Riboswitches and the RNA world

Cold Spring Harbor Perspectives in Biology

Volumn 4, Issue 2, 2012, Pages

  Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; REVIEW; RIBOSWITCH;

GENE EXPRESSION REGULATION, BACTERIAL; RIBOSWITCH; TRANSCRIPTION, GENETIC;

EID: 84863923278     PISSN: None     EISSN: 19430264     Source Type: Journal    
DOI: 10.1101/cshperspect.a003566     Document Type: Article

References (74)

1. André G, et al. 2008. S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum. Nucleic Acids Res 36: 5955-5969.
2. Ames TD, Breaker RR. 2009. Bacterial riboswitch discovery and analysis. In: The chemical biology of nucleic acids, Meyer G., ed., John Wiley & Sons, Ltd (in press).
3. Barrick JE, Breaker RR. 2007. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8: R239.
4. Benner SA, Ellington AD, Tauer A. 1989. Modern metabolism as a palimpsest of the RNAworld. Proc Natl Acad Sci USA 86: 7054-7058.
5. Blount KF, Breaker RR. 2006. Riboswitches as antibacterial drug targets. Nat Biotechnol 24: 1558-1564.
6. Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A. 2007. Riboswitch-dependent gene regulation and its evolution in the plant kingdom. Genes Dev 21: 2874-2879.
7. Borsuk P, Przykorska A, Blachnio K, Koper M, Pawlowicz JM, Pekala M, Weglenski P. 2007. L-arginine influences the structure and function of arginase mRNA in Aspergillus nidulans. Biol Chem 388: 135-144.
8. Breaker RR. 2002. Engineered allosteric ribozymes as biosensor components. Curr Opin Biotechnol 13: 31-39.
9. Breaker RR. 2004. Natural and engineered nucleic acids as tools to explore biology. Nature 432: 838-845.
10. Breaker RR. 2006. Riboswitches and the RNAworld. In: The RNAworld, 3rd ed., Gesteland R. F., Cech T. R., Atkins J. F., eds., Cold Spring Harbor Laboratory Press, pp. 89-107.
11. Breaker RR. 2009. Riboswitches: from ancient gene-control systems to modern drug targets. Future Microbiol 4: 771-773.
12. Brooks KM, Hampel KJ. 2009. A rate-limiting conformational step in the catalytic pathway of the glmS ribozyme. Biochemistry 48: 5669-5678.
13. Cheah MT, Wachter A, Sudarsan N, Breaker RR. 2007. Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447: 497-500.
14. Cochrane JC, Lipchock SV, Smith KD, Strobel SA. 2009. Structural and chemical basis for glucosamine-6-phosphate binding and activation of the glmS ribozyme. Biochemistry 48: 3239-3246.
15. Collins JA, Irnov I, Baker S, Winkler WC. 2007. Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 21: 3356-3368.
16. Coppins RL, Hall KB, Groisman EA. 2007. The intricate world of riboswitches. Curr Opin Microbiol 10: 176-181.
17. Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. 2005. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in a-proteobacteria. Genome Biol 6: R70.
18. Croft MT, Moulin M, Webb ME, Smith AG. 2007. Thiamine biosynthesis in algae is regulated by riboswitches. Proc Natl Acad Sci 104: 20770-20775.
19. 2+. Cell 125: 71-84.
20. Dann CE 3rd, Wakeman CA, Sieling CL, Baker SC, Ironv I, Winkler WC. 2007. Structure and mechanism of a metal-sensing regulatory RNA. Cell 130: 878-892.
21. Edwards AL, Batey RT. 2009. A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch. JMol Biol 385: 938-948.
22. Fuchs RT, Grundy FJ, Henkin TM. 2006. The SMK box is a new SAMbinding RNA for translational regulation of SAM synthase. Nat Struct Mol Biol 13: 226-233.
23. Garst AD, Edwards AL, Batey RT. 2010. Riboswitches: structures and mechanisms. Cold Spring Harb Perspect Biol doi: 10. 1101. cshperspect. a003533.
24. Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA. 1999. A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. Trends Genet 15: 439-442.
25. Gilbert SD, Rambo RP, Van Tyne D, Batey RT. 2008. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nat Struct Mol Biol 15: 177-182.
26. Gilbert SD, Stoddard CD, Wise SJ, Batey RT. 2006. Thermodynamic and kinetic characterization of ligand binding to the purine riboswitch aptamer domain. J Mol Biol 359: 754-768.
27. Grundy FJ, Henkin TM. 1998. The S box regulon: A new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 30: 737-749.
28. Gusarov I, Nudler E. 1999. The mechanism of intrinsic transcription termination. Mol Cell 3: 495-504.
29. Gutiérrez-Preciado A, Henkin TM, Grundy FJ, Yanofsky C, Merino E. 2009. Biochemical features and functional implications of the RNAbased T-box regulatory system. Microbiol Mol Biol Rev 73: 36-61.
30. Halls C, Mohr S, Del Campo M, Yang Q, Jankowsky E, Lambowitz AM. 2007. Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity. J Mol Biol 365: 835-855.
31. Hougland JL, Piccirilli JA, Forconi M, Lee J, Herschlag D. 2006. How the group I intron works: a case study of RNA structure and function. In: The RNA world, 3rd ed., Gesteland R. F., Cech T. R., Atkins J. F., eds., Cold Spring Harbor Laboratory Press, pp. 133-205.
32. Johansson J. 2009. RNA thermosensors in bacterial pathogens. Contrib Microbiol 16: 150-160.
33. Jose A, Soukup GA, Breaker RR. 2001. Cooperative binding of effectors by an allosteric ribozyme. Nucleic Acids Res 29: 1631-1637.
34. Kim JN, Breaker RR. 2008. Purine sensing by riboswitches. Biol Cell 100: 1-11.
35. Kim JN, Roth A, Breaker RR. 2007. Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine. Proc Natl Acad Sci 104: 16092-16097.
36. Klinkert B, Narberhaus F. 2009. Microbial thermosensors. Cell Mol Life Sci 66: 2661-2676.
37. Kubodera T, et al. 2003. Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitchlike domain in the 5′ UTR. FEBS Lett 555: 516-520.
38. Lee ER, Blount KF, Breaker RR. 2009. Roseoflavin is a natural antibacterial compound that binds to FMN riboswitches and regulates gene expression. RNA Biol 6: 187-194.
39. Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A. 2008. Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism. Nat Struct Mol Biol 15: 1076-1083.
40. Mandal M, Breaker RR. 2004a. Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5: 451-463.
41. Mandal M, Breaker RR. 2004b. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol 11: 29-35.
42. Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279.
43. Meyer MM, Roth A, Chervin SM, Garcia GA, Breaker RR. 2008. Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria. RNA 14: 685-695.
44. Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E. 2002. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111: 747-756.
45. Montange RK, Batey RT. 2006. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441: 1172-1175.
46. Nahvi A, Barrick JE, Breaker RR. 2004. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res 32: 143-150.
47. Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR. 2002. Genetic control by a metabolite binding mRNA. Chem Biol 9: 1043-1049.
48. Poiata E, Meyer MM, Ames TD, Breaker RR. 2009. Avariant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria. RNA 15: 2046-2056.
49. Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. 2004. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res 32: 3340-3353.
50. Roth A, Breaker RR. 2009. The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78: 305-334.
51. Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwick A, Kim JN, Welz R, et al. 2007. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nat Struct Mol Biol 14: 308-317.
52. Sharin E, Schein A, Mann H, Ben-Asouli Y, Jarrous N. 2005. RNase P: Role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis. Nucleic Acids Res 33: 5120-5132.
53. Silverman SK. 2003. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 4: 377-383.
54. Skordalakes E, Berger JM. 2003. Structure of the Rho transcription terminator: Mechanism of mRNA recognition and helicase loading. Cell 114: 135-146.
55. Sudarsan N, Barrick JE, Breaker RR. 2003. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9: 644-647.
56. Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, Roth A, Breaker RR. 2006. Tandem riboswitch architectures exhibit complex gene control functions. Science 314: 300-304.
57. Sudarsan N, Lee ER, Weinberg Z, Moy RH, Kim JN, Link KH, Breaker RR. 2008. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321: 411-413.
58. Suess B, Weigand JE. 2008. Engineered riboswitches: overview, problems and trends. RNA Biol 5: 24-29.
59. Serganov A, Yuan YR, Pikovskaya O, Polonskaia A, Malinina L, Phan AT, Hobartner C, Micura R, Breaker RR, Patel DJ. 2004. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol 11: 1729-1741.
60. Thompson KM, Syrett HA, Knudsen SM, Ellington AD. 2002. Group I aptazymes as genetic regulatory switches. BMC Biotechnol 2: 21.
61. Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. 2007. Riboswitch control of gene expression in plants by splicing and alternative 3′ processing of mRNAs. Plant Cell 19: 3437-3450.
62. Wang JX, Breaker RR. 2008. Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. Biochem Cell Biol 86: 157-168.
63. Wang JX, Lee ER, Morales DR, Lim J, Breaker RR. 2008. Riboswitches that sense S-adenosylhomocysteine and activate genes involved in coenzyme recycling. Mol Cell 28: 691-702.
64. Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. 2008. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA 14: 822-828.
65. Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy R, Breaker RR. 2010. Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaeal and their metagenomes. Genome Biol (submitted).
66. Welz R, Breaker RR. 2007. Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis. RNA 13: 573-582.
67. White HB, III. 1976. Coenzymes as fossils of an earlier metabolic state. J Mol Evol 7: 101-104.
68. Wickiser JK, Cheah MT, Breaker RR, Crothers DM. 2005a. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44: 13404-13414.
69. Wickiser JK, Winkler WC, Breaker RR, Crothers DM. 2005b. The speed ofRNAtranscription and metabolite binding kinetics operate anFMN riboswitch. Mol Cell 18: 49-60.
70. Winkler WC, Cohen-Chalamish S, Breaker RR. 2002a. An mRNA structure that controls gene expression by binding FMN. Proc Natl Acad Sci 99: 15908-15913.
71. Winkler W, Nahvi A, Breaker RR. 2002b. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419: 952-956.
72. Winkler WC, Nahvi A, Roth A, Collins JA, Breaker RR. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428: 281-286.
73. Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. 2004. Riboswitches: The oldest mechanism for the regulation of gene expression? Trends Genet 20: 44-50.
74. Yarnell WS, Roberts JW. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284: 611-615.