The functional anatomy of an intrinsic transcription terminator

EMBO Journal

Volumn 22, Issue 13, 2003, Pages 3385-3394

  Schwartz, Annie ^a   Rahmouni, A Rachid ^a   Boudvillain, Marc ^a  

^a CENTRE DE BIOPHYSIQUE MOLÉCULAIRE   (France)

Author keywords

Hairpin; Interaction; NAIM; RNA polymerase; Termination

Indexed keywords

CYTOSINE; DNA; ELONGATION FACTOR; GUANINE; RNA; RNA POLYMERASE; T7 RNA POLYMERASE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ALLOSTERISM; ARTICLE; ATOM; COMPLEX FORMATION; DISSOCIATION; DNA TEMPLATE; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; TRANSCRIPTION TERMINATION;

BASE SEQUENCE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RNA, MESSENGER; TERMINATOR REGIONS (GENETICS); TRANSCRIPTION, GENETIC;

EID: 0038601943     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/cdg310     Document Type: Article

References (45)

1. Boudvillain, M. and Pyle, A.M. (1998) Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. EMBO J., 17, 7091-7104.
2. Boudvillain, M., de Lencastre, A. and Pyle, A.M. (2000) A tertiary interaction that links active-site domains to the 5′ splice site of a group II intron. Nature, 406, 315-318.
3. Boudvillain, M., Schwartz, A. and Rahmouni, A.R. (2002) Limited topological alteration of the T7 RNA polymerase active center at intrinsic termination sites. Biochemistry, 41, 3137-3146.
4. Cheng, S.W., Lynch, E.C., Leason, K.R., Court, D.L., Shapiro, B.A. and Friedman, D.I. (1991) Functional importance of sequence in the stem-loop of a transcription terminator. Science, 254, 1205-1207.
5. Christian, E.L. and Yarus, M. (1992) Analysis of the role of phosphate oxygens in the group I intron from Tetrahymena. J. Mol. Biol., 228, 743-758.
6. d'Aubenton Carafa, Y., Brody, E. and Thermes, C. (1990) Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J. Mol. Biol., 216, 835-858.
7. Freier, S.M. and Altmann, K.H. (1997) The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically modified DNA:RNA duplexes. Nucleic Acids Res., 25, 4429-4443.
8. Gish, G. and Eckstein, F. (1988) DNA and RNA sequence determination based on phosphorothioate chemistry. Science, 240, 1520-1522.
9. Gopal, V., Brieba, L.G., Guajardo, R., McAllister, W.T. and Sousa, R. (1999) Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement. J. Mol. Biol., 290, 411-431.
10. Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
11. Gusarov, I. and Nudler, E. (1999) The mechanism of intrinsic transcription termination. Mol. Cell, 3, 495-504.
12. Gusarov, I. and Nudler, E. (2001) Control of intrinsic transcription termination by N and NusA: the basic mechanisms. Cell, 107, 437-449.
13. Hartvig, L. and Christiansen, J. (1996) Intrinsic termination of T7 RNA polymerase mediated by either RNA or DNA. EMBO J., 15, 4767-4774.
14. He, B., Rong, M., Lyakhov, D., Gartenstein, H., Diaz, G., Castagna, R., McAllister, W.T. and Durbin, R.K. (1997) Rapid mutagenesis and purification of phage RNA polymerases. Protein Expr. Purif., 9, 142-151.
15. He, B., Kukarin, A., Temiakov, D., Chin-Bow, S.T., Lyakhov, D.L., Rong, M., Durbin, R.K. and McAllister, W.T. (1998) Characterization of an unusual, sequence-specific termination signal for T7 RNA polymerase. J. Biol. Chem., 273, 18802-18811.
16. Hermann, T. and Patel, D.J. (1999) Stitching together RNA tertiary architectures. J. Mol. Biol., 294, 829-849.
17. 2+ and deoxynucleoside monophosphate incorporation into transcripts. Biochemistry, 36, 13718-13728.
18. Jeng, S.T., Gardner, J.F. and Gumport, R.I. (1990) Transcription termination by bacteriophage T7 RNA polymerase at rho-independent terminators. J. Biol. Chem., 265, 3823-3830.
19. Kashlev, M. and Komissarova, N. (2002) Transcription termination: primary intermediates and secondary adducts. J. Biol. Chem., 277, 14501-14508.
20. Komissarova, N., Becker, J., Solter, S., Kireeva, M. and Kashlev, M. (2002) Shortening of RNA:DNA hybrid in the elongation complex of RNA polymerase is a prerequisite for transcription termination. Mol. Cell, 10, 1151-1162.
21. Landick, R. (2001) RNA polymerase clamps down. Cell, 105, 567-570.
22. Lyakhov, D.L., He, B., Zhang, X., Studier, F.W., Dunn, J.J. and McAllister, W.T. (1997) Mutant bacteriophage T7 RNA polymerases with altered termination properties. J. Mol. Biol., 269, 28-40.
23. Macdonald, L.E., Zhou, Y. and McAllister, W.T. (1993) Termination and slippage by bacteriophage T7 RNA polymerase. J. Mol. Biol., 232, 1030-1047.
24. Macdonald, L.E., Durbin, R.K., Dunn, J.J. and McAllister, W.T. (1994) Characterization of two types of termination signal for bacteriophage T7 RNA polymerase. J. Mol. Biol., 238, 145-158.
25. McDowell, J.C., Roberts, J.W., Jin, D.J. and Gross, C. (1994) Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science, 266, 822-825.
26. Mooney, R.A., Artsimovitch, I. and Landick, R. (1998) Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol., 180, 3265-3275.
27. Mueller, U., Schubel, H., Sprinzl, M. and Heinemann, U. (1999) Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G·U wobble base pair at 1.16 Å resolution. RNA, 5, 670-677.
28. Murakami, K.S. and Darst, S.A. (2003) Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol., 13, 31-39.
29. Ortoleva-Donnelly, L., Kronman, M. and Strobel, S.A. (1998a) Identifying RNA minor groove tertiary contacts by nucleotide analogue interference mapping with N2-methylguanosine. Biochemistry, 37, 12933-12942.
30. Ortoleva-Donnelly, L., Szewczak, A.A., Gutell, R.R. and Strobel, S. (1998b) The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA, 4, 498-519.
31. 2-methylguanosine is iso-energetic with guanosine in RNA duplexes and GNRA tetraloops. Nucleic Acids Res., 26, 3640-3644.
32. SantaLucia, J.J., Kierzek, R. and Turner, D.H. (1992) Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science, 256, 217-219.
33. Steitz, T.A. (1998) A mechanism for all polymerases. Nature, 391, 231-232.
34. Strobel, S.A. (1999) A chemogenetic approach to RNA function/structure analysis. Curr. Opin. Struct. Biol., 9, 346-352.
35. Strobel, S.A. and Shetty, K. (1997) Defining the chemical groups essential for Tetrahymena group 1 intron function by nucleotide analog interference mapping. Proc. Natl Acad. Sci. USA, 94, 2903-2908.
36. Sugimoto, N., Nakano, M. and Nakano, S. (2000) Thermodynamics - structure relationship of single mismatches in RNA-DNA duplexes. Biochemistry, 39, 11270-11281.
37. Szewczak, A.A., Ortoleva-Donnelly, L., Ryder, S.P., Moncoeur, E. and Strobel, S.A. (1998) A minor groove RNA triple helix within the catalytic core of a group I intron. Nat. Struct. Biol., 5, 1037-1042.
38. Tahirov, T.H., Temiakov, D., Anikin, M., Patlan, V., McAllister, W.T., Vassylyev, D.G. and Yokoyama, S. (2002) Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature, 420, 43-50.
39. Temiakov, D., Anikin, M. and McAllister, W.T. (2002) Characterization of T7 RNA polymerase transcription complexes assembled on nucleic acid scaffolds. J. Biol. Chem., 277, 47035-47043.
40. Toulokhonov, I., Artsimovitch, I. and Landick, R. (2001) Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science, 292, 730-733.
41. Wilson, K.S. and von Hippel, P.H. (1994) Stability of Escherichia coli transcription complexes near an intrinsic terminator. J. Mol. Biol., 244, 36-51.
42. Wilson, K.S., Conant, C.R. and von Hippel, P.H. (1999) Determinants of the stability of transcription elongation complexes: interactions of the nascent RNA with the DNA template and the RNA polymerase. J. Mol. Biol., 289, 1179-1194.
43. Woody, A.Y., Eaton, S.S., Osumi-Davis, P.A. and Woody, R.W. (1996) Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis and transcription. Biochemistry, 35, 144-152.
44. Yarnell, W.S. and Roberts, J.W. (1999) Mechanism of intrinsic transcription termination and antitermination. Science, 284, 611-615.
45. Yin, Y.W. and Steitz, T.A. (2002) Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science, 298, 1387-1395.