Fitness-compensatory mutations in rifampicin-resistant RNA polymerase

Mol Microbiol. 2012 Jul;85(1):142-51. doi: 10.1111/j.1365-2958.2012.08099.x. Epub 2012 May 31.


Mutations in rpoB (RNA polymerase β-subunit) can cause high-level resistance to rifampicin, an important first-line drug against tuberculosis. Most rifampicin-resistant (Rif(R)) mutants selected in vitro have reduced fitness, and resistant clinical isolates of M. tuberculosis frequently carry multiple mutations in RNA polymerase genes. This supports a role for compensatory evolution in global epidemics of drug-resistant tuberculosis but the significance of secondary mutations outside rpoB has not been demonstrated or quantified. Using Salmonella as a model organism, and a previously characterized Rif(R) mutation (rpoB R529C) as a starting point, independent lineages were evolved with selection for improved growth in the presence and absence of rifampicin. Compensatory mutations were identified in every lineage and were distributed between rpoA, rpoB and rpoC. Resistance was maintained in all strains showing that increased fitness by compensatory mutation was more likely than reversion. Genetic reconstructions demonstrated that the secondary mutations were responsible for increasing growth rate. Many of the compensatory mutations in rpoA and rpoC individually caused small but significant reductions in susceptibility to rifampicin, and some compensatory mutations in rpoB individually caused high-level resistance. These findings show that mutations in different components of RNA polymerase are responsible for fitness compensation of a Rif(R) mutant.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antibiotics, Antitubercular / pharmacology*
  • Bacterial Proteins / drug effects
  • Bacterial Proteins / genetics
  • DNA-Directed RNA Polymerases / drug effects
  • DNA-Directed RNA Polymerases / genetics*
  • Genetic Fitness*
  • Microbial Sensitivity Tests
  • Mutation
  • Phenotype
  • Protein Structure, Tertiary
  • Rifampin / pharmacology*
  • Salmonella typhimurium / drug effects
  • Salmonella typhimurium / genetics*
  • Salmonella typhimurium / growth & development


  • Antibiotics, Antitubercular
  • Bacterial Proteins
  • DNA-Directed RNA Polymerases
  • RNA polymerase beta subunit
  • Rifampin