Proteome analysis of cold acclimation in sunflower

Journal of Proteome Research

Volumn 10, Issue 5, 2011, Pages 2330-2346

  Balbuena, Tiago S ^a,c   Salas, Joaquín J ^b   Martínez Force, Enrique ^b   Garcés, Rafael ^b   Thelen, Jay J ^a  

^a University of Missouri   (United States)

^b INSTITUTO DE LA GRASA   (Spain)

^c UNIVERSITY OF MISSOURI   (United States)

Author keywords

cold acclimation; GeLC MS; Helianthus annuus; mass spectrometry; spectral counting

Indexed keywords

PROTEOME;

ARTICLE; COLD ACCLIMATIZATION; COLD TREATMENT; CONTROLLED STUDY; ENERGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT LEAF; PLANT METABOLISM; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; SUNFLOWER; TANDEM MASS SPECTROMETRY;

ACCLIMATIZATION; CHROMATOGRAPHY, LIQUID; CLUSTER ANALYSIS; COLD TEMPERATURE; COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; HELIANTHUS; PLANT PROTEINS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

HELIANTHUS; HELIANTHUS ANNUUS;

EID: 79955868127     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr101137q     Document Type: Article

References (73)

1. Timperio, A. M.; Egidi, M. G.; Zolla, L. Proteomics applied on plant abiotic stresses: role of heat shock proteins (HSP) J. Proteomics 2008, 71 (4) 391-411
2. Mahajan, S. Tuteja. Cold, salinity and drought stresses: an overview Arch. Biochem. Biophys. 2005, 444 (2) 139-158 (Pubitemid 41728346)
3. John, U. P.; Polotnianka, R. M.; Sivakumaran, K. A.; Chew, O.; Mackin, L.; Kuiper, M. J.; Talbot, J. P.; Nugent, G. D.; Mautord, J.; Schrauf, G. E.; Spangenberg, G. C. Ice recrystallization inhibition proteins (IRIPs) and freeze tolerance in the cryophilic Antarctic hair grass Deschampsia antarctica E. Desv Plant, Cell Environ. 2009, 32 (4) 336-348
4. Kjellsen, T. D.; Shiryaeva, L.; Schroder, W. P.; Strimbeck, G. R. Proteomics of extreme freezing tolerance in Siberian spruce (Picea obovata) J. Proteomics 2010, 73 (5) 965-975
5. Gygi, S. P.; Rochon, Y.; Franza, R.; Aebersold, R. Correlation between protein and mRNA abundance in yeast Mol. Cell. Biol. 1999, 19 (3) 1720-1730 (Pubitemid 29098230)
6. Ideker, T.; Thorsson, V.; Ranish, J. A.; Christmas, R.; Buhler, J.; Eng, J. K.; Bumgarner, R.; Goodlett, D. R.; Aebersold, R.; Hood, L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network Science 2001, 292 (5518) 929-934 (Pubitemid 32422490)
7. Hajduch, M.; Hearne, L. B.; Miernyk, J. A.; Casteel, J. E.; Joshi, T.; Agrawal, G. K.; Song, Z.; Zhou, M.; Xu, D.; Thelen, J. J. Systems analysis of seed filling in Arabidopsis: using general linear modeling to assess concordance of transcript and protein expression Plant Physiol. 2010, 152 (4) 2078-2087
8. Renaut, J.; Hausman, J. F.; Bassett, C.; Artlip, T.; Cauchie, H. M.; Witter, E.; Wisniewski, M. Quantitative proteomic analysis of short photoperiod and low-tamperature responses in bark tissues of peach (Prunus persica L. Batsch) Tree Genet. Genomes 2008, 4 (4) 589-600
9. Amme, S.; Matros, A.; Schlesier, B.; Mock, H. P. Proteome analysis of cold stress response in Arabidopsis thaliana using DIGE-technology J. Exp. Bot. 2006, 57 (7) 1537-1546
10. Bae, M. S.; Cho, E. J.; Choi, E. Y.; Park, O. K. Analysis of the Arabidopsis nuclear proteome and its response to cold stress Plant J. 2003, 36 (5) 652-663 (Pubitemid 37496493)
11. Bressan, R. A.; Zhang, C.; Zhang, H.; Hasegawa, P. M.; Bohnert, H. J.; Zhu, J. K. Learning from the Arabidopsis experience: the next gene search paradigm Plant Physiol. 2001, 127 (4) 1354-1360 (Pubitemid 34049998)
12. Gao, F.; Zhou, Y.; Zhu, W.; Li, X.; Fan, L.; Zhang, G. Proteomic analysis of cold stress-responsive proteins in Tellungiella rosette leaves Planta 2009, 230 (5) 1033-1046
13. Wang, X.; Yang, P.; Zhang, X.; Xu, Y.; Kuang, T.; Shen, S.; He, Y. Proteomic analysis of the cold stress response in the moss, Physcomitrella patens Proteomics 2009, 9 (19) 4529-4538
14. Imin, N.; Kerim, T.; Rolfe, B. G.; Weinman, J. J. Effect of early cold stress on the maturation of rice anthers Proteomics 2004, 4 (7) 1873-1882 (Pubitemid 38880348)
15. Cui, S.; Huang, F.; Wang, J.; Ma, X.; Cheng, Y.; Liu, J. A proteomic analysis of cold stress responses in rice seedlings Proteomics 2005, 5 (12) 3162-3172 (Pubitemid 41176484)
16. Murphy, D. J. Improvement of industrial oil crops. In Industrial crops and uses; Singh, B., Ed.; CABI International: Cambridge, 2010; pp 183 - 206.
17. Dosio, G. A. A.; Aguirrezabal, L. A. N.; Andrade, F. H.; Pereyra, V. R. Solar radiation intercepted during seed filling and oil production in two sunflower hybrids Crop. Sci. 2000, 40 (6) 1637-1644 (Pubitemid 32062589)
18. Blamey, F. P. C.; Zollinger, R. K.; Schneiter, A. A. Sunflower production and culture. In Sunflower technology and production; Schneiter, A. A., Ed.; American Society of Agronomy: Madison, 1997; pp 595 - 670.
19. Sarmiento, C.; Garces, R.; Mancha, M. Oleate desaturation and acyl turnover in sunflower (Helianthus annuus L.) seed lipids during rapid temperature adaptation Planta 1998, 205 (4) 595-600 (Pubitemid 28320412)
20. Perez-Vich, B.; Fernández, J.; Garcés, R.; Fernández-Martínez, J. M. Inheritance of high palmitic acid content in the seed oil of sunflower mutant CAS-5 Theor. Appl. Genet. 1999, 98 (3-4) 496-501 (Pubitemid 29172812)
21. Hajduch, M.; Ganapathy, A.; Stein, J. W.; Thelen, J. J. 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. 2005, 137 (4) 1397-1419 (Pubitemid 43119338)
22. Shevchenko, A.; Tomas, H.; Havlis, J.; Olsen, J. V.; Mann, M. In-gel digestion for mass spectrometric characterization of proteins and proteomes Nat. Protoc. 2007, 1 (6) 2856-2860
23. Wernersson, R. Virtual Ribosome-a comprehensive DNA translation tool with support for integration of sequence feature annotation Nucleic Acids Res. 2006, 34, W385-W388
24. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74 (20) 5383-5392 (Pubitemid 35215372)
25. Fu, X.; Gharib, S. A.; Green, P. S.; Aitken, M. L.; Frazer, D. A.; Park, D. R.; Vaisar, T.; Heinecke, J. W. Spectral index for assessment of differential protein expression in shotgun proteomics J. Proteome Res. 2008, 7 (3) 845-854
26. Childs, K. L.; Hamilton, J. P.; Zhu, W.; Ly, E.; Cheung, F.; Wu, H.; Rabinowicz, P. D.; Town, C. D.; Buell, C. R.; Chan, A. P. The TIGR plant transcript assemblies database Nucleic Acids Res. 2007, 35, D846-D851
27. Bevan, M.; Bancroft, I.; Bent, E.; Love, K.; Goodman, H.; Dean, C.; Bergkamp, R.; Dirkse, W.; van Staveren, M.; Stiekema, W.; Drost, L.; Ridley, P.; Hudson, S. A.; Patel, K.; Murphy, G.; Piffanelli, P.; Wedler, H.; Wedler, E.; Wambutt, R.; Weitzenegger, T.; Pohl, T. M.; Terryn, N.; Gielen, J.; Villarroel, R.; de Clerck, R.; van Montagu, M.; Lecharny, A.; Auborg, S.; Gy, I.; Kreis, M.; Lao, N.; Kavanagh, T.; Hempel, S.; Kotter, P.; Entian, K. D.; Rieger, M.; Schaeffer, M.; Funk, B.; Mueller-Auer, S.; Silvey, M.; James, R.; Montfort, A.; Pons, A.; Puigdomenech, P.; Douka, A.; Voukelatou, E.; Milioni, D.; Hatzopoulos, P.; Piravandi, E.; Obermaier, B.; Hilbert, H.; Dusterhoft, A.; Moores, T.; Jones, J. D.; Eneva, T.; Palme, K.; Benes, V.; Rechman, S.; Ansorge, W.; Cooke, R.; Berger, C.; Delseny, M.; Voet, M.; Volckaert, G.; Mewes, H. W.; Klosterman, S.; Schueller, C.; Chalwatzis, N. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana Nature 1998, 391 (6666) 485-488 (Pubitemid 28086548)
28. Caraux, G.; Pinloche, S. PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order Bioinformatics 2005, 21 (7) 1280-1281 (Pubitemid 40467961)
29. Meunier, B.; Bouley, J.; Plec, I.; Bernard, C.; Picard, B.; Hocquette, J. F. Data analysis methods for detection of differential protein expression in two-dimensional gel electrophoresis Anal. Biochem. 2005, 340 (2) 226-230 (Pubitemid 40544861)
30. Stevenson, S. E.; Chu, Y.; Ozias-Akins, P.; Thelen, J. J. Validation of gel-free, label-free quantitative proteomics approaches: applications for seed allergen profiling J. Proteomics 2009, 72 (3) 555-566
31. Little, K. M.; Lee, J. K.; Ley, K. ReSASC: a resampling-based algorithm to determine differential protein expression from spectral count data Proteomics 2010, 10 (6) 1212-1222
32. Gao, B. B.; Stuart, L.; Feener, E. P. Label-free quantitative analysis of one-dimensional PAGE LC/MS/MS proteome: application on angiotensin II-stimulated smooth muscle cells secretome Mol. Cell. Proteomics 2008, 7 (12) 2399-2409
33. Chelius, D.; Bondarenko, P. V. Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry J. Proteome Res. 2002, 1 (4) 317-323 (Pubitemid 36395872)
34. Wang, W.; Zhou, H.; Lin, H.; Roy, S.; Shaler, T. A.; Hill, L. R.; Norton, S.; Kumar, P.; Anderle, M.; Becker, C. H. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards Anal. Chem. 2003, 75 (18) 4818-4826 (Pubitemid 37139783)
35. Wiener, M. C.; Sachs, J. R.; Deyanova, E. G.; Yates, N. A. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures Anal. Chem. 2004, 76 (20) 6085-6096 (Pubitemid 39382956)
36. Liu, H.; Sadygov, R. G.; Yates, J. R. A model for random sampling and estimation of relative abundance in shotgun proteomics Anal. Chem. 2004, 76 (14) 4193-4201 (Pubitemid 38943698)
37. Venable, J. D.; Dong, M. Q.; Wohlschlegel, J.; Dillin, A.; Yates, J. R. Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra Nat. Methods 2004, 1 (1) 1-7
38. Old, W. M.; Meyer-Arendt, K.; Aveline-Wolf, L.; Pierce, K. G.; Mendoza, A.; Sevinsky, J. R.; Resing, K. A.; Ahn, N. G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics Mol. Cell. Proteomics 2005, 4 (10) 1487-1502 (Pubitemid 41555475)
39. Hua, J. From freezing to scorching, transcriptional responses to temperature variation in plants Curr. Opin. Plant Biol. 2009, 12 (5) 568-573
40. Chinnusamy, V.; Zhu, J.; Zhu, J. K. Cold stress regulation of gene expression in plants Trends Plant Sci. 2007, 12 (10) 444-451 (Pubitemid 47465035)
41. Hannah, M. A.; Wiese, D.; Freund, S.; Fiehn, O.; Heyer, A. G.; Hincha, D. K. Natural genetic variation of freezing tolerance in Arabidopsis Plant Physiol. 2006, 142 (1) 98-112 (Pubitemid 44412233)
42. Cook, D.; Fowler, S.; Fiehn, O.; Thomashow, M. F. A prominent role for the CBF cold response pathway in configuring the low-tamperature metabolome of Arabidopsis Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (42) 15243-15248 (Pubitemid 39391749)
43. Kaplan, F.; Kopka, J.; Haskell, D. W.; Zhao, W.; Schiller, K. C.; Gatzke, N.; Sung, D. Y.; Guy, C. L. Exploring the temperature-stress metabolome of Arabidopsis Plant Physiol. 2004, 136 (4) 4159-4168
44. Abreu, E. F. M.; Aragao, F. J. L. Isolation and characterization of a myo-inositol-1-phosphate synthase gene from yellow passion fruit (Passiflora edulis f. flavicarpa) expressed during seed development and environmental stress Ann. Bot. 2007, 99 (2) 285-292 (Pubitemid 47355899)
45. Chen, H.; Xiong, L. Myo-inositol-1-phosphate synthase is required for polar auxin transport and organ development J. Biol. Chem. 2010, 285 (31) 24238-24247
46. Bohnert, H. J.; Sheveleva, E. Plant stress adaptations-making metabolism move Curr. Opin. Plant Biol. 1998, 1 (3) 267-274
47. Majee, M.; Maitra, S.; Dastidar, K. G.; Pattnaik, S.; Chatterjee, A.; Hait, C. C.; Das, K. P.; Majumder, A. L. A novel salt-tolerant L-myo-inositol-1-phosphate synthase from Porteresia coarctata (Roxb.) Tateoka, a halophytic wild rice J. Biol. Chem. 2004, 279 (27) 28539-28552
48. Das-Chatterjee, A.; Goswami, L.; Maitra, S.; Dastidar, K. G.; Ray, S.; Majumder, A. L. Introgression of a novel salt-tolerant L-myo-inositol 1-phosphate synthase from Porteresia coarctata (Roxb.) Tateoka (PcIN01) confers salt tolerance to evolutionary diverse organisms FEBS Lett. 2006, 580 (16) 3980-3988 (Pubitemid 43964922)
49. Torabinejad, J.; Donahue, J. L.; Gunesekera, B. N.; Allen-Daniels, M. J.; Gillaspy, G. E. VTC4 is a bifunctional enzyme that affects myoinositol and ascorbate biosynthesis in plants Plant Physiol. 2009, 150 (2) 951-961
50. Zuther, E.; Buchel, K.; Hundertmark, M.; Stitt, M.; Hincha, D. K.; Heyer, A. G. The role of raffinose in the cold acclimation response of Arabidopsis thaliana FEBS Lett. 2004, 576 (1) 169-173 (Pubitemid 39330478)
51. Charron, J. B. F.; Ouellet, F.; Pelletier, M.; Danyluk, J.; Chauve, C.; Sarhan, F. Identification, expression, and evolutionary analyses of plant lipocalins Plant Physiol. 2005, 139 (4) 2017-2028 (Pubitemid 43899836)
52. Charron, J. B. F.; Breton, G.; Badawi, M.; Sarhan, F. Molecular and structural analyses of a novel temperature stress-induced lipocalin from wheat and Arabidopsis FEBS Lett. 2002, 517 (1) 129-132 (Pubitemid 34327644)
53. Ndong, C.; Danyluk, J.; Huner, N. P. A.; Sarhan, F. Survey of gene expression in winter rye during changes in growth temperature, irradiance or excitation pressure Plant Mol. Biol. 2001, 45 (6) 691-703 (Pubitemid 33635758)
54. Lee, S. C.; Lee, M. Y.; Kim, S. J.; Jun, S. H.; An, G.; Kim, S. R. Characterization of an abiotic stress-inducible dehydrin gene, OsDhn1, in rice (Oryza sativa L.) Mol. Cells 2005, 19 (2) 212-218
55. Ohno, R.; Takami, S.; Nakamura, C. Kinetics of transcript and protein accumulation of a low-molecular-weight wheat LEA D-11 dehydrin in response to low temperature J. Plant Physiol. 2003, 160 (2) 193-200 (Pubitemid 36242507)
56. Porat, R.; Pasentsis, K.; Rozentzvieg, D.; Gerasopoulos, D.; Falara, V.; Samach, A.; Lurie, S.; Kanellis, A. K. Isolation of a dehydrin cDNA from orange and grapefruit citrus fruit that is specifically induced by the combination of heat followed by chilling temperatures Physiol. Plantarum 2004, 120 (2) 256-264 (Pubitemid 38126913)
57. Nylander, M.; Svensson, J.; Palva, E. T.; Welin, B. V. Stress-induced accumulation and tissue-specific localization of dehydrins in Arabidopsis thaliana Plant Mol. Biol. 2001, 45 (3) 263-279 (Pubitemid 32235166)
58. Kawamura, Y.; Uemura, M. Mass spectrometric approach for identifying putative plasma membrane proteins of Arabidopsis leaves associated with cold acclimation Plant J. 2003, 36 (2) 141-154 (Pubitemid 37293056)
59. Marian, C. O.; Krebs, S.; Arora, R. Dehydrin variability among rhododendron species: a 25-kDa dehydrin is conserved and associated with cold acclimation across diverse species New Phytol. 2003, 161 (3) 773-780 (Pubitemid 38193015)
60. Renault, J.; Hoffmann, L.; Hausman, J. F. Biochemical and physiological mechanisms related to cold acclimation and enhanced freezing tolerance in poplar plantlets Physiol. Plantarum 2005, 125 (1) 82-94 (Pubitemid 41265081)
61. Kontunen-Soppela, S.; Laine, K. Seasonal fluctuation of dehydrins is related to osmotic status in Scots pine needles Trees 2001, 15 (7) 425-430 (Pubitemid 33065905)
62. Rorat, T. Plant dehydrins-tissue location, structure and function Cell. Mol. Biol. Lett. 2006, 11 (4) 536-556 (Pubitemid 46708880)
63. Plaxton, W. C. The organization and regulation of plant glycolysis Annu. Rev. Plant Physiol. Plant Mol. Biol. 1996, 47, 185-214
64. Shetty, S.; Ganachari, M.; Liu, M. C.; Azghani, A.; Muniyappa, H.; Idell, S. Regulation of urokinase receptor expression by phosphoglycerate kinase is independent of its catalytic activity Am. J. Physiol. Lung Cell. Mol. Physiol. 2005, 289 (4) L591-L598
65. Ahn, C. S.; Lee, J. H.; Hwang, A. R.; Kim, W. T.; Pai, H. S. Prohibitin is involved in mitochondrial biogenesis in plants Plant J. 2006, 46 (4) 658-667
66. Byun, Y. J.; Kim, H. J.; Lee, D. H. LongSAGE analysis of the early response to cold stress in Arabidopsis leaf Planta 2009, 229 (6) 1181-1200
67. Ali, G. M.; Komatsu, S. Proteomic analysis of rice leaf sheath during drought stress J. Proteome Res. 2006, 5 (2) 396-403 (Pubitemid 43222308)
68. Jiang, Y.; Yang, Bo.; Harris, N. S.; Deyholos, M. K. Comparative proteomic analysis of NaCl stress-responsive proteins in Arabidopsis roots J. Exp. Bot. 2007, 58 (13) 3591-3607 (Pubitemid 350232995)
69. Yan, S.; Tang, Z.; Su, W. Sun. Proteomic analysis of salt stress-responsive proteins in rice roots Proteomics 2005, 5 (1) 235-244 (Pubitemid 40189654)
70. +: a class of chaperone-like ATPase associated with the assembly, operation, and disassembly of protein complexes Genome Res. 1999, 9 (1) 27-43 (Pubitemid 29095146)
71. Ito, K.; Akiyama, Y. Cellular functions, mechanism of action, and regulation of FtsH protease Annu. Rev. Microbiol. 2005, 59, 211-231 (Pubitemid 41507430)
72. Komatsu, S.; Kato, A. Varietal differences in protein phosphorylation during cold treatment of rice leaves Phytochemistry 1997, 45 (7) 1329-1335 (Pubitemid 27294950)
73. Mauro, S.; Dainese, P.; Lannoye, R.; Bassi, R. Cold-resistant and cold-sensitive maize lines differ in the phosphorylation of the photosystem II subunit CP29 Plant Physiol. 1997, 115 (1) 171-180 (Pubitemid 28378809)