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Escherichia coli σ70 senses sequence and conformation of the promoter spacer region

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Singh, Shivani S., Typas, Athanasios, Hengge, Regine and Grainger, David C.. (2011) Escherichia coli σ70 senses sequence and conformation of the promoter spacer region. Nucleic Acids Research, Vol.39 (No.12). pp. 5109-5118. ISSN 1362-4962

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Official URL: http://dx.doi.org/10.1093/nar/gkr080

Abstract

In bacteria, promoter identification by RNA polymerase is mediated by a dissociable p factor. The housekeeping σ70 factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the ‘-10’ and ‘-35’ hexamers. These elements are separated by ‘spacer’ DNA, the sequence of which is generally considered unimportant. Here, we use a combination of bioinformatics, genetics and biochemistry to show that σ70 can sense the sequence and conformation of the promoter spacer region. Our data illustrate how alterations in spacer region sequence can increase promoter activity. This stimulatory effect requires σ70 side chain R451, which is located in close proximity to the non-template strand at promoter position -18. Conversely, R451 is not required to mediate transcriptional stimulation by improvement of the -10 element. Mutation of σ70 residue R451, which is highly conserved, results in reduced growth rate, consistent with a central role in promoter recognition.

Item Type:	Journal Article
Subjects:	Q Science > QR Microbiology
Divisions:	Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH):	Escherichia coli -- Genetics, RNA polymerases, Promoters (Genetics)
Journal or Publication Title:	Nucleic Acids Research
Publisher:	Oxford University Press
ISSN:	1362-4962
Date:	11 March 2011
Volume:	Vol.39
Number:	No.12
Page Range:	pp. 5109-5118
Identification Number:	10.1093/nar/gkr080
Status:	Peer Reviewed
Access rights to Published version:	Open Access
Funder:	Wellcome Trust (London, England), Deutsche Forschungsgemeinschaft (DFG)
Grant number:	He1556/12-1 (DFG)
References:	1. Burgess,R.R., Travers,A.A., Dunn,J.J. and Bautz,E.K. (1969) Factor stimulating transcription by RNA polymerase. Nature, 221, 43–46. 2. Gruber,T.M. and Gross,C.A. (2003) Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol., 57, 441–466. 3. Paget,M.S. and Helmann,J.D. (2003) The sigma70 family of sigma factors. Genome Biol., 4, 203. 4. Hsu,L.M. (2002) Promoter clearance and escape in prokaryotes. Biochim. Biophys. Acta., 1577, 191–207. 5. Barne,K.A., Bown,J.A., Busby,S.J. and Minchin,S.D. (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. 6. Pribnow,D. (1975) Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc. Natl Acad. Sci. USA, 72, 784–788. 7. Pribnow,D. (1975) Bacteriophage T7 early promoters: nucleotide sequences of two RNA polymerase binding sites. J. Mol. Biol., 99, 419–443. 8. Maniatis,T., Ptashne,M., Backman,K., Kield,D., Flashman,S., Jeffrey,A. and Maurer,R. (1975) Recognition sequences of repressor and polymerase in the operators of bacteriophage lambda. Cell, 5, 109–113. 9. Hawley,D.K. and McClure,W.R. (1983) Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res., 11, 2237–2255. 10. Mitchell,J.E., Zheng,D., Busby,S.J. and Minchin,S.D. (2003) Identification and analysis of ‘extended -10’ promoters in Escherichia coli. Nucleic Acids Res., 31, 4689–4695. 11. Gross,C.A., Chan,C., Dombroski,A., Gruber,T., Sharp,M., Tupy,J. and Young,B. (1998) The functional and regulatory roles of sigma factors in transcription. Cold Spring Harbor Symp. Quant. Biol., 63, 141–155. 12. Murakami,K.S., Masuda,S., Campbell,E.A., Muzzin,O. and Darst,S.A. (2002) Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science, 17, 1285–1290. 13. Campbell,E.A., Muzzin,O., Chlenov,M., Sun,J.L., Olson,C.A., Weinman,O., Trester-Zedlitz,M.L. and Darst,S.A. (2002) Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol. Cell, 9, 527–539. 14. Siebenlist,U., Simpson,R.B. and Gilbert,W. (1980) E. coli RNA polymerase interacts homologously with two different promoters. Cell, 20, 269–281. 15. Siebenlist,U. and Gilbert,W. (1980) Contacts between Escherichia coli RNA polymerase and an early promoter of phage T7. Proc. Natl Acad. Sci. USA, 77, 122–126. 16. Rosenberg,M. and Court,D. (1979) Regulatory sequences involved in the promotion and termination of RNA transcription. Annu. Rev. Genet., 13, 319–353. 17. 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. 18. Liu,M., Tolstorukov,M., Zhurkin,V., Garges,S. and Adhya,S. (2002) 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. 19. Hook-Barnard,I.G. and Hinton,D.M. The promoter spacer influences transcription initiation via sigma70 region 1.1 of Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA, 106, 737–742. 20. Page,L., Griffiths,L. and Cole,J.A. (1990) Different physiological roles of two independent pathways for nitrite reduction to ammonia by enteric bacteria. Arch. Microbiol., 154, 349–354. 21. Casadaban,M.J. (1976) Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage lambda and Mu. J. Mol. Biol., 5, 541–555. 22. Conter,A., Menchon,C. and Gutierrez,C. (1997) Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12. J. Mol. Biol., 273, 75–83. 23. Kolb,A., Kotlarz,D., Kusano,S. and Ishihama,A. (1995) Selectivity of the Escherichia coli RNA polymerase Esigma38 for overlapping promoters and ability to support CRP activation. Nucleic Acids Res., 23, 819–826. 24. Lodge,J., Fear,J., Busby,S., Gunasekaran,P. and Kamini,N.R. (1992) Broad host range plasmids carrying the Escherichia coli lactose and galactose operons. FEMS Microbiol. Lett., 74, 271–276. 25. Islam,M.S., Bingle,L.E.H., Pallen,M.J. and Busby,S.J.W. (2011) Organisation of the LEE1 operon regulatory region of enterohaemorrhagic Escherichia coli O157:H7 and activation by GrlA. Mol. Microbiol., 79, 468–483. 26. Rhodius,V.A. and Busby,S.J. (2000) Interactions between activating region 3 of the Escherichia coli cyclic AMP receptor protein and region 4 of the RNA polymerase sigma(70) subunit: application of suppression genetics. J. Mol. Biol., 299, 311–324. 27. Grainger,D.C., Belyaeva,T.A., Lee,D.J., Hyde,E.I. and Busby,S.J. (2004) Transcription activation at the Escherichia coli melAB promoter: interactions of MelR with the C-terminal domain of the RNA polymerase alpha subunit. Mol. Microbiol., 51, 1311–1320. 28. Savery,N., Belyaeva,T. and Busby,S. (1996) Introduction to protein: DNA interactions, DNase I footprinting, hydroxyl radical footprinting, permanganate footprinting and supplementary protocols. In Docherty,K. (ed.), Essential Techniques: Gene Transcription. BIOS Scientific Publishers, Oxford, pp. 1–33. 29. Miller,J. (1972) Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 30. Vlahovicek,K., Kaja´ n,L. and Pongor,S. (2003) DNA analysis servers: plot.it, bend.it, model.it and IS. Nucleic Acids Res., 31, 3686–3687. 31. Yamashino,T., Kakeda,M., Ueguchi,C. and Mizuno,T. (1994) An analogue of the DnaJ molecular chaperone whose expression is controlled by sigma s during the stationary phase and phosphate starvation in Escherichia coli. Mol. Microbiol., 13, 475–483. 32. Typas,A. and Hengge,R. (2006) Role of the spacer between the -35 and -10 regions in sigmaS promoter selectivity in Escherichia coli. Mol. Microbiol., 59, 1037–1051. 33. Fenton,M.S., Lee,S.J. and Gralla,J.D. (2000) Escherichia coli promoter opening and -10 recognition: mutational analysis of sigma70. EMBO J., 19, 1130–1137. 34. Busby,S., Truelle,N., Spassky,A., Dreyfus,M. and Buc,H. (1984) The selection and characterisation of two novel mutations in the overlapping promoters of the Escherichia coli galactose operon. Gene, 28, 201–209. 35. Thouvenot,B., Charpentier,B. and Branlant,C. (2004) The strong efficiency of the Escherichia coli gapA P1 promoter depends on a complex combination of functional determinants. Biochem. J., 383, 371–382. 36. Gaal,T., Barkei,J., Dickson,R.R., deBoer,H.A., deHaseth,P.L., Alavi,H. and Gourse,R.L. (1989) Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants. J. Bacteriol., 171, 4852–4861. 37. Colland,F., Fujita,N., Kotlarz,D., Bown,J.A., Meares,C.F., 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. 38. Buckle,M., Buc,H. and Travers,A. (1992) DNA deformation in nucleoprotein complexes between RNA polymerase, cAMP receptor protein and the lac UV5 promoter probed by singlet oxygen. EMBO J., 11, 2619–2652.
URI:	http://wrap.warwick.ac.uk/id/eprint/35918