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Gene Review

rpoB  -  RNA polymerase, beta subunit

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK3978, JW3950, ftsR, groN, nitB, ...
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Disease relevance of rpoB

  • DNA segments of various sizes, which cover the rifd allele of the rpoB gene, were cloned into lambda vector phages [1].
  • Thus, the B. subtilis rpoB region differs from its E. coli counterpart in both genetic and transcriptional organization [2].
  • Cloning and physical mapping of the Staphylococcus aureus rplL, rpoB and rpoC genes, encoding ribosomal protein L7/L12 and RNA polymerase subunits beta and beta' [3].
  • The resulting protein chip was used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides, as well as a single-base mutation in rpoB gene from Mycobacterium tuberculosis, with high specificity [4].
  • Primers were designed to amplify the rpoB gene of Neisseria meningitidis [5].

High impact information on rpoB

  • Systematic dissection of a approximately 1 kb fragment determined that the rpoB promoter is contained in a 15-nucleotide segment (-14 to +1) upstream of the transcription initiation site (+1) [6].
  • Particular mutations in the rpoB gene were able to suppress negative effects that certain dnaA mutations had on the replication of lambda plasmids; this suppression was allele-specific [7].
  • An element that reduces the level of distal gene expression to one-sixth is located on a fragment which spans the rplL-rpoB intercistronic region [8].
  • Interaction between mutations of ribosomes and RNA polymerase: a pair of strA and rif mutants individually temperature-insensitive but temperature-sensitive in combination [9].
  • Introduction of the nonpermissive rif allele to the permissive strA strain reduces or abolishes the transcription of T7 genome [10].

Chemical compound and disease context of rpoB


Biological context of rpoB

  • Both transcriptional (operon) and translational (gene) fusions of either rpoB or rpoC to the lacZ reporter were used to monitor their in vivo expression by inserting single copies of these fusions into the bacterial chromosome on integration-proficient lambda vectors [16].
  • The rpoB and rpoC mutants suggested that zwittermicin A might inhibit transcription, DNA replication, DNA gyrase or topoisomerase I; however, we found no further evidence to support any of these as the target for zwittermicin A [17].
  • The results suggest that deltapsi drives zwittermicin A uptake, and that, unlike other antibiotics for which resistance maps in rpoB or rpoC, zwittermicin A does not cause the rapid cessation of DNA or RNA synthesis, suggesting a unique mechanism of antibiosis [17].
  • Furthermore, experiments with the overexpressing plasmids confirm the requirement for a portion of the rplL-rpoB intercistronic region in the vicinity of the RNaseIII processing site for the efficient translation of the beta subunit mRNA [18].
  • A series of transcriptional and translational fusions of the gene for the beta subunit of RNA polymerase (rpoB) to the lacZ reporter gene have been constructed on lambda vectors [18].

Anatomical context of rpoB


Associations of rpoB with chemical compounds

  • A second class of zwittermicin A-resistant mutants was aminoglycoside sensitive and was affected in rpoB and rpoC, genes that encode subunits of RNA polymerase [17].
  • Here, we have shown that the introduction of a certain Rif(r) rpoB mutation into a B. subtilis strain resulted in cells that overproduce an aminosugar antibiotic 3,3'-neotrehalosadiamine (NTD), the production of which is dormant in the wild-type strain [19].
  • These three mutations are of particular interest because, unlike rpoB8, they do not increase termination at all rho-dependent and rho-independent terminators. rpoB211 and rpoB212 both change Asn-1072 to His in conserved region H of rpoB (betaN1072H), whereas rpoC214 changes Arg-352 to Cys in conserved region C of rpoC (beta'R352C) [20].
  • Two rpoB mutations that suppress the temperature defect of the dnaA46 mutation in initiation of replication were tested for effects on attenuation in the tryptophan operon [14].
  • Such strains may contain as many as four or five different mutations, and M. tuberculosis strains that are resistant to both streptomycin and rifampin contain mutations in the rpsL and rpoB genes, respectively [21].

Other interactions of rpoB

  • This region is almost certainly equivalent to the rif locus, located near to fus at interval 12/13 on the S. aureus linkage map [3].
  • Sequenced spontaneous extragenic suppressors of dksA polyauxotrophy are frequently the same T563P rpoB allele that suppresses a ppGpp(0) phenotype [22].
  • The gene was designated coaA and localized between argEH and rpoB near min 90 of the chromosome [23].
  • The chloroplast genome contains sequences homologous to the Escherichia coli rpoA, rpoB and rpoC genes [24].
  • The second case involves suppression of a temperature-sensitive gyrB mutation by a rifampin-resistant allele of rpoB, the gene encoding the beta subunit of RNA polymerase [25].

Analytical, diagnostic and therapeutic context of rpoB

  • Experiments using promoter probe vectors and site-directed mutagenesis located a major rpoB promoter overlapping the 3'-coding region of orf23, 250 nucleotides upstream from the beta initiation codon [2].
  • Transformation, via homologous recombination, was demonstrated by DNA sequencing of PCR products containing the three mutations in the Rifr region of rickettsial rpoB [26].
  • Complementation tests established that the mutations were in rpoB, the structural gene for the beta subunit of ribonucleic acid polymerase [27].
  • Sequence analysis of rpoB, both from these isolates of S. pneumoniae and from two strains of S. mitis, reveals that, among a number of clinical isolates, resistance to rifampicin in S. pneumoniae has arisen by point mutation [28].
  • Restriction enzyme analysis indicated that this DNA fragment was located on the B. burgdorferi chromosomal map between rpoB and p22A; its direction of transcription was towards p22A [29].


  1. Contranscription of genes for RNA polymerase subunits beta and beta' with genes for ribosomal proteins in Escherichia coli. Yamamoto, M., Nomura, M. Proc. Natl. Acad. Sci. U.S.A. (1978) [Pubmed]
  2. Genetic and transcriptional organization of the region encoding the beta subunit of Bacillus subtilis RNA polymerase. Boor, K.J., Duncan, M.L., Price, C.W. J. Biol. Chem. (1995) [Pubmed]
  3. Cloning and physical mapping of the Staphylococcus aureus rplL, rpoB and rpoC genes, encoding ribosomal protein L7/L12 and RNA polymerase subunits beta and beta'. Aboshkiwa, M., al-Ani, B., Coleman, G., Rowland, G. J. Gen. Microbiol. (1992) [Pubmed]
  4. A MutS-based protein chip for detection of DNA mutations. Bi, L.J., Zhou, Y.F., Zhang, X.E., Deng, J.Y., Zhang, Z.P., Xie, B., Zhang, C.G. Anal. Chem. (2003) [Pubmed]
  5. Molecular characterization of rifampin-resistant Neisseria meningitidis. Carter, P.E., Abadi, F.J., Yakubu, D.E., Pennington, T.H. Antimicrob. Agents Chemother. (1994) [Pubmed]
  6. In vitro characterization of the tobacco rpoB promoter reveals a core sequence motif conserved between phage-type plastid and plant mitochondrial promoters. Liere, K., Maliga, P. EMBO J. (1999) [Pubmed]
  7. DnaA-stimulated transcriptional activation of orilambda: Escherichia coli RNA polymerase beta subunit as a transcriptional activator contact site. Szalewska-Pałasz, A., Wegrzyn, A., Błaszczak, A., Taylor, K., Wegrzyn, G. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  8. Control features within the rplJL-rpoBC transcription unit of Escherichia coli. Barry, G., Squires, C.L., Squires, C. Proc. Natl. Acad. Sci. U.S.A. (1979) [Pubmed]
  9. Interaction between mutations of ribosomes and RNA polymerase: a pair of strA and rif mutants individually temperature-insensitive but temperature-sensitive in combination. Chakrabarti, S.L., Gorini, L. Proc. Natl. Acad. Sci. U.S.A. (1977) [Pubmed]
  10. A link between streptomycin and rifampicin mutation. Chakrabarti, S.L., Gorini, L. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  11. Molecular characterization of rpoB mutations conferring cross-resistance to rifamycins on methicillin-resistant Staphylococcus aureus. Wichelhaus, T.A., Schäfer, V., Brade, V., Böddinghaus, B. Antimicrob. Agents Chemother. (1999) [Pubmed]
  12. Amino acid residues involved in substrate recognition of the Escherichia coli Orf135 protein. Iida, E., Satou, K., Mishima, M., Kojima, C., Harashima, H., Kamiya, H. Biochemistry (2005) [Pubmed]
  13. rpoB mutation in Escherichia coli alters control of ribosome synthesis by guanosine tetraphosphate. Little, R., Ryals, J., Bremer, H. J. Bacteriol. (1983) [Pubmed]
  14. Effect of dnaA and rpoB mutations on attenuation in the trp operon of Escherichia coli. Atlung, T., Hansen, F.G. J. Bacteriol. (1983) [Pubmed]
  15. Participation of Rho-dependent transcription termination in oxidative stress sensitivity caused by an rpoB mutation. Kawamura, N., Kurokawa, K., Ito, T., Hamamoto, H., Koyama, H., Kaito, C., Sekimizu, K. Genes Cells (2005) [Pubmed]
  16. Synthesis of the beta and beta' subunits of Escherichia coli RNA polymerase is autogenously regulated in vivo by both transcriptional and translational mechanisms. Dykxhoorn, D.M., St Pierre, R., Linn, T. Mol. Microbiol. (1996) [Pubmed]
  17. Genetic analysis of zwittermicin A resistance in Escherichia coli: effects on membrane potential and RNA polymerase. Stabb, E.V., Handelsman, J. Mol. Microbiol. (1998) [Pubmed]
  18. Autogenous regulation of the RNA polymerase beta subunit of Escherichia coli occurs at the translational level in vivo. Passador, L., Linn, T. J. Bacteriol. (1989) [Pubmed]
  19. RNA polymerase mutation activates the production of a dormant antibiotic 3,3'-neotrehalosadiamine via an autoinduction mechanism in Bacillus subtilis. Inaoka, T., Takahashi, K., Yada, H., Yoshida, M., Ochi, K. J. Biol. Chem. (2004) [Pubmed]
  20. Amino acid substitutions in the two largest subunits of Escherichia coli RNA polymerase that suppress a defective Rho termination factor affect different parts of the transcription complex. Heisler, L.M., Feng, G., Jin, D.J., Gross, C.A., Landick, R. J. Biol. Chem. (1996) [Pubmed]
  21. Genetic antagonism and hypermutability in Mycobacterium smegmatis. Karunakaran, P., Davies, J. J. Bacteriol. (2000) [Pubmed]
  22. DksA affects ppGpp induction of RpoS at a translational level. Brown, L., Gentry, D., Elliott, T., Cashel, M. J. Bacteriol. (2002) [Pubmed]
  23. Isolation and characterization of temperature-sensitive pantothenate kinase (coaA) mutants of Escherichia coli. Vallari, D.S., Rock, C.O. J. Bacteriol. (1987) [Pubmed]
  24. 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]
  25. Rifampin and rpoB mutations can alter DNA supercoiling in Escherichia coli. Drlica, K., Franco, R.J., Steck, T.R. J. Bacteriol. (1988) [Pubmed]
  26. Transformation of Rickettsia prowazekii to rifampin resistance. Rachek, L.I., Tucker, A.M., Winkler, H.H., Wood, D.O. J. Bacteriol. (1998) [Pubmed]
  27. Rifampin resistance mutations that alter the efficiency of transcription termination at the tryptophan operon attenuator. Yanofsky, C., Horn, V. J. Bacteriol. (1981) [Pubmed]
  28. Molecular evolution of rifampicin resistance in Streptococcus pneumoniae. Enright, M., Zawadski, P., Pickerill, P., Dowson, C.G. Microb. Drug Resist. (1998) [Pubmed]
  29. Identification and mapping of a chromosomal gene cluster of Borrelia burgdorferi containing genes expressed in vivo. Aron, L., Toth, C., Godfrey, H.P., Cabello, F.C. FEMS Microbiol. Lett. (1996) [Pubmed]
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