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J Bacteriol. 1996 Oct; 178(19): 5719–5731.
PMCID: PMC178412

Transcription of the mutL repair, miaA tRNA modification, hfq pleiotropic regulator, and hflA region protease genes of Escherichia coli K-12 from clustered Esigma32-specific promoters during heat shock.


The amiB-mutL-miaA-hfq-hflX-hflK-hflC superoperon of Escherichia coli contains genes that are important for diverse cellular functions, including DNA mismatch repair (mutL), tRNA modification (miaA), pleiotropic regulation (hfq), and proteolysis (hflX-hflK-hflC). We show that this superoperon contains three E simga(32)-dependent heat shock promoters, P(mutL)HS,P(miaA)HS, and P1(hfq)HS, in addition to four E sigma(70)-dependent promoters, P(mutL), P(miaA), P2(hfq), and P3(hfq). Transcripts from P(mutL)HS and P(miaA)HS were most prominent in vivo during extreme heat shock (50 degrees C), whereas P1(hfq)HS transcripts were detectable under nonshock conditions and increased significantly after heat shock at 50 degrees C. The P(mutL)HS, P(miaA)HS, and P1(hfq)HS transcripts were not detected in an rpoH null mutant. All three promoters were transcribed by E sigma (32) in vitro at 37 degrees C and contain -35 and -10 regions that resemble the E sigma(32) consensus. In experiments to assess the possible physiological relevance of the P(mutL)HS and P(miaA)HS promoters, we found that E. coli prototrophic strain MG 1655 increased in cell mass and remained nearly 100% viable for several hours at 50 degrees C in enriched media. In these cells, a significant fraction of mutL and hfq-hflA region transcripts were from P(mutL)HS and P1(hfq)HS, respectively, and the amounts of the miaA, hfq, hflX, hflK, and hflC transcripts increased in comparison with those in nonstressed cells. The cellular amounts of MutL and the hfq gene product (HF-I protein) were maintained during heat shock at 44 or 50 degrees C. Consistent with their expression patterns, miaA and hfq were essential for growth and viability, respectively, at temperatures of 45 degrees C and above. Together, these results suggest that there is a class of E sigma(32) promoters that functions mainly at high temperatures to ensure E. coli function and survival.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Arps PJ, Winkler ME. Structural analysis of the Escherichia coli K-12 hisT operon by using a kanamycin resistance cassette. J Bacteriol. 1987 Mar;169(3):1061–1070. [PMC free article] [PubMed]
  • Blaszczak A, Zylicz M, Georgopoulos C, Liberek K. Both ambient temperature and the DnaK chaperone machine modulate the heat shock response in Escherichia coli by regulating the switch between sigma 70 and sigma 32 factors assembled with RNA polymerase. EMBO J. 1995 Oct 16;14(20):5085–5093. [PMC free article] [PubMed]
  • Boyce JM, Evans EJ, Jr, Evans DG, DuPont HL. Production of heat-stable, methanol-soluble enterotoxin by Yersinia enterocolitica. Infect Immun. 1979 Aug;25(2):532–537. [PMC free article] [PubMed]
  • Brown L, Elliott T. Efficient translation of the RpoS sigma factor in Salmonella typhimurium requires host factor I, an RNA-binding protein encoded by the hfq gene. J Bacteriol. 1996 Jul;178(13):3763–3770. [PMC free article] [PubMed]
  • Caillet J, Droogmans L. Molecular cloning of the Escherichia coli miaA gene involved in the formation of delta 2-isopentenyl adenosine in tRNA. J Bacteriol. 1988 Sep;170(9):4147–4152. [PMC free article] [PubMed]
  • Charpentier B, Branlant C. The Escherichia coli gapA gene is transcribed by the vegetative RNA polymerase holoenzyme E sigma 70 and by the heat shock RNA polymerase E sigma 32. J Bacteriol. 1994 Feb;176(3):830–839. [PMC free article] [PubMed]
  • Cheng HH, Echols H. A class of Escherichia coli proteins controlled by the hflA locus. J Mol Biol. 1987 Aug 5;196(3):737–740. [PubMed]
  • Cheng HH, Muhlrad PJ, Hoyt MA, Echols H. Cleavage of the cII protein of phage lambda by purified HflA protease: control of the switch between lysis and lysogeny. Proc Natl Acad Sci U S A. 1988 Nov;85(21):7882–7886. [PMC free article] [PubMed]
  • Chuang SE, Blattner FR. Characterization of twenty-six new heat shock genes of Escherichia coli. J Bacteriol. 1993 Aug;175(16):5242–5252. [PMC free article] [PubMed]
  • Connolly DM, Winkler ME. Genetic and physiological relationships among the miaA gene, 2-methylthio-N6-(delta 2-isopentenyl)-adenosine tRNA modification, and spontaneous mutagenesis in Escherichia coli K-12. J Bacteriol. 1989 Jun;171(6):3233–3246. [PMC free article] [PubMed]
  • Connolly DM, Winkler ME. Structure of Escherichia coli K-12 miaA and characterization of the mutator phenotype caused by miaA insertion mutations. J Bacteriol. 1991 Mar;173(5):1711–1721. [PMC free article] [PubMed]
  • Cowing DW, Gross CA. Interaction of Escherichia coli RNA polymerase holoenzyme containing sigma 32 with heat shock promoters. DNase I footprinting and methylation protection. J Mol Biol. 1989 Dec 5;210(3):513–520. [PubMed]
  • Damagnez V, Doutriaux MP, Radman M. Saturation of mismatch repair in the mutD5 mutator strain of Escherichia coli. J Bacteriol. 1989 Aug;171(8):4494–4497. [PMC free article] [PubMed]
  • Díaz I, Ehrenberg M. ms2i6A deficiency enhances proofreading in translation. J Mol Biol. 1991 Dec 20;222(4):1161–1171. [PubMed]
  • Droffner ML, Yamamoto N. Prolonged environmental stress via a two step process selects mutants of Escherichia, Salmonella and Pseudomonas that grow at 54 degrees C. Arch Microbiol. 1991;156(4):307–311. [PubMed]
  • Erickson JW, Vaughn V, Walter WA, Neidhardt FC, Gross CA. Regulation of the promoters and transcripts of rpoH, the Escherichia coli heat shock regulatory gene. Genes Dev. 1987 Jul;1(5):419–432. [PubMed]
  • Feng G, Tsui HC, Winkler ME. Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells. J Bacteriol. 1996 Apr;178(8):2388–2396. [PMC free article] [PubMed]
  • Feng G, Winkler ME. Single-step purifications of His6-MutH, His6-MutL and His6-MutS repair proteins of escherichia coli K-12. Biotechniques. 1995 Dec;19(6):956–965. [PubMed]
  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. [PubMed]
  • Franze de Fernandez MT, Hayward WS, August JT. Bacterial proteins required for replication of phage Q ribonucleic acid. Pruification and properties of host factor I, a ribonucleic acid-binding protein. J Biol Chem. 1972 Feb 10;247(3):824–831. [PubMed]
  • Frederico LA, Kunkel TA, Shaw BR. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry. 1990 Mar 13;29(10):2532–2537. [PubMed]
  • Hagervall TG, Ericson JU, Esberg KB, Li JN, Björk GR. Role of tRNA modification in translational fidelity. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):263–266. [PubMed]
  • Herman C, Ogura T, Tomoyasu T, Hiraga S, Akiyama Y, Ito K, Thomas R, D'Ari R, Bouloc P. Cell growth and lambda phage development controlled by the same essential Escherichia coli gene, ftsH/hflB. Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10861–10865. [PMC free article] [PubMed]
  • Herman C, Thévenet D, D'Ari R, Bouloc P. Degradation of sigma 32, the heat shock regulator in Escherichia coli, is governed by HflB. Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3516–3520. [PMC free article] [PubMed]
  • Hiratsu K, Shinagawa H, Makino K. Mode of promoter recognition by the Escherichia coli RNA polymerase holoenzyme containing the sigma S subunit: identification of the recognition sequence of the fic promoter. Mol Microbiol. 1995 Dec;18(5):841–850. [PubMed]
  • Jishage M, Ishihama A. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of sigma 70 and sigma 38. J Bacteriol. 1995 Dec;177(23):6832–6835. [PMC free article] [PubMed]
  • Kajitani M, Ishihama A. Identification and sequence determination of the host factor gene for bacteriophage Q beta. Nucleic Acids Res. 1991 Mar 11;19(5):1063–1066. [PMC free article] [PubMed]
  • Kajitani M, Kato A, Wada A, Inokuchi Y, Ishihama A. Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta. J Bacteriol. 1994 Jan;176(2):531–534. [PMC free article] [PubMed]
  • Kaminski PA, Desnoues N, Elmerich C. The expression of nifA in Azorhizobium caulinodans requires a gene product homologous to Escherichia coli HF-I, an RNA-binding protein involved in the replication of phage Q beta RNA. Proc Natl Acad Sci U S A. 1994 May 24;91(11):4663–4667. [PMC free article] [PubMed]
  • Kohara Y, Akiyama K, Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. [PubMed]
  • Kröger M, Wahl R. Compilation of DNA sequences of Escherichia coli K12 (ECD and ECDC; update 1995). Nucleic Acids Res. 1996 Jan 1;24(1):29–31. [PMC free article] [PubMed]
  • Kroh HE, Simon LD. The ClpP component of Clp protease is the sigma 32-dependent heat shock protein F21.5. J Bacteriol. 1990 Oct;172(10):6026–6034. [PMC free article] [PubMed]
  • Kushner SR, Nagaishi H, Clark AJ. Indirect suppression of recB and recC mutations by exonuclease I deficiency. Proc Natl Acad Sci U S A. 1972 Jun;69(6):1366–1370. [PMC free article] [PubMed]
  • Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. [PubMed]
  • Lesley SA, Jovanovich SB, Tse-Dinh YC, Burgess RR. Identification of a heat shock promoter in the topA gene of Escherichia coli. J Bacteriol. 1990 Dec;172(12):6871–6874. [PMC free article] [PubMed]
  • Lieb M. Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites. J Bacteriol. 1987 Nov;169(11):5241–5246. [PMC free article] [PubMed]
  • Lieb M. Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair. Genetics. 1991 May;128(1):23–27. [PMC free article] [PubMed]
  • Lieb M, Rehmat S. Very short patch repair of T:G mismatches in vivo: importance of context and accessory proteins. J Bacteriol. 1995 Feb;177(3):660–666. [PMC free article] [PubMed]
  • Lisser S, Margalit H. Compilation of E. coli mRNA promoter sequences. Nucleic Acids Res. 1993 Apr 11;21(7):1507–1516. [PMC free article] [PubMed]
  • Loewen PC, Hengge-Aronis R. The role of the sigma factor sigma S (KatF) in bacterial global regulation. Annu Rev Microbiol. 1994;48:53–80. [PubMed]
  • Maurelli AT. Temperature regulation of virulence genes in pathogenic bacteria: a general strategy for human pathogens? Microb Pathog. 1989 Jul;7(1):1–10. [PubMed]
  • Mellon I, Champe GN. Products of DNA mismatch repair genes mutS and mutL are required for transcription-coupled nucleotide-excision repair of the lactose operon in Escherichia coli. Proc Natl Acad Sci U S A. 1996 Feb 6;93(3):1292–1297. [PMC free article] [PubMed]
  • Modrich P. Mechanisms and biological effects of mismatch repair. Annu Rev Genet. 1991;25:229–253. [PubMed]
  • Modrich P. Mismatch repair, genetic stability and tumour avoidance. Philos Trans R Soc Lond B Biol Sci. 1995 Jan 30;347(1319):89–95. [PubMed]
  • Muffler A, Fischer D, Hengge-Aronis R. The RNA-binding protein HF-I, known as a host factor for phage Qbeta RNA replication, is essential for rpoS translation in Escherichia coli. Genes Dev. 1996 May 1;10(9):1143–1151. [PubMed]
  • Nakao H, Watanabe H, Nakayama S, Takeda T. yst gene expression in Yersinia enterocolitica is positively regulated by a chromosomal region that is highly homologous to Escherichia coli host factor 1 gene (hfq). Mol Microbiol. 1995 Dec;18(5):859–865. [PubMed]
  • Newlands JT, Gaal T, Mecsas J, Gourse RL. Transcription of the Escherichia coli rrnB P1 promoter by the heat shock RNA polymerase (E sigma 32) in vitro. J Bacteriol. 1993 Feb;175(3):661–668. [PMC free article] [PubMed]
  • Noble JA, Innis MA, Koonin EV, Rudd KE, Banuett F, Herskowitz I. The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain. Proc Natl Acad Sci U S A. 1993 Nov 15;90(22):10866–10870. [PMC free article] [PubMed]
  • Petrullo LA, Gallagher PJ, Elseviers D. The role of 2-methylthio-N6-isopentenyladenosine in readthrough and suppression of nonsense codons in Escherichia coli. Mol Gen Genet. 1983;190(2):289–294. [PubMed]
  • Phillips TA, VanBogelen RA, Neidhardt FC. lon gene product of Escherichia coli is a heat-shock protein. J Bacteriol. 1984 Jul;159(1):283–287. [PMC free article] [PubMed]
  • Raina S, Georgopoulos C. A new Escherichia coli heat shock gene, htrC, whose product is essential for viability only at high temperatures. J Bacteriol. 1990 Jun;172(6):3417–3426. [PMC free article] [PubMed]
  • Raina S, Georgopoulos C. The htrM gene, whose product is essential for Escherichia coli viability only at elevated temperatures, is identical to the rfaD gene. Nucleic Acids Res. 1991 Jul 25;19(14):3811–3819. [PMC free article] [PubMed]
  • Savva D. Spontaneous mutation rates in continuous cultures: the effect of some environmental factors. Microbios. 1982;33(132):81–92. [PubMed]
  • Schaaper RM, Radman M. The extreme mutator effect of Escherichia coli mutD5 results from saturation of mismatch repair by excessive DNA replication errors. EMBO J. 1989 Nov;8(11):3511–3516. [PMC free article] [PubMed]
  • Shi X, Bennett GN. Plasmids bearing hfq and the hns-like gene stpA complement hns mutants in modulating arginine decarboxylase gene expression in Escherichia coli. J Bacteriol. 1994 Nov;176(21):6769–6775. [PMC free article] [PubMed]
  • Smith KC. Spontaneous mutagenesis: experimental, genetic and other factors. Mutat Res. 1992 Aug;277(2):139–162. [PubMed]
  • Squires CL, Pedersen S, Ross BM, Squires C. ClpB is the Escherichia coli heat shock protein F84.1. J Bacteriol. 1991 Jul;173(14):4254–4262. [PMC free article] [PubMed]
  • Tanaka K, Takayanagi Y, Fujita N, Ishihama A, Takahashi H. Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3511–3515. [PMC free article] [PubMed]
  • Taylor WE, Straus DB, Grossman AD, Burton ZF, Gross CA, Burgess RR. Transcription from a heat-inducible promoter causes heat shock regulation of the sigma subunit of E. coli RNA polymerase. Cell. 1984 Sep;38(2):371–381. [PubMed]
  • Tsui HC, Leung HC, Winkler ME. Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12. Mol Microbiol. 1994 Jul;13(1):35–49. [PubMed]
  • Tsui HT, Mandavilli BS, Winkler ME. Nonconserved segment of the MutL protein from Escherichia coli K-12 and Salmonella typhimurium. Nucleic Acids Res. 1992 May 11;20(9):2379–2379. [PMC free article] [PubMed]
  • Tsui HC, Winkler ME. Transcriptional patterns of the mutL-miaA superoperon of Escherichia coli K-12 suggest a model for posttranscriptional regulation. Biochimie. 1994;76(12):1168–1177. [PubMed]
  • Tsui HC, Zhao G, Feng G, Leung HC, Winkler ME. The mutL repair gene of Escherichia coli K-12 forms a superoperon with a gene encoding a new cell-wall amidase. Mol Microbiol. 1994 Jan;11(1):189–202. [PubMed]
  • VanBogelen RA, Acton MA, Neidhardt FC. Induction of the heat shock regulon does not produce thermotolerance in Escherichia coli. Genes Dev. 1987 Aug;1(6):525–531. [PubMed]
  • Wang FJ, Reiss C. The collision of cotranscribing E. coli RNA polymerases studied in vitro. Biochem Mol Biol Int. 1993 Aug;30(5):969–981. [PubMed]
  • Zhao G, Winkler ME. Kinetic limitation and cellular amount of pyridoxine (pyridoxamine) 5'-phosphate oxidase of Escherichia coli K-12. J Bacteriol. 1995 Feb;177(4):883–891. [PMC free article] [PubMed]
  • Zhou YN, Kusukawa N, Erickson JW, Gross CA, Yura T. Isolation and characterization of Escherichia coli mutants that lack the heat shock sigma factor sigma 32. J Bacteriol. 1988 Aug;170(8):3640–3649. [PMC free article] [PubMed]

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