Use of the rpoB gene to determine the specificity of base substitution mutations on the Escherichia coli chromosome

DNA Repair (Amst). 2003 May 13;2(5):593-608. doi: 10.1016/s1568-7864(03)00024-7.


Mutations in the rpoB gene of Escherichia coli result in resistance to the antibiotic rifampicin (Rif(r)) by altering the beta subunit of RNA polymerase. Previous studies have identified 39 single base substitutions in the rpoB gene that lead to Rif(r) at 37 degrees C and an additional two mutations that result in temperature sensitive cells. We have extended this work and identified an additional 30 single base substitutions that result in the Rif(r) phenotype. With these mutations the rpoB/Rif(r) system now allows the monitoring of 69 base substitutions at 37 degrees at 37 sites (base pairs) distributed among 24 coding positions. Each of the six possible base substitutions is represented by 8-17 mutations. More than 90% of the mutations are within a small enough region of the rpoB gene to allow PCR amplification with a single pair of oligonucleotide primers, followed by sequencing with a single primer, leading to rapid analysis of numerous mutations. The remaining mutations can be monitored using an additional primer pair. To calibrate this system we sequenced over 500 mutations in rpoB occurring spontaneously or generated by different mutagens and mutators with known specificity. These results show that rpoB/Rif(r) is an accurate and easy to employ detection system, and offers the advantage of allowing analysis of mutations occurring on the chromosome rather than on an extrachromosomal element. The mutS, mutT, mutY, M mutators, as well as the mutagenic agents ethyl methanesulfonate (EMS), ultraviolet (UV) irradiation, 2-aminopurine (2AP), 5-azacytidine (5AZ), and cisplatin (CPT) gave results predicted by their characterized specificities. The number of different sequence contexts is sufficient to reveal significant hotspots among the spontaneous mutS, 2-aminopurine, ultraviolet light, 5-azacytidine, and cisplatin mutational spectra. The cisplatin distribution is particularly striking, with 68% of the mutations resulting from an A:T-->T:A transversion at a single site. Because of the conservation of key regions of RNA polymerase among many microorganisms, using the Rif(r)/rpoB system may be a general method for studying mutational processes in microorganisms without well developed genetic systems.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • 2-Aminopurine / chemistry
  • Adenosine Triphosphatases / genetics
  • Antibiotics, Antitubercular / pharmacology
  • Azacitidine / chemistry
  • Bacterial Proteins / genetics
  • Binding, Competitive
  • Chromosomes / ultrastructure*
  • Cisplatin / pharmacology
  • Cross-Linking Reagents / pharmacology
  • DNA Repair*
  • DNA-Binding Proteins*
  • DNA-Directed RNA Polymerases / genetics*
  • Drug Resistance, Bacterial
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / genetics
  • Ethyl Methanesulfonate / chemistry
  • MutS DNA Mismatch-Binding Protein
  • Mutation*
  • Phenotype
  • Phosphoric Monoester Hydrolases / genetics
  • Pyrophosphatases
  • Rifampin / pharmacology
  • Temperature
  • Ultraviolet Rays


  • Antibiotics, Antitubercular
  • Bacterial Proteins
  • Cross-Linking Reagents
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • 2-Aminopurine
  • Ethyl Methanesulfonate
  • DNA-Directed RNA Polymerases
  • RNA polymerase beta subunit
  • Phosphoric Monoester Hydrolases
  • Adenosine Triphosphatases
  • Pyrophosphatases
  • mutT protein, E coli
  • MutS DNA Mismatch-Binding Protein
  • MutS protein, E coli
  • Azacitidine
  • Cisplatin
  • Rifampin