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RNA Sensors of Intracellular Metabolites

  • Chapter
Regulatory RNAs in Prokaryotes

Abstract

Gene expression in bacteria can be controlled through many different possible regulatory strategies. The “expression” of a given gene can be described as a function of all of the molecular processes involved in the conversion of the gene’s information first into messenger RNA (mRNA) transcripts and then into the corresponding proteins. Therefore, one approach for defining the different possible types of bacterial regulatory strategies is to consider the various stages along the informationprocessing pathway from DNA to protein (Fig 1).

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References

  • Amster-Choder O, Wright A (1992) Modulation of the dimerization of a transcriptional antiterminator protein by phosphorylation. Science 257: 1395–1398

    Article  PubMed  CAS  Google Scholar 

  • Artsimovitch I, Landick R (2000) Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc Natl Acad Sci USA 97: 7090–7095

    Article  PubMed  CAS  Google Scholar 

  • Arvidson DN, Bruce C, Gunsalus RP (1986) Interaction of the Trp repressor with its ligand, L-tryptophan. J Biol Chem 261: 238–243

    PubMed  CAS  Google Scholar 

  • Babitzke P, Yanofsky C (1993) Reconstitution of Bacillus subtilis trp attenuation in vitro with TRAP, the trp RNA-binding attenuation protein. Proc Natl Acad Sci USA 90: 133–137

    Article  PubMed  CAS  Google Scholar 

  • Baker CS, Morozov I, Suzuki K, Romeo T, Babitzke P (2002) CsrA regulates glycogen biosynthesis by preventing translation of glgC in Escherichia coli. Mol Microbiol 44: 1599–1610

    Article  PubMed  CAS  Google Scholar 

  • Barrick JE, Breaker RR (2007) The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biol 8: R239

    Article  PubMed  CAS  Google Scholar 

  • Bechhofer DH (2009) Messenger RNA decay and maturation in Bacillus subtilis. Prog Mol Biol Transl Sci 85: 231–271

    Article  PubMed  CAS  Google Scholar 

  • Belasco JG (2010) All things must pass: contrasts and commonalities in eukaryotic and bacterial mRNA decay. Nat Rev Mol Cell Biol 11: 467–478

    Article  PubMed  CAS  Google Scholar 

  • Blount KF, Breaker RR (2006) Riboswitches as antibacterial drug targets. Nat Biotechnol 24: 1558–1564

    Article  PubMed  CAS  Google Scholar 

  • Brown L, Elliott T (1997) Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium. J Bacteriol 179: 656–662

    PubMed  CAS  Google Scholar 

  • Browning DR, Busby SJ (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2: 57–65

    Article  PubMed  CAS  Google Scholar 

  • Burmann BM, Schweimer K, Luo X, Wahl MC, Stitt BL, Gottesman ME, Rösch P (2010) A NusE:NusG complex links transcription and translation. Science 328: 501–504

    Article  PubMed  CAS  Google Scholar 

  • Butler JS, Springer M, Dondon J, Grunberg-Manago M (1986) Posttranscriptional autoregulation of Escherichia coli threonyl tRNA synthetase expression in vivo. J Bacteriol 165:198–203

    PubMed  CAS  Google Scholar 

  • Collins JA, Irnov I, Baker S, Winkler WC (2007) Mechanism of mRNA destabilization by the glmS ribozyme. Genes Dev 21: 3356–3368

    Article  PubMed  CAS  Google Scholar 

  • Condon C (2010) What is the role of RNase J in mRNA turnover? RNA Biol 7: 316–321

    Article  PubMed  CAS  Google Scholar 

  • Cruz-Vera LR, Gong M, Yanofsky C (2008) Physiological effects of anti-TRAP protein activity and tRNA(Trp) charging on trp operon expression in Bacillus subtilis. J Bacteriol 190: 1937–1945

    Article  PubMed  CAS  Google Scholar 

  • Daldrop P, Reyes FE, Robinson DA, Hammond CM, Lilley DM, Batey RT, Brenk R (2011) Novel ligands for a purine riboswitch discovered by RNA-ligand docking. Chem Biol 18: 324–335

    Article  PubMed  CAS  Google Scholar 

  • Dallas A, Moore PB. (1997) The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. Structure 5: 1639–1653

    Article  PubMed  CAS  Google Scholar 

  • Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37: D136–140

    Article  PubMed  CAS  Google Scholar 

  • Gilbert SD, Mediatore SJ, Batey RT (2006) Modified pyrimidines specifically bind the purine riboswitch. J Am Chem Soc 128: 14214–14215

    Article  PubMed  CAS  Google Scholar 

  • Gollnick P, Babitzke P (2002) Transcription attenuation. Biochem Biophys Acta 1577: 240–250

    Article  PubMed  CAS  Google Scholar 

  • Gottesman S (2004) The small RNA regulators of Escherichia coli: roles and mechanisms. Annu Rev Microbiol 58: 303–328

    Article  PubMed  CAS  Google Scholar 

  • Gottesman S, Storz G (2010) Bacterial small RNA regulators: Versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 1: 1–16

    Google Scholar 

  • Green NJ, Grundy FJ, Henkin TM (2010) The T box mechanism: tRNA as a regulatory molecule. FEBS Lett 584: 318–324

    Article  PubMed  CAS  Google Scholar 

  • Greive SJ, von Hippel PH (2005) Thinking quantitatively about transcriptional regulation. Nat Rev Mol Cell Biol 6: 221–232

    Article  PubMed  CAS  Google Scholar 

  • Grundy FJ, Henkin TM (2003) The T box and S box transcription termination control systems. Front Biosci 8: d20–31

    Article  PubMed  CAS  Google Scholar 

  • Grundy FJ, Henkin TM (1993) tRNA as a positive regulator of transcription antitermination in B. subtilis. Cell 74: 475–482

    Article  PubMed  CAS  Google Scholar 

  • Grundy FJ, Hodil SE, Rollins SM, Henkin TM (1997) Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination. J Bacteriol 179: 2587–2594

    PubMed  CAS  Google Scholar 

  • Grundy FJ, Winkler WC, Henkin TM (2002) tRNA-mediated transcription antitermination in vitro: Codon—anticodon pairing independent of the ribosome. Proc Natl Acad Sci USA 99: 11121–11126.

    Article  PubMed  CAS  Google Scholar 

  • Herbert KM, Greenleaf WJ, Block SM (2008) Single-molecule studies of RNA polymerase: motoring along. Annu Rev Biochem 77: 148–176

    Article  CAS  Google Scholar 

  • Irnov I, Winkler WC (2010) A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol Microbiol 76: 559–575

    Article  PubMed  CAS  Google Scholar 

  • Johansen LE, Nygaard P, Lassen C, Agerso Y, Saxild HH (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

    Article  PubMed  CAS  Google Scholar 

  • Kim JN, Blount KF, Lim J, Link KH, Breaker R. (2009) Design and antimicrobial action of purine analogs that bind guanine riboswitches. ACS Chem Biol 4: 915–27

    Article  PubMed  CAS  Google Scholar 

  • Klein DJ, Ferré-D’Amaré AR (2006) Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313: 1752–1756

    Article  PubMed  CAS  Google Scholar 

  • Klein DJ, Schmeing TM, Moore PB, Steitz TA (2001) The kink-turn: a new RNA secondary structure motif. EMBO J 20: 4214–4221

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O’Reilly M, O’Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Séror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100: 4678–4683

    Article  PubMed  CAS  Google Scholar 

  • Kulshina N, Baird NJ, Ferré-D’Amaré AR (2009) Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol 16: 1212–1217

    Article  PubMed  CAS  Google Scholar 

  • Landick R, Turnbough CL, Yanofsky C (1996) Transcription Attenuation. In: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia and Salmonella cellular and molecular biology. ASM Press, Washington, DC pp 1263–1286

    Google Scholar 

  • Landick R (2006) The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans 34: 1062–1066

    Article  PubMed  CAS  Google Scholar 

  • Larson MH, Landick R, Block SM (2011) Single-molecule studies of RNA polymerase: one singular sensation, every little step it takes.

    Google Scholar 

  • Lease RA, Cusick ME, Belfort M (1998) Riboregulation in Escherichia coli DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc Natl Acad Sci 95: 12456–12461

    Article  PubMed  CAS  Google Scholar 

  • Lemay JF, Desnoyers G, Blouin S, Heppell B, Bastet L, St-Pierre P, Massé E, Lafontaine DA (2011) Comparative study between transcriptionally-and translationally-acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet 7: e1001278

    Article  PubMed  CAS  Google Scholar 

  • Lemay JF, Lafontaine DA (2007) Core requirements of the adenine riboswitch aptamer for ligand binding. RNA 13:339–350

    Article  PubMed  CAS  Google Scholar 

  • Lemay JF, Penedo JC, Tremblay R, Lilley DMJ, Lafontaine DA (2006) Folding of the adenine riboswitch. Chem Biol 13:857–868

    Article  PubMed  CAS  Google Scholar 

  • Leontis NB, Westhof E (1998) A common motif organizes the structure of multi-helix loops in 16S and 23S ribosomal RNAs. J Mol Biol 283: 571–583

    Article  PubMed  CAS  Google Scholar 

  • Ling B, Dong L, Zhang R, Wang Z, Liu Y, Liu C (2009) Theoretical studies on the interaction of modified pyrimidines and purines with purin riboswitch. J Mol Graph Model 28: 37–45

    Article  PubMed  CAS  Google Scholar 

  • Liu MY, Gui G, Wei B, Preston JF, Oakford L, Yuksel U, Giedroc DP, Romeo T (1997) The RNA molecule CsrB binds to the global regulatory protein CsrA and antagonizes its activity in Escherichia coli. J Biol Chem 272: 17502–17510

    Article  PubMed  CAS  Google Scholar 

  • Liu MY, Romeo T (1997) The global regulator CsrA of Escherichia coli is a specific mRNAbinding protein. J Bacteriol 179: 4639–4642

    PubMed  CAS  Google Scholar 

  • Luo D, Condon C, Grunberg-Manago M, Putzer H (1998) In vitro and in vivo secondary structure probing of the thrS leader in Bacillus subtilis. Nucleic Acids Res 26: 5379–5387

    Article  PubMed  CAS  Google Scholar 

  • Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S (1998) DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci 95: 12462–12467

    Article  PubMed  CAS  Google Scholar 

  • Majdalani N, Vanderpool CK, Gottesman S (2005) Bacterial small RNA regulators. Crit Rev Biochem Mol 40: 93–113

    Article  CAS  Google Scholar 

  • Mandal M, Breaker RR (2004) Adenine riboswitches and gene activation by disruption of a transcription terminator. Nat Struct Mol Biol 11: 29–35

    Article  PubMed  CAS  Google Scholar 

  • Moine H, Romby P, Springer M, Grunberg-Manago M, Ebel JP, Ehresmann C, Ehresmann B (1988) Messenger RNA structure and gene regulation at the translational level in Escherichia coli: the case of threonine:tRNAThr ligase. Proc Natl Acad Sci US 85: 7892–7896

    Article  CAS  Google Scholar 

  • Møller T, Franch T, Højrup P, Keene DR, Bächinger HP, Brennan FG, Valentin-Hansen P (2002) Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol Cell 9: 23–30

    Article  PubMed  Google Scholar 

  • Morita T, Maki K, Aiba H (2005) RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev 19: 2176–2186

    Article  PubMed  CAS  Google Scholar 

  • Mooney RA, Darst SA, Landick R (2005) Sigma and RNA polymerase: an on-again, off-again relationship? Mol Cell 21: 335–345

    Article  CAS  Google Scholar 

  • Mulhbacher J, Brouillette E, Allard M, Fortier LC, Malouin F, Lafontaine DA (2010) Novel riboswitch ligand analogs as selective inhibitors of guanine-related metabolic pathways. PLos Pathog 6: e1000865

    Article  PubMed  CAS  Google Scholar 

  • Navarro Llorens JM, Tormo A, Martinez-Garcia E (2010) Stationary phase in Gram-negative bacteria. FEMS Microbiol Rev 34: 476–495

    Article  PubMed  CAS  Google Scholar 

  • Nudler E, Gottesman ME (2002) Transcription termination and anti-termination in E. coli. Genes Cells 7: 755–768

    Article  PubMed  CAS  Google Scholar 

  • Pan T, Artsimovitch I, Fang X, Landick R, Sosnick TR (1999) Folding of a large ribozyme during transcription and the effect of the elongation factor NusA. Proc Natl Acad Sci USA 96: 9545–9550

    Article  PubMed  CAS  Google Scholar 

  • Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J (2009) Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation. Nat Struct Mol Biol 16: 840–846

    Article  PubMed  CAS  Google Scholar 

  • Putzer H, Condon C, Brechemier-Baey D, Brito R, Grunberg-Manago M (2002) Transfer RNAmediated antitermination in vitro. Nucleic Acids Res 30: 3026–3033

    Article  PubMed  CAS  Google Scholar 

  • Rieder R, Lang K, Graber D, Micura R (2007) Ligand-induced folding of the adenosinedeaminase A-riboswitch and implications on riboswitch translational control. Chembiochem 8:896–902

    Article  PubMed  CAS  Google Scholar 

  • Rieder U, Kreutz C, Micura R (2010) Folding of a transcriptionally acting preQ1 riboswitch. Proc Natl Acad Sci USA 107: 10804–10809

    Article  PubMed  CAS  Google Scholar 

  • Roberts JW, Shankar S, Filter JJ (2008) RNA polymerase elongation factors. Annu Rev Microbiol 62: 211–233

    Article  PubMed  CAS  Google Scholar 

  • Rollins SM, Grundy FJ, Henkin TM (1997) Analysis of cis-acting sequence and structural elements required for antitermination of the Bacillus subtilis tyrS gene. Mol Microbiol 25: 411–421

    Article  PubMed  CAS  Google Scholar 

  • Roth A, Breaker RR (2009) The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 78: 305–34

    Article  PubMed  CAS  Google Scholar 

  • Schilling O, Langbein I, Müller M, Schmalisch MH, Stülke J (2004) A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity. Nucleic Acids Res 32: 2853–2864

    Article  PubMed  CAS  Google Scholar 

  • Schnetz K, Stülke J, Gertz S, Krüger S, Krieg M, Hecker M, Rak B (1996) LicT, a Bacillus subtilis transcriptional antiterminator protein of the BglG family. J Bacteriol 178: 1971–1979

    PubMed  CAS  Google Scholar 

  • Schmalisch MH, Bachem S, Stülke J (2003) Control of the Bacillus subtilis antiterminator protein GlcT by phosphorylation. Elucidation of the phosphorylation chain leading to inactivation of GlcT. J Biol Chem 278: 51108–51115

    Article  PubMed  CAS  Google Scholar 

  • Schroeder KT, McPhee SA, Ouellet J, Lilley DM (2010) A structural database for k-turn motifs in RNA. RNA 16: 1463–1468

    Article  PubMed  CAS  Google Scholar 

  • Seliverstov AV, Putzer H, Gelfand MS, Lyubetsky VA (2005) Comparative analysis of RNA regulatory elements of amino acid metabolism genes in Actinobacteria. BMC Microbiol 5: 54

    Article  PubMed  CAS  Google Scholar 

  • Serganov A, Patel DJ (2007) Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat Rev Genet 8:776–790

    Article  PubMed  CAS  Google Scholar 

  • 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: 1729–41

    Article  PubMed  CAS  Google Scholar 

  • Shimaoka M, Takenaka Y, Mihara Y, Kurahashi O, Kawasaki H, Matsui H (2006) Effects of xapA and guaA disruption on inosine accumulation in Escherichia coli. Biosci Biotechnol Biochem 70: 3069–3072

    Article  PubMed  CAS  Google Scholar 

  • Sledjeski D, Gottesman S (1995) A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherechia coli. Proc Natl Acad Sci 92: 2003–2007

    Article  PubMed  CAS  Google Scholar 

  • Sledjeski DD, Whitman C, Zhang A (2001) Hfq is necessary for riboregulation by the untranslated RNA DsrA. J Bacteriol 183: 1997–2005

    Article  PubMed  CAS  Google Scholar 

  • Slock J, Stahly DP, Han CY, Six EW, Crawford IP (1990) An apparent Bacillus subtilis folic acid biosynthetic operon containing pab, an amphibolic trpG gene, a third gene required for synthesis of para-aminobenzoic acid, and the dihydropteroate synthase gene. J Bacteriol 172: 7211–7226

    PubMed  CAS  Google Scholar 

  • Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA (2009) Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol 16: 1218–1223

    Article  PubMed  CAS  Google Scholar 

  • Stülke J (2002) Control of transcription termination in bacteria by RNA-binding proteins that modulate RNA structures. Arch Microbiol 177: 433–440

    Article  PubMed  CAS  Google Scholar 

  • Stülke J, Arnaud M, Rapoport G, Martin-Verstraete (1998) PRD—a protein domain involved in PTS-dependent induction and carbon catabolite repression of catabolic operons in bacteria. Mol Microbiol 28: 865–874

    Article  PubMed  Google Scholar 

  • Stülke J, Martin-Verstraete I, Zagorec M, Rose M, Klier A, Rapoport G (1997) Induction of the Bacillus subtilis ptsGHI operon by glucose is controlled by a novel antiterminator, GlcT. Mol Microbiol 1997 25: 65–78

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Switzer RL (2009) Discoveries in bacterial nucleotide metabolism. J Biol Chem 284: 6585–6594

    Article  PubMed  CAS  Google Scholar 

  • Timmermans J, Van Melderen L (2010) Post-transcriptional global regulation by CsrA in bacteria. Cell Mol Life Sci 67: 2897–2908

    Article  PubMed  CAS  Google Scholar 

  • Turnbough CL Jr, Switzer RL (2008) Regulation of pyrimidine biosynthetic gene expression in bacteria: repression without repressors. Microbiol Mol Biol Rev 72: 266–300

    Article  PubMed  CAS  Google Scholar 

  • Valbuzzi A, Gollnick P, Babitzke P, Yanofsky C (2002) The anti-trp RNA-binding attenuation protein (Anti-TRAP), AT, recognizes the tryptophan-activated RNA binding domain of the TRAP regulatory protein. J Biol Chem 277: 10608–10613

    Article  PubMed  CAS  Google Scholar 

  • Vassylyev DG (2009) Elongation by RNA polymerase: a race through roadblocks. Curr Opin Struct Biol 19: 691–700

    Article  PubMed  CAS  Google Scholar 

  • Vitreschak AG, Mironov AA, Lyubetsky VA, Gelfand MS (2008) Comparative genomic analysis of T-box regulatory systems in bacteria. RNA 14: 717–735

    Article  PubMed  CAS  Google Scholar 

  • Wang J, Nikonowicz EP (2010) Solution structure of the K-turn and Specifier Loop Domains from the Bacillus subtilis tyrS T-box leader RNA. J Mol Biol 408: 99–117

    Article  CAS  Google Scholar 

  • Waters LS, Storz G (2009) Regulatory RNAs in bacteria. Cell 136: 615–628

    Article  PubMed  CAS  Google Scholar 

  • Wei BL, Brun-Zinkernagel AM, Simecka JW, Pruss BM, Babitzke P, Romeo T (2001) Positive regulation of motility and flhDC expression by the RNA-binding protein CsrA of Escherichia coli. Mol Microbiol 40: 245–256

    Article  PubMed  CAS  Google Scholar 

  • Weisberg RA, Gottesman ME (1999) Processive antitermination. J Bacteriol 181: 359–367

    PubMed  CAS  Google Scholar 

  • Wickiser JK, Cheah MT, Breaker RR, Crothers DM (2005a) The kinetics of ligand binding by an adenine-sensing riboswitch. Biochemistry 44: 13404–13414

    Article  PubMed  CAS  Google Scholar 

  • Wickiser JK, Winkler WC, Breaker RR, Crothers D (2005b) The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 18:49–60

    Article  PubMed  CAS  Google Scholar 

  • Winkler WC (2007) RNA-Mediated Regulation in Bacillus subtilis. In: Graumann P (ed) Bacillus: Cellular and Molecular Biology. Caister Academic Press, Friedberg pp 167–214

    Google Scholar 

  • Winkler WC, Grundy FJ, Murphy BA, Henkin TM (2001) The GA motif: An RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. RNA 7: 1165–1172

    Article  PubMed  CAS  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Yanofsky C (2000) Transcription attenuation: once viewed as a novel regulatory strategy. J Bacteriol 182: 1–8

    Article  PubMed  CAS  Google Scholar 

  • Zhang RG, Joachimiak A, Lawson CL, Schevitz RW, Otwinowski Z, Sigler PB (1987) The crystal structure of trp aporepressor at 1.8 A shows how binding tryptophan enhances DNA affinity. Nature 327: 591–97

    Article  PubMed  CAS  Google Scholar 

  • Zhang A, Wassarman KM, Rosenow C, Tjaden BC, Storz G, Gottesman S (2003) Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol 50: 1111–1124

    Article  PubMed  CAS  Google Scholar 

  • Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetzky O (1994) The solution structures of the trp repressor-operator DNA complex. J Mol Biol 238:592–614

    Article  PubMed  CAS  Google Scholar 

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Zacharia, V., Lafontaine, D., Winkler, W.C. (2012). RNA Sensors of Intracellular Metabolites. In: Regulatory RNAs in Prokaryotes. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0218-3_11

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