarantee maintenance of intracellular organelle organization. Rabs in turn interact with effectors, and effectors such as the lysosomal HOPS complex not only bind SNAREs but also catalyze their assembly and thus drive membrane fusion (Fig. 3 A). The spatiotemporal regulation of GEF activation is therefore at the heart of organelle biogenesis and maturation, and thus membrane trafficking. Within this section, we will now broaden our view by comparing different regulatory principles of GEFs.Open in a separate windowFigure 3.Regulatory mechanisms influence the activity of GEFs.(A) Hierarchical cascade of factors controlling membrane fusion. GEFs integrate various signals and initiate a cascade of protein activities, finally leading to membrane fusion. Signaling lipids, the presence of cargo proteins, upstream GTPases, and kinases influence the activity of GEFs and therefore determine Rab GTPase activation. Consequently, effector proteins such as tethering factors are recruited. This ultimately leads to SNARE-mediated lipid bilayer mixing and membrane fusion. (B) A Rab cascade in yeast exocytosis. Active Ypt32 and PI4P (yellow) on late Golgi compartments and secretory vesicles recruit the GEF Sec2, which in turn promotes activation and stable membrane insertion of the Rab Sec4. (C) Mon1-Ccz1 regulation by phosphorylation. Mon1-Ccz1 is recruited to and activated on LEs by coincidence detection of membrane-associated Rab5 and PI3P (red, Fig. 1 C) and promotes stable membrane insertion of Rab7. This process is terminated by Mon1-Ccz1 phosphorylation by the type I casein kinase Yck3 in yeast (orange). (D) A positive feedback loop of GEF activation on endocytic vesicles and EEs. The Rab5 GEF Rabex-5 binds ubiquitinated cargo on endocytic vesicles and is autoinhibited. Rab5 recruits Rabaptin-5, which binds Rabex-5 and releases the GEF from autoinhibition, generating a positive feedback loop. (E) Membrane factors determine GEF activity of TRAPPII at the trans-Golgi. TRAPPII activity for the Rab Ypt32 requires membrane-associated Arf1 and PI4P. (F) The length of the hypervariable domain of Golgi Rabs defines the substrate specificity for TRAPP complexes. The yeast Rab GTPases Ypt1 and Ypt32 differ in the length of their C-terminal HVD (box). TRAPPII and TRAPPIII complexes have the same active site, which is positioned away from the membrane, and thus discriminate Rab accessibility. (G) Phosphorylation as a mechanism to promote GEF activity. DENND1 GEF activity is autoinhibited, which is released by Akt-mediated phosphorylation. For details, see text.A Rab cascade in exocytosisAnother well-characterized Rab cascade is involved in the exocytic transport of secretory vesicles from the trans-Golgi network to the plasma membrane. At the trans-Golgi, the GEF transport protein particle II (TRAPPII) activates the Rab GTPase Ypt32, which then recruits the GEF Sec2 to secretory vesicles. Sec2 in turn activates the Rab Sec4, which binds the Sec15 subunit of the Exocyst tethering complex and allows vesicles to dock and fuse with the plasma membrane (Fig. 3 B; Walch-Solimena et al., 1997; Ortiz et al., 2002; Dong et al., 2007; Itzen et al., 2007). This cascade is conserved in humans. During ciliogenesis at the plasma membrane, the Ypt32 homologue Rab11 recruits the GEF Rabin 8, which in turn activates the human Sec4 homologue Rab8, a process regulated by phosphorylation (Hattula et al., 2002; Wang et al., 2015; Knödler et al., 2010). Interestingly, yeast Sec2 not only is a GEF, but also interacts with the Sec4 effector Sec15 (Medkova et al., 2006), a principle also observed in the endocytic Rab5 activation cycle, where the GEF Rabex5 interacts with the Rab5 effector Rabaptin-5. This dual role may also apply to Mon1-Ccz1, as the Mon1 homologue in C. elegans, SAND1, and yeast Mon1-Ccz1 can bind the HOPS tethering complex (Poteryaev et al., 2010; Nordmann et al., 2010).At the Golgi, phosphatidylinositol-4-phosphate (PI4P) contributes to directionality and spatiotemporal regulation of the exocytic Rab cascade. Sec2 binds both Ypt32 and PI4P on secretory vesicles via two binding sites, a process called coincidence detection. However, PI4P binding inhibits the interaction of Sec2 with Sec15. As vesicles reach the cell periphery, PI4P levels drop by the activity of Osh4, a lipid transporter, which allows Sec2 to bind the Exocyst subunit rather than Ypt32 (Ling et al., 2014; Mizuno-Yamasaki et al., 2010). In addition, Sec2 is phosphorylated by the plasma membrane–localized casein kinases Yck1 and Yck2 (Stalder et al., 2013; Stalder and Novick, 2016), resulting in effector recruitment rather than further Rab activation.Such a regulation may also apply to yeast Mon1-Ccz1. Anionic phospholipids and PI3P support Mon1-Ccz1 recruitment to liposomes and vacuoles (Langemeyer et al., 2020; Cabrera et al., 2014; Lawrence et al., 2014), whereas phosphorylation of the complex by the casein kinase Yck3 inhibits the binding of Mon1-Ccz1 to the Rab5-like Ypt10 and consequently reduces its GEF activity toward Rab7 (Fig. 3 C; Langemeyer et al., 2020). These observations suggest that the phosphorylation of GEFs by kinases may be a general regulatory principle in Rab cascades.Autoinhibition controls the Rab5 GEFAnother widely used regulatory mechanism is the autoinhibition of GEFs to control their activity. This has been analyzed in detail for the early endosomal Rab5-specific GEF Rabex-5, which interacts with the Rab5-effector Rabaptin-5 (Horiuchi et al., 1997). One factor for Rabex-5 recruitment to endocytic vesicles are ubiquitinated cargo proteins at the plasma membrane (Fig. 3 D; Mattera et al., 2006; Lee et al., 2006). Yet, isolated Rabex-5 has only low GEF activity in vitro (Delprato and Lambright, 2007). Structural analysis revealed that binding of Rabaptin-5 to Rabex-5 causes a rearrangement in the Rabex-5 C-terminus, which releases the GEF from autoinhibition and therefore facilitates nucleotide exchange of Rab5 (Delprato and Lambright, 2007; Zhang et al., 2014). On endosomes, increasing amounts of Rab5-GTP further promotes recruitment of the Rabex-5–Rabaptin-5 complex, resulting in a positive feedback loop of Rab5 activation and GEF recruitment (Lippé et al., 2001). Overall, Rabex-5 GEF activity is regulated by autoinhibition, a feedback loop with the Rab5 effector protein Rabaptin-5, and ubiquitinated cargo, which guarantees precise timing in establishing a Rab5-positive endosome. Of note, the Mon1 subunit of the Rab7 GEF can displace Rabex-5 from endosomal membranes (Poteryaev et al., 2010), which suggests a negative feedback loop of the Rab5 activation cascade once the next GEF is present.Regulation of Arf1 GEFs at different Golgi subcompartmentsThese key principles of GEF regulation in GTPase cascades are also found for Arf GTPases. Arf GTPases are soluble in their GDP-bound state by shielding their N-terminal myristate anchor in a hydrophobic pocket. Like Rabs, Arf GTPases are activated by specific GEFs, and their inactivation requires a specific GAP (Sztul et al., 2019). However, this review only highlights some key findings in the regulation of Rab GEFs and does not address regulation of the corresponding GAPs. Once activated, Arfs insert their lipid anchor and an adjacent amphipathic helix into membranes and are then able to bind effector proteins (Sztul et al., 2019). One of the best-studied Arf-GEFs is Sec7, which activates Arf1, an Arf GTPase involved in intra-Golgi trafficking (Achstetter et al., 1988). Studies on yeast Sec7 revealed that the protein is autoinhibited in solution and depends on three small GTPases—Arf1, the Rab Ypt1, and the Arf-like Arl1—for recruitment to the Golgi, a process supported by anionic lipids found in the late Golgi compartment. Importantly, the late Golgi Rabs Ypt31/32 strongly stimulate GEF activity (McDonold and Fromme, 2014; Richardson et al., 2012, 2016), indicating allosteric activation, as observed for Rab5-dependent Mon1-Ccz1 activation (Langemeyer et al., 2020). In this process, Sec7 dimerizes and promotes Arf1 recruitment and thus establishes a positive feedback loop. Interestingly, membrane binding of two additional Arf1 GEFs of the early Golgi, Gea1/2, depends on Rab1/Ypt1 and neutral membranes. Under these conditions, Gea1/2 is released from autoinhibition, although no positive feedback loop was observed (Gustafson and Fromme, 2017). Thus, Arf GEF regulation and Arf activation are tightly linked to multiple small GTPases and the membrane environment to establish Golgi compartments.Regulation and specificity of TRAPP complexes at the GolgiArf1 activation is also linked to the activation of Golgi-specific Rabs. Arf1-GTP binds to the highly conserved TRAPP GEF complexes at the Golgi (Fig. 3 E). Yeast and mammalian cells contain two TRAPP complexes. In yeast, both complexes share seven core components. TRAPPIII in addition contains Trs85, while accessory TRAPPII subunits are instead Trs130, Trs120, Trs65, and Tca17. Metazoan TRAPP complexes contain additional subunits (Lipatova and Segev, 2019).Interestingly, both complexes share the same catalytic site for Rab1/Ypt1 and Rab11/Ypt32. However, TRAPPIII provides GEF activity toward Rab1/Ypt1. Initially, it was proposed that TRAPPII can activate both Rab1/Ypt1 and Rab11/Ypt32 (Thomas et al., 2019, 2018; Thomas and Fromme, 2016; Riedel et al., 2018); however, it was recently shown that the TRAPPII complex is specific for Rab11/Ypt32 (Riedel et al., 2018; Thomas et al., 2019). Reconstitution of GEF activity on liposomes helped here to unravel TRAPP complex substrate specificity, since in solution assays are not adequate to address some of the features important for specific interactions: Rab11/Ypt32 has a longer HVD between the prenyl anchor and the GTPase domain compared with Rab1/Ypt1 (Fig. 3 F, box). The HVD not only binds TRAPPII but also stretches a longer distance from the membrane (Fig. 3 F). Thereby it allows Rab11/Ypt32, but not Rab1/Ypt1, to reach the active site of membrane-bound TRAPPII. Thus, substrate specificity is controlled by the distance of the GTPase domain from the membrane surface, since the active site seems to be located on the opposing site of the complex from the site of membrane interaction (Fig. 3 F; Thomas et al., 2019). The smaller TRAPPIII has its active site closer to the membrane, binds Ypt1 via its shorter HVD, and facilitates its activation, while Ypt32 with its longer HVD may be positioned too far away from the active site. In addition, both complexes require their respective membrane environment for optimal activity, indicating how Arf and Rab GEFs cooperate in Golgi biogenesis.The GEF DENND1 requires Arf5 for Rab35 activationRecently, another example of Arf-mediated Rab activation was reported (Kulasekaran et al., 2021). Rab35, an endocytic Rab found at the plasma membrane and REs (Sato et al., 2008; Kouranti et al., 2006), is involved in cell adhesion and cell migration by controlling the trafficking of β1-integrin and the EGF receptor (Klinkert and Echard, 2016; Allaire et al., 2013). Arf5 binds the Rab35 GEF DENND1 and stimulates its GEF activity, with dysregulation of this cascade linked to glioblastoma growth (Kulasekaran et al., 2021). DENND1 GEF activity is initially autoinhibited and relieved by phosphorylation via the central Akt kinase (Fig. 3 G; Kulasekaran et al., 2015). Similarly, another DENN-domain containing GEF, DENND3, is phosphorylated by the autophagy-specific ULK kinase and then activates Rab12, a small GTPase involved in autophagosome trafficking (Xu et al., 2015). Thus, it seems that Rab GEF activation is more generally linked to other trafficking proteins, such as Arfs, and controlled by kinases and likely also phosphatases.Lessons from reconstitutionOrganelle biogenesis and maintenance in the endomembrane system are tightly linked to the correct spatial and temporal activation of Rab GTPases. A small yeast cell gets by with 11 Rabs, while human cells encode >60 (Hutagalung and Novick, 2011). Rab activation, and therefore membrane identity, of each organelle depends on the cognate GEF. This puts GEFs into the driver’s seat of any Rab-directed function at cellular membranes. It seems that GEFs integrate, by several regulatory loops, incoming signals from various sources such as membrane composition, cargo proteins, upstream GTPases, or kinases/phosphatases (Fig. 3 A). Yet our insights on the specific membrane targeting and regulation of GEFs remain incomplete for want of available experimental approaches. We briefly discuss here how recent advances on the reconstitution of GEF-mediated Rab activation at model membranes have advanced our understanding of organelle maturation and biogenesis.Reconstitution of any reaction to uncover the essential constituents is limited by the available tools. GEFs, Rabs, Sec18/Munc1 proteins, tethering factors, and SNAREs are for instance required for membrane fusion (Fig. 3 A). Initial assays focused on SNAREs and revealed their important but rather inefficient fusogenicity (Weber et al., 1998). Further analyses uncovered critical activation steps for SNAREs (Malsam et al., 2012; Pobbati et al., 2006; Südhof and Rothman, 2009; Jahn and Scheller, 2006), yet fusion at physiological SNARE concentrations in various in vitro systems does not occur, unless assisted by chaperoning Sec1/Munc18 proteins and tethering factors (Bharat et al., 2014; Lai et al., 2017; Mima and Wickner, 2009; Ohya et al., 2009; Wickner and Rizo, 2017). Most tethers again depend on Rabs for their localization, and Rab localization to membranes requires a GEF (Cabrera and Ungermann, 2013), whose activity can be a limiting factor for fusion (Langemeyer et al., 2020, 2018b). The long avenue of understanding the mechanism and regulation of membrane fusion exemplifies the challenges in dissecting the complexity of a cellular reaction, but also demonstrates the powerful insights obtained from reconstitution of these processes.GEFs determine the localization of the corresponding Rab, and consequently, Rabs follow their GEF if they are mistargeted (Gerondopoulos et al., 2012; Blümer et al., 2013; Cabrera and Ungermann, 2013). However, these anchor-away approaches completely bypass the tight cellular regulation of GEF activation by the mistargeting and additional overexpression of the GEF protein and may allow only statements about GEF/substrate specificity. The spatiotemporal activation of each GEF at the right organelle is vital for the timing of all downstream reactions. GEFs are recruited to membranes by coincidence detection, which includes membrane lipids such as PIPs, membrane packaging defects, and peripheral membrane proteins such as upstream Rabs or other small GTPases. This recruitment is often accompanied by the release from autoinhibition, which may be triggered or inhibited by other regulatory processes such as phosphorylation. It comes as no surprise that pathogens such as Legionella and Salmonella take advantage of the central function of GEFs to establish and nourish their intracellular organellar niche by manipulating small GTPase activity (Spanò and Galán, 2018).To understand the specificity of Rab GEFs (and GAPs), mostly very simplified systems were used. Most GEF assays analyze soluble Rabs loaded with fluorescent 2′-O-(N-methylanthraniloyl) (MANT)-nucleotide or radioactively labeled GTP/GDP and soluble GEF in a test tube, where nucleotide exchange activity is observed upon addition of unlabeled nucleotide (Fig. 4 A). This strategy allows the identification of substrate (Rab) specificity of GEFs, but could also lead to misleading results, as pointed out earlier on the example of the TRAPP complexes and Rab1/Ypt1 or Rab11/Ypt32. In addition, GEF-Rab pairs negatively regulated by one of the above principles could easily be missed.Open in a separate windowFigure 4.Approaches to determine GEF activity in vitro. Methods to determine GEF activity for Mon1-Ccz1. In all approaches, Rab7 is preloaded with fluorescent MANT-GDP. Fluorescence decreases upon GEF-mediated nucleotide exchange. (A) GEF assays. (Ai) In-solution Rab GEF assay. Mon1-Ccz1 (blue, Bulli/Rmc1/C18orf8 subunit, indicated by unlabeled hexagon) and Rab7 (gray) are freely diffusible in the test tube, which results in random collision and Rab activation. (Aii) GEF-mediated activation of artificially recruited Rab7 on liposomes. Rab7 with a C-terminal 6xHis-tag is permanently immobilized on membranes containing the cationic lipid DOGS-NTA. Mon1-Ccz1 unspecifically binds to this membrane surface and activates Rab7. Diffusion is limited to the membrane surface, thus increasing chances of interactions. (Aiii) Reconstitution of Rab5-mediated Rab7 activation by Mon1-Ccz1 on liposomes. Chemically activated, prenylated Rab5 (green), delivered to the membrane by the Rab Escort Protein (REP), allows Mon1-Ccz1 recruitment and Rab7 activation from the GDI complex (see text for further details). (B) Summary of Ai–Aiii. pren., prenylation.As Rabs and GEFs function on membranes, we and others adopted strategies for measuring Rab activation by GEFs on membranes (Fig. 4 B). In a first approach, Rab and other small GTPases (Sot et al., 2013; Schmitt et al., 1994) were immobilized with C-terminal hexahistidine tags on liposomes containing the polycationic lipid 1,2-dioleoyl-sn-glycero-3-[(N-(5-amino-1-carboxypentyl)iminodiacetic acid)succinyl] (DOGS-NTA) and observed higher activity of the added GEF (Cabrera et al., 2014; Thomas and Fromme, 2016). A drawback of this technique is the artificial membrane composition. To avoid potential artifacts of unnaturally charged membranes and permanently membrane-bound Rab, recent studies relied on prenylated Rabs in complex with GDI. Reflecting the natural source of the cytoplasmic Rab pool, this complex was used as a GEF substrate in the presence of liposomes mimicking the natural membrane composition (Cezanne et al., 2020; Bezeljak et al., 2020; Langemeyer et al., 2020, 2018b; Thomas et al., 2018, 2019; Thomas and Fromme, 2016).Even though these observations are recent, the outcome and the understanding of GEF regulation is encouraging. For the Rab5 GEF complex consisting of Rabex5 and Rabaptin5, GEF-dependent Rab5 recruitment to membranes revealed a self-organizing system, nonlinear Rab5 patterning, and collective switching of the Rab5 population (Bezeljak et al., 2020; Cezanne et al., 2020). This is in agreement with mathematical modeling and predictions on bistability and ultrasensitivity of Rab networks (Del Conte-Zerial et al., 2008; Barr, 2013). For the Golgi-resident TRAPPII and TRAPPIII complexes, the membrane composition, the length of the Rab HVD, and the presence of membrane-bound Arf1 determined the GEF specificity for their Rabs (Fig. 3 F; Thomas et al., 2019, 2018; Thomas and Fromme, 2016; Riedel et al., 2018), which is nicely supported by recent structural analyses of yeast and metazoan TRAPPIII (Galindo et al., 2021; Joiner et al., 2021)Our own data uncovered that the yeast and metazoan Mon1-Ccz1(-RMC1) complex required membrane-bound Rab5-GTP to activate Rab7 out of the GDI complex (Langemeyer et al., 2020). Surprisingly, Rab5-GTP not only determined membrane binding of Mon1-Ccz1, but also activated the GEF on membranes by a yet-unknown mechanism (Fig. 1 C). Phosphorylation of yeast Mon1-Ccz1 by the casein kinase Yck3 inhibited this activation, demonstrating possible regulation of GEF activity (Fig. 3 C). Importantly, this finding agrees with the observed Rab5-to-Rab7 switch in vivo (Poteryaev et al., 2010; Rink et al., 2005).Taken together, the available tools open exciting avenues for our understanding of organelle maturation. Reconstitution will allow the investigation of an entire Rab cascade and its regulation by kinases or membrane lipids. It will be possible to determine the cross-talk with lipid kinases and observe possible regulatory loops between Rabs and PI kinases (Tremel et al., 2021). We are confident that such analyses, complemented by in vivo analyses of Rabs or other small GTPases and their GEFs, will clarify the underlying mechanism of organelle maturation and biogenesis along the endomembrane system of eukaryotic cells.     

FERONIA and Her Pals: Functions and Mechanisms

Current research into the FERONIA family of receptor kinases highlights both questions and opportunities for understanding signaling strategies in plant growth and survival.FERONIA and 16 closely related proteins form a distinct clade within the Arabidopsis (Arabidopsis thaliana) superfamily of receptor-like kinases (RLKs), transmembrane proteins with an extracellular domain for signal perception and a cytoplasmic domain that phosphorylates target molecules and induces cellular responses to incoming signals. Several members of this family, such as THESEUS1 and ANXUR1,2, are known to play distinct roles in growth and reproduction; FERONIA is unique in being critically involved in both plant growth and reproduction. The FERONIA family of proteins from Arabidopsis is distinguished from other RLKs by having extracellular protein motifs that share homology with malectin, an animal protein with the capacity to bind dimeric and oligomeric Glc. The possibility that these malectin-like motifs might interact with carbohydrates has generated widespread speculations that these receptor kinases could act as cell-wall sensors, communicating perturbations at the frontline of cell-cell and plant-environment interaction to the cytoplasm to induce responses. Here, we discuss emerging understanding of the functional roles and signaling mechanisms of FERONIA and its related proteins. We also highlight pressing questions, as well as the functional potential of the broader malectin-like domain-containing RLK family that exists across the plant kingdom. We believe FERONIA and her pals provide a rich ground for research with many emerging opportunities for uncovering novel insights into how plants strive for growth and survival.FERONIA/SIRÈNE was first identified genetically more than ten years ago as a key regulator of female fertility in Arabidopsis (Rotman et al., 2003; Huck et al., 2003). It was later determined to be a receptor kinase (Escobar-Restrepo et al., 2007) and one of 17 closely related receptor-like kinases (RLKs) in Arabidopsis (Fig. 1; Hèmaty and Höfte, 2008; Boisson-Dernier et al., 2011; Cheung and Wu, 2011). The name FERONIA (after an Etruscan goddess of fertility) will be used from hereon. Arabidopsis has more than 600 RLKs (Shiu and Bleecker, 2003). Several discoveries made at about the same time led to an extraordinary level of interest in FERONIA and related RLKs. These include: (1) a member of this group, THESEUS1 (named after the Greek mythological figure that slew Procustes the brigand) is a critical regulator of cell growth and appears to function as a surveyor of cell-wall status (Hèmaty et al., 2007); (2) FERONIA functions broadly throughout development and is fundamental to cell and plant growth (Guo et al., 2009; Deslauriers and Larsen, 2010; Duan et al., 2010); and (3) a closely related pair of these RLKs, ANXUR1 and ANXUR2 (named after the consort of FERONIA), is essential for male fertility (Boisson-Dernier et al., 2009; Miyazaki et al., 2009). Last but not least was the report of malectin, a novel protein from animals with the capacity to bind dimeric and oligomeric Glc-binding protein (Schallus et al., 2008) and the realization that FERONIA and related RLKs contain malectin-like motifs (PFAM CL0468) in their extracellular domains (Fig. 1). This led to widespread speculations that FERONIA and related RLKs might interact with carbohydrate moieties and function as sensors of perturbations in the cell wall, communicating conditions at the cell surface to induce appropriate cellular responses (Hèmaty and Höfte, 2008; Boisson-Dernier et al., 2011; Cheung and Wu, 2011; Lindner et al., 2012). FERONIA and related malectin-like domain-containing RLKs are often referred to as the CrRLK1-like RLKs (see e.g. Nibau and Cheung, 2011), after its founding member identified in Catharanthus roseus, CrRLK1 (Schulze-Muth et al., 1996), but for which no functional work has been reported. THESEUS1 was the first member of the group for which a clear functional role was demonstrated, and FERONIA is the most prevalently studied among these RLKs. To provide a functional context for our discussion here, we will refer to the FERONIA-related RLKs in Arabidopsis as the THESEUS1/FERONIA-related RLK family. We update current knowledge about these RLKs from Arabidopsis and highlight pressing questions and emerging opportunities from these and related malectin-like domain-containing RLKs, which are present throughout the plant kingdom (Hèmaty and Höfte, 2008; Antolin-Llovera et al., 2014; Nguyen et al., 2015).Open in a separate windowFigure 1.FERONIA protein domain structure and phylogenetic tree of the Arabidopsis THESEUS1/FERONIA receptor kinase family. A, Deduced FERONIA structural domains. SS, ECD, TM are, respectively, signal peptide, extracellular domain, transmembrane domain. MALA and MALB are tandem malectin-like domains. exJM, extracellular juxtamembrane region. Numbers indicate amino acid residues. B, The THESEUS1/FERONIA protein family.

ADVANCES

• FERONIA and related RLKs have extracellular motifs homologous with the diglucose-binding protein malectin, so potentially interact with cell wall carbohydrates and mediate wall-related activities.
• FERONIA controls growth and female fertility, mediates hormone- and pathogen-induced responses, and is required for a normal cell wall.
• FERONIA is a receptor for RALF1, a peptide regulatory factor, which affects phosphorylation of FERONIA and the key cell growth regulator H⁺-ATPase.
• FERONIA-related THESEUS1 suppresses growth in cellulose-deficient mutants, suggesting a role as surveyor of wall conditions.
• FERONIA homologs ANXUR1 and ANXUR2 ensure pollen tube integrity and male fertility.
• FERONIA, ANXUR1, and ANXUR2 signaling collectively involves a GPI-AP, a MLO protein, the RHO GTPase switch, NADPH oxidases, and a receptor-like cytoplasmic kinase; ROS and Ca²⁺ are key elements in their functions.

Extracellular homology with malectin (Schallus et al., 2008; Fig. 1A) distinguishes the THESEUS1/FERONIA-related RLKs from other members of the Arabidopsis RLK family. Malectin, named after its in vitro ability to bind maltose (Glc α1-4 Glc), is a conserved animal protein located in the lumen of the endoplasmic reticulum where it is involved in protein quality control in the early steps of secretion (Schallus et al., 2008; Qin et al., 2012). A majority of the Arabidopsis THESEUS1/FERONIA family (Fig. 1B) has tandem malectin-like motifs (Fig. 1A; Boisson-Dernier et al., 2011) in their extracellular domains. We focus our discussion on FERONIA, THESEUS1, and three other members of the family, ANXUR1, ANXUR2, and ERULUS/[Ca²⁺]_cyt-associated Protein Kinase1, for which clear biological roles have been demonstrated (Miyazaki et al., 2009; Boisson-Dernier et al., 2009; Bai et al., 2014). A contribution to cell growth and morphogenesis has also been reported for HERCULES1 (Guo et al., 2009) and CURVY (Gachomo et al., 2014), but details regarding their functions remain limited.     

Pharmacological targeting of guanosine monophosphate synthase suppresses melanoma cell invasion and tumorigenicity

Malignant melanoma possesses one of the highest metastatic potentials among human cancers. Acquisition of invasive phenotypes is a prerequisite for melanoma metastases. Elucidation of the molecular mechanisms underlying melanoma invasion will greatly enhance the design of novel agents for melanoma therapeutic intervention. Here, we report that guanosine monophosphate synthase (GMPS), an enzyme required for the de novo biosynthesis of GMP, has a major role in invasion and tumorigenicity of cells derived from either BRAF^V600E or NRAS^Q61R human metastatic melanomas. Moreover, GMPS levels are increased in metastatic human melanoma specimens compared with primary melanomas arguing that GMPS is an attractive candidate for anti-melanoma therapy. Accordingly, for the first time we demonstrate that angustmycin A, a nucleoside-analog inhibitor of GMPS produced by Streptomyces hygroscopius efficiently suppresses melanoma cell invasion in vitro and tumorigenicity in immunocompromised mice. Our data identify GMPS as a powerful driver of melanoma cell invasion and warrant further investigation of angustmycin A as a novel anti-melanoma agent.Malignant melanoma is one of the most aggressive types of human cancers. Its ability to metastasize in combination with resistance to conventional anticancer chemotherapy makes melanoma extremely difficult to cure, and the median survival of patients with metastatic melanoma is 8.5 months.^{1, 2, 3} A better understanding of the biology behind melanoma aggressiveness is imperative to facilitate the development of novel anti-melanoma strategies.Melanoma and other cancers cells have been shown to strongly rely on de novo nucleotide biosynthesis^{4, 5} and often overexpress several biosynthetic enzymes involved in these pathways.^{6, 7, 8, 9} Recently, we have identified a fundamental connection between melanoma invasion and biosynthesis of guanylates,⁸ suggesting that distortion of the guanylate metabolism facilitates melanoma progression.Guanosine monophosphate reductase (GMPR) reduces GMP to one of its precursors, inosine monophosphate (IMP), and depletes intracellular GTP pools (Figure 1a). We have recently demonstrated that GMPR suppresses melanoma cell invasion and growth of human melanoma cell xenografts. These findings tightly linked guanylate production to the invasive potential of melanoma cells.⁸Open in a separate windowFigure 1GMPS contributes to the invasive capability of melanoma cells. (a) Simplified schematic of the metabolic pathway for guanylates production. (b) SK-Mel-103 and SK-Mel-28 cells were transduced with a control vector or two independent shRNAs to GMPS and tested for invasion through Matrigel (left panel). Where indicated, cells were incubated with 100 μM guanosine for 24 h before the assay and guanosine supplementation was maintained throughout the experimental procedure. The data represent the average ± S.E.M. of at least two independent experiments. GMPS suppression was verified by immunoblotting (right panel). (c) Cells transduced as in (a) were plated on coverslips coated with FITC-conjugated gelatin. After 16 h cells were fixed with 4% PFA and stained for actin (rhodamine-conjugated phallodin) and nuclei (Hoechst). Where indicated, cells were incubated with 100 μM guanosine for 24 h before the assay and guanosine supplementation was maintained throughout the experimental procedure. At least 25 cells/sample were imaged to assess the number of cells with gelatin degradation. The data represent the average ± S.E.M. of two independent experiments. *P<0.05, **P<0.001 compared with control; ^#P<0.05, ^##P<0.001 compared with untreated cells. Statistics performed with Student''s t-Test. See also Supplementary Figure S1Of the several enzymes involved in guanylate biosynthesis, inositol monophosphate dehydrogenases 1 and 2 (IMPDH-1, -2), functional antagonists of GMPR (Figure 1a), have been targeted clinically with several drugs including the most specific one, mycophenolic acid (MPA) and its salt, mycophenolate mofetil (MMF).^{10, 11, 12, 13} Nonetheless, prior studies demonstrated that MPA possesses poor anti-tumor activity,^{14, 15} and it is primarily used as an immunosuppressing agent in organ transplantation.^{10, 11, 12}GMP synthase (GMPS) is the other functional antagonist of GMPR. GMPS catalyzes the amination of xanitol monophosphate (XMP) to GMP to promote GTP synthesis (Figure 1a).^{16, 17} Most of the studies on GMPS have been performed in bacteria, yeast, and insects, where GMPS has been shown to have a key role in sporulation, pathogenicity, and axon guidance, respectively.^{18, 19, 20} Mammalian GMPS has been the subject of several studies addressing its unconventional (GMP-unrelated) roles in the regulation of activity of ubiquitin-specific protease 7 (USP7).^{21, 22, 23, 24} However, because of the newly revealed importance of guanylate metabolism in control of melanoma cell invasion and tumorigenicity,⁸ GMPS emerges as an attractive target for anti-cancer therapy.In the late 1950s, a specific inhibitor of bacterial GMPS, angustmycin A (also known as decoyinine), has been isolated from Streptomyces hygroscopius as a potential antibiotic with sporulation-inducing activity in Bacillus subtilis.^{25, 26, 27, 28, 29} Its anti-tumor activity has never been experimentally explored. In the current study, we investigated the role of GMPS in regulation of melanoma invasion and tumorigenicity, and explored the possibility of targeting GMPS by angustmycin A as a novel anti-melanoma strategy.     

In Vivo Chemical and Structural Analysis of Plant Cuticular Waxes Using Stimulated Raman Scattering Microscopy

The cuticle is a ubiquitous, predominantly waxy layer on the aerial parts of higher plants that fulfils a number of essential physiological roles, including regulating evapotranspiration, light reflection, and heat tolerance, control of development, and providing an essential barrier between the organism and environmental agents such as chemicals or some pathogens. The structure and composition of the cuticle are closely associated but are typically investigated separately using a combination of structural imaging and biochemical analysis of extracted waxes. Recently, techniques that combine stain-free imaging and biochemical analysis, including Fourier transform infrared spectroscopy microscopy and coherent anti-Stokes Raman spectroscopy microscopy, have been used to investigate the cuticle, but the detection sensitivity is severely limited by the background signals from plant pigments. We present a new method for label-free, in vivo structural and biochemical analysis of plant cuticles based on stimulated Raman scattering (SRS) microscopy. As a proof of principle, we used SRS microscopy to analyze the cuticles from a variety of plants at different times in development. We demonstrate that the SRS virtually eliminates the background interference compared with coherent anti-Stokes Raman spectroscopy imaging and results in label-free, chemically specific confocal images of cuticle architecture with simultaneous characterization of cuticle composition. This innovative use of the SRS spectroscopy may find applications in agrochemical research and development or in studies of wax deposition during leaf development and, as such, represents an important step in the study of higher plant cuticles.The majority of land plants possess an extracellular, waxy cuticle that covers the surface of their aerial parts and protects them against desiccation, external physical and chemical stresses, and a variety of biological agents (Grncarevic and Radler, 1967; Barthlott and Neinhuis, 1997; Krauss et al., 1997; Ristic and Jenks, 2002; Yeats and Rose, 2013). The cuticle is a composite layer composed mainly of cutin and overlaid by cuticular waxes. Cutin is a macromolecular structure consisting primarily of hexadecanoic (palmitic) and octadecenoic (vaccenic) acids that are covalently linked by ester bonds to generate a rigid, three-dimensional network that is embedded with polysaccharides. Cuticular waxes are composed of long-chain (C₂₀–C₄₀) aliphatic molecules derived from fatty acids (Samuels et al., 2008), and studies over the last several decades have identified structural and regulatory constituents of the biosynthetic pathways of cuticular components (Kolattukudy, 1981; Beisson et al., 2012). In addition to the physiochemical properties conferred by its lipid components, the architecture of the cuticle plays an essential role in physiological function. For example, through understanding the properties of the cuticular structure, the extraordinary superhydrophobicity of the Lotus spp. leaf has been mimicked in micro- and nanotechnology to generate self-cleaning surfaces (Bhushan and Jung, 2006; Bhushan et al., 2009; Koch et al., 2009).As may be expected, given the diversity of plants, the habitats they inhabit, and individual life histories, the morphology and composition of plant cuticle varies extensively between and within species and includes plate-, needle-, and pillar-shaped wax crystals (Barthlott et al., 2008). In some species, cuticular wax composition is known to vary with depth, giving rise to chemically distinguishable layers (Yeats and Rose, 2013). Finally, the cuticle is increasingly shown to be important in development (Koornneef et al., 1989; Yeats and Rose, 2013) and pathogenesis (Lee and Dean, 1994; Gilbert et al., 1996; Bessire et al., 2007; Delventhal et al., 2014). It is therefore unsurprising that interest in cuticle composition, structure, and physiology is increasing (Buschhaus et al., 2014; Hen-Avivi et al., 2014; Heredia-Guerrero et al., 2014; Xu et al., 2014). Moreover, a greater understanding of the relationship between structure and chemical composition of cuticle waxes is vital for enhancing agriculture yields, as it will further our knowledge of how plants regulate water balance and inform the application of nutrition (foliar feeds) and pesticides, leading to improved formulation strategies for agrochemicals.The chemical composition and topological architecture of cuticular waxes are both critical for optimal physiological function. Analyses of these essential properties have typically been performed separately. Cuticle wax composition is normally determined using gas chromatography; cuticle ultrastructure may be analyzed using destructive imaging techniques such as scanning electron microscopy (SEM; Baker and Holloway, 1971; Jetter et al., 2000; Barthlott et al., 2008) and laser desorption ionizing mass spectroscopy (Jun et al., 2010) or, in vivo, using nondestructive real-time techniques, including white-light scanning interferometry (Kim et al., 2011), atomic force microscopy (Koch et al., 2004), confocal microscopy in reflectance mode (Veraverbeke et al., 2001), fluorescence microscopy of chemical stains (Pighin et al., 2004), coherent anti-Stokes Raman scattering (CARS) microscopy (Yu et al., 2008; Weissflog et al., 2010), and total internal reflection Raman spectroscopy (Greene and Bain, 2005). Despite the advances in our understanding of the cuticle that have been made with these techniques, there is a great need for techniques that combine chemical and structural information to provide in situ high-resolution chemical analysis of epicuticle waxes.Techniques based on vibrational spectroscopy offer in situ chemical analysis derived from the vibrational frequencies of molecular bonds within a sample. However, due to water absorption and the intrinsically low spatial resolution associated with the long infrared (IR) wavelengths required to directly excite molecular vibrations, IR absorption techniques have limited value for bioimaging. Raman scattering, however, provides analysis of vibrational frequencies by examining the inelastic scattering of visible light. Raman scattered light is frequency shifted with respect to the incident light by discrete amounts that correspond to the vibrational frequencies of molecular bonds within the sample. The spectrum of Raman scattered light consists of a series of discrete peaks that each correspond to a molecular bond and can be regarded as a chemical fingerprint holding a wealth of information regarding chemical composition. Unfortunately, Raman scattering is an extremely weak effect, and typical signals from biological samples are at least six orders of magnitude weaker than those from fluorescent labels. This severely limits the application of Raman for studying living systems because long acquisition times (100 ms–1 s per pixel) and relatively high excitation powers (several hundred milliwatts) are required to image most biomolecules with sufficient sensitivity. Furthermore, the lack of sensitivity is compounded by autofluorescence, which in plant tissues completely overwhelms the Raman signal, prohibiting its application in planta.Far stronger Raman signals can be obtained using coherent Raman scattering (CRS; Min et al., 2011). CRS achieves a Raman signal enhancement by focusing the excitation energy onto a specific molecular vibrational frequency (Fig. 1A). A pump and Stokes beam, with frequencies ω_p and ω_S, respectively, are incident upon the sample, with their frequency difference (ω_p–ω_S) tuned to match the molecular vibrational frequency of interest. Under this resonant condition, the excitation fields efficiently drive bonds to produce a strong nonlinear coherent Raman signal. When applied in microscopy format, the nonlinear nature of the CRS process confines the signal to a submicron focus that can be scanned in space, allowing three-dimensional confocal-like mapping of biomolecules. CRS microscopy has particular advantages for bioimaging: (1) Chemically specific contrast is derived from the vibrational signature of endogenous biomolecules within the sample, negating the need for extraneous labels/stains; (2) Low-energy, near-IR excitation wavelengths can be employed, which reduces photodamage and increases depth penetration into scattering tissues; and (3) The CRS process does not leave sample molecules in an excited state, does not suffer from photobleaching, and can be used for time course studies.Open in a separate windowFigure 1.Schematic representation of the two CRS processes: CARS and SRS. A, Energy level diagrams for the CARS and SRS processes, showing the pump (green), Stokes (red), and anti-Stokes (blue) photon energies. B, Diagrammatic representation of the input and output spectra for CARS and SRS, showing the gain and loss in the pump (red) and Stokes (green) beams, respectively. ΔI_S, Change in Stokes beam intensity; ΔI_p, change in pump beam intensity. C, Diagrammatic representation of the modulation transfer detection scheme used to detect stimulated Raman gain and loss with high sensitivity.CRS microscopy may be achieved by detecting either CARS or stimulated Raman scattering (SRS).     

Comparison of Isoflurane and α-Chloralose in an Anesthetized Swine Model of Acute Pulmonary Embolism Producing Right Ventricular Dysfunction

Pulmonary embolism (PE) is a leading cause of sudden cardiac death, and a model is needed for testing potential treatments. In developing a model, we compared the hemodynamic effects of isoflurane and α-chloralose in an acute swine model of PE because the choice of anesthesia will likely affect the cardiovascular responses of an animal to PE. At baseline, swine that received α-chloralose (n = 6) had a lower heart rate and cardiac output and higher SpO_2, end-tidal CO_2, and mean arterial pressure than did those given isoflurane (n = 9). After PE induction, swine given α-chloralose compared with isoflurane exhibited a lower heart rate (63 ± 10 compared with 116 ± 15 bpm) and peripheral arterial pressure (52 ± 12 compared with 61 ± 12 mm Hg); higher SpO₂ (98% ± 3% compared with 95% ± 1%), end-tidal CO₂ (35 ± 4 compared with 32 ± 5), and systolic blood pressure (121 ± 8 compared with 104 ± 20 mm Hg); and equivalent right ventricular:left ventricular ratios (1.32 ± 0.50 compared with 1.23 ± 0.19) and troponin I mean values (0.09 ± 0.07 ng/mL compared with 0.09 ± 0.06 ng/mL). Isoflurane was associated with widely variable fibrinogen and activated partial thromboplastin time. Intraexperiment mortality was 0 of 6 animals for α-chloralose and 2 of 9 swine for isoflurane. All swine anesthetized with α-chloralose survived with sustained pulmonary hypertension, RV-dilation-associated cardiac injury without the confounding vasodilatory or coagulatory effects of isoflurane. These data demonstrate the physiologic advantages of α-chloralose over isoflurane for anesthesia in a swine model of severe submassive PE.Abbreviations: LV, left ventricle; PAP, pulmonary arterial pressure; PE, pulmonary embolism; RV, right ventriclePulmonary embolism (PE) is one of the leading causes of noncardiac sudden death in Western nations and is the third most common cause of cardiovascular morbidity.^4,6,7,18 In survivors, severe PE damages the right heart, leading to a clinical course complicated by hypotension and circulatory shock, suggesting acute right heart failure in about 10% of patients and followed by persistent pulmonary hypertension or right ventricular dysfunction and dyspnea in at least 15% of patients.^{9,15,16,23,29} To test treatments to reduce right heart failure, a standardized model that is repeatable, accurate, and precise and that mimics the gross pathologic, cardiovascular, pulmonary, autonomic, hematologic, biochemical, and cellular characteristics of PE in humans with disease is needed.⁸Three lines of rationale favor domestic pigs as a model for PE. Several publications, using different methods of anesthesia, have found that swine manifest hemodynamic responses similar to those of humans in the presence of autologous PE, including elevated heart rate, decreased cardiac output, and reduced oxygen saturation.^2,12,30 Swine have similar platelet concentrations, and their coagulation profile on thromboelastography has been shown to be similar to humans, with the exception of higher fibrin crosslinking but less fibrin, leading to resistance to plasmin.^5,11,19,34 Market swine, which would otherwise be destined for slaughter, are relatively cost effective compared with other large animals and are of sufficient size for placement of an adult pulmonary arterial catheter for measurement of pulmonary vascular resistance in a closed-chest preparation.In view of the differences in the hemodynamic effects of different anesthetic agents, the choice of anesthesia will likely affect the cardiovascular responses of an animal to PE. However, current literature lacks a methodologic publication that compares the cardiovascular, right ventricular, pulmonary, and hematologic responses to PE in closed-chest swine models incorporating different anesthetic regimens.Figure 1 presents features of an ideal animal model for the purpose of testing treatments for PE. To develop a swine model of PE that closely resembles this physiologic ideal model, we induced PE in swine maintained in a surgical plane of anesthesia with either isoflurane or α-chloralose. Each of these agents has potential advantages and disadvantages. Isoflurane can be titrated minute by minute but causes undesirable vasodilation, whereas α-chloralose is believed to preserve cardiovascular reflexes but requires heating to dissolve and continuous infusion or repeated boluses.^26,35 We hypothesized that, compared with isoflurane, α-chloralose would meet more of the features described in Figure 1.Open in a separate windowFigure 1.Desirable features of large animal model of severe submassive PE designed for translational research.     

Simultaneous Raman Microspectroscopy and Fluorescence Imaging of Bone Mineralization in Living Zebrafish Larvae

Confocal Raman microspectroscopy and fluorescence imaging are two well-established methods providing functional insight into the extracellular matrix and into living cells and tissues, respectively, down to single molecule detection. In living tissues, however, cells and extracellular matrix coexist and interact. To acquire information on this cell-matrix interaction, we developed a technique for colocalized, correlative multispectral tissue analysis by implementing high-sensitivity, wide-field fluorescence imaging on a confocal Raman microscope. As a proof of principle, we study early stages of bone formation in the zebrafish (Danio rerio) larvae because the zebrafish has emerged as a model organism to study vertebrate development. The newly formed bones were stained using a calcium fluorescent marker and the maturation process was imaged and chemically characterized in vivo. Results obtained from early stages of mineral deposition in the zebrafish fin bone unequivocally show the presence of hydrogen phosphate containing mineral phases in addition to the carbonated apatite mineral. The approach developed here opens significant opportunities in molecular imaging of metabolic activities, intracellular sensing, and trafficking as well as in vivo exploration of cell-tissue interfaces under (patho-)physiological conditions.Understanding fundamental biological processes relies on probing intra- and extracellular environments, targeted delivery inside living cells and tissues, and real-time detection and imaging of chemical markers and biomolecules (1,2). Typically, information about molecules in cellular environments is obtained by fluorescence microscopy (3). This is a powerful imaging tool for localizing and imaging samples but requires fluorescent labels and markers and lacks capabilities for quantitative mapping of the chemical composition in complex systems. In this regard, confocal Raman spectroscopic imaging is becoming increasingly popular for label-free chemical detection, due to the inherent scattering nature of all biomolecules (4,5). However, confocal Raman imaging alone does not allow live, high-resolution imaging of larger regions of interest in complex biological tissues. Transcutaneous Raman spectroscopy has the potential as a tool for in vivo bone quality assessment (6), whereas the time- and space-resolved Raman spectroscopy allows the visualization in vivo of the distributions of molecular species in human and yeast cells (4,5,7). Here we developed a correlative Raman and fluorescence imaging method that combines the strengths and compensates for the shortcomings of each of these imaging modalities and allows studying in vivo processes in complex animal models such as zebrafish larvae. There are two main advantages of this approach over previous studies (8,9): low light intensity and high acquisition rate, making it well suited for real-time investigation of live samples.Fig. 1, a and b, shows a schematic representation of the experimental setup and of the optical path, respectively. The two techniques are implemented on a commercially available Raman microscope body to perform simultaneously confocal Raman spectroscopy and wide-field fluorescence imaging (see the Supporting Material for details of components). Briefly, the multimodality of the setup is provided by a combination of dichroic mirrors (DM 1–3) and filters that at turns reflect or transmit the excitation and emission signals. This combination of optics allows simultaneous collection of fluorescence images (2560 × 2160 pixels at 30 fps) with excitation at 400 and 490 nm and spatially resolved Raman spectra with excitation at 633 nm.Open in a separate windowFigure 1Fluorescence imaging of zebrafish larvae. (a) Cartoon of the experimental setup showing how the different modules are assembled onto the microscope for the simultaneous use of confocal Raman spectroscopy and fluorescence imaging. (b) Schematic representation of the optical path. (c) Fluorescence image of calcium-containing tissues, and fluids stained with calcein blue and excited at 400 nm (top). Endothelial cells of transgenic tg(fli1:EGFP)y1 zebrafish excited at 490 nm (bottom).As a proof of principle, we have studied the different mineral phases involved in bone formation of the zebrafish larvae. The bone development process involves the transport of ions to specific cells (osteoblasts) that are responsible for the subsequent mineral formation and deposition. The mineral phase in these cells is a poorly characterized disordered calcium phosphate (10–12). The mineral-bearing intracellular vesicles release their content into the extracellular collagen fibrils, where the mineral subsequently crystallizes as carbonated hydroxyapatite (13). Very little is known about the phase transformations the mineral undergoes after the deposition into the collagen matrix in vivo. Raman spectroscopy studies of bone tissue in organ cultures evidenced that the inorganic mineral deposition proceeds through transient intermediates including octacalcium phosphate-like (OCP) minerals (14).To assess the feasibility of imaging a vertebrate organism, fluorescence images of an entire zebrafish larva (Fig. 1 c) were acquired with the correlative fluorescence-Raman setup. The two images in Fig. 1 c were composed by merging several low-magnification (10×) fluorescence images. Larvae of transgenic zebrafish Tg(fli:EGFP); nac mutants (albino fish) expressing EGFP in the cytoplasm of endothelial cells was used. The newly formed bones were stained by soaking the live embryo noninvasively in the calcium markers calcein blue 0.2% wt or calcein green 0.2% wt.The calcein blue marker is excited at 400 nm. It is labeling bones and can be also detected as a fluorescent marker not associated with formed bones (e.g., stomach) (Fig. 1 c, top). At 490 nm, calcein green and endothelial cells within blood vessels expressing EGFP are excited (Fig. 1 c, bottom). Because EGFP and calcein blue have significantly different excitation and emissions spectra, dual staining with calcein blue (as a mineral marker) and EGFP allows fast-switching dual-wavelength fluorescence imaging. Furthermore, because the spectra of the calcium markers and EGFP do not extend beyond the Raman laser, these fluorophores are appropriate candidates for experiments requiring Raman and fluorescence imaging. The dual-excitation offers the capability of mapping several tissues in a single experiment at the video rate. This, in principle, could be used to probe different parameters of the microenvironment (e.g., pH (15), temperature (16), viscosity (17), and calcium concentration (18)) using wavelength-ratiometric fluorescence imaging which, in correlation with confocal Raman spectroscopy, could open new strategies in studies of the microenvironmental properties in living tissues.The fin rays of zebrafish are a simple, growing bone-model system, in which the fins are gradually mineralized within spatially resolved regions (19). Raman spectroscopy revealed details of the calcein green-stained fin where new bone is deposited (Fig. 2). In Fig. 2 a, a fluorescence image of a zebrafish larva analogous to the top image in Fig. 1 c is shown. The right inset in Fig. 3 b shows higher-magnification (60× water-immersion objective) details of the calcein green-stained fin typical of newly deposited bone. Raman spectra of progressively mineralized bone tissue were acquired within representative regions (Fig. 2 b; numbered 1–4). The spectra exhibit characteristic bands that can be assigned to the organic protein extracellular matrix (amide I, amide III, Phe, C-H, etc.) and the inorganic mineral content (v₁, v₂, v₄ of PO₄³⁻).Open in a separate windowFigure 2Correlative fluorescence-Raman imaging of zebrafish fin bone maturation. (a) Low-resolution (10×) fluorescence image of zebrafish stained with calcein green, with high-resolution (60×) details (right inset in panel b) of a representative fin ray region where Raman spectra (b) of progressively mineralized bone tissue were acquired (numbered 1–4). (Left inset in panel b) Integral of the orientation independent mineral band (v₂) where a clear drop of the mineral content can be observed.The analyses of the orientation-independent v₂ phosphate band revealed a clear drop in the mineral content based on the intensity integral (left inset in Fig. 2 b). Assuming that the spectrum collected in region 4 contains only organic matrix (very small phosphate-related peaks) and by subtracting it from the spectrum of mineral-rich bone region (spectrum 1, proximal part of the tail bone), spectral features of only the mineral phase can be plotted (black line). In addition to the phosphate (PO₄³⁻) and carbonate (CO₃²⁻) bands assignable to the carbonated apatite phase characteristic of the more mature bone mineral, several peaks related to the hydrogen phosphate (HPO₄²⁻) species can be clearly distinguished.The HPO₄²⁻ peaks are characteristic of the OCP mineral phase that has been postulated, together with amorphous calcium phosphate, as an intermediate mineral phase in the process of bone maturation (10,13,14,20), but never observed directly in living animals. Our findings show in vivo potential of the correlative setup envisioned by Crane et al. (14) and confirm that the mineral maturation indeed proceeds through an OCP-like mineral phase. Further analysis of the mineral spectrum in Fig. 2 b reveals an extremely broad band in the region 800–1100 cm⁻¹. This envelope can be related to hydrogenated phosphate species typical of amorphous calcium phosphate precipitated in an acidic environment (see Fig. S1 in the Supporting Material), suggesting that this phase is also contributing to the maturation process.In conclusion, the methodology developed here allows for unprecedented chemical characterization of fluorescently-labeled biological tissues in vivo. The approach is suitable for long-term in vivo characterization of zebrafish bone mineralization under (patho-)physiological conditions. Furthermore, the setup can be upgraded to host other advance fluorescence imaging techniques such as super-resolution microscopy (e.g., photoactivated localization microscopy), two-photon excitation, and Forster resonance energy transfer or fluorescence lifetime imaging microscopy, and be applied on both in vivo and in vitro specimens. This opens significant opportunities in molecular imaging of metabolic activities, intracellular sensing, and trafficking as well as in vivo exploration of cell-tissue interfaces.