924 Nucleic Acids Research, 2011, Vol. 39, No. 3 existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions. Proc. Natl Acad. Sci. USA, 91, 7573–7577. 10. Gardella,T., Moyle,H. and Susskind,M.M. (1989) A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter speciﬁcity. J. Mol. Biol., 206, 579–590. 11. Keener,J. and Nomura,M. (1993) Dominant lethal phenotype of a mutation in the 35 recognition region of Escherichia coli sigma 70. Proc. Natl Acad. Sci. USA, 90, 1751–1755. 12. 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. 13. Marr,M.T. and Roberts,J.W. (1997) Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science, 276, 1258–1260. 14. Siegele,D.A., Hu,J.C., Walter,W.A. and Gross,C.A. (1989) Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase. J. Mol. Biol., 206, 591–603. 15. Zuber,P., Healy,J., Carter,H.L. 3rd, Cutting,S., Moran,C.P. Jr and Losick,R. (1989) Mutation changing the speciﬁcity of an RNA polymerase sigma factor. J. Mol. Biol., 206, 605–614. 16. Chang,B.Y., Shyu,Y.T. and Doi,R.H. (1992) The interaction between Bacillus subtilis sigma-A (sigma A) factor and RNA polymerase with promoters. Biochimie, 74, 601–612. 17. Chen,Y.F. and Helmann,J.D. (1995) The Bacillus subtilis ﬂagellar regulatory protein sigma D: overproduction, domain analysis and DNA-binding properties. J. Mol. Biol., 249, 743–753. 18. Kudo,T. and Doi,R.H. (1981) Free sigma factor of Escherichia coli RNA polymerase can bind to DNA. J. Biol. Chem., 256, 9778–9781. 19. Kudo,T., Jaffe,D. and Doi,R.H. (1981) Free sigma subunit of Bacillus subtilis RNA polymerase binds to DNA. Mol. Gen. Genet., 181, 63–68. 20. Ramesh,U. and Meares,C.F. (1989) Footprint of the sigma protein. Biochem. Biophys. Res. Commun., 160, 121–125. 21. Wellman,A. and Meares,C.F. (1991) Footprint of the sigma protein: a re-examination. Biochem. Biophys. Res. Commun., 177, 140–144. 22. Dombroski,A.J., Walter,W.A. and Gross,C.A. (1993) Amino-terminal amino acids modulate sigma-factor DNA-binding activity. Genes Dev., 7, 2446–2455. 23. Dombroski,A.J., Walter,W.A., Record,M.T. Jr, Siegele,D.A. and Gross,C.A. (1992) Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit speciﬁcity of binding to promoter DNA. Cell, 70, 501–512. 24. Camarero,J.A., Shekhtman,A., Campbell,E.A., Chlenov,M., Gruber,T.M., Bryant,D.A., Darst,S.A., Cowburn,D. and Muir,T.W. (2002) Autoregulation of a bacterial sigma factor explored by using segmental isotopic labeling and NMR. Proc. Natl Acad. Sci. USA, 99, 8536–8541. 25. Schwartz,E.C., Shekhtman,A., Dutta,K., Pratt,M.R., Cowburn,D., Darst,S. and Muir,T.W. (2008) A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. Chem. Biol., 15, 1091–1103. 26. Borukhov,S. and Severinov,K. (2002) Role of the RNA polymerase sigma subunit in transcription initiation. Res. Microbiol., 153, 557–562. 27. Kuznedelov,K., Minakhin,L., Niedziela-Majka,A., Dove,S.L., Rogulja,D., Nickels,B.E., Hochschild,A., Heyduk,T. and Severinov,K. (2002) A role for interaction of the RNA polymerase ﬂap domain with the sigma subunit in promoter recognition. Science, 295, 855–857. 28. Zhang,G., Campbell,E.A., Minakhin,L., Richter,C., Severinov,K. and Darst,S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A˚ resolution. Cell, 98, 811–824. 29. Young,B.A., Anthony,L.C., Gruber,T.M., Arthur,T.M., Heyduk,E., Lu,C.Z., Sharp,M.M., Heyduk,T., Burgess,R.R. and Gross,C.A. (2001) A coiled-coil from the RNA polymerase beta’ subunit allosterically induces selective nontemplate strand binding by sigma(70). Cell, 105, 935–944. 30. Dombroski,A.J., Johnson,B.D., Lonetto,M. and Gross,C.A. (1996) The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing. Proc. Natl Acad. Sci. USA, 93, 8858–8862. 31. Harley,C.B. and Reynolds,R.P. (1987) Analysis of E. coli promoter sequences. Nucleic Acids Res., 15, 2343–2361. 32. Hawley,D.K. and McClure,W.R. (1983) Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res., 11, 2237–2255. 33. Helmann,J.D. (1995) Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res., 23, 2351–2360. 34. Aoyama,T., Takanami,M., Ohtsuka,E., Taniyama,Y., Marumoto,R., Sato,H. and Ikehara,M. (1983) Essential structure of E. coli promoter: effect of spacer length between the two consensus sequences on promoter function. Nucleic Acids Res., 11, 5855–5864. 35. Jaurin,B., Grundstrom,T., Edlund,T. and Normark,S. (1981) The E. coli beta-lactamase attenuator mediates growth rate-dependent regulation. Nature, 290, 221–225. 36. Russell,D.R. and Bennett,G.N. (1982) Construction and analysis of in vivo activity of E. coli promoter hybrids and promoter mutants that alter the 35 to 10 spacing. Gene, 20, 231–243. 37. Hidalgo,E. and Demple,B. (1997) Spacing of promoter elements regulates the basal expression of the soxS gene and converts SoxR from a transcriptional activator into a repressor. EMBO J., 16, 1056–1065. 38. Mandecki,W. and Reznikoff,W.S. (1982) A lac promoter with a changed distance between 10 and 35 regions. Nucleic Acids Res., 10, 903–912. 39. Parkhill,J. and Brown,N.L. (1990) Site-speciﬁc insertion and deletion mutants in the mer promoter-operator region of Tn501; the nineteen base-pair spacer is essential for normal induction of the promoter by MerR. Nucleic Acids Res., 18, 5157–5162. 40. Auble,D.T. and deHaseth,P.L. (1988) Promoter recognition by Escherichia coli RNA polymerase. Inﬂuence of DNA structure in the spacer separating the 10 and 35 regions. J. Mol. Biol., 202, 471–482. 41. Ayers,D.G., Auble,D.T. and deHaseth,P.L. (1989) Promoter recognition by Escherichia coli RNA polymerase. Role of the spacer DNA in functional complex formation. J. Mol. Biol., 207, 749–756. 42. McKane,M. and Gussin,G.N. (2000) Changes in the 17 bp spacer in the PR promoter of bacteriophage lambda affect steps in open complex formation that precede DNA strand separation. J. Mol. Biol., 299, 337–349. 43. Mulligan,M.E., Brosius,J. and McClure,W.R. (1985) Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter. J. Biol. Chem., 260, 3529–3538. 44. Stefano,J.E. and Gralla,J.D. (1982) Spacer mutations in the lac ps promoter. Proc. Natl Acad. Sci. USA, 79, 1069–1072. 45. Travers,A.A. (1987) Structure and function of E. coli promoter DNA. CRC Crit. Rev. Biochem., 22, 181–219. 46. Warne,S.E. and deHaseth,P.L. (1993) Promoter recognition by Escherichia coli RNA polymerase. Effects of single base pair deletions and insertions in the spacer DNA separating the 10 and 35 regions are dependent on spacer DNA sequence. Biochemistry, 32, 6134–6140. 47. Chang,B.Y. and Doi,R.H. (1990) Overproduction, puriﬁcation, and characterization of Bacillus subtilis RNA polymerase sigma A factor. J. Bacteriol., 172, 3257–3263. 48. Chang,B.Y. and Doi,R.H. (1993) Conformational properties of Bacillus subtilis RNA polymerase sigma A factor during transcription initiation. Biochem. J., 294, 43–47. 49. Hofer,B., Muller,D. and Koster,H. (1985) The pathway of E. coli RNA polymerase–promoter complex formation as visualized by footprinting. Nucleic Acids Res., 13, 5995–6013. 50. Schickor,P., Metzger,W., Werel,W., Lederer,H. and Heumann,H. (1990) Topography of intermediates in transcription initiation of E. coli. EMBO J., 9, 2215–2220. 51. Huang,X., Lopez de Saro,F.J. and Helmann,J.D. (1997) Sigma factor mutations affecting the sequence-selective interaction of