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Gene Review

rpoA  -  RNA polymerase, alpha subunit

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK3282, JW3257, pez, phs, sez
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Disease relevance of rpoA

  • The rpoA gene specifies a protein of 339 amino acids with deduced molecular mass of 36,510 Da, exhibiting 64.3 and 70.7% similarity over its entire length to Escherichia coli and B. subtilis alpha subunits, respectively [1].
  • The rpoA gene, encoding the alpha subunit of RNA polymerase, was cloned from Streptomyces coelicolor A3(2) [1].
  • The Salmonella typhimurium phs chromosomal locus essential for the reduction of thiosulfate to hydrogen sulfide was cloned, and some features of its regulation were examined [2].

High impact information on rpoA

  • We isolated two rpoD mutants with such properties, but no rpoA mutant with similar properties [3].
  • DNA sequence determination of several 'Lac-' mutant rpoA genes revealed that all had mutations clustered within a short segment near the C-terminus of alpha, between amino acid residues 265 and 270 [4].
  • This mutation was mapped by marker rescue to within a 182bp region near the 3' end of rpoA and was subsequently transferred to a plasmid by recombination in vivo [5].
  • The rpoA341 (phs) mutation of Escherichia coli results in decreased expression of several positively regulated operons and has been mapped to within or very near the rpoA gene encoding the alpha subunit of RNA polymerase [5].
  • We have shown that plasmid-directed synthesis of the wild-type alpha subunit can complement the defective phenotypes associated with this mutation consistent with its proposed location within rpoA [5].

Chemical compound and disease context of rpoA

  • The phs locus conferred H2S production on Escherichia coli, suggesting that it contains the structural gene for thiosulfate reductase [2].
  • The genes for 1,2-propanediol degradation (pdu) and B12 synthesis (cob), along with the genes for sulfur reduction (ttr, phs, and asr), constitute more than 1% of the Salmonella genome and are all absent from E. coli [6].

Biological context of rpoA


Anatomical context of rpoA


Associations of rpoA with chemical compounds

  • Both the mutant rpoA genes were found to carry a single base transition which leads to a substitution of Cys for Arg at the position 191 (rpoA101) or 45 (rpoA112), respectively [9].
  • We have shown that a second mutation to auxotrophy, cymX, which is satisfied by either methionine or cysteine, is closely linked to phs [13].

Other interactions of rpoA

  • The rpoA-rplQ intercistronic region shows strong primary, and potential secondary structural homologies with the S4-binding sites on 16S rRNA and S13 mRNA [7].
  • A lacZ-rpoA gene-fusion has been constructed and expressed in E. coli [12].

Analytical, diagnostic and therapeutic context of rpoA


  1. Molecular analysis of RNA polymerase alpha subunit gene from Streptomyces coelicolor A3(2). Cho, E.J., Bae, J.B., Kang, J.G., Roe, J.H. Nucleic Acids Res. (1996) [Pubmed]
  2. Cloning of the phs genetic locus from Salmonella typhimurium and a role for a phs product in its own induction. Fong, C.L., Heinzinger, N.K., Tongklan, S., Barrett, E.L. J. Bacteriol. (1993) [Pubmed]
  3. 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]
  4. Mapping the cAMP receptor protein contact site on the alpha subunit of Escherichia coli RNA polymerase. Zou, C., Fujita, N., Igarashi, K., Ishihama, A. Mol. Microbiol. (1992) [Pubmed]
  5. Escherichia coli rpoA mutation which impairs transcription of positively regulated systems. Thomas, M.S., Glass, R.E. Mol. Microbiol. (1991) [Pubmed]
  6. The alternative electron acceptor tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar typhimurium on ethanolamine or 1,2-propanediol. Price-Carter, M., Tingey, J., Bobik, T.A., Roth, J.R. J. Bacteriol. (2001) [Pubmed]
  7. Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4? Meek, D.W., Hayward, R.S. Nucleic Acids Res. (1984) [Pubmed]
  8. Isolation of mutations in the alpha operon of Escherichia coli that suppress the transcriptional defect conferred by a mutation in the porin regulatory gene envZ. Garrett, S., Silhavy, T.J. J. Bacteriol. (1987) [Pubmed]
  9. Sequence analysis of two temperature-sensitive mutations in the alpha subunit gene (rpoA) of Escherichia coli RNA polymerase. Igarashi, K., Fujita, N., Ishihama, A. Nucleic Acids Res. (1990) [Pubmed]
  10. Rice chloroplast RNA polymerase genes: the absence of an intron in rpoC1 and the presence of an extra sequence in rpoC2. Shimada, H., Fukuta, M., Ishikawa, M., Sugiura, M. Mol. Gen. Genet. (1990) [Pubmed]
  11. Mutations affecting two adjacent amino acid residues in the alpha subunit of RNA polymerase block transcriptional activation by the bacteriophage P2 Ogr protein. Ayers, D.J., Sunshine, M.G., Six, E.W., Christie, G.E. J. Bacteriol. (1994) [Pubmed]
  12. The plastid rpoA gene encoding a protein homologous to the bacterial RNA polymerase alpha subunit is expressed in pea chloroplasts. Purton, S., Gray, J.C. Mol. Gen. Genet. (1989) [Pubmed]
  13. Genetic studies of the phs locus of Escherichia coli, a mutation causing pleiotropic lesions in metabolism and pH homeostasis. Rowland, G.C., Giffard, P.M., Booth, I.R. FEBS Lett. (1984) [Pubmed]
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