Multigenic families and proteomics: Extended protein characterization as a tool for paralog gene identification

Proteomics

Volumn 5, Issue 2, 2005, Pages 450-460

  Delalande, François ^a   Carapito, Christine ^a,b   Brizard, Jean Paul ^b   Brugidou, Christophe ^b   Van Dorsselaer, Alain ^a  

^a Lab Spectrom Masse Bio Organique   (France)

^b INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

Multigenic family; Paralog gene; Post transcriptional gene silencing; Rice genome

Indexed keywords

FRUCTOSE BISPHOSPHATE ALDOLASE; PEPTIDE; RNA;

AMINO ACID SEQUENCE; ARTICLE; GENE IDENTIFICATION; GENE MUTATION; GENE SILENCING; GENOME; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE ANALYSIS; PLANT; PLANT VIRUS; PRIORITY JOURNAL; PROTEOMICS; RICE; RICE YELLOW MOTTLE VIRUS; RNA INTERFERENCE;

CHAPERONIN 60; CHROMATOGRAPHY, GEL; CHROMATOGRAPHY, LIQUID; CHROMOSOMES, PLANT; DATABASES, GENETIC; DATABASES, PROTEIN; DISCRIMINANT ANALYSIS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FREEZE DRYING; FRUCTOSE-BISPHOSPHATE ALDOLASE; GENE EXPRESSION; GENE SILENCING; GENES, PLANT; MASS SPECTROMETRY; MITOCHONDRIAL PROTEINS; MULTIGENE FAMILY; NANOTECHNOLOGY; ORYZA SATIVA; PHENYLALANINE AMMONIA-LYASE; PLANT PROTEINS; PLANT VIRUSES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; REPRODUCIBILITY OF RESULTS; RNA INTERFERENCE; SEQUENCE ANALYSIS, PROTEIN;

ANIMALIA; ORYZA SATIVA; RICE YELLOW MOTTLE VIRUS;

EID: 13844319213     PISSN: 16159853     EISSN: None     Source Type: Journal    
DOI: 10.1002/pmic.200400954     Document Type: Article

References (49)

1. Goff, S. A., Ricke, D., Lan, T. H., Presting, G. et al., Science 2002, 296, 92-100.
2. Yu, J., Hu, S., Wang, J., Wong, G. K. et al., Science 2002, 296, 79-92.
3. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K. et al., Nature 2002, 420, 312-316.
4. Feng, Q., Zhang, Y., Hao, P., Wang, S. et al., Nature 2002, 420, 316-320.
5. Siré, C., Brugidou, C., Virologie 2002, 6, 431-443.
6. Hibino, H., Annu. Rev. Phytopathol, 1996, 34, 249-274.
7. Bakker, W., Netherlands Plant Pathol. 1970, 77, 201-206.
8. Opalka, N., Tihova, M., Brugidou, C., Kumar, A. et al., J. Mol. Biol. 2000, 303, 197-211.
9. Fargette, D., Pinel, A., Abubakar, Z., Traore, O. et al., J. Virol. 2004, 78, 3252-3261.
10. Ventelon-Debout, M., Delalande, F, Brizard, J. P., Diemer, H. et al., Proteomics 2004, 4, 216-225.
11. Wang, M. B., Waterhouse, P. M., Curr. Opin. Plant Biol. 2002, 5, 146-150.
12. Brummell, D. A., Balint-Kurti, P. J., Harpster, M. H., Palys, J. M. et al., Plant J. 2003, 33, 793-800.
13. Wesley, S. V., Helliwell, C. A., Smith, N. A., Wang, M. B. et al., Plant J. 2001, 27, 581-590.
14. Baulcombe, D. C., Curr. Opin. Plant Biol. 1999, 2, 109-113.
15. Wassenegger, M., Pelissier, T., Plant Mol. Biol. 1998, 37, 349-362.
16. Depicker, A., Montagu, M. V., Curr. Opin. Cell Biol. 1997, 9, 373-382.
17. Stam, M., Mol. J. N. M., Kooter, J. M., Ann. Bot. 1997, 79, 3-12.
18. van der Krol, A. R., Mur, L. A., de Lange, P., Mol, J. N. et al., Plant Mol. Biol. 1990, 14, 457-466.
19. Pickett, F. B., Meeks-Wagner, D. R., Plant Cell 1995, 7, 1347-1356.
20. Wolfe, K. H., Shields, D. C., Nature 1997, 387, 708-713.
21. Semple, C., Wolfe, K. H., J. Mol. Evol. 1999, 48, 555-564.
22. Initiative, A. G., Nature 2000, 408, 796-815.
23. Zhang, J., Trends Ecol. Evol. 2003, 18, 292-298.
24. Doyle, J. J., Gaut, B. S., Plant Mol. Biol. 2000, 42, 1-23.
25. Cannon, S. B., Young, N. D., BMC Bioinformatics 2003, 4, 35.
26. Eng, J. K., McCormack, A. L., Yates, J. R., 3rd, J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
27. Mann, M., Wilm, M., Anal. Chem. 1994, 66, 4390-439.
28. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C. et al., Proc Natl Acad Sci U.S.A. 1993, 90, 5011-5015.
29. Yates, J. R., 3rd, Speicher, S., Griffin, P. R., Hunkapiller, T., Anal. Biochem. 1993, 214, 397-408.
30. Yates, J. R., 3rd, Eng, J. K., McCormack, A. L., Schieltz, D., Anal. Chem. 1995, 67, 1426-1436.
31. Choudhary, J. S., Blackstock, W. P., Creasy, D. M., Cottrell, J. S., Proteomics 2001, 1, 651-667.
32. Mann, M., Pandey, A., Trends Biochem. Sci. 2001, 26, 54-61.
33. Choudhary, J. S., Blackstock, W. P., Creasy, D. M., Cottrell, J. S., Trends Biotechnol. 2001, 19, S17-S22.
34. Giddings, M. C., Shah, A. A., Gesteland, R., Moore, B., Proc Natl Acad Sci U.S.A. 2003, 100, 20-25.
35. Kuster, B., Mortensen, P., Andersen, J. S., Mann, M., Proteomics 2001, 1, 641-650.
36. Jaffe, J. D., Berg, H. C., Church, G. M., Proteomics 2004, 4, 59-77.
37. Brugidou, C., Opalka, N., Yeager, M., Beachy, R. N. et al., Virology 2002, 297, 98-108.
38. Richert, S., Luche, S., Chevallet, M., Van Dorsselaer, A. et al., Proteomics 2004, 4, 909-916.
39. Yuan, Q., Ouyang, S., Liu, J., Suh, B. et al., Nucleic Acids Res. 2003, 31, 229-233.
40. Arumuganathan, K., Earle, E. D., Plant Mol. Biol. Rep. 1991, 9, 208-219.
41. Perkins, D. N., Pappin, D. J., Creasy, D. M. Cottrell, J. S., Electrophoresis 1999, 20, 3551-3567.
42. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. et al., Nucleic Acids Res. 2000, 28, 15-18.
43. Rutherford, K., Parkhill, J., Crook, J., Horsnell, T. et al., Bioinformatics 2000, 16, 944-945.
44. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J. et al., Nucleic Acids Res. 1997, 25, 3389-3402.
45. Yuan, J., Amend, A., Borkowski, J., DeMarco, R. et al., Bioinformatics 1999, 15, 862-863.
46. Devor, E. J., Moffat-Wilson, K. A., Hum. Biol. 2003, 75, 661-672.
47. Srikantha, T., Landsman, D., Bustin, M., J. Mol. Biol. 1987, 197, 405-413.
48. Washburn, M. P., Wolters, D., Yates, J. R., 3rd, Nat. Biotechnol. 2001, 19, 242-247.
49. Liu, H., Lin, D., Yates, J. R., 3rd, Biotechniques 2002, 32, 898-902.