Phosphoproteomic analysis of seed maturation in arabidopsis, rapeseed, and soybean

Plant Physiology

Volumn 159, Issue 1, 2012, Pages 517-528

  Meyer, Louis J ^a   Gao, Jianjiong ^b   Xu, Dong ^b   Thelen, Jay J ^a  

^a University of Missouri   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRASSICA NAPUS; GLYCINE MAX;

EID: 84860549883     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.111.191700     Document Type: Article

References (51)

1. Agrawal GK, Hajduch M, Graham K, Thelen JJ (2008) In-depth investigation of the soybean seed-filling proteome and comparison with a parallel study of rapeseed. Plant Physiol 148: 504-518
2. Agrawal GK, Thelen JJ (2006) Large scale identification and quantitative profiling of phosphoproteins expressed during seed filling in oilseed rape. Mol Cell Proteomics 5: 2044-2059
3. Altenhoff AM, Dessimoz C (2009) Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 5: e1000262
4. Baud S, Lepiniec L (2009) Regulation of de novo fatty acid synthesis in maturing oilseeds of Arabidopsis. Plant Physiol Biochem 47: 448-455
5. Bi YM, Zhang Y, Signorelli T, Zhao R, Zhu T, Rothstein S (2005) Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate-inducible member important for chlorophyll synthesis and glucose sensitivity. Plant J 44: 680-692
6. de la Fuente van Bentem S, Hirt H (2009) Protein tyrosine phosphorylation in plants: more abundant than expected? Trends Plant Sci 14: 71-76
7. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4: 207-214
8. Fait A, Angelovici R, Less H, Ohad I, Urbanczyk-Wochniak E, Fernie AR, Galili G (2006) Arabidopsis seed development and germination is associated with temporally distinct metabolic switches. Plant Physiol 142: 839-854
9. Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171: 501-523
10. Gao J, Agrawal GK, Thelen JJ, Xu D (2009) P3DB: a plant protein phosphorylation database. Nucleic Acids Res 37: D960-D962
11. Gao J, Thelen JJ, Dunker AK, Xu D (2010) Musite, a tool for global prediction of general and kinase-specific phosphorylation sites. Mol Cell Proteomics 9: 2586-2600
12. Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36: 3420-3435
13. Grimsrud PA, den Os D, Wenger CD, Swaney DL, Schwartz D, Sussman MR, Ané JM, Coon JJ (2010) Large-scale phosphoprotein analysis in Medicago truncatula roots provides insight into in vivo kinase activity in legumes. Plant Physiol 152: 19-28
14. Gutierrez L, Van Wuytswinkel O, Castelain M, Bellini C (2007) Combined networks regulating seed maturation. Trends Plant Sci 12: 294-300
15. Hajduch M, Ganapathy A, Stein JW, Thelen JJ (2005) A systematic proteomic study of seed filling in soybean: establishment of high-resolution two-dimensional reference maps, expression profiles, and an interactive proteome database. Plant Physiol 137: 1397-1419
16. Hajduch M, Hearne LB, Miernyk JA, Casteel JE, Joshi T, Agrawal GK, Song Z, Zhou M, Xu D, Thelen JJ (2010) Systems analysis of seed filling in Arabidopsis: using general linear modeling to assess concordance of transcript and protein expression. Plant Physiol 152: 2078-2087
17. Hajduch M, Matusova R, Houston NL, Thelen JJ (2011) Comparative proteomics of seed maturation in oilseeds reveals differences in intermediary metabolism. Proteomics 11: 1619-1629
18. Houston NL, Hajduch M, Thelen JJ (2009) Quantitative proteomics of seed filling in castor: comparison with soybean and rapeseed reveals differences between photosynthetic and nonphotosynthetic seed metabolism. Plant Physiol 151: 857-868
19. Hu W, Ma H (2006) Characterization of a novel putative zinc finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development. Plant J 45: 399-422
20. Huang Y, Li H, Gupta R, Morris PC, Luan S, Kieber JJ (2000) ATMPK4, an Arabidopsis homolog of mitogen-activated protein kinase, is activated in vitro by AtMEK1 through threonine phosphorylation. Plant Physiol 122: 1301-1310
21. Huber SC (2007) Exploring the role of protein phosphorylation in plants: from signaling to metabolism. Biochem Soc Trans 35: 23-32
22. Hundertmark M, Hincha DK (2008) LEA (late embryogenesis abundant) proteins and their encoding genes in Arabidopsis thaliana. BMC Genomics 9: 118
23. Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, Obradovic Z, Dunker AK (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 32: 1037-1049
24. Irar S, Oliveira E, Pagès M, Goday A (2006) Towards the identification of late-embryogenic-abundant phosphoproteome in Arabidopsis by 2-DE and MS. Proteomics (Suppl 1) 6: S175-S185
25. Ishihama Y, Rappsilber J, Mann M (2006) Modular stop and go extraction tips with stacked disks for parallel and multidimensional peptide fractionation in proteomics. J Proteome Res 5: 988-994
26. Jones SI, Gonzalez DO, Vodkin LO (2010) Flux of transcript patterns during soybean seed development. BMC Genomics 11: 136
27. Katavic V, Agrawal GK, Hajduch M, Harris SL, Thelen JJ (2006) Protein and lipid composition analysis of oil bodies from two Brassica napus cultivars. Proteomics 6: 4586-4598
28. Kim MJ, Go YS, Lee SB, Kim YS, Shin JS, Min MK, Hwang I, Suh MC (2010) Seed-expressed casein kinase I acts as a positive regulator of the SeFAD2 promoter via phosphorylation of the SebHLH transcription factor. Plant Mol Biol 73: 425-437
29. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659
30. Liu PP, Koizuka N, Martin RC, Nonogaki H (2005) The BME3 (Blue Micropylar End 3) GATA zinc finger transcription factor is a positive regulator of Arabidopsis seed germination. Plant J 44: 960-971
31. MacLean D, Burrell MA, Studholme DJ, Jones AM (2008) PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data. BMC Res Notes 1: 30
32. Manfield IW, Devlin PF, Jen CH, Westhead DR, Gilmartin PM (2007) Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family. Plant Physiol 143: 941-958
33. Nakagami H, Sugiyama N, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K (2010) Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol 153: 1161-1174
34. Ndassa YM, Orsi C, Marto JA, Chen S, Ross MM (2006) Improved immobilized metal affinity chromatography for large-scale phosphoproteomics applications. J Proteome Res 5: 2789-2799
35. Nühse TS, Peck SC, Hirt H, Boller T (2000) Microbial elicitors induce activation and dual phosphorylation of the Arabidopsis thaliana MAPK 6. J Biol Chem 275: 7521-7526
36. Pandey GK, Grant JJ, Cheong YH, Kim BG, Li L, Luan S (2005) ABR1, an APETALA2-domain transcription factor that functions as a repressor of ABA response in Arabidopsis. Plant Physiol 139: 1185-1193
37. Reiland S, Messerli G, Baerenfaller K, Gerrits B, Endler A, Grossmann J, Gruissem W, Baginsky S (2009) Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol 150: 889-903
38. Ruuska SA, Schwender J, Ohlrogge JB (2004) The capacity of green oilseeds to utilize photosynthesis to drive biosynthetic processes. Plant Physiol 136: 2700-2709
39. Schwartz D, Gygi SP (2005) An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol 23: 1391-1398
40. Schwender J, Goffman F, Ohlrogge JB, Shachar-Hill Y (2004) Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds. Nature 432: 779-782
41. Schwender J, Ohlrogge JB, Shachar-Hill Y (2003) A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos. J Biol Chem 278: 29442-29453
42. Sonmez C, Bäurle I, Magusin A, Dreos R, Laubinger S, Weigel D, Dean C (2011) RNA 39 processing functions of Arabidopsis FCA and FPA limit intergenic transcription. Proc Natl Acad Sci USA 108: 8508-8513
43. Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y (2007) Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol Cell Proteomics 6: 1103-1109
44. Sugiyama N, Nakagami H, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y (2008) Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol 4: 193
45. Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V (2005) InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem 77: 4626-4639
46. Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28: 33-36
47. Thelen JJ, Ohlrogge JB (2002) Metabolic engineering of fatty acid biosynthesis in plants. Metab Eng 4: 12-21
48. Thingholm TE, Jensen ON, Robinson PJ, Larsen MR (2008) SIMAC (sequential elution from IMAC), a phosphoproteomics strategy for the rapid separation of monophosphorylated from multiply phosphorylated peptides. Mol Cell Proteomics 7: 661-671
49. Wang H, Guo J, Lambert KN, Lin Y (2007) Developmental control of Arabidopsis seed oil biosynthesis. Planta 226: 773-783
50. Weber H, Borisjuk L, Wobus U (2005) Molecular physiology of legume seed development. Annu Rev Plant Biol 56: 253-279
51. Zheng Z, Xu X, Crosley RA, Greenwalt SA, Sun Y, Blakeslee B, Wang L, Ni W, Sopko MS, Yao C, et al (2010) The protein kinase SnRK2.6 mediates the regulation of sucrose metabolism and plant growth in Arabidopsis. Plant Physiol 153: 99-113