Regulation of bacterial gene expression by riboswitches.

Riboswitches are structured domains that usually reside in the noncoding regions of mRNAs, where they bind metabolites and control gene expression. Like their protein counterparts, these RNA gene control elements form highly specific binding pockets for the target metabolite and undergo allosteric changes in structure. Numerous classes of riboswitches are present in bacteria and they comprise a common and robust metabolite-sensing system.

[1]  D. Patel,et al.  RNA-structural Mimicry in Escherichia coli Ribosomal Protein L4-dependent Regulation of the S10 Operon* , 2003, Journal of Biological Chemistry.

[2]  E. Nudler,et al.  The mechanism of intrinsic transcription termination. , 1999, Molecular cell.

[3]  T. Henkin,et al.  Interaction between the acceptor end of tRNA and the T box stimulates antitermination in the Bacillus subtilis tyrS gene: a new role for the discriminator base , 1994, Journal of bacteriology.

[4]  R. Kadner,et al.  Adenosylcobalamin inhibits ribosome binding to btuB RNA. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[5]  M. Gelfand,et al.  Riboswitches: the oldest mechanism for the regulation of gene expression? , 2004, Trends in genetics : TIG.

[6]  W. Winkler Metabolic monitoring by bacterial mRNAs , 2005, Archives of Microbiology.

[7]  R. A. Kreneva,et al.  Genetic mapping of regulatory mutations ofBacillus subtilis riboflavin operon , 1990, Molecular and General Genetics MGG.

[8]  G. Storz,et al.  Controlling mRNA stability and translation with small, noncoding RNAs. , 2004, Current opinion in microbiology.

[9]  E. Nudler,et al.  The riboswitch control of bacterial metabolism. , 2004, Trends in biochemical sciences.

[10]  M. Green,et al.  Controlling gene expression in living cells through small molecule-RNA interactions. , 1998, Science.

[11]  T. Henkin,et al.  tRNA-mediated transcription antitermination in vitro: Codon–anticodon pairing independent of the ribosome , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Jimin Wang,et al.  The structure of a ribosomal protein S8/spc operon mRNA complex. , 2004, RNA.

[13]  A. Serganov,et al.  Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.

[14]  Irina Artsimovitch,et al.  Information Processing by RNA Polymerase: Recognition of Regulatory Signals during RNA Chain Elongation , 1998, Journal of bacteriology.

[15]  Eric Westhof,et al.  RNA as a Drug Target: The Case of Aminoglycosides , 2003, Chembiochem : a European journal of chemical biology.

[16]  H. Paulus,et al.  Research letterFine-structure mapping of cis-acting control sites in the lysC operon of Bacillus subtilis , 1992 .

[17]  M. Gelfand,et al.  A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes. , 1999, Trends in genetics : TIG.

[18]  Jeffrey E. Barrick,et al.  New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[19]  Andrew D Ellington,et al.  Group I aptazymes as genetic regulatory switches , 2002, BMC biotechnology.

[20]  O. Schilling,et al.  A protein-dependent riboswitch controlling ptsGHI operon expression in Bacillus subtilis: RNA structure rather than sequence provides interaction specificity. , 2004, Nucleic acids research.

[21]  S. Kochhar,et al.  Lysine-induced premature transcription termination in the lysC operon of Bacillus subtilis. , 1996, Microbiology.

[22]  A. Ellington,et al.  Simultaneous detection of diverse analytes with an aptazyme ligase array. , 2003, Analytical biochemistry.

[23]  E. Westhof,et al.  Riboswitch structures: purine ligands replace tertiary contacts. , 2005, Chemistry & biology.

[24]  T. Steitz,et al.  The kink‐turn: a new RNA secondary structure motif , 2001, The EMBO journal.

[25]  R. Breaker,et al.  Adenine riboswitches and gene activation by disruption of a transcription terminator , 2004, Nature Structural &Molecular Biology.

[26]  M. Gelfand,et al.  Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. , 2004, Nucleic acids research.

[27]  D. Ebbole,et al.  Cloning and characterization of a 12-gene cluster from Bacillus subtilis encoding nine enzymes for de novo purine nucleotide synthesis. , 1987, The Journal of biological chemistry.

[28]  J. Miranda-Ríos,et al.  A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Vitaly Epshtein,et al.  The riboswitch-mediated control of sulfur metabolism in bacteria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Jean-Jacques Toulmé,et al.  Regulating eukaryotic gene expression with aptamers , 2004, FEBS letters.

[31]  R. D'Amato,et al.  Exogenous control of mammalian gene expression through modulation of RNA self-cleavage , 2004, Nature.

[32]  J. Stülke Control of transcription termination in bacteria by RNA-binding proteins that modulate RNA structures , 2002, Archives of Microbiology.

[33]  T. Henkin,et al.  Solution structure of the Bacillus subtilis T-box antiterminator RNA: seven nucleotide bulge characterized by stacking and flexibility. , 2003, Journal of molecular biology.

[34]  C. Wilson,et al.  Inducible regulation of the S. cerevisiae cell cycle mediated by an RNA aptamer-ligand complex. , 2001, Bioorganic & medicinal chemistry.

[35]  Nobuo Yamashita,et al.  Thiamine‐regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch‐like domain in the 5′‐UTR , 2003, FEBS letters.

[36]  Paul R Copeland,et al.  Regulation of gene expression by stop codon recoding: selenocysteine. , 2003, Gene.

[37]  P. Bevilacqua,et al.  A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding. , 2003, Journal of molecular biology.

[38]  R. Montange,et al.  Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine , 2004, Nature.

[39]  D. Patel,et al.  Adaptive recognition by nucleic acid aptamers. , 2000, Science.

[40]  C. Yanofsky,et al.  Regulation by transcription attenuation in bacteria: how RNA provides instructions for transcription termination/antitermination decisions. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[41]  T. Henkin,et al.  The GA motif: an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic RNAs. , 2001, RNA.

[42]  T. Henkin,et al.  The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in Gram‐positive bacteria , 1998, Molecular microbiology.

[43]  H. Schwalbe,et al.  An intermolecular base triple as the basis of ligand specificity and affinity in the guanine- and adenine-sensing riboswitch RNAs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[44]  J. Vogel,et al.  RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. , 2003, Nucleic acids research.

[45]  R. Breaker,et al.  Selection in vitro of allosteric ribozymes. , 2004, Methods in molecular biology.

[46]  H. White Coenzymes as fossils of an earlier metabolic state , 1976, Journal of Molecular Evolution.

[47]  R. Breaker,et al.  Control of gene expression by a natural metabolite-responsive ribozyme , 2004, Nature.

[48]  Zasha Weinberg,et al.  A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression , 2004, Science.

[49]  Ronald R. Breaker,et al.  Kinetics of RNA Degradation by Specific Base Catalysis of Transesterification Involving the 2‘-Hydroxyl Group , 1999 .

[50]  David J. Worhunsky,et al.  Translational repression mechanisms in prokaryotes , 2003, Molecular microbiology.

[51]  J. Roth,et al.  Regulation of cobalamin biosynthetic operons in Salmonella typhimurium , 1987, Journal of bacteriology.

[52]  M. Springer,et al.  Translational feedback regulation of the gene for L35 in Escherichia coli requires binding of ribosomal protein L20 to two sites in its leader mRNA: a possible case of ribosomal RNA-messenger RNA molecular mimicry. , 2002, RNA.

[53]  S. Altuvia,et al.  Alternative mRNA structures of the cIII gene of bacteriophage lambda determine the rate of its translation initiation. , 1989, Journal of molecular biology.

[54]  J. Doudna,et al.  Ribozyme structures and mechanisms. , 2001, Annual review of biophysics and biomolecular structure.

[55]  Ronald R. Breaker,et al.  Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression , 2002, Nature.

[56]  P. Babitzke,et al.  The trp RNA-Binding Attenuation Protein of Bacillus subtilis Regulates Translation of the Tryptophan Transport Gene trpP (yhaG) by Blocking Ribosome Binding , 2004, Journal of bacteriology.

[57]  C. Oubridge,et al.  RNA-binding proteins: TRAPping RNA bases , 2000, Current Biology.

[58]  R. Breaker Engineered allosteric ribozymes as biosensor components. , 2002, Current opinion in biotechnology.

[59]  Ronald R. Breaker,et al.  Natural and engineered nucleic acids as tools to explore biology , 2004, Nature.

[60]  R. Losick,et al.  Bacillus Subtilis and Its Closest Relatives: From Genes to Cells , 2001 .

[61]  M. Gelfand,et al.  Comparative Genomics of Thiamin Biosynthesis in Procaryotes , 2002, The Journal of Biological Chemistry.

[62]  M. Gelfand,et al.  Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. , 2002, Nucleic acids research.

[63]  M. Ptashne,et al.  Genes and Signals , 2001 .

[64]  G. F. Joyce The antiquity of RNA-based evolution , 2002, Nature.

[65]  R. Breaker,et al.  An mRNA structure that controls gene expression by binding FMN , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[66]  L. Argaman,et al.  fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex. , 2000, Journal of molecular biology.

[67]  RNA Mimicry in the Translational Apparatus , 1998 .

[68]  Y. Lu,et al.  Fine-structure mapping of cis-acting control sites in the lysC operon of Bacillus subtilis. , 1992, FEMS microbiology letters.

[69]  P. Babitzke Regulation of transcription attenuation and translation initiation by allosteric control of an RNA-binding protein: the Bacillus subtilis TRAP protein. , 2004, Current opinion in microbiology.

[70]  R R Breaker,et al.  Relationship between internucleotide linkage geometry and the stability of RNA. , 1999, RNA.

[71]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[72]  T. Henkin,et al.  Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[73]  R. Breaker,et al.  Immobilized RNA switches for the analysis of complex chemical and biological mixtures , 2001, Nature Biotechnology.

[74]  B. Sullenger,et al.  Aptamers: an emerging class of therapeutics. , 2005, Annual review of medicine.

[75]  Jeffrey E. Barrick,et al.  Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria , 2003, Cell.

[76]  Margaret S. Ebert,et al.  An mRNA structure in bacteria that controls gene expression by binding lysine. , 2003, Genes & development.

[77]  D. Crothers,et al.  The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. , 2005, Molecular cell.

[78]  T. Henkin,et al.  tRNA as a positive regulator of transcription antitermination in B. subtilis , 1993, Cell.

[79]  H. Zalkin,et al.  Identification of the Bacillus subtilis pur operon repressor. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[80]  T. Henkin,et al.  tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene. , 2000, RNA.

[81]  M. Grunberg‐Manago,et al.  Transfer RNA-mediated antitermination in vitro. , 2002, Nucleic acids research.

[82]  S. K. Desai,et al.  Genetic screens and selections for small molecules based on a synthetic riboswitch that activates protein translation. , 2004, Journal of the American Chemical Society.

[83]  S. Busby,et al.  The regulation of bacterial transcription initiation , 2004, Nature Reviews Microbiology.

[84]  P. Romby,et al.  Bacterial translational control at atomic resolution. , 2003, Trends in genetics : TIG.

[85]  Ali Nahvi,et al.  Genetic control by a metabolite binding mRNA. , 2002, Chemistry & biology.

[86]  Jeffrey E. Barrick,et al.  Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. , 2004, Nucleic acids research.

[87]  M. Gelfand,et al.  Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? , 2003, Nucleic acids research.

[88]  F. Narberhaus,et al.  mRNA-mediated detection of environmental conditions , 2002, Archives of Microbiology.

[89]  Ali Nahvi,et al.  An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.

[90]  L. Christiansen,et al.  Xanthine metabolism in Bacillus subtilis: characterization of the xpt-pbuX operon and evidence for purine- and nitrogen-controlled expression of genes involved in xanthine salvage and catabolism , 1997, Journal of bacteriology.

[91]  M. Lewis,et al.  Lac repressor-operator complex. , 1997, Current opinion in structural biology.

[92]  C. Condon RNA Processing and Degradation in Bacillus subtilis , 2003, Microbiology and Molecular Biology Reviews.

[93]  Jeffrey W. Roberts,et al.  Mechanism of intrinsic transcription termination and antitermination. , 1999, Science.

[94]  R. Kadner,et al.  Conserved structural and regulatory regions in the Salmonella typhimurium btuB gene for the outer membrane vitamin B12 transport protein. , 1992, Research in microbiology.

[95]  T. Henkin,et al.  The L box regulon: Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[96]  P. Cossart,et al.  An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes , 2002, Cell.

[97]  R. Breaker,et al.  Gene regulation by riboswitches , 2004, Nature Reviews Molecular Cell Biology.

[98]  Andrew Wright,et al.  Transcriptional antitermination in the bgl operon of E. coli is modulated by a specific RNA binding protein , 1990, Cell.

[99]  R R Breaker,et al.  Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. , 2001, RNA.

[100]  T. Henkin,et al.  Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination , 1997, Journal of bacteriology.

[101]  Andrey A Mironov,et al.  Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. , 2003, RNA.

[102]  Barbara Fink,et al.  Conditional gene expression by controlling translation with tetracycline-binding aptamers. , 2003, Nucleic acids research.

[103]  S. Gottesman The small RNA regulators of Escherichia coli: roles and mechanisms*. , 2004, Annual review of microbiology.

[104]  Jeffrey E. Barrick,et al.  Metabolite-binding RNA domains are present in the genes of eukaryotes. , 2003, RNA.

[105]  J. Szulmajster,et al.  Regulation of dihydrodipicolinate synthase and aspartate kinase in Bacillus subtilis , 1975, Journal of bacteriology.

[106]  Evgeny Nudler,et al.  Sensing Small Molecules by Nascent RNA A Mechanism to Control Transcription in Bacteria , 2002, Cell.

[107]  T. Henkin,et al.  The T box and S box transcription termination control systems. , 2003, Frontiers in bioscience : a journal and virtual library.

[108]  P. Moore,et al.  Structural motifs in RNA. , 1999, Annual review of biochemistry.

[109]  Gary D. Stormo,et al.  Do mRNAs act as direct sensors of small molecules to control their expression? , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[110]  R. Breaker,et al.  Genetic Control by Metabolite‐Binding Riboswitches , 2003, Chembiochem : a European journal of chemical biology.

[111]  F. Borne,et al.  Isolation and identification of mutants constitutive for aspartokinase III synthesis in Escherichia coli K 12. , 1980, Biochimie.