Towards a comprehensive understanding of Bacillus subtilis cell physiology by physiological proteomics

Proteomics

Volumn 4, Issue 12, 2004, Pages 3727-3750

  Hecker, Michael ^a   Völker, Uwe ^a,b  

^a UNIVERSITY OF GREIFSWALD   (Germany)

^b MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

Author keywords

Bacillus subtilis; Physiological proteomics; Review; SigB; Stress adaptation reactions

Indexed keywords

MESSENGER RNA; PROTEOME;

BACILLUS SUBTILIS; BACTERIAL CELL; BACTERIAL GROWTH; BACTERIAL METABOLISM; CELL FUNCTION; CELL GROWTH; DNA MICROARRAY; FERMENTATION; GENE EXPRESSION; GENOMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN QUALITY; PROTEIN SECRETION; PROTEIN STABILITY; PROTEIN SYNTHESIS; PROTEOMICS; REVIEW;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; GLUCOSE; KINETICS; MODELS, BIOLOGICAL; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATIVE STRESS; PROTEIN ARRAY ANALYSIS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; PROTEOMICS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; TIME FACTORS;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

EID: 10644274361     PISSN: 16159853     EISSN: None     Source Type: Journal    
DOI: 10.1002/pmic.200401017     Document Type: Review

References (122)

1. Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A. et al., Science 1995, 269, 496-512.
2. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M. et al., Nature 1997, 390, 249-256.
3. Sonenshein, A. L., Hoch, J. A., Losick, R. (Eds.), Bacillus subtilis and its Closest Relatives. From Genes to Cells, ASM Press, Washington, DC 2002.
4. Schumann, W., Ehrlich, D., Ogasawara, N. (Eds.), Functional Analysis of Bacterial Genes: A Practical Manual, John Wiley & Sons, Chichester 2001.
5. Streips, U. N., Polio, F. W., J. Bacteriol. 1985, 162, 434-437.
6. Richter, A., Hecker, M., FEMS Microbiol. Lett. 1986, 36, 69-71.
7. O'Farrell, P. H., J. Biol. Chem. 1975, 250, 4007-4021.
8. Klose, J., Humangenetik 1975, 26, 231-243.
9. Scheele, G. A., J. Biol. Chem. 1975, 250, 5375-5385.
10. MacGillivray, A. J., Rickwood, D., Eur. J. Biochem. 1974, 41, 181-190.
11. Herendeen, S. L., VanBogelen, R. A., Neidhardt, F. C., J. Bacteriol. 1979, 139, 185-194.
12. VanBogelen, R. A., Kelley, P. M., Neidhardt, F. C., J. Bacteriol. 1987, 169, 26-32.
13. Link, A. J., Trends Biotechnol. 2002, 20, S8-13.
14. Gevaert, K., Van Damme, J., Goethals, M., Thomas, G. R. et al., Mol Cell Proteomics 2002, 1, 896-903.
15. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Nat Biotechnol 1999, 17, 994-999.
16. Washburn, M. P., Wolters, D., Yates III, J. R., Nat. Biotechnol. 2001, 19, 242-247.
17. Lu, Y., Bottari, P., Turecek, F., Aebersold, R., Gelb, M. H., Anal Chem 2004, 76, 4104-4111.
18. Jaffe, J. D., Berg, H. C., Church, G. M., Proteomics 2004, 4, 59-77.
19. Lipton, M. S., Pasa-Tolic, L., Anderson, G. A., Anderson, D. J. et al., Proc. Natl. Acad. Sci. USA 2002, 99, 11049-11054.
20. Taoka, M., Yamauchi, Y., Shinkawa, T., Kaji, H. et al., Mol Cell Proteomics 2004, 3, 780-787.
21. Eymann, C., Dreisbach, A., Albrecht, D., Bernhardt, J. et al., Proteomics 2004, 4, 2849-2876.
22. Bunai, K., Ariga, M., Inoue, T., Nozaki, M. et al., Electrophoresis 2004, 25, 141-155.
23. Bremer, H., Dennis, P., in: Neidhardt, F., Curtiss, R., Ingraham, J. L., Lin, E. C. C. et al. (Eds.), Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC 1996, pp. 1553-1569.
24. McHardy, A. C., Pühler, A., Kalinowski, J., Meyer, F., Proteomics 2004, 4, 46-58.
25. Rocha, E. P., Danchin, A., Mol. Biol. Evol. 2004, 21, 108-116.
26. Kobayashi, K., Ehrlich, S. D., Albertini, A., Amati, G. et al., Proc. Natl. Acad. Sci. USA 2003, 100, 4678-4683.
27. Tobisch, S., Zühlke, D., Bernhardt, J., Stülke, J., Hecker, M., J. Bacteriol. 1999, 181, 6996-7004.
28. Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M. et al., Mol. Microbiol. 2001, 41, 409-422.
29. Ludwig, H., Rebhan, N., Blencke, H. M., Merzbacher, M., Stulke, J., Mol. Microbiol. 2002, 45, 543-553.
30. Hecker, M., Schumann, W., Völker, U., Mol. Microbiol. 1996, 19, 417-428.
31. Hecker, M., Völker, U., Adv. Microbial. Physiol. 2001, 44, 35-91.
32. Smith, M. W., Neidhardt, F. C., J. Bacteriol. 1983, 154, 344-350.
33. Bernhardt, J., Büttner, K., Scharf, C., Hecker, M., Electrophoresis 1999, 20, 2225-2240.
34. Hecker, M., Völker, U., FEMS Microbiol. Ecol. 1990, 74, 197-213.
35. Price, C. W., in: Storz, G., Hengge-Aronis, R. (Eds.), Bacterial Stress Responses, ASM Press, Washington, DC 2000, pp. 179-197.
36. Hengge-Aronis, R., in: Storz, G., Hengge-Aronis, R. (Eds.), Bacterial Stress Responses, ASM, Washington, DC 2000, pp. 161-178.
37. Price, C. W., in: Sonenshein, A. L., Hoch, J. A., Losick, R. (Eds.), Bacillus subtilis and its Closest Relatives. From Genes to Cells, ASM Press, Washington, DC 2002, pp. 369-384.
38. Eymann, C., Homuth, G., Scharf, C., Hecker, M., J. Bacteriol. 2002, 184, 2500-2520.
39. Wendrich, T. M., Marahiel, M. A., Mol. Microbiol. 1997, 26, 65-79.
40. Rhaese, H. J., Dichtelmuller, H., Grade, R., Eur. J. Biochem. 1975, 56, 385-392.
41. Cashel, M., Gentry, D. R., Hernandez, V. J., Vinella, D., in: Neidhardt, F. C., Curtiss III, R., Ingraham, J. L., Lin, E. C. C. et al. (Eds.), Escherichia coli and Salmonella: Cellular and Molecular Biology, ASM Press, Washington, DC 1996, pp. 1458-1496.
42. Ochi, K., Kandala, J. C., Freese, E., J. Biol. Chem. 1981, 256, 6866-6875.
43. Lopez, J. M., Marks, C. L., Freese, E., Biochim. Biophys. Acta 1979, 587, 238-252.
44. Lopez, J. M., Dromerick, A., Freese, E., J. Bacteriol. 1981, 146, 605-613.
45. Ratnayake-Lecamwasam, M., Serror, P., Wong, K. W., Sonenshein, A. L., Genes. Dev. 2001, 15, 1093-1103.
46. Molle, V., Nakaura, Y., Shivers, R. P., Yamaguchi, H. et al., J. Bacteriol. 2003, 185, 1911-1922.
47. Inaoka, T., Takahashi, K., Ohnishi-Kameyama, M., Yoshida, M., Ochi, K., J. Biol. Chem. 2003, 278, 2169-2176.
48. Inaoka, T., Ochi, K., J. Bacteriol. 2002, 184, 3923-3930.
49. Mascher, T., Margulis, N. G., Wang, T., Ye, R. W., Helmann, J. D., Mol. Microbiol. 2003, 50, 1591-1604.
50. Hecker, M., Völker, U., Mol. Microbiol. 1998, 29, 1129-1136.
51. Cao, M., Wang, T., Ye, R., Helmann, J. D., Mol. Microbiol. 2002, 45, 1267-1276.
52. Cao, M., Helmann, J. D., J. Bacteriol. 2004, 186, 1136-1146.
53. Wiegert, T., Homuth, G., Versteeg, S., Schumann, W., Mol. Microbiol. 2001, 41, 59-71.
54. Martinez-Antonio, A., Collado-Vides, J., Curr. Opin. Microbiol 2003, 6, 482-489.
55. von Mering, C., Zdobnov, E. M., Tsoka, S., Ciccarelli, F. D. et al., Proc. Natl. Acad. Sci. USA 2003, 100, 15428-15433.
56. Bork, P., Orengo, C. A., Curr. Opin. Struct. Biol. 2004, 14, 261-263.
57. Pragai, Z., Harwood, C. R., Microbiology 2002, 148, 1593-1602.
58. Leichert, L. I., Scharf, C., Hecker, M., J. Bacteriol. 2003, 185, 1967-1975.
59. Drzewiecki, K., Eymann, C., Mittenhuber, G., Hecker, M., J. Bacteriol. 1998, 180, 6674-6680.
60. Varon, D., Brody, M. S., Price, C. W., Mol. Microbiol. 1996, 20, 339-350.
61. Hecker, M., Adv. Biochem. Eng. Biotechnol. 2003, 83, 57-92.
62. Luhn, S., Berth, M., Hecker, M., Bernhardt, J., Proteomics 2003, 3, 1117-1127.
63. Bernhardt, J., Weibezahn, J., Scharf, C., Hecker, M., Genome Res. 2003, 13, 224-237.
64. VanBogelen, R. A., Schiller, E. E., Thomas, J. D., Neidhardt, F. C., Electrophoresis 1999, 20, 2149-2159.
65. Voigt, B., Schweder, T., Becher, D., Ehrenreich, A. et al., Proteomics 2004, 4, 1465-1490.
66. Antelmann, H., Darmon, E., Noone, D., Veening, J. W. et al., Mol. Microbiol. 2003, 49, 143-156.
67. Guay, D. R., Drugs 2001, 61, 353-364.
68. Bandow, J. E., Brötz, H., Leichert, L. I., Labischinski, H., Hecker, M., Antimicrob. Agents Chemother. 2003, 47, 948-955.
69. Beyer, D., Kroll, H. P., Endermann, R., Schiffer, G. et al., Antimicrob. Agents Chemother. 2004, 48, 525-532.
70. VanBogelen, R. A., Neidhardt, F. C., Proc. Natl. Acad. Sci. USA 1990, 57, 5589-5593.
71. Yoshida, K., Kobayashi, K., Miwa, Y., Kang, C. M. et al., Nucleic Acids Res. 2001, 29, 683-692.
72. Jürgen, B., Hanschke, R., Sarvas, M., Hecker, M., Schweder, T., Appl. Microbiol. Biotechnol. 2001, 55, 326-332.
73. Mäder, U., Antelmann, H., Buder, T., Dahl, M. K. et al., Mol. Genet. Genomics 2002, 268, 455-467.
74. Mäder, U., Homuth, G., Scharf, C., Büttner, K. et al., J. Bacteriol. 2002, 184, 4288-4295.
75. Mostertz, J., Scharf, C., Hecker, M., Homuth, G., Microbiology 2004, 150, 497-512.
76. Graumann, P., Schröder, K., Schmid, R., Marahiel, M. A., J. Bacteriol. 1996, 178, 4611-4619.
77. Beckering, C. L., Steil, L., Weber, M. H., Völker, U., Marahiel, M. A., J. Bacteriol. 2002, 184, 6395-6402.
78. Weber, H., Engelmann, S., Becher, D., Hecker, M., Mol. Microbiol. 2004, 52, 133-140.
79. Saghatelian, A., Jessani, N., Joseph, A., Humphrey, M., Cravatt, B. F., Proc. Natl. Acad. Sci. USA 2004, 101, 10000-10005.
80. Jessani, N., Cravatt, B. F., Curr. Opin. Chem. Biol. 2004, 8, 54-59.
81. Noirot-Gros, M. F., Dervyn, E., Wu, L. J., Mervelet, P. et al., Proc. Natl. Acad. Sci. USA 2002, 99, 8342-8347.
82. Gavin, A. C., Bosche, M., Krause, R., Grandi, P. et al., Nature 2002, 415, 141-147.
83. Shapiro, L., McAdams, H. H., Losick, R., Science 2002, 298, 1942-1946.
84. Shapiro, L., Losick, R., Science 1997, 276, 712-718.
85. Ben-Yehuda, S., Rudner, D. Z., Losick, R., Science 2003, 299, 532-536.
86. Errington, J., Daniel, R. A., Scheffers, D. J., Microbiol. Mol. Biol. Rev. 2003, 67, 52-65.
87. Errington, J., Nat. Cell Biol. 2003, 5, 175-178.
88. Wu, L. J., Errington, J., Cell 2004, 117, 915-925.
89. Mascarenhas, J., Soppa, J., Strunnikov, A. V., Graumann, P. L., EMBO J. 2002, 27, 3108-3118.
90. Ben-Yehuda, S., Losick, R., Cell 2002, 109, 257-266.
91. Gueiros-Filho, F. J., Losick, R., Genes Dev. 2002, 16, 2544-2556.
92. Antelmann, H., Tjalsma, H., Voigt, B., Ohlmeier, S. et al., Genome Res. 2001, 11, 1484-1502.
93. van Dijl, J. M., Braun, P. G., Robinson, C., Quax, W. J. et al., J Biotechnol. 2002, 98, 243-254.
94. Antelmann, H., Yamamoto, H., Sekiguchi, J., Hecker, M., Proteomics 2002, 2, 591-602.
95. Hirose, I., Sano, K., Shioda, I., Kumano, M. et al., Microbiology 2000, 146, 65-75.
96. Tjalsma, H., Antelmann, H., Jongbloed, J. D., Braun, P. G. et al., Microbiol. Mol. Biol. Rev. 2004, 68, 207-233.
97. Bandow, J. E., Becher, D., Büttner, K., Hochgrafe, F. et al., Proteomics 2003, 3, 299-306.
98. Madec, E., Stensballe, A., Kjellstrom, S., Cladiere, L. et al., J. Mol. Biol. 2003, 330, 459-472.
99. Madec, E., Laszkiewicz, A., Iwanicki, A., Obuchowski, M., Seror, S., Mol. Microbiol. 2002, 46, 571-586.
100. Wagner, E., Luche, S., Penna, L., Chevallet, M. et al., Biochem J 2002, 366, 777-785.
101. Yang, K. S., Kang, S. W., Woo, H. A., Hwang, S. C. et al., J. Biol. Chem. 2002, 277, 38029-38036.
102. Rabilloud, T., Heller, M., Gasnier, F., Luche, S. et al., J. Biol. Chem. 2002, 277, 19396-19401.
103. Dukan, S., Nystrom, T., Genes Dev. 1998, 12, 3431-3441.
104. Dukan, S., Farewell, A., Ballesteros, M., Taddei, F. et al., Proc. Natl. Acad. Sci. USA 2000, 97, 5746-5749.
105. Mostertz, J., Hecker, M., Mol. Genet. Genomics 2003, 269, 640-648.
106. Jenal, U., Hengge-Aronis, R., Curr. Opin. Microbiol. 2003, 6, 163-172.
107. Krüger, E., Witt, E., Ohlmeier, S., Hanschke, R., Hecker, M., J. Bacteriol. 2000, 182, 3259-3265.
108. Krüger, E., Zühlke, D., Witt, E., Ludwig, H., Hecker, M., EMBO J. 2001, 20, 852-863.
109. Kock, H., Gerth, U., Hecker, M., Mol. Microbiol. 2004, 51, 1087-1102.
110. Bernhardt, J., Völker, U., Völker, A., Antelmann, H. et al., Microbiology 1997, 143, 999-1017.
111. Boylan, S. A., Redfield, A. R., Price, C. W., J. Bacteriol. 1993, 175, 3957-3963.
112. Boylan, S. A., Thomas, M. D., Price, C. W., J. Bacteriol. 1991, 173, 7856-7866.
113. Price, C. W., Fawcett, P., Ceremonie, H., Su, N. et al., Mol. Microbiol. 2001, 41, 757-774.
114. Igo, M., Losick, R., J. Mol. Biol. 1986, 191, 615-624.
115. Helmann, J. D., Wu, M. F., Kobel, P. A., Gamo, F. J. et al., J. Bacteriol. 2001, 183, 7318-7328.
116. Völker, U., Engelmann, S., Maul, B., Riethdorf, S. et al., Microbiology 1994, 140, 741-752.
117. Antelmann, H., Bernhardt, J., Schmid, R., Mach, H. et al., Electrophoresis 1997, 18, 1451-1463.
118. Petersohn, A., Brigulla, M., Haas, S., Hoheisel, J. D. et al., J. Bacteriol. 2001, 183, 5617-5631.
119. Petersohn, A., Bernhardt, J., Gerth, U., Höper, D. et al., J. Bacteriol. 1999, 181, 5718-5724.
120. Völker, U., Maul, B., Hecker, M., J. Bacteriol. 1999, 181, 3942-3948.
121. Gaidenko, T. A., Price, C. W., J. Bacteriol. 1998, 180, 3730-3733.
122. Brigulla, M., Hoffmann, T., Krisp, A., Völker, A. et al., J. Bacteriol. 2003, 185, 4305-4314.