The green proteome: Challenges in plant proteomics

Frontiers in Plant Science

Volumn 2, Issue MAR, 2011, Pages

  Heazlewood, Joshua L ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84873028352     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2011.00006     Document Type: Article

References (42)

1. Ahn, N. G., Shabb, J. B., Old, W. M., and Resing, K. A. (2007). Achieving in-depth proteomics profiling by mass spectrometry. ACS Chem. Biol. 2, 39-52.
2. Arabidopsis Genome Initiative. (2000). Analysis of the genome sequence of the fowering plant Arabidopsis thaliana. Nature 408, 796-815.
3. Baerenfaller, K., Grossmann, J., Grobei, M. A., Hull, R., Hirsch-Hoffmann, M., Yalovsky, S., Zimmermann, P., Grossniklaus, U., Gruissem, W., and Baginsky, S. (2008). Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320, 938-941.
4. Castellana, N. E., Payne, S. H., Shen, Z., Stanke, M., Bafna, V., and Briggs, S. P. (2008). Discovery and revision of Arabidopsis genes by proteogenomics. Proc. Natl. Acad. Sci. U.S.A. 105, 21034-21038.
5. Deutsch, E. W., Lam, H., and Aebersold, R. (2008). PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9, 429-434.
6. Eubel, H., Meyer, E. H., Taylor, N. L., Bussell, J. D., O'Toole, N., Heazlewood, J. L., Castleden, I., Small, I. D., Smith, S. M., and Millar, A. H. (2008). Novel proteins, putative membrane transporters, and an integrated metabolic network are revealed by quantitative proteomic analysis of Arabidopsis cell culture peroxisomes. Plant Physiol. 148, 1809-1829.
7. Ferro, M., Brugière, S., Salvi, D., Seigneurin-Berny, D., Court, M., Moyet, L., Ramus, C., Miras, S., Mellal, M., Le Gall, S., Kieffer-Jaquinod, S., Bruley, C., Garin, J., Joyard, J., Masselon, C., and Rolland, N. (2010). AT_CHLORO, A comprehensive chloroplast pro-teome database with subplastidial localization and curated information on envelope proteins. Mol. Cell. Proteomics 9, 1063-1084.
8. Gao, J., Agrawal, G. K., Thelen, J. J., and Xu, D. (2009). P3DB: a plant protein phosphorylation database. Nucleic Acids Res. 37, D960-D962.
9. Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B. M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W. L., Chen, L., Cooper, B., Park, S., Wood, T. C., 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, R. M., 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.
10. Gruhler, A., Schulze, W. X., Matthiesen, R., Mann, M., and Jensen, O. N. (2005). Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol. Cell. Proteomics 4, 1697-1709.
11. Han, X., Aslanian, A., and Yates, J. R. III. (2008). Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 12, 483-490.
12. Heazlewood, J. L., Durek, P., Hummel, J., Selbig, J., Weckwerth, W., Walther, D., and Schulze, W. X. (2008). PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res. 36, D1015-D1021.
13. Heazlewood, J. L., and Millar, A. H. (2006). "Plant pro-teomics: challenges and resources," in Plant Proteomics, ed. C. Finnie (Oxford: Blackwell Publishing), 1-31.
14. Heazlewood, J. L., Verboom, R. E., Tonti-Filippini, J., Small, I., and Millar, A. H. (2007). SUBA: the Arabidopsis sub cellular database. Nucleic Acids Res. 35, D213-D218.
15. Huang, S., Taylor, N. L., Narsai, R., Eubel, H., Whelan, J., and Millar, A. H. (2009). Experimental analysis of the rice mitochondrial proteome, its biogenesis, and heterogeneity. Plant Physiol. 149, 719-734.
16. Hynek, R., Svensson, B., Jensen, O. N., Barkholt, V., and Finnie, C. (2009). The plasma membrane proteome of germinating barley embryos. Proteomics 9, 3787-3794.
17. Isaacson, T., Damasceno, C. M. B., Saravanan, R. S., He, Y., Catala, C., Saladie, M., and Rose, J. K. C. (2006). Sample extraction techniques for enhanced proteomic analysis of plant tissues. Nat. Protoc. 1, 769-774.
18. Joshi, H. J., Hirsch-Hoffmann, M., Baerenfaller, K., Gruissem, W., Baginsky, S., Schmidt, R., Schulze, W. X., Sun, Q., van Wijk, K., Egelhofer, V., Wienkoop, S., Weckwerth, W., Bruley, C., Rolland, R., Toyoda, T., Nakagam, H., Jones, A., Briggs, S. P., Castleden, I., Tanz, S., Millar, A. H., and Heazlewood, J. L. (2011). MASCP gator: an aggregation portal for the visualization of Arabidopsis proteomics data. Plant Physiol. 155, 259-270.
19. Kerk, N. M., Ceserani, T., Tausta, S. L., Sussex, I. M., and Nelson, T. M. (2003). Laser capture micro dissection of cells from plant tissues. Plant Physiol. 132, 27-35.
20. Lalonde, S., Sero, A., Pratelli, R. j., Pilot, G., Chen, J., Sardi, M. I., Parsa, S. A., Kim, D.-Y., Acharya, B. R., Stein, E.V., Hu, H.-C., Villiers, F., Takeda, K., Yang, Y., Han, Y. S., Schwacke, R., Chiang, W., Kato, N., Loqu, D., Assmann, S. M., Kwak, J. M., Schroeder, J., Rhee, S. Y., and Frommer, W. B. (2010). A membrane protein/ signaling protein interaction network for Arabidopsis version AMPv2. Front. Physiol. 1:24. doi: 10.3389/ fphys.2010.00024
21. Lange, V., Picotti, P., Domon, B., and Aebersold, R. (2008). Selected reaction monitoring for quantitative pro-teomics: a tutorial. Mol. Syst. Biol. 4, 222.
22. MacLean, D., Burrell, M. A., Studholme, D. J., and Jones, A. M. (2008). PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data. BMC Res. Notes 1, 30. doi: 10.1186/1756-0500-1-30
23. Mann, M. (2006). Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 7, 952-958.
24. Mann, M., and Jensen, O. N. (2003). Proteomic analysis of post-translational modifcations. Nat. Biotechnol. 21, 255-261.
25. Marouga, R., David, S., and Hawkins, E. (2005). The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem. 382, 669-678.
26. Nakagami, H., Sugiyama, N., Mochida, K., Daudi, A., Yoshida, Y., Toyoda, T., Tomita, M., Ishihama, Y., and Shirasu, K. (2010). Large-scale comparative phospho-proteomics identifies conserved phosphorylation sites in plants. Plant Physiol. 153, 1161-1174.
27. Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., and Aebersold, R. (2009). Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138, 795-806.
28. Polpitiya, A. D., Qian, W.-J., Jaitly, N., Petyuk, V. A., Adkins, J. N., Camp, D. G., Anderson, G. A., and Smith, R. D. (2008). DAnTE: a statistical tool for quantitative analysis of-omics data. Bioinformatics 24, 1556-1558.
29. Rappsilber, J., and Mann, M. (2002). What does it mean to identify a protein in proteomics? Trends Biochem. Sci. 27, 74-78.
30. Salehi-Reyhani, A., Kaplinsky, J., Burgin, E., Novakova, M., deMello, A. J., Templer, R. H., Parker, P., Neil, M. A. A., Ces, O., French, P., Willison, K. R., and Klug, D. (2011). A first step towards practical single cell pro-teomics: a microfuidic antibody capture chip with TIRF detection. Lab Chip 11, 1256-1261.
31. Schulze, W. X., and Usadel, B. (2010). Quantization in mass-spectrometry-based proteomics. Annu. Rev. Plant Biol. 61, 491-516.
32. Sheoran, I. S., Ross, A. R. S., Olson, D. J. H., and Sawhney, V. K. (2007). Proteomic analysis of tomato (Lycopersicon esculentum) pollen. J. Exp. Bot. 58, 3525-3535.
33. Sheoran, I. S., Ross, A. R. S., Olson, D. J. H., and Sawhney, V. K. (2009). Compatibility of plant protein extraction methods with mass spectrometry for proteome analysis. Plant Sci. 176, 99-104.
34. Sun, Q., Zybailov, B., Majeran, W., Friso, G., Olinares, P. D. B., and van Wijk, K. J. (2009). PPDB, the plant proteomics database at Cornell. Nucleic Acids Res. 37, D969-D974.
35. Taylor, N. L., Heazlewood, J. L., and Millar, A. H. (2011). The Arabidopsis thaliana 2D gel mitochondrial proteome: refining the value of reference maps for assessing protein abundance, contaminants and post-translational modifications. Proteomics. doi: 10.1002/pmic.201000620. [Epub ahead of print].
36. Thome, M., Skrablin, M. D., and Brandt, S. P. (2006). Tissue-specific mechanical microdissection of higher plants. Physiol. Plant. 128, 383-390.
37. Vizcaíno, J. A., Côté, R., Reisinger, F., M. Foster, Mueller, M., Rameseder, J., Hermjakob, H., and Martens, L. (2009). A guide to the proteomics identifcations database proteomics data repository. Proteomics 9, 4276-4283.
38. Weckwerth, W., Baginsky, S., van Wijk, K., Heazlewood, J. L., and Millar, A. H. (2008). The multinational Arabidopsis steering subcommittee for proteomics assembles the largest proteome database resource for plant systems biology. J. Proteome Res. 7, 4209-4210.
39. Wienkoop, S., Zoeller, D., Ebert, B., Simon-Rosin, U., Fisahn, J., Glinski, M., and Weckwerth, W. (2004). Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification. Phytochemistry 65, 1641-1649.
40. Wilkins, M. (2009). Proteomics data mining. Expert Rev. Proteomics 6, 599-603.
41. Zieske, L. R. (2006). A perspective on the use of iTRAQ™ reagent technology for protein complex and profiling studies. J. Exp. Bot. 57, 1501-1508.
42. Zybailov, B., Rutschow, H., Friso, G., Rudella, A., Emanuelsson, O., Sun, Q., and van Wijk, K. J. (2008). Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS ONE 3, e1994. doi: 10.1371/journal.pone.0001994