Cell wall proteomics of crops

Frontiers in Plant Science

Volumn 4, Issue FEB, 2013, Pages

  Komatsu, Setsuko ^a   Yanagawa, Yuki ^b  

^a NATIONAL INSTITUTE OF CROP SCIENCE   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

Cell wall; Crop; Drought stress; Flooding stress; Proteomics

Indexed keywords

EID: 84899677746     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2013.00017     Document Type: Review

References (60)

1. Averyhart-Fullard, V., Datta, K., and Marcus, A. (1988). A hydroxyproline-rich protein in the soybean cell wall. Proc. Natl. Acad. Sci. U.S.A. 85, 1082-1085.
2. Baxter-Burrell, A., Yang, Z., Springer, P. S., and Bailey-Serres, J. (2002). RopGAP4-dependent Rop GTPase rheostat control of Arabidopsis oxygen deprivation tolerance. Science 296, 2026-2028.
3. Bayer, E. M., Bottrill, A. R., Walshaw, J., Vigouroux, M., Naldrett, M. J., Thomas, C. L., et al. (2006). Arabidopsiscell wall proteome defined using multidimensional protein identification technology. Proteomics 6, 301-311.
4. Bhushan, D., Pandey, A., Chattopadhyay, A., Choudhary, M. K., Chakraborty, S., Datta, A., et al. (2006). Extracellular matrix proteome of chickpea (Cicer arietinum L.) illustrates pathway abundance, novel protein functions and evolutionary perspect. J. Proteome Res. 5, 1711-1720.
5. Bhushan, D., Pandey, A., Choudhary, M. K., Datta, A., Chakraborty, S., and Chakraborty, N. (2007). Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress. Mol. Cell. Proteomics 6, 1868-1884.
6. Boudart, G., Jamet, E., Rossignol, M., Lafitte, C., Borderies, G., Jauneau, A., et al. (2005). Cell wall proteins in apoplastic fluids of Arabidopsis thaliana rosettes: identification by mass spectrometry and bioinformatics. Proteomics 5, 212-221.
7. Chen, X. Y., Kim, S. T., Cho, W. K., Rim, Y., Kim, S., Kim, S. W., et al. (2009). Proteomics of weakly bound cell wall proteins in rice calli. J. Plant Physiol. 166, 675-685.
8. Chivasa, S., Ndimba, B. K., Simon, W. J., Robertson, D., Yu, X. L., Knox, J. P., et al. (2002). Proteomic analysis of theArabidopsis thaliana cell wall. Electrophoresis 23, 1754-1765.
9. Chivasa, S., Simon, W. J., Yu, X.-L., Yalpani, N., and Slabas, A. R. (2005). Pathogen elicitor-induced changes in the maize extracellular matrix proteome. Proteomics 5, 4894-4904.
10. Cho, W. K., Chen, X. Y., Chu, H., Rim, Y., Kim, S., Kim, S. T., et al. (2009). Proteomic analysis of the secretome of rice calli. Physiol. Plant. 135, 331-341.
11. Cosgrove, D. J. (2001). Wall structure and wall loosening. A look backwards and forwards. Plant Physiol. 125, 131-134.
12. Dahal, D., Pich, A., Braun, H. P., and Wydra, K. (2010). Analysis of cell wall proteins regulated in stem of susceptible and resistant tomato species after inoculation with Ralstonia solanacearum: a proteomic approach. Plant Mol. Biol. 73, 643-658.
13. Demura, T., and Ye, Z.-H. (2010). Regulation of plant biomass production. Curr. Opin. Plant Biol. 13, 299-304.
14. Devos, M. K., and Gale, D. M. (2000). Genome relationships: the grass model in current research. Plant Cell 12, 637-643.
15. Dordas, C., Hasinoff, B. B., Rivoal, J., and Hill, R. D. (2004). Class-1 hemoglobins, nitrate and NO levels in anoxic maize cell-suspension cultures. Planta 219, 66-72.
16. Flint-Garcia, S. A., Thuillet, A. C., Yu, J., and Pressoir, G. (2005). Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J. 44, 1054-1064.
17. Garcia, R., Bermejo, C., Grau, C., Perez, R., Rodriguez-Pena, J. M., Francois, J., et al. (2004). The global transcriptional response to transient cell wall damage in Saccharomyces cerevisiae and its regulation by the cell integrity signaling pathway. J. Biol. Chem. 279, 15183-15195.
18. Haridas, V., Higuchi, M., Jaytilake, G. S., Baily, D., Mujoo, K., Blake, M. E., et al. (2001). Avicins: triterpenoid saponins from Acacia victoriae (Bentham) induce apoptosis by mitochondrial perturbation. Proc. Natl. Acad. Sci. U.S.A. 98, 5821-5826.
19. Hoecker, N., Lamkemeyer, T., Sarholz, B., Paschold, A., Fladerer, C., Madlung, J., et al. (2008). Analysis of nonadditive protein accumulation in young primary roots of a maize (Zea mays L.) F1-hybrid compared to its parental inbred lines. Proteomics 8, 3882-3894.
20. Huckelhoven, R. (2007). Cell wall-associated mechanisms of disease resistance and susceptibility. Annu. Rev. Phytopathol. 45, 101-127.
21. Jamet, E., Albenne, C., Boudart, G., Irshad, M., Canut, H., and Pont-Lezica, R. (2008a). Recent advances in plant cell wall proteomics. Proteomics 8, 893-908.
22. Jamet, E., Boudart, G., Borderies, G., Charmont, S., Lafitte, C., Rossignol, M., et al. (2008b). Isolation of plant cell wall proteins. Methods Mol. Biol. 425, 187-201.
23. Jamet, E., Canut, H., Boudart, G., and Pont-Lezica, R. F. (2006). Cell wall proteins: a new insight through proteomics. Trends Plant Sci. 11, 33-39.
24. Jung, Y. H., Jeong, S. H., Kim, S. H., Singh, R., Lee, J. E., Cho, Y. S., et al. (2008). Systematic secretome analyses of rice leaf and seed callus suspension-cultured cells: workflow development and establishment of high-density two-dimensional gel reference maps. J. Proteome Res. 7, 5187-5210.
25. Katayose, Y., Kanamori, H., Shimomura, M., Ohyanagi, H., Ikawa, H., Minami, H., et al. (2012). DaizuBase, an integrated soybean genome database including BAC-based physical maps. Breed. Sci. 61, 661-664.
26. Komatsu, S., Hiraga, S., and Yanagawa, Y. (2012). Proteomics techniques for the development of flood tolerant crops. J. Proteome Res. 11, 68-78.
27. Komatsu, S., Kobayashi, Y., Nishizawa, K., Nanjo, Y., and Furukawa, K. (2010). Comparative proteomics analysis of differentially expressed proteins in soybean cell wall during flooding stress. Amino Acids 39, 1435-1449.
28. Kong, F. J., Oyanagi, A., and Komatsu, S. (2009). Cell wall proteome of wheat roots under flooding stress using gel-based and LC MS/MS-based proteomics approaches. Biochim. Biophys. Acta 1804, 124-136.
29. Lim, S., Chisholm, K., Coffin, R. H., Peters, R. D., Al-Mughrabi, K. I., Wang-Pruski, G., et al. (2012). Protein profiling in potato (Solanum tuberosum L.) leaf tissues by differential centrifugation. J. Proteome Res. 11, 2594-2601.
30. Liu, F., Vantoai, T., Moy, L., Bock, G., Linford, L. D., and Quackenbush, J. (2005). Global transcription profiling reveals novel insights into hypoxic response in Arabidopsis. Plant Physiol. 137, 1115-1129.
31. Ma, J., Morrow, D. J., Fernandes, J., and Walbot, V. (2006). Comparative profiling of the sense and antisense transcriptome of maize lines. Genome Biol. 7:R22. doi: 10.1186/gb-2006-7-3-r22
32. Mattana, M., Coraggio, I., Bertani, A., and Reggiani, R. (1994). Expression of the enzyme of nitrate reduction during the anaerobic germination of rice. Plant Physiol. 106, 1605-1608.
33. Millar, D. J., Whitelegge, J. P., Bindschedler, L. V., Rayon, C., Boudet, A. M., Rossignol, M., et al. (2009). The cell wall and secretory proteome of a tobacco cell line synthesizing secondary wall. Proteomics 9, 2355-2372.
34. Minic, Z., Jamet, E., Négroni, L., Arsene der Garabedian, P., Zivy, M., and Jouanin, L. (2007). A sub-proteome ofArabidopsis thaliana mature stems trapped on Concanavalin A is enriched in cell wall glycoside hydrolases. J. Exp. Bot. 58, 2503-2512.
35. Moore, J. P., Nguema-Ona, E., Chevalier, L., Lindsey, G. G., Brandt, W. F., Lerouge, P., et al. (2006). Response of the leaf cell wall to desiccation in the resurrection plant Myrothamnus flabellifolius. Plant Physiol. 141, 651-662.
36. Pandey, A., Rajamani, U., Verma, J., Subba, P., Chakraborty, N., Datta, A., et al. (2010). Identification of extracellular matrix proteins of rice (Oryza sativa L.) involved in dehydration-responsive network: a proteomic approach. J. Proteome Res. 9, 3443-3464.
37. Pauly, M., and Keegstra, K. (2010). Plant cell wall polymers as precursors for biofuels. Curr. Opin. Plant Biol. 13, 305-312.
38. Pereira, C. S., Ribeiro, J. M., Vatulescu, A. D., Findlay, K., MacDougall, A. J., and Jackson, P. A. (2011). Extensin network formation in Vitis vinifera callus cells is an essential and causal event in rapid and H(2)O(2)-induced reduction in primary cell wall hydration. BMC Plant Biol. 11:106. doi: 10.1186/1471-2229-11-106
39. Reggiani, R. (2006). A role for ethylene in low-oxygen signaling in rice roots. Amino Acids 30, 299-301.
40. Rice Full-Length cDNA Consortium. (2003). Collection mapping, and annotation of over 28000 cDNA clones from japonica rice. Science 301, 376-379.
41. Roberts, K. (2001). How the cell wall acquired a cellular context. Plant Physiol. 125, 127-130.
42. Rossignol, M., Peltier, J.-B., Mock, H.-P., Matros, A., Maldonado, A. M., and Jorrin, J. V. (2006). Plant proteome analysis: a 2004-2006 update. Proteomics 6, 5529-5548.
43. Saab, I. N., and Sachs, M. M. (1996). A flooding-induced xyloglucan endotransglycosylase homolog in maize is responsive to ethylene and associated with aerenchyma. Plant Physiol. 112, 385-391.
44. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Nakao, M., et al. (2008). Genome structure of the legume, Lotus japonicus. DNA Res. 15, 227-239.
45. Schmutz, J., Cannon, S. B., Schlueter, J., Ma, J., Mitros, T., Nelson, W., et al. (2010). Genome sequence of the palaeopolyploid soybean. Nature 463, 178-183.
46. Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., et al. (2009). The B73 maize genome: complexity, diversity, and dynamics. Science 326, 1112-1115.
47. Soares, N. C., Francisco, R., Ricardo, C. P., and Jackson, P. A. (2007). Proteomics of ionically bound and soluble extracellular proteins in Medicago truncatula leaves. Proteomics 7, 2070-2082.
48. Soares, N. C., Francisco, R., Vielba, J. M., Ricardo, C. P., and Jackson, P. A. (2009). Associating wound-related changes in the apoplast proteome of Medicago with early steps in the ROS signal-transduction pathway. J. Proteome Res. 8, 2298-2309.
49. Somerville, C., Bauer, S., Brininstool, G., Facette, M., Hamann, T., Milne, J., et al. (2004). Toward a systems approach to understanding plant cell walls. Science 306, 2206-2211.
50. Stupar, R. M., and Springer, N. M. (2006). Cis-transcripioanl variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics 173, 2199-2210.
51. The International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature436, 793-800.
52. The Rice Annotation Project. (2007). Crated genome annotation of Oryza sativa ssp. Japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17, 175-183.
53. Vicre, M., Lerouxel, O., Farrant, J., Lerouge, P., and Driouich, A. (2004). Composition and desiccation-induced alterations of the cell wall in the resurrection plant Craterostigma wilmsii. Physiol. Plant. 120, 229-239.
54. Wang, S. B., Hu, Q., Sommerfeld, M., and Chen, F. (2004). Cell wall proteomics of the green alga Haematococcus pluvialis (Chlorophyceae). Proteomics 4, 692-708.
55. Watson, B. S., Lei, Z., Dixon, R. A., and Sumner, L. W. (2004). Proteomics of Medicago sativa cell walls. Phytochemistry 65, 1709-1720.
56. Young, N. D., Debellé, F., Oldroyd, G. E., Geurts, R., Cannon, S. B., Udvardi, M. K., et al. (2011). The Medicagogenome provides insight into the evolution of rhizobial symbioses. Nature 480, 520-524.
57. Zhang, Y., Giboulot, A., Zivy, M., Valot, B., Jamet, E., and Albenne, C. (2011). Combining various strategies to increase the coverage of the plant cell wall glycoproteome. Phytochemistry 72, 1109-1123.
58. Zhou, L., Bokhari, S. A., Dong, C. J., and Liu, J. Y. (2011). Comparative proteomics analysis of the root apoplasts of rice seedlings in response to hydrogen peroxide. PLoS ONE 6:e16723. doi: 10.1371/journal.pone.0016723
59. Zhu, J., Alvarez, S., Marsh, E. L., Lenoble, M. E., Cho, I. J., Sivaguru, M., et al. (2007). Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically bound proteins under water deficit. Plant Physiol. 145, 1533-1548.
60. Zhu, J., Chen, S., Alvarez, S., Asirvatham, V. S., Schachtman, D. P., Wu, Y., et al. (2006). Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins. Plant Physiol. 140, 311-325.