RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

Proc Natl Acad Sci U S A. 2010 Nov 23;107(47):20500-5. doi: 10.1073/pnas.0911253107. Epub 2010 Nov 5.


Specific small deletions within the rpoC gene encoding the β'-subunit of RNA polymerase (RNAP) are found repeatedly after adaptation of Escherichia coli K-12 MG1655 to growth in minimal media. Here we present a multiscale analysis of these mutations. At the physiological level, the mutants grow 60% faster than the parent strain and convert the carbon source 15-35% more efficiently to biomass, but grow about 30% slower than the parent strain in rich medium. At the molecular level, the kinetic parameters of the mutated RNAP were found to be altered, resulting in a 4- to 30-fold decrease in open complex longevity at an rRNA promoter and a ∼10-fold decrease in transcriptional pausing, with consequent increase in transcript elongation rate. At a genome-scale, systems biology level, gene expression changes between the parent strain and adapted RNAP mutants reveal large-scale systematic transcriptional changes that influence specific cellular processes, including strong down-regulation of motility, acid resistance, fimbria, and curlin genes. RNAP genome-binding maps reveal redistribution of RNAP that may facilitate relief of a metabolic bottleneck to growth. These findings suggest that reprogramming the kinetic parameters of RNAP through specific mutations allows regulatory adaptation for optimal growth in new environments.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Adaptation, Physiological / genetics*
  • Base Sequence
  • Chromatin Immunoprecipitation
  • Culture Media / chemistry
  • DNA Primers / genetics
  • DNA-Directed RNA Polymerases / genetics*
  • Escherichia coli / enzymology*
  • Escherichia coli / growth & development*
  • Escherichia coli Proteins / genetics*
  • Evolution, Molecular*
  • Gene Expression Profiling
  • Gene Knockout Techniques
  • Kinetics
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Protein Array Analysis
  • Sequence Analysis, DNA
  • Sequence Deletion / genetics
  • Transcription, Genetic / physiology


  • Culture Media
  • DNA Primers
  • Escherichia coli Proteins
  • beta' subunit of RNA polymerase
  • DNA-Directed RNA Polymerases

Associated data

  • GEO/GSE15500