The riboswitch control of bacterial metabolism

Trends in Biochemical Sciences

Volumn 29, Issue 1, 2004, Pages 11-17

  Nudler, Evgeny ^a   Mironov, Alexander S ^b  

^a NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

^b STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; BACTERIAL RNA; BINDING PROTEIN; COBAMAMIDE; COCARBOXYLASE; FLAVINE ADENINE NUCLEOTIDE; FLAVINE MONONUCLEOTIDE; LYSINE; RIBOFLAVIN; RNA; S ADENOSYLMETHIONINE; SIGNAL PEPTIDE; TRP RNA BINDING ATTENUATION PROTEIN; UNCLASSIFIED DRUG;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BACILLUS SUBTILIS; BACTERIAL METABOLISM; BACTERIUM; CHEMISTRY; ESCHERICHIA COLI; GENE ACTIVATION; GENE EXPRESSION REGULATION; GENE REPRESSION; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; GENETICS; METABOLIC REGULATION; METABOLISM; MOLECULAR EVOLUTION; NONHUMAN; OPERON; PRIORITY JOURNAL; PURINE METABOLISM; REGULATORY MECHANISM; REVIEW; RNA BINDING; RNA PROBE; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; TRANSLATION REGULATION; VITAMIN METABOLISM;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA;

EID: 0346687595     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2003.11.004     Document Type: Review

References (53)

1. Yanofsky C., et al. Some novel transcription attenuation mechanisms used by bacteria. Biochimie. 78:1996;1017-1024.
2. Babitzke P., et al. TRAP, the trp RNA-binding attenuation protein of Bacillus subtilis, is a multisubunit complex that appears to recognize G/UAG repeats in the trpEDCFBA and trpG transcripts. J. Biol. Chem. 269:1994;16597-16604.
3. Babitzke P., Gollnick P. Posttranscription initiation control of tryptophan metabolism in Bacillus subtilis by the trp RNA-binding attenuation protein (TRAP), anti-TRAP, and RNA structure. J. Bacteriol. 183:2001;5795-5802.
4. Rutberg B. Antitermination of transcription of catabolic operons. Mol. Microbiol. 23:1997;413-421.
5. Stulke J. Control of transcription termination in bacteria by RNA-binding proteins that modulate RNA structures. Arch. Microbiol. 177:2002;433-440.
6. Romby P., Springer M. Bacterial translational control at atomic resolution. Trends Genet. 19:2003;155-161.
7. Landick R., et al. Transcription attenuation. Neidhardt. Escherichia coli and Salmonella Typhimurium. 1996;1263-1286 American Society for Microbiology.
8. Grundy F.J., Henkin T.M. The T box and S box transcription termination control systems. Front. Biosci. 8:2003;d20-d31.
9. Perkins J.B., Pero J. Biosynthesis of riboflavin, biotin, folic acid, and cobalamin. Sonenshein A.L., Hoch J.A., Losick R. Bacillus Subtillis and Its Closest Relatives: from Genes to Cells. 2002;271-286 ASM Press.
10. Gelfand M.S., et al. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 15:1999;439-442.
11. Kreneva R.A., Perumov D.A. Genetic mapping of regulatory mutations of Bacillus subtilis riboflavin operon. Mol. Gen. Genet. 222:1990;467-469.
12. Gusarov I., et al. Primary structure and functional activity of the Bacillus subtilis ribC gene. Mol Biol (Mosk). 31:1997;820-825.
13. Mack M.A., et al. Regulation of riboflavin biosynthesis in Bacillus subtilis is affected by the activity of the flavokinase/flavin adenine dinucleotide synthetase encoded by ribC. J. Bacteriol. 180:1998;950-955.
14. Mironov A.S., et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell. 111:2002;747-756.
15. Winkler W.C., et al. An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. U. S. A. 99:2002;15908-15913.
16. Vitreschak A.G., et al. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 30:2002;3141-3151.
17. Begley T.P., et al. Thiamin biosynthesis in prokaryotes. Arch. Microbiol. 171:1999;293-300.
18. Petersen L.A., Downs D.M. Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis. J. Bacteriol. 179:1997;4894-4900.
19. Miranda-Rios J., et al. Expression of thiamin biosynthetic genes (thiCOGE) and production of symbiotic terminal oxidase cbb3 in Rhizobium etli. J. Bacteriol. 179:1997;6887-6893.
20. Miranda-Rios J., et al. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl. Acad. Sci. U. S. A. 98:2001;9736-9741.
21. Rodionov D.A., et al. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J. Biol. Chem. 277:2002;48949-48959.
22. Stormo G.D., Ji Y. Do mRNAs act as direct sensors of small molecules to control their expression? Proc. Natl. Acad. Sci. U. S. A. 98:2001;9465-9467.
23. Winkler W., et al. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 419:2002;952-956.
24. Sudarsan N., et al. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA. 9:2003;644-647.
25. Wei B.Y., et al. Conserved structural and regulatory regions in the Salmonella typhimurium btuB gene for the outer membrane vitamin B12 transport protein. Res. Microbiol. 143:1992;459-466.
26. Escalante-Semerena J.C., Roth J.R. Regulation of cobalamin biosynthetic operons in Salmonella typhimurium. J. Bacteriol. 169:1987;2251-2258.
27. Lundrigan M.D., et al. Transcribed sequences of the Escherichia coli btuB gene control its expression and regulation by vitamin B12. Proc. Natl. Acad. Sci. U. S. A. 88:1991;1479-1483.
28. Richter-Dahlfors A.A., et al. Vitamin B12 repression of the cob operon in Salmonella typhimurium: translational control of the cbiA gene. Mol. Microbiol. 13:1994;541-553.
29. Richter-Dahlfors A.A., Andersson D.I. Cobalamin (vitamin B12) repression of the Cob operon in Salmonella typhimurium requires sequences within the leader and the first translated open reading frame. Mol. Microbiol. 6:1992;743-749.
30. Ravnum S., Andersson D.I. Vitamin B12 repression of the btuB gene in Salmonella typhimurium is mediated via a translational control which requires leader and coding sequences. Mol. Microbiol. 23:1997;35-42.
31. Nou X., Kadner R.J. Coupled changes in translation and transcription during cobalamin-dependent regulation of btuB expression in Escherichia coli. J. Bacteriol. 180:1998;6719-6728.
32. Nou X., Kadner R.J. Adenosylcobalamin inhibits ribosome binding to btuB RNA. Proc. Natl. Acad. Sci. U. S. A. 97:2000;7190-7195.
33. Nahvi A., et al. Genetic control by a metabolite binding mRNA. Chem. Biol. 9:2002;1043-1049.
34. Ravnum S., Andersson D.I. An adenosyl-cobalamin (coenzyme-B12)-repressed translational enhancer in the cob mRNA of Salmonella typhimurium. Mol. Microbiol. 39:2001;1585-1594.
35. Franklund C.V., Kadner R.J. Multiple transcribed elements control expression of the Escherichia coli btuB gene. J. Bacteriol. 179:1997;4039-4042.
36. Vitreschak A.G., et al. Regulation of the vitamin B(12) metabolism and transport in bacteria by a conserved RNA structural element. RNA. 9:2003;1084-1097.
37. Grundy F.J., Henkin T.M. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol. Microbiol. 30:1998;737-749.
38. Auger S., et al. The metIC operon involved in methionine biosynthesis in Bacillus subtilis is controlled by transcription antitermination. Microbiology. 148:2002;507-518.
39. Yocum R.R., et al. Cloning and characterization of the metE gene encoding S-adenosylmethionine synthetase from Bacillus subtilis. J. Bacteriol. 178:1996;4604-4610.
40. McDaniel B.A., et al. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl. Acad. Sci. U. S. A. 100:2003;3083-3088.
41. Epshtein V., et al. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. U. S. A. 100:2003;5052-5056.
42. Winkler W.C., et al. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 10:2003;701-707.
43. Mansilla M.C., et al. Transcriptional control of the sulfur-regulated cysH operon, containing genes involved in L-cysteine biosynthesis in Bacillus subtilis. J. Bacteriol. 182:2000;5885-5892.
44. Mandal M., et al. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell. 113:2003;577-586.
45. Lu Y., et al. Fine-structure mapping of cis-acting control sites in the lysC operon of Bacillus subtilis. FEMS Microbiol. Lett. 71:1992;23-27.
46. Kochhar S., Paulus H. Lysine-induced premature transcription termination in the lysC operon of Bacillus subtilis. Microbiology. 142:1996;1635-1639.
47. Patte J.C., et al. The leader sequence of the Escherichia coli lysC gene is involved in the regulation of LysC synthesis. FEMS Microbiol. Lett. 169:1998;165-170.
48. Switzer R.L., et al. Purine, pyrimidine, and pyridine nucleotide metabolism. Sonenshein A.L., Hoch J.A., Losick R. Bacillus Subtillis and Its Closest Relatives: from Genes to Cells. 2002;255-269 ASM Press.
49. Christiansen L.C., et al. Xanthine metabolism in Bacillus subtilis: characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism. J. Bacteriol. 179:1997;2540-2550.
50. Ebbole D.J., Zalkin H. Detection of pur operon-attenuated mRNA and accumulated degradation intermediates in Bacillus subtilis. J. Biol. Chem. 263:1988;10894-10902.
51. Johansen L.E., et al. Definition of a second Bacillus subtilis pur regulon comprising the pur and xpt-pbuX operons plus pbuG, nupG (yxjA), and pbuE (ydhL). J. Bacteriol. 185:2003;5200-5209.
52. Fan P., et al. Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol. 258:1996;480-500.
53. Kiga D., et al. An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition. Nucleic Acids Res. 26:1998;1755-1760.