Expression, Prediction and Function of the Thylakoid Proteome in Higher Plants and Green Algae

  • Klaas van Wijk
Part of the Advances in Photosynthesis and Respiration book series (AIPH, volume 23)

The thylakoid membrane system contains not only the photosynthetic electron transport chain, with about 100 proteins, but also many additional peripheral and integral thylakoid proteins, most of which do not have a known function. Many of these additional thylakoid proteins are expected to be involved in binding and stabilization of cofactors, or folding and turnover of thylakoid proteins.


Matrix Assisted Laser Desorption Ionization Thylakoid Membrane Thylakoid Protein Thylakoid Membrane Protein Lumenal Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Aebersold R and Mann M (2003) Mass spectrometry-based pro-teomics. Nature 422: 198-207PubMedGoogle Scholar
  2. Aro EM and Ohad I (2003) Redox regulation of thylakoid protein phosphorylation. Antioxid Redox Signal 5: 55-67PubMedGoogle Scholar
  3. Aro EM, Rokka A and Vener AV (2004) Determination of phos-phoproteins in higher plant thylakoids. Methods Mol Biol 274: 271-286PubMedGoogle Scholar
  4. Bae MS, Cho EJ, Choi EY and Park OK (2003) Analysis of the Arabidopsis nuclear proteome and its response to cold stress. Plant J 36: 652-663PubMedGoogle Scholar
  5. Bennett J, Shaw EK and Michel H (1988) Cytochrome b6f complex is required for phosphorylation of light-harvesting chlorophyll a/b complex II in chloroplast photosynthetic mem-branes. Eur J Biochem 171: 95-100PubMedGoogle Scholar
  6. Ben-Shem A, Frolow F and Nelson N (2003) Crystal structure of plant photosystem I. Nature 426: 630-635PubMedGoogle Scholar
  7. Blonder J, Goshe MB, Moore RJ, Pasa-Tolic L, Masselon CD, Lipton MS and Smith RD (2002) Enrichment of inte-gral membrane proteins for proteomic analysis using liquid chromatography-tandem mass spectrometry. J Proteome Res 1: 351-360PubMedGoogle Scholar
  8. Blonder J, Conrads TP, Yu LR, Terunuma A, Janini GM, Issaq HJ, Vogel JC and Veenstra TD (2004a) A detergent- and cyanogen bromide-free method for integral membrane proteomics: ap-plication to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics 4: 31-45Google Scholar
  9. Blonder J, Hale ML, Lucas DA, Schaefer CF, Yu LR, Conrads TP, Issaq HJ, Stiles BG and Veenstra TD (2004b) Proteomic analysis of detergent-resistant membrane rafts. Electrophore-sis 25: 1307-1318Google Scholar
  10. Casano LM, Lascano HR, Martin M and Sabater B (2004) Topol-ogy of the plastid Ndh complex and its NDH-F subunit in thylakoid membranes. Biochem J 382: 145-155PubMedGoogle Scholar
  11. Chen M, Choi Y, Voytas DF and Rodermel S (2000) Mutations in the Arabidopsis VAR2 locus cause leaf variegation due to the loss of a chloroplast FtsH protease. Plant J 22: 303-313PubMedGoogle Scholar
  12. Dennison C and Lovrien R (1997) Three phase partitioning: con-centration and purification of proteins. Protein Exp Purif 11: 149-161Google Scholar
  13. Diner BA, Ries DF, Cohen BN and Metz JG (1988) COOH-terminal processing of polypeptide D1 of the photosystem II reaction center of Scenedesmus obliquus is necessary for the assembly of the oxygen-evolving complex. J Biol Chem 263: 8972-8980PubMedGoogle Scholar
  14. Eichacker LA and Henry R (2001) Function of a chloroplast SRP in thylakoid protein export. Biochim Biophys Acta 1541: 120-134.PubMedGoogle Scholar
  15. Elrad D and Grossman AR (2004) A genome’s-eye view of the light-harvesting polypeptides of Chlamydomonas reinhardtii. Curr Genet 45: 61-75PubMedGoogle Scholar
  16. Ferro M, Seigneurin-Berny D, Rolland N, Chapel A, Salvi D, Garin J and Joyard J (2000) Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast mem-brane proteins. Electrophoresis 21: 3517-3526PubMedGoogle Scholar
  17. 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: 325-345PubMedGoogle Scholar
  18. Fincher V, Dabney-Smith C and Cline K (2003) Functional as-sembly of thylakoid delta pH-dependent/Tat protein transport pathway components in vitro. Eur J Biochem 270: 4930-4941PubMedGoogle Scholar
  19. Friso G, Giacomelli L, Ytterberg AJ, Peltier JB, Rudella A, Sun Q and Wijk KJ (2004) In-depth analysis of the thylakoid mem-brane proteome of Arabidopsis thaliana chloroplasts: new proteins, new functions, and a plastid proteome database. Plant Cell 16: 478-499PubMedGoogle Scholar
  20. Gallardo K, Job C, Groot SP, Puype M, Demol H, Vandekerck-hove J and Job D (2002) Proteomics of Arabidopsis seed ger-mination. A comparative study of wild- type and gibberellin-deficient seeds. Plant Physiol 129: 823-837PubMedGoogle Scholar
  21. Gallardo K, Le Signor C, Vandekerckhove J, Thompson RD and Burstin J (2003) Proteomics of Medicago truncatula seed de-velopment establishes the time frame of diverse metabolic processes related to reserve accumulation. Plant Physiol 133: 664-682PubMedGoogle Scholar
  22. Ganeteg U, Kulheim C, Andersson J and Jansson S (2004) Is each light-harvesting complex protein important for plant fitness? Plant Physiol 134: 502-509PubMedGoogle Scholar
  23. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Re-mor 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 organi-zation of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147PubMedGoogle Scholar
  24. Ge Y, Lawhorn BG, ElNaggar M, Strauss E, Park JH, Begley TP and McLafferty FW (2002) Top down characterization of larger proteins (45 kDa) by electron capture dissociation mass spectrometry. J Am Chem Soc 124: 672-678PubMedGoogle Scholar
  25. Giglione C and Meinnel T (2001) Organellar peptide deformy-lases: universality of the N-terminal methionine cleavage mechanism. Trends Plant Sci 6: 566-572.PubMedGoogle Scholar
  26. Giglione C, Vallon O and Meinnel T (2003) Control of protein life-span by N-terminal methionine excision. EMBO J 22: 13-23PubMedGoogle Scholar
  27. Gomez SM, Nishio JN, Faull KF and Whitelegge JP (2002) The chloroplast grana proteome defined by intact mass measure-ments from liquid chromatography mass spectrometry. Mol Cell Proteomics 1: 46-59PubMedGoogle Scholar
  28. Gomez SM, Bil KY, Aguilera R, Nishio JN, Faull KF and White-legge JP (2003) Transit peptide cleavage sites of integral thy-lakoid membrane proteins. Mol Cell Proteomics 2: 1068-1085PubMedGoogle Scholar
  29. Goshe MB and Smith RD (2003) Stable isotope-coded proteomic mass spectrometry. Curr Opin Biotechnol 14: 101-109PubMedGoogle Scholar
  30. Gupta R, He Z and Luan S (2002a) Functional relationship of cytochrome c(6) and plastocyanin in Arabidopsis. Nature 417: 567-571Google Scholar
  31. Gupta R, Mould RM, He Z and Luan S (2002b) A chloroplast FKBP interacts with and affects the accumulation of Rieske subunit of cytochrome bf complex. Proc Nat Acad Sci USA 99: 15806-15811Google Scholar
  32. Gutman BL and Niyogi KK (2004) Chlamydomonas and Ara-bidopsis. A dynamic duo. Plant Physiol 135: 607-610PubMedGoogle Scholar
  33. Hansson M and Vener AV (2003) Identification of three previ-ously unknown in vivo protein phosphorylation sites in thy-lakoid membranes of Arabidopsis thaliana. Mol Cell Pro-teomics 2: 550-559Google Scholar
  34. Hind G, Marshak DR and Coughlan SJ (1995) Spinach thylakoid polyphenol oxidase: cloning, characterization, and relation to a putative protein kinase. Biochemistry 34: 8157-8164PubMedGoogle Scholar
  35. Hippler M, Klein J, Fink A, Allinger T and Hoerth P (2001) To-wards functional proteomics of membrane protein complexes: analysis of thylakoid membranes from Chlamydomonas rein-hardtii. Plant J 28: 595-606PubMedGoogle Scholar
  36. 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 I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michal-ickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtele-jnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, 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: 180-183PubMedGoogle Scholar
  37. Hsu JL, Huang SY, Chow NH and Chen SH (2003) Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 75: 6843-6852PubMedGoogle Scholar
  38. Huber CG, Timperio AM and Zolla L (2001) Isoforms of photo-system II antenna proteins in different plant species revealed by liquid chromatography-electrospray ionization mass spectrometry. J Biol Chem 276: 45755-45761PubMedGoogle Scholar
  39. Inagaki N, Yamamoto Y, Mori H and Satoh K (1996) Carboxyl-terminal processing protease for the D1 precursor protein: cloning and sequencing of the spinach cDNA. Plant Mol Biol 30: 39-50PubMedGoogle Scholar
  40. Keegstra K and Cline K (1999) Protein import and routing sys-tems of chloroplasts. Plant Cell 11: 557-570PubMedGoogle Scholar
  41. Kelleher NL (2004) Top-down proteomics. Anal Chem 76: 197A-203APubMedGoogle Scholar
  42. Kelleher NL, Zubarev RA, Bush K, Furie B, Furie BC, McLaf-ferty FW and Walsh CT (1999) Localization of labile post-translational modifications by electron capture dissociation: the case of gamma-carboxyglutamic acid. Anal Chem 71: 4250-4253PubMedGoogle Scholar
  43. Kessler F, Schnell D and Blobel G (1999) Identification of pro-teins associated with plastoglobules isolated from pea ( Pisum sativum L.) chloroplasts. Planta 208: 107-113PubMedGoogle Scholar
  44. Kieselbach T, Hagman A, Andersson B and Schr öder WP (1998) The thylakoid lumen of chloroplasts. Isolation and character-ization. J Biol Chem 273: 6710-6716PubMedGoogle Scholar
  45. Klostermann E, Droste Gen Helling I, Carde JP and Schune-mann D (2002) The thylakoid membrane protein ALB3 associates with the cpSecY- translocase in Arabidopsis thaliana. Biochem J 368: 777-781PubMedGoogle Scholar
  46. Koussevitzky S, Ne’eman E and Harel E (2004) Import of polyphenol oxidase by chloroplasts is enhanced by methyl jas-monate. Planta 219: 412-419PubMedGoogle Scholar
  47. Krogh A, Larsson B, von Heijne G and Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580PubMedGoogle Scholar
  48. Kyte J and Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132PubMedGoogle Scholar
  49. Lew S and London E (1997) Simple procedure for reversed-phase high-performance liquid chromatographic purification of long hydrophobic peptides that form transmembrane helices. Anal Biochem 251: 113-116PubMedGoogle Scholar
  50. Liao DI, Qian J, Chisholm DA, Jordan DB and Diner BA (2000) Crystal structures of the photosystem II D1 C-terminal pro-cessing protease. Nat Struct Biol 7: 749-753PubMedGoogle Scholar
  51. Lindahl M, Tabak S, Cseke L, Pichersky E, Andersson B and Adam Z (1996) Identification, characterization, and molecu-lar cloning of a homologue of the bacterial FtsH protease in chloroplasts of higher plants. J Biol Chem 271: 29329-29334PubMedGoogle Scholar
  52. Luche S, Santoni V and Rabilloud T (2003) Evaluation of non-ionic and zwitterionic detergents as membrane protein sol-ubilizers in two-dimensional electrophoresis. Proteomics 3: 249-253PubMedGoogle Scholar
  53. Mattoo AK and Edelman M (1987) Intramembrane translocation and posttranslational palmitoylation of the chloroplast 32-kDa herbicide-binding protein. Proc Nat Acad Sci USA 84: 1497-1501PubMedGoogle Scholar
  54. McLafferty FW, Fridriksson EK, Horn DM, Lewis MA and Zubarev RA (1999) Techview: biochemistry. Biomolecule mass spectrometry. Science 284: 1289-1290PubMedGoogle Scholar
  55. Michel H, Hunt DF, Shabanowitz J and Bennett J (1988) Tandem mass spectrometry reveals that three photosystem II proteins of spinach chloroplasts contain N-acetyl-O-phosphothreonine at their NH2 termini. J Biol Chem 263: 1123-1130PubMedGoogle Scholar
  56. Michel H, Griffin PR, Shabanowitz J, Hunt DF and Bennett J (1991) Tandem mass spectrometry identifies sites of three post-translational modifications of spinach light-harvesting chlorophyll protein II. Proteolytic cleavage, acetylation, and phosphorylation. J Biol Chem 266: 17584-17591PubMedGoogle Scholar
  57. Molloy MP, Herbert BR, Williams KL and Gooley AA (1999) Extraction of Escherichia coli proteins with organic solvents prior to two-dimensional electrophoresis. Electrophoresis 20: 701-704PubMedGoogle Scholar
  58. Moore M, Goforth RL, Mori H and Henry R (2003) Functional interaction of chloroplast SRP/FtsY with the ALB3 translo-case in thylakoids: substrate not required. J Cell Biol 162: 1245-1254PubMedGoogle Scholar
  59. Mori H and Cline K (2001) Post-translational protein transloca-tion into thylakoids by the Sec and DeltapH-dependent path-ways. Biochim Biophys Acta 1541: 80-90PubMedGoogle Scholar
  60. Moseley JL, Allinger T, Herzog S, Hoerth P, Wehinger E, Mer-chant S and Hippler M (2002) Adaptation to Fe-deficiency requires remodeling of the photosynthetic apparatus. EMBO J 21: 6709-6720PubMedGoogle Scholar
  61. Munekage Y, Hojo M, Meurer J, Endo T, Tasaka M and Shikanai T (2002) PGR5 is involved in cyclic electron flow around pho-tosystem I and is essential for photoprotection in Arabidopsis. Cell 110: 361-371PubMedGoogle Scholar
  62. Newman SM, Eannetta NT, Yu H, Prince JP, de Vicente MC, Tanksley SD and Steffens JC (1993) Organisation of the tomato polyphenol oxidase gene family. Plant Mol Biol 21: 1035-1051PubMedGoogle Scholar
  63. Nixon PJ, Trost JT and Diner BA (1992) Role of the carboxy terminus of polypeptide D1 in the assembly of a functional water-oxidizing manganese cluster in photosystem II of the cyanobacterium Synechocystis sp. PCC 6803: assembly re-quires a free carboxyl group at C-terminal position 344. Bio-chemistry 31: 10859-10871Google Scholar
  64. Oblong JE and Lamppa GK (1992) Identification of two struc-turally related proteins involved in proteolytic processing of precursors targeted to the chloroplast. EMBO J 11: 4401-4409PubMedGoogle Scholar
  65. Oelm üller R, Herrmann RG and Pakrasi HB (1996) Molecular studies of CtpA, the carboxyl-terminal processing protease for the D1 protein of the photosystem II reaction center in higher plants. J Biol Chem 271: 21848-21852Google Scholar
  66. Ong SE, Foster LJ and Mann M (2003) Mass spectrometric-based approaches in quantitative proteomics. Methods 29: 124-130PubMedGoogle Scholar
  67. Ort DR and Yocum CF (eds) (1996) Oxygenic photosynthesis: the light reactions, Advances in Photosynthesis, Vol 4. Kluwer Academic Publishers, Dordrecht, The NetherlandsGoogle Scholar
  68. Parmryd I, Shipton CA, Swiezewska E, Dallner G and Andersson B (1997) Chloroplastic prenylated proteins. FEBS Lett 414: 527-531PubMedGoogle Scholar
  69. Patrie SM, Charlebois JP, Whipple D, Kelleher NL, Hendrick-son CL, Quinn JP, Marshall AG and Mukhopadhyay B (2004) Construction of a hybrid quadrupole/fourier transform ion cyclotron resonance mass spectrometer for versatile MS/MS above 10 kDa. J Am Soc Mass Spectrom 15: 1099-1108PubMedGoogle Scholar
  70. Patterson SD and Aebersold RH (2003) Proteomics: the first decade and beyond. Nat Genet 33 (Suppl): 311-323PubMedGoogle Scholar
  71. Peltier G and Cournac L (2002) Chlororespiration. Annu Rev Plant Biol 53: 523-550Google Scholar
  72. Peltier JB, Friso G, Kalume DE, Roepstorff P, Nilsson F, Adamska I and van Wijk KJ (2000) Proteomics of the chloroplast. Sys-tematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12: 319-342PubMedGoogle Scholar
  73. 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: 211-236PubMedGoogle Scholar
  74. Peltier JB, Ytterberg AJ, Sun Q and Van Wijk KJ (2004) New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast and versatile fractionation strategy. J Biol Chem 279: 49367-49383PubMedGoogle Scholar
  75. Pursiheimo S, Rintamaki E, Baena-Gonzalez E and Aro EM (1998) Thylakoid protein phosphorylation in evolutionally di-vergent species with oxygenic photosynthesis. FEBS Lett 423: 178-182PubMedGoogle Scholar
  76. Reisfeld A, Mattoo AK and Edelman M (1982) Processing of a chloroplast-translated membrane protein in vivo. Analysis of the rapidly synthesized 32,000-dalton shield protein and its precursor in Spirodela oligorrhiza. Eur J Biochem 124: 125-129PubMedGoogle Scholar
  77. Rey P, Gillet B, Romer S, Eymery F, Massimino J, Peltier G and Kuntz M (2000) Over-expression of a pepper plastid lipid-associated protein in tobacco leads to changes in plastid ultrastructure and plant development upon stress. Plant J 21: 483-494PubMedGoogle Scholar
  78. Richter S and Lamppa GK (1998) A chloroplast processing en-zyme functions as the general stromal processing peptidase. Proc Nat Acad Sci USA 95: 7463-7468PubMedGoogle Scholar
  79. Robinson C, Thompson SJ and Woolhead C (2001) Multiple pathways used for the targeting of thylakoid proteins in chloro-plasts. Traffic 2: 245-251PubMedGoogle Scholar
  80. Rochaix JD (2002) Chlamydomonas, a model system for study-ing the assembly and dynamics of photosynthetic complexes. FEBS Lett 529: 34-38PubMedGoogle Scholar
  81. Rochaix J-D, Goldschmidt-Clermont M and Merchant S (eds) (1998) The molecular biology of chloroplasts and mitochon-dria in Chlamydomonas. Advances in Photosynthesis, Vol 7. Kluwer Academic Publishers, Dordrecht, the NetherlandsGoogle Scholar
  82. Sakamoto W, Zaltsman A, Adam Z and Takahashi Y (2003) Co-ordinated regulation and complex formation of yellow var-iegated1 and yellow variegated2, chloroplastic FtsH metallo-proteases involved in the repair cycle of photosystem II in Arabidopsis thylakoid membranes. Plant Cell 15: 2843-2855PubMedGoogle Scholar
  83. Santoni V, Molloy M and Rabilloud T (2000) Membrane proteins and proteomics: un amour impossible? Electrophoresis 21: 1054-1070PubMedGoogle Scholar
  84. Sazanov LA, Burrows PA and Nixon PJ (1998) The plastid ndh genes code for an NADH-specific dehydrogenase: isolation of a complex I analogue from pea thylakoid membranes. Proc Nat Acad Sci USA 95: 1319-1324PubMedGoogle Scholar
  85. Scheller HV, Jensen PE, Haldrup A, Lunde C and Knoetzel J (2001) Role of subunits in eukaryotic photosystem I. Biochim Biophys Acta 1507: 41-60PubMedGoogle Scholar
  86. Schiltz S, Gallardo K, Huart M, Negroni L, Sommerer N and Burstin J (2004) Proteome reference maps of vegetative tissues in pea. An investigation of nitrogen mobilization from leaves during seed filling. Plant Physiol 135: 2241-2260PubMedGoogle Scholar
  87. Schubert M, Petersson UA, Haas BJ, Funk C, Schroder WP and Kieselbach T (2002) Proteome map of the chloroplast lumen of Arabidopsis thaliana. J Biol Chem 277: 8354-8365PubMedGoogle Scholar
  88. Schuenemann D, Amin P, Hartmann E and Hoffman NE (1999) Chloroplast SecY is complexed to SecE and involved in the translocation of the 33-kDa but not the 23-kDa subunit of the oxygen-evolving complex. J Biol Chem 274: 12177-12182PubMedGoogle Scholar
  89. Seigneurin-Berny D, Rolland N, Garin J and Joyard J (1999) Technical advance: differential extraction of hydrophobic pro-teins from chloroplast envelope membranes: a subcellular-specific proteomic approach to identify rare intrinsic mem-brane proteins. Plant J 19: 217-228PubMedGoogle Scholar
  90. Shestakov SV, Anbudurai PR, Stanbekova GE, Gadzhiev A, Lind LK and Pakrasi HB (1994) Molecular cloning and character-ization of the ctpA gene encoding a carboxyl-terminal pro-cessing protease. Analysis of a spontaneous photosystem II-deficient mutant strain of the cyanobacterium Synechocystis sp. PCC 6803. J Biol Chem 269: 19354-19359PubMedGoogle Scholar
  91. Shi LX and Schroder WP (2004) The low molecular mass sub-units of the photosynthetic supracomplex, photosystem II. Biochim Biophys Acta 1608: 75-96PubMedGoogle Scholar
  92. Sommer A, Ne’eman E, Steffens JC, Mayer AM and Harel E (1994) Import, targeting, and processing of a plant polyphenol oxidase. Plant Physiol 105: 1301-1311PubMedGoogle Scholar
  93. Stauber EJ, Fink A, Markert C, Kruse O, Johanningmeier U and Hippler M (2003) Proteomics of Chlamydomonas reinhardtii light-harvesting proteins. Eukaryot Cell 2: 978-994PubMedGoogle Scholar
  94. Steen H and Mann M (2004) The ABC’s (and XYZ’s) of peptide sequencing. Nat Rev Mol Cell Biol 5: 699-711PubMedGoogle Scholar
  95. Storf S, Stauber EJ, Hippler M and Schmid VH (2004) Pro-teomic analysis of the photosystem I light-harvesting an-tenna in tomato ( Lycopersicon esculentum). Biochemistry 43: 9214-9224PubMedGoogle Scholar
  96. Stroebel D, Choquet Y, Popot JL and Picot D (2003) An atypical haem in the cytochrome b(6)f complex. Nature 426: 413-418PubMedGoogle Scholar
  97. Su Q and Boschetti A (1993) Partial purification and properties of enzymes involved in the processing of a chloroplast import protein from Chlamydomonas reinhardii. Eur J Biochem 217: 1039-1047PubMedGoogle Scholar
  98. Sun Q, Emanuelsson O and van Wijk KJ (2004) Analysis of cu-rated and predicted plastid subproteomes of Arabidopsis. Sub-cellular compartmentalization leads to distinctive proteome properties. Plant Physiol 135: 723-734PubMedGoogle Scholar
  99. Takahashi Y, Yasui TA, Stauber EJ and Hippler M (2004) Com-parison of the subunit compositions of the PSI-LHCI super-complex and the LHCI in the green alga Chlamydomonas rein-hardtii. Biochemistry 43: 7816-7823PubMedGoogle Scholar
  100. Tarr GE and Crabb JW (1983) Reverse-phase high-performance liquid chromatography of hydrophobic proteins and fragments thereof. Anal Biochem 131: 99-107PubMedGoogle Scholar
  101. Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY and Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37: 914-939PubMedGoogle Scholar
  102. Tu CJ, Peterson EC, Henry R and Hoffman NE (2000) The L18 domain of light-harvesting chlorophyll proteins binds to cpSRP43. J Biol Chem 275: 13187-13190PubMedGoogle Scholar
  103. van Wijk KJ (2000) Proteomics of the chloroplast: experimenta-tion and prediction. Trends Plant Sci 5: 420-425Google Scholar
  104. van Wijk K (2004) Plastid proteomics. Plant Physiol Biochem 42: 963-977PubMedGoogle Scholar
  105. VanderVere PS, Bennett TM, Oblong JE and Lamppa GK (1995) A chloroplast processing enzyme involved in precursor matu-ration shares a zinc-binding motif with a recently recognized family of metalloendopeptidases. Proc Nat Acad Sci USA 92: 7177-7181PubMedGoogle Scholar
  106. Vener AV, Harms A, Sussman MR and Vierstra RD (2001) Mass spectrometric resolution of reversible protein phosphorylation in photosynthetic membranes of Arabidopsis thaliana. J Biol Chem 276: 6959-6966PubMedGoogle Scholar
  107. Washburn MP, Wolters D and Yates JR, 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19: 242-247PubMedGoogle Scholar
  108. Weigel M, Pesaresi P and Leister D (2003) Tracking the function of the cytochrome c6-like protein in higher plants. Trends Plant Sci 8: 513-517PubMedGoogle Scholar
  109. Westerlund I, Von Heijne G and Emanuelsson O (2003) LumenP-a neural network predictor for protein localization in the thy-lakoid lumen. Protein Sci 12: 2360-2366PubMedGoogle Scholar
  110. Whitelegge JP, Gomez SM and Faull KF (2003) Proteomics of membrane proteins. Adv Protein Chem 65: 271-307PubMedGoogle Scholar
  111. Wollman FA, Minai L and Nechushtai R (1999) The biogenesis and assembly of photosynthetic proteins in thylakoid mem-branes. Biochim Biophys Acta 1411: 21-85PubMedGoogle Scholar
  112. Wu CC and Yates JR (2003) The application of mass spec-trometry to membrane proteomics. Nat Biotechnol 21: 262-267PubMedGoogle Scholar
  113. Yamamoto Y, Inagaki N and Satoh K (2001) Overexpression and characterization of carboxyl-terminal processing protease for precursor D1 protein: regulation of enzyme-substrate inter-action by molecular environments. J Biol Chem 276: 7518-7525PubMedGoogle Scholar
  114. Yu F, Park S and Rodermel SR (2004) The Arabidopsis FtsH metalloprotease gene family: interchangeability of sub-units in chloroplast oligomeric complexes. Plant J 37: 864-876PubMedGoogle Scholar
  115. Zabrouskov V, Giacomelli L, Van Wijk KJ and McLafferty FW (2003) A new approach for plant proteomics: characterization of chloroplast proteins of Arabidopsis thaliana by top-down mass spectrometry. Mol Cell Proteomics 2: 1253-1260PubMedGoogle Scholar
  116. Zer H and Ohad I (2003) Light, redox state, thylakoid-protein phosphorylation and signaling gene expression. Trends Biochem Sci 28: 467-470PubMedGoogle Scholar
  117. Zhang H and Cramer WA (2004) Purification and crystallization of the cytochrome b6f complex in oxygenic photosynthesis. Methods Mol Biol 274: 67-78PubMedGoogle Scholar
  118. Zhong R, Wan J, Jin R and Lamppa G (2003) A pea antisense gene for the chloroplast stromal processing peptidase yields seedling lethals in Arabidopsis: survivors show defective GFP import in vivo. Plant J 34: 802-812PubMedGoogle Scholar
  119. 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: 1938-1950PubMedGoogle Scholar
  120. 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: 198-214PubMedGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Klaas van Wijk
    • 1
  1. 1.Department of Plant BiologyCornell UniversityIthacaUSA

Personalised recommendations