Multiple Sequence Motifs in the Rubisco Small Subunit Transit Peptide Independently Contribute to Toc159-Dependent Import of Proteins into Chloroplasts

A large number of plastid proteins encoded by the nuclear genome are posttranslationally imported into plastids by at least two distinct mechanisms: the Toc159-dependent and Toc132/Toc120-dependent pathways. Light-induced photosynthetic proteins are imported through the Toc159-dependent pathway, whereas constitutive housekeeping plastid proteins are imported into plastids through the Toc132/Toc120 pathway. However, it remains unknown which features of the plastid protein transit peptide (TP) determine the import pathway. We have discovered sequence elements of the Rubisco small subunit TP (RbcS-tp) that play a role in determining import through the Toc159-dependent pathway in vivo. We generated multiple hybrid mutants using the RbcS-tp and the E1α-subunit of pyruvate dehydrogenase TP (E1α-tp) as representative peptides mediating import through the Toc159-dependent and Toc159-independent pathways, respectively. Import experiments using these hybrid mutants in wild-type and ppi2 mutant protoplasts revealed that multiple sequence motifs in the RbcS-tp independently contribute to Toc159-dependent protein import into chloroplasts. One of these motifs is the group of serine residues located in the N-terminal 12-amino acid segment and the other is the C-terminal T5 region of the RbcS-tp ranging from amino acid positions 41 to 49. Based on these findings, we propose that multiple sequence elements in the RbcS-tp contribute independently to Toc159-dependent import of proteins into chloroplasts.The plastid is a crucial organelle in plant cells. It plays a role in critical cellular processes such as photosynthesis, ATP generation, amino acid metabolism, and synthesis of fatty acids and lipid components. Accordingly, a large number of proteins are required for all these activities in plastids. Some of these proteins are encoded by the chloroplast genetic system and are translated in the plastids. However, most plastid proteins (over 90%) are encoded by the nuclear genome and are imported into plastids from the cytosol posttranslationally (Kessler and Schnell, 2006; Jarvis, 2008).Most plastid interior proteins that undergo posttranslational import from the cytosol contain a cleavable N-terminal targeting signal, a transit peptide (TP), of 50 to 70 amino acid residues (Jarvis, 2008; Lee et al., 2008). However, recently, some plastid interior proteins have been identified that do not have the N-terminal canonical TP (Miras et al., 2002, 2007; Nada and Soll, 2004). The long TP consists of multiple domains or motifs that encode information for preprotein import into plastids (von Heijne et al., 1989; Pilon et al., 1995; Rensink et al., 2000; Lee et al., 2006, 2008). The preproteins transit through the cytosol as unfolded protein. During passage through the cytosol, they may form a complex with heat shock proteins, such as Hsp70 and Hsp90, and guidance factors such as 14-3-3 (May and Soll, 2000; Qbadou et al., 2006). However, 14-3-3 may not be essential for the targeting of these proteins to chloroplasts (Lee et al., 2002, 2006; Nakrieko et al., 2004). To cross the two envelope membranes, the TP interacts with components of the Toc and Tic complexes located at the outer and inner envelopes of chloroplasts, respectively (Jarvis, 2008). These include members of the Toc159 family, Toc33/Toc34, Toc75, and Tic20. At the late stage or after translocation, the TP is recognized and cleaved off by stromal processing peptidases (Richter and Lamppa, 1999; Chen and Li, 2007).Despite extensive study of the TPs, it is not fully understood how the information encoded in these peptides is decoded by the plastid protein import machinery. TPs display some degree of similarity in their amino acid composition, including a higher content of Ala, Gly, and the hydroxylated amino acids Ser and Thr, and a lack of acidic amino acids (von Heijne et al., 1989; Bruce, 2001; Zhang and Glaser, 2002). However, it is clear that the entire family of TPs, termed the transit peptidome, cannot be represented by a single consensus sequence. Growing evidence has pointed to a functional classification of TPs. The first indication is that the transit peptidome may be classified into two groups: Toc159-dependent and Toc159-independent TPs (Ivanova et al., 2004; Kubis et al., 2004; Smith et al., 2004). The TPs that confer Toc159 dependence in protein import are typically used by light-induced photosynthetic proteins, whereas Toc159-independent TPs are used by nonphotosynthetic and housekeeping proteins (Kessler and Schnell, 2006). This was clearly demonstrated in the ppi2 mutant that has a T-DNA insertion in atTOC159 (Smith et al., 2004). In accord with this observation, the expression of atTOC159 is high in young and photosynthetic tissues whereas atTOC132 and atTOC120 are expressed uniformly in all plant tissues at low levels (Kubis et al., 2004). In addition, in nonphotosynthetic tissues, such as roots, the mRNA level of atTOC132 or atTOC120 is much higher than that of atTOC159. These results are consistent with the hypothesis that TPs may contain sequence motifs that determine the targeting pathway. However, the sequence information that confers Toc159 dependence or Toc132/120 dependence on these proteins during protein import remains unknown. In addition, Lee et al. (2008) recently demonstrated that the transit peptidome may be divided into several groups based on critical sequence motifs present in the TP. However, the role of the sequence motifs embedded in the TPs is not entirely clear yet with respect to translocation through the envelope membranes and also to the molecular machinery that recognizes these sequence motifs. Furthermore, the sequence information that confers Toc159 dependence or Toc132/120 dependence in protein import on these proteins remains unknown.The Rubisco small subunit (RbcS) and E1α TPs (RbcS-tp and E1α-tp) confer Toc159 dependence and Toc159 independence in protein import into chloroplasts, respectively (Smith et al., 2004). In this study, using these two TPs, we have determined the RbcS-tp sequence motifs that confer Toc159 dependence. Here, we have demonstrated that Toc159-dependent protein import is mediated independently by multiple sequence motifs: one of them is the group of Ser residues located in the N-terminal 12-amino acid segment and the other is in the C-terminal region ranging from amino acid positions 41 to 49.     

The Acidic A-Domain of Arabidopsis Toc159 Occurs as a Hyperphosphorylated Protein

The translocon at the outer membrane of the chloroplast assists the import of a large class of preproteins with amino-terminal transit sequences. The preprotein receptors Toc159 and Toc33 in Arabidopsis (Arabidopsis thaliana) are specific for the accumulation of abundant photosynthetic proteins. The receptors are homologous GTPases known to be regulated by phosphorylation within their GTP-binding domains. In addition to the central GTP-binding domain, Toc159 has an acidic N-terminal domain (A-domain) and a C-terminal membrane-anchoring domain (M-domain). The A-domain of Toc159 is dispensable for its in vivo activity in Arabidopsis and prone to degradation in pea (Pisum sativum). Therefore, it has been suggested to have a regulatory function. Here, we show that in Arabidopsis, the A-domain is not simply degraded but that it accumulates as a soluble, phosphorylated protein separated from Toc159. However, the physiological relevance of this process is unclear. The data show that the A-domain of Toc159 as well as those of its homologs Toc132 and Toc120 are targets of a casein kinase 2-like activity.The Toc and Tic complexes cooperate to import nuclear-encoded chloroplast preproteins from the cytosol (Jarvis, 2008; Kessler and Schnell, 2009). Initially, incoming preproteins encounter the receptors Toc159 and Toc34 at the chloroplast surface. Both are GTP-binding proteins and share sequence homology in their G-domains. While Toc34 is anchored in the outer membrane by a short hydrophobic C-terminal tail, the triple-domain Toc159 is inserted via a largely hydrophilic 52-kD M-domain. In addition to the G- and M-domains, Toc159 has a large acidic A-domain covering the N-terminal half of the protein. Arabidopsis (Arabidopsis thaliana) encodes two isoforms of Toc34 (Toc33 and Toc34) and four of Toc159 (Toc159, Toc132, Toc120, and Toc90; Jackson-Constan and Keegstra, 2001). The Toc159 isoforms have a similar domain structure, but they differ from each other in length and sequence of their A-domain (Hiltbrunner et al., 2001a). However, Toc90 does not have an acidic domain at all and only consists of the G- and M-domains (Hiltbrunner et al., 2004). It has been demonstrated that the A-domain of AtToc159 and AtToc132 have properties of intrinsically disordered proteins (Hernández Torres et al., 2007; Richardson et al., 2009), suggesting an involvement of the A-domain in transient and multiple protein-protein interactions possibly with the transit peptides of preproteins. Toc34 and Toc159 together with the Toc75 channel constitute the Toc-core complex (Schleiff et al., 2003) and are required for the accumulation of highly abundant photosynthesis-associated proteins in the chloroplast. The Arabidopsis deletion mutants of Toc33 (ppi1; Jarvis et al., 1998) and Toc159 (ppi2; Bauer et al., 2000) have indicative phenotypes of their role in chloroplast biogenesis, respectively pale green and albino. Complementation experiments of the ppi2 mutant have established that the G- and M-domains have essential functions whereas the A-domain is dispensable (Lee et al., 2003; Agne et al., 2009). In preceding studies, possibly influenced by the model organism and experimental tools, Toc159 occurred in different forms. Initially, Toc159 was identified in pea (Pisum sativum) as an 86-kD protein lacking the entire A-domain (Hirsch et al., 1994; Bolter et al., 1998). In addition to its membrane-associated form, Arabidopsis Toc159 has been found as a soluble protein (Hiltbrunner et al., 2001b). However, the function and the fate of the A-domain as well as that of soluble Toc159 remain unknown and a matter of debate.Not only GTP binding and hydrolysis by the Toc GTPases but also phosphorylation is known as a regulatory mechanism of chloroplast protein import at the Toc complex level (Oreb et al., 2008b). First, some precursor proteins, such as the small subunit of Rubisco, may be phosphorylated in their transit sequence by a cytosolic kinase (Martin et al., 2006). Phosphorylation promotes binding to a 14-3-3 protein and cytosolic Hsp70 in the guidance complex that delivers the phosphorylated preprotein to the Toc complex (May and Soll, 2000). Second, both Toc159 and Toc34 are known to be phosphorylated and independently so by distinct kinases, OEK70 and OEK98, respectively (Fulgosi and Soll, 2002). These two kinase activities have been located to the outer envelope membrane, but their molecular identification is still pending. Phosphorylation of the Toc GTPases may occur in the GTP-binding domains (Oreb et al., 2008a). For Toc34, data on the site (Ser-113 in pea and Ser-181 in Arabidopsis) and effects of phosphorylation are available (Jelic et al., 2002, 2003). It imposes a negative regulation on the Toc complex by inhibiting GTP and preprotein binding to Toc34, reducing its ability to bind Toc159 and to assemble into the Toc complex (Oreb et al., 2008a). The in vivo mutational analysis in Arabidopsis indicated that phosphorylation at Toc34 represents a nonessential mechanism (Aronsson et al., 2006; Oreb et al., 2007). Despite the 86-kD proteolytic fragment of Toc159 being a major phosphoprotein in the pea outer chloroplast membrane (Fulgosi and Soll, 2002), little is known of the molecular and regulatory mechanisms of Toc159 phosphorylation. In this study, we report that the A-domain of Toc159 can be purified as a stable fragment. Moreover, it is hyperphosphorylated, hinting at an important and highly regulated functional role. Our data suggest that Toc159 is the target of casein kinase 2 (CK2)-like and membrane-associated kinase activities.     

Chloroplast Hsp93 Directly Binds to Transit Peptides at an Early Stage of the Preprotein Import Process

Three stromal chaperone ATPases, cpHsc70, Hsp90C, and Hsp93, are present in the chloroplast translocon, but none has been shown to directly bind preproteins in vivo during import, so it remains unclear whether any function as a preprotein-translocating motor and whether they have different functions during the import process. Here, using protein crosslinking followed by ionic detergent solubilization, we show that Hsp93 directly binds to the transit peptides of various preproteins undergoing active import into chloroplasts. Hsp93 also binds to the mature region of a preprotein. A time course study of import, followed by coimmunoprecipitation experiments, confirmed that Hsp93 is present in the same complexes as preproteins at an early stage when preproteins are being processed to the mature size. In contrast, cpHsc70 is present in the same complexes as preproteins at both the early stage and a later stage after the transit peptide has been removed, suggesting that cpHsc70, but not Hsp93, is important in translocating processed mature proteins across the envelope.Most chloroplast proteins are encoded by the nuclear genome as higher M_r preproteins that are fully synthesized in the cytosol before being imported into the chloroplast. The import process is initiated by binding of the N-terminal transit peptide of the preprotein to the translocon at the outer envelope membrane of chloroplasts (TOC) complex, in which Toc159 and Toc34 function as receptors and Toc75 is the outer membrane channel. This step is followed by binding of the transit peptide to the translocon at the inner envelope membrane of chloroplasts (TIC) machinery, the central components of which include the Tic20/Tic56/Tic100/Tic214 channel complex and Tic110. Tic110 functions as the stromal receptor for transit peptides and also as a scaffold for tethering other translocon components (for reviews, see Li and Chiu, 2010; Shi and Theg, 2013; Paila et al., 2015). The actual translocation of the bound preproteins across the envelope is powered by hydrolysis of ATP in the stroma (Pain and Blobel, 1987; Theg et al., 1989), and it is therefore assumed that some stromal ATPase motor proteins bind the preproteins as they emerge from the inner membrane and use the energy of ATP hydrolysis to translocate the preproteins across the envelope into the stroma.Three stromal ATPases have been identified in the translocon complex: cpHsc70 (chloroplast heat shock cognate protein 70 kD), Hsp90C (chloroplast heat shock protein 90), and Hsp93/ClpC (93-kD heat shock protein). Hsp93, the first to be identified, belongs to the Hsp100 subfamily of AAA+ proteins (ATPases associated with various cellular activities) and was detected in coimmunoprecipitation experiments in complexes containing other translocon components and preproteins undergoing import (Akita et al., 1997; Nielsen et al., 1997; Chou et al., 2003; Rosano et al., 2011). In Arabidopsis (Arabidopsis thaliana), Hsp93 exists as two isoforms encoded by the genes HSP93III and HSP93V. Removal of the more abundant Hsp93V results in protein import defects, while double knockout of the two genes causes lethality (Constan et al., 2004; Kovacheva et al., 2007; Chu and Li, 2012; Lee et al., 2015). Purified recombinant Hsp93III can bind to the transit peptide of pea (Pisum sativum) ferredoxin-NADP+ reductase in vitro (Rosano et al., 2011). In addition, the N-terminal domain of Hsp93 is critical both for its in vivo functions and its association with chloroplast membranes and Tic110, suggesting that one of the major functions of Hsp93 requires it to be localized at the envelope with Tic110 (Chu and Li, 2012). However, because many prokaryotic Hsp100 family proteins function as the regulatory components of the Clp proteases (Kress et al., 2009; Nishimura and van Wijk, 2015), and, in Arabidopsis, some Clp proteolytic core components have also been found at the envelope fraction, it has been proposed that Hsp93 is involved in degradation of misfolded or damaged proteins at the envelope (Sjögren et al., 2014). However, whether the Clp proteolytic core can form a stable complex with Hsp93 in higher plant chloroplasts remains to be shown.In mitochondria and the endoplasmic reticulum, protein import is driven by the Hsp70 family of proteins. In chloroplasts, accumulating evidence also supports that Hsp70 is important for chloroplast protein import. Purified recombinant Hsp70 can bind in vitro to the transit peptide of the small subunit of RuBP carboxylase preprotein (prRBCS; Ivey et al., 2000). Stromal Hsp70 can be coimmunoprecipitated with preproteins undergoing import and with other translocon components, and mutations resulting in reduced or altered stromal Hsp70 activity cause protein import defects (Shi and Theg, 2010; Su and Li, 2010). Recently, it has been shown, in moss, that increasing the K_m for Hsp70 ATP hydrolysis results in an increased K_m for ATP usage in chloroplast protein import, indicating that stromal Hsp70 is indeed one of the proteins supplying ATP-derived energy to power import (Liu et al., 2014). Finally, stromal Hsp90C has been shown to be part of active translocon complexes in coimmunoprecipitation experiments (Inoue et al., 2013). As further evidence that Hsp90 is important for protein import into chloroplasts, the Hsp90 ATPase activity inhibitor radicicol reversibly inhibits the import of preproteins into chloroplasts (Inoue et al., 2013).Presence of the three ATPases in the translocon was demonstrated by coimmunoprecipitation after solubilization of chloroplast membranes under conditions that preserve the large membrane protein complexes, either by solubilization with nonionic detergents or by treating chloroplasts with crosslinkers that link all proteins in a complex together (Akita et al., 1997; Nielsen et al., 1997; Shi and Theg, 2010; Su and Li, 2010; Inoue et al., 2013). These complexes contain translocon components that directly bind to preproteins, and also other proteins that are associated with these translocon components but have no direct contacts with the preproteins. For example, Nielsen et al. (1997) demonstrated the presence of Hsp93 in the translocon by binding of prRBCS to isolated pea chloroplasts and then solubilization of chloroplast membranes with the nonionic detergent decylmaltoside. Under these conditions, an anti-Hsp93 antibody specifically immunoprecipitated Hsp93 together with Toc159, Toc75, Toc34, Tic110, and prRBCS (Nielsen et al., 1997). The result showed that Hsp93 is in the same complexes with these proteins but did not provide information whether Hsp93 directly binds to them. It is possible that Hsp93 only has direct contacts with, for example, Tic110, which then binds to prRBCS. Direct binding, in particular to the transit peptide region, would provide strong evidence that an ATPase functions as a protein translocating motor, rather than in assisting the assembly of other translocon components or in the folding or degradation of imported proteins. Furthermore, if all three ATPases were found to be involved in preprotein translocation, it would be important to understand how they work together; for example, whether they preferentially bind different preproteins, bind to different regions of a preprotein, or act at different stages of the import process.Here, we examined whether Hsp93 can directly bind to preproteins undergoing import into chloroplasts, and compared the timing of the binding of Hsp93 and cpHsc70 to the preproteins. We used isolated pea chloroplasts, rather than isolated Arabidopsis chloroplasts, because pea chloroplasts exhibit more robust import ability (Fitzpatrick and Keegstra, 2001). Various crosslinkers that react with cysteines were then used to achieve more specific crosslinkings, followed by solubilization with the ionic detergent lithium dodecyl sulfate (LDS) to thoroughly solubilize chloroplast membranes and to disrupt noncovalent protein-protein interactions. Our results show that Hsp93 directly binds to preproteins undergoing import. Import time course experiments further revealed that Hsp93 functions primarily during the early stage of import, whereas cpHsc70 associates with substrates being imported at both the early stage and a later stage after transit peptide removal.     

Functional Analysis of the Hsp93/ClpC Chaperone at the Chloroplast Envelope

The Hsp100-type chaperone Hsp93/ClpC has crucial roles in chloroplast biogenesis. In addition to its role in proteolysis in the stroma, biochemical and genetic evidence led to the hypothesis that this chaperone collaborates with the inner envelope TIC complex to power preprotein import. Recently, it was suggested that Hsp93, working together with the Clp proteolytic core, can confer a protein quality control mechanism at the envelope. Thus, the role of envelope-localized Hsp93, and the mechanism by which it participates in protein import, remain unclear. To analyze the function of Hsp93 in protein import independently of its ClpP association, we created a mutant of Hsp93 affecting its ClpP-binding motif (PBM) (Hsp93[P-]), which is essential for the chaperone’s interaction with the Clp proteolytic core. The Hsp93[P-] construct was ineffective at complementing the pale-yellow phenotype of hsp93 Arabidopsis (Arabidopsis thaliana) mutants, indicating that the PBM is essential for Hsp93 function. As expected, the PBM mutation negatively affected the degradation activity of the stromal Clp protease. The mutation also disrupted association of Hsp93 with the Clp proteolytic core at the envelope, without affecting the envelope localization of Hsp93 itself or its association with the TIC machinery, which we demonstrate to be mediated by a direct interaction with Tic110. Nonetheless, Hsp93[P-] expression did not detectably improve the protein import efficiency of hsp93 mutant chloroplasts. Thus, our results do not support the proposed function of Hsp93 in protein import propulsion, but are more consistent with the notion of Hsp93 performing a quality control role at the point of import.Chloroplasts are essential organelles in plant cells as they are responsible for performing a variety of functions (Jarvis and López-Juez, 2013). Although chloroplasts have their own genome (encoding approximately 100 proteins), the majority of the proteins found in these organelles are nucleus-encoded (approximately 3,000) (Leister, 2003), synthesized in the cytosol, and imported into the chloroplast as precursor proteins (preproteins), each one with a cleavable N-terminal extension or transit peptide (Shi and Theg, 2013a; Paila et al., 2015). The preprotein import mechanism is initiated by the interaction of the transit peptide with the translocon at the outer envelope membrane of chloroplasts (TOC) complex and subsequently involves transport through the translocon at the inner envelope membrane of chloroplasts (TIC) machinery in an energy-dependent process (Theg et al., 1989; Shi and Theg, 2013b). The Tic110 and Tic40 components have long been described as central TIC components, but these proteins were absent from a recently described 1-MD TIC complex (consisting of Tic20, Tic56, Tic100, and Tic214; Kovács-Bogdan et al., 2010; Nakai, 2015). One possible explanation is that two TIC complexes act sequentially during protein import (e.g. a Tic110-containing complex may act downstream of the 1-MD complex). A TIC complex associated import motor is proposed to exist at the stromal side of the inner envelope, and several stromal chaperones, including Hsp93/ClpC and Hsp70, have been proposed to act as motors to drive protein translocation into the stroma (for review, see Flores-Pérez and Jarvis, 2013).Hsp93 is closely related to bacterial ClpC and is a member of the Class I subfamily of Hsp100 chaperones, which themselves belong to the wider AAA+ (ATPases associated with various cellular activities) superfamily (Hanson and Whiteheart, 2005; Flores-Pérez and Jarvis, 2013). AAA+ enzymes are involved in a variety of cellular processes, such as protein folding, unfolding for proteolysis, and disassembly of protein aggregates or protein complexes. Although AAA+ chaperones are well characterized in bacteria, they are found in all kingdoms (Hanson and Whiteheart, 2005). Such proteins possess one or two nucleotide binding domains, both of which contain conserved Walker A and B motifs. These chaperones may also contain a conserved ClpP-binding motif (PBM), or P-loop, which is essential for interaction with the unrelated, proteolytic ClpP subunit (Weibezahn et al., 2004; Hanson and Whiteheart, 2005).In the chloroplast, Hsp93/ClpC partitions between the inner envelope membrane and the chloroplast stroma. Most Hsp93/ClpC protein is located in the stroma. Nonetheless, a large proportion of the total chloroplast Hsp93/ClpC pool (30%) associates with the envelope (Sjögren et al., 2014). Hsp93 has frequently been copurified with TIC and TOC complex components, which led to the hypothesis that it provides the driving force for preprotein import (Akita et al., 1997; Nielsen et al., 1997). Also, Hsp93 was found to specifically coimmunoprecipitate with preproteins under limiting ATP conditions and to stably bind to transit peptides in vitro (Nielsen et al., 1997; Rosano et al., 2011). Genetic and molecular studies have suggested that it functions in close association with Tic110 and Tic40 (Chou et al., 2003; Kovacheva et al., 2005; Chou et al., 2006). More recently, it was shown that the N-terminal domain of Hsp93 is important for its membrane association (Chu and Li, 2012). Despite all this evidence, the nature of the interaction between Hsp93 and the TIC apparatus has not been fully characterized.Analysis of mutants also supported the involvement of the Hsp93 chaperone in protein import. In Arabidopsis (Arabidopsis thaliana), two homologous genes, atHSP93-V (CLPC1) and atHSP93-III (CLPC2), code for Hsp93/ClpC, and the resulting protein isoforms share 91% amino acid sequence identity (Kovacheva et al., 2007). The Hsp93-V protein is the most abundant isoform, and mutations in the atHSP93-V gene lead to a pale-green plant phenotype with protein import defective chloroplasts. In contrast, atHSP93-III knockout plants are indistinguishable from the wild type, most likely due to the compensatory presence of functionally redundant and abundant atHsp93-V (Kovacheva et al., 2005, 2007). Complete loss of both proteins in Arabidopsis is lethal during embryo development, whereas double mutants lacking Hsp93-V but retaining partial Hsp93-III activity are viable but exhibit severe chlorosis and protein import defects (Kovacheva et al., 2007).More typically, as expected by its close relationship to bacterial orthologs, Hsp93/ClpC is a functional component of the caseinolytic protease (Clp) in the chloroplast stroma, where it recognizes and unfolds substrates for degradation (Shanklin et al., 1995). Significantly, the Clp proteolytic core is also bound to the envelope membranes, in quantities which are sufficient to bind to all of the similarly localized Hsp93/ClpC (Sjögren et al., 2014). This recent finding suggested a role for the Clp protease in protein quality control at the envelope. The structure of the Clp protease complex comprises a cylinder-like protease core and an AAA+ chaperone ring complex, and it is generally conserved throughout evolution (Nishimura and van Wijk, 2015). In Arabidopsis, the plastid Clp proteolytic core contains two distinct heptameric rings (the P-ring consisting of ClpP3-P6 and the R-ring consisting of ClpP1 and ClpR1-R4; Sjögren et al., 2006), and attached to this are accessory ClpT proteins involved in core assembly (Sjögren and Clarke, 2011). Several studies have shown that deficiency of the proteolytic subunits of the core complex leads to sick plant phenotypes (Sjögren et al., 2004; Rudella et al., 2006; Sjögren et al., 2006), highlighting the essential nature of Clp proteolytic activity to chloroplast function and plant viability.As described above, the putative interacting partners of Hsp93 at the envelope are Tic110 and Tic40. Tic110 is a highly abundant protein and is essential for plastid biogenesis (Inaba et al., 2005; Kovacheva et al., 2007). It has two N-terminal transmembrane α-helices, and it projects a large C-terminal hydrophilic domain into the stroma (Jackson et al., 1998; Inaba et al., 2003). A stromal region proximal to the second transmembrane helix selectively associates with transit peptides, serving as a docking site for preproteins as they emerge from the TIC channel (Inaba et al., 2003). The hydrophilic domain of algal Tic110 possesses a rod-shaped helix-repeat structure similar to HEAT-repeat domains (and plant Tic110 proteins are predicted to be similar), and these typically function as scaffolds for protein-protein interactions (Tsai et al., 2013). Tic40 is topologically similar to Tic110 and is proposed to act as a cochaperone in the preprotein import motor (Chou et al., 2003). In the corresponding model, a transit peptide emerging from the TIC channel binds to the stromal domain of Tic110; this binding causes a conformational change of Tic110 to recruit Tic40, which in turn triggers transit peptide release to enable association of the preprotein with Hsp93 (Inaba et al., 2003; Chou et al., 2006). Finally, Tic40 is proposed to stimulate ATP hydrolysis by Hsp93 so that the chaperone pulls the preprotein into the stroma (Chou et al., 2006).Although there is good evidence that Hsp93 is involved in protein import, the ability of Hsp93 to associate with the Clp protease core means that, in principle, any aspect of the hsp93 mutant phenotype could be due to disruption of the ClpP-linked functions of the protein. Bearing this in mind, we aimed to further characterize the role of Hsp93 at the inner envelope membrane. First, we analyzed the putative interactions of Hsp93 with the TIC components, Tic110 and Tic40, in a complementary set of in vitro and in vivo studies. Second, we evaluated the proposed role of Hsp93 in protein import independently of its role in proteolysis by creating a PBM mutant of the major Hsp93 isoform, atHsp93-V, and studying its activity in planta.     

Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis

The nucleus-encoded mitochondria-targeted proteins, multiple organellar RNA editing factors (MORF3, MORF5, and MORF6), interact with Arabidopsis (Arabidopsis thaliana) PURPLE ACID PHOSPHATASE2 (AtPAP2) located on the chloroplast and mitochondrial outer membranes in a presequence-dependent manner. Phosphorylation of the presequence of the precursor MORF3 (pMORF3) by endogenous kinases in wheat germ translation lysate, leaf extracts, or STY kinases, but not in rabbit reticulocyte translation lysate, resulted in the inhibition of protein import into mitochondria. This inhibition of import could be overcome by altering threonine/serine residues to alanine on the presequence, thus preventing phosphorylation. Phosphorylated pMORF3, but not the phosphorylation-deficient pMORF3, can form a complex with 14-3-3 proteins and HEAT SHOCK PROTEIN70. The phosphorylation-deficient mutant of pMORF3 also displayed faster rates of import when translated in wheat germ lysates. Mitochondria isolated from plants with altered amounts of AtPAP2 displayed altered protein import kinetics. The import rate of pMORF3 synthesized in wheat germ translation lysate into pap2 mitochondria was slower than that into wild-type mitochondria, and this rate disparity was not seen for pMORF3 synthesized in rabbit reticulocyte translation lysate, the latter translation lysate largely deficient in kinase activity. Taken together, these results support a role for the phosphorylation and dephosphorylation of pMORF3 during the import into plant mitochondria. These results suggest that kinases, possibly STY kinases, and AtPAP2 are involved in the import of protein into both mitochondria and chloroplasts and provide a mechanism by which the import of proteins into both organelles may be coordinated.Chloroplasts and mitochondria are endosymbiotic organelles that are intimately involved in energy metabolism in plants (Araújo et al., 2014). The majority of proteins located in chloroplasts and mitochondria are encoded in the nucleus, translated in the cytosol, and imported into the organelles (Murcha et al., 2014). For both chloroplasts and mitochondria, over 1,000 different proteins are required to be specifically imported into each organelle. Furthermore, while most proteins are imported specifically into one organelle, a significant number of proteins are dually targeted to both via ambiguous targeting signals (Carrie et al., 2009a; Ye et al., 2012, 2015). The sorting of proteins to chloroplast and mitochondria is achieved through the inclusion of targeting signals in newly synthesized proteins that act in combination with receptor domains present in outer membrane multisubunit protein complexes to specifically direct proteins to their destination compartments (Jarvis, 2008; Shi and Theg, 2013; Murcha et al., 2014). Chloroplast targeting signals (transit peptides) and mitochondrial targeting signals (presequences) are recognized by receptors on the translocase of the outer chloroplast envelope (TOC) and the translocase of the outer mitochondria membrane (TOM), respectively (Ye et al., 2015). In addition to the targeting signals and protein receptors, it has been proposed that cytosolic chaperone proteins may also play a role in maintaining precursor proteins in an import-competent state and may play a role in determining targeting specificity. However, in plants, the role of cytosolic chaperones has only been characterized to some extent for protein import into chloroplasts (Jarvis, 2008; Fellerer et al., 2011; Flores-Pérez and Jarvis, 2013; Lee et al., 2013; Schweiger et al., 2013) but not into mitochondria.In addition to cytosolic chaperone factors, three STY kinases are also involved in phosphorylating the transit peptides of several chloroplast precursor proteins, such as the precursor for the small subunit of Rubisco (pSSU) and the precursor for HIGH CHLOROPHYLL FLUORESCENCE136 (pHCF136), but not the presequence of the tobacco (Nicotiana tabacum) precursor for the β-subunit of the mitochondria ATP synthase (pF1β; Martin et al., 2006; Lamberti et al., 2011a, 2011b). In addition, a pea (Pisum sativum) 14-3-3 protein has also been reported to bind to the phosphorylated Ser on the transit peptide of pSSU but not to an S→A mutant. The formation of the pSSU/14-3-3/HEAT SHOCK PROTEIN70 (HSP70) complex enhances the kinetics of the import of pSSU into chloroplasts, as free pSSU is imported relatively slowly (May and Soll, 2000). Phosphatase inhibitors, NaF and NaMoO₄, inhibit pSSU import into plastids in a reversible manner, suggesting that the dephosphorylation of the phosphorylated transit peptide of pSSU is required for import (Flügge and Hinz, 1986; Waegemann and Soll, 1996). A model for pSSU recognition and TOC translocation has been proposed in which the transit peptide of pSSU is phosphorylated at Ser-34 and the transit peptide binds to Toc33 and Toc159 to form a trimeric complex (Becker et al., 2004; Oreb et al., 2011). Hydrolysis of GTP at Toc33 dissociates it from the complex, and an as yet unknown phosphatase dephosphorylates pSer-34 on pSSU, allowing import to proceed through the combined action of Toc159 and Toc75 (Becker et al., 2004; Oreb et al., 2011). Phosphorylation seems to affect import, as phosphomimicking transit peptides of pSSU and pHCF136 reduced their import rates into chloroplasts (Lamberti et al., 2011a; Nickel et al., 2015).Unlike chloroplast import, there is no evidence that the phosphorylation and dephosphorylation of plant mitochondrial presequences are required for efficient protein import. In yeast (Saccharomyces cerevisiae), Tom22 functions as a cytosolic facing receptor and transfers precursor proteins to the Tom40 channel. It can be phosphorylated by Casein Kinase2 (CK2) and the mitochondria-bound CK1 to stimulate the activity and assembly of the TOM complex (Harbauer et al., 2014). Protein Kinase A (PKA) can phosphorylate Tom22, impairing its import rate. Thus, PKA, CK1, and CK2 act antagonistically. It has also been demonstrated that the cyclin-dependent kinase CDK1 stimulated assembly of the TOM complex by the phosphorylation of Tom6, an accessory subunit of the TOM complex, enhancing its import into mitochondria (Gerbeth et al., 2013). Thus, in yeast mitochondria, the phosphorylation of the protein import machinery itself appears to play a role in import.While the overall theme of mitochondrial protein targeting, machinery, and pathways utilized is conserved between different systems, significant variations have been observed in plants. First, the plant outer mitochondrial protein receptor Tom20 is not an ortholog to the yeast or mammalian receptors (Perry et al., 2006). Structural studies on the plant Tom20 import receptor suggest a discontinuous bidentate hydrophobic binding mechanism, somewhat different from that observed in other systems (Rimmer et al., 2011). Furthermore, plant mitochondria are required to distinguish between chloroplast and mitochondrial proteins. Transit peptides and presequences display some similarities in that both are enriched in positively charged residues. However, while mitochondrial presequences are proposed to form α-amphiphilic structures, chloroplast transit peptides do not and, instead, are predicted to form β-sheet secondary structures (Zhang and Glaser, 2002). The identification of a plant-specific outer membrane receptor, Toc64, involved in the import of specific precursor proteins (Chew et al., 2004) highlights the possibility of additional and varied mechanisms between plant mitochondrial protein targeting and other systems.Previously, we identified an outer mitochondrial membrane protein, called PURPLE ACID PHOSPHATASE2 (AtPAP2), that is also dually targeted to the outer envelope in chloroplasts (Sun et al., 2012a, 2012b). Similar to Toc33/34 and Tom20, AtPAP2 is anchored on the outer membranes by a C-terminal transmembrane motif. Overexpression of AtPAP2 resulted in an altered growth phenotype with elevated ATP levels (Sun et al., 2012b); thus, the function of this protein was investigated. Here, we show that the phosphorylation and dephosphorylation of the presequence of the precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 (pMORF3) alter the kinetics of its import in Arabidopsis (Arabidopsis thaliana). Furthermore, it was shown that the phosphorylation of pMORF3, when translated in wheat germ lysate (WGL), resulted in relatively slow import kinetics, and the inhibition of phosphorylation by site-directed mutagenesis resulted in faster import kinetics. Together, these results show that the phosphorylation and dephosphorylation of a mitochondrial precursor protein play a role in its rate of import. The roles of the outer membrane AtPAP2 protein and STY kinases were also investigated, supporting a role for phosphorylation and dephosphorylation in the import of some precursor proteins into plant mitochondria.     

Pea Chloroplast DnaJ-J8 and Toc12 Are Encoded by the Same Gene and Localized in the Stroma

Toc12 is a novel J domain-containing protein identified in pea (Pisum sativum) chloroplasts. It was shown to be an integral outer membrane protein localizing in the intermembrane space of the chloroplast envelope. Furthermore, Toc12 was shown to associate with an intermembrane space Hsp70, suggesting that Toc12 is important for protein translocation across the chloroplast envelope. Toc12 shares a high degree of sequence similarity with Arabidopsis (Arabidopsis thaliana) DnaJ-J8, which has been suggested to be a soluble protein of the chloroplast stroma. Here, we isolated genes encoding DnaJ-J8 from pea and found that Toc12 is a truncated clone of one of the pea DnaJ-J8s. Protein import analyses indicate that Toc12 and DnaJ-J8s possess a cleavable transit peptide and are localized in the stroma. Arabidopsis mutants with T-DNA insertions in the DnaJ-J8 gene show no defect in chloroplast protein import. Implications of these results in the energetics and mechanisms of chloroplast protein import are discussed.Most chloroplast proteins are encoded by the nuclear genome and synthesized in the cytosol as higher molecular mass precursors with an N-terminal extension known as the transit peptide. Precursor proteins are imported into chloroplasts through a translocon complex located at the chloroplast envelope. Translocon components associated with the outer membrane are called Toc (for translocon of the outer envelope membrane of chloroplast) proteins, and those associated with the inner membrane are called Tic (for translocon of the inner envelope membrane of chloroplast) proteins. Cleavage of the transit peptide from the precursor by a specific stromal processing peptidase during translocation results in the production of the lower molecular mass mature protein. Various translocon components have been assigned functions in the basic steps of the import process (for review, see Inaba and Schnell, 2008; Jarvis, 2008; Li and Chiu, 2010). For example, Toc159 (the no. indicates the calculated molecular mass of the protein) and Toc34 are receptors for the transit peptides, and Toc75 is the protein-translocating channel across the outer membrane. Toc64, on the other hand, has a dual function: it serves as a docking site for the cytosolic Hsp90 through its cytosolic domain and as a scaffold for translocon components located in the intermembrane space through its intermembrane space domain (Qbadou et al., 2007).Protein import into chloroplasts involves at least two distinct ATP-consuming steps. The first step is called “early import intermediate” or “docking,” in which less than 100 μm ATP is required and precursors are translocated across the outer membrane and come into contact with translocon components in the inner membrane (Olsen et al., 1989; Kouranov and Schnell, 1997; Inaba et al., 2003; Inoue and Akita, 2008). It has been shown that the ATP is used in the intermembrane space (Olsen and Keegstra, 1992), most likely by a yet unidentified intermembrane space Hsp70 called imsHsp70 or Hsp70-IAP (ims for “intermembrane space” and IAP for “import intermediate-associated protein”; Marshall et al., 1990; Schnell et al., 1994; Qbadou et al., 2007). The second ATP-consuming step is the complete translocation of precursors across the two envelope membranes into the stroma. This step requires about 1 mm ATP. The ATP is most likely used by the stromal Hsp93 and chloroplast Hsc70 associated with the translocon to drive protein translocation into the stroma (Nielsen et al., 1997; Shi and Theg, 2010; Su and Li, 2010).Hsp70 family proteins are involved in many cellular processes, including protein folding, protein translocation across membranes, and regulation of protein degradation. Hsp70 proteins are often recruited to perform a certain function by specifically localized J domain-containing proteins. The J domain-containing proteins interact with Hsp70 when Hsp70 is bound to ATP and stimulate ATP hydrolysis by Hsp70. The specific J domain-containing cochaperone that recruits the stromal chloroplast Hsc70 to the inner envelope membrane to assist in protein translocation has not been identified. The specific J domain-containing cochaperone for imsHsp70 for its function in protein import into chloroplasts is proposed to be a protein named Toc12 (Becker et al., 2004).Toc12 was identified as a novel J domain-containing protein from pea (Pisum sativum) chloroplasts. It belongs to the type III J domain proteins containing only the J domain without the Gly- and Phe-rich domain (G/F domain) and the zinc-finger domain originally found in Escherichia coli DnaJ. It has been shown that the protein is synthesized at its mature size of 103 amino acids without a cleavable transit peptide. After import, the protein has been shown to anchor in the outer membrane by its N-terminal part, which has been suggested to form a β-barrel-type domain. Its C-terminal part, composed of the J domain, has been shown to localize in the intermembrane space. Toc12 has been shown to associate with imsHsp70. Toc12 and imsHsp70 interact with the intermembrane space domain of Toc64, which in turn associates with another intermembrane space translocon component, Tic22. It is proposed that the Toc12-imsHsp70-Toc64-Tic22 complex mediates protein translocation across the intermembrane space through specific precursor binding and ATP hydrolysis (Becker et al., 2004; Qbadou et al., 2007). However, the existence of imsHsp70 has only been shown on immunoblots by its reactivity to the monoclonal antibody SPA820 raised against human Hsp70. Its encoding gene has never been identified. The Arabidopsis (Arabidopsis thaliana) Hsp70 gene family has 14 members. Only two of them are localized in chloroplasts, and both have been shown to locate in the stroma (Ratnayake et al., 2008; Su and Li, 2008). A recent study has further shown that the major protein recognized by the SPA820 antibody in pea chloroplasts is located in the stroma, indicating that imsHsp70 is most likely a stromal protein (Ratnayake et al., 2008).Most translocon components were originally identified from pea chloroplasts. While all translocon components identified from pea have easily recognizable Arabidopsis homologs, Toc12 seems to be an exception. The Arabidopsis gene suggested to be the pea TOC12 homolog, At1g80920 (Inoue, 2007; Jarvis, 2008), encodes a protein that is much larger than pea Toc12 and is annotated as J8 (referred to as AtJ8 herein). The entire pea Toc12 has a high sequence similarity to the N-terminal two-thirds of AtJ8. AtJ8 contains an extra C-terminal domain of 60 amino acids that is highly conserved among J8 proteins from other higher plants. However, in contrast to pea Toc12, AtJ8 is predicted to locate in the stroma (Miernyk, 2001; www.arabidopsis.org). Indeed, a fusion protein consisting of the first 80 amino acids of AtJ8 fused at the N terminus of GFP was imported into the chloroplast stroma, and approximately 46 amino acids from the N terminus were processed after import (Lee et al., 2008), indicating that the first 46 amino acids of AtJ8 function as a cleavable stroma-targeting transit peptide. A T-DNA insertion in the AtJ8 gene that causes the truncation of the last three amino acids results in no visible phenotype. However, detailed analyses indicate that the mutant has lower CO₂ assimilation and Rubisco activity than the wild type (Chen et al., 2010).We are interested in identifying J domain-containing proteins interacting with stromal Hsp70. As part of the initial effort, we investigated the suborganellar location of J8 and examined the relationship between Toc12 and J8. We found that, in pea, there are at least two genes encoding J8, which we named PsJ8a and PsJ8b. TOC12 represents part of PsJ8b. Toc12, AtJ8, and the two PsJ8 proteins could be imported into chloroplasts and processed to stromally localized soluble mature proteins. Four alleles of AtJ8 mutants were analyzed, but none of them showed any defect in the import of various chloroplast precursor proteins.     

Characterization of the Possible Roles for B Class MADS Box Genes in Regulation of Perianth Formation in Orchid

To investigate sepal/petal/lip formation in Oncidium Gower Ramsey, three paleoAPETALA3 genes, O. Gower Ramsey MADS box gene5 (OMADS5; clade 1), OMADS3 (clade 2), and OMADS9 (clade 3), and one PISTILLATA gene, OMADS8, were characterized. The OMADS8 and OMADS3 mRNAs were expressed in all four floral organs as well as in vegetative leaves. The OMADS9 mRNA was only strongly detected in petals and lips. The mRNA for OMADS5 was only strongly detected in sepals and petals and was significantly down-regulated in lip-like petals and lip-like sepals of peloric mutant flowers. This result revealed a possible negative role for OMADS5 in regulating lip formation. Yeast two-hybrid analysis indicated that OMADS5 formed homodimers and heterodimers with OMADS3 and OMADS9. OMADS8 only formed heterodimers with OMADS3, whereas OMADS3 and OMADS9 formed homodimers and heterodimers with each other. We proposed that sepal/petal/lip formation needs the presence of OMADS3/8 and/or OMADS9. The determination of the final organ identity for the sepal/petal/lip likely depended on the presence or absence of OMADS5. The presence of OMADS5 caused short sepal/petal formation. When OMADS5 was absent, cells could proliferate, resulting in the possible formation of large lips and the conversion of the sepal/petal into lips in peloric mutants. Further analysis indicated that only ectopic expression of OMADS8 but not OMADS5/9 caused the conversion of the sepal into an expanded petal-like structure in transgenic Arabidopsis (Arabidopsis thaliana) plants.The ABCDE model predicts the formation of any flower organ by the interaction of five classes of homeotic genes in plants (Yanofsky et al., 1990; Jack et al., 1992; Mandel et al., 1992; Goto and Meyerowitz, 1994; Jofuku et al., 1994; Pelaz et al., 2000, 2001; Theißen and Saedler, 2001; Pinyopich et al., 2003; Ditta et al., 2004; Jack, 2004). The A class genes control sepal formation. The A, B, and E class genes work together to regulate petal formation. The B, C, and E class genes control stamen formation. The C and E class genes work to regulate carpel formation, whereas the D class gene is involved in ovule development. MADS box genes seem to have a central role in flower development, because most ABCDE genes encode MADS box proteins (Coen and Meyerowitz, 1991; Weigel and Meyerowitz, 1994; Purugganan et al., 1995; Rounsley et al., 1995; Theißen and Saedler, 1995; Theißen et al., 2000; Theißen, 2001).The function of B group genes, such as APETALA3 (AP3) and PISTILLATA (PI), has been thought to have a major role in specifying petal and stamen development (Jack et al., 1992; Goto and Meyerowitz, 1994; Krizek and Meyerowitz, 1996; Kramer et al., 1998; Hernandez-Hernandez et al., 2007; Kanno et al., 2007; Whipple et al., 2007; Irish, 2009). In Arabidopsis (Arabidopsis thaliana), mutation in AP3 or PI caused identical phenotypes of second whorl petal conversion into a sepal structure and third flower whorl stamen into a carpel structure (Bowman et al., 1989; Jack et al., 1992; Goto and Meyerowitz, 1994). Similar homeotic conversions for petal and stamen were observed in the mutants of the AP3 and PI orthologs from a number of core eudicots such as Antirrhinum majus, Petunia hybrida, Gerbera hybrida, Solanum lycopersicum, and Nicotiana benthamiana (Sommer et al., 1990; Tröbner et al., 1992; Angenent et al., 1993; van der Krol et al., 1993; Yu et al., 1999; Liu et al., 2004; Vandenbussche et al., 2004; de Martino et al., 2006), from basal eudicot species such as Papaver somniferum and Aquilegia vulgaris (Drea et al., 2007; Kramer et al., 2007), as well as from monocot species such as Zea mays and Oryza sativa (Ambrose et al., 2000; Nagasawa et al., 2003; Prasad and Vijayraghavan, 2003; Yadav et al., 2007; Yao et al., 2008). This indicated that the function of the B class genes AP3 and PI is highly conserved during evolution.It has been thought that B group genes may have arisen from an ancestral gene through multiple gene duplication events (Doyle, 1994; Theißen et al., 1996, 2000; Purugganan, 1997; Kramer et al., 1998; Kramer and Irish, 1999; Lamb and Irish, 2003; Kim et al., 2004; Stellari et al., 2004; Zahn et al., 2005; Hernandez-Hernandez et al., 2007). In the gymnosperms, there was a single putative B class lineage that duplicated to generate the paleoAP3 and PI lineages in angiosperms (Kramer et al., 1998; Theißen et al., 2000; Irish, 2009). The paleoAP3 lineage is composed of AP3 orthologs identified in lower eudicots, magnolid dicots, and monocots (Kramer et al., 1998). Genes in this lineage contain the conserved paleoAP3- and PI-derived motifs in the C-terminal end of the proteins, which have been thought to be characteristics of the B class ancestral gene (Kramer et al., 1998; Tzeng and Yang, 2001; Hsu and Yang, 2002). The PI lineage is composed of PI orthologs that contain a highly conserved PI motif identified in most plant species (Kramer et al., 1998). Subsequently, there was a second duplication at the base of the core eudicots that produced the euAP3 and TM6 lineages, which have been subject to substantial sequence changes in eudicots during evolution (Kramer et al., 1998; Kramer and Irish, 1999). The paleoAP3 motif in the C-terminal end of the proteins was retained in the TM6 lineage and replaced by a conserved euAP3 motif in the euAP3 lineage of most eudicot species (Kramer et al., 1998). In addition, many lineage-specific duplications for paleoAP3 lineage have occurred in plants such as orchids (Hsu and Yang, 2002; Tsai et al., 2004; Kim et al., 2007; Mondragón-Palomino and Theißen, 2008, 2009; Mondragón-Palomino et al., 2009), Ranunculaceae, and Ranunculales (Kramer et al., 2003; Di Stilio et al., 2005; Shan et al., 2006; Kramer, 2009).Unlike the A or C class MADS box proteins, which form homodimers that regulate flower development, the ability of B class proteins to form homodimers has only been reported in gymnosperms and in the paleoAP3 and PI lineages of some monocots. For example, LMADS1 of the lily Lilium longiflorum (Tzeng and Yang, 2001), OMADS3 of the orchid Oncidium Gower Ramsey (Hsu and Yang, 2002), and PeMADS4 of the orchid Phalaenopsis equestris (Tsai et al., 2004) in the paleoAP3 lineage, LRGLOA and LRGLOB of the lily Lilium regale (Winter et al., 2002), TGGLO of the tulip Tulipa gesneriana (Kanno et al., 2003), and PeMADS6 of the orchid P. equestris (Tsai et al., 2005) in the PI lineage, and GGM2 of the gymnosperm Gnetum gnemon (Winter et al., 1999) were able to form homodimers that regulate flower development. Proteins in the euAP3 lineage and in most paleoAP3 lineages were not able to form homodimers and had to interact with PI to form heterodimers in order to regulate petal and stamen development in various plant species (Schwarz-Sommer et al., 1992; Tröbner et al., 1992; Riechmann et al., 1996; Moon et al., 1999; Winter et al., 2002; Kanno et al., 2003; Vandenbussche et al., 2004; Yao et al., 2008). In addition to forming dimers, AP3 and PI were able to interact with other MADS box proteins, such as SEPALLATA1 (SEP1), SEP2, and SEP3, to regulate petal and stamen development (Pelaz et al., 2000; Honma and Goto, 2001; Theißen and Saedler, 2001; Castillejo et al., 2005).Orchids are among the most important plants in the flower market around the world, and research on MADS box genes has been reported for several species of orchids during the past few years (Lu et al., 1993, 2007; Yu and Goh, 2000; Hsu and Yang, 2002; Yu et al., 2002; Hsu et al., 2003; Tsai et al., 2004, 2008; Xu et al., 2006; Guo et al., 2007; Kim et al., 2007; Chang et al., 2009). Unlike the flowers in eudicots, the nearly identical shape of the sepals and petals as well as the production of a unique lip in orchid flowers make them a very special plant species for the study of flower development. Four clades (1–4) of genes in the paleoAP3 lineage have been identified in several orchids (Hsu and Yang, 2002; Tsai et al., 2004; Kim et al., 2007; Mondragón-Palomino and Theißen, 2008, 2009; Mondragón-Palomino et al., 2009). Several works have described the possible interactions among these four clades of paleoAP3 genes and one PI gene that are involved in regulating the differentiation and formation of the sepal/petal/lip of orchids (Tsai et al., 2004; Kim et al., 2007; Mondragón-Palomino and Theißen, 2008, 2009). However, the exact mechanism that involves the orchid B class genes remains unclear and needs to be clarified by more experimental investigations.O. Gower Ramsey is a popular orchid with important economic value in cut flower markets. Only a few studies have been reported on the role of MADS box genes in regulating flower formation in this plant species (Hsu and Yang, 2002; Hsu et al., 2003; Chang et al., 2009). An AP3-like MADS gene that regulates both floral formation and initiation in transgenic Arabidopsis has been reported (Hsu and Yang, 2002). In addition, four AP1/AGAMOUS-LIKE9 (AGL9)-like MADS box genes have been characterized that show novel expression patterns and cause different effects on floral transition and formation in Arabidopsis (Hsu et al., 2003; Chang et al., 2009). Compared with other orchids, the production of a large and well-expanded lip and five small identical sepals/petals makes O. Gower Ramsey a special case for the study of the diverse functions of B class MADS box genes during evolution. Therefore, the isolation of more B class MADS box genes and further study of their roles in the regulation of perianth (sepal/petal/lip) formation during O. Gower Ramsey flower development are necessary. In addition to the clade 2 paleoAP3 gene OMADS3, which was previously characterized in our laboratory (Hsu and Yang, 2002), three more B class MADS box genes, OMADS5, OMADS8, and OMADS9, were characterized from O. Gower Ramsey in this study. Based on the different expression patterns and the protein interactions among these four orchid B class genes, we propose that the presence of OMADS3/8 and/or OMADS9 is required for sepal/petal/lip formation. Further sepal and petal formation at least requires the additional presence of OMADS5, whereas large lip formation was seen when OMADS5 expression was absent. Our results provide a new finding and information pertaining to the roles for orchid B class MADS box genes in the regulation of sepal/petal/lip formation.     

Calcineurin B-Like Protein-Interacting Protein Kinase CIPK21 Regulates Osmotic and Salt Stress Responses in Arabidopsis

The role of calcium-mediated signaling has been extensively studied in plant responses to abiotic stress signals. Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) constitute a complex signaling network acting in diverse plant stress responses. Osmotic stress imposed by soil salinity and drought is a major abiotic stress that impedes plant growth and development and involves calcium-signaling processes. In this study, we report the functional analysis of CIPK21, an Arabidopsis (Arabidopsis thaliana) CBL-interacting protein kinase, ubiquitously expressed in plant tissues and up-regulated under multiple abiotic stress conditions. The growth of a loss-of-function mutant of CIPK21, cipk21, was hypersensitive to high salt and osmotic stress conditions. The calcium sensors CBL2 and CBL3 were found to physically interact with CIPK21 and target this kinase to the tonoplast. Moreover, preferential localization of CIPK21 to the tonoplast was detected under salt stress condition when coexpressed with CBL2 or CBL3. These findings suggest that CIPK21 mediates responses to salt stress condition in Arabidopsis, at least in part, by regulating ion and water homeostasis across the vacuolar membranes.Drought and salinity cause osmotic stress in plants and severely affect crop productivity throughout the world. Plants respond to osmotic stress by changing a number of cellular processes (Xiong et al., 1999; Xiong and Zhu, 2002; Bartels and Sunkar, 2005; Boudsocq and Lauriére, 2005). Some of these changes include activation of stress-responsive genes, regulation of membrane transport at both plasma membrane (PM) and vacuolar membrane (tonoplast) to maintain water and ionic homeostasis, and metabolic changes to produce compatible osmolytes such as Pro (Stewart and Lee, 1974; Krasensky and Jonak, 2012). It has been well established that a specific calcium (Ca²⁺) signature is generated in response to a particular environmental stimulus (Trewavas and Malhó, 1998; Scrase-Field and Knight, 2003; Luan, 2009; Kudla et al., 2010). The Ca²⁺ changes are primarily perceived by several Ca²⁺ sensors such as calmodulin (Reddy, 2001; Luan et al., 2002), Ca²⁺-dependent protein kinases (Harper and Harmon, 2005), calcineurin B-like proteins (CBLs; Luan et al., 2002; Batistič and Kudla, 2004; Pandey, 2008; Luan, 2009; Sanyal et al., 2015), and other Ca²⁺-binding proteins (Reddy, 2001; Shao et al., 2008) to initiate various cellular responses.Plant CBL-type Ca²⁺ sensors interact with and activate CBL-interacting protein kinases (CIPKs) that phosphorylate downstream components to transduce Ca²⁺ signals (Liu et al., 2000; Luan et al., 2002; Batistič and Kudla, 2004; Luan, 2009). In several plant species, multiple members have been identified in the CBL and CIPK family (Luan et al., 2002; Kolukisaoglu et al., 2004; Pandey, 2008; Batistič and Kudla, 2009; Weinl and Kudla, 2009; Pandey et al., 2014). Involvement of specific CBL-CIPK pair to decode a particular type of signal entails the alternative and selective complex formation leading to stimulus-response coupling (D’Angelo et al., 2006; Batistič et al., 2010).Several CBL and CIPK family members have been implicated in plant responses to drought, salinity, and osmotic stress based on genetic analysis of Arabidopsis (Arabidopsis thaliana) mutants (Zhu, 2002; Cheong et al., 2003, 2007; Kim et al., 2003; Pandey et al., 2004, 2008; D’Angelo et al., 2006; Qin et al., 2008; Tripathi et al., 2009; Held et al., 2011; Tang et al., 2012; Drerup et al., 2013; Eckert et al., 2014). A few CIPKs have also been functionally characterized by gain-of-function approach in crop plants such as rice (Oryza sativa), pea (Pisum sativum), and maize (Zea mays) and were found to be involved in osmotic stress responses (Mahajan et al., 2006; Xiang et al., 2007; Yang et al., 2008; Tripathi et al., 2009; Zhao et al., 2009; Cuéllar et al., 2010).In this report, we examined the role of the Arabidopsis CIPK21 gene in osmotic stress response by reverse genetic analysis. The loss-of-function mutant plants became hypersensitive to salt and mannitol stress conditions, suggesting that CIPK21 is involved in the regulation of osmotic stress response in Arabidopsis. These findings are further supported by an enhanced tonoplast targeting of the cytoplasmic CIPK21 through interaction with the vacuolar Ca²⁺ sensors CBL2 and CBL3 under salt stress condition.     

Focus on Ethylene: Ethylene and the Regulation of Physiological and Morphological Responses to Nutrient Deficiencies

To cope with nutrient deficiencies, plants develop both morphological and physiological responses. The regulation of these responses is not totally understood, but some hormones and signaling substances have been implicated. It was suggested several years ago that ethylene participates in the regulation of responses to iron and phosphorous deficiency. More recently, its role has been extended to other deficiencies, such as potassium, sulfur, and others. The role of ethylene in so many deficiencies suggests that, to confer specificity to the different responses, it should act through different transduction pathways and/or in conjunction with other signals. In this update, the data supporting a role for ethylene in the regulation of responses to different nutrient deficiencies will be reviewed. In addition, the results suggesting the action of ethylene through different transduction pathways and its interaction with other hormones and signaling substances will be discussed.When plants suffer from a mineral nutrient deficiency, they develop morphological and physiological responses (mainly in their roots) aimed to facilitate the uptake and mobilization of the limiting nutrient. After the nutrient has been acquired in enough quantity, these responses need to be switched off to avoid toxicity and conserve energy. In recent years, different plant hormones (e.g. ethylene, auxin, cytokinins, jasmonic acid, abscisic acid, brassinosteroids, GAs, and strigolactones) have been implicated in the regulation of these responses (Romera et al., 2007, 2011, 2015; Liu et al., 2009; Rubio et al., 2009; Kapulnik et al., 2011; Kiba et al., 2011; Iqbal et al., 2013; Zhang et al., 2014).Before the 1990s, there were several publications relating ethylene and nutrient deficiencies (cited in Lynch and Brown [1997] and Romera et al. [1999]) without establishing a direct implication of ethylene in the regulation of nutrient deficiency responses. In 1994, Romera and Alcántara (1994) published an article in Plant Physiology suggesting a role for ethylene in the regulation of Fe deficiency responses. In 1999, Borch et al. (1999) showed the participation of ethylene in the regulation of P deficiency responses. Since then, evidence has been accumulating in support of a role for ethylene in the regulation of both Fe (Romera et al., 1999, 2015; Waters and Blevins, 2000; Lucena et al., 2006; Waters et al., 2007; García et al., 2010, 2011, 2013, 2014; Yang et al., 2014) and P deficiency responses (Kim et al., 2008; Lei et al., 2011; Li et al., 2011; Nagarajan and Smith, 2012; Wang et al., 2012, 2014c). Both Fe and P may be poorly available in most soils, and plants develop similar responses under their deficiencies (Romera and Alcántara, 2004; Zhang et al., 2014). More recently, a role for ethylene has been extended to other deficiencies, such as K (Shin and Schachtman, 2004; Jung et al., 2009; Kim et al., 2012), S (Maruyama-Nakashita et al., 2006; Wawrzyńska et al., 2010; Moniuszko et al., 2013), and B (Martín-Rejano et al., 2011). Ethylene has also been implicated in both N deficiency and excess (Tian et al., 2009; Mohd-Radzman et al., 2013; Zheng et al., 2013), and its participation in Mg deficiency has been suggested (Hermans et al., 2010).In this update, we will review the information supporting a role for ethylene in the regulation of different nutrient deficiency responses. For information relating ethylene to other aspects of plant mineral nutrition, such as N₂ fixation and responses to excess of nitrate or essential heavy metals, the reader is referred to other reviews (for review, see Maksymiec, 2007; Mohd-Radzman et al., 2013; Steffens, 2014).