Unexpected versatility in bacterial riboswitches

Trends in Genetics

Volumn 31, Issue 3, 2015, Pages 150-156

  Mellin, J R ^a,b,c   Cossart, Pascale ^a,b,c  

^a INSTITUT PASTEUR   (France)

^b INSERM   (France)

^c CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; MESSENGER RNA; RHO FACTOR; RIBONUCLEASE E; UNTRANSLATED RNA; BACTERIAL PROTEIN; COMPLEMENTARY RNA; RIBONUCLEASE; RIBOSWITCH;

5' UNTRANSLATED REGION; BIOTECHNOLOGY; GENE EXPRESSION REGULATION; GENE PRODUCT; GENETIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; REVIEW; RIBOSWITCH; RNA TRANSCRIPTION; SENSOR; GENETIC TRANSCRIPTION; GENETICS;

BACTERIA (MICROORGANISMS);

BACTERIAL PROTEINS; ENDORIBONUCLEASES; GENE EXPRESSION REGULATION, BACTERIAL; RIBOSWITCH; RNA, ANTISENSE; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

EID: 84923594078     PISSN: 01689525     EISSN: 13624555     Source Type: Journal    
DOI: 10.1016/j.tig.2015.01.005     Document Type: Review

References (63)

1. Grundy F.J., et al. Interaction between the acceptor end of tRNA and the T box stimulates antitermination in the Bacillus subtilis tyrS gene: a new role for the discriminator base. J. Bacteriol. 1994, 176:4518-4526.
2. Grundy F.J., Henkin T.M. tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell 1993, 74:475-482.
3. Winkler W.C., et al. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 2004, 428:281-286.
4. Grundy F.J., et al. The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:12057-12062.
5. Mandal M., et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 2004, 306:275-279.
6. Winkler W., et al. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002, 419:952-956.
7. Nahvi A., et al. Genetic control by a metabolite binding mRNA. Chem. Biol. 2002, 9:1043.
8. Winkler W.C., et al. An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:15908-15913.
9. Winkler W.C., et al. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 2003, 10:701-707.
10. Mironov A.S., et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 2002, 111:747-756.
11. Dann C.E., et al. Structure and mechanism of a metal-sensing regulatory RNA. Cell 2007, 130:878-892.
12. Baker J.L., et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 2012, 335:233-235.
13. Epshtein V., et al. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:5052-5056.
14. Breaker R.R. Prospects for riboswitch discovery and analysis. Mol. Cell 2011, 43:867-879.
15. Wang J.X., et al. Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol. Cell 2008, 29:691-702.
16. Mandal M., Breaker R.R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat. Struct. Mol. Biol. 2004, 11:29-35.
17. Rodionov D.A., et al. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res. 2004, 32:3340-3353.
18. Rodionov D.A., et al. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J. Biol. Chem. 2003, 278:41148-41159.
19. Mellin J.R., et al. A riboswitch-regulated antisense RNA in Listeria monocytogenes. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:13132-13137.
20. André G., et al. S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res. 2008, 36:5955-5969.
21. Jeter R.M. Cobalamin-dependent 1,2-propanediol utilization by Salmonella typhimurium. J. Gen. Microbiol. 1990, 136:887-896.
22. Rondon M.R., Escalante-Semerena J.C. The poc locus is required for 1,2-propanediol-dependent transcription of the cobalamin biosynthetic (cob) and propanediol utilization (pdu) genes of Salmonella typhimurium. J. Bacteriol. 1992, 174:2267-2272.
23. Bobik T.A., et al. A single regulatory gene integrates control of vitamin B12 synthesis and propanediol degradation. J. Bacteriol. 1992, 174:2253-2266.
24. Mellin J.R., et al. Riboswitches. Sequestration of a two-component response regulator by a riboswitch-regulated noncoding RNA. Science 2014, 345:940-943.
25. DebRoy S., et al. Riboswitches. A riboswitch-containing sRNA controls gene expression by sequestration of a response regulator. Science 2014, 345:937-940.
26. Del Papa M.F., Perego M. Ethanolamine activates a sensor histidine kinase regulating its utilization in Enterococcus faecalis. J. Bacteriol. 2008, 190:7147-7156.
27. Hollands K., et al. Riboswitch control of Rho-dependent transcription termination. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:5376-5381.
28. Hollands K., et al. Unusually long-lived pause required for regulation of a Rho-dependent transcription terminator. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:E1999-E2007.
29. Livny J., Waldor M.K. Mining regulatory 5'UTRs from cDNA deep sequencing datasets. Nucleic Acids Res. 2010, 38:1504-1514.
30. Irnov I., et al. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res. 2010, 38:6637-6651.
31. Bastet L., et al. New insights into riboswitch regulation mechanisms. Mol. Microbiol. 2011, 80:1148-1154.
32. Caron M-P., et al. Dual-acting riboswitch control of translation initiation and mRNA decay. Proc. Natl. Acad. Sci. U.S.A. 2012, 109:E3444-E3453.
33. 2+ targets the mgtA transcript for degradation by RNase E. FEMS Microbiol. Lett. 2008, 280:226-234.
34. Groher F., Suess B. Synthetic riboswitches - a tool comes of age. Biochim. Biophys. Acta 2014, 1839:964-973.
35. Ceres P., et al. Engineering modular 'ON' RNA switches using biological components. Nucleic Acids Res. 2013, 41:10449-10461.
36. Muranaka N., Yokobayashi Y. Posttranscriptional signal integration of engineered riboswitches yields band-pass output. Angew. Chem. Int. Ed. Engl. 2010, 49:4653-4655.
37. Ceres P., et al. Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth. Biol. 2013, 2:463-472.
38. Desai S.K., Gallivan J.P. Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. J. Am. Chem. Soc. 2004, 126:13247-13254.
39. Hanson S., et al. Tetracycline-aptamer-mediated translational regulation in yeast. Mol. Microbiol. 2003, 49:1627-1637.
40. Weigand J.E., et al. Screening for engineered neomycin riboswitches that control translation initiation. RNA 2008, 14:89-97.
41. Lynch S.A., et al. A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function. Chem. Biol. 2007, 14:173-184.
42. Suess B., et al. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res. 2003, 31:1853-1858.
43. Topp S., et al. Synthetic riboswitches that induce gene expression in diverse bacterial species. Appl. Environ. Microbiol. 2010, 76:7881-7884.
44. Seeliger J.C., et al. A riboswitch-based inducible gene expression system for mycobacteria. PLoS ONE 2012, 7:e29266.
45. Kötter P., et al. A fast and efficient translational control system for conditional expression of yeast genes. Nucleic Acids Res. 2009, 37:e120.
46. Rudolph M.M., et al. Synthetic riboswitches for the conditional control of gene expression in Streptomyces coelicolor. Microbiology 2013, 159:1416-1422.
47. Nakahira Y., et al. Theophylline-dependent riboswitch as a novel genetic tool for strict regulation of protein expression in cyanobacterium Synechococcus elongatus PCC 7942. Plant Cell Physiol. 2013, 54:1724-1735.
48. Win M.N., Smolke C.D. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:14283-14288.
49. Win M.N., et al. Frameworks for programming biological function through RNA parts and devices. Chem. Biol. 2009, 16:298-310.
50. Thompson K.M., et al. Group I aptazymes as genetic regulatory switches. BMC Biotechnol. 2002, 2:21.
51. Chen Y.Y., et al. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:8531-8536.
52. Bayer T.S., Smolke C.D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 2005, 23:337-343.
53. Beisel C.L., et al. Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol. Syst. Biol. 2008, 4:224.
54. Qi L., et al. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res. 2012, 40:5775-5786.
55. Callura J.M., et al. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:15898-15903.
56. Topp S., Gallivan J.P. Guiding bacteria with small molecules and RNA. J. Am. Chem. Soc. 2007, 129:6807-6811.
57. Cho E.J., et al. Applications of aptamers as sensors. Annu. Rev. Anal. Chem. 2009, 2:241-264.
58. Strack R.L., Jaffrey S.R. New approaches for sensing metabolites and proteins in live cells using RNA. Curr. Opin. Chem. Biol. 2013, 17:651-655.
59. Henkin T.M. Riboswitch RNAs: using RNA to sense cellular metabolism. Genes Dev. 2008, 22:3383-3390.
60. Fowler C.C., et al. Using a riboswitch sensor to examine coenzyme B12 metabolism and transport in E. coli. Chem. Biol. 2010, 17:756-765.
61. Paige J.S., et al. Fluorescence imaging of cellular metabolites with RNA. Science 2012, 335:1194.
62. Paige J.S., et al. RNA mimics of green fluorescent protein. Science 2011, 333:642-646.
63. Kellenberger C.A., et al. RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP. J. Am. Chem. Soc. 2013, 135:4906-4909.