Medicago PhosphoProtein Database: A repository for Medicago truncatula phosphoprotein data

Frontiers in Plant Science

Volumn 3, Issue JUN, 2012, Pages

  Rose, Christopher M ^a   Venkateshwaran, Muthusubramanian ^a   Grimsrud, Paul A ^a   Westphall, Michael S ^a   Sussman, Michael R ^a   Coon, Joshua J ^a,b   Ané, Jean Michel ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

CAD; ETD; Medicago truncatula; Phosphoproteome; Proteomics

Indexed keywords

EID: 84873736627     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2012.00122     Document Type: Review

References (57)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
2. Ané, J. M., Zhu, H., and Frugoli, J. (2008). Recent advances in Medicago truncatula genomics. Int. J. Plant Genomics 2008, 256597.
3. Arrighi, J. F., Barre, A., Ben Amor, B., Bersoult, A., Soriano, L. C., Mirabella, R., de Carvalho-Niebel, F., Journet, E. P., Gherardi, M., Huguet, T., Geurts, R., Dénarié, J., Rouge, P., and Gough, C. (2006). The Medicago truncatula lysin [corrected] motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes. Plant Physiol.142, 265-279.
4. Ben Amor, B., Shaw, S. L., Oldroyd, G. E. D., Maillet, F., Penmetsa, R. V., Cook, D., Long, S. R., Dénarié, J., and Gough, C. (2003). The NFP locus of Medicago truncatula controls an early step of nod factor signal transduction upstream of a rapid calcium flux and root hair deformation. Plant J. 34, 495-506.
5. Bonfante, P., and Genre, A. (2010). Mechanisms underlying beneficial plant-fungus interactions in mycorrhizal symbiosis. Nat. Commun. 1, 48.
6. Brelles-Marino, G. Q., and Ané, J. M. (2008). "Nod factors and the molecular dialogue in the rhizobia-legume interaction, " in Nitrogen Fixation Research Progress, ed. G. N. Couto (New York: Nova Science Publishers, Inc.), 173-227.
7. Brown, J. W., Shaw, P. J., Shaw, P., and Marshall, D. F. (2005). Arabidopsis nucleolar protein database (AtNoPDB). Nucleic Acids Res. 33, D633-D636.
8. Chen, T., Zhu, H., Ke, D., Cai, K., Wang, C., Gou, H., Hong, Z., and Zhang, Z. (2012). A MAP kinase kinase interacts with SymRK and regulates nodule organogenesis in Lotus japonicus. Plant Cell 24, 823-838.
9. Colditz, F., and Braun, H. P. (2010). Medicago truncatula proteomics. J. Proteomics 73, 1974-1985.
10. Cook, D. R. (1999). Medicago truncatula-a model in the making! Curr. Opin. Plant Biol. 2, 301-304.
11. Dénarié, J., Debellé, F., and Promé, J. C. (1996). Rhizobium lipo-chitooligosaccharide nodulation factors: signaling molecules mediating recognition and morphogenesis. Annu. Rev. Biochem. 65, 503-535.
12. Durek, P., Schmidt, R., Heazlewood, J. L., Jones, A., MacLean, D., Nagel, A., Kersten, B., and Schulze, W. X. (2010). PhosPhAt: the Arabidopsis thaliana phosphorylation site database. an update. Nucleic Acids Res. 38, D828-D834.
13. Ehrhardt, D. W., Wais, R., and Long, S. R. (1996). Calcium spiking in plant root hairs responding to rhizobium nodulation signals. Cell 85, 673-681.
14. Endre, G., Kereszt, A., Kevei, Z., Mihacea, S., Kaló, P., and Kiss, G. B. (2002). A receptor kinase gene regulating symbiotic nodule development. Nature 417, 962-966.
15. Ferro, M., Brugiere, 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 proteome database with subplastidial localization and curated information on envelope proteins. Mol. Cell. Proteomics 9, 1063-1084.
16. Gao, J., Agrawal, G. K., Thelen, J. J., and Xu, D. (2009). P3DB: a plant protein phosphorylation database. Nucleic Acids Res. 37, D960-D962.
17. Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004). Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964.
18. Graham, P. H., and Vance, C. P. (2003). Legumes: importance and constraints to greater use. Plant Physiol. 131, 872-877.
19. Grimsrud, P. A., den Os, D., Wenger, C. D., Swaney, D. L., Schwartz, D., Sussman, M. R., Ane, J. M., and Coon, J. J. (2010). Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol. 152, 19-28.
20. Heazlewood, J. L., Verboom, R. E., Tonti-Filippini, J., Small, I., and Millar, A. H. (2007). SUBA: the Arabidopsissubcellular database. Nucleic Acids Res. 35, D213-D218.
21. Horvath, B., Yeun, L. H., Domonkos, A., Halasz, G., Gobbato, E., Ayaydin, F., Miro, K., Hirsch, S., Sun, J., Tadege, M., Ratet, P., Mysore, K. S., Ane, J. M., Oldroyd, G. E., and Kalo, P. (2011). Medicago truncatula IPD3 is a member of the common symbiotic signaling pathway required for rhizobial and mycorrhizal symbioses. Mol. Plant Microbe Interact. 24, 1345-1358.
22. Huber, S. C. (2007). Exploring the role of protein phosphorylation in plants: from signalling to metabolism. Biochem. Soc. Trans. 35, 28-32.
23. Hummel, J., Niemann, M., Wienkoop, S., Schulze, W., Steinhauser, D., Selbig, J., Walther, D., and Weckwerth, W. (2007). ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics 8, 216. doi: 10.1186/1471-2105-8-216
24. Jayaraman, D., Forshey, K. L., Grimsrud, P. A., and Ané, J. M. (2012). Leveraging proteomics to understand plant-microbe interactions. Front. Plant Sci. 3:44. doi: 10.3389/fpls.2012.00044
25. Jones, K. M., Kobayashi, H., Davies, B. W., Taga, M. E., and Walker, G. C. (2007). How rhizobial symbionts invade plants: the Sinorhizobium-Medicago model. Nat. Rev. Microbiol. 5, 619-633.
26. Kevei, Z., Lougnon, G., Mergaert, P., Horvath, G. V., Kereszt, A., Jayaraman, D., Zaman, N., Marcel, F., Regulski, K., Kiss, G. B., Kondorosi, A., Endre, G., Kondorosi, E., and Ané, J. M. (2007). 3-hydroxy-3-methylglutaryl coenzyme a reductase 1 interacts with NORK and is crucial for nodulation in Medicago truncatula. Plant Cell 19, 3974-3989.
27. Kleffmann, T., Hirsch-Hoffmann, M., Gruissem, W., and Baginsky, S. (2006). Plprot: a comprehensive proteome database for different plastid types. Plant Cell Physiol. 47, 432-436.
28. 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.
29. Laugesen, S., Messinese, E., Hem, S., Pichereaux, C., Grat, S., Ranjeva, R., Rossignol, M., and Bono, J. J. (2006). Phosphoproteins analysis in plants: a proteomic approach. Phytochemistry 67, 2208-2214.
30. Lefebvre, B., Timmers, T., Mbengue, M., Moreau, S., Herve, C., Toth, K., Bittencourt-Silvestre, J., Klaus, D., Deslandes, L., Godiard, L., Murray, J. D., Udvardi, M. K., Raffaele, S., Mongrand, S., Cullimore, J., Gamas, P., Niebel, A., and Ott, T. (2010). A remorin protein interacts with symbiotic receptors and regulates bacterial infection. Proc. Natl. Acad. Sci. U.S.A. 107, 2343-2348.
31. Lévy, J., Bres, C., Geurts, R., Chalhoub, B., Kulikova, O., Duc, G., Journet, E. P., Ané, J. M., Lauber, E., Bisseling, T., Dénarié, J., Rosenberg, C., and Debellé, F. (2004). A putative Ca2+ and calmodulin-dependent protein kinase required for bacterial and fungal symbioses. Science 303, 1361-1364.
32. Lima, L., Seabra, A., Melo, P., Cullimore, J., and Carvalho, H. (2006). Phosphorylation and subsequent interaction with 14-3-3 proteins regulate plastid glutamine synthetase in Medicago truncatula. Planta 223, 558-567.
33. Limpens, E., Mirabella, R., Fedorova, E., Franken, C., Franssen, H., Bisseling, T., and Geurts, R. (2005). Formation of organelle-like N2-fixing symbiosomes in legume root nodules is controlled by DMI2. Proc. Natl. Acad. Sci. U.S.A.102, 10375-10380.
34. Lippert, D., Yuen, M., and Bohlmann, J. (2009). Spruce proteome DB: a resource for conifer proteomics research. Tree Genet. Genomes 5, 723-727.
35. Mbengue, M., Camut, S., de Carvalho-Niebel, F., Deslandes, L., Froidure, S., Klaus-Heisen, D., Moreau, S., Rivas, S., Timmers, T., Herve, C., Cullimore, J., and Lefebvre, B. (2010). The Medicago truncatula E3 ubiquitin ligase PUB1 interacts with the LYK3 symbiotic receptor and negatively regulates infection and nodulation. Plant Cell 22, 3474-3488.
36. McAlister, G. C., Phanstiel, D., Wenger, C. D., Lee, M. V., and Coon, J. J. (2010). Analysis of tandem mass spectra by FTMS for improved large-scale proteomics with superior protein quantification. Anal. Chem. 82, 316-322.
37. Messinese, E., Mun, J. H., Yeun, L. H., Jayaraman, D., Rouge, P., Barre, A., Lougnon, G., Schornack, S., Bono, J. J., Cook, D. R., and Ané, J. M. (2007). A novel nuclear protein interacts with the symbiotic DMI3 calcium-and calmodulin-dependent protein kinase of Medicago truncatula. Mol. Plant Microbe Interact. 20, 912-921.
38. Nesvizhskii, A. I., and Aebersold, R. (2005). Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440.
39. Peck, S. C. (2006). Phosphoproteomics in Arabidopsis: moving from empirical to predictive science. J. Exp. Bot.57, 1523-1527.
40. Peiter, E., Sun, J., Heckmann, A. B., Venkateshwaran, M., Riely, B. K., Otegui, M. S., Edwards, A., Freshour, G., Hahn, M. G., Cook, D. R., Sanders, D., Oldroyd, G. E., Downie, J. A., and Ané, J. M. (2007). The Medicago truncatulaDMI1 protein modulates cytosolic calcium signaling. Plant Physiol. 145, 192-203.
41. Reumann, S., Ma, C., Lemke, S., and Babujee, L. (2004). AraPerox. A database of putative Arabidopsis proteins from plant peroxisomes. Plant Physiol. 136, 2587-2608.
42. Riely, B. K., Ane, J. M., Penmetsa, R. V., and Cook, D. R. (2004). Genetic and genomic analysis in model legumes bring nod-factor signaling to center stage. Curr. Opin. Plant Biol. 7, 408-413.
43. Riely, B. K., Mun, J. H., and Ane, J. M. (2006). Unravelling the molecular basis for symbiotic signal transduction in legumes. Mol. Plant Pathol. 7, 197-207.
44. Rode, C., Senkler, M., Klodmann, J., Winkelmann, T., and Braun, H. P. (2011). GelMap-a novel software tool for building and presenting proteome reference maps. J. Proteomics 74, 2214-2219.
45. Ruiz-Lozano, J. M., Azcon, R., and Gomez, M. (1995). Effects of arbuscular-mycorrhizal glomus species on drought tolerance: physiological and nutritional plant responses. Appl. Environ. Microbiol. 61, 456-460.
46. Sakata, K., Ohyanagi, H., Nobori, H., Nakamura, T., Hashiguchi, A., Nanjo, Y., Mikami, Y., Yunokawa, H., and Komatsu, S. (2009). Soybean proteome database: a data resource for plant differential omics. J. Proteome Res. 8, 3539-3548.
47. Schutzendubel, A., and Polle, A. (2002). Plant responses to abiotic stresses: heavy metal-induced oxidative stress and protection by mycorrhization. J. Exp. Bot. 53, 1351-1365.
48. Schwartz, D., and Gygi, S. P. (2005). An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat. Biotechnol. 23, 1391-1398.
49. Shimoda, Y., Han, L., Yamazaki, T., Suzuki, R., Hayashi, M., and Imaizumi-Anraku, H. (2012). Rhizobial and fungal symbioses show different requirements for calmodulin binding to calcium calmodulin-dependent protein kinase inLotus japonicus. Plant Cell 24, 304-321.
50. Smit, P., Limpens, E., Geurts, R., Fedorova, E., Dolgikh, E., Gough, C., and Bisseling, T. (2007). Medicago LYK3, an entry receptor in rhizobial nodulation factor signaling. Plant Physiol. 145, 183-191.
51. Sun, Q., Zybailov, B., Majeran, W., Friso, G., Olinares, P. D., and van Wijk, K. J. (2009). PPDB, the plant proteomics database at cornell. Nucleic Acids Res. 37, D969-D974.
52. Swaney, D. L., McAlister, G. C., and Coon, J. J. (2008). Decision tree-driven tandem mass spectrometry for shotgun proteomics. Nat. Methods 5, 959-964.
53. Syka, J. E., Coon, J. J., Schroeder, M. J., Shabanowitz, J., and Hunt, D. F. (2004). Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 101, 9528-9533.
54. Thoquet, P., Gherardi, M., Journet, E. P., Kereszt, A., Ane, J. M., Prosperi, J. M., and Huguet, T. (2002). The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes. BMC Plant. Biol. 2, 1. doi: 10.1186/1471-2229-2-1
55. Venkateshwaran, M., and Ané, J. M. (2011). "Legumes and nitrogen fixation: physiological, molecular, evolutionary perspective and applications, " in The Molecular Basis of Nutrient Use Efficiency in Crops, eds M. Hawkesford and P. Barraclough (Hoboken, NJ: John Wiley & Sons), 457-489.
56. Wienkoop, S., Larrainzar, E., Glinski, M., Gonzalez, E. M., Arrese-Igor, C., and Weckwerth, W. (2008). Absolute quantification of Medicago truncatula sucrose synthase isoforms and N-metabolism enzymes in symbiotic root nodules and the detection of novel nodule phosphoproteins by mass spectrometry. J. Exp. Bot. 59, 3307-3315.
57. Young, N. D., Debelle, F., Oldroyd, G. E., Geurts, R., Cannon, S. B., Udvardi, M. K., Benedito, V. A., Mayer, K. F., Gouzy, J., Schoof, H., Van de Peer, Y., Proost, S., Cook, D. R., Meyers, B. C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A. K., Murray, J. D., Naoumkina, M. A., Rosen, B., Silverstein, K. A., Tang, H., Rombauts, S., Zhao, P. X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, X., Doyle, J. J., Dudez, A. M., Farmer, A. D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., Gonzalez, A. J., Green, P. J., Hallab, A., Hartog, M., Hua, A., Humphray, S. J., Jeong, D. H., Jing, Y., Jocker, A., Kenton, S. M., Kim, D. J., Klee, K., Lai, H., Lang, C., Lin, S., Macmil, S. L., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E. L., Mun, J. H., Najar, F. Z., Nicholson, C., Noirot, C., O'Bleness, M., Paule, C. R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E. F., Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Severin, A. J., Sherrier, D. J., Shi, R., Sims, S., Singer, S. R., Sinharoy, S., Sterck, L., Viollet, A., Wang, B. B., Wang, K., Wang, M., Wang, X., Warfsmann, J., Weissenbach, J., White, D. D., White, J. D., Wiley, G. B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L., Zuber, A., Denarie, J., Dixon, R. A., May, G. D., Schwartz, D. C., Rogers, J., Quetier, F., Town, C. D., and Roe, B. A. (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480, 520-524.