1,545
Views
14
CrossRef citations to date
0
Altmetric
RNA Family

Four RNA families with functional transient structures

&
Pages 5-20 | Received 02 Jul 2014, Accepted 25 Nov 2014, Published online: 31 Mar 2015

References

  • Burge, S. W. et al. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 2013; 41: D226-32.
  • Nahvi, A. et al. Genetic control by a metabolite binding mRNA. Chem. Biol. 2002; 9: 1043-1049.
  • Winkler, W., Nahvi, A. & Breaker, R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 2002; 419: 952-956.
  • Winkler, W., Cohen-Chalamish, S. & Breaker, R. An mRNA structure that controls gene expression by binding FMN. PNAS 2002; 99: 15908-15913.
  • Lai, D., Proctor, J. & Meyer, I. On the importance of cotranscriptional RNA structure formation. RNA 2013; 19: 1461-1473.
  • Wong, T., Sosnick, T. & Pan, T. Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. PNAS 2007; 104: 17995-18000.
  • Van Meerten, D., Girard, G. & Van Duin, J. Translational control by delayed RNA folding: Identification of the kinetic trap. RNA 2001; 7: 483-494.
  • Groeneveld, H., Thimon, K. & van Duin, J. Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding? RNA 1995; 1: 79-88.
  • Kolter, R. & Yanofsky, C. Attenuation in amino acid biosynthetic operons. Annu Rev Genet 1982; 16: 113-34.
  • Yanofsky, C. Attenuation in the control of expression of bacterial operons. Nature 1981; 289: 751-758.
  • 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 Structural Biology 2003; 10: 701-707.
  • Chadalavada, D. M., Knudsen, S. M., Nakano, S. & Bevilacqua, P. C. A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. J Mol Biol 2000; 301: 349-367.
  • Chadalavada, D. M., Gratton, E. A. & Bevilacqua, P. C. The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting. Biochemistry 2010; 49: 5321-30.
  • Zhu, J., Steif, A., Proctor, J. & Meyer, I. Transient RNA structure features are evolutionarily conserved and can be computationally predicted. Nucleic Acids Res 2013; 41: 6273-6285.
  • Rose, J. K. & Yanofsky, C. Interaction of the operator of the tryptophan operon with repressor. PNAS 1974; 71: 3134-38.
  • Bennett, G. N. & Yanofsky, C. Sequence analysis of operator constitutive mutants of the tryptophan operon of Escherichia coli. J Mol Biol 1978; 121: 179-192.
  • Yanofsky, C. Tryptophan biosynthesis in Escherichia coli. genetic determination of the proteins involved. JAMA 1971; 218: 1026-1035.
  • Stroynowski, I., van Cleemput, M. & Yanofsky, C. Superattenuation in the tryptophan operon of Serratia marcescens. Nature 1982; 298: 38-41.
  • Squires, C. et al. Nucleotide sequence of the 5′ end of tryptophan messenger RNA of Escherichia coli. J Mol Biol 1976; 103: 351-81.
  • Bertrand, K., Korn, L. J., Lee, F. & Yanofsky, C. The attenuator of the tryptophan operon of Escherichia coli: Heterogeneous 3′-OH termini in vivo and deletion mapping of functions. J Mol Biol 1977; 117: 227-47.
  • Oppenheim, D., Bennett, G. & Yanofsky, C. Escherichia coli RNA polymerase and trp repressor interaction with the promoter-operator region of the tryptophan operon of Salmonella typhimurium. J Mol Biol 1980; 144: 133-42.
  • Rose, J. K., Squires, C. L., Yanofsky, C., Yang, H. L. & Zubay, G. Regulation of in vitro transcription of the tryptophan operon by purified RNA polymerase in the presence of partially purified repressor and tryptophan. Nature new Biol 1973; 245: 133-37.
  • Imamoto, F. Immediate cessation of transcription of the operator-proximal region of the tryptophan operon in Escherichia coli after repression of the operon. Nature 1968; 220: 31-34.
  • Hiraga, S. & Yanofsky, C. Inhibition of the progress of transcription on the tryptophan operon of Escherichia coli. J Mol Biol 1973; 79: 339-49.
  • Jackson, E. & Yanofsky, C. Region between the operator and first structural gene of the tryptophan operon of Escherichia coli may have a regulatory function. J Mol Biol 1973; 76: 89-101.
  • Bertrand, K., Squires, C. & Yanofsky, C. Transcription termination in vivo in the leader region of the tryptophan operon of Escherichia coli. J Mol Biol 1976; 103: 319-37.
  • Lee, F., Squires, C. L., Squires, C. & Yanofsky, C. Termination of transcription in vitro in the Escherichia coli tryptophan operon leader region. J Mol Biol 1976; 103: 383-393.
  • Bronson, M. J., Squires, C. & Yanofsky, C. Nucleotide sequences from tryptophan messenger RNA of Escherichia coli: the sequence corresponding to the amino-terminal region of the first polypeptide specified by the operon. PNAS 1973; 70: 2335-9.
  • Miozzari, G. F. & Yanofsky, C. Translation of the leader region of the Escherichia coli tryptophan operon. J.Bact 1978; 133: 1457-1466.
  • Yanofsky, C. & Soil, L. Mutations affecting tRNATrp and its charging and their effect on regulation of transcription termination at the attenuator of the tryptophan operon. J Mol Biol 1977; 113: 663-677.
  • Zurawski, G., Elseviers, D., Stauffer, G. V. & Yanofsky, C. Translational control of transcription termination at the attenuator of the Escherichia coli tryptophan operon. PNAS 1978; 75: 5988-92.
  • Lee, F. & Yanofsky, C. Transcription termination at the trp operon attenuators of Escherichia coli and Salmonella typhimurium: RNA secondary structure and regulation of termination. PNAS 1977; 74: 4365-9.
  • Oxender, D., Zurawski, G. & Yanofsky, C. Attenuation in the Escherichia coli tryptophan operon: role of RNA secondary structure involving the tryptophan codon region. PNAS 1979; 76: 5524-5528.
  • Bertrand, K. & Yanofsky, C. Regulation of transcription termination in the leader region of the tryptophan operon of Escherichia coli involves tryptophan or its metabolic product. J Mol Biol 1976; 103: 339-49.
  • Lee, F., Bertrand, K., Bennett, G. & Yanofsky, C. Comparison of the nucleotide sequences of the initial transcribed regions of the tryptophan operons of Escherichia coli and Salmonella typhimurium. J Mol Biol 1978; 121: 193-217.
  • Miozzari, G. F. & Yanofsky, C. The regulatory region of the trp operon of Serratia marcescens. Nature 1978; 276: 684-9.
  • Miozzari, G F. & Yanofsky, C. Naturally occurring promoter down mutation: Nucleotide sequence of the trp promoter/operator/leader region of Shigella dysenteriae 16. PNAS 1978; 75: 5580-4.
  • Farnham, P. J. & Platt, T. A model for transcription termination suggested by studies on the trp attenuator in vitro using base analogs. Cell 1980; 20: 739-48.
  • Farnham, P. J. & Platt, T. Effects of DNA base analogs on transcription termination at the tryptophan operon attenuator of Escherichia coli. PNAS 1982; 79: 998-1002.
  • Zurawski, G. & Yanofsky, C. Escherichia coli tryptophan operon leader mutations, which relieve transcription termination, are cis-dominant to trp leader mutations, which increase transcription termination. J Mol Biol 1980; 142: 123-9.
  • Stauffer, G. V., Zurawski, G. & Yanofsky, C. Single base-pair alterations in the Escherichia coli trp operon leader region that relieve transcription termination at the trp attenuator. PNAS 1978; 75: 4833-7.
  • Stroynowski, I. & Yanofsky, C. Transcript secondary structures regulate transcription termination at the attenuator of S. marcescens tryptophan operon. Nature 1982; 298: 34-38.
  • Winkler, M. E., Mullis, K., Barnett, J., Stroynowski, I. & Yanofsky, C. Transcription termination at the tryptophan operon attenuator is decreased in vitro by an oligomer complementary to a segment of the leader transcript. PNAS 1982; 79: 2181-5.
  • Bollback, J. P. & Huelsenbeck, Phylogeny J. P., genome evolution, and host specificity of single-stranded RNA bacteriophage (family Leviviridae). J Mol Evol 2001; 52: 117-128.
  • Furuse, K. Distribution of coliphages in the environment: general considerations. In: Goyal SM (ed) Phage ecology (Wiley, New York, 1987).
  • Crawford, E. M. & Gesteland, R. F. The adsorption of bacteriophage R17. Virology 1964; 22: 165-167.
  • Bradley, D. E. Shortening of Pseudomonas aeruginosa pili after RNA-phage adsorption. J Gen Microbiol 1972; 72: 303-319.
  • Shapiro, L. & Bendis, I. RNA phages of bacteria other than E. coli. In: N Zinder (ed) RNA phages (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1975).
  • Miyake, T. et al. Grouping of RNA phages based on template specificity of their RNA replicases. PNAS 1971; 68: 2022-2024.
  • Murphy, F. A. et al. Virus taxonomy: The classification and nomenclature of viruses. The sixth report of the International Committee on Taxonomy of Viruses (Springer-Verlag, Vienna, 1995).
  • Geis, M. et al. Folding kinetics of large RNAs. J Mol Biol 2008; 379: 160-173.
  • van Himbergen, J., van Geffen, B. & van Duin, J. Translational control by a long range RNA-RNA interaction; a basepair substitution analysis. Nucleic Acids Res 1993; 21: 1713-7.
  • Kolakofsky, D. & Weissmann, C. Possible mechanism for transition of viral RNA from polysome to replication complex. Nature (London) New Biol 1971; 231: 42-46.
  • Klovins, J., Tsareva, N. A., de Smit, M. H., Berzins, V. & van Duin, J. Rapid evolution of translational control mechanisms in RNA genomes. J Mol Biol 1997; 265: 372-84.
  • Robertson, H. D. & Lodish, H. F. Messenger characteristics of nascent bacteriophage RNA. PNAS 1970; 67: 710-716.
  • van Duin, J. Single-stranded RNA bacteriophage. In: Calendar R, ed. The bacteriophages, vol 1 (Plenum Press, New York, 1988).
  • Beekwilder, J., Nieuwenhuizen, R., Poot, R. & van Duin, J. Secondary structure model for the first three domains of Qbeta RNA. Control of A-protein synthesis. J Mol Biol 1996; 256: 8-19.
  • Skripkin, E. A., Adhin, M. R., de Smit, M. H. & van Duin, J. Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance. J Mol Biol 1990; 211: 447-63.
  • Olsthoorn, R. C., Licis, N. & van Duin, J. Leeway and constraints in the forced evolution of a regulatory RNA helix. EMBO J 1994; 13: 2660-8.
  • Poot, R. A., Tsareva, N. V., Boni, I. V. & van Duin, J. RNA folding kinetics regulates translation of phage MS2 maturation gene. PNAS 1997; 94: 10110-5.
  • de Smit, M. H. & van Duin, J. Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis. PNAS 1990; 87: 7668-7672.
  • Kondo, M. Structure and function of RNA replicase of bacteriophage Qβ. Arch Int Physiol Biochim 1975; 83: 909-948.
  • Lai, M. M. The molecular biology of hepatitis delta virus. Annu Rev Biochem 1995; 64: 259-286.
  • Ferre-D′Amare, A. R., Zhou, K. & Doudna, J. A. Crystal structure of a hepatitis delta virus ribozyme. Nature 1998; 395: 567-74.
  • Wang, K. S. et al. Structure, sequence and expression of the hepatitis delta (delta) viral genome. Nature 1986; 323: 508-514.
  • Kos, A., Dijkema, R., Arnberg, A. C., van der Meide, P. H. & Schellekens, H. The hepatitis delta (delta) virus possesses a circular RNA. Nature 1986; 323: 558-560.
  • Makino, S. et al. Molecular cloning and sequencing of a human hepatitis delta (delta) virus RNA. Nature 1987; 329: 343-346.
  • Kuo, M. Y. et al. Molecular cloning of hepatitis delta virus RNA from an infected woodchuck liver: sequence, structure, and applications. J Virol 1988; 62: 1855-1861.
  • Lazinski, D. & Taylor, J. Regulation of the hepatitis delta virus ribozymes: to cleave or not to cleave? RNA 1995; 1: 225-233.
  • Been, M. D. & Wickham, G. S. Self-cleaving ribozymes of hepatitis delta virus RNA. Eur. J.Biochem 1997; 247, 741--753.
  • Perrotta, A. T. & Been, M. D. The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant. Nucleic Acids Res 1990; 18: 6821-6827.
  • Rosenstein, S. P. & Been, M. D. Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures. Nucleic Acids Res 1991; 19: 5409-16.
  • Woodson, S. & Cech, T. Alternative secondary structures in the 5′ exon affect both forward and reverse self-splicing of the tetrahymena intervening sequence RNA. Biochemistry 1991; 30: 2042-2050.
  • Woodson, S. Exon sequences distant from the splice junction are required for efficient self-splicing of the tetrahymena IVS. Nucleic Acids Res 1992; 20: 4027-4032.
  • Nikolcheva, T. & Woodson, S. Facilitation of group 1 splicing in vivo: Misfolding of the Tetrahymena IVS and the role of ribosomal RNA exons. J Mol Biol 1999; 292: 557-567.
  • Perrotta, A. & Been, M. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta-virus RNA. Nature 1991; 350: 434-436.
  • Tanner, N. K. et al. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses. Curr Biol 1994; 4: 488-498.
  • Perrotta, A. T. & Been, M. D. Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage. Nucleic Acids Res 1996; 24: 1314-1321.
  • Matysiak, M., Wrzesinski, J. & Ciesiolka, J. Sequential folding of the genomic ribozyme of the hepatitis delta virus: structural analysis of RNA transcription intermediates. J Mol Biol 1999; 291: 283-294.
  • Perrotta, A., Nikiforova, O. & Been, M. A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduces kinetic trapping of inactive conformations. Nucleic Acids Res 1999; 27: 795-802.
  • Mathews, D., Sabina, J., Zuker, M. & Turner, D. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999; 288: 911-940.
  • Zuker, M., Mathews, D. & Turner, D. Algorithms and thermodynamics for RNA secondary structure prediction practical guide In RNA Biochemistry and Biotechnology, J.B.B.R.C. Clark (Ed.), NATO ASI Series (Kluwer Academic Publishers, Dordrecht, the Netherlands, 1999).
  • Zhu, J. & Wartell, R. The effect of base sequence on the stability of RNA and DNA single base bulges. Biochemistry 1999; 38: 15986-15993.
  • Chadalavada, D. M., Senchak, S. E. & Bevilacqua, P. C. The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of pseudoknots. J Mol Biol 2002; 317: 559-575.
  • Benner, S., Ellington, A. & Tauer, A. Modern metabolism as a palimpsest of the RNA world. PNAS 1989; 86: 7054-7058.
  • Joyce, G. The antiquity of RNA-based evolution. Nature 2002; 418: 214-221.
  • Mironov, A. et al. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell 2002; 111: 747-756.
  • Haller, A., Rieder, U., Aigner, M., Blanchard, S. C. & Micura, R. Conformational capture of the SAM-II riboswitch. Nat Chem Biol 2011; 7: 393-400.
  • Grundy, F. & Henkin, T. The s box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Mol Microbiol 1998; 30: 737-749.
  • Nudler, E. & Mironov, A. The riboswitch control of bacterial metabolism. Trends Biochem Sci 2004; 29: 11-17.
  • Epshtein, V., Mironov, A. & Nudler, E. The riboswitch-mediated control of sulfur metabolism in bacteria. PNAS 2003; 100: 5052-5056.
  • Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 2013; 29: 2933-2935.
  • Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Sayers, E. W. Genbank. Nucleic Acids Res 2009; 37: D26-31.
  • Griffiths-Jones, S. RALEE--RNA ALignment editor in Emacs. Bioinformatics 2005; 21: 257-259.
  • Edgar, R. C. Search and clustering orders of magnitude faster than blast. Bioinformatics 2010; 26: 2460-2461.
  • Lai, D., Proctor, J., Zhu, J. & Meyer, I. R-chie: a web server and r package for visualizing RNA secondary structures. Nucleic Acids Res 2012; 40:e95.
  • Montange, R. K & Batey, R. T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 2006; 441: 1172-1175.
  • Darty, K., Denise, A., & Ponty, Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009; 25 (15):1974-1975.