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.     

Variability and Constancy in Cellular Growth of Arabidopsis Sepals

Growth of tissues is highly reproducible; yet, growth of individual cells in a tissue is highly variable, and neighboring cells can grow at different rates. We analyzed the growth of epidermal cell lineages in the Arabidopsis (Arabidopsis thaliana) sepal to determine how the growth curves of individual cell lineages relate to one another in a developing tissue. To identify underlying growth trends, we developed a continuous displacement field to predict spatially averaged growth rates. We showed that this displacement field accurately describes the growth of sepal cell lineages and reveals underlying trends within the variability of in vivo cellular growth. We found that the tissue, individual cell lineages, and cell walls all exhibit growth rates that are initially low, accelerate to a maximum, and decrease again. Accordingly, these growth curves can be represented by sigmoid functions. We examined the relationships among the cell lineage growth curves and surprisingly found that all lineages reach the same maximum growth rate relative to their size. However, the cell lineages are not synchronized; each cell lineage reaches this same maximum relative growth rate but at different times. The heterogeneity in observed growth results from shifting the same underlying sigmoid curve in time and scaling by size. Thus, despite the variability in growth observed in our study and others, individual cell lineages in the developing sepal follow similarly shaped growth curves.Cells undergo multiple rounds of growth and division to create reproducible tissues. In some plant tissues, such as expanding cotyledons, reproducibility can occur on a cellular level during specific intervals of development, where cotyledon cells exhibit uniform cellular growth (Zhang et al., 2011). However, several studies on cell division and growth in other developing plant tissues have demonstrated that plant cells exhibit considerable cell-to-cell variability during development (Meyer and Roeder, 2014). For example, in both the Arabidopsis (Arabidopsis thaliana) meristem and leaf epidermis, cells show spatiotemporal variation in individual cell growth rates (GRs; Asl et al., 2011; Elsner et al., 2012; Kierzkowski et al., 2012; Uyttewaal et al., 2012). Furthermore, cell divisions have been observed with marked randomness in their timing and orientation (Roeder et al., 2010; Besson and Dumais, 2011; Roeder, 2012). In this study, we identify a hidden, underlying pattern in the seemingly random GR (Box 1) of cells during the formation of sepals in Arabidopsis.Open in a separate windowBox 1.Definitions of GR terms. (For details on the calculations, see “Materials and Methods.”)Plant cell growth is defined as an increase in cell size due to an irreversible expansion of the cell wall. Neighboring cells physically accommodate one another during plant growth because their cell walls are glued together with a pectin-rich middle lamella, which prevents cell mobility. The cell wall is a thin, stiff layer composed of a polymer matrix including cellulose, hemicellulose, and pectin (Somerville et al., 2004; Cosgrove, 2005). Plant cells change their size and shape by modifying their turgor pressure and/or the mechanical properties of their walls, such as elasticity, plasticity, and extensibility. Growing plant cells exert forces on their neighbors through their walls, and cell wall stresses created by these forces feed back to alter the growth anisotropy (Hamant et al., 2008; Sampathkumar et al., 2014). Although these feedbacks can coordinate growth, they may also amplify differences in growth between neighboring cells (Uyttewaal et al., 2012).Two competing computational models have proposed explanations of the cellular heterogeneity observed in growing tissues by making different assumptions about how cells grow. In the first, it is assumed that relative growth rates (RGRs) of all cells are uniform in space and time, whereas variation in the timing of division causes the heterogeneity of cell sizes (Roeder et al., 2010). This model suggests that cell divisions cut the sepal into semiindependent cells, which grow uniformly within the expanding organ (Kaplan and Hagemann, 1991). The second model postulates the reverse process: timing of cell division is uniform, but cellular growth is variable and depends on the size of the cell (Asl et al., 2011). This model suggests that cells are autonomous. Currently, there is biological evidence for both models. Variability in cell division timing is observed in sepals and meristems, whereas variability in cellular GRs has been observed in leaves and meristem cells (Reddy et al., 2004; Roeder et al., 2010; Asl et al., 2011; Elsner et al., 2012; Kierzkowski et al., 2012; Uyttewaal et al., 2012). Thus, the debate on how the growth of individual cells within an organ relates to one another remains unresolved.The identification of underlying patterns in noisy cellular growth processes is challenging. Technical difficulties include the capability for cellular-resolution imaging of the tissue at sufficiently small time intervals. Previous studies (Zhang et al., 2011; Elsner et al., 2012; Kierzkowski et al., 2012) did not image and track individual cells, or they had a coarse time resolution, with 11- to 48-h intervals between images, which may have hidden important temporal dynamics. We studied growing cells in the Arabidopsis sepal, which allows for live imaging with cellular resolution at 6-h intervals (Roeder et al., 2010). The sepal is the leaf-like outermost floral organ of Arabidopsis (Fig. 1) with four sepals of stereotypical size produced per flower. Its accessibility for live imaging makes the sepal an excellent system for studying organogenesis (Roeder et al., 2010, 2011, 2012; Qu et al., 2014). Sepals exhibit high cellular variability in the timing of division and endoreduplication, an alternative cell cycle in which a cell replicates its DNA but fails to divide (Roeder et al., 2010). Furthermore, quantifying cell growth in sepals may shed light on growth mechanisms of other plant organs, such as leaves (Poethig and Sussex, 1985; Roeder et al., 2010).Open in a separate windowFigure 1.Diverse sizes of Arabidopsis sepal cells. A, Four sepals (s) are the outermost green leaf-like floral organs in Arabidopsis. B and C, Scanning electron micrographs of a mature Arabidopsis sepal show that the outer epidermal cells have a wide range of sizes. Asterisks mark some of the largest cells (giant cells) that can span 1/4 the length of the sepal. Scale = 100 µm.Another key challenge in analyzing cellular growth is the identification of trends in noisy data. Inaccuracies in data acquisition, such as segmentation errors, and noisy growth of individual cells can hide meaningful spatiotemporal trends in growth. GRs measured over longer time intervals will have reduced noise, but they may also obscure important temporal dynamics. Alternatively, previous studies have examined growth of the whole organ or its subregions to avoid cellular noise (De Veylder et al., 2001; Mündermann et al., 2005; Rolland-Lagan et al., 2005, 2014; Kuchen et al., 2012; Remmler and Rolland-Lagan, 2012). However, precise cellular patterns are not resolved. In our study, we use cellular resolution data to define spatially averaged kinematics while keeping the full temporal resolution to identify course-grained spatial trends in the dynamics of cellular growth (Box 1).We analyze the relationships among the growth of individual cell lineages in a developing Arabidopsis sepal by live imaging and computational analyses. We have developed continuous low-order displacement fields to represent the spatially averaged kinematics of the sepal (Box 1). We find that the growth of the tissue surface area, cell lineage area, and wall length follows S curves, suggesting that their GRs vary over time. Additionally, we find that there is a linear correlation between the maximum GR (i.e. size increase per hour) and the size of the cell. We furthermore find that each sepal cell lineage reaches the same maximum RGR (i.e. GR divided by size). However, each cell reaches the maximum RGR at a different time during its development, generating the observed heterogeneity. Thus, we find underlying similarities in the growth curves of sepal cells.     

AUXIN RESPONSE FACTOR17 Is Essential for Pollen Wall Pattern Formation in Arabidopsis

In angiosperms, pollen wall pattern formation is determined by primexine deposition on the microspores. Here, we show that AUXIN RESPONSE FACTOR17 (ARF17) is essential for primexine formation and pollen development in Arabidopsis (Arabidopsis thaliana). The arf17 mutant exhibited a male-sterile phenotype with normal vegetative growth. ARF17 was expressed in microsporocytes and microgametophytes from meiosis to the bicellular microspore stage. Transmission electron microscopy analysis showed that primexine was absent in the arf17 mutant, which leads to pollen wall-patterning defects and pollen degradation. Callose deposition was also significantly reduced in the arf17 mutant, and the expression of CALLOSE SYNTHASE5 (CalS5), the major gene for callose biosynthesis, was approximately 10% that of the wild type. Chromatin immunoprecipitation and electrophoretic mobility shift assays showed that ARF17 can directly bind to the CalS5 promoter. As indicated by the expression of DR5-driven green fluorescent protein, which is an synthetic auxin response reporter, auxin signaling appeared to be specifically impaired in arf17 anthers. Taken together, our results suggest that ARF17 is essential for pollen wall patterning in Arabidopsis by modulating primexine formation at least partially through direct regulation of CalS5 gene expression.In angiosperms, the pollen wall is the most complex plant cell wall. It consists of the inner wall, the intine, and the outer wall, the exine. The exine is further divided into sexine and nexine layers. The sculptured sexine includes three major parts: baculum, tectum, and tryphine (Heslop-Harrison, 1971; Piffanelli et al., 1998; Ariizumi and Toriyama, 2011; Fig. 1A). Production of a functional pollen wall requires the precise spatial and temporal cooperation of gametophytic and sporophytic tissues and metabolic events (Blackmore et al., 2007). The intine layer is controlled gametophytically, while the exine is regulated sporophytically. The sporophytic tapetum cells provide material for pollen wall formation, while primexine determines pollen wall patterning (Heslop-Harrison, 1968).Open in a separate windowFigure 1.Schematic representation of the pollen wall and primexine development. A, The innermost layer adjacent to the plasma membrane is the intine. The bacula (Ba), tectum (Te), and tryphine (T) make up the sexine layer. The nexine is located between the intine and the sexine layers. The exine includes the nexine and sexine layers. B, Primexine (Pr) appears between callose (Cl) and plasma membrane (Pm) at the early tetrad stage (left panel). Subsequently, the plasma membrane becomes undulated (middle panel) and sporopollenin deposits on the peak of the undulated plasma membrane to form bacula and tectum (right panel).After meiosis, four microspores were encased in callose to form a tetrad. Subsequently, the primexine develops between the callose layer and the microspore membrane (Fig. 1B), and the microspore plasma membrane becomes undulated (Fig. 1B; Fitzgerald and Knox, 1995; Southworth and Jernstedt, 1995). Sporopollenin precursors then accumulate on the peak of the undulated microspore membrane to form the bacula and tectum (Fig. 1B; Fitzgerald and Knox, 1995). After callose degradation, individual microspores are released from the tetrad, and the bacula and tectum continue to grow into exine with further sporopollenin deposition (Fitzgerald and Knox, 1995; Blackmore et al., 2007).The callose has been reported to affect primexine deposition and pollen wall pattern formation. The peripheral callose layer, secreted by the microsporocyte, acts as the mold for primexine (Waterkeyn and Bienfait, 1970; Heslop-Harrison, 1971). CALLOSE SYNTHASE5 (CalS5) is the major enzyme responsible for the biosynthesis of the callose peripheral of the tetrad (Dong et al., 2005; Nishikawa et al., 2005). Mutation of Cals5 and abnormal CalS5 pre-mRNA splicing resulted in defective peripheral callose deposition and primexine formation (Dong et al., 2005; Nishikawa et al., 2005; Huang et al., 2013). Besides CalS5, four membrane-associated proteins have also been reported to be involved in primexine formation: DEFECTIVE EXINE FORMATION1 (DEX1; Paxson-Sowders et al., 1997, 2001), NO EXINE FORMATION1 (NEF1; Ariizumi et al., 2004), RUPTURED POLLEN GRAIN1 (RPG1; Guan et al., 2008; Sun et al., 2013), and NO PRIMEXINE AND PLASMA MEMBRANE UNDULATION (NPU; Chang et al., 2012). Mutation of DEX1 results in delayed primexine formation (Paxson-Sowders et al., 2001). The primexine in nef1 is coarse compared with the wild type (Ariizumi et al., 2004). The loss-of-function rpg1 shows reduced primexine deposition (Guan et al., 2008; Sun et al., 2013), while the npu mutant does not deposit any primexine (Chang et al., 2012). Recently, it was reported that Arabidopsis (Arabidopsis thaliana) CYCLIN-DEPENDENT KINASE G1 (CDKG1) associates with the spliceosome to regulate the CalS5 pre-mRNA splicing for pollen wall formation (Huang et al., 2013). Clearly, disrupted primexine deposition leads to aberrant pollen wall patterning and ruptured pollen grains in these mutants.The plant hormone auxin has multiple roles in plant reproductive development (Aloni et al., 2006; Sundberg and Østergaard, 2009). Knocking out the two auxin biosynthesis genes, YUC2 and YUC6, caused an essentially sterile phenotype in Arabidopsis (Cheng et al., 2006). Auxin transport is essential for anther development; defects in auxin flow in anther filaments resulted in abnormal pollen mitosis and pollen development (Feng et al., 2006). Ding et al. (2012) showed that the endoplasmic reticulum-localized auxin transporter PIN8 regulates auxin homeostasis and male gametophyte development in Arabidopsis. Evidence for the localization, biosynthesis, and transport of auxin indicates that auxin regulates anther dehiscence, pollen maturation, and filament elongation during late anther development (Cecchetti et al., 2004, 2008). The role of auxin in pollen wall development has not been reported.The auxin signaling pathway requires the auxin response factor (ARF) family proteins (Quint and Gray, 2006; Guilfoyle and Hagen, 2007; Mockaitis and Estelle, 2008; Vanneste and Friml, 2009). ARF proteins can either activate or repress the expression of target genes by directly binding to auxin response elements (AuxRE; TGTCTC/GAGACA) in the promoters (Ulmasov et al., 1999; Tiwari et al., 2003). The Arabidopsis ARF family contains 23 members. A subgroup in the ARF family, ARF10, ARF16, and ARF17, are targets of miRNA160 (Okushima et al., 2005b; Wang et al., 2005). Plants expressing miR160-resistant ARF17 exhibited pleiotropic developmental defects, including abnormal stamen structure and reduced fertility (Mallory et al., 2005). This indicates a potential role for ARF17 in plant fertility, although the detailed function remains unknown. In addition, ARF17 was also proposed to negatively regulate adventitious root formation (Sorin et al., 2005; Gutierrez et al., 2009), although an ARF17 knockout mutant was not reported and its phenotype is unknown.In this work, we isolated and characterized a loss-of-function mutant of ARF17. Results from cytological observations suggest that ARF17 controls callose biosynthesis and primexine deposition. Consistent with this, the ARF17 protein is highly abundant in microsporocytes and tetrads. Furthermore, we demonstrate that the ARF17 protein is able to bind the promoter region of CalS5. Our results suggest that ARF17 regulates pollen wall pattern formation in Arabidopsis.     

Mitofusins: ubiquitylation promotes fusion

Mitochondrial genes including Mfn2 are at the center of many diseases, underscoring their potential as a therapeutical target. The Chen group now identified 15-oxospiramilactone as a chemical inhibitor of the mammalian deubiquitylase USP30, acting on Mfn1 and Mfn2.Mitofusins, Fzo1 in yeast and Mfn1 and Mfn2 in mammals, are ubiquitylated and this post-translational modification has both positive and negative consequences on mitochondrial fusion¹. The process of ubiquitylation requires enzymes belonging to three classes of proteins called E1, E2 and E3, which catalyze a cascade of successive steps leading to the covalent attachment of the modifier to its target protein². Deubiquitylating enzymes render this modification reversible, thus offering further possibilities for regulation². Ubiquitylation of mitofusins leads to their proteolyic breakdown, inhibiting fusion of mitochondria that consequently undergo fragmentation (Figure 1, left panel)^1,3. For example in response to mitochondrial depolarization or apoptotic stimuli, E3 ligases like Parkin and Huwe1 ubiquitylate and target Mfn1 and Mfn2 to the proteasome (Figure 1, left panel)^3,4. However, ubiquitylation of mitofusins is a dual process and a non-proteolytic role of mitofusin ubiquitylation that promotes mitochondrial fusion is now emerging¹. This opposing mechanism was first described in yeast, where the isopeptidases Ubp12 and Ubp2 that deubiquitylate Fzo1 have been identified⁵. Inhibition and activation of mitochondrial fusion by ubiquitylation enable different morphologies of mitochondria ranging from a multitude of small organelles to a hyperconnected network (Figure 1)⁵. In a recent paper published in Cell Research, Yue et al.⁶ reveal that a similar process is present in mammalian cells. The authors report that the isopeptidase USP30 acts on ubiquitylated forms of Mfn1 and Mfn2 that stimulate mitochondrial fusion (Figure 1, right panel). This discovery identifies for the first time in mammals a positive role of ubiquitylation in the regulation of Mfn1 and Mfn2 fusion activity⁶.Open in a separate windowFigure 1Dual roles of ubiquitylation and deubiquitylation of mitofusins Mfn1 and Mfn2, the key effectors for mitochondrial fusion, in regulating mitochondrial fusion. On one hand, ubiquitylation of Mfn1 and Mfn2 by E3 ligases like Parkin or Huwe1 targets their proteasomal degradation and inhibits mitochondrial fusion, which results in mitochondrial fragmentation due to unopposed fission events. On the other hand, ubiquitylation of Mfn1 and Mfn2 by an unknown E3 ligase enhances their activity and promotes mitochondrial fusion. This positive regulation is counteracted by the deubiquitylase USP30, targeted by the small molecule inhibitor 15-oxospiramilactone.Moreover, Yue et al.⁶ identified the first small molecule inhibitor of mitochondrial fusion, 15-oxospiramilactone, which targets USP30 in both human and mouse cell lines. 15-oxospiramilactone is a semi-synthetic diterpene alkaloid of 330 Da that can be chemically synthetized through an oxidation reaction from spiramines extracted from the roots of a Chinese herbal medicine Spiraea japonica (Rosaceae). Inhibition of USP30 increased ubiquitylation of Mfn1 and Mfn2 and led to an elongation of the mitochondrial network (Figure 1, right panel)^6,7. USP30 is a cysteine ubiquitin isopeptidase N-terminally anchored to the outer membrane of mitochondria, which was previously shown to regulate mitochondrial morphology dependent on Mfn1 and Mfn2⁷. USP30 knockdown leads to mitochondrial elongation, a phenotype rescued by ectopic expression of wild-type USP30, while the catalytically inactive mutant C77S USP30 failed to revert⁷. Yue et al.⁶ show that 15-oxospiramilactone directly interacts with USP30, which also depends on its catalytically active cysteine, and inhibits the DUB activity of USP30 on tetraubiquitin chains. Moreover, they demonstrate that inhibition of USP30 and subsequent mitochondrial elongation are due to stimulated mitochondrial fusion activity, apparently with no influence on mitochondrial fission⁶. Concomitantly, cells showed increased ubiquitylation of Mfn1 and Mfn2 without significant changes in protein turnover of these two proteins⁶. Therefore, in analogy to findings in yeast, ubiquitylation of Mfn1 and Mfn2 can either signal them to activate mitochondrial fusion or in contrast promote their proteasomal degradation, resulting in mitochondrial fission (Figure 1).Importantly, 15-oxospiramilactone reverts the mitochondrial fragmentation phenotype of single Mfn-knockout (Mfn1^−/− or Mfn2^−/−) cells, suggesting that mitochondrial fusion depends on the ubiquitylation of both mitofusin proteins⁶. In yeast, the importance of ubiquitylation was proven by directly attaching a deubiquitylase to Fzo1, which resulted in a non-ubiquitylated and non-functional Fzo1 protein⁵. In addition, the identification and the subsequent mutagenesis study of the ubiquitylation sites in Fzo1 confirmed an interplay between ubiquitylation and oligomerization in mitochondrial fusion in S. cerevisiae⁵. Impairing the yeast E3 ligase SCF^Mdm30 inhibited mitochondrial fusion and, conversely, ablation of UBP12 led to more fusion events^5,8. Given this new identification of USP30 as the functional orthologue of the yeast Ubp12, future studies will certainly aim at the identification of the E3 ligase counterpart of SCF^Mdm30 and ubiquitylation sites in Mfn1 and Mfn2. In addition to USP30 inhibition, other conditions leading to mitochondrial hyperfusion have been previously observed, such as mild stress conditions that increase reactive oxygen species (ROS)⁹. Importantly, oxidative stress and mitochondrial fusion are directly linked as ROS induces disulphide switching of Mfn2 to oligomeric forms that promote mitochondrial fusion⁹. It would be interesting to investigate whether 15-oxospiramilactone also affects the generation of disulphide-mediated mitofusin oligomers, thus activating mitochondrial fusion.Mutations in Mfn2 are causative for the Charcot-Marie-Tooth type 2A neuropathy, an autosomal dominant disorder of the peripheral nervous system that mainly affects axons and lower extremities¹. Deficiencies in Parkin and Mfn2 ubiquitylation were also linked to Parkinson''s disease³. In addition to neuropathies, Mfn2 is associated to other diseases like cardiomyophathies and diabetes¹. Yue et al.⁶ found that 15-oxospiramilactone reverted phenotypes arising from the lack of Mfn1 or Mfn2. It restored the normal distribution of mtDNA, allowed recovery of the ΔΨm and increased the ATP levels and OXPHOS capacity of the rebuilt mitochondrial network. Therefore, this study potentiates 15-oxospiramilactone for therapeutical benefit. The anti-cancer properties of 15-oxospiramilactone, also named S3 or NC043, have been previously reported^10,11. It inhibits Wnt/β-catenin signaling and colon cancer cell tumorigenesis in a xenograft model¹⁰. Moreover, 15-oxospiramilactone increases Bim expression and apoptosis to inhibit tumor growth from Bax^−/−/Bak^−/− cells implanted in mice¹¹. However, Yue et al.⁶ show that the effect of 15-oxospiramilactone in mitochondrial fusion is independent of apoptosis and suggest that the difference is due to drug concentration. Indeed, previous anti-cancer studies used 15-oxospiramilactone at a concentration range of 3.75-15 μM^10,11, whereas 2 μM suffice to inhibit USP30⁶. Further studies are needed to address the clinical relevance of 15-oxospiramilactone and USP30 in Mfn2-associated diseases.     

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.     

Cytokinetic astralogy

Division plane specification in animal cells has long been presumed to involve direct contact between microtubules of the anaphase mitotic spindle and the cell cortex. In this issue, von Dassow et al. (von Dassow et al. 2009. J. Cell. Biol. doi:10.1083/jcb.200907090) challenge this assumption by showing that spindle microtubules can effectively position the division plane at a distance from the cell cortex.Cell division, or cytokinesis, is accomplished via constriction of an equatorially localized contractile ring composed of filamentous actin and myosin II (Rappaport, 1996). Accurate division plane specification is essential to properly partition the cytoplasm and permit each daughter cell to receive a single copy of the genome. To ensure this accuracy, microtubules of the mitotic spindle signal to the cell cortex upon anaphase onset and promote assembly of the contractile ring between the separating chromosomes. The precise mechanism by which microtubules position the contractile ring, however, remains elusive.Early models on the nature of the spindle-derived signal proposed that astral rays (later found to be microtubules) position the division plane by either locally promoting contractility at the cell equator or inhibiting contractility at the cell poles (Rappaport, 1996). Recent evidence, though, suggests that distinct microtubule populations within a single cell provide multiple signals to promote accurate division (Canman et al., 2003; Bringmann and Hyman, 2005; Chen et al., 2008; Foe and von Dassow, 2008; von Dassow, 2009).The anaphase mitotic spindle contains several subtypes of microtubules, each of which is likely to contribute to division plane specification. Although kinetochore microtubules drive chromosome segregation during anaphase, nonkinetochore microtubules extend and maintain close proximity with the assembling central spindle (Mastronarde et al., 1993). Central spindle microtubules are highly stable (Salmon et al., 1976) and organize into an antiparallel bundled array between the separating chromosomes (Mastronarde et al., 1993). Preventing central spindle assembly usually results in a complete failure in cytokinesis, and prevents division plane specification in many cell types (Glotzer, 2005). Astral microtubules, however, are highly dynamic and grow out circumferentially from the centrosomes toward the cell cortex. Increasing evidence suggests that the astral microtubule signal inhibits contractility (see below; Canman et al., 2000; Kurz et al., 2002; Lewellyn et al., 2009).Regardless of the mechanism of division plane specification via microtubules, nearly all current models depend on direct contact between microtubules of the mitotic spindle and the cell cortex. Most of these models were based on observations that at the time of division plane specification, astral microtubules contact the cell cortex in nearly all systems studied. Nonkinetochore and/or central spindle microtubules have also been proposed to deliver critical contractile signals to the cell equator (Murata-Hori and Wang, 2002; Canman et al., 2003; Somers and Saint, 2003; Verbrugghe and White, 2004; Lewellyn et al., 2009; Vale et al., 2009). Yet in many cell types (especially early embryos), central spindle microtubules are at some distance from the cell cortex during division plane specification. Despite this, signal delivery for both astral and central spindle microtubules was proposed to occur via direct transport along microtubules to the cell cortex. The study of von Dassow et al. in this issue, however, indicates that accurate division plane specification does not require any close microtubule/cortical contact and may occur via a diffusion-based mechanism (see also Salmon and Wolniak, 1990).By treating echinoderm and Xenopus embryos with controlled levels of trichostatin A (TSA), which destabilizes acetylated dynamic microtubules via inhibition of the tubulin deacetylase HDAC6 (Matsuyama et al., 2002), von Dassow et al. (2009) were able to preferentially prevent astral microtubule growth while leaving central spindle microtubules intact. TSA treatment did not block anaphase onset or central spindle assembly, but resulted in the complete disruption of all direct microtubule contact with the cell cortex. Nevertheless, TSA-treated cells were able to undergo cytokinesis successfully (Fig. 1 A). The lack of astral microtubules in TSA-treated cells was also recapitulated by double centrosome ablation, and again the cells were able to undergo cytokinesis (Fig. 1 B). In both experiments, cytokinesis occurred in a timely manner, but the contractile ring was broader than in control cells. Together, these data suggest that spindle microtubules are sufficient to provide a diffusible stimulatory signal capable of defining the cell division plane without any direct contact with the cell cortex (von Dassow et al., 2009).Open in a separate windowFigure 1.Testing models of division plane specification by targeting distinct microtubule populations. By selectively eliminating astral microtubules with either controlled TSA-treatment (A) or by double centrosome ablation (B), von Dassow et al. (2009) provide strong evidence that microtubule contact with the cell cortex is not essential for successful cytokinesis. When a single centrosome was ablated, the division plane was displaced away from the ablated aster (B); this suggests that astral microtubules provide an inhibitory signal. Further, anucleate cells would only complete cytokinesis if the intracentrosomal distance exceeded the distance from the centrosomes to the cell cortex (C).The authors noticed that cytokinesis occurred selectively at a position with reduced microtubule density in control cells; therefore, they explored the role of astral microtubules in division plane positioning. By selectively ablating one centrosome just before anaphase onset, von Dassow et al. (2009) were also able to provide strong support for an inhibitory role of astral microtubules in division plane specification. When a single centrosome was ablated, the division plane was displaced away from the remaining astral microtubules and toward the ablated centrosome (Fig. 1 B). Further evidence for an inhibitory role of astral microtubules in cytokinesis came from close examination of the intracentrosomal distance in anucleate cells that were able to undergo cytokinesis relative to those that were not. Cells were only able to undergo cytokinesis when the intracentrosomal distance exceeded the distance from the centrosomes to the cell cortex (Fig. 1 C), which suggests that cytokinesis requires an aster-free zone. The authors propose a mechanism in these anucleate cells whereby global activation of contractility drives division plane specification refined by a zone of astral separation (von Dassow et al., 2009). However, one possibility is that a central spindle still forms in these anucleate cells and thus provides the same diffusion-based signal that promotes division in cells without asters. Indeed, antiparallel arrays of bundled microtubules that resemble the central spindle are known to form between asters without intervening chromosomes in other systems (Savoian et al., 1999).To summarize, the results described by von Dassow et al. (2009) support a model in which central spindle microtubules provide a diffusible stimulatory signal to promote the assembly of a broad contractile ring, which is then refined by astral microtubules into a tight contractile ring. It is tempting to speculate on the molecular nature of this diffusible signal and mechanism of the astral refinement during cytokinesis. Signaling via the small GTPase Rho is required for cytokinesis and is dependent on spindle microtubules (Bement et al., 2005; Piekny et al., 2005). von Dassow et al. (2009) showed that in TSA-treated cells lacking astral microtubules, the equatorial zone of active Rho GTPase is broader relative to control cells. Rho activation is promoted (at least in part) via the central spindle–localized GTP exchange factor, ECT2 (Glotzer, 2005). In parallel, the GTPase-activating protein (GAP) CYK4/MgcRacGAP also associates with the central spindle, where it acts to both limit the zone of Rho activity (Miller and Bement, 2009) and to promote the inactivation of another small GTPase, Rac (D''Avino et al., 2004; Yoshizaki et al., 2004; Canman et al., 2008). Perhaps in parallel to central spindle mediated activation of Rho signaling, local inactivation of the inhibitory Rac signal via CYK4 GAP activity would further specify the division plane, even at a distance (Fig. 2). When the dynamic asters are present, they could then additionally amplify Rac signaling at the cell poles via a similar mechanism to what occurs during cell motility (Wittmann and Waterman-Storer, 2001). This local feedback loop would reinforce the positive signal coming from the central spindle via Rho activation and could help delimit active Rho at the cell equator (Fig. 2). Certainly, understanding how Rho activation can be propagated to the cell cortex via diffusion in such an accurate manner will be a major future challenge.Open in a separate windowFigure 2.Model for central spindle–mediated signaling via Rho family small GTPases. Central spindle–localized guanine nucleotide exchange factor ECT2 leads to Rho activation at the cell equator. At the same time, central spindle–localized CYK4 (a Rho family GAP) would also locally inactivate the inhibitory Rac signal. Further refinement of the zone of active Rho by astral microtubule–activated Rac could then sharpen the Rho zone into a tight contractile ring.     

Focus Issue on Plant Cell Walls: Sequencing around 5-Hydroxyconiferyl Alcohol-Derived Units in Caffeic Acid O-Methyltransferase-Deficient Poplar Lignins

Caffeic acid O-methyltransferase (COMT) is a bifunctional enzyme that methylates the 5- and 3-hydroxyl positions on the aromatic ring of monolignol precursors, with a preference for 5-hydroxyconiferaldehyde, on the way to producing sinapyl alcohol. Lignins in COMT-deficient plants contain benzodioxane substructures due to the incorporation of 5-hydroxyconiferyl alcohol (5-OH-CA), as a monomer, into the lignin polymer. The derivatization followed by reductive cleavage method can be used to detect and determine benzodioxane structures because of their total survival under this degradation method. Moreover, partial sequencing information for 5-OH-CA incorporation into lignin can be derived from detection or isolation and structural analysis of the resulting benzodioxane products. Results from a modified derivatization followed by reductive cleavage analysis of COMT-deficient lignins provide evidence that 5-OH-CA cross couples (at its β-position) with syringyl and guaiacyl units (at their O-4-positions) in the growing lignin polymer and then either coniferyl or sinapyl alcohol, or another 5-hydroxyconiferyl monomer, adds to the resulting 5-hydroxyguaiacyl terminus, producing the benzodioxane. This new terminus may also become etherified by coupling with further monolignols, incorporating the 5-OH-CA integrally into the lignin structure.Lignins are polymeric aromatic constituents of plant cell walls, constituting about 15% to 35% of the dry mass (Freudenberg and Neish, 1968; Adler, 1977). Unlike other natural polymers such as cellulose or proteins, which have labile linkages (glycosides and peptides) between their building units, lignins’ building units are combinatorially linked with strong ether and carbon-carbon bonds (Sarkanen and Ludwig, 1971; Harkin, 1973). It is difficult to completely degrade lignins. Lignins are traditionally considered to be dehydrogenative polymers derived from three monolignols, p-coumaryl alcohol 1h (which is typically minor), coniferyl alcohol 1g, and sinapyl alcohol 1s (Fig. 1; Sarkanen, 1971). They can vary greatly in their composition in terms of their plant and tissue origins (Campbell and Sederoff, 1996). This variability is probably determined and regulated by different activities and substrate specificities of the monolignol biosynthetic enzymes from different sources, and by the carefully controlled supply of monomers to the lignifying zone (Sederoff and Chang, 1991).Open in a separate windowFigure 1.The monolignols 1, and marker compounds 2 to 4 resulting from incorporation of novel monomer 15h into lignins: thioacidolysis monomeric marker 2, dimers 3, and DFRC dimeric markers 4.Recently there has been considerable interest in genetic modification of lignins with the goal of improving the utilization of lignocellulosics in various agricultural and industrial processes (Baucher et al., 2003; Boerjan et al., 2003a, 2003b). Studies on mutant and transgenic plants with altered monolignol biosynthesis have suggested that plants have a high level of metabolic plasticity in the formation of their lignins (Sederoff et al., 1999; Ralph et al., 2004). Lignins in angiosperm plants with depressed caffeic acid O-methyltransferase (COMT) were found to derive from significant amounts of 5-hydroxyconiferyl alcohol (5-OH-CA) monomers 15h (Fig. 1) substituting for the traditional monomer, sinapyl alcohol 1s (Marita et al., 2001; Ralph et al., 2001a, 2001b; Jouanin et al., 2004; Morreel et al., 2004b). NMR analysis of a ligqnin from COMT-deficient poplar (Populus spp.) has revealed that novel benzodioxane structures are formed through β-O-4 coupling of a monolignol with 5-hydroxyguaiacyl units (resulting from coupling of 5-OH-CA), followed by internal trapping of the resultant quinone methide by the phenolic 5-hydroxyl (Ralph et al., 2001a). When the lignin was subjected to thioacidolysis, a novel 5-hydroxyguaiacyl monomer 2 (Fig. 1) was found in addition to the normal guaiacyl and syringyl thioacidolysis monomers (Jouanin et al., 2000). Also, a new compound 3g (Fig. 1) was found in the dimeric products from thioacidolysis followed by Raney nickel desulfurization (Lapierre et al., 2001; Goujon et al., 2003).Further study with the lignin using the derivatization followed by reductive cleavage (DFRC) method also confirmed the existence of benzodioxane structures, with compounds 4 (Fig. 1) being identified following synthesis of the authentic parent compounds 9 (Fig. 2). However, no 5-hydroxyguaiacyl monomer could be detected in the DFRC products. These facts imply that the DFRC method leaves the benzodioxane structures fully intact, suggesting that the method might therefore be useful as an analytical tool for determining benzodioxane structures that are linked by β-O-4 ethers. Using a modified DFRC procedure, we report here on results that provide further evidence for the existence of benzodioxane structures in lignins from COMT-deficient plants, that 5-OH-CA is behaving as a rather ideal monolignol that can be integrated into plant lignins, and demonstrate the usefulness of the DFRC method for determining these benzodioxane structures.Open in a separate windowFigure 2.Synthesis of benzodioxane DFRC products 12 (see later in Fig. 6 for their structures). i, NaH, THF. ii, Pyrrolidine. iii, 1g or 1s, benzene/acetone (4/1, v/v). iv, DIBAL-H, toluene. v, Iodomethane-K₂CO₃, acetone. vi, Ac₂O pyridine.