Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

• Published in: Proceedings of the National Academy of Sciences - PNAS 2012-10, Vol.109 (41), p.E2774-E2783
• Main Authors: Lee, Heewook, Popodi, Ellen, Tang, Haixu, Foster, Patricia L
• Format: Article
• Language: English
• Subjects: Adenosine Triphosphatases - genetics; bacteria; base pair mismatch; Base Sequence; Binding Sites - genetics; Biological Sciences; DNA Methylation; DNA Mismatch Repair - genetics; DNA repair; DNA Replication - genetics; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; E coli; environmental factors; Escherichia coli; Escherichia coli - genetics; Escherichia coli Proteins - genetics; Genes, Bacterial - genetics; Genetics; genome; Genome, Bacterial - genetics; Genomes; INDEL Mutation; Monte Carlo Method; Mutation; Mutation Rate; MutL Proteins; PNAS Plus; Point Mutation; Polymorphism, Single Nucleotide; Selection, Genetic; sequence analysis; Sequence Analysis, DNA - methods
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1210309109

Knowledge of the rate and nature of spontaneous mutation is fundamental to understanding evolutionary and molecular processes. In this report, we analyze spontaneous mutations accumulated over thousands of generations by wild-type Escherichia coli and a derivative defective in mismatch repair (MMR), the primary pathway for correcting replication errors. The major conclusions are (i) the mutation rate of a wild-type E. coli strain is ∼1 × 10 ⁻³ per genome per generation; (ii) mutations in the wild-type strain have the expected mutational bias for G:C > A:T mutations, but the bias changes to A:T > G:C mutations in the absence of MMR; (iii) during replication, A:T > G:C transitions preferentially occur with A templating the lagging strand and T templating the leading strand, whereas G:C > A:T transitions preferentially occur with C templating the lagging strand and G templating the leading strand; (iv) there is a strong bias for transition mutations to occur at 5′ApC3′/3′TpG5′ sites (where bases 5′A and 3′T are mutated) and, to a lesser extent, at 5′GpC3′/3′CpG5′ sites (where bases 5′G and 3′C are mutated); (v) although the rate of small (≤4 nt) insertions and deletions is high at repeat sequences, these events occur at only 1/10th the genomic rate of base-pair substitutions. MMR activity is genetically regulated, and bacteria isolated from nature often lack MMR capacity, suggesting that modulation of MMR can be adaptive. Thus, comparing results from the wild-type and MMR-defective strains may lead to a deeper understanding of factors that determine mutation rates and spectra, how these factors may differ among organisms, and how they may be shaped by environmental conditions.