Molecular chaperones involved in chloroplast protein import

Characterization of a novel γ-type carbonic anhydrase, Sjγ-CA2, in Saccharina japonica: Insights into carbon concentration mechanism in macroalgae

Carbonic anhydrase (CA) is a crucial component of CO2-concentrating mechanism (CCM) in macroalgae. In Saccharina japonica, an important brown seaweed, 11 CAs, including 5 α-, 3 β-, and 3 γ-CAs, have been documented. Among them, one α-CA and one β-CA were localized in the periplasmic space, one α-CA was found in the chloroplast, and one γ-CA was situated in mitochondria. Notably, the known γ-CAs have predominantly been identified in mitochondria. In this study, we identified a chloroplastic γ-type CA, Sjγ-CA2, in S. japonica. Based on the reported amino acid sequence of Sjγ-CA2, the epitope peptide for monoclonal antibody production was selected as 165 Pro-305. After purification and specificity identification, anti-SjγCA2 monoclonal antibody was employed in immunogold electron microscopy. The results illustrated that Sjγ-CA2 was localized in the chloroplasts of both gametophytes and sporophytes of S. japonica. Subsequently, immunoprecipitation coupled with LC-MS/MS analysis revealed that Sjγ-CA2 mainly interacted with photosynthesis-related proteins. Moreover, the first 65 amino acids at N-terminal of Sjγ-CA2 was identified as the chloroplast transit peptide by the transient expression of GFP-SjγCA2 fused protein in tabacco. Real-time PCR results demonstrated an up-regulation of the transcription of Sjγ-CA2 gene in response to high CO2 concentration. These findings implied that Sjγ-CA2 might contribute to minimizing the leakage of CO2 from chloroplasts and help maintaining a high concentration of CO2 around Rubisco.

Molecular Bases of Heat Stress Responses in Vegetable Crops With Focusing on Heat Shock Factors and Heat Shock Proteins

The effects of the climate change including an increase in the average global temperatures, and abnormal weather events such as frequent and severe heatwaves are emerging as a worldwide ecological concern due to their impacts on plant vegetation and crop productivity. In this review, the molecular processes of plants in response to heat stress-from the sensing of heat stress, the subsequent molecular cascades associated with the activation of heat shock factors and their primary targets (heat shock proteins), to the cellular responses-have been summarized with an emphasis on the classification and functions of heat shock proteins. Vegetables contain many essential vitamins, minerals, antioxidants, and fibers that provide many critical health benefits to humans. The adverse effects of heat stress on vegetable growth can be alleviated by developing vegetable crops with enhanced thermotolerance with the aid of various genetic tools. To achieve this goal, a solid understanding of the molecular and/or cellular mechanisms underlying various responses of vegetables to high temperature is imperative. Therefore, efforts to identify heat stress-responsive genes including those that code for heat shock factors and heat shock proteins, their functional roles in vegetable crops, and also their application to developing vegetables tolerant to heat stress are discussed.

Novel high resolution melting (HRM) and snapback assays for simultaneous detection and differentiation of Plasmodium ovale spp

Plasmodium ovale spp. are two of the six species of apicomplexan parasites belonging to the genus Plasmodium commonly causing disease in humans. A recent phylogeny study has identified both Plasmodium ovale species (P. ovale curtisi and P. ovale wallikeri) as two sympatric occurring species. The actual prevalence and clinical relevance of P. ovale spp. are likely underestimated due to low parasitemia and mixed infections, which pose a major challenge to microscopic diagnosis and are frequently undetectable using malaria Rapid Diagnostic Tests (RDTs). The aim of this work is to develop a HRM-based assay for simultaneous detection and differentiation of P. ovale wallikeri and P. ovale curtisi. Thirty three well-documented P. ovale spp. samples from previous studies were used for this study. The newly developed High Resolution Melting (HRM) assay targeting the apicoplast genome was highly specific to both P. ovale species. Adding a snapback tail at the 5' end of the forward primer for a nested HRM PCR, increased the melting temperature (Tm) difference between the two species. To our knowledge this study reports the first direct HRM assay developed on the apicoplast genome, specific for both P. ovale species. This method provides added value to the WHO open request of developing new practical malaria diagnostic methods for the malaria elimination program and could contribute to a quick and efficient diagnosis of low-level parasitemia, symptomatic or asymptomatic, as well as mixed or single P. ovale infections.

Eukaryotic Hsp70 chaperones in the intermembrane space of chloroplasts

MAIN CONCLUSION

Multiple eukaryotic Hsp70 typically localized in the cytoplasm are also distributed to the intermembrane space of chloroplasts and might thereby represent the missing link in energizing protein translocation. Protein translocation into organelles is a central cellular process that is tightly regulated. It depends on signals within the preprotein and on molecular machines catalyzing the process. Molecular chaperones participate in transport and translocation of preproteins into organelles to control folding and to provide energy for the individual steps. While most of the processes are explored and the components are identified, the transfer of preproteins into and across the intermembrane space of chloroplasts is not yet understood. The existence of an energy source in this compartment is discussed, because the required transit peptide length for successful translocation into chloroplasts is shorter than that found for mitochondria where energy is provided exclusively by matrix chaperones. Furthermore, a cytosolic-type Hsp70 homologue was proposed as component of the chloroplast translocon in the intermembrane space energizing the initial translocation. The molecular identity of such intermembrane space localized Hsp70 remained unknown, which led to a controversy concerning its existence. We identified multiple cytosolic Hsp70s by mass spectrometry on isolated, thermolysin-treated Medicago sativa chloroplasts. The localization of these Hsp70s of M. sativa or Arabidopsis thaliana in the intermembrane space was confirmed by a self-assembly GFP-based in vivo system. The localization of cytosolic Hsp70s in the stroma of chloroplasts or different mitochondrial compartments could not be observed. Similarly, we could not identify any cytosolic Hsp90 in the intermembrane space of chloroplast. With respect to our results we discuss the possible targeting and function of the Hsp70 found in the intermembrane space.

GUN1, a Jack-Of-All-Trades in Chloroplast Protein Homeostasis and Signaling

The GENOMES UNCOUPLED 1 (GUN1) gene has been reported to encode a chloroplast-localized pentatricopeptide-repeat protein, which acts to integrate multiple indicators of plastid developmental stage and altered plastid function, as part of chloroplast-to-nucleus retrograde communication. However, the molecular mechanisms underlying signal integration by GUN1 have remained elusive, up until the recent identification of a set of GUN1-interacting proteins, by co-immunoprecipitation and mass-spectrometric analyses, as well as protein-protein interaction assays. Here, we review the molecular functions of the different GUN1 partners and propose a major role for GUN1 as coordinator of chloroplast translation, protein import, and protein degradation. This regulatory role is implemented through proteins that, in most cases, are part of multimeric protein complexes and whose precise functions vary depending on their association states. Within this framework, GUN1 may act as a platform to promote specific functions by bringing the interacting enzymes into close proximity with their substrates, or may inhibit processes by sequestering particular pools of specific interactors. Furthermore, the interactions of GUN1 with enzymes of the tetrapyrrole biosynthesis (TPB) pathway support the involvement of tetrapyrroles as signaling molecules in retrograde communication.

Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection

RNA viruses often depend on host factors for multiplication inside cells due to the constraints of their small genome size and limited coding capacity. One such factor that has been exploited by several plant and animal viruses is heat shock protein 70 (HSP70) family homologs which have been shown to play roles for different viruses in viral RNA replication, viral assembly, disassembly, and cell-to-cell movement. Using next generation sequence analysis, we reveal that several isoforms of Hsp70 and Hsc70 transcripts are induced to very high levels during cucumber necrosis virus (CNV) infection of Nicotiana benthamiana and that HSP70 proteins are also induced by at least 10-fold. We show that HSP70 family protein homologs are co-opted by CNV at several stages of infection. We have found that overexpression of Hsp70 or Hsc70 leads to enhanced CNV genomic RNA, coat protein (CP), and virion accumulation, whereas downregulation leads to a corresponding decrease. Hsc70-2 was found to increase solubility of CNV CP in vitro and to increase accumulation of CNV CP independently of viral RNA replication during coagroinfiltration in N. benthamiana. In addition, virus particle assembly into virus-like particles in CP agroinfiltrated plants was increased in the presence of Hsc70-2. HSP70 was found to increase the targeting of CNV CP to chloroplasts during infection, reinforcing the role of HSP70 in chloroplast targeting of host proteins. Hence, our findings have led to the discovery of a highly induced host factor that has been co-opted to play multiple roles during several stages of the CNV infection cycle.

IMPORTANCE

Because of the small size of its RNA genome, CNV is dependent on interaction with host cellular components to successfully complete its multiplication cycle. We have found that CNV induces HSP70 family homologs to a high level during infection, possibly as a result of the host response to the high levels of CNV proteins that accumulate during infection. Moreover, we have found that CNV co-opts HSP70 family homologs to facilitate several aspects of the infection process such as viral RNA, coat protein and virus accumulation. Chloroplast targeting of the CNV CP is also facilitated, which may aid in CNV suppression of host defense responses. Several viruses have been shown to induce HSP70 during infection and others to utilize HSP70 for specific aspects of infection such as replication, assembly, and disassembly. We speculate that HSP70 may play multiple roles in the infection processes of many viruses.

A census of nuclear cyanobacterial recruits in the plant kingdom

The plastids and mitochondria of the eukaryotic cell are of endosymbiotic origin. These events occurred ~2 billion years ago and produced significant changes in the genomes of the host and the endosymbiont. Previous studies demonstrated that the invasion of land affected plastids and mitochondria differently and that the paths of mitochondrial integration differed between animals and plants. Other studies examined the reasons why a set of proteins remained encoded in the organelles and were not transferred to the nuclear genome. However, our understanding of the functional relations of the transferred genes is insufficient. In this paper, we report a high-throughput phylogenetic analysis to identify genes of cyanobacterial origin for plants of different levels of complexity: Arabidopsis thaliana, Chlamydomonas reinhardtii, Physcomitrella patens, Populus trichocarpa, Selaginella moellendorffii, Sorghum bicolor, Oryza sativa, and Ostreococcus tauri. Thus, a census of cyanobacterial gene recruits and a study of their function are presented to better understand the functional aspects of plastid symbiogenesis. From algae to angiosperms, the GO terms demonstrated a gradual expansion over functionally related genes in the nuclear genome, beginning with genes related to thylakoids and photosynthesis, followed by genes involved in metabolism, and finally with regulation-related genes, primarily in angiosperms. The results demonstrate that DNA is supplied to the nuclear genome on a permanent basis with no regard to function, and only what is needed is kept, which thereby expands on the GO space along the related genes.

Quantitative analysis of the chloroplast molecular chaperone ClpC/Hsp93 in Arabidopsis reveals new insights into its localization, interaction with the Clp proteolytic core, and functional importance

The molecular chaperone ClpC/Hsp93 is essential for chloroplast function in vascular plants. ClpC has long been held to act both independently and as the regulatory partner for the ATP-dependent Clp protease, and yet this and many other important characteristics remain unclear. In this study, we reveal that of the two near-identical ClpC paralogs (ClpC1 and ClpC2) in Arabidopsis chloroplasts, along with the closely related ClpD, it is ClpC1 that is the most abundant throughout leaf maturation. An unexpectedly large proportion of both chloroplast ClpC proteins (30% of total ClpC content) associates to envelope membranes in addition to their stromal localization. The Clp proteolytic core is also bound to envelope membranes, the amount of which is sufficient to bind to all the similarly localized ClpC. The role of such an envelope membrane Clp protease remains unclear although it appears uninvolved in preprotein processing or Tic subunit protein turnover. Within the stroma, the amount of oligomeric ClpC protein is less than that of the Clp proteolytic core, suggesting most if not all stromal ClpC functions as part of the Clp protease; a proposal supported by the near abolition of Clp degradation activity in the clpC1 knock-out mutant. Overall, ClpC appears to function primarily within the Clp protease, as the principle stromal protease responsible for maintaining homeostasis, and also on the envelope membrane where it possibly confers a novel protein quality control mechanism for chloroplast preprotein import.

Proteomic analysis of differentially expressed proteins induced by salicylic acid in suspension-cultured ginseng cells

In this study, optimized 2-DE sample preparation methodologies were established for suspension-cultured ginseng cells. Three commonly used protein extraction methods (Trichloroacetic acid-acetone, urea/thiourea and phenol extraction method) were evaluated for proteomic analysis of suspension cultures of ginseng. A comparative analysis of suspension-cultured ginseng cells proteome induced by salicylic acid (SA) was reported. The results demonstrated that phenol extraction method was the best method based on protein extraction efficiency and the good quality of 2-DE patterns for suspension-cultured ginseng cells. Fifteen differentially expressed proteins induced by salicylic acid in suspension-cultured ginseng cells were identified by MALDI-TOF-MS. These identified proteins were involved in defense and stress response, energy metabolism, signal transduction/transcription, protein synthesis and metabolism, and photosynthesis. Chaperonin 60, related to defense responses, was more abundant in suspension-cultured ginseng cells after application of SA. Vacuolar ATPase subunit B was newly induced in SA treatment.

Molecular chaperone involvement in chloroplast protein import

Chloroplasts are organelles of endosymbiotic origin that perform essential functions in plants. They contain about 3000 different proteins, the vast majority of which are nucleus-encoded, synthesized in precursor form in the cytosol, and transported into the chloroplasts post-translationally. These preproteins are generally imported via envelope complexes termed TOC and TIC (Translocon at the Outer/Inner envelope membrane of Chloroplasts). They must navigate different cellular and organellar compartments (e.g., the cytosol, the outer and inner envelope membranes, the intermembrane space, and the stroma) before arriving at their final destination. It is generally considered that preproteins are imported in a largely unfolded state, and the whole process is energy-dependent. Several chaperones and cochaperones have been found to mediate different stages of chloroplast import, in similar fashion to chaperone involvement in mitochondrial import. Cytosolic factors such as Hsp90, Hsp70 and 14-3-3 may assist preproteins to reach the TOC complex at the chloroplast surface, preventing their aggregation or degradation. Chaperone involvement in the intermembrane space has also been proposed, but remains uncertain. Preprotein translocation is completed at the trans side of the inner membrane by ATP-driven motor complexes. A stromal Hsp100-type chaperone, Hsp93, cooperates with Tic110 and Tic40 in one such motor complex, while stromal Hsp70 is proposed to act in a second, parallel complex. Upon arrival in the stroma, chaperones (e.g., Hsp70, Cpn60, cpSRP43) also contribute to the folding, assembly or onward intraorganellar guidance of the proteins. In this review, we focus on chaperone involvement during preprotein translocation at the chloroplast envelope. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.

Heat shock response in photosynthetic organisms: membrane and lipid connections

The ability of photosynthetic organisms to adapt to increases in environmental temperatures is becoming more important with climate change. Heat stress is known to induce heat-shock proteins (HSPs) many of which act as chaperones. Traditionally, it has been thought that protein denaturation acts as a trigger for HSP induction. However, increasing evidence has shown that many stress events cause HSP induction without commensurate protein denaturation. This has led to the membrane sensor hypothesis where the membrane's physical and structural properties play an initiating role in the heat shock response. In this review, we discuss heat-induced modulation of the membrane's physical state and changes to these properties which can be brought about by interaction with HSPs. Heat stress also leads to changes in lipid-based signaling cascades and alterations in calcium transport and availability. Such observations emphasize the importance of membranes and their lipids in the heat shock response and provide a new perspective for guiding further studies into the mechanisms that mediate cellular and organismal responses to heat stress.

A Toxoplasma gondii mutant highlights the importance of translational regulation in the apicoplast during animal infection

Toxoplasma gondii is an obligate intracellular parasite of all warm-blooded animals. We previously described a forward genetic screen to identify T. gondii mutants defective in the establishment of a chronic infection. One of the mutants isolated was disrupted in the 3' untranslated region (3'UTR) of an orthologue of bacterial translation elongation factor G (EFG). The mutant does not have a growth defect in tissue culture. Genetic complementation of this mutant with the genomic locus of TgEFG restores virulence in an acute infection mouse model. Epitope tagged TgEFG localized to the apicoplast, via a non-canonical targeting signal, where it functions as an elongation factor for translation in the apicoplast. Comparisons of TgEFG expression constructs with wild-type or mutant 3'UTRs showed that a wild-type 3'UTR is necessary for translation of TgEFG. In tissue culture, the TgEFG transcript is equally abundant in wild-type and mutant parasites; however, during an animal infection, the TgEFG transcript is increased more than threefold in the mutant. These results highlight that in tissue culture, translation in the apicoplast can be diminished, but during an animal infection, translation in the apicoplast must be fully functional.

The motors of protein import into chloroplasts

Chloroplast function is largely dependent on its resident proteins, most of which are encoded by the nuclear genome and are synthesized in cytosol. Almost all of these are imported through the translocons located in the outer and inner chloroplast envelope membranes. The motor protein that provides the driving force for protein import has been proposed to be Hsp93, a member of the Hsp100 family of chaperones residing in the stroma. Combining in vivo and in vitro approaches, recent publications have provided multiple lines of evidence demonstrating that a stromal Hsp70 system is also involved in protein import into this organelle. Thus it appears that protein import into chloroplasts is driven by two motor proteins, Hsp93 and Hsp70. A perspective on collaboration between these two chaperones is discussed.

Insights into the Clp/HSP100 chaperone system from chloroplasts of Arabidopsis thaliana

HSP100 proteins are molecular chaperones involved in protein quality control. They assist in protein (un)folding, prevent aggregation, and are thought to participate in precursor translocation across membranes. Caseinolytic proteins ClpC and ClpD from plant chloroplasts belong to the HSP100 family. Their role has hitherto been investigated by means of physiological studies and reverse genetics. In the present work, we employed an in vitro approach to delve into the structural and functional characteristics of ClpC2 and ClpD from Arabidopsis thaliana (AtClpC2 and AtClpD). They were expressed in Escherichia coli and purified to near-homogeneity. The proteins were detected mainly as dimers in solution, and, upon addition of ATP, the formation of hexamers was observed. Both proteins exhibited basal ATPase activity (K(m), 1.42 mm, V(max), 0.62 nmol/(min × μg) for AtClpC2 and K(m) ∼19.80 mm, V(max) ∼0.19 nmol/(min × μg) for AtClpD). They were able to reactivate the activity of heat-denatured luciferase (∼40% for AtClpC2 and ∼20% for AtClpD). The Clp proteins tightly bound a fusion protein containing a model transit peptide. This interaction was detected by binding assays, where the chaperones were selectively trapped by the transit peptide-containing fusion, immobilized on glutathione-agarose beads. Association of HSP100 proteins to import complexes with a bound transit peptide-containing fusion was also observed in intact chloroplasts. The presented data are useful to understand protein quality control and protein import into chloroplasts in plants.

The apicomplexan plastid and its evolution

Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid-the apicoplast. Although its tiny genome and even the entire nuclear genome has been sequenced for several organisms bearing the organelle, the reason for its existence remains largely obscure. Some of the functions of the apicoplast, including housekeeping ones, are significantly different from those of other plastids, possibly due to the organelle's unique symbiotic origin.

Distinct regions at the N-terminus of the Cucumber necrosis virus coat protein target chloroplasts and mitochondria

Cucumber necrosis virus (CNV) is a spherical virus consisting of 180 identical coat protein (CP) subunits. The N-terminus of the CP subunit contains a 58aa RNA binding (R) domain and a 34aa arm that connects the R domain to the shell. These regions are known to play critical roles in virus assembly and disassembly. It has recently been shown that a region encompassing the arm can function as a chloroplast transit peptide (TP) in infected plants and that targeting may represent a means for virus particle disassembly. In this study, we further delineate the TP region and show that a 22aa sequence at the N-terminus of the shell enhances chloroplast targeting. We also demonstrate that R domain specifically co-localizes with mitochondria in agroinfiltrated plants. Deletion analyses show that the N-terminal 39 amino acids of the R domain are sufficient for mitochondrial targeting and that this region contains features typical of mitochondrial presequences. The R/arm region is found to be dually targeted to mitochondria and chloroplasts suggesting that this region of the CP plays a critical role in determining the fate of CP during the infection process.

Computational analysis of the evolution of 1-deoxy-D-xylulose-5-phosphate Reductoisomerase, an important enzyme in plant terpene biosynthesis

Isoprenoids are a highly diverse and important group of natural compounds. The enzyme 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) catalyzes a key regulatory step in the non-mevalonate isoprenoid biosynthetic pathway in eubacteria and in plant plastids. For example, in Artemisia annua DXR participates in regulation of the biosynthesis of artemisinin, an important antimalarial drug. We performed phylogenetic analysis using DXR protein sequences from a model prokaryote, Escherichia coli, a picoplanktonic alga, Ostreococcus lucimarinus, and higher plants. The functional domain of DXR was conserved, allowing molecular evolutionary comparisons of both prokaryotic and eukaryotic sequences of DXR. Despite this conservation, for some plant species such as Campthoteca acuminata and Arabidopsis thaliana, phylogenetic relationships of their lineages were consistently violated. Our analysis revealed that plant DXR has an N-terminal transit domain that is likely bipartite, consisting of a chloroplast transit peptide (cTP) and a lumen transit peptide (lTP). Several features observed in the lTP suggest that, while DXR is targeted to the chloroplast, it is localized to the thylakoid lumen. These features include a twin arginine motif, a hydrophobic region, and a proline-rich region. The transit peptide also showed putative motifs for a 14-3-3 binding site with a chaperone phosphorylation site at Thr.

Why chloroplasts and mitochondria contain genomes

Chloroplasts and mitochondria originated as bacterial symbionts. The larger, host cells acquired genetic information from their prokaryotic guests by lateral gene transfer. The prokaryotically-derived genes of the eukaryotic cell nucleus now function to encode the great majority of chloroplast and mitochondrial proteins, as well as many proteins of the nucleus and cytosol. Genes are copied and moved between cellular compartments with relative ease, and there is no established obstacle to successful import of any protein precursor from the cytosol. Yet chloroplasts and mitochondria have not abdicated all genes and gene expression to the nucleus and to cytosolic translation. What, then, do chloroplast- and mitochondrially-encoded proteins have in common that confers a selective advantage on the cytoplasmic location of their genes? The proposal advanced here is that co-location of chloroplast and mitochondrial genes with their gene products is required for rapid and direct regulatory coupling. Redox control of gene expression is suggested as the common feature of those chloroplast and mitochondrial proteins that are encoded in situ. Recent evidence is consistent with this hypothesis, and its underlying assumptions and predictions are described.

The TOC complex: preprotein gateway to the chloroplast

Photosynthetic eukaryotes strongly depend on chloroplast metabolic pathways. Most if not all involve nuclear encoded proteins. These are synthesized as cytosolic preproteins with N-terminal, cleavable targeting sequences (transit peptide). Preproteins are imported by a major pathway composed of two proteins complexes: TOC and TIC (Translocon of the Outer and Inner membranes of the Chloroplasts, respectively). These selectively recognize the preproteins and facilitate their transport across the chloroplast envelope. The TOC core complex consists of three types of components, each belonging to a small family: Toc34, Toc75 and Toc159. Toc34 and Toc159 isoforms represent a subfamily of the GTPase superfamily. The members of the Toc34 and Toc159 subfamily act as GTP-dependent receptors at the chloroplast surface and distinct members of each occur in defined, substrate-specific TOC complexes. Toc75, a member of the Omp85 family, is conserved from prokaryotes and functions as the unique protein-conducting channel at the outer membrane. In this review we will describe the current state of knowledge regarding the composition and function of the TOC complex.

A stromal heat shock protein 70 system functions in protein import into chloroplasts in the moss Physcomitrella patens

Heat shock protein 70s (Hsp70s) are encoded by a multigene family and are located in different cellular compartments. They have broad-ranging functions, including involvement in protein trafficking, prevention of protein aggregation, and assistance in protein folding. Hsp70s work together with their cochaperones, J domain proteins and nucleotide exchange factors (e.g., GrpEs), in a functional cycle of substrate binding and release accompanied by ATP hydrolysis. We have taken advantage of the gene targeting capability of the moss Physcomitrella patens to investigate the functions of chloroplast Hsp70s. We identified four Hsp70 genes and two GrpE cochaperone homolog genes (CGE) in moss that encode chloroplast proteins. Disruption of one of the Hsp70 genes, that for Hsp70-2, caused lethality, and protein import into heat-shocked chloroplasts isolated from temperature-sensitive hsp70-2 mutants was appreciably impaired. Whereas the double cge null mutant was not viable, we recovered a cge1 null/cge2 knock down mutant in which Hsp70-2 was upregulated. Chloroplasts isolated from this mutant demonstrated a defect in protein import. In addition, two different precursors staged as early import intermediates could be immunoprecipitated with an Hsp70-2-specific antibody. This immunoprecipitate also contained Hsp93 and Tic40, indicating that it represents a precursor still in the Toc/Tic translocon. Together, these data indicate that a stromal Hsp70 system plays a crucial role in protein import into chloroplasts.

Comparative analyses of the proteomes of leaves and flowers at various stages of development reveal organ-specific functional differentiation of proteins in soybean

The functional differentiation of protein networks in individual organs and tissues of soybean at various developmental stages was investigated by proteomic approach. Protein extraction by Mg/NP-40 buffer followed by alkaline phenol-based method was optimized for proteomic analysis. Proteome analyses of leaves at various developmental stages showed 26 differentially expressed proteins, wherein proteins in translocon at the outer/inner envelope membrane of chloroplast protein-transport machineries increased significantly at the first trifoliate. Immunoblot analysis showed chaperonin-60 expressed abundantly in young leaves, whereas HSP 70 and ATP-synthase beta were constitutively expressed in all tissues. The net photosynthesis rate and chlorophyll content showed an age-dependent correlation in leaves. These results suggest that proteins involved in carbon assimilation, folding and assembly, and energy may work synchronously and show a linear correlation to photosynthesis at developmental stages of leaves. Comparison of flower bud and flower proteome reveals 29 differentially expressed proteins, wherein proteins involved in mitochondrial protein transport and assembly, secondary metabolism, and pollen-tube growth were up-regulated during flower development. Together, these results suggest that during developmental stages, each type of tissue is associated with a specific group of proteins; wherein proteins involved in energy, sugar metabolism, and folding, assembly, and destination may play pivotal roles in the maturation process of each organ or tissue.

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 E1alpha-subunit of pyruvate dehydrogenase TP (E1alpha-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.

Comparative proteomic analysis of bacterial wilt susceptible and resistant tomato cultivars

To investigate the molecular mechanisms of bacterial resistance in susceptible and resistant cultivars of tomato, a proteomic approach was adopted. Four cultivars of tomato were selected on the basis of their response to bacterial (Pseudomonas solanacearum) inoculation wherein cultivar Roma and Riogarande, and cultivar Pusa Ruby and Pant Bahr were considered as resistant and susceptible cultivars, respectively. Proteins were extracted from leaves of 3-week-old seedlings of the four cultivars and separated by 2-DE. A total of nine proteins were found to be differentially expressed between the susceptible and resistant cultivars. Amino acid sequences of these proteins were determined with a protein sequencer. The identified proteins belongs to the categories of energy, protein destination and storage, and defense. Of these proteins, a 60kDa chaperonin and an apical membrane antigen were significantly upregulated in resistant cultivars compared with susceptible cultivars. Application of jasmonic acid and salicylic acid resulted in significant changes in levels of apical membrane antigen and protein disulfide-isomerase. Taken together, these results suggest that apical membrane antigen might be involved in bacterial resistance process through salicylic acid induced defense mechanism signaling in tomato plants.

Cellular pathology and histopathology of hypo-salinity exposure on the coral Stylophora pistillata

Coral reefs can experience extreme salinity changes, particularly hypo-salinity, as a result of storms, heavy rainy seasons (e.g., monsoons), and coastal runoff. Field and laboratory observations have documented that corals exposed to hypo-saline conditions can undergo extensive bleaching and mortality. There is controversy in the literature as to whether hypo-saline conditions induce a pathological response in corals, and if there is a relationship between decreasing salinity treatment and pathological responses. To test the hypothesis that hypo-salinity exposure does not have a pathological effect on coral, we used histological and cellular diagnostic methods to characterize the pathology in hypo-salinity-exposed corals. Colonies of Stylophora pistillata were exposed to five salinity concentrations [39 parts per thousand (ppt), 32 ppt, 28 ppt, 24 ppt, and 20 ppt] that may realistically occur on a reef. Histological examination indicated an increasing severity of pathomorphologies associated with decreasing salinity, including increased tissue swelling, degradation and loss of zooxanthellae, and tissue necrosis. Pulse-amplitude modulated chlorophyll fluorimetry kinetics demonstrated a decreasing photosynthetic efficiency with decreasing salinity conditions. Cytochrome P450 levels were affected by even slight changes in salinity concentration suggesting that detoxification pathways, as well as several endocrine pathways, may be adversely affected. Finally, these studies demonstrated that hypo-saline conditions can induce an oxidative-stress response in both the host and in its algal symbiont, and in so doing, may synergistically increase oxidative-stress burdens. As with other types of environmental stresses, exposure to hypo-saline conditions may have long-term consequences on coral physiology.

Mitochondrial and plastid evolution in eukaryotes: an outsiders' perspective

The eukaryotic organelles mitochondrion and plastid originated from eubacterial endosymbionts. Here we propose that, in both cases, prokaryote-to-organelle conversion was driven by the internalization of host-encoded factors progressing from the outer membrane of the endosymbionts towards the intermembrane space, inner membrane and finally the organelle interior. This was made possible by an outside-to-inside establishment in the endosymbionts of host-controlled protein-sorting components, which enabled the gradual integration of organelle functions into the nuclear genome. Such a convergent trajectory for mitochondrion and plastid establishment suggests a novel paradigm for organelle evolution that affects theories of eukaryogenesis.

Molecular characterization of cotton 14-3-3L gene preferentially expressed during fiber elongation

The 14-3-3 protein, highly conserved in all eukaryotic cells, is an important regulatory protein. It plays an important role in the growth, amplification, apoptosis, signal transduction, and other crucial life activities of cells. A cDNA encoding a putative 14-3-3 protein was isolated from cotton fiber cDNA library. The cDNA, designated as Gh14-3-3L (Gossypium hirsutum 14-3-3-like), is 1,029 bp in length (including a 762 bp long open reading frame and 5'-/3'-untranslated regions) and deduced a protein with 253 amino acids. The Gh14-3-3L shares higher homology with the known plant 14-3-3 proteins, and possesses the basic structure of 14-3-3 proteins: one dimeric domain, one phosphoralated-serine rich motif, four CC domains, and one EF Hand motif. Northern blotting analysis showed that Gh14-3-3L was predominantly expressed during early fiber development, and reached to the peak of expression in 10 days post anthers (DPA) fiber cells, suggesting that the gene may be involved in regulating fiber elongation. The gene is also expressed at higher level in both ovule and petal, but displays lower or undetectable level of activity in other tissues of cotton.

Revaluating the evolution of the Toc and Tic protein translocons

The origin of the plastid from a cyanobacterial endosymbiont necessitated the establishment of specialized molecular machines (translocons) to facilitate the import of nuclear-encoded proteins into the organelle. To improve our understanding of the evolution of the translocons at the outer and inner envelope membrane of chloroplasts (Toc and Tic, respectively), we critically reassess the prevalent notion that their subunits have a function exclusive to protein import. We propose that many translocon components are multifunctional, conserving ancestral pre-endosymbiotic properties that predate their recruitment into the primitive translocon (putatively composed of subunits Toc34, Toc75 and Tic110 and associated chaperones). Multifunctionality seems to be a hallmark of the Tic complex, in which protein import is integrated with a broad array of plastid processes.

Characterization of hemizygous deletions in citrus using array-comparative genomic hybridization and microsynteny comparisons with the poplar genome

BACKGROUND

Many fruit-tree species, including relevant Citrus spp varieties exhibit a reproductive biology that impairs breeding and strongly constrains genetic improvements. In citrus, juvenility increases the generation time while sexual sterility, inbreeding depression and self-incompatibility prevent the production of homozygous cultivars. Genomic technology may provide citrus researchers with a new set of tools to address these various restrictions. In this work, we report a valuable genomics-based protocol for the structural analysis of deletion mutations on an heterozygous background.

RESULTS

Two independent fast neutron mutants of self-incompatible clementine (Citrus clementina Hort. Ex Tan. cv. Clemenules) were the subject of the study. Both mutants, named 39B3 and 39E7, were expected to carry DNA deletions in hemizygous dosage. Array-based Comparative Genomic Hybridization (array-CGH) using a Citrus cDNA microarray allowed the identification of underrepresented genes in these two mutants. Subsequent comparison of citrus deleted genes with annotated plant genomes, especially poplar, made possible to predict the presence of a large deletion in 39B3 of about 700 kb and at least two deletions of approximately 100 and 500 kb in 39E7. The deletion in 39B3 was further characterized by PCR on available Citrus BACs, which helped us to build a partial physical map of the deletion. Among the deleted genes, ClpC-like gene coding for a putative subunit of a multifunctional chloroplastic protease involved in the regulation of chlorophyll b synthesis was directly related to the mutated phenotype since the mutant showed a reduced chlorophyll a/b ratio in green tissues.

CONCLUSION

In this work, we report the use of array-CGH for the successful identification of genes included in a hemizygous deletion induced by fast neutron irradiation on Citrus clementina. The study of gene content and order into the 39B3 deletion also led to the unexpected conclusion that microsynteny and local gene colinearity in this species were higher with Populus trichocarpa than with the phylogenetically closer Arabidopsis thaliana. This work corroborates the potential of Citrus genomic resources to assist mutagenesis-based approaches for functional genetics, structural studies and comparative genomics, and hence to facilitate citrus variety improvement.

Secretion without Golgi

A growing number of proteins devoid of signal peptides have been demonstrated to be released through the non-classical pathways independent of endoplasmic reticulum and Golgi. Among them are two potent proangiogenic cytokines FGF1 and IL1alpha. Stress-induced transmembrane translocation of these proteins requires the assembly of copper-dependent multiprotein release complexes. It involves the interaction of exported proteins with the acidic phospholipids of the inner leaflet of the cell membrane and membrane destabilization. Not only stress, but also thrombin treatment and inhibition of Notch signaling stimulate the export of FGF1. Non-classical release of FGF1 and IL1alpha presents a promising target for treatment of cardiovascular, oncologic, and inflammatory disorders.

Targeting of nucleus-encoded proteins to chloroplasts in plants

Most chloroplast proteins are encoded in the nucleus and synthesized on free, cytosolic ribosomes in precursor form. Each precursor has an amino-terminal extension called a transit peptide, which directs the protein through a post-translational targeting pathway and is removed upon arrival inside the organelle. This 'protein import' process is mediated by the coordinate action of two multiprotein complexes, one in each of the envelope membranes: the TOC and TIC (Translocon at the Outer/ Inner envelope membrane of Chloroplasts) machines. Many components of these complexes have been identified biochemically in pea; these include transit peptide receptors, channel proteins, and molecular chaperones. Intriguingly, the Arabidopsis genome encodes multiple, homologous genes for receptor components of the TOC complex. Careful analysis indicated that the different receptor isoforms operate in different import pathways with distinct precursor recognition specificities. These 'substrate-specific' import pathways might play a role in the differentiation of different plastid types, and/or act to prevent deleterious competition effects between abundant and nonabundant precursors. Until recently, all proteins destined for internal chloroplast compartments were thought to possess a cleavable transit peptide, and to engage the TOC/TIC machinery. New studies using proteomics and other approaches have revealed that this is far from true. Remarkably, a significant number of chloroplast proteins are transported via a pathway that involves the endoplasmic reticulum and Golgi apparatus. Other recent reports have elucidated an intriguing array of protein targeting routes leading to the envelope membranes themselves.

Chloroplast biogenesis: control of plastid development, protein import, division and inheritance

The chloroplast is a multi-copy cellular organelle that not only performs photosynthesis but also synthesizes amino acids, lipids and phytohormones. The plastid also responds to environmental stimuli such as gravitropism. Biogenesis of chloroplasts is initiated from proplastids in shoot meristems, and involves a series of important events. In the last decade, considerable progress has been made towards understanding various aspects of chloroplast biogenesis at the molecular level, via studies in model systems such as Arabidopsis. This review focuses on two important aspects of chloroplast biogenesis, synthesis/assembly and division/transmission. Chloroplasts originated through endosymbiosis from an ancestor of extant cyanobacteria, and thus contain their own genomes. DNA in chloroplasts is organized into complexes with proteins, and these are called nucleoids. The synthesis of chloroplast proteins is regulated at various steps. However, a majority of proteins are synthesized in the cytosol, and their proper import into chloroplast compartments is a prerequisite for chloroplast development. Fundamental aspects of plastid gene expression/regulation and chloroplast protein transport are described, together with recent proteome analyses of the organelle. Chloroplasts are not de novo synthesized, but instead are propagated from pre-existing plastids. In addition, plastids are transmitted from generation to generation with a unique mode of inheritance. Our current knowledge on the division machinery and the inheritance of plastids is described.

Transit peptide diversity and divergence: A global analysis of plastid targeting signals

Proteins are targeted to plastids by N-terminal transit peptides, which are recognized by protein import complexes in the organelle membranes. Historically, transit peptide properties have been defined from vascular plant sequences, but recent large-scale genome sequencing from the many plastid-containing lineages across the tree of life has provided a much broader representation of targeted proteins. This includes the three lineages containing primary plastids (plants and green algae, rhodophytes and glaucophytes) and also the seven major lineages that contain secondary plastids, "secondhand" plastids derived through eukaryotic endosymbiosis. Despite this extensive spread of plastids throughout Eukaryota, an N-terminal transit peptide has been maintained as an essential plastid-targeting motif. This article provides the first global comparison of transit peptide composition and summarizes conservation of some features, the loss of an ancestral motif from the green lineages including plants, and modifications to transit peptides that have occurred in secondary and even tertiary plastids.

The E3 ligase AtCHIP ubiquitylates FtsH1, a component of the chloroplast FtsH protease, and affects protein degradation in chloroplasts

The Arabidopsis E3 ligase AtCHIP was found to interact with FtsH1, a subunit of the chloroplast FtsH protease complex. FtsH1 can be ubiquitylated by AtCHIP in vitro, and the steady-state level of FtsH1 is reduced in AtCHIP-over-expressing plants under high-intensity light conditions, suggesting that the ubiquitylation of FtsH1 by AtCHIP might lead to the degradation of FtsH1 in vivo. Furthermore, the steady-state level of another subunit of the chloroplast FtsH protease complex, FtsH2, is also reduced in AtCHIP-over-expressing plants under high-intensity light conditions, and FtsH2 interacts physically with AtCHIP in vivo, suggesting the possibility that FtsH2 is also a substrate protein for AtCHIP in plant cells. A substrate of FtsH protease in vivo, the photosystem II reaction center protein D1, is not efficiently removed by FtsH in AtCHIP-over-expressing plants under high-intensity light conditions, supporting the assumption that FtsH subunits are substrates of AtCHIP in vivo, and that AtCHIP over-expression may lead to a reduced level of FtsH in chloroplasts. AtCHIP interacts with cytosolic Hsp70 and the precursors of FtsH1 and FtsH2 in the cytoplasm, and Hsp70 also interacts with FtsH1, and these protein-protein interactions appear to be increased under high-intensity light conditions, suggesting that Hsp70 might be partly responsible for the increased degradation of the substrates of Hsp70, such as FtsH1 and FtsH2, in AtCHIP-over-expressing plants under high-intensity light conditions. Therefore, AtCHIP, together with Hsp70, may play an important role in protein quality control in chloroplasts.

A substrate-independent, 14:3:3 protein-mediated plastid import pathway of NADPH:protochlorophyllide oxidoreductase A

Plastids are semiautonomous organelles that contain only limited coding information in their own DNA. Because most of their genome was transferred to the nucleus after their endosymbiotic origin, plastids must import the major part of their protein constituents from the cytosol. The exact role of cytosolic targeting factors in the regulation of plastid protein import has not been determined. Here, we report that the nucleus-encoded NADPH:protochlorophyllide (Pchlide) oxidoreductase A plastid precursor (pPORA) can use two different plastid import pathways that differ by the requirements for cytosolic 14:3:3 proteins and Hsp70. pPORA synthesized in a wheat germ lysate segregated into different precursor fractions. While import of free pPORA and only Hsp70-complexed pPORA was Pchlide-dependent and involved the previously identified Pchlide-dependent translocon, 14:3:3 protein- and Hsp70-complexed pPORA was transported into Pchlide-free chloroplasts through the Toc75-containing standard translocon at the outer chloroplast membrane/translocon at the inner chloroplast membrane machinery. A 14:3:3 protein binding site was identified in the mature region of the (35)S-pPORA, which governed 14:3:3 protein- and Hsp70-mediated, Pchlide-independent plastid import. Collectively, our results reveal that the import of pPORA into the plastids is tightly regulated and involves different cytosolic targeting factors and plastid envelope translocon complexes.

Chloroplast envelope membranes: a dynamic interface between plastids and the cytosol

Chloroplasts are bounded by a pair of outer membranes, the envelope, that is the only permanent membrane structure of the different types of plastids. Chloroplasts have had a long and complex evolutionary past and integration of the envelope membranes in cellular functions is the result of this evolution. Plastid envelope membranes contain a wide diversity of lipids and terpenoid compounds serving numerous biochemical functions and the flexibility of their biosynthetic pathways allow plants to adapt to fluctuating environmental conditions (for instance phosphate deprivation). A large body of knowledge has been generated by proteomic studies targeted to envelope membranes, thus revealing an unexpected complexity of this membrane system. For instance, new transport systems for metabolites and ions have been identified in envelope membranes and new routes for the import of chloroplast-specific proteins have been identified. The picture emerging from our present understanding of plastid envelope membranes is that of a key player in plastid biogenesis and the co-ordinated gene expression of plastid-specific protein (owing to chlorophyll precursors), of a major hub for integration of metabolic and ionic networks in cell metabolism, of a flexible system that can divide, produce dynamic extensions and interact with other cell constituents. Envelope membranes are indeed one of the most complex and dynamic system within a plant cell. In this review, we present an overview of envelope constituents together with recent insights into the major functions fulfilled by envelope membranes and their dynamics within plant cells.

Import and localisation of nucleoside diphosphate kinase 2 in chloroplasts

Nucleoside diphosphate kinases (NDPKs) are key enzymes that are involved in the homeostasis of nucleoside triphosphates (NTPs). Different isoforms exist, which are found in diverse cell compartments, for example the cytosol, mitochondria, and plant chloroplasts. NDPK2 of Pisum sativum has been shown to be localised in chloroplasts. Two forms of different size have been reported in plastids and it has been speculated that they function in distinct suborganellar compartments. We investigated the import behaviour and localisation of these two isoforms. Our results indicate that they do not differ in their route of entry into the organelle and both forms end up in the chloroplast stroma.

Protein export from Plasmodium parasites

Many prokaryotic and eukaryotic intracellular pathogens survive by altering the host cell through the export of proteins. In contrast to the well-studied prokaryotic export systems, knowledge of protein export in eukaryotic pathogens is scant. The recent discovery that a short protein sequence targets a protein for export from the malaria parasite Plasmodium falciparum has shed light on the possible mechanism of proteins export and has allowed the preliminary identification of several hundred exported proteins. Among the exported proteins are the members of the paralogous protein families, previously identified exported proteins and many uncharacterized proteins. The interaction of the parasite with the host cell is thus much more complex, and involves more parasite proteins, than previously thought.

Downregulation of ClpR2 leads to reduced accumulation of the ClpPRS protease complex and defects in chloroplast biogenesis in Arabidopsis

Plastids contain tetradecameric Clp protease core complexes, with five ClpP Ser-type proteases, four nonproteolytic ClpR, and two associated ClpS proteins. Accumulation of total ClpPRS complex decreased twofold to threefold in an Arabidopsis thaliana T-DNA insertion mutant in CLPR2 designated clpr2-1. Differential stable isotope labeling of the ClpPRS complex with iTRAQ revealed a fivefold reduction in assembled ClpR2 accumulation and twofold to fivefold reductions in the other subunits. A ClpR2:(his)(6) fusion protein that incorporated into the chloroplast ClpPRS complex fully complemented clpr2-1. The reduced accumulation of the ClpPRS protease complex led to a pale-green phenotype with delayed shoot development, smaller chloroplasts, decreased thylakoid accumulation, and increased plastoglobule accumulation. Stromal ClpC1 and 2 were both recruited to the thylakoid surface in clpr2-1. The thylakoid membrane of clpr2-1 showed increased carotenoid content, partial inactivation of photosystem II, and upregulated thylakoid proteases and stromal chaperones, suggesting an imbalance in chloroplast protein homeostasis and a well-coordinated network of proteolysis and chaperone activities. Interestingly, a subpopulation of PsaF and several light-harvesting complex II proteins accumulated in the thylakoid with unprocessed chloroplast transit peptides. We conclude that ClpR2 cannot be functionally replaced by other ClpP/R homologues and that the ClpPRS complex is central to chloroplast biogenesis, thylakoid protein homeostasis, and plant development.

Protein import into chloroplasts: an ever-evolving storyThis review is one of a selection of papers published in the Special Issue on Plant Cell Biology

Chloroplasts are but one type of a diverse group of essential organelles that distinguish plant cells and house many critical biochemical pathways, including photosynthesis. The biogenesis of plastids is essential to plant growth and development and relies on the targeting and import of thousands of nuclear-encoded proteins from the cytoplasm. The import of the vast majority of these proteins is dependent on translocons located in the outer and inner envelope membranes of the chloroplast, termed the Toc and Tic complexes, respectively. The core components of the Toc and Tic complexes have been identified within the last 12 years; however, the precise functions of many components are still being elucidated, and new components are still being identified. In Arabidopsis thaliana (and other species), many of the components are encoded by more than one gene, and it appears that the isoforms differentially associate with structurally distinct import complexes. Furthermore, it appears that these complexes represent functionally distinct targeting pathways, and the regulation of import by these separate pathways may play a role in the differentiation and specific functions of distinct plastid types during plant growth and development. This review summarizes these recent discoveries and emphasizes the mechanisms of differential Toc complex assembly and substrate recognition.

A proteomic approach to study pea (Pisum sativum) responses to powdery mildew (Erysiphe pisi)

As a global approach to gain a better understanding of the mechanisms involved in pea resistance to Erysiphe pisi, changes in the leaf proteome of two pea genotypes differing in their resistance phenotype were analyzed by a combination of 2-DE and MALDI-TOF/TOF MS. Leaf proteins from control non-inoculated and inoculated susceptible (Messire) and resistant (JI2480) plants were resolved by 2-DE, with IEF in the 5-8 pH range and SDS-PAGE on 12% gels. CBB-stained gels revealed the existence of quantitative and qualitative differences between extracts from: (i) non-inoculated leaves of both genotypes (77 spots); (ii) inoculated and non-inoculated Messire leaves (19 spots); and (iii) inoculated and non-inoculated JI2480 leaves (12 spots). Some of the differential spots have been identified, after MALDI-TOF/TOF analysis and database searching, as proteins belonging to several functional categories, including photosynthesis and carbon metabolism, energy production, stress and defense, protein synthesis and degradation and signal transduction. Results are discussed in terms of constitutive and induced elements involved in pea resistance against Erysiphe pisi.

Mechanisms of protein import and routing in chloroplasts

The vast majority of the approximately 3000 different proteins required to build a fully functional chloroplast are encoded by the nuclear genome and translated on cytosolic ribosomes. As chloroplasts are each surrounded by a double-membrane system, or envelope, sophisticated mechanisms are necessary to mediate the import of these nucleus-encoded proteins into chloroplasts. Once inside the organelle, many chloroplast proteins engage one of four additional protein sorting mechanisms that direct targeting to the internal thylakoid membrane system.