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Gene Review

rpoH  -  RNA polymerase, sigma 32 (sigma H) factor

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK3445, JW3426, fam, hin, htpR
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Disease relevance of rpoH

  • Induction of heat shock proteins in Escherichia coli is caused by a transient increase in the cellular level of sigma 32 (the rpoH gene product), a protein required for transcription of heat shock genes [1].
  • The rpoH gene encoding the heat-shock sigma factor of Pseudomonas putida was cloned by using its ability to complement the temperature-sensitive growth of the Escherichia coli rpoH mutant [2].
  • The Caulobacter heat shock sigma factor gene rpoH is positively autoregulated from a sigma32-dependent promoter [3].
  • Primary amino acid sequence comparisons demonstrate that R. sphaeroides RpoH(II) belongs to a phylogenetically distinct group with RpoH orthologs from alpha-proteobacteria that contain two rpoH genes [4].
  • We report the role of a gene (rpoH) from the facultative phototroph Rhodobacter sphaeroides that encodes a protein (sigma37) similar to Escherichia coli sigma32 and other members of the heat shock family of eubacterial sigma factors [5].

High impact information on rpoH

  • The htpR gene of E. coli encodes a positive regulator of the heat-shock response [6].
  • To understand the mechanism of heat induction of sigma32 synthesis further, we analyzed expression of rpoH-lacZ gene fusions with altered stability of mRNA structure before and after heat shock [7].
  • These regulatory defects are due to the loss of normal control over the synthesis and stability of sigma 32, the alternate RNA polymerase sigma-factor required for heat shock gene expression [8].
  • The rpoH gene of Escherichia coli encodes sigma 32, the 32-kD sigma-factor responsible for the heat-inducible transcription of the heat shock genes. rpoH is transcribed from at least three promoters [9].
  • The chromosomal rpoH gene and RpoH sigma factor did not appear to be required for pap transcription, and the thermoregulation of pilus gene transcription must be different from that of the heat shock regulon [10].

Chemical compound and disease context of rpoH

  • The addition of isopropyl thio-beta-D-galactoside (IPTG) to Escherichia coli cells containing multiple copies of the heat shock regulatory gene htpR (rpoH) under the control of an IPTG-inducible promoter (P-tac) induced 15 of the 17 polypeptides of the heat shock (HTP) regulon [11].
  • The ampicillin resistance gene in Escherichia coli, chloramphenicol acetyltransferase gene in different gram-negative strains, and RNA polymerase sigma factor (rpoD) gene in Aeromonas spp. could be detected under identical permeabilization conditions [12].
  • One of the amber mutations, dnaG24 which maps proximal to the NH2-terminus of the dnaG gene, exerted a polar effect on the synthesis of RNA polymerase sigma factor in E. coli [13].

Biological context of rpoH

  • The observation that heat shock proteins are induced by some abnormal, rapidly degraded polypeptides, and that strains with mutations in the rpoH gene, the positive regulator of heat shock gene expression, are defective in proteolysis, has led to the proposal that heat shock proteins are required for normal degradation of polypeptides [14].
  • We previously showed that heat-induced translation of sigma 32-beta-galactosidase fusion protein encoded by an rpoH-lacZ gene fusion was mediated by an mRNA secondary structure formed between two 5'-proximal segments (A and B) of rpoH coding sequence spanning some 200 nt [1].
  • DNase I footprint analysis indicated that dnaA protein protected specific sites within the rpoH promoter region [15].
  • Furthermore, some of the compensatory mutations resulted in super-repressed (non-inducible) phenotypes, suggesting that the heat induction depends on a specific nucleotide sequence(s) as well as the mRNA secondary structure within the 5'-proximal regulatory segment of rpoH coding region [16].
  • Extended protection against lysis occurred when overproduction of heat shock proteins was induced artificially in cells that contained a plasmid with the rpoH+ gene under control of the tac promoter [17].

Anatomical context of rpoH

  • Mutations in the rpoH gene, encoding sigma 32, an alternative factor required for transcription of the heat shock genes, result in the extensive aggregation of virtually all cellular proteins and formation of inclusion bodies both under stress and non-stress conditions [18].
  • Suppression of the Escherichia coli rpoH opal mutation by ribosomes lacking S15 protein [19].
  • This study identifies a gene for a plastid RNA polymerase sigma factor and indicates that there may be a family of nuclear-encoded sigma factors that recognize promoters in subsets of plastid genes and regulate differential gene expression at the transcriptional level [20].

Associations of rpoH with chemical compounds

  • Dissection of the rpoH promoter region allowed us to localize the glucose-sensitive promoter to the 110-base-pair (bp) segment directly upstream of the rpoH coding region [21].
  • One mutation has been sequenced and causes a leucine-to-tryptophan change 7 amino acids from the carboxyl terminus of the rpoH gene product [22].
  • Studies of rpoH transcription in vitro demonstrated that RNA polymerase-sigma 70 can transcribe from the P5 promoter only in the presence of cAMP and its receptor protein [21].
  • All rpoH mutants tested showed a weak but significant response to ethanol [23].
  • The mutants can grow only at temperatures below 34 degrees C-35 degrees C. Heat, ethanol, and coumermycin induce major heat shock proteins in the wild-type but not in the htpR mutants [24].

Regulatory relationships of rpoH

  • dnaA protein regulates transcriptions of the rpoH gene of Escherichia coli [15].
  • We present evidence that the rate of expression of the dnaJ protein is increased by heat shock under the control of the htpR (rpoH) gene product [25].

Other interactions of rpoH

  • Chromosomal clpB transcripts also increased upon temperature upshift and were totally absent in the rpoH deletion strain [26].
  • We determined the relative positions of most of these genes and show that the rpoH gene lies immediately downstream of the last gene (ftsX) of a cell division operon and is transcribed in the same direction [27].
  • Strains bearing mutations in oxyR and rpoH were the most hypersensitive to these compounds [28].
  • However, the data reported here demonstrate that the 20-kDa protein is not required for high-level CytA production in E. coli strains carrying mutations in rpoH, groEL, or dnaK, all of which affect the proteolytic ability of the cells [29].
  • Promoter mapping experiments and Northern (RNA) analysis showed that the htpY gene belongs to the classical heat shock gene family, because the transcription from its major promoter is under the positive control of the rpoH gene product (sigma 32) and resembles canonical E sigma 32-transcribed consensus promoter sequences [30].

Analytical, diagnostic and therapeutic context of rpoH

  • Reverse transcription-PCR (RT-PCR) methods were developed for detecting mRNA from rpoH, groEL, and tufA genes. mRNA from all three genes was detected immediately after the cells had been killed by heat or ethanol but gradually disappeared with time when dead cells were held at room temperature [31].
  • Isolation and sequence analysis of rpoH genes encoding sigma 32 homologs from gram negative bacteria: conserved mRNA and protein segments for heat shock regulation [32].
  • The isolated C. crescentus gene complements the growth defect of an E. coli rpoH deletion strain at 37 degrees C, and Western blot (immunoblot) analysis confirmed that the gene product is related to the E. coli sigma32 protein [33].
  • Northern blot analysis showed that the level of rpoH mRNA was clearly increased at 20 degrees C, a temperature that induces heat shock in this organism [34].
  • Hybridization to a PCR product derived from conserved sigma-factor sequences led to the identification of two Sinorhizobium meliloti DNA segments that display significant sequence similarity to the family of rpoH genes encoding the sigma(32) (RpoH) heat-shock transcription factors [35].


  1. A distinct segment of the sigma 32 polypeptide is involved in DnaK-mediated negative control of the heat shock response in Escherichia coli. Nagai, H., Yuzawa, H., Kanemori, M., Yura, T. Proc. Natl. Acad. Sci. U.S.A. (1994) [Pubmed]
  2. Cloning and sequencing of rpoH and identification of ftsE-ftsX in Pseudomonas putida PpG1. Aramaki, H., Sagara, Y., Fujita, M. DNA Res. (1999) [Pubmed]
  3. The Caulobacter heat shock sigma factor gene rpoH is positively autoregulated from a sigma32-dependent promoter. Wu, J., Newton, A. J. Bacteriol. (1997) [Pubmed]
  4. Activity of Rhodobacter sphaeroides RpoHII, a second member of the heat shock sigma factor family. Green, H.A., Donohue, T.J. J. Bacteriol. (2006) [Pubmed]
  5. Metabolic roles of a Rhodobacter sphaeroides member of the sigma32 family. Karls, R.K., Brooks, J., Rossmeissl, P., Luedke, J., Donohue, T.J. J. Bacteriol. (1998) [Pubmed]
  6. The htpR gene product of E. coli is a sigma factor for heat-shock promoters. Grossman, A.D., Erickson, J.W., Gross, C.A. Cell (1984) [Pubmed]
  7. Translational induction of heat shock transcription factor sigma32: evidence for a built-in RNA thermosensor. Morita, M.T., Tanaka, Y., Kodama, T.S., Kyogoku, Y., Yanagi, H., Yura, T. Genes Dev. (1999) [Pubmed]
  8. DnaK, DnaJ, and GrpE heat shock proteins negatively regulate heat shock gene expression by controlling the synthesis and stability of sigma 32. Straus, D., Walter, W., Gross, C.A. Genes Dev. (1990) [Pubmed]
  9. Identification of the sigma E subunit of Escherichia coli RNA polymerase: a second alternate sigma factor involved in high-temperature gene expression. Erickson, J.W., Gross, C.A. Genes Dev. (1989) [Pubmed]
  10. Regulatory genes in the thermoregulation of Escherichia coli pili gene transcription. Göransson, M., Forsman, K., Uhlin, B.E. Genes Dev. (1989) [Pubmed]
  11. Induction of the heat shock regulon does not produce thermotolerance in Escherichia coli. VanBogelen, R.A., Acton, M.A., Neidhardt, F.C. Genes Dev. (1987) [Pubmed]
  12. Recognition of individual genes in diverse microorganisms by cycling primed in situ amplification. Kenzaka, T., Tamaki, S., Yamaguchi, N., Tani, K., Nasu, M. Appl. Environ. Microbiol. (2005) [Pubmed]
  13. Amber dnaG mutation exerting a polar effect on the synthesis of RNA polymerase sigma factor in Escherichia coli. Nakamura, Y. Mol. Gen. Genet. (1984) [Pubmed]
  14. Escherichia coli heat shock gene mutants are defective in proteolysis. Straus, D.B., Walter, W.A., Gross, C.A. Genes Dev. (1988) [Pubmed]
  15. dnaA protein regulates transcriptions of the rpoH gene of Escherichia coli. Wang, Q.P., Kaguni, J.M. J. Biol. Chem. (1989) [Pubmed]
  16. Heat induction of sigma 32 synthesis mediated by mRNA secondary structure: a primary step of the heat shock response in Escherichia coli. Yuzawa, H., Nagai, H., Mori, H., Yura, T. Nucleic Acids Res. (1993) [Pubmed]
  17. Lysis of Escherichia coli by the bacteriophage phi X174 E protein: inhibition of lysis by heat shock proteins. Young, K.D., Anderson, R.J., Hafner, R.J. J. Bacteriol. (1989) [Pubmed]
  18. Protein aggregation and inclusion body formation in Escherichia coli rpoH mutant defective in heat shock protein induction. Gragerov, A.I., Martin, E.S., Krupenko, M.A., Kashlev, M.V., Nikiforov, V.G. FEBS Lett. (1991) [Pubmed]
  19. Suppression of the Escherichia coli rpoH opal mutation by ribosomes lacking S15 protein. Yano, R., Yura, T. J. Bacteriol. (1989) [Pubmed]
  20. Molecular characterization of a positively photoregulated nuclear gene for a chloroplast RNA polymerase sigma factor in Cyanidium caldarium. Liu, B., Troxler, R.F. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  21. Transcriptional regulation of the heat shock regulatory gene rpoH in Escherichia coli: involvement of a novel catabolite-sensitive promoter. Nagai, H., Yano, R., Erickson, J.W., Yura, T. J. Bacteriol. (1990) [Pubmed]
  22. Mutations in the rpoH (htpR) gene of Escherichia coli K-12 phenotypically suppress a temperature-sensitive mutant defective in the sigma 70 subunit of RNA polymerase. Grossman, A.D., Zhou, Y.N., Gross, C., Heilig, J., Christie, G.E., Calendar, R. J. Bacteriol. (1985) [Pubmed]
  23. The use of operon fusions in studies of the heat-shock response: effects of altered sigma 32 on heat-shock promoter function in Escherichia coli. Yano, R., Imai, M., Yura, T. Mol. Gen. Genet. (1987) [Pubmed]
  24. Heat shock regulatory gene (htpR) of Escherichia coli is required for growth at high temperature but is dispensable at low temperature. Yura, T., Tobe, T., Ito, K., Osawa, T. Proc. Natl. Acad. Sci. U.S.A. (1984) [Pubmed]
  25. The nucleotide sequence of the Escherichia coli K12 dnaJ+ gene. A gene that encodes a heat shock protein. Bardwell, J.C., Tilly, K., Craig, E., King, J., Zylicz, M., Georgopoulos, C. J. Biol. Chem. (1986) [Pubmed]
  26. Expression of ClpB, an analog of the ATP-dependent protease regulatory subunit in Escherichia coli, is controlled by a heat shock sigma factor (sigma 32). Kitagawa, M., Wada, C., Yoshioka, S., Yura, T. J. Bacteriol. (1991) [Pubmed]
  27. The Escherichia coli heat shock regulatory gene is immediately downstream of a cell division operon: the fam mutation is allelic with rpoH. Crickmore, N., Salmond, G.P. Mol. Gen. Genet. (1986) [Pubmed]
  28. Interaction of lead nitrate and cadmium chloride with Escherichia coli K-12 and Salmonella typhimurium global regulatory mutants. LaRossa, R.A., Smulski, D.R., Van Dyk, T.K. J. Ind. Microbiol. (1995) [Pubmed]
  29. Effect of a 20-kilodalton protein from Bacillus thuringiensis subsp. israelensis on production of the CytA protein by Escherichia coli. Visick, J.E., Whiteley, H.R. J. Bacteriol. (1991) [Pubmed]
  30. The Escherichia coli heat shock gene htpY: mutational analysis, cloning, sequencing, and transcriptional regulation. Missiakas, D., Georgopoulos, C., Raina, S. J. Bacteriol. (1993) [Pubmed]
  31. Detection of mRNA by reverse transcription-PCR as an indicator of viability in Escherichia coli cells. Sheridan, G.E., Masters, C.I., Shallcross, J.A., MacKey, B.M. Appl. Environ. Microbiol. (1998) [Pubmed]
  32. Isolation and sequence analysis of rpoH genes encoding sigma 32 homologs from gram negative bacteria: conserved mRNA and protein segments for heat shock regulation. Nakahigashi, K., Yanagi, H., Yura, T. Nucleic Acids Res. (1995) [Pubmed]
  33. Isolation, identification, and transcriptional specificity of the heat shock sigma factor sigma32 from Caulobacter crescentus. Wu, J., Newton, A. J. Bacteriol. (1996) [Pubmed]
  34. The rpoH gene encoding heat shock sigma factor sigma(32) of psychrophilic bacterium Colwellia maris. Yamauchi, S., Okuyama, H., Nishiyama, Y., Hayashi, H. Extremophiles (2006) [Pubmed]
  35. Identification of the heat-shock sigma factor RpoH and a second RpoH-like protein in Sinorhizobium meliloti. Oke, V., Rushing, B.G., Fisher, E.J., Moghadam-Tabrizi, M., Long, S.R. Microbiology (Reading, Engl.) (2001) [Pubmed]
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