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

TitleRNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.
Publication TypeJournal Article
Year of Publication2010
AuthorsConrad TM, Frazier M, Joyce AR, Cho B-K, Knight EM, Lewis NE, Landick R, Palsson BØ
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue47
Pagination20500-5
PubMed Date2010 Nov 23
ISSN1091-6490
KeywordsAdaptation, Physiological, Base Sequence, Chromatin Immunoprecipitation, Culture Media, DNA Primers, DNA-Directed RNA Polymerases, Escherichia coli, Escherichia coli Proteins, Evolution, Molecular, Gene Expression Profiling, Gene Knockout Techniques, Kinetics, Molecular Sequence Data, Mutagenesis, Site-Directed, Protein Array Analysis, Sequence Analysis, DNA, Sequence Deletion, Transcription, Genetic
Abstract

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.

Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID21057108

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