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Proteomic Studies in Plants

  • Park, Ohk-Mae K. (Kumho Life and Environmental Science Laboratory)
  • Published : 2004.01.31

Abstract

Proteomics is a leading technology for the high-throughput analysis of proteins on a genome-wide scale. With the completion of genome sequencing projects and the development of analytical methods for protein characterization, proteomics has become a major field of functional genomics. The initial objective of proteomics was the large-scale identification of all protein species in a cell or tissue. The applications are currently being extended to analyze various functional aspects of proteins such as post-translational modifications, protein-protein interactions, activities and structures. Whereas the proteomics research is quite advanced in animals and yeast as well as Escherichia coli, plant proteomics is only at the initial phase. Major studies of plant proteomics have been reported on subcellular proteomes and protein complexes (e.g. proteins in the plasma membranes, chloroplasts, mitochondria and nuclei). Here several plant proteomics studies will be presented, followed by a recent work using multidimensional protein identification technology (MudPIT).

Keywords

References

  1. Aebersold, R. and Mann, M. (2003) Mass spectrometry-based proteomics. Nature 422, 198-207. https://doi.org/10.1038/nature01511
  2. Appella, E., Padlan, E. A. and Hunt, D. F. (1995) Analysis of the structure of naturally processed peptides bound by class I and class II major histocompatibility complex molecules. EXS 73, 105-119.
  3. Bae, M. S., Cho, E. J., Choi, E.-Y. and Park, O. K. (2003) Analysis of the Arabidopsis nuclear proteome and its response to cold stress. Plant J. 36, 652-663. https://doi.org/10.1046/j.1365-313X.2003.01907.x
  4. Borner, G. H., Lilley, K. S., Stevens, T. J. and Dupree, P. (2003) Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis. Plant Physiol. 132, 568-577. https://doi.org/10.1104/pp.103.021170
  5. Borner, G. H., Sherrier, D. J., Stevens, T. J., Arkin, I. T. and Dupree, P. (2002) Prediction of glycosylphosphatidylinositolanchored proteins in Arabidopsis. A genomic analysis. Plant Physiol. 129, 486-499. https://doi.org/10.1104/pp.010884
  6. Chivasa, S., Ndimba, B. K., Simon, W. J., Robertson, D., Yu, X. L., Knox, J. P., Bolwell, P. and Slabas, A. R. (2002) Proteomic analysis of the Arabidopsis thaliana cell wall. Electrophoresis 23, 1754-1765. https://doi.org/10.1002/1522-2683(200206)23:11<1754::AID-ELPS1754>3.0.CO;2-E
  7. Corthals, G. L., Wasinger, V. C., Hochstrasser, D. F. and Sanchez, J. C. (2000) The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 21, 1104-1115. https://doi.org/10.1002/(SICI)1522-2683(20000401)21:6<1104::AID-ELPS1104>3.0.CO;2-C
  8. Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F. and Whitehouse, C. M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71. https://doi.org/10.1126/science.2675315
  9. 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.
  10. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147. https://doi.org/10.1038/415141a
  11. Gomez, S. M., Nishio, J. N., Faull, K. F. and Whitelegge, J. P. (2002) The chloroplast grana proteome defined by intact mass measurements from liquid chromatography mass spectrometry. Mol. Cell Proteomics 1, 46-59. https://doi.org/10.1074/mcp.M100007-MCP200
  12. Gorg, A. (1991) Two-dimensional electrophoresis. Nature 349, 545-546. https://doi.org/10.1038/349545a0
  13. Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y. and Aebersold, R. (2000) Evaluation of two-dimensional gel electrophoresisbased proteome analysis technology. Proc. Natl. Acad. Sci. USA 97, 9390-9395. https://doi.org/10.1073/pnas.160270797
  14. Han, D. K., Eng, J., Zhou, H. and Aebersold R. (2001) Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946-951. https://doi.org/10.1038/nbt1001-946
  15. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183. https://doi.org/10.1038/415180a
  16. Houseman, B. T. and Mrksich, M. (2002) Towards quantitative assays with peptide chips: a surface engineering approach. Trends Biotechnol. 20, 279-281. https://doi.org/10.1016/S0167-7799(02)01984-4
  17. Huber, C. G., 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. https://doi.org/10.1074/jbc.M106700200
  18. Jung, E., Heller, M., Sanchez, J. C. and Hochstrasser, D. F. (2000) Proteomics meets cell biology: the establishment of subcellular proteomes. Electrophoresis 21, 3369-3377. https://doi.org/10.1002/1522-2683(20001001)21:16<3369::AID-ELPS3369>3.0.CO;2-7
  19. Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. 60, 2299-2301. https://doi.org/10.1021/ac00171a028
  20. Kawamura, Y. and Uemura, M. (2003) Mass spectrometric approach for identifying putative plasma membrane proteins of Arabidopsis leaves associated with cold acclimation. Plant J. 36, 141-154. https://doi.org/10.1046/j.1365-313X.2003.01864.x
  21. Keegstra, K. and Cline, K. (1999) Protein import and routing systems of chloroplasts. Plant Cell 11, 557-570. https://doi.org/10.1105/tpc.11.4.557
  22. Kersten, B., Burkle, L., Kuhn, E. J., Giavalisco, P., Konthur, Z., Lueking, A., Walter, G., Eickhoff, H. and Schneider, U. (2002) Large-scale plant proteomics. Plant Mol. Biol. 48, 133-141. https://doi.org/10.1023/A:1013784205292
  23. Koller, A., Washburn, M. P., Lange, B. M., Andon, N. L., Deciu, C., Haynes, P. A., Hays, L., Schieltz, D., Ulaszek, R., Wei, J., Wolters, D. and Yates, J. R. 3rd. (2002) Proteomic survey of metabolic pathways in rice. Proc. Natl. Acad. Sci. USA 99, 11969-11974. https://doi.org/10.1073/pnas.172183199
  24. Komatsu, S., Konishi, H., Shen, S. and Yang, G. (2003) Rice proteomics: a step toward functional analysis of the rice genome. Mol. Cell Proteomics 2, 2-10. https://doi.org/10.1074/mcp.R200008-MCP200
  25. Kruft, V., Eubel, H., Jansch, L., Werhahn, W. and Braun, H. P. (2001) Proteomic approach to identify novel mitochondrial proteins in Arabidopsis. Plant Physiol. 127, 1694-1710. https://doi.org/10.1104/pp.010474
  26. MacBeath, G. (2002) Protein microarrays and proteomics. Nat. Genet. Suppl. 32, 526-532. https://doi.org/10.1038/ng1037
  27. Mann, M. and Jensen, O. N. (2003) Proteomic analysis of posttranslational modifications. Nat. Biotechnol. 21, 255-261. https://doi.org/10.1038/nbt0303-255
  28. Millar, A. H., Sweetlove, L. J., Giege, P. and Leaver, C. J. (2001) Analysis of the Arabidopsis mitochondrial proteome. Plant Physiol. 127, 1711-1727. https://doi.org/10.1104/pp.010387
  29. Mitchell, P. (2002) A perspective on protein microarrays. Nat. Biotechnol. 20, 225-229. https://doi.org/10.1038/nbt0302-225
  30. Ndimba, B. K., Chivasa, S., Hamilton, J. M., Simon, W. J. and Slabas, A. R. (2003) Proteomic analysis of changes in the extracellular matrix of Arabidopsis cell suspension cultures induced by fungal elicitors. Proteomics 3, 1047-1059. https://doi.org/10.1002/pmic.200300413
  31. Pandey, A. and Mann, M. (2000) Proteomics to study genes and genomes. Nature 405, 837-846. https://doi.org/10.1038/35015709
  32. Patterson, S. D. and Aebersold, R. H. (2003) Proteomics: the first decade and beyond. Nat. Genet. Suppl. 33, 311-323. https://doi.org/10.1038/ng1106
  33. Peltier, J. B., Friso, G., Kalume, D. E., Roepstorff, P., Nilsson, F., Adamska, I. and van Wijk, K. J. (2000) Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12, 319-342. https://doi.org/10.1105/tpc.12.3.319
  34. Peltier, J. B., Ytterberg, J., Liberles, D. A., Roepstorff, P. and van Wijk, K. J. (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. https://doi.org/10.1074/jbc.M010503200
  35. Phizicky, E., Bastiaens, P. I., Zhu, H., Snyder, M. and Fields, S. (2003) Protein analysis on a proteomic scale. Nature 422, 208-215. https://doi.org/10.1038/nature01512
  36. Premstaller, A., Oberacher, H., Walcher, W., Timperio, A.-M., Zolla, L., Chervet, J.-P, Cavusoglu, N., Van Dorsellaer, A. and Huber, C. G. (2001) High-performance liquid chromatographyelectrospray ionization mass spectrometry using monolithic capillary columns for proteomic studies. Anal. Chem. 73, 2390- 2396. https://doi.org/10.1021/ac010046q
  37. Prime, T., Sherrier, D., Mahon, P., Packman, L. and Dupree, P. (2000) A proteomic analysis of organelles from Arabidopsis thaliana. Electrophoresis 21, 3488-3499. https://doi.org/10.1002/1522-2683(20001001)21:16<3488::AID-ELPS3488>3.0.CO;2-3
  38. Rakwal, R. and Agrawal, G. K. (2003) Rice proteomics: current status and future perspectives. Electrophoresis 24, 3378-3389. https://doi.org/10.1002/elps.200305586
  39. Rouquie, D., Peltier, J. B., MarquisMansion, M., Tournaire, C., Doumas, P. and Rossignol, M. (1997) Construction of a directory of tobacco plasma membrane proteins by combined two-dimensional gel electrophoresis and protein sequencing. Electrophoresis 18, 654-660. https://doi.org/10.1002/elps.1150180352
  40. Santoni, V., Kieffer, S., Desclaux, D., Masson, F. and Rabilloud, T. (2000) Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties. Electrophoresis 21, 3329-3344. https://doi.org/10.1002/1522-2683(20001001)21:16<3329::AID-ELPS3329>3.0.CO;2-F
  41. Santoni, V., Rouquie, D., Doumas, P., Mansion, M., Boutry, M., Degand, H., Dupree, P., Packman, L., Sherrier, J., Prime, T., Bauw, G., Posada, E., Rouze, P., Dehais, P., Sahnoun, I., Barlier, I. and Rossignol, M. (1998) Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J. 16, 633-641. https://doi.org/10.1046/j.1365-313x.1998.00335.x
  42. Schweitzer, B., Roberts, S., Grimwade, B., Shao, W., Wang, M., Fu, Q., Shu, Q., Laroche, I., Zhou, Z., Tchernev, V. T., Christiansen, J., Velleca, M. and Kingsmore, S. F. (2002) Multiplexed protein profiling on microarrays by rolling-circle mplification. Nat. Biotechnol. 20, 359-365. https://doi.org/10.1038/nbt0402-359
  43. Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen, P., Shevchenko, A., Boucherie, H. and Mann, M. (1996) Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. USA 93, 14440-14445. https://doi.org/10.1073/pnas.93.25.14440
  44. van Wijk, K. J. (2001) Challenges and prospects of plant proteomics. Plant Physiol. 126, 501-508. https://doi.org/10.1104/pp.126.2.501
  45. Vener, A. V., Harms, A., Sussman, M. R. and Vierstra, R. D. (2001) Mass spectrometric resolution of reversible protein phosphorylation in photosynthetic membranes of Arabidopsis thaliana. J. Biol. Chem. 276, 6959-6966. https://doi.org/10.1074/jbc.M009394200
  46. Washburn, M. P., Wolters, D. and Yates, J. R. 3rd. (2001) Largescale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247. https://doi.org/10.1038/85686
  47. Werhahn, W. and Braun, H. P. (2002) Biochemical dissection of the mitochondrial proteome from Arabidopsis thaliana by three-dimensional gel electrophoresis. Electrophoresis 23, 640-646. https://doi.org/10.1002/1522-2683(200202)23:4<640::AID-ELPS640>3.0.CO;2-F
  48. Werhahn, W., Niemeyer, A., Jansch, L., Kruft, V., Schmitz, U. K. and Braun, H. P. (2001) Purification and characterization of the preprotein translocase of the outer mitochondrial membrane from Arabidopsis. Identification of multiple forms of TOM20. Plant Physiol. 125, 943-954. https://doi.org/10.1104/pp.125.2.943
  49. Whitelegge, J. P. (2002) Plant proteomics: BLASTing out of a MudPIT. Proc. Natl. Acad. Sci. USA 99, 11564-11566. https://doi.org/10.1073/pnas.192449199
  50. Whitelegge, J. P., Gundersen, C. B. and Faull, K. F. (1998) Electrospray-ionization mass spectrometry of intact intrinsic membrane proteins. Protein Sci. 7, 1423-1430. https://doi.org/10.1002/pro.5560070619
  51. Wilkins, M. R., Pasquali, C., Appel, R. D., Ou, K., Golaz, O., Sanchez, J. C., Yan, J. X., Gooley, A. A., Hughes, G., Humphery-Smith, I., Williams, K. L. and Hochstrasser, D. F. (1996) From proteins to proteomes: large scale protein identification by two-dimensional electrophoresis and amino acid analysis. Biotechnology 14, 61-65. https://doi.org/10.1038/nbt0196-61
  52. Wolters, D. A., Washburn, M. P. and Yates, J. R. 3rd. (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690. https://doi.org/10.1021/ac010617e
  53. Zivy, M. and de Vienne, D. (2000) Proteomics: a link between genomics, genetics and physiology. Plant Mol. Biol. 44, 575-580. https://doi.org/10.1023/A:1026525406953
  54. Zolla, L., Rinalducci, S., Timperio, A. M. and Huber, C. G. (2002) Proteomics of light-harvesting proteins in different plant species. Analysis and comparison by liquid chromatographyelectrospray ionization mass spectrometry. Photosystem I. Plant Physiol. 130, 1938-1950. https://doi.org/10.1104/pp.009803
  55. Zolla, L., Timperio, A. M., Walcher, W. and Huber, C. G. (2003) Proteomics of light-harvesting proteins in different plant species. Analysis and comparison by liquid chromatographyelectrospray ionization mass spectrometry. Photosystem II. Plant Physiol. 131, 198-214. https://doi.org/10.1104/pp.012823

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