Escherichia coli promoter opening and -10 recognition: Mutational analysis of σ70

EMBO Journal

Volumn 19, Issue 5, 2000, Pages 1130-1137

  Fenton, M S ^a   Lee, S J ^a   Gralla, J D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Escherichia coli; Fork junction; Promoter; 70

Indexed keywords

DOUBLE STRANDED DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; DNA BINDING; ESCHERICHIA COLI; GENE MUTATION; GENETIC TRANSCRIPTION; HALF LIFE TIME; NONHUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; DNA, BACTERIAL; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); SIGMA FACTOR;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0034161515     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/19.5.1130     Document Type: Article

References (35)

1. Barne KA, Bown JA, Busby SJ and Minchin SD (1997) Region 2.5 of the Escherichia coli RNA polymerase σ70 subunit is responsible for the recognition of the ‘extended‐10’ motif at promoters. EMBO J, 16, 4034–4040.
2. Bown JA, Owens JT, Meares CF, Fujita N, Ishihama A, Busby SJ and Minchin SD (1999) Organization of open complexes at Escherichia coli promoters. Location of promoter DNA sites close to region 2.5 of the σ70 subunit of RNA polymerase. J Biol Chem, 274, 2263–2270.
3. Buckle M, Pemberton IK, Jacquet MA and Buc H (1999) The kinetics of sigma subunit directed promoter recognition by E.coli RNA polymerase. J Mol Biol, 285, 955–964.
4. Callaci S and Heyduk T (1998) Conformation and DNA binding properties of a single‐stranded DNA binding region of σ70 subunit from Escherichia coli RNA polymerase are modulated by an interaction with the core enzyme. Biochemistry, 37, 3312–3320.
5. Cheetham GM, Jeruzalmi D and Steitz TA (1999) Structural basis for initiation of transcription from an RNA polymerase–promoter complex. Nature, 399, 80–83.
6. Coleman JE and Oakley JL (1980) Physical chemical studies of the structure and function of DNA binding (helix‐destabilizing) proteins. CRC Crit Rev Biochem, 7, 247–289.
7. Colland F, Fujita N, Kotlarz D, Bown JA, Meares CF, Ishihama A and Kolb A (1999) Positioning of sigma (S), the stationary phase sigma factor, in Escherichia coli RNA polymerase–promoter open complexes. EMBO J, 18, 4049–4059.
8. Daniels D, Zuber P and Losick R (1990) Two amino acids in an RNA polymerase sigma factor involved in the recognition of adjacent base pairs in the −10 region of a cognate promoter. Proc Natl Acad Sci USA, 87, 8075–8079.
9. Guo Y and Gralla JD (1998) Promoter opening via a DNA fork junction binding activity. Proc Natl Acad Sci USA, 95, 11655–11660.
10. Guo Y, Wang L and Gralla JD (1999) A fork junction DNA–protein switch that controls promoter melting by the bacterial enhancer‐dependent sigma factor. EMBO J, 18, 3736–3745.
11. Hawley DK and McClure WR (1983) Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res, 11, 2237–2255.
12. Helmann JD and Chamberlin MJ (1988) Structure and function of bacterial sigma factors. Annu Rev Biochem, 57, 839–872.
13. Helmann JD and 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.
14. Huang X, Lopez de Saro FJ and Helmann JD (1997) σ factor mutations affecting the sequence‐selective interaction of RNA polymerase with −10 region single‐stranded DNA. Nucleic Acids Res, 25, 2603–2609.
15. Jones CH and Moran CP,Jr (1992) Mutant sigma factor blocks transition between promoter binding and initiation of transcription. Proc Natl Acad Sci USA, 89, 1958–1962.
16. Juang YL and Helmann JD (1994) A promoter melting region in the primary sigma factor of Bacillus subtilis. Identification of functionally important aromatic amino acids. J Mol Biol, 235, 1470–1488.
17. Kainz M and Roberts J (1992) Structure of transcription elongation complexes in vivo. Science, 255, 838–841.
18. Keilty S and Rosenberg M (1987) Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J Biol Chem, 262, 6389–6395.
19. Kenney TJ, York K, Youngman P and Moran CP,Jr (1989) Genetic evidence that RNA polymerase associated with σA factor uses a sporulation‐specific promoter in Bacillus subtilis. Proc Natl Acad Sci USA, 86, 9109–9113.
20. Kirkegaard K, Buc H, Spassky A and Wang JC (1983) Mapping of single‐stranded regions in duplex DNA at the sequence level: single‐strand‐specific cytosine methylation in RNA polymerase–promoter complexes. Proc Natl Acad Sci USA, 80, 2544–2548.
21. Lau AY, Scharer OD, Samson L, Verdine GL and Ellenberger T (1998) Crystal structure of a human alkylbase‐DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Cell, 95, 249–258.
22. Malhotra A, Severinova E and Darst SA (1996) Crystal structure of a σ70 subunit fragment from E.coli RNA polymerase. Cell, 87, 127–136.
23. Marr MT and Roberts JW (1997) Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science, 276, 1258–1260.
24. Polyakov A, Severinova E and Darst SA (1995) Three‐dimensional structure of E.coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell, 83, 365–373.
25. Roberts CW and Roberts JW (1996) Base‐specific recognition of the nontemplate strand of promoter DNA by E.coli RNA polymerase. Cell, 86, 495–501.
26. Roe JH, Burgess RR and Record MT,Jr (1985) Temperature dependence of the rate constants of the Escherichia coli RNA polymerase–λ PR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening. J Mol Biol, 184, 441–453.
27. Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K and Gourse RL (1993) A third recognition element in bacterial promoters: DNA binding by the α subunit of RNA polymerase. Science, 262, 1407–1413.
28. Sasse‐Dwight S and Gralla JD (1989) KMnO 4 as a probe for lac promoter DNA melting and mechanism in vivo. J Biol Chem, 264, 8074–8081.
29. Sharp MM, Chan CL, Lu CZ, Marr MT, Nechaev S, Merritt EW, Severinov K, Roberts JW and Gross CA (1999) The interface of sigma with core RNA polymerase is extensive, conserved and functionally specialized. Genes Dev, 13, 3015–3026.
30. Siegele DA, Hu JC, Walter WA and Gross CA (1989) Altered promoter recognition by mutant forms of the σ70 subunit of Escherichia coli RNA polymerase. J Mol Biol, 206, 591–603.
31. Stefano JE, Ackerson JW and Gralla JD (1980) Alterations in two conserved regions of promoter sequence lead to altered rates of polymerase binding and levels of gene expression. Nucleic Acids Res, 8, 2709–2723.
32. Tatti KM and Moran CP,Jr (1995) σE changed to σB specificity by amino acid substitutions in its −10 binding region. J Bacteriol, 177, 6506–6509.
33. Waldburger C, Gardella T, Wong R and Susskind MM (1990) Changes in conserved region 2 of Escherichia coli σ70 affecting promoter recognition. J Mol Biol, 215, 267–276.
34. Wilson C and Dombroski AJ (1997) Region 1 of σ70 is required for efficient isomerization and initiation of transcription by Escherichia coli RNA polymerase. J Mol Biol, 267, 60–74.
35. Zuber P, Healy J, Carter HL,III, Cutting S, Moran CP,Jr and Losick R (1989) Mutation changing the specificity of an RNA polymerase sigma factor. J Mol Biol, 206, 605–614.