Identification of Mitochondrial Coenzyme A Transporters from Maize and Arabidopsis

Plants make coenzyme A (CoA) in the cytoplasm but use it for reactions in mitochondria, chloroplasts, and peroxisomes, implying that these organelles have CoA transporters. A plant peroxisomal CoA transporter is already known, but plant mitochondrial or chloroplastic CoA transporters are not. Mitochondrial CoA transporters belonging to the mitochondrial carrier family, however, have been identified in yeast (Saccharomyces cerevisiae; Leu-5p) and mammals (SLC25A42). Comparative genomic analysis indicated that angiosperms have two distinct homologs of these mitochondrial CoA transporters, whereas nonflowering plants have only one. The homologs from maize (Zea mays; GRMZM2G161299 and GRMZM2G420119) and Arabidopsis (Arabidopsis thaliana; At1g14560 and At4g26180) all complemented the growth defect of the yeast leu5Δ mitochondrial CoA carrier mutant and substantially restored its mitochondrial CoA level, confirming that these proteins have CoA transport activity. Dual-import assays with purified pea (Pisum sativum) mitochondria and chloroplasts, and subcellular localization of green fluorescent protein fusions in transiently transformed tobacco (Nicotiana tabacum) Bright Yellow-2 cells, showed that the maize and Arabidopsis proteins are targeted to mitochondria. Consistent with the ubiquitous importance of CoA, the maize and Arabidopsis mitochondrial CoA transporter genes are expressed at similar levels throughout the plant. These data show that representatives of both monocotyledons and eudicotyledons have twin, mitochondrially located mitochondrial carrier family carriers for CoA. The highly conserved nature of these carriers makes possible their reliable annotation in other angiosperm genomes.CoA acts as an acyl carrier in many reactions of primary and secondary metabolism, and some 8% of the nearly 4,900 enzymes described in the Enzyme Commission database are CoA dependent (Bairoch, 2000). CoA occupies a central position in lipid metabolism, respiration, gluconeogenesis, and other pathways (Leonardi et al., 2005). It is present in all forms of life, but while all organisms can synthesize it from pantothenate (vitamin B₅), only prokaryotes, plants, and fungi are able to synthesize pantothenate; animals obtain pantothenate from the diet (Daugherty et al., 2002; Leonardi et al., 2005; Webb and Smith, 2011).In plants, the steps that convert pantothenate to CoA are almost certainly cytosolic (Webb and Smith, 2011; Gerdes et al., 2012). CoA, however, is required in mitochondria for the citric acid cycle, in chloroplasts for fatty acid synthesis, and in peroxisomes for β-oxidation. CoA, therefore, must be imported into these organelles from the cytosol, and indeed, early work demonstrated a CoA transport system in potato (Solanum tuberosum) mitochondria (Neuburger et al., 1984). Yeast (Saccharomyces cerevisiae) and mammalian mitochondria and peroxisomes likewise import CoA because they cannot make it (Fiermonte et al., 2009; Agrimi et al., 2012b). The compartmentation of CoA in all eukaryotes appears to be closely regulated, with cytosol and organelles maintaining separate CoA pools whose levels can modulate fluxes through CoA-dependent reactions (Hunt and Alexson, 2002; Leonardi et al., 2005; De Marcos Lousa et al., 2013).Mitochondrial CoA transporters belonging to the mitochondrial carrier family (MCF) have been identified in yeast (Leu-5p; Prohl et al., 2001) and human (SLC25A42; Fiermonte et al., 2009). Furthermore, peroxisomal CoA carriers from human (SLC25A17; Agrimi et al., 2012b) and Arabidopsis (Arabidopsis thaliana; peroxisomal CoA and NAD carrier [PXN]; Agrimi et al., 2012a) have also been identified. However, no transporters for CoA are known for plant mitochondria or chloroplasts (Palmieri et al., 2011; Gerdes et al., 2012).In this study, a comparative genomic analysis first identified close Arabidopsis and maize (Zea mays) homologs of the yeast and mammalian mitochondrial CoA carriers as candidates for the missing plant mitochondrial or chloroplast transporters. Experimental evidence then demonstrated that the candidate proteins transport CoA when expressed in yeast, that they are targeted to mitochondria in vitro and in planta, and that they are expressed throughout the plant.     

Regulation of Microbe-Associated Molecular Pattern-Induced Hypersensitive Cell Death,Phytoalexin Production,and Defense Gene Expression by Calcineurin B-Like Protein-Interacting Protein Kinases,OsCIPK14/15, in Rice Cultured Cells

Although cytosolic free Ca²⁺ mobilization induced by microbe/pathogen-associated molecular patterns is postulated to play a pivotal role in innate immunity in plants, the molecular links between Ca²⁺ and downstream defense responses still remain largely unknown. Calcineurin B-like proteins (CBLs) act as Ca²⁺ sensors to activate specific protein kinases, CBL-interacting protein kinases (CIPKs). We here identified two CIPKs, OsCIPK14 and OsCIPK15, rapidly induced by microbe-associated molecular patterns, including chitooligosaccharides and xylanase (Trichoderma viride/ethylene-inducing xylanase [TvX/EIX]), in rice (Oryza sativa). Although they are located on different chromosomes, they have over 95% nucleotide sequence identity, including the surrounding genomic region, suggesting that they are duplicated genes. OsCIPK14/15 interacted with several OsCBLs through the FISL/NAF motif in yeast cells and showed the strongest interaction with OsCBL4. The recombinant OsCIPK14/15 proteins showed Mn²⁺-dependent protein kinase activity, which was enhanced both by deletion of their FISL/NAF motifs and by combination with OsCBL4. OsCIPK14/15-RNAi transgenic cell lines showed reduced sensitivity to TvX/EIX for the induction of a wide range of defense responses, including hypersensitive cell death, mitochondrial dysfunction, phytoalexin biosynthesis, and pathogenesis-related gene expression. On the other hand, TvX/EIX-induced cell death was enhanced in OsCIPK15-overexpressing lines. Our results suggest that OsCIPK14/15 play a crucial role in the microbe-associated molecular pattern-induced defense signaling pathway in rice cultured cells.Calcium ions regulate diverse cellular processes in plants as a ubiquitous internal second messenger, conveying signals received at the cell surface to the inside of the cell through spatial and temporal concentration changes that are decoded by an array of Ca²⁺ sensors (Reddy, 2001; Sanders et al., 2002; Yang and Poovaiah, 2003). Several families of Ca²⁺ sensors have been identified in higher plants. The best known are calmodulins (CaMs) and CaM-related proteins, which typically contain four EF-hand domains for Ca²⁺ binding (Zielinski, 1998). Unlike mammals, which possess single molecular species of CaM, plants have at least three distinct molecular species of CaM playing diverse physiological functions and whose expression is differently regulated (Yamakawa et al., 2001; Luan et al., 2002; Karita et al., 2004; Takabatake et al., 2007). The second major class is exemplified by the Ca²⁺-dependent protein kinases, which contain CaM-like Ca²⁺-binding domains and a kinase domain in a single protein (Harmon et al., 2000). In addition, a new family of Ca²⁺ sensors was identified as calcineurin B-like (CBL) proteins, which consists of proteins similar to both the regulatory β-subunit of calcineurin and the neuronal Ca²⁺ sensor in animals (Liu and Zhu, 1998; Kudla et al., 1999).Unlike CaMs, which interact with a large variety of target proteins, CBLs specifically target a family of protein kinases referred to as CBL-interacting protein kinases (CIPKs) or SnRK3s (for sucrose nonfermenting 1-related protein kinases type 3), which are most similar to the SNF family protein kinases in yeast (Luan et al., 2002). A database search of the Arabidopsis (Arabidopsis thaliana) genome sequence revealed 10 CBL and 25 CIPK homologues (Luan et al., 2002). Expression patterns of these Ca²⁺ sensors and protein kinases suggest their diverse functions in different signaling processes, including light, hormone, sugar, and stress responses (Batistic and Kudla, 2004). AtCBL4/Salt Overly Sensitive3 (SOS3) and AtCIPK24/SOS2 have been shown to play a key role in Ca²⁺-mediated salt stress adaptation (Zhu, 2002). The CBL-CIPK system has been shown to be involved in signaling pathways of abscisic acid (Kim et al., 2003a), sugar (Gong et al., 2002a), gibberellins (Hwang et al., 2005), salicylic acid (Mahajan et al., 2006), and K⁺ channel regulation (Li et al., 2006; Lee et al., 2007; for review, see Luan, 2009; Batistic and Kudla, 2009). However, physiological functions of most of the family members still remain largely unknown.Plants respond to pathogen attack by activating a variety of defense responses, including the generation of reactive oxygen species (ROS), synthesis of phytoalexins, expression of pathogenesis-related (PR) genes, cell cycle arrest, and mitochondrial dysfunction followed by a form of hypersensitive cell death known as the hypersensitive response (Nürnberger and Scheel, 2001; Greenberg and Yao, 2004; Kadota et al., 2004b). Transient membrane potential changes and Ca²⁺ influx are involved at the initial stage of defense responses (Kuchitsu et al., 1993; Pugin et al., 1997; Blume et al., 2000; Kadota et al., 2004a). Many kinds of defense responses are prevented when Ca²⁺ influx is compromised by Ca²⁺ chelators (Nürnberger and Scheel, 2001; Lecourieux et al., 2002). Since complex spatiotemporal patterns of cytosolic free Ca²⁺ concentration have been suggested to play pivotal roles in defense signaling (Nürnberger and Scheel, 2001; Sanders et al., 2002), multiple Ca²⁺ sensor proteins and their effectors should function in the defense signaling pathways. Although possible involvement of some CaM isoforms (Heo et al., 1999; Yamakawa et al., 2001), Ca²⁺-dependent protein kinases (Romeis et al., 2000, 2001; Ludwig et al., 2005; Kobayashi et al., 2007; Yoshioka et al., 2009), as well as Ca²⁺ regulation of EF-hand-containing enzymes such as ROS-generating NADPH oxidase (Ogasawara et al., 2008) have been suggested, other Ca²⁺-regulated signaling components still remain to be identified. No CBLs or CIPKs have so far been implicated as signaling components in defense signaling.N-Acetylchitooligosaccharides, chitin fragments, are microbe-associated molecular patterns (MAMPs) that are recognized by plasma membrane receptors (Kaku et al., 2006; Miya et al., 2007) and induce a variety of defense responses, such as membrane depolarization (Kuchitsu et al., 1993; Kikuyama et al., 1997), ion fluxes (Kuchitsu et al., 1997), ROS production (Kuchitsu et al., 1995), phytoalexin biosynthesis (Yamada et al., 1993), and induction of PR genes (Nishizawa et al., 1999), without hypersensitive cell death in rice (Oryza sativa) cells. In contrast, a fungal proteinaceous elicitor, xylanase from Trichoderma viride (TvX)/ethylene-inducing xylanase (EIX), which is recognized by two putative plasma membrane receptors, LeEix1 and LeEix2 (Ron and Avni, 2004), triggers hypersensitive cell death along with different kinetics of ROS production and activation of a mitogen-activated protein kinase, OsMPK6, previously named as OsMPK2 or OsMAPK6, in rice cells (Kurusu et al., 2005). These two fungal MAMPs thus provide excellent model systems to study innate immunity in rice cells.This study identified two CIPKs involved in various MAMP-induced layers of defense responses, including PR gene expression, phytoalexin biosynthesis, mitochondrial dysfunction, and cell death, in rice. Molecular characterization of these CIPKs, including interaction with the putative Ca²⁺ sensors as well as their physiological functions, is discussed.     

Integrating Image-Based Phenomics and Association Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice

Salinity affects a significant portion of arable land and is particularly detrimental for irrigated agriculture, which provides one-third of the global food supply. Rice (Oryza sativa), the most important food crop, is salt sensitive. The genetic resources for salt tolerance in rice germplasm exist but are underutilized due to the difficulty in capturing the dynamic nature of physiological responses to salt stress. The genetic basis of these physiological responses is predicted to be polygenic. In an effort to address this challenge, we generated temporal imaging data from 378 diverse rice genotypes across 14 d of 90 mm NaCl stress and developed a statistical model to assess the genetic architecture of dynamic salinity-induced growth responses in rice germplasm. A genomic region on chromosome 3 was strongly associated with the early growth response and was captured using visible range imaging. Fluorescence imaging identified four genomic regions linked to salinity-induced fluorescence responses. A region on chromosome 1 regulates both the fluorescence shift indicative of the longer term ionic stress and the early growth rate decline during salinity stress. We present, to our knowledge, a new approach to capture the dynamic plant responses to its environment and elucidate the genetic basis of these responses using a longitudinal genome-wide association model.Nearly one-third of the 54 million ha of the highly saline soils in the world are located in South and Southeast Asia. Rice (Oryza sativa), which is the primary source of calories and protein for these two regions, is very sensitive to salinity stress, with even moderate salinity levels known to decrease yields by 50% (Zeng et al., 2002). Projected sea level rise due to climate change is expected to increase saltwater ingress in coastal rice-growing regions of South and Southeast Asia. Therefore, development of salt-tolerant rice cultivars is essential to maintain rice productivity in the salinity-affected regions globally.Salt tolerance, defined as the ability to maintain growth and productivity in saline conditions, is a complex polygenic trait that may be influenced by distinct physiological mechanisms (Munns et al., 1982; Munns and Termaat, 1986; Cheeseman, 1988; Munns and Tester, 2008; Horie et al., 2012; for a comprehensive review of genes involved in salinity tolerance in rice, see Negrão et al., 2011) At the cellular level, plants respond to saline conditions in two phases, namely an osmotic (shoot ion independent) and an ionic stress phase, which can occur in an overlapping manner with varying intensity during the course of salinity stress (Munns and Termaat, 1986; Munns, 2002; Munns and James, 2003; Munns and Tester, 2008; Horie et al., 2012). During the osmotic stress phase, which occurs soon after the onset of salinity, the reduction in external osmotic potential disrupts water uptake and impedes cell expansion, which, at the whole plant level, leads to reduced growth rate (Matsuda and Riazi, 1981; Munns and Passioura, 1984; Rawson and Munns, 1984; Azaizeh and Steudle, 1991; Fricke and Peters, 2002; Fricke, 2004; Boursiac et al., 2005). As salinity stress persists over several days and weeks, sodium ions (Na⁺) accumulate to toxic levels, resulting in cell death and precocious leaf senescence (Lutts and Bouharmont, 1996; Munns, 2002; Munns and James, 2003; Ghanem et al., 2008). This is typically observed during the ionic phase of the salinity response (Munns, 2002; Munns and James, 2003; Munns and Tester, 2008). Plants possess distinct mechanisms to adapt to these osmotic and ionic stresses that are controlled by a suite of genes (Apse et al., 1999; Carvajal et al., 1999; Halfter et al., 2000; Ishitani et al., 2000; Shi et al., 2000; Zeng and Shannon, 2000; Rus et al., 2001; Berthomieu et al., 2003; Martínez-Ballesta et al., 2003; Boursiac et al., 2005, 2008; Ren et al., 2005; Huang et al., 2006; Davenport et al., 2007; Obata et al., 2007; Székely et al., 2008; Horie et al., 2011; Rivandi et al., 2011; Asano et al., 2012; Munns et al., 2012; Latz et al., 2013; Schmidt et al., 2013; Campo et al., 2014; Choi et al., 2014; Liu et al., 2014). The genetic basis of temporal adaptive responses to salinity stress remains to be explored in rice and other crops. This is primarily due to challenges in capturing the dynamic physiological responses to salinity for a large number of genotypes in a nondestructive manner. Manual phenotyping to detect incremental changes in growth rate during the osmotic stress and slight shifts in leaf color due to ionic stress is difficult to quantify for a large number of genotypes.In rice, at least one major quantitative trait loci (QTL; saltol) for salinity tolerance has been characterized based on end point measurements of biomass, senescence/injury, and Na⁺ and K⁺ concentrations (Bonilla et al., 2002; Lin et al., 2004; Thomson et al., 2010). SHOOT K⁺ CONTENT1 (SKC1) is the causative gene underlying the saltol region. SKC1 encodes a Na⁺-selective high-affinity potassium transporter that regulates Na⁺/K⁺ homeostasis during salinity stress (Ren et al., 2005). High levels of Na⁺ displace cellular K⁺, an essential element for several enzymatic reactions and physiological processes (Gierth and Mäser, 2007). The ability to maintain cellular K⁺ levels during salinity through the action of Na⁺-selective potassium transporters or Na⁺/H⁺ antiporters is a well-characterized tolerance mechanism in cereals including rice (Ren et al., 2005; Sunarpi et al., 2005; Huang et al., 2006; Møller et al., 2009; Mian et al., 2011; Munns et al., 2012).Numerous studies have utilized conventional linkage mapping to identify QTL for morphological and physiological responses to salinity in rice using discrete end point measurements (Bonilla et al., 2002; Lin et al., 2004; Ren et al., 2005; Negrão et al., 2011; Wang et al., 2012). However, the physiological adaptation to saline conditions is a complex continuous process that develops over time. While some accessions will exhibit similar end point phenotypic values, the genetic and physiological mechanisms giving rise to the similar phenotypes may be very different and the growth trajectories throughout the experiment may be distinct. Although single time point studies have yielded important information regarding the genetic basis of salinity tolerance, such approaches are too simple to reveal the genetic architecture of stress adaptation. With the advent of high-throughput image-based phenotyping platforms, it is now feasible to quantify dynamic responses during the stress treatment for a large number of genotypes (Berger et al., 2010; Golzarian et al., 2011; Chen et al., 2014; Honsdorf et al., 2014).Image-based phenotyping has been combined with genome-wide association studies (GWAS) and linkage mapping to examine the genetic basis of complex developmental processes (Busemeyer et al., 2013; Moore et al., 2013; Topp et al., 2013; Slovak et al., 2014; Würschum et al., 2014; Yang et al., 2014; Bac-Molenaar et al., 2015). Moreover, the introduction of the time axis provides a better understanding of the physiological processes underlying complex stress and developmental responses compared with single end point measurements (Zhang et al., 2012; Moore et al., 2013; Brown et al., 2014; Chen et al., 2014; Slovak et al., 2014; Bac-Molenaar et al., 2015). However, to date, no studies have implemented an association mapping approach using image-derived phenotypes to address the genetic basis of dynamic stress responses in plants. Image-based phenotyping offers several advantages over conventional phenotyping: (1) quantitative measurements can be recorded over discrete time points to capture morphological and physiological responses in a nondestructive manner, and (2) the use of various types of spectral imaging address phenotypes that are not detectable to the human eye such as chlorophyll fluorescence and leaf water content. Integrating dynamic phenotypic data and association mapping has the potential to query genetic diversity across hundreds of accessions for complex traits and provides much higher resolution compared with conventional linkage mapping. Here, we explored the dynamic growth and chlorophyll responses to salinity of a diverse set of rice accessions using high-throughput visible and fluorescence imaging. To assess the genetic basis of plant growth in saline conditions, a logistic model was used to describe the temporal growth responses and was incorporated into the statistical framework necessary for association mapping. Coupled with temporal fluorescence imaging, we present, to our knowledge, new insights into the genetic architecture of osmotic and ionic responses during salinity stress in rice.     

Lipoate-Protein Ligase and Octanoyltransferase Are Essential for Protein Lipoylation in Mitochondria of Arabidopsis

Prosthetic lipoyl groups are required for the function of several essential multienzyme complexes, such as pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase (KGDH), and the glycine cleavage system (glycine decarboxylase [GDC]). How these proteins are lipoylated has been extensively studied in prokaryotes and yeast (Saccharomyces cerevisiae), but little is known for plants. We earlier reported that mitochondrial fatty acid synthesis by ketoacyl-acyl carrier protein synthase is not vital for protein lipoylation in Arabidopsis (Arabidopsis thaliana) and does not play a significant role in roots. Here, we identify Arabidopsis lipoate-protein ligase (AtLPLA) as an essential mitochondrial enzyme that uses octanoyl-nucleoside monophosphate and possibly other donor substrates for the octanoylation of mitochondrial PDH-E2 and GDC H-protein; it shows no reactivity with bacterial and possibly plant KGDH-E2. The octanoate-activating enzyme is unknown, but we assume that it uses octanoyl moieties provided by mitochondrial β-oxidation. AtLPLA is essential for the octanoylation of PDH-E2, whereas GDC H-protein can optionally also be octanoylated by octanoyltransferase (LIP2) using octanoyl chains provided by mitochondrial ketoacyl-acyl carrier protein synthase to meet the high lipoate requirement of leaf mesophyll mitochondria. Similar to protein lipoylation in yeast, LIP2 likely also transfers octanoyl groups attached to the H-protein to KGDH-E2 but not to PDH-E2, which is exclusively octanoylated by LPLA. We suggest that LPLA and LIP2 together provide a basal protein lipoylation network to plants that is similar to that in other eukaryotes.Lipoic acid (LA; 6,8-dithiooctanoic acid) prosthetic groups are essential for the catalytic activity of four important multienzyme complexes in plants and other organisms: pyruvate dehydrogenase (PDH), α-ketoglutarate dehydrogenase (KGDH), branched-chain α-ketoacid dehydrogenase (BCDH), and the Gly cleavage system (glycine decarboxylase [GDC]; Perham, 2000; Douce et al., 2001; Mooney et al., 2002). In all these multienzyme complexes, LA is covalently attached to the ε-amino group of a particular lysyl residue of the respective protein subunit. Lipoylated E2 subunits of PDH, KGDH, and BCDH are dihydrolipoyl acyltransferases that interact with E1 and E3 subunits to pass acyl intermediates to CoA (Mooney et al., 2002). By contrast, the lipoylated H-protein of GDC acts as a cosubstrate of three other GDC proteins and has no enzymatic activity itself (Douce et al., 2001). In the course of their respective reaction cycles, LA becomes reduced to dihydrolipoic acid. Most of these enzymes are confined to the mitochondrion. As the only exception, PDH is also present in plastids, where it provides acetyl-CoA for fatty acid biosynthesis (Ohlrogge et al., 1979; Lernmark and Gardeström, 1994; Lin et al., 2003).Mitochondria and plastids each have their own route of de novo LA synthesis, both of which start with the synthesis of protein-bound octanoyl chains (Shimakata and Stumpf, 1982; Ohlrogge and Browse, 1995; Wada et al., 1997; Gueguen et al., 2000; Yasuno et al., 2004). These octanoyl moieties are passed on by organelle-specific octanoyltransferases (Wada et al., 2001a, 2001b) to the respective target apoproteins where lipoyl synthase (LIP1) inserts two sulfur atoms to finally produce functional lipoyl groups (Yasuno and Wada, 1998, 2002; Zhao et al., 2003). A similar pathway has been identified in mammalian mitochondria (Morikawa et al., 2001; Witkowski et al., 2007). In quantitative terms, leaf mesophyll mitochondria have an extraordinarily high requirement for lipoate, because they contain very large amounts of GDC to catalyze the photorespiratory Gly-to-Ser conversion (Bauwe et al., 2010). For this reason, leaf mesophyll mitochondria are the major site of LA synthesis in plants (Wada et al., 1997).It was thought that the octanoyl chains provided by mitochondrial β-ketoacyl-acyl carrier protein synthase (mtKAS) represent the solitary source for protein lipoylation in plant mitochondria (Yasuno et al., 2004). As we reported earlier, however, leaves of mtKAS-deficient knockout mutants show considerable lipoylation of mitochondrial PDH-E2 and KGDH-E2 subunits and some residual lipoylation of GDC H-protein; roots are not at all impaired. Accordingly, the phenotype of such mutants can be fully cured in the low-photorespiratory condition of elevated CO₂ (Ewald et al., 2007). These observations indicated that plant mitochondria, in addition to the mtKAS-LIP2-LIP1 route of protein lipoylation, can resort to an alternative pathway. This would not be uncommon. In Escherichia coli, for example, a salvage pathway utilizes free octanoate or LA in an ATP-dependent two-step reaction catalyzed by the bifunctional enzyme lipoate-protein ligase A (LPLA; Morris et al., 1995). Archaea (Christensen and Cronan, 2009; Posner et al., 2009) and vertebrates (Tsunoda and Yasunobu, 1967) require two separate enzymes to first activate octanoate or LA to lipoyl-nucleoside monophosphate (NMP) and then, in a second step, to convey the activated lipoyl group to the respective target proteins. The lipoate-activating enzyme (LAE) of mammals was identified as a refunctioned medium-chain acyl-CoA synthetase that utilizes GTP to produce lipoyl-GMP (Fujiwara et al., 2001). LIP3 from yeast (Saccharomyces cerevisiae) can use octanoyl-CoA to octanoylate apoE2 proteins (Hermes and Cronan, 2013), whereas octanoyl groups from fatty acid biosynthesis are first attached to H-protein and then passed on to apoE2 proteins (Schonauer et al., 2009).The physiological significance of lipoyl-protein ligases in plants is not exactly known. Such enzymes do not operate in plastids (Ewald et al., 2014) but could be present in mitochondria. A single-gene-encoded LPLA with predicted mitochondrial localization has been identified in rice (Oryza sativa; Kang et al., 2007). Complementation studies with the lipoylation-deficient E. coli mutant TM137 (Morris et al., 1995) suggested that OsLPLA belongs to the bifunctional type of LPLAs. We report the identification of the homologous enzyme in Arabidopsis (Arabidopsis thaliana), provide evidence for its mitochondrial location, and show that Arabidopsis LPLA requires a separate enzyme for octanoate/lipoate activation. We also examine the interplay between LPLA, LIP2, and the mtKAS route of protein lipoylation and suggest a model for protein lipoylation in plant mitochondria.     

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.     

Refining the Definition of Plant Mitochondrial Presequences through Analysis of Sorting Signals,N-Terminal Modifications,and Cleavage Motifs

Mitochondrial protein import is a complex multistep process from synthesis of proteins in the cytosol, recognition by receptors on the organelle surface, to translocation across one or both mitochondrial membranes and assembly after removal of the targeting signal, referred to as a presequence. In plants, import has to further discriminate between mitochondria and chloroplasts. In this study, we determined the precise cleavage sites in the presequences for Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) mitochondrial proteins using mass spectrometry by comparing the precursor sequences with experimental evidence of the amino-terminal peptide from mature proteins. We validated this method by assessments of false-positive rates and comparisons with previous available data using Edman degradation. In total, the cleavable presequences of 62 proteins from Arabidopsis and 52 proteins from rice mitochondria were determined. None of these proteins contained amino-terminal acetylation, in contrast to recent findings for chloroplast stromal proteins. Furthermore, the classical matrix glutamate dehydrogenase was detected with intact and amino-terminal acetylated sequences, indicating that it is imported into mitochondria without a cleavable targeting signal. Arabidopsis and rice mitochondrial presequences had similar isoelectric points, hydrophobicity, and the predicted ability to form an amphiphilic α-helix at the amino-terminal region of the presequence, but variations in length, amino acid composition, and cleavage motifs for mitochondrial processing peptidase were observed. A combination of lower hydrophobicity and start point of the amino-terminal α-helix in mitochondrial presequences in both Arabidopsis and rice distinguished them (98%) from Arabidopsis chloroplast stroma transit peptides. Both Arabidopsis and rice mitochondrial cleavage sites could be grouped into three classes, with conserved −3R (class II) and −2R (class I) or without any conserved (class III) arginines. Class II was dominant in both Arabidopsis and rice (55%–58%), but in rice sequences there was much less frequently a phenylalanine (F) in the −1 position of the cleavage site than in Arabidopsis sequences. Our data also suggest a novel cleavage motif of (F/Y)↓(S/A) in plant class III sequences.Plant mitochondria play a key role in energy production and metabolism that requires the import and assembly of at least 1,000 proteins. Protein import into mitochondria begins with synthesis of the precursor protein in the cytosol, followed by binding to various proteins in the cytosol, binding to receptors on the outer mitochondrial membrane, translocation across one or both mitochondrial membranes, removal of the targeting signal, termed a presequence, and intraorganellar sorting and assembly. A variety of studies have shown that there is no primary amino acid sequence conservation among presequences, but they do have a high proportion of positively charged residues and the capacity to form an amphiphilic α-helix (Roise et al., 1986; von Heijne, 1986). Many mitochondrial presequences have a loosely conserved motif near the cleavage site comprising an Arg residue at the −2 and/or −3 position (von Heijne et al., 1989; Schneider et al., 1998). This Arg has been experimentally shown to be an important recognition site for the mitochondrial processing peptidase (MPP; Arretz et al., 1994; Ogishima et al., 1995; Tanudji et al., 1999). MPP is a heterodimeric enzyme that contains two similar subunits: α-MPP is involved in binding precursor proteins and β-MPP catalyzes the cleavage of the presequence (Kitada et al., 1995; Luciano et al., 1997). In yeast and mammals, MPP is a soluble protein located in the matrix, but in plants, MPP is integrated into the inner membrane-bound cytochrome b/c₁ complex (Braun et al., 1992; Eriksson et al., 1994; Glaser and Dessi, 1999).The mechanism through which the targeting signal binds to a receptor protein has been revealed by NMR studies and the crystal structure of rat Tom20 (for translocase of the outer membrane) with a bound presequence (Abe et al., 2000; Saitoh et al., 2007). A dynamic binding model in which different hydrophobic residues in the presequence interact with Tom20 has been proposed. Thus, the presequence has mobility in the binding site via hydrophobic interactions, with several different binding states being possible. This model accounts for the ability of a single Tom20 in yeast to bind to a diverse array of presequences. Although plants contain a protein that is called Tom20 and that has a receptor function in mitochondrial import, it is not orthologous to yeast or mammalian Tom20 (Perry et al., 2006; Lister et al., 2007). However, the NMR structure of plant Tom20 reveals a similar hydrophobic binding pocket. This has been highlighted as a case of convergent evolution of a receptor that uses a similar mechanism of binding to recognize presequences (Lister and Whelan, 2006). Although structural studies reveal the importance of hydrophobic residues for presequence binding, several studies on yeast, mammals, and plants reveal an important role for positively charged residues in presequences for import into mitochondria (Lister et al., 2005; Neupert and Herrmann, 2007). These positively charged residues may play a role in positioning the amphiphilic α-helix for binding to Tom20 and also in subsequent translocation into and across the pores forming proteins of the TOM and TIM (for translocase of the inner membrane) complexes. Movement of the presequence into and across a translocase is explained by the binding chain hypothesis (Pfanner and Geissler, 2001). According to this hypothesis, a presequence binds to higher affinity sites in the import apparatus until it is “trapped” on the inside of the inner membrane by a combination of electrostatic interactions, the net negative charge on the inside of the inner membrane, and binding to matrix-located HSP70 (Zhang and Glaser, 2002).In addition to the fact that plant Tom20s are not orthologous to other Tom20s, plant mitochondria also lack the other two receptor components that have been functionally characterized in yeast, namely Tom70 and Tom22 (Lister et al., 2007). Furthermore, mitochondrial and plastid targeting signals contain significant similarities in plants; thus, plant mitochondrial presequences have evolved to differentiate from the large number and abundant nature of plastid proteins requiring import from the cytosol (Macasev et al., 2000). This raises the question of how similar plant mitochondrial targeting signals are to those of yeast and how they are differentiated from plastid transit peptides. To adequately address these questions, a large number of presequences need to be assembled to define motifs that differentiate presequence classes. Traditionally, the N-terminal sequences of plant mitochondrial proteins have been obtained by Edman degradation either from purified mitochondrial protein complexes or in proteome studies (Braun and Schmitz, 1995; Jänsch et al., 1996; Millar et al., 1998, 1999; Kruft et al., 2001; Bardel et al., 2002). The presequences could only be obtained by comparison of these N-terminal sequences with the preprotein sequence deduced from full-length cDNA sequences, which were only available in a small number of cases. Glaser et al. (1998) presented a list of approximately 100 plant mitochondrial presequences; these were mainly derived from prediction and/or comparisons in homologous cDNA-derived protein sequences with a core set of 31 experimentally proven presequences for plant mitochondrial proteins. Later analysis of 58 experimentally proven plant mitochondrial presequences deposited in the Swiss-Prot database revealed two major classes containing an Arg residue at positions −2 and −3 and one class without any conserved Arg residues (Zhang et al., 2001; Zhang and Glaser, 2002). However, this data set relied on the sequences available at the time that were from a variety of plant species and contained redundant orthologs from similar proteins. This data set also clearly focused on dicot plants, as less than 20% of the sequences were from monocot species.In the chloroplast, N-terminal modification of chloroplast proteins has been shown to be important for protein viability (Pesaresi et al., 2003). N-terminal acetylation can be detected by high-resolution mass spectrometry (MS) through a change in mass of the N-terminal peptide. The recent systematic analysis of the Arabidopsis (Arabidopsis thaliana) chloroplast proteome revealed 47 stroma proteins with N-acetylated residues and 62 without N-acetylated residues (Zybailov et al., 2008). The detection of N-terminal and non-N-terminal acetylated proteins by identifications of semitryptic peptides also allowed analysis of the cleavage sites and potential motifs for cleavage by processing peptidases (Zybailov et al., 2008). However, no systematic experimental analysis of N-terminal modifications and potential cleavage sites of plant mitochondrial proteins has been carried out to date using such an MS approach.In this study, we have determined Arabidopsis and rice (Oryza sativa) mitochondrial protein-targeting presequences and cleavage sites using an MS approach after gel- or liquid chromatography (LC)-based separation and also identified a range of N-terminal modifications of mitochondrial proteins. Validation of this method was performed by false-positive analysis and comparison with previous results in Arabidopsis using an Edman degradation approach (Kruft et al., 2001). We compared the characteristics of the generated Arabidopsis and rice mitochondrial presequences and the cleavage site motifs. Comparison with experimentally proven yeast mitochondrial presequences and Arabidopsis plastid stroma transit peptides allowed consideration of some evolutionary questions and insights into the different signal-recognizing mechanism(s) used to distinguish between organelles.     

Role of the Rice Hexokinases OsHXK5 and OsHXK6 as Glucose Sensors

The Arabidopsis (Arabidopsis thaliana) hexokinase 1 (AtHXK1) is recognized as an important glucose (Glc) sensor. However, the function of hexokinases as Glc sensors has not been clearly demonstrated in other plant species, including rice (Oryza sativa). To investigate the functions of rice hexokinase isoforms, we characterized OsHXK5 and OsHXK6, which are evolutionarily related to AtHXK1. Transient expression analyses using GFP fusion constructs revealed that OsHXK5 and OsHXK6 are associated with mitochondria. Interestingly, the OsHXK5ΔmTP-GFP and OsHXK6ΔmTP-GFP fusion proteins, which lack N-terminal mitochondrial targeting peptides, were present mainly in the nucleus with a small amount of the proteins seen in the cytosol. In addition, the OsHXK5NLS-GFP and OsHXK6NLS-GFP fusion proteins harboring nuclear localization signals were targeted predominantly in the nucleus, suggesting that these OsHXKs retain a dual-targeting ability to mitochondria and nuclei. In transient expression assays using promoter∷luciferase fusion constructs, these two OsHXKs and their catalytically inactive alleles dramatically enhanced the Glc-dependent repression of the maize (Zea mays) Rubisco small subunit (RbcS) and rice α-amylase genes in mesophyll protoplasts of maize and rice. Notably, the expression of OsHXK5, OsHXK6, or their mutant alleles complemented the Arabidopsis glucose insensitive2-1 mutant, thereby resulting in wild-type characteristics in seedling development, Glc-dependent gene expression, and plant growth. Furthermore, transgenic rice plants overexpressing OsHXK5 or OsHXK6 exhibited hypersensitive plant growth retardation and enhanced repression of the photosynthetic gene RbcS in response to Glc treatment. These results provide evidence that rice OsHXK5 and OsHXK6 can function as Glc sensors.In higher plants, sugars are known to function as signaling molecules in addition to being a fundamental source of fuel for carbon and energy metabolism. Indeed, sugars have been shown to regulate physiological processes during the entire plant life cycle, from germination to flowering and senescence, and to function during defense responses to biotic and abiotic stresses (Jang and Sheen, 1994; Jang et al., 1997; Perata et al., 1997; Smeekens and Rook, 1997; Smeekens, 1998; Wingler et al., 1998; Rolland et al., 2001, 2006; Leon and Sheen, 2003; Gibson, 2005; Biemelt and Sonnewald, 2006; Seo et al., 2007). Therefore, to sustain normal plant growth and development, rigorous sugar sensing and signaling systems are important for coordinating and modulating many essential metabolic pathways.Glc, one of the main products of photosynthesis, is the most widely recognized sugar molecule that regulates plant signaling pathways (Koch, 1996; Yu et al., 1996; Ho et al., 2001; Chen, 2007). Yeast (Saccharomyces cerevisiae) has several Glc sensors, including the hexokinase ScHXK2, Glc transporter-like proteins Sucrose nonfermenting 3 (Snf3) and Restores glucose transport 2 (Rgt2), and G protein-coupled receptor Gpr1. These sensors have been reported to sense the internal and external Glc status as part of mechanisms controlling cell growth and gene expression (Rolland et al., 2001; Lemaire et al., 2004; Santangelo, 2006). Similarly, recent studies in plants have unveiled sugar sensing and signaling systems mediated by hexokinase as a Glc sensor or G protein-coupled receptors in a hexokinase-independent way (Rolland et al., 2001, 2002, 2006; Chen et al., 2003; Moore et al., 2003; Holsbeeks et al., 2004; Cho et al., 2006b; Huang et al., 2006). In addition, plant Snf1-related protein kinase 1 (SnRK1), which is an ortholog of the yeast Snf1, plays important roles linking sugar signal, as well as stress and developmental signals, for the global regulation of plant metabolism, energy balance, growth, and survival (Baena-González et al., 2007; Lu et al., 2007; Baena-González and Sheen, 2008).In addition to the catalytic role of hexokinase in plants, which is to facilitate hexose phosphorylation to form hexose-6-P, the role of hexokinase as an evolutionarily conserved Glc sensor was first recognized from biochemical, genetic, and molecular studies of Arabidopsis (Arabidopsis thaliana) hexokinase 1 (AtHXK1) transgenic plants and glucose insensitive2 (gin2) mutants (Jang et al., 1997; Rolland et al., 2002; Harrington and Bush, 2003; Moore et al., 2003; Cho et al., 2006b). Transgenic plants expressing catalytically inactive AtHXK1 mutant alleles in the gin2 mutant background have provided compelling evidence that the catalytic and sensory functions of AtHXK1 are uncoupled in the Arabidopsis plant (Moore et al., 2003). Furthermore, proteomics and yeast two-hybrid interaction experiments have revealed that in the nucleus, AtHXK1 interacts with two partners, the vacuolar H⁺-ATPase B1 and the 19S regulatory particle of proteasome subunit, to directly control the expression of specific photosynthetic genes (Cho et al., 2006b; Chen, 2007). In these studies, the interactions between AtHXK1 and vacuolar H⁺-ATPase B1 or 19S regulatory particle of proteasome subunit appeared not to require the enzymatic activity of AtHXK1. In the tomato (Solanum lycopersicum) plant, AtHXK1 expression causes a reduction in photosynthesis, growth inhibition, and the induction of rapid senescence (Dai et al., 1999), which are all characteristics of sugar sensing and signaling in photosynthetic tissues. With the exception of Arabidopsis HXK1, the role of hexokinases as Glc sensors has yet to be demonstrated in other plant species (Halford et al., 1999; Veramendi et al., 2002; Rolland et al., 2006).Hexokinases have been shown to associate with various subcellular compartments, including mitochondria, chloroplasts, Golgi complexes, endoplasmic reticula, plasma membranes, and cytosols, suggesting numerous distinct intracellular functions (Schleucher et al., 1998; Wiese et al., 1999; Frommer et al., 2003; Olsson et al., 2003; Giese et al., 2005; Cho et al., 2006a; Kandel-Kfir et al., 2006; Rezende et al., 2006; Damari-Weissler et al., 2007). In yeast, the Glc sensor ScHXK2 has a nuclear localization signal (NLS) within its N-terminal domain and resides partly in the nucleus in addition to the cytosol (Herrero et al., 1998; Randez-Gil et al., 1998). Furthermore, the nuclear localization of ScHXK2 is required for Glc repression of several genes, such as SUC2, HXK1, and GLK1 (Herrero et al., 1998; Rodríguez et al., 2001). A portion of cellular AtHXK1, which is predominantly associated with mitochondria, was also found to reside in the nucleus (Yanagisawa et al., 2003; Cho et al., 2006b). Under conditions of Glc excess, it has thus been hypothesized that nuclear AtHXK1 binds its substrate Glc, resulting in the suppression of target gene expression (Cho et al., 2006b; Chen, 2007).We have previously isolated 10 rice (Oryza sativa) hexokinases, OsHXK1 through OsHXK10, and demonstrated that all of these subtypes possess hexokinase activity (Cho et al., 2006a). The results of this previous study showed that OsHXK4 and OsHXK7 reside in the chloroplast stroma and cytosol, respectively. Based on sequence similarity and subcellular localization, we have identified two rice hexokinases homologous to AtHXK1, OsHXK5 and OsHXK6. The subcellular localization of OsHXK5 and OsHXK6, observed with GFP fusion constructs, suggested that OsHXK5 and OsHXK6 retain a dual-targeting ability to mitochondria and nuclei. This finding prompted us to examine whether these homologues play a role in Glc sensing and signaling in rice. To address this question, we observed the function of OsHXK5 and OsHXK6 in mesophyll protoplasts of maize (Zea mays) and rice and in transgenic rice plants. In addition, we transformed the Arabidopsis gin2-1 mutant with either wild-type or catalytically inactive alleles of OsHXK5 and OsHXK6 and analyzed their sugar sensing and signaling characteristics. Finally, the conserved role of hexokinase as a Glc sensor in Arabidopsis and rice plants is discussed.