The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch

Molecular Cell

Volumn 18, Issue 1, 2005, Pages 49-60

  Wickiser, J Kenneth ^a,b   Winkler, Wade C ^a,c   Breaker, Ronald R ^a   Crothers, Donald M ^a  

^a YALE UNIVERSITY   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLAVINE MONONUCLEOTIDE; LIGAND; MESSENGER RNA; RNA POLYMERASE;

ALLOSTERISM; ARTICLE; BACILLUS SUBTILIS; BINDING KINETICS; HUMAN; METABOLITE; POLYMERIZATION; PROTEIN FUNCTION; RNA TRANSCRIPTION; THERMODYNAMICS; TRANSCRIPTION TERMINATION;

BACILLUS SUBTILIS;

EID: 15944382675     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2005.02.032     Document Type: Article

References (42)

1. I. Artsimovitch, and R. Landick Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals Proc. Natl. Acad. Sci. USA 97 2000 7090 7095
2. M.S. Carlomagno, and A. Nappo NusA modulates intragenic termination by different pathways Gene 308 2003 115 128
3. D.M. Crothers, P.E. Cole, C.W. Hilbers, and R.G. Shulman The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA J. Mol. Biol. 87 1974 63 88
4. V. Epshtein, and E. Nudler Cooperation between RNA polymerase molecules in transcription elongation Science 300 2003 801 805
5. P.J. Farnham, J. Greenblatt, and T. Platt Effects of NusA protein on transcription termination in the tryptophan operon of Escherichia coli Cell 29 1982 945 951
6. F. Gong, and C. Yanofsky A transcriptional pause synchronizes translation with transcription in the tryptophanase operon leader region J. Bacteriol. 185 2003 6472 6476
7. F.J. Grundy, and T.M. Henkin Kinetic analysis of tRNA-directed transcription antitermination of the Bacillus subtilis glyQS gene in vitro J. Bacteriol. 186 2004 5392 5399
8. I. Gusarov, and E. Nudler The mechanism of intrinsic transcription termination Mol. Cell 3 1999 495 504
9. I. Gusarov, and E. Nudler Control of intrinsic transcription termination by N and NusA: the basic mechanisms Cell 107 2001 437 449
10. D.C. Haines, I.F. Sevrioukova, and J.A. Peterson The FMN-binding domain of cytochrome P450BM-3: resolution, reconstitution, and flavin analogue substitution Biochemistry 39 2000 9419 9429
11. N. Komissarova, and M. Kashlev Functional topography of nascent RNA in elongation intermediates of RNA polymerase Proc. Natl. Acad. Sci. USA 95 1998 14699 14704
12. T. Kubodera, M. Watanabe, K. Yoshiuchi, N. Yamashita, A. Nishimura, S. Nakai, K. Gomi, and H. Hanamoto 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
13. R. Landick, D. Wang, and C.L. Chan Quantitative analysis of transcriptional pausing by Escherichia coli RNA polymerase: his leader pause site as paradigm Methods Enzymol. 274 1996 334 353
14. M. Mandal, and R.R. Breaker Gene regulation by riboswitches Nat. Rev. Mol. Cell Biol. 5 2004 451 463
15. M. Mandal, B. Boese, J.E. Barrick, W.C. Winkler, and R.R. Breaker Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria Cell 113 2003 577 586
16. M. Mandal, M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo, and R.R. Breaker A glycine-dependent riboswitch that uses cooperative binding to control gene expression Science 306 2004 275 279
17. B.A. McDaniel, F.J. Grundy, I. Artsimovitch, and T.M. Henkin 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
18. A.S. Mironov, I. Gusarov, R. Rafikov, L.E. Lopez, K. Shatalin, R.A. Kreneva, D.A. Perumov, and E. Nudler Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria Cell 111 2002 747 756
19. J.A. Monforte, J.D. Kahn, and J.E. Hearst RNA folding during transcription by Escherichia coli RNA polymerase analyzed by RNA self-cleavage Biochemistry 29 1990 7882 7890
20. A. Nahvi, N. Sudarsan, M.S. Ebert, X. Zou, K.L. Brown, and R.R. Breaker Genetic control by a metabolite binding mRNA Chem. Biol. 9 2002 1043
21. E. Nudler, and A.S. Mironov The riboswitch control of bacterial metabolism Trends Biochem. Sci. 29 2004 11 17
22. T. Pan, I. Artsimovitch, X.W. Fang, R. Landick, and T.R. Sosnick Folding of a large ribozyme during transcription and the effect of the elongation factor NusA Proc. Natl. Acad. Sci. USA 96 1999 9545 9550
23. D.R. Phillips, S.M. Cutts, C.M. Cullinane, and D.M. Crothers High-resolution transcription assay for probing drug-DNA interactions at individual drug sites Methods Enzymol. 340 2001 466 485
24. R. Reynolds, and M.J. Chamberlin Parameters affecting transcription termination by Escherichia coli RNA. II. Construction and analysis of hybrid terminators J. Mol. Biol. 224 1992 53 63
25. G. Rhodes, and M.J. Chamberlin Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase. I. Isolation of ternary complexes and the kinetics of elongation J. Biol. Chem. 249 1974 6675 6683
26. D.A. Rodionov, A.G. Vitreschak, A.A. Mironov, and M.S. Gelfand Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems Nucleic Acids Res. 32 2004 3340 3353
27. D.W. Selinger, R.M. Saxena, K.J. Cheung, G.M. Church, and C. Rosenow Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation Genome Res. 13 2003 216 223
28. G.A. Soukup, and R.R. Breaker Relationship between internucleotide linkage geometry and the stability of RNA RNA 5 1999 1308 1325
29. N. Sudarsan, J.E. Barrick, and R.R. Breaker Metabolite-binding RNA domains are present in the genes of eukaryotes RNA 9 2003 644 647
30. N. Sudarsan, J.K. Wickiser, S. Nakamura, M.S. Ebert, and R.R. Breaker An mRNA structure in bacteria that controls gene expression by binding lysine Genes Dev. 17 2003 2688 2697
31. A.G. Vitreschak, D.A. Rodionov, A.A. Mironov, and M.S. Gelfand Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation Nucleic Acids Res. 30 2002 3141 3151
32. A.G. Vitreschak, D.A. Rodionov, A.A. Mironov, and M.S. Gelfand Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 20 2004 44 50
33. K.S. Wilson, and P.H. von Hippel Transcription termination at intrinsic terminators: the role of the RNA hairpin Proc. Natl. Acad. Sci. USA 92 1995 8793 8797
34. M.E. Winkler, and C. Yanofsky Pausing of RNA polymerase during in vitro transcription of the tryptophan operon leader region Biochemistry 20 1981 3738 3744
35. W.C. Winkler, and R.R. Breaker Genetic control by metabolite-binding riboswitches ChemBioChem 4 2003 1024 1032
36. W.C. Winkler, S. Cohen-Chalamish, and R.R. Breaker An mRNA structure that controls gene expression by binding FMN Proc. Natl. Acad. Sci. USA 99 2002 15908 15913
37. W.C. Winkler, A. Nahvi, and R.R. Breaker Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Nature 419 2002 952 956
38. W.C. Winkler, A. Nahvi, N. Sudarsan, J.E. Barrick, and R.R. Breaker An mRNA structure that controls gene expression by binding S-adenosylmethionine Nat. Struct. Biol. 10 2003 701 707
39. W.C. Winkler, A. Nahvi, A. Roth, J.A. Collins, and R.R. Breaker Control of gene expression by a natural metabolite-responsive ribozyme Nature 428 2004 281 286
40. A.V. Yakhnin, and P. Babitzke NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism in vitro Proc. Natl. Acad. Sci. USA 99 2002 11067 11072
41. W.S. Yarnell, and J.W. Roberts Mechanism of intrinsic transcription termination and antitermination Science 284 1999 611 615
42. H. Zhang, and R.L. Switzer Transcriptional pausing in the Bacillus subtilis pyr operon in vitro: a role in transcriptional attenuation? J. Bacteriol. 185 2003 4764 4771