Rice proteomics: A step toward functional analysis of the rice genome

Rice Functional Genomics: Challenges, Progress and Prospects

Volumn , Issue , 2007, Pages 61-89

  Komatsu, Setsuko ^a  

^a NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84875969832     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/0-387-48914-2_5     Document Type: Chapter

References (76)

1. Abbasi F, Komatsu S (2004) A proteomic approach to analyze salt-responsive proteins in rice leaf sheath. Proteomics 4:2072-2081.
2. Abubakar Z, Ali F, Pinel A, Traore O, N'Guessan P, Notteghem JL, Kimmins F, Konate G, Fargette D (2003) Phylogeography of Rice yellow mottle virus in Africa. J Gen Virol 84:733-743.
3. Agrawal GK, Rakwal R, Yonekura M, Kubo A, Saji H (2002) Proteome analysis of differentially displayed proteins as a tool for investigating ozone stress in rice (Oryza sativa L.) seedlings. Proteomics 2:974-959.
4. Ali GM, Komatsu S (2006) Proteomic analysis of rice leaf sheath during drought stress. J Proteome Res 5:396-403.
5. Brugidou C, Opalka N, Yeager M, Beachy RN, Fauquet C (2002) Stability of rice yellow mottle virus and cellular compartmentalization during the infection process in Oryza sativa (L.). Virology 297:98-108.
6. Casimaro I, Marchant A, Bhalerao RP, Beeckman T, Dhooge S, Swarup R, Graham N, Inze D, Sandberg G, Casero PJ, Bennett M (2001) Auxin transport promotes Arabidopsis lateral root initiation. Plant Cell 13:843-852.
7. Chameides WL, Saylor RD, Cowling EB (1997) Ozone pollution in the rural United States and the new NAAQS. Science 276:916.
8. Cleveland DW, Fisher SG, Kirschner MW, Laemmli UK (1977) Peptide mapping by limited proteolysis in sodium dodecyl sulphate and analysis by gel electrophoresis. J Biol Chem 252:1102-1106.
9. Cui S, Huang F, Wang J, Ma X, Cheng Y, Liu J (2005) A proteomic analysis of cold stress responses in rice seedlings. Proteomics 5:3162-3172.
10. Dani V, Simon WJ, Duranti M, Croy RR (2005) Changes in the tobacco leaf apoplast proteome in response to salt stress. Proteomics 5:737-745.
11. Devos KM, Gale MD (2000) Genome relationships: The grass model in current research. Plant Cell 12:637-646.
12. Eubel H, Braun H-P, Millar H (2005) Blue-native PAGE in plants: A tool in analysis of protein-protein interactions. Plant Methods 1:1-13.
13. Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Zhang Y, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B. (2002) Sequence and analysis of rice chromosome 4. Nature 420:316-320.
14. Fukuda M, Islam N, Woo SH, Yamagishi A, Takaoka M, Hirano H (2003) Assessing matrix assisted laser desorption/ionization-time of flight-mass spectrometry as a means of rapid embryo protein identification in rice. Electrophoresis 24:1219-1329.
15. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971-1974.
16. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, 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 RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
17. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999a) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotech 17:994-999.
18. Gygi SP, Rochon Y, Franza BR, Aebersold M (1999b) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720-1730.
19. Hajheidari M, Abdollahian-Noghabi M, Askari H, Heidari M, Sadeghian SY, Ober ES, Hosseini-Salekdeh G (2005) Proteome analysis of sugar beet leaves under drought stress. Proteomics 5:950-960.
20. Heazlewood JL, Howell KA, Whelan J, Millar AH (2003) Towards an analysis of the rice mitochondrial proteome. Plant Physiol 132:230-242.
21. Hirano H, Kawasaki H, Sassa H (2000) Two-dimensional gel electrophoresis using immobilized pH gradient tube gels. Electrophoresis 21:440-445.
22. Hooley R (1994) Gibberellins: Perception, transduction and responses. Plant Mol Biol 26:1529-1555.
23. Imin N, Kerim T, Weinman JJ, Rolfe BG (2001) Characterization of rice anther proteins expressed at the young microspore stage. Proteomics 1:149-1161.
24. Immler D, Gremm D, Kirsch D, Spengler B, Presek P, Meyer HE (1998) Identification of phosphorylated proteins from thrombin-activated human platelets isolated by two-dimensional gel electrophoresis by electrospray ionization-tandem mass spectrometry (ESI-MS/MS) and liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS). Electrophoresis 19:1015-1023.
25. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793-800.
26. Islam N, Lonsdala M, Upadhyaya NM, Higgins TJ, Hirano H, Akhurst R (2004) Protein extraction from mature rice leaves for two-dimensional gel electrophoresis and its application in proteome analysis. Proteomics 4:1903- 1908.
27. Kerim T, Imin N, Weinman JJ, Rolfe BG (2003) Proteome analysis of male gametophyte development in rice anthers. Proteomics 3:738-751.
28. Khan M, Takasaki H, Komatsu S (2005) Comprehensive phosphoproteome analysis in rice and identification of phosphoproteins responsive to different hormones/stresses. J. Proteome Res 4:1592-1599.
29. Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A (2003) Collection, mapping, and annotation of over 28, 000 cDNA clones from japonica rice. Science 301:376-379.
30. Kim KM, Kwon YS, Lee JJ, Eun MY, Sohn JK (2004) QTL mapping and molecular marker analysis for the resistance of rice to ozone. Mol Cells 17 151-155.
31. Kim ST, Cho KS, Yu S, Kim SG, Hong JC, Han C-D, Bae DW, Nam MH, Kang KY (2003) Proteomic analysis of differentially expressed proteins induced by rice blast fungus and elicitor in suspension-cultured rice cells. Proteomics 3:2368-2378.
32. Koller A, Washburn MP, Lange BM, Andon NL, Deciu C, Haynes PA, Hays L, Schieltz D, Ulaszek R, Wei J, Wolters D, Yates JR 3rd (2002) Proteomic survey of metabolic pathways in rice. Proc Natl Acad Sci USA 99:11969- 11974.
33. Komatsu S (2005) Rice proteome database: A step toward functional analysis of the rice genome. Plant Mol Biol 59:179-190.
34. Komatsu S, Tanaka N (2004) Rice proteome analysis: A step toward functional analysis of the rice genome. Proteomics 4:938-949.
35. Komatsu S, Kajiwara H, Hirano H (1993) A rice protein library: A data-file of rice proteins separated by two-dimensional electrophoresis. Theor Appl Genet 86:935-942.
36. Komatsu S, Masuda T, Abe K (1996) Phosphorylation of a protein (pp56) is related to the regeneration of rice cultured suspension cells. Plant Cell Physiol 37:748-753.
37. Komatsu S, Muhammad A, Rakwal R (1999a) Separation and characterization of proteins from green and etiolated shoots of rice (Oryza sativa L.): Towards a rice proteome. Electrophoresis 20:630-636.
38. Komatsu S, Rakwal R, Li Z (1999b) Separation and characterization of proteins in rice (Oryza sativa) suspension cultured cells. Plant Cell, Tissue Organ Culture 55:183-192.
39. Komatsu S, Konishi H, Shen S, Yang G (2003) Rice proteomics: A step toward functional analysis of the rice genome. Mol Cell Proteomics 2:2-10.
40. Komatsu S, Kojima K, Suzuki K, Ozaki K, Higo K (2004) Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: Its status in 2003. Nucl Acids Res 32:388-392.
41. Komatsu S, Zang X, Tanaka N (2006) Comparison of two proteomics techniques used to identify proteins regulated by gibberellin in rice. J. Proteome Res 5:270-276.
42. Konishi H, Komatsu S (2003) A proteomics approach to investigating promotive effects of brassinolide on lamina inclination and root growth in rice seedlings. Biol Pharm Bull 26:401-408.
43. Konishi H, Ishiguro K, Komatsu S (2001) A proteomics approach towards understanding blast fungus infection of rice grown under different levels of nitrogen fertilization. Proteomics 1:1162-1171.
44. Larsen MR, Sorensen GL, Fey SJ, Larsen PM, Roepstorff P (2001) Phosphoproteomics: Evaluation of the use of enzymatic de-phosphorylation and differential mass spectrometric peptide mass mapping for site specific phosphorylation assignment in proteins separated by gel electrophoresis. Proteomics 1:223-238.
45. Leung K-C, Li H-Y, Mishra G, Vhye M-L (2004) ACBP4 and ACBP5, novel Arabidopsis acyl-CoA-binding proteins with kelch motifs that bind oleoyl- CoA. Plant Mol Biol 55:297-309.
46. Leustek T, Martin MN, Bick J-A, Davies JP (2000) Pathways and regulation of sulfur metabolism revealed through molecular and genetic studies. Annu Rev Plant Physiol Plant Mol Biol 51:141-165.
47. Lonhosky PM, Zhang X, Honavar VG, Dobbs DL, Fu A, Rodermel SR (2004) A proteomic analysis of maize chloroplast biogenesis. Plant Physiol 134:560- 574.
48. Lyons JM (1973) Chilling injury in plants. Annu Rev Plant Physiol 24:445-446.
49. Mikami S, Hori H, Mitsui T (2001) Separation of distinct components of rice Golgi complex by sucrose density gradient centrifugation. Plant Sci 161:665- 675.
50. O'Farrell PH (1975) High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250:4007-4021.
51. Oguchi K, Tanaka N, Komatsu S, Akao S (2004a) Methylmalonate- semialdehyde dehydrogenase is induced in auxin- And zinc-stimulated root formation in rice. Plant Cell Rep 22:848-858.
52. Oguchi K, Tanaka N, Komatsu S, Akao S (2004b) Characterization of NADPHdependent oxidoreductase from rice induced by auxin and zinc. Physiol Plant 121:124-131.
53. Pinel A, N'Guessan P, Bousalem M, Fargette D (2000) Molecular variability of geographically distinct isolates of Rice yellow mottle virus in Africa. Arch Virol 145:1621-1638.
54. Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755-1767.
55. Rabilloud T (2002) Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2:3-10.
56. Raison JK, Lyons JM, Keith AD (1971) Temperature-induced phase changes in mitochondrial membranes detected by spin labeling. J Biol Chem 246:4036- 4040.
57. Rakwal R, Komatsu S (2000) Role of jasmonate in the rice (Oryza sativa L.) selfdefense mechanism using proteome analysis. Electrophoresis 21:2492-2500.
58. Resing KA, Ahn NG (1997) Protein phosphorylation analysis by electrospray ionization-mass spectrometry. Methods Enzymol 283:29-44.
59. Rose JK, Bashir S, Giovannoni JJ, Jahn MM, Saravanan RS (2004) Tackling the plant proteome: Practical approaches, hurdle hurdles and experimental tools. Plant J 39:715-733.
60. Salekdeh GH, Siopongco J, Ghareyazie B, Bennett J (2002) Proteomic analysis of rice leaves during drought stress and recovery. Proteomics 2:1131-1145.
61. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim HI, Eun MY, Yano M, Jiang J, Gojobori T (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312-316.
62. Sasse JM (1997) Recent progress in brassinosteroids research. Physiol Plant 100:696-701.
63. Shen S, Matsubae M, Takao T, Tanaka N, Komatsu S (2002) A proteomic analysis of leaf sheath from rice. J Biochem 132:613-620.
64. Shen S, Sharma A, Komatsu S (2003) Characterization of proteins responsive to gibberellin in the leaf-sheath of rice (Oryza sativa L.) seedling using proteome analysis. Biol Pharm Bull 26:129-136.
65. Suarez-Lopez P (2005) Long-range signaling in plant reproductive development. Int J Dev Biol 49:761-771.
66. Tanaka N, Fujita M, Handa H, Murayama S, Uemura M, Kawamura Y, Mitsui T, Mikami S, Tozawa Y, Yoshinaga T, Komatsu S (2004a) Proteomics of the rice cell: Systematic identification of the protein population in subcellular compartments. Mol Gen Genomics 271:566-576.
67. Tanaka N, Konishi H, Khan M, Komatsu S (2004b) Proteome analysis of rice tissues separated and visualized by two-dimensional electrophoresis: Approach to investigating the gibberellin regulated proteins. Mol Gen Genomics 270:485-496.
68. Tanaka N, Mitsui S, Nobori H, Yanagi K, Komatsu S (2005) Expression and function of proteins during development of the basal region in rice seedlings. Mol Cell Proteomics 4:796-808.
69. Tsugita A, Kawakami T, Uchiyama Y, Kamo M, Miyatake N, Nozu Y (1994) Separation and characterization of rice proteins. Electrophoresis 15:708-720.
70. Valent B, Farrall L, Chumley FG (1991) Magnaporthe grisea genes for pathogenicity and virulence identified through a series of backcrosses. Genetics 127:87-101.
71. Ventelon-Debout M, Delalande F, Brizard J-P, Diemer H, Van Dorsselaer A, Brugidou C (2004) Proteome analysis of cultivar-specific deregulations of Oryza sativa indica and O. sativa japonica cellular suspensions undergoing Rice yellow mottle virus infection. Proteomics 4:216-225.
72. Whitelegge JP (2002) Plant proteomics: BLASTing out of a MudPIT. Proc Natl Acad Sci USA 99:11564-11566.
73. Yan S, Tang Z, Su W, Sun W (2005) Proteomic analysis of salt stress-responsive proteins in rice root. Proteomics 5:235-244.
74. Yang G, Inoue A, Takasaki H, Kaku H, Akao S, Komatsu S (2005) A proteomic approach to analyze auxin and zinc-responsive protein in rice. J Proteome Res 4:456-463.
75. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92.
76. Zhong B, Karibe H, Komatsu S, Ichimura H, Nagamura Y, Sasaki T, Hirano H (1997) Screening of rice genes from a cDNA based on the sequence data-file of proteins separated by two-dimensional electrophoresis. Breeding Sci 47:255-251.