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Gene Review

rpoD  -  RNA polymerase, sigma 70 (sigma D) factor

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK3057, JW3039, alt
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Disease relevance of rpoD


High impact information on rpoD

  • We isolated two rpoD mutants with such properties, but no rpoA mutant with similar properties [6].
  • The rpoD mutations altered amino acids within and near the first helix of the putative helix-turn-helix (HTH) motif in the carboxy-terminal region of sigma 70 [6].
  • The mutant results from a single base pair substitution in the rpoD gene that causes a Glu to Gly change at position 458 of sigma70 [7].
  • A dominant lethal mutation in the Escherichia coli rpoD gene, which encodes sigma 70, the promoter recognition subunit of RNA polymerase, was isolated after random mutagenesis [8].
  • Implications of the sequence homologies found among htpR, rpoD, and nusA proteins are discussed [9].

Chemical compound and disease context of rpoD

  • A simplified DNA-directed in vitro system which measures synthesis of the NH2-terminal dipeptides of gene products has been used to study the expression of rpoD, the gene coding for the sigma subunit of Escherichia coli RNA polymerase [10].
  • Sequencing data indicated that the RNA polymerase sigma 43 operon of Bacillus subtilis consisted of three genes, P23 (function unknown), dnaE (DNA primase), and rpoD (sigma 43) (Wang and Doi 1986a) [11].
  • An allele of rpoD (rpoD1181) that results in increased synthesis of the pyrimidine moiety of thiamine in Salmonella enterica was identified [12].
  • Three genes (hrd) homologous to the rpoD gene of Escherichia coli, that encode sigma factor-like proteins, have been cloned from DNA of the candicidin-producing strain Streptomyces griseus IMRU 3570 [13].
  • 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 [14].

Biological context of rpoD

  • The most significant differences between the two operons are observed in the molecular size of the first genes (P23 and rpsU), the complete lack of amino acid homology between P23 and S21, the molecular weights of the two rpoD genes, the size of the intercistronic region between the first two genes, and the regulatory elements of the operon [15].
  • The complete nucleotide sequence of a 5 kb fragment including the entire rpoD gene revealed the presence of two other genes preceding rpoD in the order P23-dnaE-rpoD [15].
  • With plasmid pMRG-1, which contains only the internal promoters, only rpoD expression was observed [10].
  • Bacillus subtilis dnaE encodes a protein essential for DNA replication and is tightly linked to rpoD, the gene for the major sigma factor of RNA polymerase [16].
  • Both dnaE and rpoD were transcribed in the same direction, counterclockwise on the chromosome [17].

Associations of rpoD with chemical compounds


Physical interactions of rpoD

  • The rpoD gene is part of a complex operon which also includes the genes for ribosomal protein S21 (rpsU) and primase (dnaG) [10].

Other interactions of rpoD

  • Primary promoters have been identified upstream of the structural genes, but there are secondary (internal) promoters within the dnaG gene that are involved in the expression of rpoD [10].
  • All the lineages examined, however, contain the intact forms of sigma70 (sigmaD, the rpoD gene product) and sigma54 (sigmaN, the rpoN gene product) [20].
  • Comparison of the katF sequence to the sequence of rpoD, which encodes the sigma subunit of RNA polymerase, revealed a 181 bp region with 65% homology and a 38 bp segment that was 87% homologous [21].
  • These findings indicate that the genetic structure of the leuA-rpoD1 locus in M. aeruginosa K-81 significantly differs from those of known leuA and rpoD loci found in other bacteria [22].
  • The interaction between IHF and the NusA protein has been investigated further in studies on the in vitro expression of the genes for the beta (rpoB) and sigma (rpoD) subunits of RNA polymerase, both known to be stimulated by NusA [23].

Analytical, diagnostic and therapeutic context of rpoD

  • However, [Gly434]sigma70, which contains a mutation at the DNA-binding rpoD box region, also migrates as a 70-kDa protein on SDS/PAGE [24].
  • RESULTS: On immunoblotting assays, MYC-X-5/1 reacted with the 90-kDa protein in the E. coli RNA polymerase preparations and with the 90-kDa protein over-expressed in E. coli carrying the plasmid with the rpoD insert [25].
  • A genetic cross between T4alt and T4mod phages yielded alt mod recombinant progeny which could not ADP ribosylate RNA polymerase at all, yet grew apparently normally [26].


  1. The operon that encodes the sigma subunit of RNA polymerase also encodes ribosomal protein S21 and DNA primase in E. coli K12. Burton, Z.F., Gross, C.A., Watanabe, K.K., Burgess, R.R. Cell (1983) [Pubmed]
  2. A strong sequence homology exists between the major RNA polymerase sigma factors of Bacillus subtilis and Escherichia coli. Gitt, M.A., Wang, L.F., Doi, R.H. J. Biol. Chem. (1985) [Pubmed]
  3. A missense mutation in rpoD results in an A-signalling defect in Myxococcus xanthus. Davis, J.M., Mayor, J., Plamann, L. Mol. Microbiol. (1995) [Pubmed]
  4. Genetic and molecular analysis of the rpoD gene from Lactococcus lactis. Araya, T., Ishibashi, N., Shimamura, S., Tanaka, K., Takahashi, H. Biosci. Biotechnol. Biochem. (1993) [Pubmed]
  5. Multiple principal sigma factor homologs in eubacteria: identification of the "rpoD box". Tanaka, K., Shiina, T., Takahashi, H. Science (1988) [Pubmed]
  6. Role of the sigma 70 subunit of RNA polymerase in transcriptional activation by activator protein PhoB in Escherichia coli. Makino, K., Amemura, M., Kim, S.K., Nakata, A., Shinagawa, H. Genes Dev. (1993) [Pubmed]
  7. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. Barne, K.A., Bown, J.A., Busby, S.J., Minchin, S.D. EMBO J. (1997) [Pubmed]
  8. Dominant lethal phenotype of a mutation in the -35 recognition region of Escherichia coli sigma 70. Keener, J., Nomura, M. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  9. 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]
  10. In vitro stimulation of Escherichia coli RNA polymerase sigma subunit synthesis by NusA protein. Peacock, S., Lupski, J.R., Godson, G.N., Weissbach, H. Gene (1985) [Pubmed]
  11. Promoter switching during development and the termination site of the sigma 43 operon of Bacillus subtilis. Wang, L.F., Doi, R.H. Mol. Gen. Genet. (1987) [Pubmed]
  12. A mutant allele of rpoD results in increased conversion of aminoimidazole ribotide to hydroxymethyl pyrimidine in Salmonella enterica. Dougherty, M.J., Downs, D.M. J. Bacteriol. (2004) [Pubmed]
  13. Three genes hrdB, hrdD and hrdT of Streptomyces griseus IMRU 3570, encoding sigma factor-like proteins, are differentially expressed under specific nutritional conditions. Marcos, A.T., Gutiérrez, S., Díez, B., Fernández, F.J., Oguiza, J.A., Martín, J.F. Gene (1995) [Pubmed]
  14. 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]
  15. Nucleotide sequence and organization of Bacillus subtilis RNA polymerase major sigma (sigma 43) operon. Wang, L.F., Doi, R.H. Nucleic Acids Res. (1986) [Pubmed]
  16. Bacillus subtilis dnaE encodes a protein homologous to DNA primase of Escherichia coli. Wang, L.F., Price, C.W., Doi, R.H. J. Biol. Chem. (1985) [Pubmed]
  17. Genetic mapping of rpoD implicates the major sigma factor of Bacillus subtilis RNA polymerase in sporulation initiation. Price, C.W., Doi, R.H. Mol. Gen. Genet. (1985) [Pubmed]
  18. Promotion, termination, and anti-termination in the rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli K-12. Lupski, J.R., Ruiz, A.A., Godson, G.N. Mol. Gen. Genet. (1984) [Pubmed]
  19. Cloning, sequencing, and expression of the rpoD gene encoding the primary sigma factor of Xanthomonas campestris. Tseng, Y.S., Yu, C.T., Tseng, Y.H., Yang, M.T. Biochem. Biophys. Res. Commun. (1997) [Pubmed]
  20. Variation in RNA polymerase sigma subunit composition within different stocks of Escherichia coli W3110. Jishage, M., Ishihama, A. J. Bacteriol. (1997) [Pubmed]
  21. Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a novel sigma transcription factor. Mulvey, M.R., Loewen, P.C. Nucleic Acids Res. (1989) [Pubmed]
  22. A novel genetic organization: the leuA-rpoD1 locus in the cyanobacterium Microcystis aeruginosa K-81. Asayama, M., Kabasawa, M., Shirai, M. Biochim. Biophys. Acta (1997) [Pubmed]
  23. Escherichia coli integration host factor inhibits the NusA stimulation of RNA polymerase sigma subunit synthesis in vitro. Peacock, S., Weissbach, H. Arch. Biochem. Biophys. (1985) [Pubmed]
  24. Mutations in the 1.1 subdomain of Escherichia coli sigma factor sigma70 and disruption of its overall structure. Gopal, V., Chatterji, D. Eur. J. Biochem. (1997) [Pubmed]
  25. Identification of epitope recognized by an anti-c-myc monoclonal antibody that cross-reacts with E. coli sigma factor using phage display libraries. Ikegaki, N., Tang, X.X., Kay, B.K., Kennett, R.H. Immunotechnology (1996) [Pubmed]
  26. ADP ribosylation of Escherichia coli RNA polymerase is nonessential for bacteriophage T4 development. Goff, C.G., Setzer, J. J. Virol. (1980) [Pubmed]
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