Molecular basis of gene regulation by the THI-box riboswitch

Molecular Microbiology

Volumn 67, Issue 4, 2008, Pages 793-803

  Ontiveros Palacios, Nancy ^a   Smith, Angela M ^b   Grundy, Frank J ^b   Soberon, Mario ^a   Henkin, Tina M ^b   Miranda Ríos, Juan ^a  

^a INSTITUTO DE BIOTECNOLOGÍA   (Mexico)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COCARBOXYLASE; RIBONUCLEASE H; RNA;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIUM MUTANT; ENZYME DEGRADATION; ESCHERICHIA COLI; GENE EXPRESSION; NONHUMAN; PHENOTYPIC VARIATION; PRIORITY JOURNAL; RIBOSOME SUBUNIT; RIBOSWITCH; TRANSLATION REGULATION;

BINDING SITES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; NUCLEIC ACID CONFORMATION; REGULATORY SEQUENCES, RIBONUCLEIC ACID; RIBOSOME SUBUNITS, SMALL, BACTERIAL; RNA, BACTERIAL; RNA, MESSENGER; THIAMINE; THIAMINE PYROPHOSPHATE; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 38449096224     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2007.06088.x     Document Type: Article

References (44)

1. Abreu-Goodger, C., Ontiveros-Palacios, N., Ciria, R. Merino, E. (2004) Conserved regulatory motifs in bacteria: riboswitches and beyond. Trends Genet 20 : 475 479.
2. Batifoulier, F., Verny, M.-A., Besson, C., Demigne, C. Rémésy, C. (2005) Determination of thiamin and its phosphate esters in rat tissues analyzed as thiochromes on a RP-amide C16 column. J Chromatogr B Analyt Technol Biomed Life Sci 816 : 67 72.
3. Cheah, M.T., Wachter, A., Sudarsan, N. Breaker, R.R. (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447 : 497 500.
4. Edwards, T.E. Ferré-D'Amaré, A.R. (2006) Crystal structure of the THI-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14 : 360 402.
5. MK box is a new SAM binding RNA element that regulates translation of bacterial SAM synthetase genes. Nat Struct Mol Biol 13 : 226 233.
6. MK box translational riboswitch RNA. Proc Natl Acad Sci USA 104 : 4876 4880.
7. Grundy, F.J. Henkin, T.M. (1993) tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell 74 : 475 482.
8. Grundy, F.J. Henkin, T.M. (2004) Kinetic analysis of tRNA-directed transcription antitermination of the Bacillus subtilis glyQS gene in vitro. J Bacteriol 186 : 5392 5399.
9. Grundy, F.J. Henkin, T.M. (2006) From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements. Crit Rev Biochem Mol 41 : 329 338.
10. Grundy, F.J., Moir, T.R., Haldeman, M.T. Henkin, T.M. (2002) Sequence requirements for terminators and antiterminators in the T box transcription antitermination system: disparity between conservation and functional requirements. Nucleic Acids Res 30 : 1646 1655.
11. Grundy, F.J., Lehman, S.C. Henkin, T.M. (2003) The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci USA 100 : 12057 12062.
12. Grundy, F.J., Yousef, M.R. Henkin, T.M. (2005) Monitoring uncharged tRNA during transcription of the Bacillus subtilis glyQS gene. J Mol Biol 346 : 73 81.
13. Johansen, L.E., Nygaard, P., Lassen, C., Agerso, Y. Saxild, H.H. (2003) 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 : 5200 5209.
14. Kawasaki, T. (1986) Determination of thiamine and its phosphate esters by high-performance liquid chromatography. Methods Enzymol 122 : 15 20.
15. Kubodera, T., Watanabe, M., Yoshiuchi, K., Yamashita, N., Nishimura, A., Nakai, S., et al. (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.
16. Lang, K., Rieder, R. Micura, R. (2007) Ligand-induced folding of the thiM TPP riboswitch investigated by a structure-based fluorescence spectroscopic approach. Nucleic Acids Res 35 : 5370 5378.
17. Lemay, J.F., Penedo, J.C., Tremblay, R., Lilley, D.M. Lafontaine, D.A. (2006) Folding of the adenine riboswitch. Chem Biol 13 : 857 868.
18. McDaniel, B.A.M., Grundy, F.J., Artsimovitch, I. 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 USA 100 : 3083 3088.
19. McDaniel, B.A., Grundy, F.J. Henkin, T.M. (2005) A tertiary structural element in S box leader RNAs is required for S-adenosylmethionine-directed transcription termination. Mol Microbiol 57 : 1008 1021.
20. Mandal, M. Breaker, R.R. (2004) Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struc Mol Biol 11 : 29 35.
21. Mandal, M., Boese, B., Barrick, J.E., Winkler, W.C. Breaker, R.R. (2003) Riboswiches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113 : 577 586.
22. Mandal, M., Lee, M., Barrick, J.E., Weinberg, Z., Emilsson, G.M., Ruzzo, W.L. Breaker, R.R. (2004) A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306 : 275 279.
23. Mathews, D.H., Sabina, J., Zuker, M. Turner, D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288 : 911 940.
24. Mayer, G., Raddatz, M.-S.L., Grunwald, J.D. Famulok, M. (2007) RNA ligands that distinguish metabolite-induced conformations in the TPP riboswitch. Angew Chem Int Ed 46 : 557 560.
25. Miller, J. (1972) Experiments in Molecular Genetics. Cold Spring Harbor, NY : Cold Spring Harbor Laboratory.
26. Miranda-Ríos, J. (2007) The THI-box riboswitch, or how RNA binds thiamin pyrophosphate. Structure 15 : 259 265.
27. 3 in Rhizobium etli. J Bacteriol 179 : 6887 6893.
28. Miranda-Ríos, J., Navarro, M. Soberon, M. (2001) A conserved RNA structure (thi-box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc Natl Acad Sci USA 98 : 9736 9741.
29. Mironov, A.S., Gusarov, I., Rafikov, R., Lopez, L.E., Shatalin, K., Kreneva, R.A., et al. (2002) Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111 : 747 756.
30. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C. Ferrin, T.E. (2004) ucsf Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25 : 1605 1612.
31. Powers, T. Noller, H.R. (1991) A functional pseudoknot in 16S ribosomal RNA. EMBO J 10 : 2203 2214.
32. Rentmeister, A., Mayer, G., Kuhn, N. Famulok, M. (2007) Conformational changes in the expression domain of the Escherichia coli thiM riboswitch. Nucleic Acids Res 35 : 3713 3722.
33. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A. Gelfand, M.S. (2002) Comparative genomics of thiamin biosynthesis in prokaryotes. New genes and regulatory mechanisms. J Biol Chem 277 : 48949 48959.
34. Serganov, A., Polonskaia, A., Phan, A.T., Breaker, R.R. Patel, D.J. (2006) Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441 : 1167 1171.
35. Simons, R.W., Houman, F. Kleckner, N. (1987) Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53 : 85 96.
36. Sudarsan, N., Barrick, J.E. Breaker, R.R. (2003) Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9 : 644 647.
37. Thore, S., Leibundgut, M. Ban, N. (2006) Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312 : 1208 1211.
38. Wachter, A., Tunc-Ozdemir, M., Grove, B.C., Green, P.J., Shintani, D.K. Breaker, R.R. (2007) Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell (in press). doi:10.1105/tpc.107.053645
39. Wickiser, J.K., Cheah, M.T., Breaker, R.R. Crothers, D.M. (2005a) The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44 : 13404 13414.
40. Wickiser, J.K., Winkler, W.C., Breaker, R.R. Crothers, D.M. (2005b) The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 18 : 49 60.
41. Winkler, W., Nahvi, A. Breaker, R.R. (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419 : 952 956.
42. Yanisch-Perron, C., Vieira, J. Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33 : 103 119.
43. Yousef, M.R., Grundy, F.J. Henkin, T.M. (2003) tRNA requirements for glyQS antitermination: a new twist on tRNA. RNA 9 : 1148 1156.
44. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31 : 3406 3415.