Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 9, 2012, Pages 3323-3328

  Perdrizet II, George A ^a   Artsimovitch, Irina ^b   Furman, Ran ^b   Sosnick, Tobin R ^a   Pan, Tao ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Gene regulation; Metabolism; Translational control

Indexed keywords

APTAMER; CIS ACTING ELEMENT; COBAMAMIDE; ESCHERICHIA COLI PROTEIN; PROTEIN BTUB; RNA POLYMERASE; UNCLASSIFIED DRUG;

5' UNTRANSLATED REGION; ARTICLE; BACTERIAL GENE; CATALYSIS; ENVIRONMENTAL FACTOR; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN ISOLATION; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; RIBOSOME; RIBOSWITCH; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION REGULATION; TRANSLATION INITIATION;

5' UNTRANSLATED REGIONS; APTAMERS, NUCLEOTIDE; BACTERIAL OUTER MEMBRANE PROTEINS; BASE SEQUENCE; COBAMIDES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; INVERTED REPEAT SEQUENCES; MEMBRANE TRANSPORT PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; OSMOLAR CONCENTRATION; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; REGULATORY SEQUENCES, NUCLEIC ACID; RIBOSOMES; RIBOSWITCH; RNA FOLDING; RNA POLYMERASE I; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 84857771826     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1113086109     Document Type: Article

References (33)

1. Oxender DL, Zurawski G, Yanofsky C (1979) Attenuation in the Escherichia coli tryptophan operon: Role of RNA secondary structure involving the tryptophan codon region. Proc Natl Acad Sci USA 76:5524-5528. (Pubitemid 10161653)
2. May GE, Olson S, McManus CJ, Graveley BR (2011) Competing RNA secondary structures are required for mutually exclusive splicing of the Dscam exon 6 cluster. RNA 17:222-229.
3. Roland KL, Liu CG, Turnbough CL, Jr (1988) Role of the ribosome in suppressing transcriptional termination at the pyrBI attenuator of Escherichia coli K-12. Proc Natl Acad Sci USA 85:7149-7153.
4. Winkler WC, Breaker RR (2005) Regulation of bacterial gene expression by riboswitches. Annu Rev Microbiol 59:487-517. (Pubitemid 41507440)
5. Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007) Control of alternative RNA splicing and gene expression by eukaryotic riboswitches. Nature 447:497-500. (Pubitemid 46816734)
6. Nahvi A, Barrick JE, Breaker RR (2004) Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Res 32:143-150. (Pubitemid 38228613)
7. Nahvi A, et al. (2002) Genetic control by a metabolite binding mRNA. Chem Biol 9:1043-1049. (Pubitemid 35273725)
8. Wickiser JK, Winkler WC, Breaker RR, Crothers DM (2005) The speed of RNA transcription and metabolite binding kinetics operate an FMN riboswitch. Mol Cell 18:49-60. (Pubitemid 40444647)
9. Vogel U, Jensen KF (1994) The RNA chain elongation rate in Escherichia coli depends on the growth rate. J Bacteriol 176:2807-2813. (Pubitemid 24152923)
10. Tolic-Norrelykke SF, Engh AM, Landick R, Gelles J (2004) Diversity in the rates of transcript elongation by single RNA polymerase molecules. J Biol Chem 279:3292-3299. (Pubitemid 38140563)
11. Bevilacqua PC, Blose JM (2008) Structures, kinetics, thermodynamics, and biological functions of RNA hairpins. Annu Rev Phys Chem 59:79-103. (Pubitemid 351703380)
12. 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. (Pubitemid 30431422)
13. Wong TN, Sosnick TR, Pan T (2007) Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci USA 104:17995-18000. (Pubitemid 350210809)
14. Nechooshtan G, Elgrably-Weiss M, Sheaffer A, Westhof E, Altuvia S (2009) A pH-responsive riboregulator. Genes Dev 23:2650-2662.
15. Wong TN, Pan T (2009) RNA folding during transcription: Protocols and studies. Methods Enzymol 468:167-193.
16. Lemay JF, et al. (2011) Comparative study between transcriptionally- and translationally- acting adenine riboswitches reveals key differences in riboswitch regulatory mechanisms. PLoS Genet 7:e1001278.
17. Nou X, Kadner RJ (2000) Adenosylcobalamin inhibits ribosome binding to btuB RNA. Proc Natl Acad Sci USA 97:7190-7195. (Pubitemid 30431439)
18. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410.
19. Larkin MA, et al. (2007) Clustal W and Clustal X version 2. Bioinformatics 23:2947-2948.
20. Hofacker IL, Fekete M, Stadler PF (2002) Secondary structure prediction for aligned RNA sequences. J Mol Biol 319:1059-1066. (Pubitemid 34729418)
21. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36:W70-74.
22. Nawrocki EP, Kolbe DL, Eddy SR (2009) Infernal 1.0: Inference of RNA alignments. Bioinformatics 25:1335-1337.
23. Zarrinkar PP, Williamson JR (1994) Kinetic intermediates in RNA folding. Science 265:918-924. (Pubitemid 24281488)
24. Treiber DK, Williamson JR (2000) Kinetic oligonucleotide hybridization for monitoring kinetic folding of large RNAs. Methods Enzymol 317:330-353. (Pubitemid 30418094)
25. Vassylyev DG, et al. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417:712-719. (Pubitemid 34640620)
26. Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I (2007) Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448:157-162. (Pubitemid 47067370)
27. Landick R, Stewart J, Lee DN (1990) Amino acid changes in conserved regions of the beta-subunit of Escherichia coli RNA polymerase alter transcription pausing and termination. Genes Dev 4:1623-1636.
28. Artsimovitch I, Chu C, Lynch AS, Landick R (2003) A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science 302:650-654. (Pubitemid 37310922)
29. Svetlov V, Belogurov GA, Shabrova E, Vassylyev DG, Artsimovitch I (2007) Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res 35:5694-5705. (Pubitemid 47506287)
30. 2+-dependent folding of a large ribozyme without kinetic traps. Nat Struct Biol 6:1091-1095.
31. Rangan P, Masquida B, Westhof E, Woodson SA (2003) Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc Natl Acad Sci USA 100:1574-1579. (Pubitemid 36254489)
32. Burns CM, Richardson LV, Richardson JP (1998) Combinatorial effects of NusA and NusG on transcription elongation and Rho-dependent termination in Escherichia coli. J Mol Biol 278:307-316. (Pubitemid 28220906)
33. Hufton SE, et al. (1995) Structure-function analysis of the vitamin B12 receptor of Escherichia coli by means of informational suppression. Mol Microbiol 15:381-393.