Putting the pieces together: high-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus

Molecular and Cellular Proteomics

Volumn 12, Issue 1, 2013, Pages 106-119

  Abraham, Paul ^a,b   Gannone, Richard J ^b   Adams, Rachel M ^a,b   Kalluri, Udaya ^b   Tuskan, Gerald A ^b   Hettich, Robert L ^b  

^a UNIVERSITY OF TENNESSEE   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYSIS OF VARIANCE; ARTICLE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ION TRAP MASS SPECTROMETRY; LEAF DEVELOPMENT; MASS SPECTROMETER; NONHUMAN; PEPTIDE ANALYSIS; PEPTIDE MAPPING; PHOTOSYNTHESIS; PLANT LEAF; PLANT ROOT; PLANT STEM; POPULUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN ISOLATION; PROTEOMICS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TANDEM MASS SPECTROMETRY;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; PLANT LEAVES; PLANT PROTEINS; POPULUS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; TANDEM MASS SPECTROMETRY;

POPULUS;

EID: 84871882222     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M112.022996     Document Type: Article

References (57)

1. Ahrens, C. H., Brunner, E., Qeli, E., Basler, K., and Aebersold, R. (2010) Generating and navigating proteome maps using mass spectrometry. Nat. Rev. Mol. Cell Biol. 11, 789-801
2. Tuskan, G. A., DiFazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R., R., Bhalerao, R. P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G. L., Cooper, D., Coutinho, P. M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., Depamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J. C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D. R., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C. J., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de Peer, Y., and Rokhsar, D., (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596-1604 (Pubitemid 44414027)
3. Plomion, C., Lalanne, C., Claverol, S., Meddour, H., Kohler, A., Bogeat-Triboulot, M. B., Barre, A., Le Provost, G., Dumazet, H., Jacob, D., Bastien, C., Dreyer, E., de Daruvar, A., Guehl, J. M., Schmitter, J. M., Martin. F., and Bonneu, M. (2006) Mapping the proteome of poplar and application to the discovery of drought-stress responsive proteins. Proteomics 6, 6509-6527 (Pubitemid 46048390)
4. Kalluri, U. C., Hurst, G. B., Lankford, P. K., Ranjan, P., and Pelletier, D. A. (2009) Shotgun proteome profile of Populus developing xylem. Proteomics 9, 4871-4880
5. Shuford, C. M., Li, Q., Sun, Y. H., Chen, H. C., Wang, J., Shi, R., Sederoff, R. R., Chiang, V. L., and Muddiman, D. C. (2012) Comprehensive quantification of monolignol-pathway enzymes in populus trichocarpa by protein cleavage isotope dilution mass spectrometry. J Proteome Res. 11, 3390-3404
6. Abraham, P., Adams, R., Giannone, R. J., Kalluri, U., Ranjan, P., Erickson, B., Shah, M., Tuskan, G. A., and Hettich, R. L. (2012) Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J. Proteome Res. 11, 449-460
7. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. Anal. Chem. 68, 850-858
8. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd, (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (Pubitemid 32220565)
9. Botelho, D., Wall, M. J., Vieira, D. B., Fitzsimmons, S., Liu, F., and Doucette, A. (2010) Top-down and bottom-up proteomics of SDS-containing solutions following mass-based separation. J Proteome Res 9, 2863-2870
10. Wang, W., Tai, F. J., and Chen, S. N. (2008) Optimizing protein extraction from plant tissues for enhanced proteomics analysis. J. Separation Sci. 31, 2032-2039 (Pubitemid 352003186)
11. Wiśniewski, J. R., Zougman, A., Nagaraj, N., and Mann, M. (2009) Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362
12. 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 (Pubitemid 30230776)
13. Peck, S. C. (2005) Update on proteomics in Arabidopsis. Where do we go from here? Plant Physiol. 138, 591-599
14. 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 (Pubitemid 351929590)
15. Piques, M., Schulze, W. X., Höhne, M., Usadel, B., Gibon, Y., Rohwer, J., and Stitt, M. (2009) Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol. Syst. Biol. 5, 314
16. Second, T. P., Blethrow, J. D., Schwartz, J. C., Merrihew, G. E., MacCoss, M. J., Swaney, D. L., Russell, J. D., Coon, J. J., and Zabrouskov, V. (2009) Dual-pressure linear ion trap mass spectrometer improving the analysis of complex protein mixtures. Anal. Chem. 81 7757-7765
17. Giannone, R. J., Huber, H., Karpinets, T., Heimerl, T., Kuper, U., Rachel, R., Keller, M., Hettich, R. L., and Podar, M. (2011). "Proteomic characterization of cellular and molecular processes that enable the Nanoarchaeum equitans-Ignicoccus hospitalis relationship." PLoS One 6, e22942
18. Eng, J. K., Mccormack, A. L., and Yates, J. R. (1994) An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
19. Tabb, D. L., McDonald, W. H., and Yates, J. R., 3rd, (2002) DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics. J Proteome Res 1, 21-26
20. Edgar, R. C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461
21. Zybailov, B., Mosley, A. L., Sardiu, M. E., Coleman, M. K., Florens, L., and Washburn, M. P. (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5, 2339-2347 (Pubitemid 44330827)
22. Lochner, A., Giannone, R. J., Keller, M., Antranikian, G., Graham, D. E., and Hettich, R. L. (2011) Label-free quantitative proteomics for the extremely thermophilic bacterium Caldicellulosiruptor obsidiansis reveal distinct abundance patterns upon growth on cellobiose, crystalline cellulose, and switchgrass. J. Proteome Res. 10, 5302-5314
23. Yamada, T., Letunic, I., Okuda, S., Kanehisa, M., and Bork, P. (2011) iPath2.0: interactive pathway explorer. Nucleic Acids Res. 39, W412-415
24. Black, D. L. (2000) Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell 103, 367-370
25. Delalande, F., Carapito, C., Brizard, J. P., Brugidou, C., and Van Dorsselaer, A. (2005) Multigenic families and proteomics: extended protein characterization as a tool for paralog gene identification. Proteomics 5, 450-460 (Pubitemid 40262063)
26. Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data - The protein inference problem. Mol. Cell. Proteomics 4, 1419-1440 (Pubitemid 41555469)
27. Yang, X. Y., Dondeti, V. Dezube, R. Maynard, D. M. Geer, L. Y. Epstein, J. Chen, X. F. Markey S. P. and Kowalak J. A. (2004) DBParser: Web-based software for shotgun proteomic data analyses. J. Proteome Res. 3, 1002-1008 (Pubitemid 39425657)
28. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658 (Pubitemid 37082259)
29. Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K., and Nesvizhskii, A. (2004) The need for guidelines in publication of peptide and protein identification data. Mol. Cell. Proteomics 3, 531-533
30. Nagaraj, N., Kulak, N. A., Cox, J., Neuhauser, N., Mayr, K., Hoerning, O., Vorm, O., and Mann, M. (2012) System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol. Cell. Proteomics 11, M111.013722
31. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580 (Pubitemid 33032862)
32. Kuster, B., Schirle, M., Mallick, P., and Aebersold, R. (2005) Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell. Biol. 6, 577-583 (Pubitemid 40943048)
33. Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Frohlich, F., Cox, J., and Mann, M. (2011) Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol. Cell. Proteomics 10, M110.003699
34. 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
35. Kruger, N. J., and Ratcliffe, R. G. (2012) Pathways and fluxes: exploring the plant metabolic network. J. Exp. Bot. 63, 2243-2246
36. Liu, H., Sadygov, R. G., and Yates, J. R., 3rd (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193-4201 (Pubitemid 38943698)
37. Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E. L., Eddy, S. R., Bateman, A., and Finn, R. D. (2012) The Pfam protein families database. Nucleic Acids Res. 40, D290-301
38. Siemens, J., Keller, I., Sarx, J., Kunz, S., Schuller, A., Nagel, W., Schmülling, T., Parniske, M., and Ludwig-Müller, J. (2006) Transcriptome analysis of Arabidopsis clubroots indicate a key role for cytokinins in disease development. Mol. Plant Microbe Interact. 19, 480-494 (Pubitemid 43668272)
39. Ravanel, S., Gakiere, B., Job, D., and Douce, R. (1998) The specific features of methionine biosynthesis and metabolism in plants. Proc. Natl. Acad. Sci. U. S. A. 95, 7805-7812 (Pubitemid 28293335)
40. Guelette, B. S., Benning, U. F., and Hoffmann-Benning, S. (2012) Identification of lipids and lipid-binding proteins in phloem exudates from Arabidopsis thaliana. J Exp Bot 63, 3603-3616
41. Wen, J., Vanek-Krebitz, M., Hoffmann-Sommergruber, K., Scheiner, O., and Breiteneder, H. (1997) The potential of Betv1 homologues, a nuclear multigene family, as phylogenetic markers in flowering plants. Mol. Phylogenet. Evol. 8, 317-333 (Pubitemid 127348455)
42. Fujimoto, Y., Nagata, R., Fukasawa, H., Yano, K., Azuma, M., Iida, A., Sugimoto, S., Shudo, K., and Hashimoto, Y. (1998) Purification and cDNA cloning of cytokinin-specific binding protein from mung bean (Vigna radiata). Eur. J. Biochem. 258, 794-802 (Pubitemid 28557948)
43. Kleczkowski, L. A., Geisler, M., Ciereszko, I., and Johansson, H. (2004) UDP-glucose pyrophosphorylase. An old protein with new tricks. Plant Physiol. 134, 912-918 (Pubitemid 38398240)
44. Cseke, L. J., Ravinder, N., Pandey, A. K., and Podila, G. K. (2007) Identification of PTM5 protein interaction partners, a MADS-box gene involved in aspen tree vegetative development. Gene 391, 209-222 (Pubitemid 46356799)
45. Bohler, S., Sergeant, K., Lefèvre, I., Jolivet, Y., Hoffmann, L., Renaut, J., Dizengremel, P., and Hausman, J. F. (2010) Differential impact of chronic ozone exposure on expanding and fully expanded poplar leaves. Tree Physiol. 30, 1415-1432
46. Broun, P., Poindexter, P., Osborne, E., Jiang, C. Z., and Riechmann, J. L. (2004) WIN1, a transcriptional activator of epidermal wax accumulation in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 101, 4706-4711 (Pubitemid 38437475)
47. Volokita, M., Rosilio-Brami, T., Rivkin, N., and Zik, M. (2011) Combining comparative sequence and genomic data to ascertain phylogenetic relationships and explore the evolution of the large GDSL-lipase family in land plants. Mol. Biol. Evol. 28, 551-565
48. Nawrath, C. (2006) Unraveling the complex network of cuticular structure and function. Curr. Opin. Plant Biol. 9, 281-287
49. Reina, J. J., Guerrero, C., and Heredia, A. (2007) Isolation, characterization, and localization of AgaSGNH cDNA: a new SGNH-motif plant hydrolase specific to Agave americana L. leaf epidermis. J. Exp. Bot. 58, 2717-2731 (Pubitemid 47511741)
50. Kurdyukov, S., Faust, A., Nawrath, C., Bär, S., Voisin, D., Efremova, N., Franke, R., Schreiber, L., Saedler, H., Metraux, J. P., and Yephremov, A. (2006) The epidermis-specific extracellular BODYGUARD controls cuticle development and morphogenesis in Arabidopsis. Plant Cell 18, 321-339 (Pubitemid 43951296)
51. Peterhansel, C., and Maurino, V. G. (2011) Photorespiration redesigned. Plant Physiol. 155, 49-55
52. Baier, M., and Dietz, K. J. (1997) The plant 2-Cys peroxiredoxin BAS1 is a nuclear-encoded chloroplast protein: its expressional regulation, phylogenetic origin, and implications for its specific physiological function in plants. Plant J. 12, 179-190 (Pubitemid 27312774)
53. Baier, M., and Dietz, K. J. (1999) Protective function of chloroplast 2-cysteine peroxiredoxin in photosynthesis. Evidence from transgenic Arabidopsis. Plant Physiol. 119, 1407-1414 (Pubitemid 29388236)
54. Havaux, M. (1998) Carotenoids as membrane stabilizers in chloroplasts. Trends Plant Sci. 3, 147-151
55. Niyogi, K. K. (1999) Photoprotection revisited: Genetic and molecular approaches. Ann. Rev. Plant Physiol. Plant Mol. Biol. 50, 333-359
56. Havaux, M. (1998) Carotenoids as membrane stabilizers in chloroplasts. Trends Plant Sci. 3, 147-151
57. Niyogi, K. K. (1999) Photoprotection revisited: Genetic and molecular approaches. Ann. Rev. Plant Physiol. Plant Mol. Biol. 50, 333-359