Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis

RNA

Volumn 13, Issue 4, 2007, Pages 573-582

  Welz, Rüdiger ^a   Breaker, Ronald R ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

Aptamer; Metabolite binding RNA; Thiamine pyrophosphate; Transcription termination

Indexed keywords

COCARBOXYLASE;

ARTICLE; BACILLUS ANTHRACIS; BINDING AFFINITY; CONTROLLED STUDY; GENE CONTROL; GENE EXPRESSION; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; RIBOSWITCH; TRANSCRIPTION TERMINATION;

5' UNTRANSLATED REGIONS; APTAMERS, NUCLEOTIDE; BACILLUS ANTHRACIS; BASE SEQUENCE; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENES, REPORTER; GENES, SWITCH; LIGANDS; LUCIFERASES; MATHEMATICS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, MESSENGER; THIAMINE PYROPHOSPHATE; TRANSCRIPTION, GENETIC;

BACILLUS ANTHRACIS; POSIBACTERIA;

EID: 33947714417     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.407707     Document Type: Article

References (43)

1. Barrick, J.E., Corbino, K.A., Winkler, W.C., Nahvi, A., Mandal, M., Collins, J., Lee, M., Roth, A., Sudarsan, N., Jona, I., et al. 2004. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl. Acad. Sci. 101: 6421-6426.
2. Blount, K.F., Wang, J.X., Lim, J., Sudarsan, N., and Breaker, R.R. 2007. Antibacterial lysine analogs that target lysine riboswitches. Nat. Chem. Biol. 1: 44-49.
3. Corbino, K.A., Barrick, J.E., Lim, J., Welz, R., Tucker, B.J., Puskarz, I., Mandal, M., Rudnick, N.D., and Breaker, R.R. 2005. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in a-proteobacteria. Genome Biol. 6: R70.
4. Edwards, T.E. and Ferré-D'Amaré, A.R. 2006. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14: 1459-1468.
5. Epshtein, V., Mironov, A.S., and Nudler, E. 2003. The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl. Acad. Sci. 100: 5052-5056.
6. Grundy, F.J., Lehman, S.C., and Henkin, T.M. 2003. The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc. Natl. Acad. Sci. 100: 12057-12062.
7. Gusarov, I. and Nudler, E. 1999. The mechanism of intrinsic transcription termination. Mol. Cell 3: 495-504.
8. Gutierrez-Preciado, A., Jensen, R.A., Yanofsky, C., and Merino, E. 2005. New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria. Trends Genet. 21: 432-436.
9. Kubodera, T., Watanabe, M., Yoshiuchi, K., Yamashita, N., Nishimura, A., Nakai, S., Gomi, K., and Hanamoto, H. 2003. 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: 516-520.
10. Lemay, J.F., Penedo, J.C., Tremblay, R., Lilley, D.M.J., and Lafontaine, D.A. 2006. Folding of the adenine riboswitch. Chem. Biol. 13: 857-868.
11. Mandal, M. and Breaker, R.R. 2004. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 5: 451-463.
12. Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C., and Breaker, R.R. 2003. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113: 577-586.
13. Mandal, M., Lee, M., Barrick, J.E., Weinberg, Z., Emilsson, G.M., Ruzzo, W.L., and Breaker, R.R. 2004. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306: 275-279.
14. Marchler-Bauer, A., Anderson, J.B., Cherukuri, P.F., DeWeese-Scott, C., Geer, L.Y., Gwadz, M., He, S., Hurwitz, D.I., Jackson, J.D., Ke, Z., et al. 2005. CDD: A Conserved Domain Database for protein classification. Nucleic Acids Res. 33: D192-D196.
15. McDaniel, B.A.M., Grundy, F.J., Artsimovitch, I., and Henkin, T.M. 2003. Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA. Proc. Natl. Acad. Sci. 100: 3083-3088.
16. Miranda-Rios, J., Navarro, M., and Soberón, M. 2001. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl. Acad. Sci. 98: 9736-9741.
17. Mironov, A.S., Gusarov, I., Rafikov, R., Lopez, L.E., Shatalin, K., Kreneva, R.A., Perumov, D.A., and Nudler, E. 2002. Sensing small molecules by nascent RNA: A mechanism to control transcription in bacteria. Cell 111: 747-756.
18. Nahvi, A., Sudarsan, N., Ebert, M.S., Zou, X., Brown, K.L., and Breaker, R.R. 2002. Genetic control by a metabolite binding RNA. Chem. Biol. 9: 1043-1049.
19. Nahvi, A., Barrick, J.E., and Breaker, R.R. 2004. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res. 32: 143-150.
20. Puerta-Fernandez, E., Barrick, J.E., Roth, A., and Breaker, R.R. 2006. Identification of a large noncoding RNA in extremophilic eubacteria. Proc. Natl. Acad. Sci. 103: 19490-19495.
21. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A., and Gelfand, M.S. 2002. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J. Biol. Chem. 277: 48949-48959.
22. Rodionov, D.A., Dubchak, I., Arkin, A., Alm, E., and Gelfand, M.S. 2004. Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria. Genome Biol. 5: R90.
23. Seetharaman, S., Zivarts, M., Sudarsan, N., and Breaker, R.R. 2001. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat. Biotechnol. 19: 336-341.
24. Serganov, A., Polonskaia, A., Phan, A.T., Breaker, R.R., and Patel, D.J. 2006. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441: 1167-1171.
25. Soukup, G.A. and Breaker, R.R. 1999. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5: 1308-1325.
26. Soukup, J.K. and Soukup, G.A. 2004. Riboswitches exert genetic control through metabolite-induced conformational change. Curr. Opin. Struct. Biol. 14: 344-349.
27. Soukup, G.A., DeRose, E.C., Koizumi, M., and Breaker, R.R. 2001. Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 7: 524-536.
28. Sudarsan, N., Barrick, J.E., and Breaker, R.R. 2003a. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9: 644-647.
29. Sudarsan, N., Wickiser, J.K., Nakamura, S., Ebert, M.S., and Breaker, R.R. 2003b. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes & Dev. 17: 2688-2697.
30. Sudarsan, N., Cohen-Chalamish, S., Nakamura, S., Emilsson, G.M., and Breaker, R.R. 2005. Thiamine pyrophosphate riboswitches are targets for the antimicrobial compound pyrithiamine. Chem. Biol. 12: 1325-1335.
31. Sudarsan, N., Hammond, M.C., Block, K.F., Welz, R., Barrick, J.E., Roth, A., and Breaker, R.R. 2006. Tandem riboswitch architectures exhibit complex gene control functions. Science 314: 300-304.
32. Thore, S., Leibundgut, M., and Nan, N. 2006. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312: 1208-1211.
33. Vitreschak, A.G., Rodionov, D.A., Mironov, A.A., and Gelfand, M.S. 2002. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 30: 3141-3151.
34. 12 metabolism and transport in bacteria by a conserved RNA structural element. RNA 9: 1084-1097.
35. Weinberg, Z. and Ruzzo, W.L. 2006. Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics 22: 35-39.
36. Wickiser, J.K., Cheah, M.T., Breaker, R.R., and Crothers, D.M. 2005a. The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44: 13404-13414.
37. Wickiser, J.K., Winkler, W.C., Breaker, R.R., and Crothers, D.M. 2005b. The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol. Cell 18: 49-60.
38. Winkler, W.C. and Breaker, R.R. 2005. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59: 487-517.
39. Winkler, W.C., Cohen-Chalamish, S., and Breaker, R.R. 2002a. An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. 99: 15908-15913.
40. Winkler, W., Nahvi, A., and Breaker, R.R. 2002b. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419: 952-956.
41. Winkler, W.C., Nahvi, A., Sudarsan, N., Barrick, J.E., and Breaker, R.R. 2003. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nat. Struct. Biol. 10: 701-707.
42. 2+ in TPP-dependent riboswitch. FEBS Lett. 579: 2583-2588.
43. Yarnell, W.S. and Roberts, J.W. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284: 611-615.