A new basal promoter element recognized by RNA polymerase core enzyme

EMBO Journal

Volumn 30, Issue 18, 2011, Pages 3766-3775

  Yuzenkova, Yulia ^a,c   Tadigotla, Vasisht R ^b   Severinov, Konstantin ^c,d,e   Zenkin, Nikolay ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b Boston University   (United States)

^c RUTGERS UNIVERSITY   (United States)

^d The State University of New Jersey   (United States)

^e INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

Author keywords

promoter; RNA polymerase core; sigma subunit; transcription pausing; zipper domain

Indexed keywords

DNA; RNA POLYMERASE;

ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENE INTERACTION; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION;

BINDING SITES; DNA-DIRECTED RNA POLYMERASES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; THERMUS;

BACTERIA (MICROORGANISMS);

EID: 80052782406     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/emboj.2011.252     Document Type: Article

References (34)

1. Artsimovitch I (2008) Post-initiation control by the initiation factor sigma. Mol Microbiol 68: 1-3 (Pubitemid 351363779)
2. Artsimovitch I, Svetlov V, Anthony L, Burgess RR, Landick R (2000) RNA polymerases from Bacillus subtilis and Escherichia coli differ in recognition of regulatory signals in vitro. J Bacteriol 182: 6027-6035
3. Barne KA, Bown JA, Busby SJ, Minchin SD (1997) Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. EMBO J 16: 4034-4040 (Pubitemid 27281018)
4. Borukhov S, Goldfarb A (1993) Recombinant Escherichia coli RNA polymerase: purification of individually overexpressed subunits and in vitro assembly. Protein Expr Purif 4: 503-511 (Pubitemid 2007168)
5. Borukhov S, Severinov K (2002) Role of the RNA polymerase sigma subunit in transcription initiation. Res Microbiol 153: 557-562 (Pubitemid 35223308)
6. Brodolin K, Zenkin N, Mustaev A, Mamaeva D, Heumann H (2004) The sigma 70 subunit of RNA polymerase induces lacUV5 promoter-proximal pausing of transcription. Nat Struct Mol Biol 11 : 551-557 (Pubitemid 38691923)
7. Burgess RR, Anthony L (2001) How sigma docks to RNA polymer-ase and what sigma does. Curr Opin Microbiol 4: 126-131 (Pubitemid 32294412)
8. 0 subunit of RNA poly-merase that blocks growth of bacteriophage P2. J Bacteriol 178: 6991-6993 (Pubitemid 26404979)
9. Deighan P, Pukhrambam C, Nickels BE, Hochschild A (2011) Initial transcribed region sequences influence the composition and functional properties of the bacterial elongation complex. Genes Dev 25: 77-88
10. Ederth J, Artsimovitch I, Isaksson LA, Landick R (2002) The downstream DNA jaw of bacterial RNA polymerase facilitates both transcriptional initiation and pausing. J Biol Chem 277: 37456-37463
11. Estrem ST, Ross W, Gaal T, Chen ZW, Niu W, Ebright RH, Gourse RL (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev 13: 2134-2147 (Pubitemid 29407353)
12. Hatoum A, Roberts J (2008) Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation. Mol Microbiol 68: 17-28 (Pubitemid 351363781)
13. Haugen SP, Berkmen MB, Ross W, Gaal T, Ward C, Gourse RL (2006) rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase. Cell 125: 1069-1082 (Pubitemid 43866199)
14. Helmann JD, deHaseth PL (1999) Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners. Biochemistry 38: 5959-5967 (Pubitemid 29230211)
15. Hirata A, Murakami KS (2009) Archaeal RNA polymerase. Curr Opin Struct Biol 19: 724-731
16. Hook-Barnard IG, Hinton DM (2009) The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase. Proc Natl Acad Sci USA 106: 737-742
17. Kashlev M, Nudler E, Severinov K, Borukhov S, Komissarova N, Goldfarb A (1996) Histidine-tagged RNA polymerase of Escherichia coli and transcription in solid phase. Methods Enzymol 274: 326-334 (Pubitemid 26353088)
18. Kulbachinskiy A, Bass I, Bogdanova E, Goldfarb A, Nikiforov V (2004) Cold sensitivity of thermophilic and mesophilic RNA polymerases. J Bacteriol 186: 7818-7820 (Pubitemid 39463751)
19. Kuznedelov K, Korzheva N, Mustaev A, Severinov K (2002a) Structure-based analysis of RNA polymerase function: the largest subunit's rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA-DNA hybrid length. EMBO J 21: 1369-1378 (Pubitemid 34246515)
20. Kuznedelov K, Minakhin L, Niedziela-Majka A, Dove SL, Rogulja D, Nickels BE, Hochschild A, Heyduk T, Severinov K (2002b) A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295: 855-857 (Pubitemid 34118366)
21. Kuznedelov K, Minakhin L, Severinov K (2003) Preparation and characterization of recombinant Thermus aquaticus RNA polymerase. Methods Enzymol 370: 94-108 (Pubitemid 37542772)
22. Liu M, Tolstorukov M, Zhurkin V, Garges S, Adhya S (2004) A mutant spacer sequence between-35 and-10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent. Proc Natl Acad Sci USA 101: 6911-6916 (Pubitemid 38596417)
23. Mooney RA, Landick R (2003) Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev 17: 2839-2851 (Pubitemid 37463292)
24. Murakami KS, Darst SA (2003) Bacterial RNA polymerases: the wholo story. Curr Opin Struct Biol 13: 31-39 (Pubitemid 36170252)
25. Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA (2002) Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296: 1285-1290 (Pubitemid 34522778)
26. Naryshkin N, Revyakin A, Kim Y, Mekler V, Ebright RH (2000) Structural organization of the RNA polymerase-promoter open complex. Cell 101: 601-611
27. Nechaev S, Geiduschek EP (2006) The role of an upstream promoter interaction in initiation of bacterial transcription. EMBO J 25: 1700-1709
28. Nickels BE, Mukhopadhyay J, Garrity SJ, Ebright RH, Hochschild A (2004) The sigma 70 subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter. Nat Struct Mol Biol 11: 544-550 (Pubitemid 38691922)
29. Polyakov A, Severinova E, Darst SA (1995) Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83: 365-373
30. Ring BZ, Yarnell WS, Roberts JW (1996) Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing. Cell 86: 485-493 (Pubitemid 26272088)
31. Schroeder LA, deHaseth PL (2005) Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases. J Biol Chem 280: 17422-17429 (Pubitemid 41389213)
32. Severinov K, Markov D, Severinova E, Nikiforov V, Landick R, Darst SA, Goldfarb A (1995) Streptolydigin-resistant mutants in an evolutionarily conserved region of the beta' subunit of Escherichia coli RNA polymerase. J Biol Chem 270: 23926-23929
33. Wada T, Yamazaki T, Kyogoku Y (2000) The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus. J Biol Chem 275: 16057-16063 (Pubitemid 30366913)
34. Zenkin N, Naryshkina T, Kuznedelov K, Severinov K (2006) The mechanism of DNA replication primer synthesis by RNA polymerase. Nature 439: 617-620 (Pubitemid 43185388)