Structural basis of transcription by bacterial and eukaryotic RNA polymerases

Current Opinion in Structural Biology

Volumn 22, Issue 1, 2012, Pages 110-118

  Sekine, Shun Ichi ^a,b   Tagami, Shunsuke ^b   Yokoyama, Shigeyuki ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; DOUBLE STRANDED DNA; EUKARYOTIC DNA DIRECTED RNA POLYMERASE; EUKARYOTIC TRANSCRIPTION FACTOR SII; GRE FACTOR HOMOLOG 1; RNA POLYMERASE II; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GFH1; TRANSCRIPTION FACTOR GRE; UNCLASSIFIED DRUG;

BACKTRACKING; BACTERIUM TRANSCRIPTION; BETA HAIRPIN; BRIDGE HELIX; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA DENATURATION; ENZYME CONFORMATION; ENZYME STRUCTURE; EUKARYOTIC TRANSCRIPTION; GENE TRANSLOCATION; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEIC ACID STRUCTURE; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN HYDROLYSIS; PROTEIN RNA BINDING; PROTEIN STRUCTURE; REVIEW; RNA CLEAVAGE; TRANSCRIPT CLEAVAGE; TRANSCRIPTION ELONGATION; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION;

DNA-DIRECTED RNA POLYMERASES; HUMANS; MICROTUBULE-ASSOCIATED PROTEINS; RNA; TRANSCRIPTION, GENETIC; TRANSCRIPTIONAL ELONGATION FACTORS;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 84857031357     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2011.11.006     Document Type: Review

References (58)

1. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science 2001, 292:1863-1876.
2. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3Å resolution. Cell 1999, 98:811-824.
3. Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Structural basis of transcription: an RNA polymerase II elongation complex at 3.3Å resolution. Science 2001, 292:1876-1882.
4. Vassylyev D.G., Vassylyeva M.N., Perederina A., Tahirov T.H., Artsimovitch I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature 2007, 448:157-162.
5. Wang D., Bushnell D.A., Huang X., Westover K.D., Levitt M., Kornberg R.D. Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Science 2009, 324:1203-1206.
6. Cheung A.C., Cramer P. Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature 2011, 471:249-253.
7. Tagami S., Sekine S., Kumarevel T., Hino N., Murayama Y., Kamegamori S., Yamamoto M., Sakamoto K., Yokoyama S. Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein. Nature 2010, 468:978-982.
8. Donahue B.A., Yin S., Taylor J.S., Reines D., Hanawalt P.C. Transcript cleavage by RNA polymerase II arrested by a cyclobutane pyrimidine dimer in the DNA template. Proc Natl Acad Sci USA 1994, 91:8502-8506.
9. Jeon C., Agarwal K. Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc Natl Acad Sci USA 1996, 93:13677-13682.
10. Marr M.T., Roberts J.W. Function of transcription cleavage factors GreA and GreB at a regulatory pause site. Mol Cell 2000, 6:1275-1285.
11. Komissarova N., Kashlev M. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded. Proc Natl Acad Sci USA 1997, 94:1755-1760.
12. Komissarova N., Kashlev M. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J Biol Chem 1997, 272:15329-15338.
13. Nudler E., Mustaev A., Lukhtanov E., Goldfarb A. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 1997, 89:33-41.
14. Fish R.N., Kane C.M. Promoting elongation with transcript cleavage stimulatory factors. Biochim Biophys Acta 2002, 1577:287-307.
15. Wind M., Reines D. Transcription elongation factor SII. Bioessays 2000, 22:327-336.
16. Borukhov S., Polyakov A., Nikiforov V., Goldfarb A. GreA protein: a transcription elongation factor from Escherichia coli. Proc Natl Acad Sci USA 1992, 89:8899-8902.
17. Reines D. Elongation factor-dependent transcript shortening by template-engaged RNA polymerase II. J Biol Chem 1992, 267:3795-3800.
18. Izban M.G., Luse D.S. The RNA polymerase II ternary complex cleaves the nascent transcript in a 3'----5' direction in the presence of elongation factor SII. Genes Dev 1992, 6:1342-1356.
19. Wang D., Hawley D.K. Identification of a 3'-->5' exonuclease activity associated with human RNA polymerase II. Proc Natl Acad Sci USA 1993, 90:843-847.
20. Erie D.A., Hajiseyedjavadi O., Young M.C., von Hippel P.H. Multiple RNA polymerase conformations and GreA: control of the fidelity of transcription. Science 1993, 262:867-873.
21. Thomas M.J., Platas A.A., Hawley D.K. Transcriptional fidelity and proofreading by RNA polymerase II. Cell 1998, 93:627-637.
22. Zenkin N., Yuzenkova Y., Severinov K. Transcript-assisted transcriptional proofreading. Science 2006, 313:518-520.
23. Gu W., Reines D. Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence. J Biol Chem 1995, 270:30441-30447.
24. Sydow J.F., Brueckner F., Cheung A.C., Damsma G.E., Dengl S., Lehmann E., Vassylyev D., Cramer P. Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Mol Cell 2009, 34:710-721.
25. Morin P.E., Awrey D.E., Edwards A.M., Arrowsmith C.H. Elongation factor TFIIS contains three structural domains: solution structure of domain II. Proc Natl Acad Sci USA 1996, 93:10604-10608.
26. Agarwal K., Baek K.H., Jeon C.J., Miyamoto K., Ueno A., Yoon H.S. Stimulation of transcript elongation requires both the zinc finger and RNA polymerase II binding domains of human TFIIS. Biochemistry 1991, 30:7842-7851.
27. Nakanishi T., Shimoaraiso M., Kubo T., Natori S. Structure-function relationship of yeast S-II in terms of stimulation of RNA polymerase II, arrest relief, and suppression of 6-azauracil sensitivity. J Biol Chem 1995, 270:8991-8995.
28. Olmsted V.K., Awrey D.E., Koth C., Shan X., Morin P.E., Kazanis S., Edwards A.M., Arrowsmith C.H. Yeast transcript elongation factor (TFIIS), structure and function. I: NMR structural analysis of the minimal transcriptionally active region. J Biol Chem 1998, 273:22589-22594.
29. Kettenberger H., Armache K.J., Cramer P. Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage. Cell 2003, 114:347-357.
30. Kettenberger H., Armache K.J., Cramer P. Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol Cell 2004, 16:955-965.
31. Wang D., Bushnell D.A., Westover K.D., Kaplan C.D., Kornberg R.D. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 2006, 127:941-954.
32. Vassylyev D.G., Vassylyeva M.N., Zhang J., Palangat M., Artsimovitch I., Landick R. Structural basis for substrate loading in bacterial RNA polymerase. Nature 2007, 448:163-168.
33. Borukhov S., Sagitov V., Goldfarb A. Transcript cleavage factors from E. coli. Cell 1993, 72:459-466.
34. Hogan B.P., Hartsch T., Erie D.A. Transcript cleavage by Thermus thermophilus RNA polymerase. Effects of GreA and anti-GreA factors. J Biol Chem 2002, 277:967-975.
35. Laptenko O., Kim S.S., Lee J., Starodubtseva M., Cava F., Berenguer J., Kong X.P., Borukhov S. pH-dependent conformational switch activates the inhibitor of transcription elongation. EMBO J 2006, 25:2131-2141.
36. Symersky J., Perederina A., Vassylyeva M.N., Svetlov V., Artsimovitch I., Vassylyev D.G. Regulation through the RNA polymerase secondary channel. Structural and functional variability of the coiled-coil transcription factors. J Biol Chem 2006, 281:1309-1312.
37. Stebbins C.E., Borukhov S., Orlova M., Polyakov A., Goldfarb A., Darst S.A. Crystal structure of the GreA transcript cleavage factor from Escherichia coli. Nature 1995, 373:636-640.
38. Lamour V., Hogan B.P., Erie D.A., Darst S.A. Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavage. J Mol Biol 2006, 356:179-188.
39. Vassylyeva M.N., Svetlov V., Dearborn A.D., Klyuyev S., Artsimovitch I., Vassylyev D.G. The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors. EMBO Rep 2007, 8:1038-1043.
40. Tuske S., Sarafianos S.G., Wang X., Hudson B., Sineva E., Mukhopadhyay J., Birktoft J.J., Leroy O., Ismail S., Clark A.D., et al. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 2005, 122:541-552.
41. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6Å resolution. Nature 2002, 417:712-719.
42. Tan L., Wiesler S., Trzaska D., Carney H.C., Weinzierl R.O. Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol 2008, 7:40.
43. Epshtein V., Mustaev A., Markovtsov V., Bereshchenko O., Nikiforov V., Goldfarb A. Swing-gate model of nucleotide entry into the RNA polymerase active center. Mol Cell 2002, 10:623-634.
44. Bar-Nahum G., Epshtein V., Ruckenstein A.E., Rafikov R., Mustaev A., Nudler E. A ratchet mechanism of transcription elongation and its control. Cell 2005, 120:183-193.
45. Tagami S., Sekine S.I., Yokoyama S. A novel conformation of RNA polymerase sheds light on the mechanism of transcription. Transcription 2011, 2:162-167.
46. Tagami S., Sekine S., Kumarevel T., Yamamoto M., Yokoyama S. Crystallization and preliminary X-ray crystallographic analysis of Thermus thermophilus transcription elongation complex bound to Gfh1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010, 66:64-68.
47. Platt T. Transcription termination and the regulation of gene expression. Annu Rev Biochem 1986, 55:339-372.
48. Roghanian M., Yuzenkova Y., Zenkin N. Controlled interplay between trigger loop and Gre factor in the RNA polymerase active centre. Nucleic Acids Res 2011, 39:4352-4359.
49. Brueckner F., Cramer P. Structural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation. Nat Struct Mol Biol 2008, 15:811-818.
50. Vassylyev D.G., Svetlov V., Vassylyeva M.N., Perederina A., Igarashi N., Matsugaki N., Wakatsuki S., Artsimovitch I. Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol 2005, 12:1086-1093.
51. Temiakov D., Zenkin N., Vassylyeva M.N., Perederina A., Tahirov T.H., Kashkina E., Savkina M., Zorov S., Nikiforov V., Igarashi N., et al. Structural basis of transcription inhibition by antibiotic streptolydigin. Mol Cell 2005, 19:655-666.
52. Opalka N., Chlenov M., Chacon P., Rice W.J., Wriggers W., Darst S.A. Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell 2003, 114:335-345.
53. Parvin J.D., Sharp P.A. DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 1993, 73:533-540.
54. Thomm M. Archaeal transcription factors and their role in transcription initiation. FEMS Microbiol Rev 1996, 18:159-171.
55. Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D. Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science 2004, 303:983-988.
56. Kostrewa D., Zeller M.E., Armache K.J., Seizl M., Leike K., Thomm M., Cramer P. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 2009, 462:323-330.
57. Liu X., Bushnell D.A., Wang D., Calero G., Kornberg R.D. Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Science 2010, 327:206-209.
58. Murakami K.S., Masuda S., Darst S.A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4Å resolution. Science 2002, 296:1280-1284.