Whole-genome mutational biases in bacteria

Abstract

A fundamental biological question is what forces shape the guanine plus cytosine (GC) content of genomes. We studied the specificity and rate of different mutational biases in real time in the bacterium Salmonella typhimurium under conditions of strongly reduced selection and in the absence of the major DNA repair systems involved in repairing common spontaneous mutations caused by oxidized and deaminated DNA bases. The mutational spectrum was determined by whole-genome sequencing of two S. typhimurium mutants that were serially passaged for 5,000 generations. Analysis of 943 identified base pair substitutions showed that 91% were GC-to-TA transversions and 7% were GC-to-AT transitions, commonly associated with 8-oxoG- and deamination-induced damages, respectively. Other types of base pair substitutions constituted the remaining 2% of the mutations. With regard to mutational biases, there was a significant increase in C-to-T transitions on the nontranscribed strand, and for highly expressed genes, C/G-to-T mutations were more common than expected; however, no significant mutational bias with regard to leading and lagging strands of replication or chromosome position were found. These results suggest that, based on the experimentally determined mutational rates and specificities, a bacterial genome lacking the relevant DNA repair systems could, as a consequence of these underlying mutational biases, very rapidly reduce its GC content.

Fig. 1.

Mutation rates to rifampicin resistance for ancestral strains and lineages after 200 growth cycles. Closed circles represent the ancestral strains before mutation accumulation; open circles represent the evolved strains. Mutation rates were increased 6-fold in the ung- and ung- vsr- mutants and ≈100-fold in the mutM- mutY- and ung- vsr- mug- mutM- mutY- mutants compared with the wild type (3 × 10⁻⁹), with no significant differences between ancestral and evolved strains.

Fig. 2.

Empirical cumulative distribution functions of (A) GC-to-TA transversions and (B) GC-to-AT transitions. If mutations are distributed randomly with regard to chromosomal location, then a linear relationship is expected, with no deviations at the origin of replication (4.08 Mbp) or terminus (1.61 Mbp).

Fig. 3.

(A) Mean fitness of the evolved strains, measured as the generation time during exponential growth in rich growth medium normalized by the generation time of the ancestral wild type included in each experiment. (B) Variance in fitness between lineages of the evolved strains.