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 deaminationinduced 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.dna repair ͉ experimental evolution ͉ gc bias ͉ mutation spectra ͉ Salmonella typhimurium A central question in evolutionary genomics is what mechanisms cause the variation observed in DNA base composition between and within genomes and how rapidly and by what mechanisms these biases might change in response to, for example, altered ecology and genetic constitution of the organism. The large range in guanine plus cytosine (GC) content among bacterial species is well established, varying between at least 17% and 75% GC, with an even larger variation in the third codon position (1). Within a genome, GC content usually is quite homogeneous and has a strong phylogenetic signal, but despite this overall homogeneity, there frequently exist strand-specific biases between the two strands of DNA such that the average nucleotide composition deviates from the theoretically expected A ϭ T and G ϭ C within each strand. Thus, most bacterial chromosomes are relatively strongly enriched in G over C and in T over A and are slightly depleted in GϩC in weakly selected positions in the leading strand compared with in the lagging strand (2). In addition, highly transcribed genes appear to show a G and T skew on the nontranscribed strand compared with poorly transcribed genes (3).Although the causes of these biases remain unclear, the biases can be expected to arise at least at three different levels. First, there might exist an underlying bias in the mutation pressure caused by unavoidable spontaneous DNA damage, such as deamination of C3U and 5-meC3T (4, 5) or oxidation of G to form 7,8-dihydro-8-oxoG (8-...

Rate and molecular spectrum of spontaneous mutations in the bacteriumEscherichia colias determined by whole-genome sequencing

“…None of these values is significantly different from expected (P ≥ 0.42 in every case). Thus, our results do not support previous observations that highly expressed genes have either high (11,35,36) or low (37-39) mutation rates. Unlike a previous report (39), we found no bias for any type of base change occurring preferentially on either the transcribed or the nontranscribed DNA strand (Table S3).…”

“…The application of whole-genome sequencing to MA lines has made this protocol an extremely valuable way to determine a complete and nearly unbiased picture of mutation profiles. Recent results from applying this protocol to microbes include the genomewide spontaneous mutational spectrum in Saccharomyces cerevisiae (10) and the mutational consequences of loss of DNA oxidative damage repair in Salmonella typhimurium (11).…”

The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia

“…Universal transition and G:C . A:T biases have also been observed in all MA studies to date (Lind and Andersson 2008;Lynch et al 2008;Denver et al 2009;Ossowski et al 2010;Lee et al 2012;Sung et al 2012a,b), corroborating previous findings using indirect methods (Hershberg and Petrov 2010;Hildebrand et al 2010). However, several additional characteristics of mutation spectra vary among species (Lynch et al 2008;Denver et al 2009;Ossowski et al 2010;Lee et al 2012;Sung et al 2012a,b), and examining the role of genome architecture, size, and lifestyle in producing these idiosyncrasies will require a considerably larger number of detailed MA studies.…”

“…The lack of mutational bias toward AT bases observed in B. cenocepacia has not been seen previously in nonmutator MA lineages of any kind (Lind and Andersson 2008;Lynch et al 2008;Denver et al 2009;Keightley et al 2009;Ossowski et al 2010;Lee et al 2012;Sung et al 2012a,b). However, selection and/or biased gene conversion must still be invoked to explain the high %GC content in B. cenocepacia (Hershberg and Petrov 2010;Hildebrand et al 2010).…”

Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea

“…However, recent studies have shown that the variation of the GC content among bacteria is driven by selection, in which mutations from GC to adenosine-thymine (AT) are more common than mutations from AT to GC (Hershberg and Petrov, 2010;Hildebrand et al, 2010;Rocha and Feil, 2010). Lind and Andersson (2008) compared the genomes of 2 Salmonella typhimurium mutants and showed a bias toward mutations from GC to AT. Rocha and Danchin (2002) suggested that GC content variation may be related to the higher energy cost and limited availability of G and C over A and T. However, many bacterial species such as Actinobacteria have a high GC content genome.…”