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Gene Review

rpoB  -  DNA-directed RNA polymerase subunit beta

Mycobacterium tuberculosis H37Rv

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Disease relevance of rpoB

  • We assessed the performance of the Genotype MTBDR line probe assay that offers the simultaneous identification of Mycobacterium tuberculosis and its resistance to rifampin (RIF) and isoniazid (INH) by detecting the most commonly found mutations in the rpoB and katG genes [1].
  • The dominant-negative mutant rpoB gene is a potential suicide gene especially for the treatment of multidrug-resistant tuberculosis once a delivery strategy is also developed [2].
  • A clinical isolate of Helicobacter pylori that developed resistance to rifabutin during therapy carried an rpoB gene that retained a wild-type cluster region sequence but had acquired a novel codon 149 (V149F) mutation [3].
  • All resistant laboratory mutants of H. pylori ATCC 43504 showed amino acid exchanges in codons 524 to 545 or codon 585 of the rpoB gene, corresponding to the gene sequences from Mycobacterium tuberculosis and Escherichia coli [4].
  • Sequencing of the rpoB gene in Legionella pneumophila and characterization of mutations associated with rifampin resistance in the Legionellaceae [5].

High impact information on rpoB

  • An array designed to determine the specific nucleotide sequence of 705 bp of the rpoB gene of Mycobacterium tuberculosis accurately detected rifampin resistance associated with mutations of 44 clinical isolates of M. tuberculosis [6].
  • However, for several species, the number of alleles in the 16S and rpoB gene sequences provided discordant estimates of the genetic diversity within a species [6].
  • An evolutionarily invariant lysine was substituted with arginine by site-directed mutagenesis in the rpoB gene [2].
  • The dominant-negative rpoB gene product inhibited a transposon-derived kanamycin-resistance gene in both M. smegmatis and M. tuberculosis H37Rv, leading to growth inhibition of the mycobacteria on solid media containing kanamycin [2].
  • IS6110 DNA fingerprinting and automated DNA sequencing of a region of the RNA polymerase beta subunit structural gene (rpoB) containing mutations that confer rifampin resistance showed that all organisms independently acquired the mono-rifampin-resistant phenotype [7].

Chemical compound and disease context of rpoB

  • In Mycobacterium tuberculosis there is a strong correlation between in-vitro resistance to rifampicin (RIF) and pyrazinamide (PZA) and mutations in rpoB and pncA, respectively [8].
  • New rpoB gene primers for detecting Rif(r) in Mycobacterium tuberculosis complex bacteria achieved 100% specificity and 88% (fresh sputa) and 92% (ethanol-preserved sputa) diagnostic sensitivity and detected up to 4 CFU/sample [9].

Biological context of rpoB


Anatomical context of rpoB

  • The system could detect mutations of the rpoB, katG, and embB genes in DNAs extracted from 45 laboratory strains and from sputum samples of 27 patients with pulmonary TB [15].
  • Mutations in the rpoB gene were identified, and the growth rates of three defined mutants were measured by competition with the susceptible parent strain in laboratory medium and by single cultures in a macrophage cell line and in laboratory medium [16].
  • The rpoB mRNA was also localised to CD68-positive cells with the morphology of macrophages and to giant cells of certain necrotic granulomas [17].

Associations of rpoB with chemical compounds

  • Sequencing of consecutive isolates identified by the National Tuberculosis Program showed 89% of isoniazid-resistant isolates could be detected by targeting just 2 codons, katG 315 and -15C-->T in the inhA promoter, while rifampin resistance will be more complex to detect, with many different mutation and insertion events in rpoB [18].
  • The most frequent mutation, encountered in 6 of 10 strains (60%), was in the rpoB gene; it occurred, at codon position 521 and resulted in leucine changed to proline [19].
  • RMP and PZA resistances are associated with multiple mutations within the rpoB and pncA genes, respectively [10].
  • Alterations in rpoB, rpsL and katG gene may be the important mechanism of M. tuberculosis resistance to RFP, SM, and INH [20].
  • There was geographic variation in the frequency of occurrence of particular rpoB mutations, with the Ser531 --> Leu/Trp codon mutation found in 59/113 of isolates [21].

Other interactions of rpoB


Analytical, diagnostic and therapeutic context of rpoB

  • Multiple mutations at a specific rpoB nucleotide in target PCR products could be identified, as could mutants that were present at > or =0.5% of the total population of target sequences [22].
  • Heteroduplex analysis of rpoB, detected 16 (76.2%) of 21 rifampin-resistant strains, whereas direct DNA sequencing detected all rifampin-resistant strains [23].
  • The nucleotide sequence diversity in 121 Mycobacterial isolates (comprised of 10 species) was examined by both conventional dideoxynucleotide sequencing of the rpoB and 16S genes and by analysis of the rpoB oligonucleotide array hybridization patterns [6].
  • Comparative evaluation of polymerase chain reaction and restriction enzyme analysis: two amplified targets, hsp65 and rpoB, for identification of cultured mycobacteria [24].
  • OBJECTIVE: To evaluate the use of denaturation high-performance liquid chromatography (dHPLC) as a rapid method to detect rifampicin (RMP) resistance based on mutations in the rpoB gene in a high-volume laboratory setting [25].


  1. Performance of the Genotype MTBDR Line Probe Assay for Detection of Resistance to Rifampin and Isoniazid in Strains of Mycobacterium tuberculosis with Low- and High-Level Resistance. Brossier, F., Veziris, N., Truffot-Pernot, C., Jarlier, V., Sougakoff, W. J. Clin. Microbiol. (2006) [Pubmed]
  2. Development of a suicide gene as a novel approach to killing Mycobacterium tuberculosis. Rom, W.N., Yie, T.A., Tchou-Wong, K.M. Am. J. Respir. Crit. Care Med. (1997) [Pubmed]
  3. Mutations in the beginning of the rpoB gene can induce resistance to rifamycins in both Helicobacter pylori and Mycobacterium tuberculosis. Heep, M., Rieger, U., Beck, D., Lehn, N. Antimicrob. Agents Chemother. (2000) [Pubmed]
  4. Rifampin and rifabutin resistance mechanism in Helicobacter pylori. Heep, M., Beck, D., Bayerdörffer, E., Lehn, N. Antimicrob. Agents Chemother. (1999) [Pubmed]
  5. Sequencing of the rpoB gene in Legionella pneumophila and characterization of mutations associated with rifampin resistance in the Legionellaceae. Nielsen, K., Hindersson, P., Hoiby, N., Bangsborg, J.M. Antimicrob. Agents Chemother. (2000) [Pubmed]
  6. Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Gingeras, T.R., Ghandour, G., Wang, E., Berno, A., Small, P.M., Drobniewski, F., Alland, D., Desmond, E., Holodniy, M., Drenkow, J. Genome Res. (1998) [Pubmed]
  7. Independent origin of mono-rifampin-resistant Mycobacterium tuberculosis in patients with AIDS. Lutfey, M., Della-Latta, P., Kapur, V., Palumbo, L.A., Gurner, D., Stotzky, G., Brudney, K., Dobkin, J., Moss, A., Musser, J.M., Kreiswirth, B.N. Am. J. Respir. Crit. Care Med. (1996) [Pubmed]
  8. Simultaneous identification and typing of multi-drug-resistant Mycobacterium tuberculosis isolates by analysis of pncA and rpoB. Brown, T.J., Tansel, O., French, G.L. J. Med. Microbiol. (2000) [Pubmed]
  9. Newly Developed Primers for Comprehensive Amplification of the rpoB Gene and Detection of Rifampin Resistance in Mycobacterium tuberculosis. Rigouts, L., Nolasco, O., de Rijk, P., Nduwamahoro, E., Van Deun, A., Ramsay, A., Arevalo, J., Portaels, F. J. Clin. Microbiol. (2007) [Pubmed]
  10. Genotypic determination of Mycobacterium tuberculosis antibiotic resistance using a novel mutation detection method, the branch migration inhibition M. tuberculosis antibiotic resistance test. Liu, Y.P., Behr, M.A., Small, P.M., Kurn, N. J. Clin. Microbiol. (2000) [Pubmed]
  11. Mutations in the rpoB and katG genes leading to drug resistance in Mycobacterium tuberculosis in Latvia. Tracevska, T., Jansone, I., Broka, L., Marga, O., Baumanis, V. J. Clin. Microbiol. (2002) [Pubmed]
  12. Prevalence of katG Ser315 substitution and rpoB mutations in isoniazid-resistant Mycobacterium tuberculosis isolates from Brazil. Höfling, C.C., Pavan, E.M., Giampaglia, C.M., Ferrazoli, L., Aily, D.C., de Albuquerque, D.M., Ramos, M.C. The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease. (2005) [Pubmed]
  13. Single-nucleotide polymorphism-based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum. Arnold, C., Westland, L., Mowat, G., Underwood, A., Magee, J., Gharbia, S. Clin. Microbiol. Infect. (2005) [Pubmed]
  14. Rifampin resistance in Mycobacterium kansasii is associated with rpoB mutations. Klein, J.L., Brown, T.J., French, G.L. Antimicrob. Agents Chemother. (2001) [Pubmed]
  15. Dual-probe assay for rapid detection of drug-resistant Mycobacterium tuberculosis by real-time PCR. Wada, T., Maeda, S., Tamaru, A., Imai, S., Hase, A., Kobayashi, K. J. Clin. Microbiol. (2004) [Pubmed]
  16. Effect of rpoB mutations conferring rifampin resistance on fitness of Mycobacterium tuberculosis. Mariam, D.H., Mengistu, Y., Hoffner, S.E., Andersson, D.I. Antimicrob. Agents Chemother. (2004) [Pubmed]
  17. Localisation of mycobacterial DNA and mRNA in human tuberculous granulomas. Fenhalls, G., Stevens-Muller, L., Warren, R., Carroll, N., Bezuidenhout, J., Van Helden, P., Bardin, P. J. Microbiol. Methods (2002) [Pubmed]
  18. Mutations prevalent among rifampin- and isoniazid-resistant Mycobacterium tuberculosis isolates from a hospital in Vietnam. Caws, M., Duy, P.M., Tho, D.Q., Lan, N.T., Hoa, D.V., Farrar, J. J. Clin. Microbiol. (2006) [Pubmed]
  19. Molecular basis of rifampin and isoniazid resistance in Mycobacterium bovis strains isolated in Sardinia, Italy. Sechi, L.A., Zanetti, S., Sanguinetti, M., Molicotti, P., Romano, L., Leori, G., Delogu, G., Boccia, S., La Sorda, M., Fadda, G. Antimicrob. Agents Chemother. (2001) [Pubmed]
  20. Molecular mechanisms of drug resistance in Mycobacterium tuberculosis clinical isolates. Wu, X., Zhang, J., Zhuang, Y., Zhang, X., Li, G., He, X. Chin. Med. J. (1999) [Pubmed]
  21. Comparison of PCR-heteroduplex characterization by automated DNA sequencing and line probe assay for the detection of rifampicin resistance in Mycobacterium tuberculosis isolates from KwaZulu-Natal, South Africa. Kiepiela, P., Bishop, K., Kormuth, E., Roux, L., York, D.F. Microb. Drug Resist. (1998) [Pubmed]
  22. Evaluation of the invader assay, a linear signal amplification method, for identification of mutations associated with resistance to rifampin and isoniazid in Mycobacterium tuberculosis. Cooksey, R.C., Holloway, B.P., Oldenburg, M.C., Listenbee, S., Miller, C.W. Antimicrob. Agents Chemother. (2000) [Pubmed]
  23. Detection of resistance to isoniazid, rifampin, and streptomycin in clinical isolates of Mycobacterium tuberculosis by molecular methods. Nachamkin, I., Kang, C., Weinstein, M.P. Clin. Infect. Dis. (1997) [Pubmed]
  24. Comparative evaluation of polymerase chain reaction and restriction enzyme analysis: two amplified targets, hsp65 and rpoB, for identification of cultured mycobacteria. Cheunoy, W., Prammananan, T., Chaiprasert, A., Foongladda, S. Diagn. Microbiol. Infect. Dis. (2005) [Pubmed]
  25. Denaturing HPLC for high-throughput screening of rifampicin-resistant Mycobacterium tuberculosis isolates. Yip, C.W., Leung, K.L., Wong, D., Cheung, D.T., Chu, M.Y., Tang, H.S., Kam, K.M. Int. J. Tuberc. Lung Dis. (2006) [Pubmed]
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