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The rpoB gene encodes the β subunit of bacterial RNA polymerase. It codes for 1342 amino acids, making it the second-largest polypeptide in the bacterial cell.[1] It is the site of mutations that confer resistance to the rifamycin antibacterial agents, such as rifampin.[2] Mutations in rpoB that confer resistance to rifamycins do so by altering residues of the rifamycin binding site on RNA polymerase, thereby reducing rifamycin binding affinity for rifamycins[3][4]

Initial studies were done by Jin and Gross to generate rpoB mutations in E. coli that conferred resistance to rifampicin. Three clusters of mutations were identified, cluster I at codons 507-533, cluster II at codons 563-572, and cluster III at codon 687.[1][5]

Nucleic acid probes can detect mutations in rpoB that confer rifampicin resistance. For Mycobacterium tuberculosis, the rifamycin-resistant mutations most commonly encountered involve codons 516, 526, and 531 (numbered, by convention, as in Escherichia coli rpoB).[6][7] For Staphylococcus aureus, the rifamycin-resistant mutation most commonly encountered involves codon 526.[8]

Some bacteria contain multiple copies of the 16S rRNA gene, which is commonly used as the molecular marker to study phylogeny. In these cases, the rpoB gene can be used to study microbial diversity.[9][10]


  1. ^ a b Goldstein, Beth P. "Resistance to rifampicin: a review". The Journal of Antibiotics. 67 (9): 625–630. doi:10.1038/ja.2014.107. 
  2. ^ Floss, H.G.; Yu, T. (2005). "Rifamycin-Mode of Action, Resistance, and Biosynthesis". Chem. Rev. 105 (2): 621–32. doi:10.1021/cr030112j. PMID 15700959. 
  3. ^ Campbell, E.A.; Korzheva, N.; Mustaev, A.; Murakami, K.; Nair, S.; Goldfarb, A.; Darst, S.A. (2001). "Structural mechanism for rifampicin inhibition of bacterial RNA polymerase". Cell. 104 (6): 901–12. doi:10.1016/S0092-8674(01)00286-0. PMID 11290327. 
  4. ^ Feklistov, A.; Mekler, V.; Jiang, Q.; Westblade, L.F.; Irschik, H.; Jansen, R.; Mustaev, A.; Darst, S.A.; Ebright, R.H. (2008). "Rifamycins do not function by allosteric modulation of binding of Mg2+ to the RNA polymerase active center". Proc Natl Acad Sci USA. 105 (39): 14820–5. doi:10.1073/pnas.0802822105. PMC 2567451Freely accessible. PMID 18787125. 
  5. ^ Jin, Ding Jun; Gross, Carol A. (1988-07-05). "Mapping and sequencing of mutations in the Escherichia colirpoB gene that lead to rifampicin resistance". Journal of Molecular Biology. 202 (1): 45–58. doi:10.1016/0022-2836(88)90517-7. 
  6. ^ Mokrousov, I.; Otten, T.; Vyshnevskiy, B.; Narvskaya, O. (2003). "Allele-Specific rpoB PCR Assays for Detection of Rifampin-Resistant Mycobacterium tuberculosis in Sputum Smears". Antimicrob Agents Chemother. 47 (7): 2231–2235. doi:10.1128/AAC.47.7.2231-2235.2003. PMC 161874Freely accessible. PMID 12821473. 
  7. ^ Telenti A; Imboden P; Marchesi F; et al. (1993). "Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis". Lancet. 341 (8846): 647–50. doi:10.1016/0140-6736(93)90417-F. PMID 8095569. 
  8. ^ Wichelhaus TA; Schäfer V; Brade V; Böddinghaus B (1999). "Molecular characterization of rpoB mutations conferring cross-resistance to rifamycins on methicillin-resistant Staphylococcus aureus". Antimicrob Agents Chemother. 43 (11): 2813–2816. PMC 89569Freely accessible. PMID 10543773. 
  9. ^ Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S (2007). "Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies". Appl. Environ. Microbiol. 73 (1): 278–88. doi:10.1128/AEM.01177-06. PMC 1797146Freely accessible. PMID 17071787. 
  10. ^ Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA (2012). "A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity". PLoS ONE. 7 (2): e30600. doi:10.1371/journal.pone.0030600. PMC 3280256Freely accessible. PMID 22355318.