Control of gene expression by a natural metabolite-responsive ribozyme (original) (raw)

• Cech, T. R. Self-splicing of group I introns. Annu. Rev. Biochem. 59, 543–568 (1990)
  Article CAS Google Scholar
• Frank, D. N. & Pace, N. R. Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu. Rev. Biochem. 67, 153–180 (1998)
  Article CAS Google Scholar
• Michel, F. & Feral, J. Structure and activities of group II introns. Annu. Rev. Biochem. 64, 435–461 (1995)
  Article CAS Google Scholar
• Doherty, E. A. & Doudna, J. A. Ribozyme structures and mechanisms. Annu. Rev. Biochem. 69, 597–615 (2000)
  Article CAS Google Scholar
• Nissen, P., Hansen, J., Ban, N., Moore, P. B. & Steitz, T. A. The structural basis of ribosome activity in peptide bond synthesis. Science 289, 920–930 (2000)
  Article ADS CAS Google Scholar
• Breaker, R. R. In vitro selection of catalytic polynucleotides. Chem. Rev. 97, 371–390 (1997)
  Article CAS Google Scholar
• Osborne, S. E. & Ellington, A. D. Nucleic acid selection and the challenge of combinatorial chemistry. Chem. Rev. 97, 349–370 (1997)
  Article CAS Google Scholar
• Soukup, G. A. & Breaker, R. R. Allosteric nucleic acid catalysts. Curr. Opin. Struct. Biol. 10, 318–325 (2000)
  Article CAS Google Scholar
• Breaker, R. R. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13, 31–39 (2002)
  Article CAS Google Scholar
• Silverman, S. K. Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA. RNA 9, 377–383 (2003)
  Article CAS Google Scholar
• Seetharaman, S., Zivarts, M., Sudarsan, N. & Breaker, R. R. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nature Biotechnol. 19, 336–341 (2001)
  Article CAS Google Scholar
• Ptashne, M. & Gann, A. Genes & Signals (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2002)
  Google Scholar
• Nahvi, A. et al. Genetic control by a metabolite-binding mRNA. Chem. Biol. 9, 1043–1049 (2002)
  Article CAS Google Scholar
• Winkler, W., Nahvi, A. & Breaker, R. R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952–956 (2002)
  Article ADS CAS Google Scholar
• Winkler, W. C., Cohen-Chalamish, S. & Breaker, R. R. An mRNA structure that controls gene expression by binding FMN. Proc. Natl Acad. Sci. USA 99, 15908–15913 (2002)
  Article ADS CAS Google Scholar
• Mironov, A. S. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 111, 747–756 (2002)
  Article CAS Google Scholar
• Winkler, W. C. & Breaker, R. R. Genetic control by metabolite-binding riboswitches. Chembiochem 4, 1024–1032 (2003)
  Article CAS Google Scholar
• Mandal, M., Boese, B., Barrick, J. E., Winkler, W. C. & Breaker, R. R. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 113, 577–586 (2003)
  Article CAS Google Scholar
• Gusarov, I. & Nudler, E. The mechanism of intrinsic transcription termination. Mol. Cell 3, 495–504 (1999)
  Article CAS Google Scholar
• Yarnell, W. S. & Roberts, J. W. Mechanism of intrinsic transcription termination and antitermination. Science 284, 611–615 (1999)
  Article ADS CAS Google Scholar
• Mandal, M. & Breaker, R. R. Adenine riboswitches and gene activation by disruption of a transcription terminator. Nature Struct. Mol. Biol. 11, 29–35 (2004)
  Article CAS Google Scholar
• Vitreschak, A. G., Rodionov, D. A., Mironov, A. A. & Gelfand, M. S. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 20, 44–50 (2004)
  Article CAS Google Scholar
• Sudarsan, N., Barrick, J. E. & Breaker, R. R. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA 9, 644–647 (2003)
  Article CAS Google Scholar
• Kubodera, T. et al. 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 (2003)
  Article CAS Google Scholar
• Barrick, J. E. et al. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proc. Natl Acad. Sci. USA (submitted)
• Milewski, S. Glucosamine-6-phosphate synthase: the multi-facets enzyme. Biochim. Biophys. Acta 1597, 173–192 (2002)
  Article CAS Google Scholar
• Winkler, W. C., Nahvi, A., Sudarsan, N., Barrick, J. E. & Breaker, R. R. An mRNA structure that controls gene expression by binding _S_-adenosylmethionine. Nature Struct. Biol. 10, 701–707 (2003)
  Article CAS Google Scholar
• Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S. & Breaker, R. R. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 17, 2688–2697 (2003)
  Article CAS Google Scholar
• Soukup, G. A. & Breaker, R. R. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5, 1308–1325 (1999)
  Article CAS Google Scholar
• Li, Y. & Breaker, R. R. Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group. J. Am. Chem. Soc. 121, 5364–5372 (1999)
  Article CAS Google Scholar
• Emilsson, G. M., Nakamura, S., Roth, A. & Breaker, R. R. Ribozyme speed limits. RNA 9, 907–918 (2003)
  Article CAS Google Scholar
• Breaker, R. R. et al. A common speed limit for RNA-cleaving ribozymes and deoxyribozymes. RNA 9, 949–957 (2003)
  Article CAS Google Scholar
• Tang, J. & Breaker, R. R. Rational design of allosteric ribozymes. Chem. Biol. 4, 453–459 (1997)
  Article CAS Google Scholar
• Soukup, G. A. & Breaker, R. R. Engineering precision RNA molecular switches. Proc. Natl Acad. Sci. USA 96, 3584–3589 (1999)
  Article ADS CAS Google Scholar
• Koizumi, M., Soukup, G. A., Kerr, J. Q. & Breaker, R. R. Allosteric selection of ribozymes that respond to the second messengers cGMP and cAMP. Nature Struct. Biol. 6, 1062–1071 (1999)
  Article CAS Google Scholar
• Breaker, R. R. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13, 31–39 (2002)
  Article CAS Google Scholar
• Soukup, G. A., DeRose, E. C., Koizumi, M. & Breaker, R. R. Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 7, 524–536 (2001)
  Article CAS Google Scholar
• Abrash, H. I., Cheung, C.-C. S. & Davis, J. C. The nonenzymic hydrolysis of nucleoside 2′,3′-phosphates. Biochemistry 6, 1303 (1967)
  Article Google Scholar
• Saville, B. J. & Collins, R. A. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell 61, 685–696 (1990)
  Article CAS Google Scholar
• Joyce, G. F. The antiquity of RNA-based evolution. Nature 418, 214–221 (2002)
  Article ADS CAS Google Scholar
• Miller, J. H. A Short Course in Bacterial Genetics 72 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1992)
  Google Scholar