RNA polymerase structure and function at lac operon

Comptes Rendus - Biologies

Volumn 328, Issue 6 SPEC. ISS., 2005, Pages 576-587

  Borukhov, Sergei ^a   Lee, Jookyung ^a  

^a UMDNJ School of Osteopathic Medicine   (United States)

Author keywords

CAP; Lac operon; Lac repressor; RNA polymerase; Transcription initiation

Indexed keywords

CYCLIC AMP BINDING PROTEIN; RNA POLYMERASE;

ENZYME ACTIVITY;

CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME STRUCTURE; ESCHERICHIA COLI; GENE EXPRESSION; GENE SEQUENCE; GENETIC TRANSCRIPTION; LACTOSE OPERON; MOLECULAR INTERACTION; MOLECULAR MECHANICS; NONHUMAN; PROTEIN FUNCTION; REGULATORY MECHANISM; REVIEW; RNA SYNTHESIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 20444414890     PISSN: 16310691     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.crvi.2005.03.007     Document Type: Short Survey

References (58)

1. F. Jacob J. Monod Genetic regulatory mechanisms in the synthesis of proteins J. Mol. Biol. 3 1961 318-356
2. J.H. Miller W.S. Reznikoff (Eds.) The Operon 1978 Cold Spring Harbor Laboratory Press Cold Spring Harbor
3. G. Zhang E.A. Campbell L. Minakhin C. Richter K. Severinov S.A. Darst Crystal structure of Thermus aquaticus core RNA polymerase at 3.3-Å resolution Cell 98 1999 811-824
4. D.G. Vassylyev S. Sekine O. Laptenko J. Lee M.N. Vassylyeva S. Borukhov S. Yokoyama Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6-Å resolution Nature 417 2002 712-719
5. K.S. Murakami S. Masuda S.A. Darst Structural basis of transcription initiation: RNA polymerase holoenzyme at 4-Å resolution Science 296 2002 1280-1284
6. P. Cramer D.A. Bushnell R.D. Kornberg Structural basis of transcription: RNA polymerase II at 2.8-angstrom resolution Science 292 2001 1863-1876
7. A.L. Gnatt P. Cramer J. Fu D.A. Bushnell R.D. Kornberg Structural basis of transcription: An RNA polymerase II elongation complex at 3.3-Å resolution Science 292 2001 1876-1882
8. K.S. Murakami S. Masuda E.A. Campbell O. Muzzin S.A. Darst Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex Science 296 2002 1285-1290
9. E.A. Campbell O. Muzzin M. Chlenov J.L. Sun C.A. Olson O. Weinman M.L. Trester-Zedlitz S.A. Darst Structure of the bacterial RNA polymerase promoter specificity sigma subunit Mol. Cell 9 2002 527-539
10. B. Benoff H. Yang C.L. Lawson G. Parkinson J. Liu E. Blatter Y.W. Ebright H.M. Berman R.H. Ebright Structural basis of transcription activation: The CAP-alpha CTD-DNA complex Science 297 2002 1562-1566
11. D. Jain B.E. Nickels L. Sun A. Hochschild S.A. Darst Structure of a ternary transcription activation complex Mol. Cell 13 2004 45-53
12. D. Sweetser M. Nonet R.A. Young Prokaryotic and eukaryotic RNA polymerase have homologous core subunits Proc. Natl Acad. Sci. USA 84 1987 1192-1196
13. R.H. Ebright RNA Polymerase: Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II J. Mol. Biol. 304 2000 687-698
14. S.A. Darst Bacterial RNA polymerase Curr. Opin. Struct. Biol. 11 2001 155-162
15. R.R. Burgess A.A. Travers J.J. Dunn E.K.F. Bautz Factor stimulating transcription by RNA polymerase Nature 221 1969 43-44
16. C.A. Gross M.A. Lonetto R. Losick Sigma factors in: K. Yamamoto S. McKnight (Eds.) Control of Transcription 1992 Cold Spring Harbor Press Cold Spring Harbor 129-176
17. C.A. Gross C. Chan A. Dombrowski T. Gruber M. Sharp J. Tupy B. Young The functional and regulatory roles of sigma factors in transcription Cold Spring Harb. Symp. Quant. Biol. 63 1998 141-155
18. 70), promoter and the kinetics of the steps of transcription initiation, in: F.C. Neidhart (Ed.), Escherichia coli and Salmonella typhimurium, second ed., in: Cellular and Molecular Biology, vol. 1, ACM Press, Washington, DC, pp. 792-820
19. P. von Hippel An integrated model of the transcription complex in elongation, termination, and editing Science 281 1998 660-665
20. M.L. Craig O.V. Tsodikov K.L. McQuade P.E.J. Schlax M.W. Capp R.M. Saecker M.T.J. Record DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA J. Mol. Biol. 283 1998 741-756
21. J. Mukhopadhyay A.N. Kapanidis V. Mekler E. Kortkhonjia Y.W. Ebright R.H. Ebright Cell 106 2001 453-463
22. G. Bar-Nahum E. Nudler Cell 106 2001 443-451
23. J.T. Wade K. Struhl Association of RNA polymerase with transcribed regions in Escherichia coli Proc. Natl Acad. Sci. USA 101 2004 17777-17782
24. W.R. McClure Annu. Rev. Biochem. 54 1985 171-204
25. C.B. Hareley R.P. Reynolds Analysis of E. coli promoter sequences Nucleic Acids Res. 15 1987 2343-2361
26. S. Lisser H. Margalit Compilation of E. coli mRNA promoter sequences Nucleic Acids Res. 21 1993 1507-1516
27. P.L. de Haseth J.D. Helmann Open complex formation by Escherichia coli RNA polymerase: The mechanism of polymerase-induced strand separation of double helical DNA Mol. Microbiol. 16 1995 817-824
28. J. Bown K. Barne S. Minchin S. Busby Nucleic Acids Mol. Biol. 11 1997 41-52
29. R. Lutz T. Lozinski T. Ellinger H. Bujard Dissecting the functional program of Escherichia coli promoters: The combined mode of action of lac repressor and AraC activator Nucleic Acids Res. 29 2001 3873-3881
30. W. Ross K.K. Gosink J. Salomon K. Igarashi C. Zou A. Ishihama K. Severinov R.L. Gourse A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase Science 262 1993 1407-1413
31. S.T. Estrem T. Gaal W. Ross R.L. Gourse Identification of an UP element consensus sequence for bacterial promoters Proc. Natl Acad. Sci. USA 95 1998 9761-9766
32. lac promoter hyperactive and cAMP receptor protein-independent Proc. Natl Acad. Sci. USA 101 2004 6911-6916
33. I.K. Pemberton G. Muskhelishvili A.A. Travers M. Buckle The G+C-rich discriminator region of the tyrT promoter antagonizes the formation of stable preinitiation complexes J. Mol. Biol. 299 2000 859-864
34. N.V. Vo L.M. Hsu C.M. Kane M.J. Chamberlin In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape Biochemistry 42 2003 3798-3811
35. M. Liu S. Garges S. Adhya lacP1 promoter with an extended -10 motif: Pleiotropic effects of cyclic AMP protein at different steps of transcription initiation J. Biol. Chem. 279 52 2004 54552-54557
36. J. Collado-Vides B. Magasanik J.D. Gralla Control site location and transcriptional egulation in Escherichia coli Microbiol. Rev. 55 1991 371-394
37. P.J. Schlax M.W. Capp M.T. Record Jr. Inhibition of transcription initiation by lac repressor J. Mol. Biol. 245 1995 331-350
38. S. Busby R. Ebright Transcription activation by catabolite activation protein (CAP) J. Mol. Biol. 293 1999 199-213
39. S.A Darst N. Opalka P. Chacon A. Polyakov C. Richter G. Zhang W. Wriggers Conformational flexibility of bacterial RNA polymerase Proc. Natl Acad. Sci. USA 99 2002 4296-4301
40. L. Minakhin S. Nechaev E.A. Campbell K. Severinov Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription J. Bacteriol. 183 2001 71-76
41. M.N. Vassylyeva J. Lee S.I. Sekine O. Laptenko S. Kuramitsu T. Shibata Y. Inoue S. Borukhov D.G. Vassylyev S. Yokoyama Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus Acta Crystallogr. D Biol. Crystallogr. 58 2002 1497-1500
42. K.D. Westover D.A Bushnell R.D. Kornberg Structural basis of transcription: Nucleotide selection by rotation in the RNA polymerase II active center Cell 119 2004 481-489
43. K. Severinov M. Kashlev E. Severinova I. Bass K. McWilliams E. Kutter V. Nikiforov L. Snyder A. Goldfarb A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc J. Biol. Chem. 269 1994 14254-14259
44. K. Severinov A. Mustaev E. Severinova I. Bass M. Kashlev R. Landick V. Nikiforov A. Goldfarb S.A. Darst Assembly of functional Escherichia coli RNA polymerase containing beta subunit fragments Proc. Natl Acad. Sci. USA 92 1995 4591-4595
45. S. Borukhov E. Nudler RNA polymerase holoenzyme: Structure, function and biological implications Curr. Opin. Microbiol. 6 2003 93-100
46. O. Laptenko J. Lee I. Lomakin S. Borukhov Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase EMBO J. 22 2003 6322-6334
47. N. Zakharova I. Bass E. Arsenieva V. Nikiforov K. Severinov Mutations in and monoclonal antibody binding to evolutionary hypervariable region of Escherichia coli RNA polymerase beta′ subunit inhibit transcript cleavage and transcript elongation J. Biol. Chem. 273 1998 24912-24920
48. S. Borukhov K. Severinov Role of the RNA polymerase sigma subunit in transcription initiation Res. Microbiol. 153 2002 557-562
49. K.S. Murakami S.A. Darst Bacterial RNA polymerases: The wholo story Curr. Opin. Struct. Biol. 13 2003 31-39
50. 70 subunit of Escherichia coli RNA polymerase modulates the formation of stable polymerase/promoter complexes J. Mol. Biol. 309 2001 561-572
51. M.M. Sharp C.L. Chan C.Z. Lu M.T. Marr S. Nechaev E.W. Merritt K. Severinov J.W. Roberts C.A. Gross The sigma interface with core RNA polymerase is extensive, functionally specialized, and conserved Genes Dev. 13 1999 3015-3026
52. T.M. Gruber D. Markov M.M. Sharp B.A. Young C.Z. Lu H.J. Zhong I. Artsimovitch K.M. Geszvain T.M. Arthur R.R. Burgess R. Landick K. Severinov C.A. Gross Binding of the initiation factor sigma(70) to core RNA polymerase is a multistep process Mol. Cell. 8 2001 21-31
53. K. Kuznedelov L. Minakhin A. Niedziela-Majka S.L. Dove D. Rogulja B.E. Nickels A. Hochschild T. Heyduk K. Severinov A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition Science 295 2002 855-857
54. H. Chen H. Tang R.H. Ebright Functional interaction between RNA polymerase alpha subunit C-terminal domain and sigma70 in UP-element- and activator-dependent transcription Mol. Cell. 11 2003 1621-1633
55. C.L. Lawson D. Swigon K.S. Murakami S.A. Darst H.M. Berman R.E. Ebright Catabolite activator protein: DNA binding and transcription activation Curr. Opin. Struct. Biol. 14 2004 10-20
56. C.A. Gross C. Chan A. Dombroski T. Gruber M. Sharp J. Tupy B. Young The functional and regulatory roles of sigma factors in transcription Cold Spring Harb. Symp. Quant. Biol. 63 1998 141-155
57. 70 subunit is responsible for the recognition of the 'extended - 10' motif at promoters EMBO J. 16 1997 4034-4040
58. H.M. Lim H.J. Lee S. Roy S. Adhya A 'master' in base unpairing during isomerization of a promoter upon RNA polymerase binding Proc. Natl Acad. Sci. USA 98 2001 14849-14852