B. subtilis ribosomal proteins: Structural homology and post-translational modifications

Journal of Proteome Research

Volumn 8, Issue 9, 2009, Pages 4193-4206

  Lauber, Matthew A ^a   Running, William E ^a   Reilly, James P ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

B. subtilis; Post translational modifications; Protein mass spectrometry; Ribosomal proteins; S methylthioacetimidate; Sequencing errors; Structural homology; Two dimensional liquid chromatography

Indexed keywords

AMIDINE; RIBOSOME PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GROWTH; BACTERIAL STRAIN; CHEMICAL LABELING; CONTROLLED STUDY; DNA METHYLATION; GENE SEQUENCE; GENOME; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METHYLATION; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTEOMICS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; CHROMATOGRAPHY, LIQUID; CRYSTALLOGRAPHY, X-RAY; MASS SPECTROMETRY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOMICS; RIBOSOMAL PROTEINS; SEQUENCE ALIGNMENT; SOLVENTS; STRUCTURAL HOMOLOGY, PROTEIN;

BACTERIA (MICROORGANISMS); POSIBACTERIA;

EID: 70349923633     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr801114k     Document Type: Article

References (73)

1. Voet, D.; Voet, J. G. In Biochemistry, 3rd ed.; J. Wiley & Sons: Hoboken, NJ, 2004; p 1310.
2. Nissen, P.; Hansen, J.; Ban, N.; Moore, P. B.; Steitz, T. A. Science 2000, 289, 920-930.
3. Polacek, N.; Gaynor, M.; Yassin, A.; Mankin, A. S. Nature 2001, 411, 499-501.
4. Wilson, D.; Nierhaus, K. Crit. Rev. Biochem. Mol. Biol. 2005, 40, 243-267.
5. Blaha, G.; Wilson, D. N.; Stoller, G.; Fischer, G.; Willumeit, R.; Nierhaus, K. H. J. Mol. Biol. 2003, 326, 887-897.
6. Deuerling, E.; Schulze-Specking, A. Nature 1999, 400, 693-696.
7. Kramer, G. T.; Rauch, T.; Rist, W.; Vorderwuelbecke, S.; Patzelt, H.; Schulze-Specking, A.; Ban, N.; Deuerling, E.; Bukau, B. Nature 2002, 419, 171-174.
8. Wahl, M. C.; Moller, W. Curr. Protein Pept. Sci. 2002, 3, 93-106.
9. Kurland, C. G.; Jørgensen, F.; Richter, A.; Ehrenberg, M.; Bilgin, N.; Rojas, A.-M. Through the accuracy window. In The Ribosome-Structure, Function, and Evolution; Dahlberg, A., Hill, W. E., Garrett, R. A., Moore, P. B., Schlessinger, D., Warner, J. R., Eds.; American Society Microbiology: Washington, D.C., 1990; pp 513-526.
10. Kurland, C. G.; Hughes, D.; Ehrenberg, M. Escherichia coli and Salmonella. In Cellular and Molecular Biology, 2nd ed.; Neidhardt, F. C., Ed.; ASM Press: Washington, D.C., 1996; pp 974-1004.
11. Kowalak, J. A.; Walsh, K. A. Protein Sci. 1996, 5, 1625-1632.
12. Anton, B. P.; Saleh, L.; Benner, J. S.; Raleigh, E. A.; Kasif, S.; Roberts, R. J. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1826-1831.
13. Louie, D. F.; Resing, K. A.; Lewis, T. S.; Ahn, N. G. J. Biol. Chem. 1996, 271, 28189-28198.
14. Vladtmirov, S. N.; Ivanov, A. V.; Karpova, G. G.; Musolyamov, A. K.; Egorov, T. A.; Thiede, B.; Wittmann-Liebold, B.; Otto, A. Eur. J. Biochem. 1996, 239, 144-149.
15. Strader, M. B.; VerBerkmoes, N. C.; Tabb, D. L.; Connelly, H. M.; Barton, J. W.; Bruce, B. D.; Pelletier, D. A.; Davison, B. H.; Hettich, R. L.; Larimer, F. W.; Hurst, G. B. J. Proteome Res. 2004, 3, 965-978.
16. Suh, M.-J.; Hamburg, D.-M.; Gregory, S. T.; Dahlberg, A. E.; Limbach, P. A. Proteomics 2005, 5, 4818-4831.
17. Carr, J. F.; Hamburg, D. M.; Gregory, S. T.; Limbach, P. A.; Dahlberg, A. E. J. Bacteriol. 2006, 188, 2020-2023.
18. Running, W. E.; Ravipaty, S.; Karty, J. A.; Reilly, J. P. J. Proteome Res. 2007, 6, 337-347.
19. Running, W. E.; Reilly, J. P. J. Proteome Res. 2009, 8 (3), 1228-1246.
20. Sonenshein, A. L.; Hoch, J. A.; Losick, R. Bacillus subtilis and Its Closest Relatives: From Genes to Cells; ASM Press: Washington, D.C., 2002.
21. Panina, E. M.; Mironov, A. A.; Gelfand, M. S. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 9912-9917.
22. Makarova, K. S.; Ponomarev, V. A.; Koonin, E. V. Genome Biol. 2001, 2, research0033.110033.14.
23. Natori, Y.; Nanamiya, H.; Akanuma, G.; Kosono, S.; Kudo, T.; Ochi, K.; Kawamura, F. Mol. Microbiol. 2007, 63, 294-307.
24. Nanamiya, H.; Akanuma, G.; Natori, Y.; Murayama, R.; Kosono, S.; Kudo, T.; Kobayashi, K.; Ogasawara, N.; Park, S.; Ochi, K.; Kawamura, F. Mol. Microbiol. 2004, 52, 273-283.
25. Akanuma, G.; Nanamiya, H.; Natori, Y.; Nomura, N.; Kawamura, F. J. Bacteriol. 2006, 188, 2715-2720.
26. Selmer, M.; Dunham, C. M.; Murphy, F. V.; Weixlbaumer, A.; Petry, S.; Kelley, A. C.; Weir, J. R.; Ramakrishnan, V. Science 2006, 313, 1935-1942.
27. Schuwirth, B. S.; Borovinskaya, M. A.; Hau, C. W.; Zhang, W.; Vila-Sanjurjo, A.; Holton, J. M.; Cate, J. H. Science 2005, 310, 827-834.
28. Suckau, D.; Mak, M.; Przybylski, M. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 5630-5634
29. Liu, X.; Broshears, W. C.; Reilly, J. P. Anal. Biochem. 2007, 367, 13-19.
30. Janecki, D. J.; Beardsley, R. L.; Reilly, J. P. Anal. Chem. 2005, 77, 7274-7281.
31. Karty, J. A.; Running, W. E.; Reilly, J. P. J. Chromatogr. B. 2007, 847, 103-113.
32. Kunst, F.; et al. Nature 1997, 390 (6657), 249-256.
33. Kearns, D. B.; Losick, R. Mol. Microbiol. 2003, 49 (3), 581-590.
34. Arnold, R. J.; Reilly, J. P. Anal. Biochem. 1999, 269, 105-112.
35. Spedding, G. In Ribosomes and Protein Synthesis: A Pratical Approach; Rickwood, D., Hames, B. D., Eds.; Oxford Press: New York, 1990; pp 1-29.
36. Good, N. E.; Winget, G. D.; Winter, W.; Connolly, T. N.; Izawa, S.; Singh, R. M. M. Biochemistry 1966, 5 (2), 467-477
37. Read, S. M.; Northcote, D. H. Anal. Biochem. 1981, 116 (1), 53-64.
38. Beardsley, R. L.; Running, W. E.; Reilly, J. P. J. Proteome Res. 2006, 5, 2935-2946.
39. Thompson, J. D.; Higgins, D. G.; Gibson, T. J. Nucleic Acids Res. 1994, 22, 4673-4680.
40. Combet, C.; Blanchet, C.; Geourjon, C.; Deléage, G. Trends Biochem. Sci. 2000, 25, 147-150.
41. DeLano, W. L. The PyMOL Molecular Graphics System; DeLano Scientific: Palo Alto, CA, 2002.
42. Connolly, M. L. J. Appl. Crystallogr. 1983, 16, 548-558
43. Farwell, M. A.; Roberts, M. W.; Rabinowitz, J. C. Mol. Microbiol. 1992, 6 (22), 3375-3383
44. Isono, K.; Isono, S. Proc. Natl. Acad. Sci. U.S.A. 1976, 73, 767-770
45. Schmalisch, M.; Langbein, I.; Stulke, J. J. Mol. Microbiol. Biotechnol. 2002, 4, 495-501.
46. Korepanov, A. P.; Gongadze, G. M. Biochemistry (Moscow) 2004, 69, 607-611.
47. Gryaznova, O. I.; Davydova, N. L.; Gongadze, G. M.; Jonsson, B. H.; Garber, M. B.; Liljas, A. Biochimie 1996, 78, 915-919.
48. Frottin, F.; Martinez, A.; Peynot, P.; Mitra, S.; Holz, R. C.; Giglione, C.; Meinnel, T. Mol. Cell. Proteomics 2006, 5, 2336-2349.
49. Higo, K.; Otaka, E.; Osawa, S. Mol. Gen. Genet. 1982, 185, 239-244
50. Suh, J.-W.; Boylan, S. A.; Oh, S. H.; Price, C. W. Gene 1996, (169), 17-23.
51. Yasumoto, K.; Liu, H.; Jeong, S. M.; Ohashi, Y.; Kakinuma, S.; Tanaka, K.; Kawamura, F.; Yoshikawa, H.; Takahashi, H. Microbiology 1996, (142), 3039-3046.
52. Hill, F.; Gemund, C.; Benes, B.; Ansorge, W.; Gibson, T. J. EMBO Rep. 2000, 1 (1), 29-31.
53. Alix, J. Adv. Exp. Med. Biol. 1988, 231, 371-385.
54. Polevoda, B.; Sherman, F. Mol. Microbiol. 2007, 65 (3), 590-606.
55. Cameron, D. M.; Gregory, S. T.; Thompson, J.; Suh, M.-J.; Limbach, P. A.; Dahlberg, A. E. J. Bacteriol. 2004, 186 (17), 5819-5825.
56. Poncz, L.; Dearborn, D. G. J. Biol. Chem. 1983, 258 (3), 1844-1850
57. Lederer, F.; Alix, J. H.; Hayes, D. Biochem. Biophys. Res. Commun. 1977, 77 (2), 470-480
58. Dognin, M. J.; Wittmann-Liebold, B. FEBS Lett. 1977, 84 (2), 342-346
59. Brosius, J.; Chen, R. FEBS Lett. 1976, 68 (1), 105-109
60. Gordiyenko, Y.; Deroo, S.; Zhou, M.; Videler, H.; Robinson, C. V. J. Mol. Biol. 2008, 380 (2), 404-414.
61. Chang, F. N. J. Bacteriol. 1978, 135 (3), 1165-1166
62. Deusser, E.; Wittmann, H. G. Nature 1972, 238 (5362), 269-270
63. Moore, C. M.; Helmann, J. D. Curr. Opin. Microbiol. 2005, 8, 188-195.
64. Hilden, I.; Krath, B. N.; Hove-Jensen, B. J. Bacteriol. 1995, 177 (24), 7280-7284
65. Mirel, D. B.; Chamberlin, M. J. J. Bacteriol. 1989, 171 (6), 3095-3101
66. Matsuno, K.; Sonenshein, A. L. J. Bacteriol. 1999, 181 (11), 3392-3401.
67. Ando, Y.; Nakamura, K. Biosci. Biotechnol. Biochem. 2006, 70 (7), 1606-1615.
68. Nakamura, K.; Yahagi, S.-I.; Yamazaki, T.; Yamane, K. J. Biol. Chem. 1999, 274 (19), 13569-13576.
69. Vila-Sanjurjo, A.; Schuwirth, B.-S.; Hau, C. W.; Cate, J. H. D. Nat. Struct. Mol. Biol. 2004, 11, 1054-1059.
70. Ueta, M.; Yoshida, H.; Wada, C.; Baba, T.; Mori, H.; Wada, A. Genes Cells 2005, 10, 1103-1112.
71. Maki, Y.; Yoshida, H.; Wada, A. Genes Cells 2000, 5 (12), 965-974.
72. Ueta, M.; Ohniwa, R. L.; Yoshida, H.; Maki, Y.; Wada, C.; Wada, A. J. Biochem. 2008, (143), 425-433.
73. Wilson, D. N.; Nierhaus, K. H. Crit. Rev. Biochem. Mol. Biol. 2007, 42 (3), 187-219.