Trans-translation is involved in the CcpA-dependent tagging and degradation of TreP in Bacillus subtilis

Journal of Biochemistry

Volumn 145, Issue 1, 2009, Pages 59-66

  Ujiie, Hiromi ^a,b   Matsutani, Tomoko ^a   Tomatsu, Hisashi ^a   Fujihara, Ai ^a   Ushida, Chisato ^a,b   Miwa, Yasuhiko ^c   Fujita, Yasutaro ^c   Himeno, Hyouta ^a,b   Muto, Akira ^a,b  

^a HIROSAKI UNIVERSITY   (Japan)

^b IWATE UNIVERSITY   (Japan)

^c FUKUYAMA UNIVERSITY   (Japan)

Author keywords

Bacillus subtilis; CcpA; tmRNA; Trans translation; TreP

Indexed keywords

ASPARAGINE; CATABOLITE CONTROL PROTEIN A; MESSENGER RNA; PERMEASE; TREHALOSE;

ARTICLE; BACILLUS SUBTILIS; GENE SEQUENCE; GENETIC TRANSCRIPTION; NONHUMAN; PROTEIN BINDING; PROTEIN DEGRADATION; RNA TRANSLATION;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; DNA-BINDING PROTEINS; MEMBRANE TRANSPORT PROTEINS; MOLECULAR SEQUENCE DATA; PROTEIN BIOSYNTHESIS; REPRESSOR PROTEINS; RNA, BACTERIAL; RNA, MESSENGER;

BACILLUS SUBTILIS;

EID: 58149120965     PISSN: 0021924X     EISSN: 17562651     Source Type: Journal    
DOI: 10.1093/jb/mvn143     Document Type: Article

References (43)

1. Ushida, C., Himeno, H., Watanabe, T., and Muto, A. (1994) tRNA-like structures in 10Sa RNAs of Mycoplasma caplicolum and Bacillus subtilis. Nucleic Acids Res. 22, 3392-3396
2. Komine, Y., Kitabatake, M., Yokogawa, T., Nishikawa, K., and Inokuchi, H. (1994) A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc. Natl Acad. Sci. USA 91, 9223-9227
3. Tu, G.-F., Reid, G. E., Zhang, J.-G., Moritz, R. L., and Simpson, R. J. (1995) C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide. J. Biol. Chem. 270, 9322-9326
4. Keiler, K. C., Waller, P. R. H., and Sauer, R. T. (1996) Role of peptide tagging system in degradation of protein synthesized from messenger RNA. Science 271, 990-993
5. Himeno, H., Sato, M., Tadaki, T., Fukushima, M., Ushida, C., and Muto, A. (1997) In vitro trans-translation mediated by alanine charged 10Sa RNA. J. Mol. Biol. 268, 803-808
6. Herman, C., Thevenet, D., Bouloc, P., Walker, G. C., and D'Ari, R. (1998) Degradation of carboxy-termianl-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). Genes Dev. 12, 1348-1355
7. Gottesman, S., Roche, E., Zhou, Y., and Sauer, R. T. (1998) The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA RNA-tagging system. Genes Dev. 12, 1338-1347
8. Yamamoto, Y., Sunohara, T., Jojima, K., Inada, T., and Aiba, H. (2003) SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs. RNA 9, 408-418
9. Hayes, C.S. and Sauer, R.T. (2003) Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12, 903-911
10. Muto, A., Ushida, C., and Himeno, H. (1998) A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem. Sci. 23, 25-29
11. Karzai, A.W., Roch, E.D., and Sauer, R.T. (2000) The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nature Struct. Biol. 7, 449-455
12. Withey, J.H. and Friedman, D.I. (2003) A salvage pathway for protein synthesis: tmRNA and trans-translation. Annu. Rev. Microbiol. 57, 101-123
13. Moore, S.D. and Sauer, R.T. (2007) The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76, 101-124
14. Keiler, K.C. (2007) Physiology of tmRNA: what gets tagged and why? Curr. Opin. Microbiol. 10, 169-175
15. Fujihara, A., Tomatsu, H., Inagaki, S., Tadaki, T., Ushida, C., Himeno, H., and Muto, A. (2002) Detection of tmRNA-mediated trans-translation products in Bacillus subtilis. Genes Cells 7, 343-350
16. Muto, A., Fujihara, A., Ito, K., Matsuno, J., Ushida, C., and Himeno, H. (2000) Requirement of transfer-messenger RNA for the growth of Bacillus subtilis under stresses. Genes Cells 5, 627-636
17. Huang, C., Wolfgang, M. C., Withey, J., Koomey, M., and Friedman, D. I. (2000) Charged tmRNA but not tmRNA-mediated proteolysis is essential for Nisseria gonorrhoeae viability. EMBO J. 19, 1098-1107
18. Wiegert, T. and Schumann, W. (2001) SsrA-mediated tagging in Bacillus subtilis. J. Bacteriol. 183, 3885-3889
19. Stulke, J. and Hillen, M. (2000) Regulation of carbon catabolism in Bacillus subtilis. Ann. Rev. Microbiol. 54, 849-880
20. Deutscher, J., Galinier, A., and Martin-Verstraete, I. (2002) Carbohydrate uptake and metabolism in Bacillus subtilis and its Closest Relatives: From Genes to Cells (Sonenshein, A. L., Hoch, J. A., and Losick, R., eds.), pp. 129-150 ASM press, Washington, DC.
21. Fujita, Y., Miwa, Y., Tojo, S., and Hirooka, K. (2007) Carbon catabolite control and metabolic networks mediated by the CcpA protein in Bacillus subtilis in Global Regulatory Networks in Bacillus subtilis (Fujita, Y., ed.), pp. 91-110 Transworld Research Network, Kerala, India.
22. Fujita, Y., Miwa, Y., Galinier, A., and Deutscher, J. (1995) Specific recognition of the Bacillus subtilis gnt cis-acting catabolite-responsive element by a protein complex formed between CcpA and seryl-phosphorylated HPr. Mol. Microbiol. 17, 953-960
23. Miwa, Y., Nagura, K., Eguchi, S., Fukuda, H., Deutscher, J., and Fujita, Y. (1997) Catabolite repression of the Bacillus subtilis gnt operon exerted by two catabolite-responsive element. Mol. Microbiol. 23, 1203-1213
24. Miwa, Y., Nakata, A., Ogiwara, A., Yamamoto, M., and Fujita, Y. (2000) Evaluation and characterization of catabolite-responsive element (cre) of Bacillus subtilis. Nucleic Acids Res. 28, 1206-1210
25. Moreno, M.S., Schneider, B.L., Maile, R.R., Weyler, W., and Saier, M.H. Jr. (2001) Catabolite repression mediated by the CcpA protein in Bacillus subtilis: novel modes of regulation revealed by whole-genome analyses. Mol. Microbiol. 39, 1366-1381
26. Schock, F. and Dahl, M.K. (1996) Expression of the treA gene of Bacillus subtilis 168 is regulated by the repressor TreR. J. Bacteriol. 178, 4576-4581
27. Tre and a potential regulator of the trehalose operon. Gene 175, 59-63
28. Vagner, V., Dervyn, E., and Ehrlich, S. D. (1998) A vector for systematic gene inactivation in Bacillus subtilis. Microbiology 144, 3097-3104
29. Miwa, Y., Saikawa, N., and Fujita, Y. (1994) Possible function and some properties of the CcpA protein of Bacillus subtilis. Microbiology 140, 2567-2575
30. Elbashir, S.M., Lendeckel, W., and Tuschl, T. (2001) RNA interference is mediated by 21- and 22-nucletide RNAs. Genes Dev. 15, 188-200
31. Hokii, Y., Kubo, A., Ogasawara, T., Nogi, Y., Taneda, A., Arai, R., Muto, A., and Ushida, C. (2006) Twelve novel C.elegans RNA candidates isolated by two-dimensional polyacrylamide gel electrophoresis. Gene 365, 83-87
32. Kim, J.H. and Chambliss, G.H. (1997) Contacts between Bacillus subtilis catabolite regulatory protein CcpA and AmyO target site. Nucleic Acids Res. 25, 3490-3496
33. Kim, J.H., Yang, Y.K., and Chambliss, G.H. (2005) Evidence that Bacillus catabolite control protein CcpA interacts with RNA polymerase to inhibit transcription. Mol. Microbiol. 56, 155-162
34. Ayora, S., Rojo, F., Ogasawara, N., Nakai, S., and Alonso, J.C. (1996) The Mfd protein of Bacillus subtilis is involved in both transcription-coupled DNA repair and DNA recombination. J. Mol. Biol. 256, 301-318
35. Park, J-S., Marr, M.T., and Roberts, J.W. (2002) E.coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell 109, 757-767
36. Zalieckas, J.M., Wray, L.V. Jr., Ferson, A.E., and Fisher, S.H. (1998) Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons. Mol. Microbiol. 27, 1031-1038
37. Sunohara, T., Jojima, K., Yamamoto, Y., Inada, T., and Aiba, H. (2002) Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA. RNA 10, 378-386
38. Ivanova, N., Pavlov, M.Y., Felden, B., and Ehrenberg, M. (2004) Ribosome rescue by tmRNA requires truncated mRNA. J. Mol. Biol. 338, 33-41
39. Li, X., Yokota, T., Ito, K., Nakamura, Y., and Aiba, H. (2007) Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli. Mol. Microbiol. 63, 116-126
40. Roche, E.D. and Sauer, R.T. (1999) SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity. EMBO J. 18, 4579-4589
41. Roche, E.D. and Sauer, R.T. (2001) Identification of endogenous SsrA-tagged proteins reveals tagging at positions corresponding to stop codons. J. Biol. Chem. 276, 28509-28515
42. Asano, K., Kurita, D., Takada, K., Konno, T., Muto, A., and Himeno, H. (2005) Competition between trans-translation and termination or elongation of translation. Nucleic Acid Res. 33, 5544-5552
43. Abo, T., Inada, T., Ogawa, K., and Aiba, H. (2000) SsrA-mediated tagging and proteolysis of LacI and its role in the regulation of lac operon. EMBO J. 19, 3762-3769