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Gene Review

rpoD  -  RpoD protein

Escherichia coli CFT073

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Disease relevance of rpoD

  • A. capsulatum RpoD restored normal growth to E. coli strain CAG20153 under conditions that prevent expression of the endogenous rpoD [1].
  • To begin to address this gap, we identified the gene encoding the A. capsulatum major sigma factor, rpoD, which encodes a 597-amino acid protein with a predicted sequence highly similar to the major sigma factors of Solibacter usitatus Ellin6076 and Geobacter sulfurreducens PCA [1].
  • RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box [2].
  • The deduced protein is highly homologous to the SigA protein of Rhizobium meliloti (72% amino acid sequence identity) but less so to RpoD of Escherichia coli (51% identity) [3].
  • The deduced amino acid sequence of R. capsulatus RpoD protein exhibits 46.2% and 45.7% identity with housekeeping sigma factors of Pseudomonas and E. coli, respectively [4].

High impact information on rpoD

  • In contrast to other minor sigma factors, sigma 38 shares a set of amino acid sequences common among the principal sigma factors of eubacteria and is therefore a member of the RpoD-related protein family [5].
  • We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni [2].
  • The TATA-box is in some, but not all cases, preceded by a TGx, similar to an extended -10 promoter.We predicted a total of 764 presumed RpoD promoters in the C.jejuni genome, of which 654 were located upstream of annotated genes [2].
  • An evolutionary conserved "RpoD box" has been identified at the junction of subdomain 2.3/2.4 in class I and class II sigma factors and there are two tryptophan residues at position 433 and 434 which can be used as intrinsic fluorescent markers to study their structure-function relationship [6].
  • Expression of peptide fusions directed against E. coli DnaN, LpxA, RpoD, ProRS, SecA, GyrA, and Era each dramatically inhibited cell growth [7].

Biological context of rpoD

  • Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information [8].
  • The operon was cloned in three segments from Listeria monocytogenes (Lm), initially using a probe designed from a highly conserved region of RpoD [9].

Associations of rpoD with chemical compounds

  • 5. The role in uhpT transcription of portions of RNA polymerase Esigma(70) holoenzyme which affect regulation at other promoters was examined by using series of alanine substitutions throughout the C-terminal domains of RpoA (residues 255 to 329) and of RpoD (residues 570 to 613) [10].
  • Purified hexahistidine-tagged RpoD migrates at approximately 70 kDa under SDS-PAGE conditions, which is consistent with the predicted MW of 69.2 kDa, and the gene product is immunoreactive with monoclonal antibodies specific for either bacterial RpoD proteins or the N-terminal histidine tag [1].


  1. Identification and characterization of the gene encoding the Acidobacterium capsulatum major sigma factor. Sabree, Z.L., Bergendahl, V., Liles, M.R., Burgess, R.R., Goodman, R.M., Handelsman, J. Gene (2006) [Pubmed]
  2. RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. Petersen, L., Larsen, T.S., Ussery, D.W., On, S.L., Krogh, A. J. Mol. Biol. (2003) [Pubmed]
  3. Dissection of the transcription machinery for housekeeping genes of Bradyrhizobium japonicum. Beck, C., Marty, R., Kläusli, S., Hennecke, H., Göttfert, M. J. Bacteriol. (1997) [Pubmed]
  4. Cloning, nucleotide sequence and characterization of the rpoD gene encoding the primary sigma factor of Rhodobacter capsulatus. Pasternak, C., Chen, W., Heck, C., Klug, G. Gene (1996) [Pubmed]
  5. 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. Tanaka, K., Takayanagi, Y., Fujita, N., Ishihama, A., Takahashi, H. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  6. A point mutation at the junction of domain 2.3/2.4 of transcription factor sigma 70 abrogates productive transcription and restores its expected mobility on a denaturing gel. Gopal, V., Ma, H.W., Kumaran, M.K., Chatterji, D. J. Mol. Biol. (1994) [Pubmed]
  7. Intracellular expression of Peptide fusions for demonstration of protein essentiality in bacteria. Benson, R.E., Gottlin, E.B., Christensen, D.J., Hamilton, P.T. Antimicrob. Agents Chemother. (2003) [Pubmed]
  8. Computational prediction of RpoS and RpoD regulatory sites in Geobacter sulfurreducens using sequence and gene expression information. Yan, B., N????ez, C., Ueki, T., Esteve-N????ez, A., Puljic, M., Adkins, R.M., Meth??, B.A., Lovley, D.R., Krushkal, J. Gene (2006) [Pubmed]
  9. Characterization of the macromolecular synthesis (MMS) operon from Listeria monocytogenes. Metzger, R., Brown, D.P., Grealish, P., Staver, M.J., Versalovic, J., Lupski, J.R., Katz, L. Gene (1994) [Pubmed]
  10. RNA polymerase alpha and sigma(70) subunits participate in transcription of the Escherichia coli uhpT promoter. Olekhnovich, I.N., Kadner, R.J. J. Bacteriol. (1999) [Pubmed]
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