Riboswitches exert genetic control through metabolite-induced conformational change

Current Opinion in Structural Biology

Volumn 14, Issue 3, 2004, Pages 344-349

  Soukup, Juliane K ^a   Soukup, Garrett A ^b  

^a CREIGHTON UNIVERSITY   (United States)

^b CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Flavin mononucleotide; FMN; GlcN6P; Glucosamine 6 phosphate; S adenosylmethionine; SAM; Thiamine pyrophosphate; TPP; Untranslated region; UTR

Indexed keywords

RNA;

BASE PAIRING; BINDING AFFINITY; CONFORMATIONAL TRANSITION; GENE CONTROL; GENE EXPRESSION REGULATION; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; REVIEW; RNA CLEAVAGE; RNA PROCESSING; RNA STRUCTURE; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; TRANSLATION INITIATION;

GENE EXPRESSION REGULATION; NUCLEIC ACID CONFORMATION; RNA;

EID: 2942549198     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.sbi.2004.04.007     Document Type: Review

References (34)

1. Massé E., Mahdalani N., Gottesman S. Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol. 6:2003;120-124
2. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism and function. Cell. 116:2004;281-297
3. Nudler E., Mironov A.S. The riboswitch control of bacterial metabolism. Trends Biochem Sci. 29:2004;11-17
4. Winkler W.C., Breaker R.R. Genetic control by metabolite-binding riboswitches. ChemBioChem. 4:2003;1024-1032
5. 12 and modulate reporter gene expression in response to ligand.
6. Nou X., Kadner R.J. Adenosylcobalamin inhibits ribosome binding to btuB RNA. Proc Natl Acad Sci USA. 97:2000;7190-7195
7. 12 metabolism and transport in bacteria by a conserved RNA structural element. RNA. 9:2003;1084-1097
8. 12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res. 32:2004;143-150
9. Winkler W.C., Cohen-Chalamish S., Breaker R.R. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci USA. 99:2002;15908-15913
10. Vitreschak A.G., Rodionov D.A., Mironov A.A., Gelfand M.S. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 30:2002;3141-3151
11. Mironov A.S., Gusarov I., Rafikov R., Lopez L.E., Shatalin K., Kreneva R.A., Perumov D.A., Nudler E. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell. 111:2002;747-756 Another seminal paper providing evidence of the diversity of riboswitches. Premature transcription termination of thiamine and riboflavin operons was shown to be induced by direct binding of cognate ligand.
12. Winkler W., Nahvi A., Breaker R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature. 419:2002;952-956 TPP is demonstrated to bind directly to mRNA elements upstream of TPP biosynthetic genes and to modulate reporter gene expression by affecting translation initiation.
13. Miranda-Rios J., Navarro M., Soberón M. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc Natl Acad Sci USA. 98:2001;9736-9741
14. Sudarsan N., Barrick J.E., Breaker R.R. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA. 9:2003;644-647 This work details the first evidence of riboswitches in eukaryotic organisms, suggesting riboswitch control of RNA processing.
15. Kubodera T., Watanabe M., Yoshiuchi K., Yamashita N., Nishimura A., Nakai S., Gomi K., Hanamoto H. Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR. FEBS Lett. 555:2003;516-520
16. McDaniel B.A.M., Grundy F.J., Artsimovitch I., Henkin T.M. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA. Proc Natl Acad Sci USA. 100:2003;3083-3088 Mutational analyses of the UTRs of genes involved in methionine metabolism indicate the role of the mRNA in transcription termination. In addition, binding assays demonstrated direct interaction of SAM with the RNA.
17. Epshtein V., Mironov A.S., Nudler E. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc Natl Acad Sci USA. 100:2003;5052-5056
18. Winkler W.C., Nahvi A., Sudarsan N., Barrick J.E., Breaker R.R. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat Struct Biol. 10:2003;701-707
19. Kochhar S., Paulus H. Lysine-induced premature transcription termination in the lysC operon of Bacillus subtilis. Microbiology. 142:1996;1635-1639
20. Patte J.C., Akrim M., Mejean V. The leader sequence of the Escherichia coli lysC gene is involved in the regulation of LysC synthesis. FEMS Microbiol Lett. 169:1998;165-170
21. Grundy F.J., Lehman S.C., Henkin T.M. The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci USA. 100:2003;12057-12062
22. Sudarsan N., Wickiser J.K., Nakamura S., Ebert M.S., Breaker R.R. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 17:2003;2688-2697
23. Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res. 31:2003;6748-6757
24. Mandal M., Boese B., Barrick J.E., Winkler W.C., Breaker R.R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell. 113:2003;577-586 This work identifies a riboswitch that binds guanine and exerts control over the expression of genes involved in purine biosynthesis. The widespread distribution of riboswitch sequences is discussed.
25. Mandal M., Breaker R.R. Adenine riboswitches and gene activation by disruption of a transcriptional terminator. Nat Struct Mol Biol. 11:2004;29-35 The specificities of the purine riboswitches are examined. The only known example of riboswitch function in gene activation is reported.
26. Winkler W.C., Nahvi A., Roth A., Collins J.A., Breaker R.R. Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 428:2004;281-286 A novel ribozyme motif is reported, the first new natural RNA catalyst in over a decade. Moreover, the ribozyme is activated by GlcN6P and might function as a true allosteric catalyst.
27. Gold L., Polisky B., Uhlenbeck O., Yarus M. Diversity of oligonucleotide functions. Annu Rev Biochem. 64:1995;763-797
28. Hermann T., Patel D.J. Adaptive recognition by nucleic acid aptamers. Science. 287:2000;820-825
29. Gelfand M.S., Mironov A.A., Jomantas J., Kozlov Y.I., Perumov D.A. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet. 15:1999;439-442
30. Stormo G.D., Ji Y. Do mRNAs act as direct sensors of small molecules to control their expression? Proc Natl Acad Sci USA. 98:2001;9465-9467
31. Soukup G.A., Breaker R.R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA. 5:1999;1308-1325
32. Soukup G.A., Breaker R.R. Allosteric nucleic acid catalysts. Curr Opin Struct Biol. 10:2000;318-325
33. Grundy F.J., Winkler W.C., Henkin T.M. tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome. Proc Natl Acad Sci USA. 99:2002;11121-11126
34. Johansson J., Mandin P., Renzoni A., Chiaruttini C., Springer M., Cossart P. An RNA thermosensor controls expression of virulence gene in Listeria monocytogenes. Cell. 110:2002;551-561