Journal of Plant Biotechnology

The Korean Society of Plant Biotechnology (한국식물생명공학회)
권호 표지
DOI QR코드

DOI QR Code

Rice Proteomics: A Functional Analysis of the Rice Genome and Applications

프로테옴 해석에 의한 벼 게놈 기능해석과 응용

  • Woo, Sun-Hee (Division of Biological and Chemical Science, Korea Basic Science Institute) ;
  • Kim, Hong-Sig (Department of Plant Resouces, College of Agriculture, Chungbuk National University) ;
  • Song, Berm-Heun (Department of Plant Resouces, College of Agriculture, Chungbuk National University) ;
  • Lee, Chul-Won (Department of Plant Resouces, College of Agriculture, Chungbuk National University) ;
  • Park, Young-Mok (Division of Biological and Chemical Science, Korea Basic Science Institute) ;
  • Jong, Seung-Keun (Department of Plant Resouces, College of Agriculture, Chungbuk National University) ;
  • Cho, Yong-Gu (Department of Plant Resouces, College of Agriculture, Chungbuk National University)
  • 우선희 (한국기초과학지원연구원, 생명화학연구부) ;
  • 김홍식 (충북대학교 농과대학 식물자원학과) ;
  • 송범헌 (충북대학교 농과대학 식물자원학과) ;
  • 이철원 (충북대학교 농과대학 식물자원학과) ;
  • 박영목 (한국기초과학지원연구원, 생명화학연구부) ;
  • 정승근 (충북대학교 농과대학 식물자원학과) ;
  • 조용구 (충북대학교 농과대학 식물자원학과)
  • Published : 2003.09.01
Download PDF
⟨ Previous Next ⟩

Abstract

In this review, we described the catalogues of the rice proteome which were constructed in our program, and functional characterization of some of these proteins was discussed. Mass-spectrometry is the most prevalent technique to rapidly identify a large number of proteome analysis. However, the conventional Western blotting/sequencing technique has been used in many laboratories. As a first step to efficiently construct protein cata-file in proteome analysis of major cereals, we have analyzed the N-terminal sequences of 100 rice embryo proteins and 70 wheat spike proteins separated by two-dimensional electrophoresis. Edman degradation revealed the N-terminal peptide sequences of only 31 rice proteins and 47 wheat proteins, suggesting that the rest of separated protein sports are N-terminally blocked. To efficiently determine the internal sequence of blocked proteins, we have developed a modified Cleveland peptide mapping method. Using this above method, the internal sequences of all blocked rice proteins(i, e., 69 proteins) were determined. Among these 100 rice proteins, thirty were proteins for which homologous sequence in the rice genome database could be identified. However, the rest of the proteins lacked homologous proteins. This appears to be consistent with the fact that about 45% of total rice cDNA have been deposited in the EMBL database. Also, the major proteins involved in the growth and development of rice can be identified using the proteome approach. Some of these proteins, including a calcium-binding protein that tuned out to be calreticulin, gibberellin-binding protein, which is ribulose-1.5-bisphosphate carboxylase/oxygense active in rice, and leginsulin-binding protein in soybean have functions in the signal transduction pathway. Proteomics is well suited not only to determine interaction between pairs of proteins, but also to identify multisubunit complexes. Currently, a protein-protein interaction database for plant proteins(http://genome.c.kanazawa-u.ac.jp/Y2H)could be a very useful tool for the plant research community. Also, the information thus obtained from the plant proteome would be helpful in predicting the function of the unknown proteins and would be useful be in the plant molecular breeding.

Keywords

References

  1. Anderson L, Seilhamer J (1997) A comparison of selected mRNA and protein abundances inhuman liver. Electrophoresis 18: 533-537 https://doi.org/10.1002/elps.1150180333
  2. Damerval C, Le Guilloux C (1998) Characterization of novel proteins affected by the o2 mutation and expression during maize endosperm development. Mol Gen Genet 257: 354-361 https://doi.org/10.1007/s004380050657
  3. Flengsrud R (1993) Separationof acidic barley endosperm proteins by two-dimensional electrophoresis. Electrophoresis 14: 1060-1066 https://doi.org/10.1002/elps.11501401169
  4. Fukuda M, Islam N,Woo SH, Yamagishi A, Takaoka M, Hirano H(2003) Assessing matrix assisted laser desorption/ionizatirn-time of flight-mass spectrametry as a means of rapid embryo protein identification in rice. Electrophoresis 24: 1319-1329 https://doi.org/10.1002/elps.200390168
  5. Gomez L, Sanchez-Monge R, Lopez-Otin C, Salcedo G (1991) Amino acid compositions and sequence analysis of the major low Mr globulins from Triticum monococcum L endosperm. J Cereal Sci 14: 117-123 https://doi.org/10.1016/S0733-5210(09)80132-X
  6. G$\ddot{o}$rgA, Postel W,Baumer M, Weiss W(1992)Two-dimensional polyacrylamide gel electrophoresis, with immobilized pH gradients in the first dimension, of barley seed proteins: Discrimination of cultivars with different malting grades. Electrophoresis 13: 192-203 https://doi.org/10.1002/elps.1150130141
  7. Gygi SP, Rist B, Gerber SA,Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotopecoded affinity tags. Nature Biotechnol 17: 994-999 https://doi.org/10.1038/13690
  8. Hirano H (1989) Microsequence analysis of winged bean seed proteins electroblotted from two-dimensirnal gel. J Protein Chem 8: 115-130 https://doi.org/10.1007/BF01025083
  9. Hirano H(1997) Screeninq of rice genes from the cDNA catalogusing the data obtained by protein sequencing. J Protein Chem 16: 533-536 https://doi.org/10.1023/A:1026377931210
  10. Hirano H (1998) Structure and function of hormone-like peptides in plants. Danbaku, Kakusan and Kouso (in Japanese) 43: 27-39
  11. Hirano H, Komatsu S, Nakamura A, Kikuchi F, Kajiwara H, Tsunasawa S, Sakiyama F (1991) Structural homology between semidwarfism-related proteins and glutelin seed protein in rice (Oryza sattvaL). Theor Appl Genet 83: 153-158
  12. Islam N, Woo SH, Tsujimoto H, Kawasaki H, Hirano H (2002) Proteome approaches to characterize seed storage proteins related to ditelccentric chromosomes in common wheat (Triticum aestivum L). Proteomics 2: 1146-1155 https://doi.org/10.1002/1615-9861(200209)2:9<1146::AID-PROT1146>3.0.CO;2-6
  13. Ito K, Kimura Y, Sassa H, Hirano H (2000) Identification of the rice 20S proteasome subunits and analysis of their N-terminal modification. Jpn J Electrophoresis 44: 205-210 https://doi.org/10.2198/sbk.44.205
  14. Kamo M, Kawakami T, Miyatake M, TsugitaA (1995) Separation and characterization of Arabidopsis thaliana proteins by twodimensional gel electrophoresis. Electrophoresis 16: 423-430 https://doi.org/10.1002/elps.1150160169
  15. Kimura Y, Takaoka M, Tanaka S, Sassa H,Tanaka K, Polevoda B, Sherman F, Hirano H (2000) N-acetylation and proteolytic activity ofthe yeast 20S proteasome. J BioI Chem 275: 4635-4639 https://doi.org/10.1074/jbc.275.7.4635
  16. Komatsu S, Kajiwara H, Hirano H (1994) Rice protein library: A data file of rice proteins separated by two-dimensional electrophoresis. Theor Appl Genet 86: 935-942
  17. Komatsu S, Masuda T, Hirano H (1996) Rice gibberellin-binding phosphoprotein structurally related to ribulose-1,5-bisphosphate carboxylase/oxygenase activase. FEBS Lett 384: 167-171 https://doi.org/10.1016/0014-5793(96)00275-X
  18. 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 https://doi.org/10.1093/oxfordjournals.pcp.a029009
  19. KomatsuS, Li Z, Rakwal R (1999) Separation and characterization of proteins in rice (Oryza sativa L) suspension cultured cells. Plant Cell TIss Org Cult 55: 183-192 https://doi.org/10.1023/A:1006145716701
  20. Lafiandra D, Kasarda, DD (1985) One and two-dimensional polyarylamide gel electrophoresis in a single gel: Separation of wheat proteins. Cereal Chem 62: 314-319
  21. Li Z, Komatsu S (2000) Molecular cloning and characterization of calreticulin, a calcuim -binding protein involved in the regeneration of rice cultured suspension cells. Eur J Biochem 267: 737-745 https://doi.org/10.1046/j.1432-1327.2000.01052.x
  22. Lund AA, Blum PH, Bhattramakki D, ElthonTE (1998) Heat-stress response of maize mitochondria. Plant Physiol 116: 1097-1110 https://doi.org/10.1104/pp.116.3.1097
  23. Masson F, Rosegnol M(1995) Basic plasticity of protein expression in tobacco leaf plasma membrane. Plant J 8: 77-85 https://doi.org/10.1046/j.1365-313X.1995.08010077.x
  24. Matsudaira P (1987) Sequence from picomole quantities of proteins electroblotted onto polyvinylidene difluoride membranes. J BioI Chem 262: 10035-10038
  25. Oda Y, Huang K, Cross R, Cowbum D, Chait BT (1999) Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci USA 96: 6591-6596 https://doi.org/10.1073/pnas.96.12.6591
  26. Ramani S, Apte SK (1997) Transient expression of multiple genes in salinity stressed young seedlings of rice (Oryza sativaL)cv. Bura Rata. Biochem Biophys Res Commun 233: 663-667 https://doi.org/10.1006/bbrc.1997.6521
  27. Rey P, Pruvot G, Becuwe N, Eymery F, Rumeau D, Peltier G (1998) A novel thioredoxin-like protein located in the chloroplast is induced by water deficit in Solanum tuberrosum L plants. Plant J 13: 97-107 https://doi.org/10.1046/j.1365-313X.1998.00015.x
  28. Riccardi F, Gazeau P, de Vienne D, Zivy M(1998) Protein changes in response to progressive water deficit in maize. Plant Physiol 117: 1253-1263 https://doi.org/10.1104/pp.117.4.1253
  29. Rouquie D, Peltier JB, Marquis-Mansion M,Tounaire C, Doumas P, Rossignol M(1997) Construction of a directory of tobacco plasma membrane proteins by combined two-dimensional gel electrophoresis and protein sequencing. Electrophoresis 18: 654-660 https://doi.org/10.1002/elps.1150180352
  30. Santoni V, Rouquie D, Doumas P, Mansion M, Boutry M,Degand H, Depree P, Packman L, Sherrier J, Prime T, Bauw G, Posada E, Reuze P, Dehais P, Sahnoun I, Barlier I, Rossignol M(1998) Use of a proteome strategy for tagging proteins present at the plasma membrane. Plant J 16: 633-641 https://doi.org/10.1046/j.1365-313x.1998.00335.x
  31. Santoni V, DelarueM, Caboche M, Bellini C (1997) A comparison of two-dimensional electrophoresis data with phenotypical traits in Arabidopsis leads to the identification of a mutant (cri 1) that accumulates cytokinins. Planta 202: 62-69 https://doi.org/10.1007/s004250050103
  32. Sassa H, Oguchi S, Inoue T, Hirano H (2000) Primary structural features of the 20S proteasome subunits of rice (Oryza satiua L). Gene 250: 61-69 https://doi.org/10.1016/S0378-1119(00)00190-6
  33. Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Gojobori T (2002) The genome sequence structure of rice chromosome 1. Nature 420: 312-316 https://doi.org/10.1038/nature01184
  34. Thiellement H, Bahrman N, Damerval C, Plomion C, Rossignol M, Santoni V,de Vienne D, Zivy M (1999) Proteomics for genetic and physiologcal studies in plants. Electrophoresis 20: 2013-2026 https://doi.org/10.1002/(SICI)1522-2683(19990701)20:10<2013::AID-ELPS2013>3.0.CO;2-#
  35. Tsugita A, Kawakami T, Uchiyama Y, Kamo M, Miyatake N, Noze Y (1994) Separation and characterization of rice proteins. Electrophoresis 15: 708-720 https://doi.org/10.1002/elps.1150150198
  36. Velculescu YE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE, Hieter P, Vogelstein B, Kinzler KW (1997) Characterization of the yeast transcriptome. Cell 88: 243-251 https://doi.org/10.1016/S0092-8674(00)81845-0
  37. Weiss W, Huber G, Engel KH, Pethran A, Dunn M, Gooley AA, Gorg A (1997) Identification and characterization of wheat grain albumin/globulin allergens. Electrophoresis 18: 826-833 https://doi.org/10.1002/elps.1150180529
  38. Woo SH, Islam N, Takaoka M, Adachi T, Hirano H (2001) Preliminary proteome analysis of the buckwheat embryo-proteins. Adv Buckwheat Res 8: 544-548
  39. Woo SH, Fukuda M, Islam N, Takaoka M, Kawasaki H, Hirano H (2002) Effident peptide mapping and its application to identification of embryo proteins in the rice (Oryza sativa L) proteome analysis. Electrophoresis 23: 647-654 https://doi.org/10.1002/1522-2683(200202)23:4<647::AID-ELPS647>3.0.CO;2-O
  40. Woo SH, Hirano H, Jong SK (2003) Separation and characterization of spikelet proteins expressed at the young microspore stage in rice (Oryza sativa L). Kor J Crop Sci (revision)
  41. Woo SH, Higa A, Kimura M, Jong SK,Yamaguchi I (2003) Analysis of wheat lemma proteins separated by two-dimensional polyacrylamide gel electrophoresis. Biosci Biotechnol Biochem (in press)
  42. Zhang L, Zheu W,Vekulescu YE, Kem SE, Hruban RH, Hamilton SR, Vogelstein B, Kinzler KW (1997) Gene expression profiles in normal cancer cells. Science 276: 1268-1272 https://doi.org/10.1126/science.276.5316.1268
  43. Zhang Z, Komatsu S (2000) Molecular cloning and charatcerization of cDNA encoding two isoforms of ribulose-1,5-bisphosphate carboxylase/oxygenase activase in rice (Oryza sativa L.). J Biochem 128: 383-389 https://doi.org/10.1093/oxfordjournals.jbchem.a022765

Cited by

  1. Analysis of Protein Function and Comparison of Protein Expression of Different Environment in Soybean using Proteomics Techniques vol.60, pp.1, 2015, https://doi.org/10.7740/kjcs.2014.60.1.033
  2. Analysis of Serum Proteom after Intravenous Injection of cultivated wild ginseng pharmacopuncture vol.9, pp.2, 2006, https://doi.org/10.3831/KPI.2006.9.2.017
  3. Analysis of Protein Function and Comparison on Expression of Protein in Taekwang During Maturation using Proteomic Techniques vol.60, pp.1, 2015, https://doi.org/10.7740/kjcs.2014.60.1.041
  4. Analysis of Serum proteom before and after Intravenous Injection of wild ginseng herbal acupuncture vol.7, pp.3, 2004, https://doi.org/10.3831/KPI.2004.7.3.005