trends in plant science Reviews Proteomics of the chloroplast: experimentation and prediction Klaas Jan van Wijk New technologies, in combination with increasing amounts of plant genome sequence data, have opened up incredible experimental possibilities to identify the total set of chloroplast proteins (the chloroplast proteome) as well as their expression levels and post-translational modifications in a global manner. This is summarized under the term ‘proteomics’ and typically involves two-dimensional electrophoresis or chromatography, mass spectrometry and bioinformatics. Complemented with nucleotide-based global techniques, proteomics is expected to provide many new insights into chloroplast biogenesis, adaptation and function. hloroplasts are chlorophyll-containing plastids and originate from proplastids, which are generally maternally inherited via the embryo. Although the study of the chloroplast is a classic field in plant biology, there is no good overview of the total set of chloroplast proteins (the chloroplast proteome). Improvements in two-dimensional electrophoresis (2-DE) and mass spectrometry have, in combination with increasing amounts of sequence data from Arabidopsis, rice, maize and other plant species, opened up fantastic experimental possibilities enabling the chloroplast proteins as well as their expression levels and post-translational modifications to be identified rapidly. This is summarized under the term ‘proteomics’. Proteomics typically involves biochemical purification techniques such as 2-DE, chromatography or affinity purification, mass spectrometry and bioinformatics1,2. Complemented with other functional genomics techniques such as cDNA or oligonucleotide microarrrays (Box 1) and reverse genetics, a better understanding of chloroplast biogenesis, adaptation to the environment, signal transduction and metabolic pathways can be obtained. Here, we discuss in detail such an experimental approach to the characterization of the chloroplast proteome. A complete characterization includes not only the identification of proteins but also studies of their expression levels, post-translational modifications, protein–protein interactions and apparent discrepancies between the identified proteins and their predicted protein sequence from nucleotide sequencing data. We also comment on possibilities and limitations for the theoretical prediction of the chloroplast proteome based on targeting or presequence information. C Experimental characterization of the chloroplast proteome by 2-DE and mass spectrometry The improvement of 2-DE through the development of immobilized pH gradients3 and optimization of solubilization techniques4,5 now allows the reproducible separation of more than 2000 proteins on a single 2-DE gel. Such gel-separated proteins can be identified by mass spectrometry if genomic information is available1,2,6 (Box 2). In addition, mass spectrometry is a powerful tool for analyzing isoforms, secondary modifications of proteins (e.g. glycosylation and phosphorylation) and proteolysis using low amounts (picomoles to attomoles) of proteins7–9. Thus, a proteomics approach allows us to bridge the gap between genomic sequence information and the actual protein population in a cell. Proteomics is already an important tool in medical research and the analysis of yeast and prokaryotes. With the rapid progress of the sequencing of the Arabidopsis genome and ongoing EST and genomic sequencing of many agricultural crops, proteomics is 420 October 2000, Vol. 5, No. 10 bound to become another important tool for plant biology. Several plant proteomics studies have been published in recent years10. However, in these studies, protein identification was achieved through Edman sequencing, which necessarily limited the identification of proteins in terms of cost, speed and sensitivity. Mass spectrometry will allow identification at a much higher speed and with 100–1000 times less protein. Two plant proteomics studies using mass spectrometry have been published recently, one concerning anoxia tolerance in maize root tips11 and the other on pea thylakoid proteins12. An explosion of plant proteomics initiatives can be expected in the coming years. Compartmenting the chloroplast proteome From a biochemical point of view, the chloroplast can be divided into several compartments, with each compartment having its own specific subset of proteins, or subproteome. To characterize the chloroplast proteome fully, either experimentally or by prediction, it is useful (and probably essential) to subdivide the chloroplast proteome into such subproteomes13. Only then can we devise optimal experimental strategies to identify and characterize most proteins, including those that are hydrophobic5, of low abundance or transiently expressed14. For each of the chloroplast compartments, we briefly review current knowledge of each corresponding subproteome and discuss possible experimental and theoretical strategies for further characterization. Stromules, the chloroplast envelope and vesicles Starting from the cytosolic side of the chloroplast, the first compartment is the chloroplast outer and inner envelope. The envelope is the site of transport of metabolites, proteins and messengers between plastids and the cytosol15,16. The inner envelope membrane is also a site for the biosynthesis of several products (e.g. lipids and pigments15,17,18) and has also been implicated in DNA replication and transcription of the chloroplast genome19. Several protein complexes involved in the translocation of nucleus-encoded chloroplast proteins have been characterized in great detail20,21. At least 100 protein bands can be resolved on onedimensional electrophoresis (1-DE) silver- or Coomassie-stained gels of purified inner and outer membranes. However, 1-DE gels do not have sufficient resolution to obtain a global overview of the envelope proteome or to study post-translational modifications or changes in protein expression. No successful systematic analysis of the envelope proteome has been carried out to date, which is partly related to the hydrophobic nature of this subproteome. The 2-DE of envelope membrane proteins was reported to be unsuccessful in the recovery of 1360 - 1385/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved. PII: S1360-1385(00)01737-4 trends in plant science Reviews Box 1. Functional genomics tools to understand cellular processes Transcriptomics Definition Type of information Strong points Weak points Proteomics Definition Type of information Strong points Weak points • The systematic analysis of accumulated transcripts in the cell or tissue • The accumulation of transcripts, indicating the level of gene expression • Extremely sensitive • Many different transcripts can be monitored simultaneously • mRNA levels often do not correspond to protein accumulation • Cannot study post-translational modifications • Location of mRNA does not provide information about the location of the gene product • The systematic analysis of the proteins (the proteome) of a cell, tissue, organelle or membrane • The identification and expression level of the proteome • Post-translational modifications and protein– protein interactions (protein complexes) • Relatively fast and sensitive (femtomole range) identification of proteins • Protein–protein interactions can be studied • Monitors the protein directly, rather than monitoring the mRNA • With current technology, the number of proteins that can be simultaneously followed is not as high as with transcriptomics • Protein separation steps are still timeconsuming • Monitoring the expression levels of membrane proteins is technically demanding envelope proteins22, a phenomenon that has been reported for membrane proteins in general5. However, it is at least possible to resolve smaller membrane proteins (1– 4 transmembrane domains) on 2-DE gels if soluble proteins as well as lipids are removed23. A similar strategy, using extraction with organic solvents, but with 1-DE, has been used to identify several hydrophobic chloroplast envelope proteins24. In this way, the most hydrophobic proteins from chloroplast envelope preparations could be enriched while excluding more hydrophilic proteins, thereby reducing the complexity of the protein mixture. Using this method, a few integral envelope membrane proteins were identified, and ~5–10% of the total envelope protein content were estimated to be hydrophobic proteins, representing at least 15–20 different proteins24. Intriguing tube-like structures protruding out of the chloroplast envelope were detected in chloroplasts and chlorophyll-free proplastids and plastids, using transgenic plants in which green fluorescent protein (GFP) was targeted into the chloroplast25,26. This confirmed less detailed observations reported between 1960 and the 1980s (Ref. 27). These dynamic structures were named stromules (for stroma filled tubules) and sometimes interconnected different plastids with the surrounding nuclei and mitochondria. Analysis of the proteome of these stromules could provide an insight into their specific function. Microscopic and radiolabeling studies have revealed that vesicles can form at the inner chloroplast envelope and are involved in Box 2. Mass spectrometry for the analysis of proteins and peptides Mass spectrometry is the preferred method in the study of protein identification. Mass spectrometers with ‘soft’ ionization techniques allow the rapid identification of proteins provided that genomic or cDNA sequence is available. Protein identification and characterization generally involves two types of mass spectrometers: • Matrix-assisted laser desorption–ionization time-of-flight (MALDI-TOF) mass spectrometers – accurately measure the masses of a protein (mixture) or of proteolytic digests of gel separated or otherwise purified proteins. A selected protein spot is digested with a site-specific protease such as trypsin, resulting in a set of peptides. The masses of the peptides are then measured by MALDI-TOF MS, resulting in a list of peptide masses. For each entry in the nucleotide and protein databases, the masses of the predicted tryptic peptides are calculated and compared (within the experimental mass accuracy) with the list of measured peptide masses using web-based search engines (e.g. Protein Prospector, Mascot, Profound). The correct protein will have many ‘matching’ peptides. Proteins can be identified even when they consist of a mixture of two or three proteins. This method relies on the mass accuracy (5–15 ppm) and sensitivity (femtomole range) of the latest generation of MALDI-TOF MS instruments. • Tandem mass spectrometer – often coupled to liquid chromatography, using electrospray ionization with a collision cell for induced fragmentation (the technique is thus abbreviated to ESI-MS/MS). When a protein cannot be positively identified by MALDI-TOF MS, peptide sequence tags are obtained by ESI-MS/MS. The individual peptides are ‘screened’ in the first section of the tandem mass spectrometer and selected peptides are subsequently further fragmented along the protein backbone by collision with argon or nitrogen molecules. This is termed collision-induced dissociation. These peptide fragments are then separated by a second analyzer to provide amino acid sequence information. The peptide sequence tags and measured ion masses are used to search for proteins in the database using specialized software. These two types of instruments together allow the rapid identification of proteins, the accurate determination of partial amino acid sequences and the elucidation of post-translational protein modifications. lipid transfer from the inner envelope to the thylakoids15,17,28. The concept of active vesicle formation within the chloroplast was further supported in other studies29,30, and such vesicles might contain their own subproteome. A low-density chloroplast membrane fraction with an acyl lipid composition similar to inner envelopes and thylakoid membranes has been isolated from the green alga Chlamydomonas reinhardtii31. Several chloroplast mRNA binding proteins were found to be strongly enriched, suggesting that these membranes could be a site of chloroplast gene expression31. To elucidate the role of these intriguing membranes in biogenesis, a more systematic analysis of their proteins is urgently needed. Chloroplast stroma The chloroplast stroma is a compartment with a high protein content and many well known enzymes involved in carbon assimilation, as well as many biosynthetic pathways. Although best known for their role in photosynthesis, chloroplasts synthesize many essential compounds, such as plant hormones, fatty acids and lipids, amino acids, vitamins (B1, K1 and E), purine and pyrimidine nucleotides, and secondary metabolites such as October 2000, Vol. 5, No. 10 421 trends in plant science Reviews alkaloids or isoprenoids. Moreover, chloroplasts are also required for nitrogen and sulfur assimilation. In addition to these enzymes, the stroma also contains the transcriptional and translation machinery. No systematic analysis of the stromal proteome has been presented in the literature. Clearly, a large-scale protein analysis during chloroplast development, environmental changes and of (chloroplast) mutants could reveal connections between the many biosynthetic pathways and provide insight into chloroplast functions and signaling. However, it will be a challenge to resolve the proteins of lower abundance, given the presence of several abundant proteins. Removal of these dominant proteins (or protein complexes) by affinity purification or other separation techniques will probably be crucial to get a good overview of the stromal proteome. Nucleoids and plastoglobules The chloroplast genome is organized in so-called nucleoids, which are associated with the inner envelope. Nucleoids contain at least 15–20 proteins, which are poorly characterized19,32. Identification of these proteins might give us an insight into gene activation, genome organization and, possibly, DNA replication during chloroplast division. Other interesting structures in the chloroplast include the plastoglobules, which are lipid-containing particles in the stroma that are thought to serve as lipid reservoirs for thylakoid membranes. To date, two proteins (PG1 and fibrillins or PAP) have been identified33,34. Thylakoid membrane system The thylakoid membrane system contains four abundant multisubunit protein complexes (Photosystems I and II, the ATP synthase, and the cytochrome b6f complex). Together, they contain ~70 proteins and carry out the photosynthetic reactions. The thylakoid membrane might contain many other proteins that are involved in the biogenesis and regulation of these complexes35,36. This includes processes such as biosynthesis and ligation of cofactors, and the insertion, folding or degradation of proteins. Based on preliminary information and postulated functions, at least 100 proteins (many of low abundance) are expected to be present. Recently, we have initiated a systematic analysis of thylakoid proteins from pea12 (Fig. 1). We constructed high-resolution 2-DE maps of lumenal and peripheral proteins of the thylakoid membrane system purified from intact pea chloroplasts. After correction for possible isoforms and post-translational modifications, at least 200–230 different lumenal and peripheral proteins were calculated to be present. 61 proteins were identified by mass spectrometry and Edman sequencing12, of which 33 had a clear function or functional domain, whereas no function could be assigned for ten proteins. For the other 18 proteins, no corresponding ESTs or full-length genes could be identified at the time of publication, in spite of experimental determination of a significant amount of amino acid sequence. Ongoing genome sequencing is expected to identify these genes, and they can then be analyzed for functional domains. Although pea is a good model system for biochemical work, there is one important drawback to using it for proteomics studies: only a limited amount of DNA and protein sequences are available for pea, and protein identification must therefore be carried out based on the homology of pea proteins to well sequenced plant species, such as Arabidopsis thaliana. Homology-based identification with mass spectrometry data is possible12 but generally requires a larger amount of experimentally determined protein sequence tags or peptide mass fingerprints. Therefore, the use of Arabidopsis, rice or other plant species that will be completely sequenced is highly favorable. 422 October 2000, Vol. 5, No. 10 (a) Isolation of chloroplasts Purification of chloroplast subproteomes pI 3.0 10.0 (b) MW (c) Pick spots in gel digestion extraction of peptides (d) Identification by mass spectrometry MALDI-TOF ESI-MS/MS Peptide masses Sequence tags (e) Bioinformatics (f) Verification of identified proteins – analysis of targeting signals – comparison experimentally determined and – predicted MW and pI Fig. 1. Possible strategy for identifying chloroplast proteins using two-dimensional gel electrophoresis, mass spectrometry and targeting analysis. (a) Purification of intact chloroplasts followed by fractionation of different chloroplast compartments, such as thylakoids, stroma and envelope membranes. Further separation and delipidation is required for the identification of membrane proteins. (b) After isolation, chloroplast subproteomes are separated according to their isoelectric point (pI) and then according to their molecular weight (MW), resulting in a two-dimensional gel. The spots are then visualized by Coomassie blue or silver staining. (c) Individual protein spots are selected, excised from the gel and digested with a site-specific protease, resulting in a set of peptides. (d) Extracted peptides from each gel spot are measured by matrixassisted laser desorption–ionization time-of-flight (MALDI-TOF) mass spectrometry. For further identification and characterization, selected peptides are analyzed by electrospray tandem mass spectrometry (ESI-MS/MS), resulting in the generation of amino acid sequence tags. (e) The set of peptide masses measured by MALDITOF mass spectrometry are compared with the masses of the predicted peptides for each entry in the sequence databases, possibly identifying the protein. The sequence tags obtained by ESI-MS/MS are used for further confirmation of the identified protein or to analyze post-translational modifications. (f) The identified proteins are further analyzed for positive identification by analyzing targeting information, such as chloroplast transit peptide or lumenal transit peptide. In addition, the experimentally determined molecular mass and isoelectric point are compared with the predicted values, after removal of predicted (cleavable) transit peptides. trends in plant science Reviews The construction of high resolution 2-DE maps of Arabidopsis thylakoids has therefore been initiated and is well under way, with more than 1000 protein spots analyzed by matrix-assisted laser desorption–ionization time-of-flight mass spectrometry (J.B. Peltier et al., unpublished). Analysis of the integral thylakoid proteins is also in progress. These 2-DE maps can be used as reference maps to study post-translational modifications or the expression of thylakoid proteins under varying environmental conditions and during chloroplast development, or to evaluate the effect of specific gene deletions. In addition, these newly identified proteins will provide a useful database to more rationally design strategies aimed at understanding thylakoid biogenesis. Prediction of the chloroplast proteome through analysis of targeting signals Attempts have been made to predict the size of the chloroplast proteome based on location prediction programs and relationships to cyanobacterial ancestors, and estimates vary from 1950 to 2500 (Refs 37,38). Several programs are available on the Internet to predict the cellular location of a protein. For chloroplasts, two programs [PSORT and ChloroP (Box 3)] have been available for several years. Both programs were used on a set of identified nuclear encoded thylakoid proteins to test the prediction for chloroplast localization and the expected cleavage site by stromal processing peptidase(s)12. Ninety four percent of this set was correctly predicted to be located in the chloroplast by ChloroP, whereas PSORT predicted chloroplast localization for 52%. Unfortunately, ChloroP also predicts a significant number of false positives, which are mostly mitochondrial proteins: out of a test set of 715 Arabidopsis entries in the SWISS-PROT database, 11% were falsely predicted as chloroplast proteins39. However, the program TargetP has recently become available (Box 3). This is basically a retrained ChloroP integrated with a new mitochondrial predictor and a retrained version of SignalP (Box 3). TargetP is reported to be about three times better than ChloroP at discriminating between chloroplast and mitochondrial signal sequences and should therefore result in fewer false positives for chloroplast prediction40. Using N-terminal sequence information, it discriminates between proteins destined for the mitochondrion, the chloroplast, the secretory pathway and ‘other’ locations with a reported success rate of 85% on redundancyreduced test sets of mitochondrial, chloroplast, secretory, nuclear and cytosolic plant proteins. However, these test sets excluded other organelles such as vacuoles and peroxisomes. In a TargetP analysis of the complete Arabidopsis chromosomes II and IV, the number of estimated chloroplast proteins was 171 (2.2% of 7798 assigned genes; Ref. 40) if using only the highest level of confidence (corresponding to no false positives on the test sets). Allowing lower levels of confidence (or Box 3. Programs to predict the cellular location of a protein ChloroP, TargetP and SignalP http://www.cbs.dtu.dk/services/ PSORT http://psort.nibb.ac.jp/ Chloroplast and mitochondrial predictor http://www.inra.fr/Internet/Produits/Predotar/ higher sensitivity) 10% of the proteins encoded by the assigned genes on chromosomes II and IV were estimated to be located in mitochondria and 14% to be located in the chloroplast. Cleavage site prediction for identified chloroplast proteins was 40% correct when allowing an error of 62 amino acids. This prediction can only be improved after generating more experimental data. Thylakoid proteins destined for the lumen have an additional transit peptide that shows strong similarities to bacterial signal peptides21,41. In the aforementioned thylakoid proteomics study, the lumenal transit peptides of a set of 26 non-redundant proteins (16 known and 10 newly discovered) were compared by aligning the sequences according to their experimentally determined cleavage sites. As expected, the presequence and cleavage site had similar features to signal peptides in bacteria. However, the lumenal transit peptides also showed a strong presence of prolines at the end of the hydrophobic domain, a nearly complete conservation (25 out of 26) of the alanine at the 21 position and an abundance of glutamic acid at the 12 and 14 positions. The prediction program SignalP, which was originally developed to predict cleavable signal peptides of secretory proteins in bacteria and eukaryotes, also predicted lumenal transit peptides and their cleavage sites, but with mixed success12. However, if SignalP could be adapted to lumenal signal peptides by using the specific features of lumenal proteins as mentioned above, its prediction of lumenal proteins might be significantly improved. Recently, a new chloroplast and mitochondrial predictor has been developed (Box 3). This program is still in development but it is reported to be good at discriminating between proteins localized in the chloroplasts and mitochondria, and at recognizing proteins targeted to both organelles (I. Small, pers. commun.). What does this mean for the use of these programs to identify (or confirm) chloroplast proteins and their location within the chloroplast? When the complete annotated genome of Arabidopsis or other higher plants becomes available, it is expected that many chloroplast-localized proteins will be tentatively identified based on presequence information. In particular, the lumenal proteins should be predicted with high confidence and sensitivity by initial screening with TargetP set at a low confidence level (or high sensitivity) followed by analysis with SignalP in Gram-negative mode. Recognition of outer envelope proteins based on primary sequence information is difficult or impossible because most lack obvious chloroplast targeting signals42. Several tRNA synthetases have been reported to be targeted to both the mitochondria and chloroplasts43, but they are not easily recognized by prediction as chloroplast proteins. Several more dual targeted proteins are likely to be present. Other chloroplast proteins that might escape positive prediction are those targeted not via information in the N terminus but by alternative mechanisms. This could include targeting via the C terminus, as observed for plant vacuoles44 and yeast mitochondria45, or targeting via the so-called ‘hitch-hiker’ mechanism that has been observed in bacteria46, or targeting as polyproteins47. Predicting whether chloroplast membrane proteins are destined for the thylakoid membrane or the (inner) envelope is currently not possible because there are no obvious targeting signals. Thus, the most confident location prediction within the chloroplast is currently for the lumenal proteins. It is important to realize that, for these programs to work correctly, the assignment of the start methionine needs to be correct. Several cases were observed in which incorrect assignment resulted in a negative chloroplast (incorrect) prediction12. In addition, chloroplast location prediction programs cannot determine actual protein accumulation. Finally, as a word of caution, the October 2000, Vol. 5, No. 10 423 trends in plant science Reviews currently available chloroplast predictors cannot identify chloroplast proteins of the unicellular alga C. reinhardtii, which is an important model organism in the study of chloroplast biogenesis35,48. Post-translational modifications, isoforms and mRNA editing Characterization of the chloroplast proteome involves the identification not only of proteins but also of their post-translational modifications. Many post-translational modifications of chloroplast proteins have been reported, including methylation (for RbcS)49, carbamylation (for RbcS, RbcL)50, glycosylation (for CF)51 and palmitoylation (for D1)52. However, no global analysis of posttranslational modifications has been carried out to date. With the recent developments of mass spectrometry and 2-DE, such analysis is now feasible and could lead to many interesting and unexpected observations. For instance, systematic mapping of phosphorylation of chloroplast proteins during light–dark transitions is likely to reveal unexpected kinetics and substrates, possibly leading to more insight into redox-driven signal transduction chains and (de)activation mechanisms in the chloroplast. Proteomics approaches can also provide a global overview of splicing, mRNA editing and the expression of isoforms. Several cases of mRNA editing53 and splicing54 have been described for chloroplast proteins, and multigene families have been reported in pea and spinach. These phenomena can, of course, also be detected from a careful analysis of the mRNA (or cDNA), but proteomics is clearly a strong alternative or complementary way to elucidate such events. Functional proteomics of the chloroplast Protein reference maps of subfractions of various organisms constructed by 2-DE are expected to become a central tool for organizing and understanding proteomes. A few web sites with small organized 2-DE databases are already available (e.g. yeast, E. coli, plant plasma membranes and chloroplasts; Box 4). Reference 2-DE maps will be used to follow differential protein expression and post-translational modifications. A combination of proteomics with other large-scale techniques such as DNA microarrays will be needed because they are expected to be highly complementary (Box 1). DNA- and RNA-based technologies are more sensitive tools, which can handle much larger numbers of genes simultaneously. By contrast, proteomics determines the presence of the gene product directly (rather than at the mRNA level) and can also monitor post-translational modifications, including proteolysis. Only after the experimental determination of further chloroplast proteins and the cleavage site of their targeting signals can the prediction of chloroplast localization and cleavage sites be improved. To identify the functional role of newly discovered proteins, additional approaches (e.g. reverse genetics) will be needed in combination with proteomics. Systematic analysis of protein–protein interactions using non-denaturing biochemical Box 4. 2-DE databases Yeast, E. coli and others http://www.expasy.ch/ch2d/ Plant plasma membranes http://sphinx.rug.ac.be:8080/ppmdb/index.html Chloroplasts http://www.biokemi.su.se/chloroplast/ 424 October 2000, Vol. 5, No. 10 techniques (such as affinity purification and gel filtration) followed by mass spectrometry or yeast two-hybrid systems will be essential to unravel biochemical functions at a molecular level. Proteomics studies on chloroplast biogenesis mutants obtained by phenotypic screening, chlorophyll fluorescence screens55, other phenotypic criteria or reverse genetics will help to pinpoint the function of the gene products involved in chloroplast biogenesis and function. Acknowledgements I gratefully acknowledge members of my laboratory and Olof Emanuelsson for numerous stimulating discussions and critically reading the manuscript. My funding was provided by the Swedish National Research Council (NFR), the Swedish Agricultural Research Council (SJFR), the Swedish Strategic Funds (SSF) and the Carl Trygger Foundation. References 1 Roepstorff, P. (1997) Mass spectrometry in protein studies from genome to function. Curr. Opin. Biotechnol. 8, 6–13 2 Yates, J.R., III (2000) Mass spectrometry: from genomics to proteomics. Trends Genet. 16, 5–8 3 Görg, A. et al. (1988) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 9, 531–546 4 Herbert, B. (1999) Advances in protein solubilisation for two-dimensional electrophoresis. Electrophoresis 20, 660–663 5 Santoni, V. et al. (2000) Membrane proteins and proteomics: un amour impossible? Electrophoresis 21, 1054–1070 6 Dainese, P. et al. (1997) Probing protein function using a combination of gene knockout and proteome analysis by mass spectrometry. Electrophoresis 18, 432–442 7 Kuster, B. and Mann, M. (1998) Identifying proteins and post-translational modifications by mass spectrometry. Curr. Opin. Struct. Biol. 8, 393–400 8 Burlingame, A.L. et al. (1998) Mass spectrometry. Anal. Chem. 70, 647R–716R 9 Wilkins, M.R. et al. (1999) High-throughput mass spectrometric discovery of protein post-translational modifications. J. Mol. Biol. 289, 645–657 10 Thiellement, H. et al. (1999) Proteomics for genetic and physiological studies in plants. Electrophoresis 20, 2013–2026 11 Chang, W.W. et al. (2000) Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment, and identification of proteins by mass spectrometry. Plant Physiol. 122, 295–318 12 Peltier, J.B. et al. (2000) Proteomics of the chloroplast. Systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12, 319–342 13 Cordwell, S.J. et al. (2000) Subproteomics based upon protein cellular location and relative solubilities in conjunction with composite twodimensional electrophoresis gels. Electrophoresis 21, 1094–1103 14 Corthals, G.L. et al. (2000) The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 21, 1104–1115 15 Joyard, J. et al. (1998) The biochemical machinery of plastid envelope membranes. Plant Physiol. 118, 715–723 16 Soll, J. and Tien, R. (1998) Protein translocation into and across the chloroplastic envelope membranes. Plant Mol. Biol. 38, 191–207 17 Marechal, E. et al. (1997) Lipid synthesis and metabolism in the plastid envelope. Physiol. Plant 100, 65–77 18 Bruce, B.D. (1998) The role of lipids in plastid protein transport. Plant Mol. Biol. 38, 223–246 19 Sato, N. et al. (1999) Do plastid envelope membranes play a role in the expression of the plastid genome? Biochimie 81, 619–629 20 May, T. and Soll, J. (1999) Chloroplast precursor protein translocon. FEBS Lett. 452, 52–56 21 Keegstra, K. and Cline, K. (1999) Protein import and routing systems of chloroplasts. Plant Cell 11, 557–570 trends in plant science Reviews 22 Adessi, C. et al. (1997) Two-dimensional electrophoresis of membrane proteins: a current challenge for immobilized pH gradients. Electrophoresis 18, 127–135 23 Molloy, M.P. et al. (2000) Proteomic analysis of the Escherichia coli outer membrane. Eur. J. Biochem. 267, 2871–2881 24 Seigneurin-Berny, D. et al. (1999) Differential extraction of hydrophobic proteins from chloroplast envelope membranes: a subcellular-specific proteomic approach to identify rare intrinsic membrane proteins. Plant J. 19, 217–228 25 Kohler, R.H. and Hanson, M.R. (2000) Plastid tubules of higher plants are tissue specific and developmentally regulated. J. Cell Sci. 113, 81–89 26 Köhler, R.H. et al. (1997) Exchange of protein molecules through connections between higher plant plastids. Science 276, 2039–2042 27 Wildman, S.G. et al. (1962) Chloroplast and mitochondria in living plant cells: cinematographic studies. Science 138, 434–436 28 Morré, D.J. et al. (1991) Stromal low temperature compartment derived from inner membrane of the chloroplast envelope. Plant Physiol. 97, 1558–1564 29 Hugueney, P. et al. (1995) Identification of a plastid protein involved in vesicle fusion and/or membrane protein translocation. Proc. Natl. Acad. Sci. U. S. A. 92, 5630–5634 30 Park, J.M. et al. (1998) A dynamin-like protein in Arabidopsis thaliana is involved in biogenesis of thylakoid membranes. EMBO J. 17, 859–867 31 Zerges, W. and Rochaix, J.D. (1998) Low density membranes are associated with RNA-binding proteins and thylakoids in the chloroplast of Chlamydomonas reinhardtii. J. Cell. Biol. 140, 101–110 32 Sato, N. et al. (1993) Detection and characterization of a plastid envelope DNA-binding protein which may anchor plastid nucleoids. EMBO J. 12, 555–561 33 Pozueta-Romero, J. et al. (1997) A ubiquitous plant housekeeping gene, PAP, encodes a major protein component of bell pepper chromoplasts. Plant Physiol. 115, 1185–1194 34 Kessler, F. et al. (1999) Identification of proteins associated with plastoglobules isolated from pea (Pisum sativum L.) chloroplasts. Planta 208, 107–113 35 Wollman, F.A. et al. (1999) The biogenesis and assembly of photosynthetic proteins in thylakoid membranes. Biochim. Biophys. Acta 1411, 21–85 36 van Wijk, K.J. Proteins involved in biogeneis of the thylakoid membrane. In Advances in Photosynthesis: Regulatory Aspects of Photosynthesis (Vol. 8) (Andersson, B. and Aro, E-M., eds), Kluwer (in press) 37 Abdallah, F. et al. (2000) A prediction of the size and evolutionary origin of the proteome of chloroplasts of Arabidopsis. Trends Plant Sci. 5, 141–142 38 Martin, W. and Herrmann, R.G. (1998) Gene transfer from organelles to the nucleus: how much, what happens, and why? Plant Physiol. 118, 9–17 39 Emanuelsson, O. et al. (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8, 978–984 40 Emanuelsson, O. et al. (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300, 1005–1116 41 Dalbey, R.E. and Robinson, C. (1999) Protein translocation into and across the bacterial plasma membrane and the plant thylakoid membrane. Trends Biochem. Sci. 24, 17–22 42 Reumann, S. and Keegstra, K. (1999) The endosymbiotic origin of the protein import machinery of chloroplastic envelope membranes. Trends Plant Sci. 4, 302–307 43 Peeters, N.M. et al. (2000) Duplication and quadruplication of Arabidopsis thaliana cysteinyl- and asparaginyl-tRNA synthetase genes of organellar origin. J. Mol. Evol. 50, 413–423 44 Di Sansebastiano, G.P. et al. (1998) Specific accumulation of GFP in a nonacidic vacuolar compartment via a C-terminal propeptide-mediated sorting pathway. Plant J. 15, 449–457 45 Lee, C.M. et al. (1999) The DNA helicase, Hmi1p, is transported into mitochondria by a C-terminal cleavable targeting signal. J. Biol. Chem. 274, 20937–20942 46 Rodrigue, A. et al. (1999) Co-translocation of a periplasmic enzyme complex by a hitchhiker mechanism through the bacterial tat pathway. J. Biol. Chem. 274, 13223–13228 47 Mant, A. and Robinson, C. (1998) An Arabidopsis cDNA encodes an apparent polyprotein of two non-identical thylakoid membrane proteins that are associated with photosystem II and homologous to algal ycf32 open reading frames. FEBS Lett. 423, 183–188 48 Hippler, M. et al. (1998) Chlamydomonas genetics, a tool for the study of bioenergetic pathways. Biochim. Biophys. Acta 1367, 1–62 49 Grimm, R. et al. (1997) Postimport methylation of the small subunit of ribulose-1,5-bisphosphate carboxylase in chloroplasts. FEBS Lett. 408, 350–354 50 Smith, H.B. et al. (1988) Subtle alteration of the active site of ribulose bisphosphate carboxylase/oxygenase by concerted site-directed mutagenesis and chemical modification. Biochem. Biophys. Res. Commun. 152, 579–584 51 Maione, T.E. and Jagendorf, A.T. (1984) Partial deglycosylation of chloroplast coupling factor 1 (CF1) prevents the reconstitution of photophosphorylation. Proc. Natl. Acad. Sci. U. S. A. 81, 3733–3736 52 Mattoo, A.K. and Edelman, M. (1987) Intramembrane translocation and posttranslational palmitoylation of the chloroplast 32-kDa herbicide-binding protein. Proc. Natl. Acad. Sci. U. S. A. 84, 1497–1501 53 Sugita, M. and Sugiura, M. (1996) Regulation of gene expression in chloroplasts of higher plants. Plant Mol. Biol. 32, 315–326 54 Mano, S. et al. (1997) Stromal and thylakoid-bound ascorbate peroxidases are produced by alternative splicing in pumpkin. FEBS Lett. 413, 21–26 55 Meurer, J. et al. (1996) Isolation of high-chlorophyll-fluorescence mutants of Arabidopsis thaliana and their characterisation by spectroscopy, immunoblotting and northern hybridisation. Planta 198, 385–396 Klaas Jan van Wijk is at the Dept of Biochemistry, Arrhenius Laboratories, Stockholm University, S-10691 Stockholm, Sweden (tel 146 8 162420; fax 146 8 153679; e-mail [email protected]). October 2000, Vol. 5, No. 10 425
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