Update on chloroplast proteomics

Photosynthesis Research

Volumn 78, Issue 3 SPEC. ISS., 2003, Pages 181-193

  Schröder, Wolfgang P ^a,b   Kieselbach, Thomas ^c  

^a UMEÅ UNIVERSITY   (Sweden)

^b Umea Plant Science Center   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

Author keywords

Arabidopsis; Bioinformatics; Functional genomics; Proteome; Spinach; Synechocystis 6803

Indexed keywords

ARABIDOPSIS; SPINACIA OLERACEA; SYNECHOCYSTIS; SYNECHOCYSTIS SP.; SYNECHOCYSTIS SP. PCC 6803;

EID: 17544396290     PISSN: 01668595     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:PRES.0000006914.52898.67     Document Type: Short Survey

References (78)

1. Aebersold R and Mann M (2003) Mass spectrometry-based proteomics. Nature 422: 198-207
2. Alban A, David SO, Bjorkesten L, Andersson C, Sloge E, Lewis S and Currie I (2003) A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3: 36-44
3. Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, Mann M and Lamond AI (2002) Directed proteomic analysis of the human nucleolus. Curr Biol 12: 1-11
4. Apweiler R, Attwood TK, Bairoch A, Baitman A, Birney E, Biswas M, Bucher E, Cerutti L, Corpet F, Croning MDR, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJA and Zdobnov EM (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucl Acids Res 29: 37-40
5. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
6. Balmer Y, Koller A, del Val G, Manieri W, Schürmann P and Buchanan B (2003) Proteomics gives insight into the regulatory function of chloroplast thioredoxins. Proc Natl Acad Sci USA 100: 370-375
7. Bricker TM, Prevost M, Vu V, Laborde S, Womack J and Frankel LK (2001) Isolation of lumenal proteins from spinach thylakoid membranes by Triton X-114 phase partitioning. Biochim Biophys Acta 1503: 350-356
8. Choi JS, Kim DS, Lee J, Kim SJ, Kim SI, Kim YH, Hong J, Yoo JS, Suh KH and Park YM (2000) Proteome analysis of light-induced proteins in Synechocystis sp. PCC 6803: identification of proteins separated by 2D-PAGE using N-terminal sequencing and MALDI-TOF MS. Mol Cells 10: 705-711
9. Emanuelsson O, Nielsen H and von Heijne G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sits. Protein Sci 8: 978-984
10. Emanuelsson O, Nielsen H, Brunak S and von Heijne G (2000) Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 300: 1005-1016
11. Ferro M, Salvi D, Riviere-Rolland H, Vermat T, Seigneurin-Berny D, Grunwald D, Garin J, Joyard J and Rolland N (2002) Integral membrane proteins of the chloroplast envelope: identification and subcellular localization of new transporters. Proc Natl Acad Sci USA 99: 11487-11492
12. Ferro M, Salvi D, Brugiere S, Miras S, Kowalski S, Louwagie M, Garin J, Joyard J and Rolland N (2003) Proteomics of the chloroplast envelope membranes from Arabidopsis thaliana. Mol Cell Proteomics 2: 325-345
13. Fulda S, Huang F, Nilsson F, Hagemann M, and Norling B (2000) Proteomics of Synechocystis sp. strain PCC 6803. Identification of periplasmic proteins in cells grown at low and high salt concentrations. Eur J Biochem 267: 5900-5907
14. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Hofert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, Gnau V, Bauch A, Bastuck S, Huhse B, Leutwein C, Heurtier MA, Copley RR, Edelmann A, Querfurth E, Rybin V, Drewes G, Raida M, Bouwmeester T, Bork P, Seraphin B, Kuster B, Neubauer G and Superti-Furga G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147
15. Gharbi S, Gaffney P, Yang A, Zvelebil MJ, Cramer R, Waterfield MD and Timms JF (2002) Evaluation of two-dimensional differential gel electrophoresis for proteomic expression analysis of a model breast cancer cell system. Mol Cell Proteomics 1: 91-98
16. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A and Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100
17. Gomez SM, Nishio JN, Faull KF and Whitelegge JP (2002) The chloroplast grana proteome defined by intact mass measurements from liquid chromatography mass spectrometry. Mol Cell Proteomics 1: 46-59
18. Graves PR and Haystead TA (2002) Molecular biologist's guide to proteomics. Microbiol Mol Biol Rev 66: 39-63
19. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH and Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nature Biotechnol 17: 994-999
20. Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O and Salzberg SL (2002) Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol 3, research 0029.1-research 0029.12
21. Hamdan M and Righetti PG (2002) Modern strategies for protein quantification in proteome analysis: advantages and limitations. Mass Spectrom Rev 21: 287-302
22. Hippler M, Klein J, Fink A, Allinger T and Hoerth P (2001) Towards functional proteomics of membrane protein complexes: analysis of thylakoid membranes from Chlamydomonas reinhardtii. Plant J 28: 595-606
23. Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson J, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen L-H, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen B-D, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D and Tyers M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183
24. Hu Y, Wang G, Chen GY, Fu X and Yao SQ (2003) Proteome analysis of Saccharomyces cerevisiae under metal stress by two-dimensional differential gel electrophoresis. Electrophoresis 24: 1458-1470
25. Huang F, Parmryd I, Nilsson F, Persson AL, Pakrasi HB, Andersson B and Norling B (2002) Proteomics of Synechocystis sp. Strain PCC 6803: identification of plasma membrane proteins. Mol Cell Proteomics 1: 956-966
26. Huber CG, Timperio A-M and Zolla L (2001) Isoforms of Photosystem II antenna proteins in different plant species revealed by liquid chromatography-electrospray ionization mass spectrometry. J Biol Chem 276: 45755-45761
27. Jansson S (1999) A guide to the Lhc genes and their relatives in Arabiodpsis. Trends in Plant Sci 4: 236-240
28. Kashino Y, Lauber WM, Carroll JA, Wang Q, Whitmarsh J, Satoh K and Pakrasi HB (2002) Proteomic analysis of a highly active Photosystem II preparation from the cyanobacterium Synechocystis sp. PCC 6803 reveals the presence of novel polypeptides. Biochemistry 41: 8004-8012
29. Kenyon GL, DeMarini DM, Fuchs E, Galas DJ, Kirsch JF, Leyh TS, Moos WH, Petsko GA, Ringe D, Rubin GM and Sheahan LC (2002) Defining the mandate of proteomics in the post-genomics era: workshop report. Mol Cell Proteomics 1: 763-780
30. Kieselbach T and Schröder WP (2003) The proteome of the chloroplast lumen of higher plants. Photosynth Res 78: 249-264 (this issue)
31. Kieselbach T, Hagman Å, Andersson B and Schröder WP (1998) The thylakoid lumen of chloroplasts: isolation and characterization. J Biol Chem 273: 6710-6716
32. Kieselbach T, Bystedt M, Hynds P, Robinson C and Schröder WP (2000) A peroxidase homologue and novel plastocyanin located by proteomics to the Arabidopsis chloroplast thylakoid lumen. FEBS Lett 480: 271-276
33. Koo AJK and Ohlrogge JB (2002) The predicted candidates of Arabidopsis plastid inner envelope membrane proteins and their expression profiles. Plant Physiol 130: 823-836
34. Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19: 47-56
35. Mann M, Hendrickson RC and Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 70: 437-473
36. Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M and Penny D (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 99: 12246-12251
37. Motohashi K, Kondoh A, Stumpp MT and Hisabori T (2001) Comprehensive survey of proteins targeted by chloroplast thioredoxin. Proc Natl Acad Sci USA 98: 11224-11229
38. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Barell D, Bateman A, Binns D, Biswas M, Bradley P, Bork P, Bucher P, Copley RR, Courcelle M, Das U, Durbin R, Falquet L, Fleischmann W, Griffiths-Jones S, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lopez R, Letunic I, Lonsdale D, Silventoinen V, Orchard SE, Pagni M, Peyruc D, Ponting CP, Selengut JD, Servant F, Sigrist CJA, Vaughan R and Zdobnov EM (2003) The InterPro database, 2003 brings increased coverage and new features. Nucleic Acids Res 31: 315-318
39. Nakamura Y, Kaneko T and Tabata S (2000) CyanoBase, the genome database for Synechocystis sp. strain PCC6803: status for the year 2000. Nucleic Acids Res 28: 72
40. Norling B, Zak E, Andersson B and Pakrasi H (1998) 2D-isolation of pure plasma and thylakoid membranes from the cyanobacterium Synechocystis sp. PCC 6803. FEBS Lett 436: 189-192
41. Normile D and Pennisi E (2002) Rice: boiled down to bare essentials. Science 296: 32-36
42. Orchard S, Kersey P, Hermjakob H and Apweiler R (2003a) Meeting review: the HUPO proteomics standards initiative meeting: towards common standards for exchanging proteomics data. Comp Funct Genom 4: 16-19
43. Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H and Apweiler R (2003b) Meeting review: progress in establishing common standards for exchanging proteomics data: the second meeting of the HUPO proteomics standards initiative. Comp Funct Genom 4: 203-206
44. Patton WF (2000) A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21: 1123-1144
45. Patton WF, Schulenberg B and Steinberg TH (2002) Two-dimensional gel electrophoresis: better than a poke in the ICAT? Curr Opin Biotechnol 13: 321-328
46. Peltier JB, Frisco G, Kalume DE, Roepstorff P, Nilsson F, Adamska I and van Wijk KJ (2000) Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12: 319-341
47. Peltier JB, Ytterberg J, Liberles DA, Roepstorff P and van Wijk KJ (2001) Identification of a 350 kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana. J Biol Chem 276: 16318-16327
48. Peltier JB, Emanuelsson O, Kalume DE, Ytterberg J, Friso G, Rudella A, Liberles DA, Soderberg L, Roepstorff P, von Heijne G and van Wijk KJ (2002) Central functions of the lumenal and peripheral thylakoid proteome of Arabidopsis determined by experimentation and genome-wide prediction. Plant Cell 14: 211-236
49. Roberts JKM (2002) Proteomics and a future generation of plant molecular biologists. Plant Mol Biol 48: 143-154
50. Rossignol M (2001) Analysis of the plant proteome. Curr Opin Biotechnol 12: 131-134
51. Sazuka T and Ohara O (1997) Towards a proteome project of cyanobacterium Synechocystis sp. strain PCC6803: linking 130 protein spots with their respective genes. Electrophoresis 18: 1252-1258
52. Sazuka T, Yamaguchi M and Ohara O (1999) Cyano2Dbase updated: linkage of 234 protein spots to corresponding genes through N-terminal microsequencing. Electrophoresis 20: 2160-2171
53. Scherl A, Coute Y, Deon C, Calle A, Kindbeiter K, Sanchez JC, Greco A, Hochstrasser D and Diaz JJ (2002) Functional proteomic analysis of human nucleolus. Mol Biol Cell 13: 4100-4109
54. Schleiff E, Eichacker LA, Eckart K, Becker T, Mirus O, Stahl T and Soll J (2003) Prediction of the plant beta-barrel proteome: a case study of the chloroplast outer envelope. Protein Sci 12: 748-759
55. Schubert M, Petersson UA, Haas BJ, Funk C, Schröder WP and Kieselbach T (2002) Proteome map of the chloroplast lumen of Arabidopsis thaliana. J Biol Chem 277: 8354-8365
56. Shaw MM and Riederer BM (2003) Sample preparation for two-dimensional gel electrophoresis. Proteomics 3: 1408-1417
57. Taylor CF, Paton N-W, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ and Oliver SG (2003). A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nat Biotechnol 21: 247-254
58. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I and Davison M (2001) Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1: 377-396
59. Tyers M and Mann M (2003) From genomics to proteomics. Nature 422: 193-197
60. van Wijk KJ (2001) Challenges and prospects of plant proteomics. Plant Physiol 126: 501-508
61. Voss T and Haberl P (2000) Observations on the reproducibility and matching efficiency of two-dimensional electrophoresis gels: consequences for comprehensive data analysis. Electrophoresis 21: 3345-5330
62. Wang Y, Sun J and Chitnis PR (2000) Proteomic study of the peripheral proteins from thylakoid membranes of the cyanobacterium Synechocystis sp. PCC 6803. Electrophoresis 21: 1746-1754
63. Whitelegge JP, Zhang H, Aguilera R, Taylor RM and Cramer WA (2002) Full subunit coverage liquid chromatography electrospray ionization mass spectrometry (LCMS+) of an oligomeric membrane protein. Mol Cell Proteomics 1: 816-827
64. Williams KL and Hochstrasser DF (1997) Introduction to the proteome. In: Wilkins MR, Williams KL. Appel RD and Hochstrasser DF (eds), Proteome Research: New Frontiers in Functional Genomics, pp 1-12. Springer-Verlag, Berlin
65. Wilson KA, McManus MT, Gordon ME and Jordan TW (2002) The proteomics of senescence in leaves of white clover, Trifolium repens (L.). Proteomics 2: 1114-1122
66. Wortman JR, Haas BJ, Hannick LI, Smith Jr RK, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR and Town CD (2003) Annotation of the Arabidopsis genome. Plant Physiol 132: 461-468
67. Wullschleger SD, Jansson S and Taylor G (2002) Genomics and forest biology. Populus emerges as the perennial favorite. Plant Cell 14: 2651-2655
68. Yamaguchi K and Subramanian AR (2000) The plastid ribosomal proteins. Identification of all the proteins in the 50S subunit of an organelle ribosome (chloroplast). J Biol Chem 275: 28466-28482
69. Yamaguchi K and Subramanian AR (2003) Proteomic identification of all plastid-specific ribosomal proteins in higher plant chloroplast 30S ribosomal subunit. Eur J Biochem 270: 190-205
70. Yamaguchi K, von Knoblauch K and Subramanian AR (2000) The plastid ribosomal proteins. Identification of all the proteins in the 30S subunit of an organelle ribosome (chloroplast). J Biol Chem 275: 28455-28465
71. Yu S-G, Stefansson H, Romanoska E and Albertsson P-Å (1994) Two dimensional electrophoresis of thylakoid membrane proteins and its application to microsequencing. Photosynth Res 41: 475-486
72. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L and Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296: 79-92
73. Yuan Q, Quyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J and Buell CR (2003) The T1GR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res 31: 229-233
74. 6f complex. J Biol Chem 276: 38159-38165
75. 6f complex of oxygenic photosynthesis. Proc Natl Acad Sci USA 100: 5160-5163
76. Zhou H, Ranish JA, Watts JD and Aebersold R (2002) Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nat Biotechnol 20: 512-515
77. Zolla L, Rinalducci S, Timperio AM and Huber CG (2002) Proteomics of light-harvesting proteins in different plant species. Analysis and comparison by liquid chromatography-electrospray ionization mass spectrometry. Photosystem I. Plant Physiol 130: 1938-1950
78. Zolla L, Timperio AM, Walcher W and Huber CG (2003) Proteomics of light-harvesting proteins in different plant species. Analysis and comparison by liquid chromatography-electrospray ionization mass spectrometry. Photosystem II. Plant Physiol 131: 198-214