Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications

Subunits of the plastid ClpPR protease complex have differential contributions to embryogenesis, plastid biogenesis, and plant development in Arabidopsis

The plastid ClpPR protease complex in Arabidopsis thaliana consists of five catalytic ClpP and four noncatalytic ClpR subunits. An extensive analysis of the CLPR family and CLPP5 is presented to address this complexity. Null alleles for CLPR2 and CLPR4 showed delayed embryogenesis and albino embryos, with seedling development blocked in the cotyledon stage; this developmental block was overcome under heterotrophic conditions, and seedlings developed into small albino to virescent seedlings. By contrast, null alleles for CLPP5 were embryo lethal. Thus, the ClpPR proteins make different functional contributions. To further test for redundancies and functional differences between the ClpR proteins, we overexpressed full-length cDNAs for ClpR1, R2, R3, R4 in clpr1, clpr2 and clpr4 mutants. This showed that overexpression of ClpR3 can complement for the loss of ClpR1, but not for the loss of ClpR2 or ClpR4, indicating that ClpR3 can functionally substitute ClpR1. By contrast, ClpR1, R2 and R4 could not substitute each other. Double mutants of weak CLPR1 and 2 alleles were seedling lethal, showing that a minimum concentration of different ClpR proteins is essential for Clp function. Microscopy and large-scale comparative leaf proteome analyses of a CLPR4 null allele demonstrate a central role of Clp protease in chloroplast biogenesis and protein homeostasis; substrates are discussed. Lack of transcriptional and translational feedback regulation within the CLPPR gene family indicates that regulation of Clp activity occurs through Clp complex assembly and substrate delivery.

Multistep processing of an insertion sequence in an essential subunit of the chloroplast ClpP complex

In Chlamydomonas reinhardtii, the clpP1 chloroplast gene encoding one of the catalytic subunits of the ClpP protease complex contains a large in-frame insertion sequence (IS1). Based on the Escherichia coli ClpP structure, IS1 is predicted to protrude at the apical surface of the complex, likely influencing the interaction of the catalytic core with ClpC/HSP100 chaperones. Immunoblotting with an anti-ClpP1 antibody detected two immunoreactive forms of ClpP1: ClpP1(H) (59 kDa) and ClpP1(L) (25 kDa). It has been proposed that IS1 is a new type of protein intron (different from inteins). By studying transformants harboring mutations at the predicted borders of IS1 and tags at the C terminus of ClpP1 (tandem affinity purification tag, His tag, Strep.Tag) or within the IS1 sequence (3-hemagglutinin tag), we show that IS1 is not a protein intron and that ClpP1(L) results from endoproteolytic cleavage inside IS1. Processing sites have been identified in the middle of IS1 and near its C terminus. The sites can be mutated without abolishing processing.

Structure and function of a novel type of ATP-dependent Clp protease

The Clp protease is conserved among eubacteria and most eukaryotes, and uses ATP to drive protein substrate unfolding and translocation into a chamber of sequestered proteolytic active sites. The main constitutive Clp protease in photosynthetic organisms has evolved into a functionally essential and structurally intricate enzyme. The model Clp protease from the cyanobacterium Synechococcus consists of the HSP100 molecular chaperone ClpC and a mixed proteolytic core comprised of two distinct subunits, ClpP3 and ClpR. We have purified the ClpP3/R complex, the first for a Clp proteolytic core comprised of heterologous subunits. The ClpP3/R complex has unique functional and structural features, consisting of twin heptameric rings each with an identical ClpP3(3)ClpR(4) configuration. As predicted by its lack of an obvious catalytic triad, the ClpR subunit is shown to be proteolytically inactive. Interestingly, extensive modification to ClpR to restore proteolytic activity to this subunit showed that its presence in the core complex is not rate-limiting for the overall proteolytic activity of the ClpCP3/R protease. Altogether, the ClpP3/R complex shows remarkable similarities to the 20 S core of the proteasome, revealing a far greater degree of convergent evolution than previously thought between the development of the Clp protease in photosynthetic organisms and that of the eukaryotic 26 S proteasome.

Identification of new protein substrates for the chloroplast ATP-dependent Clp protease supports its constitutive role in Arabidopsis

The ATP-dependent Clp protease in plant chloroplasts consists of a heterogeneous proteolytic core containing multiple ClpP and ClpR paralogues. In this study, we have examined in detail the only viable knockout mutant to date of one of these subunits in Arabidopsis thaliana, ClpR1. Loss of ClpR1 caused a slow-growth phenotype, with chlorotic leaves during early development that later partially recovered upon maturity. Analysis of the Clp proteolytic core in the clpR1 mutant (clpR1-1) revealed approx. 10% of the wild-type levels remaining, probably due to a relative increase in the closely related ClpR3 protein and its partial substitution of ClpR1 in the core complex. A proteomic approach using an in organello proteolytic assay revealed 19 new potential substrates for the chloroplast Clp protease. Many of these substrates were constitutive enzymes involved in different metabolic pathways, including photosynthetic carbon fixation, nitrogen metabolism and chlorophyll/haem biosynthesis, whereas others function in housekeeping roles such as RNA maturation, protein synthesis and maturation, and recycling processes. In contrast, degradation of the stress-related chloroplast proteins Hsp21 (heat-shock protein 21) and lipoxygenase 2 was unaffected in the clpR1-1 line and thus not facilitated by the Clp protease. Overall, we show that the chloroplast Clp protease is principally a constitutive enzyme that degrades numerous stromal proteins, a feature that almost certainly underlies its vital importance for chloroplast function and plant viability.

NblA, a key protein of phycobilisome degradation, interacts with ClpC, a HSP100 chaperone partner of a cyanobacterial Clp protease

When cyanobacteria are starved for nitrogen, expression of the NblA protein increases and thereby induces proteolytic degradation of phycobilisomes, light-harvesting complexes of pigmented proteins. Phycobilisome degradation leads to a color change of the cells from blue-green to yellow-green, referred to as bleaching or chlorosis. As reported previously, NblA binds via a conserved region at its C terminus to the alpha-subunits of phycobiliproteins, the main components of phycobilisomes. We demonstrate here that a highly conserved stretch of amino acids in the N-terminal helix of NblA is essential for protein function in vivo. Affinity purification of glutathione S-transferase-tagged NblA, expressed in a Nostoc sp. PCC7120 mutant lacking wild-type NblA, resulted in co-precipitation of ClpC, encoded by open reading frame alr2999 of the Nostoc chromosome. ClpC is a HSP100 chaperone partner of the Clp protease. ATP-dependent binding of NblA to ClpC was corroborated by in vitro pull-down assays. Introducing amino acid exchanges, we verified that the conserved N-terminal motif of NblA mediates the interaction with ClpC. Further results indicate that NblA binds phycobiliprotein subunits and ClpC simultaneously, thus bringing the proteins into close proximity. Altogether these results suggest that NblA may act as an adaptor protein that guides a ClpC.ClpP complex to the phycobiliprotein disks in the rods of phycobilisomes, thereby initiating the degradation process.

Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels

Due to its unmatched resolution, gel electrophoresis is an indispensable tool for the analysis of diverse biomolecules. By adaptation of the electrophoretic conditions, even fragile protein complexes as parts of intracellular networks migrate through the gel matrix under sustainment of their integrity. If the thickness of such native gels is significantly increased compared to the analytical version, also high sample loads can be processed. However, the cage-like network obstructs an in-depth analysis for deciphering structure and function of protein complexes and other species. Consequently, the biomolecules have to be removed from the gel matrix into solution. Several approaches summarized in this review tackle this problem. While passive elution relies on diffusion processes, electroelution employs an electric field to force biomolecules out of the gel. An alternative procedure requires a special electrophoresis setup, the continuous elution device. In this apparatus, molecules migrate in the electric field until they leave the gel and were collected in a buffer stream. Successful isolation of diverse protein complexes like photosystems, ATP-dependent enzymes or active respiratory supercomplexes and some other bioparticles demonstrates the versatility of preparative electrophoresis. After liberating particles out of the gel cage, numerous applications are feasible. They include elucidation of the individual components up to high resolution structures of protein complexes. Therefore, preparative electrophoresis can complement standard purification methods and is in some cases superior to them.

Complexity of Hsp90 in organelle targeting

Heat shock protein 90 (Hsp90) is an abundant and highly conserved molecular chaperone. In Arabidopsis, the Hsp90 gene family consists of seven members. Here, we report that the AtHsp90-6 gene gives rise to two mRNA populations, termed AtHsp90-6L and AtHsp90-6S due to alternative initiation of transcription. The AtHsp90-6L and AtHsp90-6S transcription start sites are located 228 nucleotides upstream and 124 nucleotides downstream of the annotated translation start site, respectively. Both transcripts are detected under normal or heat-shock conditions. The inducibility of AtHsp90-6 mRNAs by heat shock implies a potential role of both isoforms in stress management. Stable transformation experiments with fusion constructs between the N-terminal part of each AtHsp90-6 isoform and green fluorescent protein indicated import of both fusion proteins into mitochondria. In planta investigation confirmed that fusion of the AtHsp90-5 N-terminus to green fluorescent protein (GFP) did result in specific chloroplastic localization. The mechanisms of regulation for mitochondria- and plastid-localized chaperone-encoding genes are not well understood. Future work is needed to address the possible roles of harsh environmental conditions and developmental processes on fine-tuning and compartmentalization of the AtHsp90-6L, AtHsp90-6S, and AtHsp90-5 proteins in Arabidopsis.

Proteomic analysis of S-nitrosylated proteins in Arabidopsis thaliana undergoing hypersensitive response

Nitric oxide (NO) has a fundamental role in the plant hypersensitive disease resistance response (HR), and S-nitrosylation is emerging as an important mechanism for the transduction of its bioactivity. A key step toward elucidating the mechanisms by which NO functions during the HR is the identification of the proteins that are subjected to this PTM. By using a proteomic approach involving 2-DE and MS we characterized, for the first time, changes in S-nitrosylated proteins in Arabidopsis thaliana undergoing HR. The 16 S-nitrosylated proteins identified are mostly enzymes serving intermediary metabolism, signaling and antioxidant defense. The study of the effects of S-nitrosylation on the activity of the identified proteins and its role during the execution of the disease resistance response will help to understand S-nitrosylation function and significance in plants.

A mutant impaired in the production of plastome-encoded proteins uncovers a mechanism for the homeostasis of isoprenoid biosynthetic enzymes in Arabidopsis plastids

The plastid-localized methylerythritol phosphate (MEP) pathway synthesizes the isoprenoid precursors for the production of essential photosynthesis-related compounds and hormones. We have identified an Arabidopsis thaliana mutant, rif1, in which posttranscriptional upregulation of MEP pathway enzyme levels is caused by the loss of function of At3g47450, a gene originally reported to encode a mitochondrial protein related to nitric oxide synthesis. However, we show that nitric oxide is not involved in the regulation of the MEP pathway and that the encoded protein is a plastid-targeted homolog of the Bacillus subtilis YqeH protein, a GTPase required for proper ribosome assembly. Consistently, in rif1 seedlings, decreased levels of plastome-encoded proteins were observed, with the exception of ClpP1, a catalytic subunit of the plastidial Clp protease complex. The unexpected accumulation of ClpP1 in plastids with reduced protein synthesis suggested a compensatory mechanism in response to decreased Clp activity levels. In agreement, a negative correlation was found between Clp protease activity and MEP pathway enzyme levels in different experiments, suggesting that Clp-mediated degradation of MEP pathway enzymes might be a mechanism used by individual plastids to finely adjust plastidial isoprenoid biosynthesis to their functional and physiological states.

Sorting signals, N-terminal modifications and abundance of the chloroplast proteome

Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins. Novel proteins include various kinases and putative nucleotide binding proteins. Based on repeated and independent MS based protein identifications requiring multiple matched peptide sequences, as well as literature, 916 nuclear-encoded proteins were assigned with high confidence to the plastid, of which 86% had a predicted chloroplast transit peptide (cTP). The protein abundance of soluble stromal proteins was calculated from normalized spectral counts from LTQ-Obitrap analysis and was found to cover four orders of magnitude. Comparison to gel-based quantification demonstrates that ‘spectral counting’ can provide large scale protein quantification for Arabidopsis. This quantitative information was used to determine possible biases for protein targeting prediction by TargetP and also to understand the significance of protein contaminants. The abundance data for 550 stromal proteins was used to understand abundance of metabolic pathways and chloroplast processes. We highlight the abundance of 48 stromal proteins involved in post-translational proteome homeostasis (including aminopeptidases, proteases, deformylases, chaperones, protein sorting components) and discuss the biological implications. N-terminal modifications were identified for a subset of nuclear- and chloroplast-encoded proteins and a novel N-terminal acetylation motif was discovered. Analysis of cTPs and their cleavage sites of Arabidopsis chloroplast proteins, as well as their predicted rice homologues, identified new species-dependent features, which will facilitate improved subcellular localization prediction. No evidence was found for suggested targeting via the secretory system. This study provides the most comprehensive chloroplast proteome analysis to date and an expanded Plant Proteome Database (PPDB) in which all MS data are projected on identified gene models.

Metabolic pathways of the wheat (Triticum aestivum) endosperm amyloplast revealed by proteomics

BACKGROUND

By definition, amyloplasts are plastids specialized for starch production. However, a proteomic study of amyloplasts isolated from wheat (Triticum aestivum Butte 86) endosperm at 10 days after anthesis (DPA) detected enzymes from many other metabolic and biosynthetic pathways. To better understand the role of amyloplasts in food production, the data from that study were evaluated in detail and an amyloplast metabolic map was outlined.

RESULTS

Analysis of 288 proteins detected in an amyloplast preparation predicted that 178 were amyloplast proteins. Criteria included homology with known plastid proteins, prediction of a plastid transit peptide for the wheat gene product or a close homolog, known plastid location of the pathway, and predicted plastid location for other members of the same pathway. Of these, 135 enzymes were arranged into 18 pathways for carbohydrate, lipid, amino acid, nucleic acid and other biosynthetic processes that are critical for grain-fill. Functions of the other proteins are also discussed.

CONCLUSION

The pathways outlined in this paper suggest that amyloplasts play a central role in endosperm metabolism. The interacting effects of genetics and environment on starch and protein production may be mediated in part by regulatory mechanisms within this organelle.

Expression of protein complexes and individual proteins upon transition of etioplasts to chloroplasts in pea (Pisum sativum)

The protein complexes of pea (Pisum sativum L.) etioplasts, etio-chloroplasts and chloroplasts were examined using 2D Blue Native/SDS-PAGE. The most prominent protein complexes in etioplasts were the ATPase and the Clp and FtsH protease complexes which probably have a crucial role in the biogenesis of etioplasts and chloroplasts. Also the cytochrome b(6)f (Cyt b(6)f) complex was assembled in the etioplast membrane, as well as Rubisco, at least partially, in the stroma. These complexes are composed of proteins encoded by both the plastid and nuclear genomes, indicating that a functional cross-talk exists between pea etioplasts and the nucleus. In contrast, the proteins and protein complexes that bind chlorophyll, with the PetD subunit and the entire Cyt b(6)f complex as an exception, did not accumulate in etioplasts. Nevertheless, some PSII core components such as PsbE and the luminal oxygen-evolvong complex (OEC) proteins PsbO and PsbP accumulated efficiently in etioplasts. After 6 h de-etiolation, a complete PSII core complex appeared with 40% of the maximal photochemical efficiency, but a fully functional PSII was recorded only after 24 h illumination. Similarly, the core complex of PSI was assembled after 6 h illumination, whereas the PSI-light-harvesting complex I was stably assembled only in chloroplasts illuminated for 24 h. Moreover, a battery of proteins responsible for defense against oxidative stress accumulated particularly in etioplasts, including the stromal and thylakoidal forms of ascorbate peroxidase, glutathione reductase and PsbS.

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.

Arabidopsis thaliana deficient in two chloroplast ascorbate peroxidases shows accelerated light-induced necrosis when levels of cellular ascorbate are low

Arabidopsis chloroplasts have a multi-layered defense against hydrogen peroxide (H(2)O(2)) that includes a stromal and thylakoid ascorbate peroxidase (sAPX and tAPX). Single and double null mutants in SAPX and TAPX (sapx and tapx) were each crossed with ascorbate deficient vtc2. The single, double and triple mutants did not show visual light stress phenotypes when grown at control or high light intensities (CL and HL; 120 and 1,000 micromol photons m(-2) s(-1)). Upon shift from CL to HL, mesophyll of expanded leaves of the triple mutant bleached within hours, with exclusion of the major vein areas; this contrasts to reported patterns of cell death under ozone treatment and calatase deficiency. tapx-vtc2 and sapx-vtc2, but not tapx-sapx or single mutants, showed limited bleaching. Bleaching and necrosis were accompanied by accumulation of H(2)O(2). Cellular concentrations of alpha-tocopherol, ascorbate and glutathione showed dramatic increase in response to HL in all eight genotypes and the four vtc2 genotypes accumulated more glutathione under CL than the others. Transcript analysis of other ROS responsive genes in vtc2 and the triple mutant showed up to 20-fold induction after transition to HL, generally irrespective of genotype. We conclude that chloroplast APX proteins in Arabidopsis can be effectively compensated by other endogenous H(2)O(2) detoxification systems, but that low cellular ascorbate levels in absence of chloroplast APX activity are detrimental to the cell during excess light.

ClpP: a distinctive family of cylindrical energy-dependent serine proteases

Processes maintaining protein homeostasis in the cell are governed by the activities of molecular chaperones that mainly assist in the folding of polypeptide chains and by a large class of proteases that regulate protein levels through degradation. ClpP proteases define a distinctive family of cylindrical, energy-dependent serine proteases that are highly conserved throughout bacteria and eukaryota. They typically interact with ATP-dependent AAA+ chaperones that bind and unfold target substrates and then translocate them into ClpP for degradation. Structural and functional studies have provided a detailed view of the mechanism of function of this class of proteases.

Chaperones and proteases--guardians of protein integrity in eukaryotic organelles

Organelles like mitochondria, chloroplasts, or the endoplasmic reticulum are essential subcompartments of eukaryotic cells that fulfill important metabolic tasks. Organellar protein homeostasis is maintained by a combination of specific protein biogenesis processes and protein quality control (PQC) mechanisms that together guarantee the functional state of the organelle. According to their endosymbiontic origin, mitochondria and chloroplasts contain internal PQC systems that consist of a cooperative network of molecular chaperones and proteases. In contrast, the endoplasmic reticulum employs the main cytosolic degradation machinery, the proteasome, for the removal of damaged or misfolded proteins. Here we present and discuss recent experimental insights into the molecular mechanisms underlying organellar PQC processes.

Distinctive types of ATP-dependent Clp proteases in cyanobacteria

Cyanobacteria are the only prokaryotes that perform oxygenic photosynthesis and are thought to be ancestors to plant chloroplasts. Like chloroplasts, cyanobacteria possess a diverse array of proteolytic enzymes, with one of the most prominent being the ATP-dependent Ser-type Clp protease. The model Clp protease in Escherichia coli consists of a single ClpP proteolytic core flanked on one or both ends by a HSP100 chaperone partner. In comparison, cyanobacteria have multiple ClpP paralogs plus a ClpP variant (ClpR), which lacks the catalytic triad typical of Ser-type proteases. In this study, we reveal that two distinct soluble Clp proteases exist in the unicellular cyanobacterium Synechococcus elongatus. Each protease consists of a unique proteolytic core comprised of two separate Clp subunits, one with ClpP1 and ClpP2, the other with ClpP3 and ClpR. Each core also associates with a particular HSP100 chaperone partner, ClpC in the case of the ClpP3/R core, and ClpX for the ClpP1/P2 core. The two adaptor proteins, ClpS1 and ClpS2 also interact with the ClpC chaperone protein, likely increasing the range of protein substrates targeted by the Clp protease in cyanobacteria. We also reveal the possible existence of a third Clp protease in Synechococcus, one which associates with the internal membrane network. Altogether, we show that presence of several distinctive Clp proteases in cyanobacteria, a feature which contrasts from that in most other organisms.

An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in plastid development

The ATP-dependent Clp protease has been well-characterized in Escherichia coli, but knowledge of its function in higher plants is limited. In bacteria, this two-component protease consists of a Ser-type endopeptidase ClpP, which relies on the ATP-dependent unfolding activity from an Hsp100 molecular chaperone to initiate protein degradation. In the chloroplasts of higher plants, multiple isoforms of the proteolytic subunit exist, with Arabidopsis having five ClpPs and four ClpP-like proteins termed ClpR predicted in its genome. In this work we characterized an Arabidopsis mutant impaired in one subunit of the chloroplast-localized Clp protease core, ClpR1. clpR1-1, a virescent mutant, carries a pre-mature stop codon in the clpR1 gene, resulting in no detectable ClpR1 protein. The accumulation of several chloroplast proteins, as well as most of the chloroplast-localized Clp protease subunits, is inhibited in clpR1-1. Unexpectedly, some plastid-encoded proteins do not accumulate, although their transcripts accumulate to wild-type levels. Maturation of 23S and 4.5S chloroplast ribosomal RNA (cp-rRNA) is delayed in clpR1-1, and both RNAs accumulate as higher molecular weight precursors. Also, chloroplasts in clpR1-1 are smaller than in wild type and have fewer thylakoid membranes with smaller grana stacks. We propose that a ClpR1-containing activity is required for chloroplast development and differentiation and in its absence both are delayed.

The chloroplast protease subunit ClpP4 is a substrate of the E3 ligase AtCHIP and plays an important role in chloroplast function

Animal CHIP proteins are chaperone-dependent E3 ubiquitin ligases that physically interact with Hsp70, Hsp90 and proteasome, promoting degradation of a selective group of non-native or damaged proteins in animal cells. The plant CHIP-like protein, AtCHIP, also plays important roles in protein turnover metabolism. AtCHIP interacts with a proteolytic subunit, ClpP4, of the chloroplast Clp protease in vivo, and ubiquitylates ClpP4 in vitro. The steady-state level of ClpP4 is reduced in AtCHIP-overexpressing plants under high-intensity light conditions, suggesting that AtCHIP targets ClpP4 for degradation and thereby regulates the Clp proteolytic activity in chloroplasts under certain stress conditions. Overexpression of ClpP4 in Arabidopsis leads to chlorotic phenotypes in transgenic plants, and chloroplast structures in the chlorotic tissues of ClpP4-overexpressing plants are abnormal and largely devoid of thylakoid membranes, suggesting that ClpP4 plays a critical role in chloroplast structure and function. As AtCHIP is a cytosolic protein that has been shown to play an important role in regulating an essential chloroplast protease, this research provides new insights into the regulatory networks controlling protein turnover catabolism in chloroplasts.

Analyses of the secretomes of Erwinia amylovora and selected hrp mutants reveal novel type III secreted proteins and an effect of HrpJ on extracellular harpin levels

SUMMARY Erwinia amylovora is a plant pathogenic enterobacterium that causes fire blight disease of apple, pear and other rosaceous plants. A type III (T3) secretion system, encoded by clustered, chromosomal hrp genes (hypersensitive response and pathogenicity), is essential for infection, but only a few proteins are known that are secreted through this pathway (the T3 'secretome'). We developed an efficient protocol for purification and concentration of extracellular proteins and used it to characterize the T3 secretome of E. amylovora Ea273 by comparing preparations from the wild-type strain with those from mutants defective in hrp secretion, regulation, or in genes encoding putative T3-secreted proteins. Proteins were resolved by gel electrophoresis and identified using mass spectrometry and a draft sequence of the E. amylovora genome. Twelve T3-secreted proteins were identified, including homologues of known effector and helper proteins, and HrpJ, a homologue of YopN of Yersinia pestis. Several previously uncharacterized T3-secreted proteins were designated as Eops for Erwinia outer proteins. Analysis of the secretome of a non-polar hrpJ mutant demonstrated that HrpJ is required for accumulation of wild-type levels of secreted harpins. HrpJ was found to be essential for pathogenesis, and to play a major role in elicitation of the hypersensitive reaction in tobacco.

The Arabidopsis ClpB/Hsp100 family of proteins: chaperones for stress and chloroplast development

The Casein lytic proteinase/heat shock protein 100 (Clp/Hsp100) proteins are chaperones that act to remodel/disassemble protein complexes and/or aggregates using the energy of ATP. In plants, one of the best-studied proteins from this family is cytosolic ClpB1 (At1g74310), better known in Arabidopsis as AtHsp101, which is a heat shock protein required for acclimation to high temperatures. Three other ClpB homologues have been identified in the Arabidopsis genome (ClpB2, ClpB3 and ClpB4; At4g14670, At5g15450 and At2g25140). To define further the roles of these chaperones in plants we investigated their intracellular localization, evolutionary relationships, patterns of expression and the phenotypes of corresponding T-DNA insertion mutants. We first found that ClpB2 was misannotated; there is no functional ClpB/Hsp100 gene at this locus. By fusing the putative transit peptides of ClpB3 and ClpB4 with GFP, we showed that these proteins are targeted to the chloroplast and mitochondrion, respectively, and we therefore designated them as ClpB-p and ClpB-m. Phylogenetic analysis supports two major lineages of ClpB proteins in plants, an 'eukaryotic', cytosol/nuclear-localized group containing AtHsp101, and an organelle-localized lineage, containing both ClpB-p and ClpB-m. Although AtHsp101, ClpB-p and ClpB-m transcripts all accumulate dramatically at high temperatures, the T-DNA insertion mutants of ClpB-p and ClpB-m show no evidence of seedling heat stress phenotypes similar to those observed in AtHsp101 mutants. Strikingly, ClpB-p knockouts were seedling lethals, failing to accumulate chlorophyll or properly develop chloroplasts. Thus, in plants, the function of ClpB/Hsp100 proteins is not restricted to heat stress, but a specific member of the family provides housekeeping functions that are essential to chloroplast development.

A nuclear-encoded ClpP subunit of the chloroplast ATP-dependent Clp protease is essential for early development in Arabidopsis thaliana

ClpP4 is a nuclear-encoded plastid protein that functions as a proteolytic subunit of the ATP-dependent Clp protease of higher plants. Given the lack of viable clpP4 knockout mutants, antisense clpP4 repression lines were prepared to study the functional importance of ClpP4 in Arabidopsis thaliana. Screening of transformants revealed viable lines with up to 90% loss of wild type levels of ClpP4 protein, while those with > 90% were severely bleached and strongly retarded in vegetative growth, failing to reach reproductive maturity. Of the viable antisense plants, repression of clpP4 expression produced a pleiotropic phenotype, of which slow growth and leaf variegation were most prominent. Chlorosis was most severe in younger leaves, with the affected regions localized around the mid-vein and exhibiting impaired chloroplast development and mesophyll cell differentiation. Chlorosis lessened during leaf expansion until all had regained the wild type appearance upon maturity. This change in phenotype correlated with the developmental expression of ClpP4 in the wild type, in which ClpP4 was less abundant in mature leaves due to post-transcriptional/translational regulation. Repression of ClpP4 caused a concomitant down-regulation of other nuclear-encoded ClpP paralogs in the antisense lines, but no change in other chloroplast-localized Clp proteins. Greening of the young chlorotic antisense plants upon maturation was accelerated by increased light, either by longer photoperiod or by higher growth irradiance; conditions that both raised levels of ClpP4 in wild type leaves. In contrast, shift to low growth irradiance decreased the relative amount of ClpP4 in wild type leaves, and caused newly developed leaves of fully greened antisense lines to regain the chlorotic phenotype.

An Arabidopsis chloroplast-targeted Hsp101 homologue, APG6, has an essential role in chloroplast development as well as heat-stress response

Analysis of albino or pale-green (apg) mutants is important for identifying nuclear genes responsible for chloroplast development and pigment synthesis. We have identified 38 apg mutants by screening 11 000 Arabidopsis Ds-tagged lines. One mutant, apg6, contains a Ds insertion in a gene encoding APG6 (ClpB3), a homologue of the heat-shock protein Hsp101 (ClpB1). We isolated somatic revertants and identified two Ds-tagged and one T-DNA-tagged mutant alleles of apg6. All three alleles gave the same pale-green phenotype. These results suggest that APG6 is important for chloroplast development. The APG6 protein contains a transit peptide and is localized in chloroplasts. The plastids of apg6 pale-green cells were smaller than those of the wild type, and contained undeveloped thylakoid membranes. APG6 mRNA accumulated in response to heat shock in various organs, but not in response to other abiotic stresses. Under normal conditions, APG6 is constitutively expressed in the root tips, the organ boundary region, the reproductive tissues of mature plants where plastids exist as proplastids, and slightly in the stems and leaves. In addition, constitutive overexpression of APG6 in transgenic plants inhibited chloroplast development and resulted in a mild pale-green phenotype. The amounts of chloroplast proteins related to photosynthesis were markedly decreased in apg6 mutants. These results suggest that APG6 functions as a molecular chaperone involved in plastid differentiation mediating internal thylakoid membrane formation and conferring thermotolerance to chloroplasts during heat stress. The APG6 protein is not only involved in heat-stress response in chloroplasts, but is also essential for chloroplast development.

Cross genome comparisons of serine proteases in Arabidopsis and rice

Background

Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. The availability of Arabidopsis thaliana and rice (Oryza sativa) genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species.

Results

Despite the differences in genome sizes between Arabidopsis and rice, we identified a very similar number of serine protease-like proteins in the two plant species (206 and 222, respectively). Nearly 40% of the above sequences were identified as potential orthologues. Atypical members could be identified in the plant genomes for Deg, Clp, Lon, rhomboid proteases and species-specific members were observed for the highly populated subtilisin and serine carboxypeptidase families suggesting multiple lateral gene transfers. DegP proteases, prolyl oligopeptidases, Clp proteases and rhomboids share a significantly higher percentage orthology between the two genomes indicating substantial evolutionary divergence was set prior to speciation. Single domain architectures and paralogues for several putative subtilisins, serine carboxypeptidases and rhomboids suggest they may have been recruited for additional roles in secondary metabolism with spatial and temporal regulation. The analysis reveals some domain architectures unique to either or both of the plant species and some inactive proteases, like in rhomboids and Clp proteases, which could be involved in chaperone function.

Conclusion

The systematic analysis of the serine protease-like proteins in the two plant species has provided some insight into the possible functional associations of previously uncharacterised serine protease-like proteins. Further investigation of these aspects may prove beneficial in our understanding of similar processes in commercially significant crop plant species.

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.

Detection and analysis of protein–protein interactions in organellar and prokaryotic proteomes by native gel electrophoresis: (Membrane) protein complexes and supercomplexes

It is an essential and challenging task to unravel protein-protein interactions in their actual in vivo context. Native gel systems provide a separation platform allowing the analysis of protein complexes on a rather proteome-wide scale in a single experiment. This review focus on blue-native (BN)-PAGE as the most versatile and successful gel-based approach to separate soluble and membrane protein complexes of intricate protein mixtures derived from all biological sources. BN-PAGE is a charge-shift method with a running pH of 7.5 relying on the gentle binding of anionic CBB dye to all membrane and many soluble protein complexes, leading to separation of protein species essentially according to their size and superior resolution than other fractionation techniques can offer. The closely related colorless-native (CN)-PAGE, whose applicability is restricted to protein species with intrinsic negative net charge, proved to provide an especially mild separation capable of preserving weak protein-protein interactions better than BN-PAGE. The essential conditions determining the success of detecting protein-protein interactions are the sample preparations, e.g. the efficiency/mildness of the detergent solubilization of membrane protein complexes. A broad overview about the achievements of BN- and CN-PAGE studies to elucidate protein-protein interactions in organelles and prokaryotes is presented, e.g. the mitochondrial protein import machinery and oxidative phosphorylation supercomplexes. In many cases, solubilization with digitonin was demonstrated to facilitate an efficient and particularly gentle extraction of membrane protein complexes prone to dissociation by treatment with other detergents. In general, analyses of protein interactomes should be carried out by both BN- and CN-PAGE.

Recent advances in the study of Clp, FtsH and other proteases located in chloroplasts

Several chloroplast proteases have been characterized in recent years. The ATP-dependent chloroplast proteases Clp and FtsH stand out because they form multi-subunit complexes consisting of different gene products. Surprisingly, both green and non-green plastids appear to contain a similar soluble Clp core proteolytic complex, consisting of five ClpP proteases, their non-catalytic ClpR homologs, and two ClpS homologs that have unknown function. Analyses of single and double FtsH1, FtsH2, FtsH5 and FtsH8 mutants, and overexpression of FtsH proteins in these Arabidopsis thaliana mutants show partial redundancies within pairs of closely related FtsH thylakoid proteins. The presence of at least one member of each pair is essential for functional accumulation. Other chloroplast proteases have also been identified recently. Future challenges include the identification of substrate recognition mechanisms and elucidating the role of proteases in chloroplast biogenesis and function.

Protein degradation machineries in plastids

Plastids undergo drastic morphological and physiological changes under different developmental stages and in response to environmental conditions. A key to accomplishing these transitions and maintaining homeostasis is the quality and quantity control of many plastid proteins by proteases and chaperones. Although a limited number of plastid proteases have been identified by biochemical approaches, recent progress in genome information revealed various plant proteases that are of prokaryotic origin and that are localized in chloroplasts. Of these, ATP-dependent proteases such as Clp, FtsH, and Lon are considered the major enzymes involved in processive degradation (gradual degradation to oligopeptides and amino acids). The basic architecture of plant ATP-dependent proteases is very similar to the architechture of bacterial enzymes, such as those in Escherichia coli, but plastid enzymes apparently have extraordinary numbers of isomers. Recent molecular genetic characterization in Arabidopsis has identified differential roles of these isomers. This review covers what is currently known about the types and function of plastid proteases together with our new observations.

The chloroplast ClpP complex in Chlamydomonas reinhardtii contains an unusual high molecular mass subunit with a large apical domain

The composition of the chloroplast-localized protease complex, ClpP, from the green alga Chlamydomonas reinhardtii was characterized by nondenaturing electrophoresis, immunoblotting and MS. The detected ClpP complex has a native mass of approximately 540 kDa, which is approximately 200 kDa higher than ClpP complexes in higher plant chloroplasts, mitochondria or bacteria. The 540-kDa ClpP complex contains two nuclear-encoded ClpP proteins (ClpP3 and P5) and five ClpR (R1, R2, R3, R4 and R6) proteins, as well two proteins, ClpP1L and ClpP1H, both probably derived from the plastid clpP1 gene. ClpP1H is 59 kDa and contains a approximately 30-kDa insertion sequence (IS1) not found in other ClpP proteins, responsible for the high MW of the complex. Based on comparison with other sequences, IS1 protrudes as an additional domain on the apical surface of the ClpP/R complex, probably preventing interaction with the HSP100 chaperone. ClpP1L is a 25-kDa protein similar in size to other ClpP proteins and could arise by post-translational processing of ClpP1H. Chloramphenicol-chase experiments show that ClpP1L and ClpP1H have a similar half-life, indicating that both are stable components of the complex. The structure of the ClpP complex is further discussed in conjunction with a phylogenetic analysis of the ClpP/R genes. A model is proposed for the evolution of the algal and plant complex from its cyanobacterial ancestor.

Functional differentiation of bundle sheath and mesophyll maize chloroplasts determined by comparative proteomics

Chloroplasts of maize (Zea mays) leaves differentiate into specific bundle sheath (BS) and mesophyll (M) types to accommodate C4 photosynthesis. Consequences for other plastid functions are not well understood but are addressed here through a quantitative comparative proteome analysis of purified M and BS chloroplast stroma. Three independent techniques were used, including cleavable stable isotope coded affinity tags. Enzymes involved in lipid biosynthesis, nitrogen import, and tetrapyrrole and isoprenoid biosynthesis are preferentially located in the M chloroplasts. By contrast, enzymes involved in starch synthesis and sulfur import preferentially accumulate in BS chloroplasts. The different soluble antioxidative systems, in particular peroxiredoxins, accumulate at higher levels in M chloroplasts. We also observed differential accumulation of proteins involved in expression of plastid-encoded proteins (e.g., EF-Tu, EF-G, and mRNA binding proteins) and thylakoid formation (VIPP1), whereas others were equally distributed. Enzymes related to the C4 shuttle, the carboxylation and regeneration phase of the Calvin cycle, and several regulators (e.g., CP12) distributed as expected. However, enzymes involved in triose phosphate reduction and triose phosphate isomerase are primarily located in the M chloroplasts, indicating that the M-localized triose phosphate shuttle should be viewed as part of the BS-localized Calvin cycle, rather than a parallel pathway.

The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts

This study presents an analysis of the stromal proteome in its oligomeric state extracted from highly purified chloroplasts of Arabidopsis thaliana. 241 proteins (88% with predicted cTP), mostly assembled in oligomeric complexes, were identified by mass spectrometry with emphasis on distinguishing between paralogues. This is critical because different paralogues in a gene family often have different subcellular localizations and/or different expression patterns and functions. The native protein masses were determined for all identified proteins. Comparison with the few well characterized stromal complexes from A. thaliana confirmed the accuracy of the native mass determination, and by extension, the usefulness of the native mass data for future in-depth protein interaction studies. Resolved protein interactions are discussed and compared with an extensive collection of native mass data of orthologues in other plants and bacteria. Relative protein expression levels were estimated from spot intensities and also provided estimates of relative concentrations of individual proteins. No such quantification has been reported so far. Surprisingly proteins dedicated to chloroplast protein synthesis, biogenesis, and fate represented nearly 10% of the total stroma protein mass. Oxidative pentose phosphate pathway, glycolysis, and Calvin cycle represented together about 75%, nitrogen assimilation represented 5-7%, and all other pathways such as biosynthesis of e.g. fatty acids, amino acids, nucleotides, tetrapyrroles, and vitamins B(1) and B(2) each represented less than 1% of total protein mass. Several proteins with diverse functions outside primary carbon metabolism, such as the isomerase ROC4, lipoxygenase 2 involved in jasmonic acid biosynthesis, and a carbonic anhydrase (CA1), were surprisingly abundant in the range of 0.75-1.5% of the total stromal mass. Native images with associated information are available via the Plastid Proteome Database.

Two novel targeting peptide degrading proteases, PrePs, in mitochondria and chloroplasts, so similar and still different

Two novel metalloproteases from Arabidopsis thaliana, termed AtPrePI and AtPrePII, were recently identified and shown to degrade targeting peptides in mitochondria and chloroplasts using an ambiguous targeting peptide. AtPrePI and AtPrePII are classified as dually targeted proteins as they are targeted to both mitochondria and chloroplasts. Both proteases harbour an inverted metal binding motif and belong to the pitrilysin subfamily A. Here we have investigated the subsite specificity of AtPrePI and AtPrePII by studying their proteolytic activity against the mitochondrial F(1)beta pre-sequence, peptides derived from the F(1)beta pre-sequence as well as non-mitochondrial peptides and proteins. The degradation products were analysed, identified by MALDI-TOF spectrometry and superimposed on the 3D structure of the F(1)beta pre-sequence. AtPrePI and AtPrePII cleaved peptides that are in the range of 10 to 65 amino acid residues, whereas folded or longer unfolded peptides and small proteins were not degraded. Both proteases showed preference for basic amino acids in the P(1) position and small, uncharged amino acids or serine residues in the P'(1) position. Interestingly, both AtPrePI and AtPrePII cleaved almost exclusively towards the ends of the alpha-helical elements of the F(1)beta pre-sequence. However, AtPrePI showed a preference for the N-terminal amphiphilic alpha-helix and positively charged amino acid residues and degraded the F(1)beta pre-sequence into 10-16 amino acid fragments, whereas AtPrePII did not show any positional preference and degraded the F(1)beta pre-sequence into 10-23 amino acid fragments. In conclusion, despite the high sequence identity between AtPrePI and AtPrePII and similarities in cleavage specificities, cleavage site recognition differs for both proteases and is context and structure dependent.

Plant serine proteases: biochemical, physiological and molecular features

In the latest two decades, the interest received by plant proteases has been on the rise. Serine proteases (EC 3.4.21)-in particular those from cucurbits, cereals and trees-share indeed a number of biochemical and physiological features, that may prove useful toward understanding of several mechanisms at the subcellular level. This critical review focuses on the characterization of most plant serine proteases, and comprehensively lists information produced by more and more sophisticated research tools that have led to the current state of the art in knowledge of these unique enzymes.

Developmental and light effects on the accumulation of FtsH protease in Arabidopsis chloroplasts--implications for thylakoid formation and photosystem II maintenance

The chloroplast ATP-dependent metalloprotease FtsH is involved in the degradation of unassembled proteins, the repair of photosystem II (PSII) from photoinhibition, and, apparently, the formation of thylakoids. In Arabidopsis, it is encoded by a family of 12 genes. However, the products of only four of them, FtsH1, 2, 5 and 8, have been found in chloroplasts to date. Mutations in two of these, FtsH2 and 5, demonstrate a visible phenotype of variegated leaves, with the phenotype of the FtsH2 mutant being more pronounced. Moreover, the degree of variegation appears to be dependent on developmental stage and environmental factors, suggesting an intricate relationship between the different gene products. To explore this, developmental and light effects on the accumulation of FtsH protease were studied in wild-type (WT) and FtsH2-mutant plants. Whereas cotyledons of the mutant were indistinguishable from those of the WT, the first true leaves were almost completely white. Subsequent leaves contained increasing proportions of green sectors. Analysis of the mRNA of the four FtsH genes, in cotyledons, first and second leaves of WT and mutant plants, revealed that: (i) transcript level increases during development, and (ii) transcript level in the mutant is higher than in the WT. FtsH protein level in the mutant was ca. 50% of that found in the WT, whereas the levels of other thylakoid proteins were the same. In individual leaves, the level of FtsH protein increased during development as well. Exposure of seedlings to different light intensities did not affect the degree of variegation, suggesting that it is due to a defect in chloroplast development rather than photobleaching. Examination of FtsH protein during exposure to high light revealed a decrease in its level, concomitant with a decrease in PSII potential, suggesting that the kinetics of photoinhibition reflects not only photodamage to PSII and induction of protective mechanisms, but also a decrease in repair capacity due to a reduction in the level of FtsH protease.

The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation

ClpP is a conserved serine-protease with two heptameric rings that enclose a large chamber containing the protease active sites. Each ClpP subunit can be divided into a handle region, which mediates ring-ring interactions, and a head domain. ClpP associates with the hexameric ATPases ClpX and ClpA, which can unfold and translocate substrate proteins through the ClpP axial pores into the protease lumen for degradation. We have determined the x-ray structure of Streptococcus pneumoniae ClpP(A153P) at 2.5 A resolution. The structure revealed two novel features of ClpP which are essential for ClpXP and ClpAP functional activities. First, the Ala --> Pro mutation disrupts the handle region, resulting in an altered ring-ring dimerization interface, which, in conjunction with biochemical data, demonstrates the unusual plasticity of this region. Second, the structure shows the existence of a flexible N-terminal loop in each ClpP subunit. The loops line the axial pores in the ClpP tetradecamer and then protrude from the protease apical surface. The sequence of the N-terminal loop is highly conserved in ClpP across all kingdoms of life. These loops are essential determinants for complex formation between ClpP and ClpX/ClpA. Mutation of several amino acid residues in this loop or the truncation of the loop impairs ClpXP and ClpAP complex formation and prevents the coupling between ClpX/ClpA and ClpP activities.

Comparative genomics and functional roles of the ATP-dependent proteases Lon and Clp during cytosolic protein degradation

The general pathway involving adenosine triphosphate (ATP)-dependent proteases and ATP-independent peptidases during cytosolic protein degradation is conserved, with differences in the enzymes utilized, in organisms from different kingdoms. Lon and caseinolytic protease (Clp) are key enzymes responsible for the ATP-dependent degradation of cytosolic proteins in Escherichia coli. Orthologs of E. coli Lon and Clp were searched for, followed by multiple sequence alignment of active site residues, in genomes from seventeen organisms, including representatives from eubacteria, archaea, and eukaryotes. Lon orthologs, unlike ClpP and ClpQ, are present in most organisms studied. The roles of these proteases as essential enzymes and in the virulence of some organisms are discussed.

Solute transporters of the plastid envelope membrane

Plastids are metabolically extraordinarily active and versatile organelles that are found in all plant cells with the exception of angiosperm pollen grains. Many of the plastid-localized biochemical pathways depend on precursors from the cytosol and, in turn, many cytosolic pathways depend on the supply of precursor molecules from the plastid stroma. Hence, a massive traffic of metabolites occurs across the permeability barrier between plastids and cytosol that is called the plastid envelope membrane. Many of the known plastid envelope solute transporters have been identified by biochemical purification and peptide sequencing. This approach is of limited use for less abundant proteins and for proteins of plastid subtypes that are difficult to isolate in preparative amounts. Hence, the majority of plastid envelope membrane transporters are not yet identified at the molecular level. The availability of fully sequenced plant genomes, the progress in bioinformatics to predict membrane transporters localized in plastids, and the development of highly sensitive proteomics techniques open new avenues toward identifying additional, to date unknown, plastid envelope membrane transporters.

Plastid proteomics

Plastids are essential organelles present in virtually all cells in plants and in green algae. The proteomes of plastids, and in particular of chloroplasts, have received significant amounts of attention in recent years. Various fractionation and mass spectrometry (MS) techniques have been applied to catalogue the chloroplast proteome and its membrane compartments. Neural network and hidden Markov models, in combination with experimentally derived filters, were used to try to predict the chloroplast subproteomes. Some of the many protein-protein interaction, as well as post-translational modifications have been characterized. Nevertheless, our understanding of the chloroplast proteome and its dynamics is very incomplete. Rapid improvements and wide-scale implementation of MS and new tools for comparative proteomics will undoubtedly accelerate this understanding in the near future. Proteomics studies often generate a large amount of data and these data are only meaningful if they can be easily accessed via the 'world-wide-web' and connected to other types of biological information. The plastid proteome data base (PPDB at http://www.ppdb.tc.cornell.edu/) and other web resources are discussed. This review will briefly summarize recent experimental and theoretical efforts, attempt to translate these data into the functions of the chloroplast and outline expectations and possibilities for (comparative) chloroplast proteomics.

Inactivation of the clpC1 gene encoding a chloroplast Hsp100 molecular chaperone causes growth retardation, leaf chlorosis, lower photosynthetic activity, and a specific reduction in photosystem content

ClpC is a molecular chaperone of the Hsp100 family. In higher plants there are two chloroplast-localized paralogs (ClpC1 and ClpC2) that are approximately 93% similar in primary sequence. In this study, we have characterized two independent Arabidopsis (Arabidopsis thaliana) clpC1 T-DNA insertion mutants lacking on average 65% of total ClpC content. Both mutants display a retarded-growth phenotype, leaves with a homogenous chlorotic appearance throughout all developmental stages, and more perpendicular secondary influorescences. Photosynthetic performance was also impaired in both knockout lines, with relatively fewer photosystem I and photosystem II complexes, but no changes in ATPase and Rubisco content. However, despite the specific drop in photosystem I and photosystem II content, no changes in leaf cell anatomy or chloroplast ultrastructure were observed in the mutants compared to the wild type. Previously proposed functions for envelope-associated ClpC in chloroplast protein import and degradation of mistargeted precursors were examined and shown not to be significantly impaired in the clpC1 mutants. In the stroma, where the majority of ClpC protein is localized, marked increases of all ClpP paralogs were observed in the clpC1 mutants but less variation for the ClpR paralogs and a corresponding decrease in the other chloroplast-localized Hsp100 protein, ClpD. Increased amounts of other stromal molecular chaperones (Cpn60, Hsp70, and Hsp90) and several RNA-binding proteins were also observed. Our data suggest that overall ClpC as a stromal molecular chaperone plays a vital role in chloroplast function and leaf development and is likely involved in photosystem biogenesis.

New Functions of the Thylakoid Membrane Proteome of Arabidopsis thaliana Revealed by a Simple, Fast, and Versatile Fractionation Strategy

Identification of membrane proteomes remains challenging. Here, we present a simple, fast, and scalable off-line procedure based on three-phase partitioning with butanol to fractionate membrane proteomes in combination with both in-gel and in-solution digestions and mass spectrometry. This should help to further accelerate the field of membrane proteomics. Using this new strategy, we analyzed the salt-stripped thylakoid membrane of chloroplasts of Arabidopsis thaliana. 242 proteins were identified, at least 40% of which are integral membrane proteins. The functions of 86 proteins are unknown; these include proteins with TPR, PPR, rhodanese, and DnaJ domains. These proteins were combined with all known thylakoid proteins and chloroplast (associated) envelope proteins, collected from primary literature, resulting in 714 non-redundant proteins. They were assigned to functional categories using a classification developed for MapMan (Thimm, O., Blasing, O., Gibon, Y., Nagel, A., Meyer, S., Kruger, P., Selbig, J., Muller, L. A., Rhee, S. Y., and Stitt, M. (2004) Plant J. 37, 914-939), updated with information from primary literature. The analysis elucidated the likely location of many membrane proteins, including 190 proteins of unknown function, holding the key to better understanding the two membrane systems. The three-phase partitioning procedure added a new level of dynamic resolution to the known thylakoid proteome. An automated strategy was developed to track possible ambiguous identifications to more than one gene model or family member. Mass spectrometry search results, ambiguities, and functional classifications can be searched via the Plastid Proteome Database.

Expression in multigene families. Analysis of chloroplast and mitochondrial proteases

The proteolytic machinery of chloroplasts and mitochondria in Arabidopsis consists primarily of three families of ATP-dependent proteases, Clp, Lon, and FtsH, and one family of ATP-independent proteases, DegP. However, the functional significance of the multiplicity of their genes is not clear. To test whether expression of specific isomers could be differently affected by growth conditions, we analyzed transcript abundance following short-term exposure to different environmental stimuli, using 70-mer oligonucleotide arrays. This analysis revealed variability in the response to high light and different temperatures within members of each family. Thirty out of the 41 tested genes were up-regulated in response to high light, including both chloroplast and mitochondrial isozymes, whereas only six and five genes responded to either high or low temperature, respectively. The extent of response was variable, ranging from 2- to 20-fold increase in the steady-state levels. Absolute transcript levels of the tested genes, compiled from one-channel arrays, were also variable. In general, transcripts encoding mitochondrial isozymes were accumulated to a lower level than chloroplastic ones. Within the FtsH family, transcript abundance of most genes correlated with the severity of mutant phenotypes in the relevant genes. This correlation was also evident at the protein level. Analysis of FtsH isozymes revealed that FtsH2 was the most abundant species, followed by FtsH5 and 8, with FtsH1 being accumulated to only 10% of FtsH2 level. These results suggest that, unlike previous expectations, the relative importance of different chloroplast protease isozymes, evidenced by mutant phenotypes at least in the FtsH family, is determined by their abundance, and not necessarily by different specific functions or specialized expression under certain conditions.

In-depth analysis of the thylakoid membrane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database

An extensive analysis of the Arabidopsis thaliana peripheral and integral thylakoid membrane proteome was performed by sequential extractions with salt, detergent, and organic solvents, followed by multidimensional protein separation steps (reverse-phase HPLC and one- and two-dimensional electrophoresis gels), different enzymatic and nonenzymatic protein cleavage techniques, mass spectrometry, and bioinformatics. Altogether, 154 proteins were identified, of which 76 (49%) were alpha-helical integral membrane proteins. Twenty-seven new proteins without known function but with predicted chloroplast transit peptides were identified, of which 17 (63%) are integral membrane proteins. These new proteins, likely important in thylakoid biogenesis, include two rubredoxins, a potential metallochaperone, and a new DnaJ-like protein. The data were integrated with our analysis of the lumenal-enriched proteome. We identified 83 out of 100 known proteins of the thylakoid localized photosynthetic apparatus, including several new paralogues and some 20 proteins involved in protein insertion, assembly, folding, or proteolysis. An additional 16 proteins are involved in translation, demonstrating that the thylakoid membrane surface is an important site for protein synthesis. The high coverage of the photosynthetic apparatus and the identification of known hydrophobic proteins with low expression levels, such as cpSecE, Ohp1, and Ohp2, indicate an excellent dynamic resolution of the analysis. The sequential extraction process proved very helpful to validate transmembrane prediction. Our data also were cross-correlated to chloroplast subproteome analyses by other laboratories. All data are deposited in a new curated plastid proteome database (PPDB) with multiple search functions (http://cbsusrv01.tc.cornell.edu/users/ppdb/). This PPDB will serve as an expandable resource for the plant community.