Accelerated gene evolution through replication–transcription conflicts

Abstract

Summary Several mechanisms that increase the rate of mutagenesis across the entire genome have been identified; however, how the rate of evolution might be promoted in individual genes is unclear. A majority of the genes in bacteria are encoded on the leading strand of replication1–4. This presumably avoids the potentially detrimental head-on collisions that occur between the replication and transcription machineries when genes are encoded on the lagging strand1–4. We identified the ubiquitous (core) genes in Bacillus subtilis and determined that 17% of them are on the lagging strand. We found a higher rate of point mutations in the core genes on the lagging strand compared to those on the leading strand, with this difference being primarily in the amino acid changing (nonsynonymous) mutations. We determined that overall, the genes under strong negative selection against amino acid changing mutations tend to be on the leading strand, co-oriented with replication. In contrast, based on the rate of convergent mutations, genes under positive selection for amino acid changing mutations are more commonly found on the lagging strand, indicating faster adaptive evolution in many genes in the head-on orientation. Increased gene length and gene expression levels are positively correlated with the rate of accumulation of nonsynonymous mutations in the head-on genes, suggesting that the conflict between replication and transcription could be a driving force behind these mutations. Indeed, using reversion assays, we show that the difference in the rate of mutagenesis of genes in the two orientations is transcription-dependent. Altogether, our findings indicate that head-on replication-transcription conflicts are more mutagenic than co-directional conflicts and that these encounters can significantly increase adaptive structural variation in the coded proteins. We propose that bacteria, and potentially other organisms, promote faster evolution of specific genes through orientation-dependent encounters between DNA replication and transcription.

An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis

“…We then determined the rate of accumulation of each type of SNP, in relation to protein length, for both strands. Our group, as well as others, has used gene length as a surrogate for conflict frequency (12,66), because replication and transcription machineries both spend an increased length of time traversing longer genes, increasing the chances for collisions. Because the analysis compares SNPs within species, the ancestral identity of a given nucleotide is unknown; thus, it is not possible to determine the directionality of the mutations.…”

“…This model was based on evolutionary analyses of several different B. subtilis genomes, where we found that highly conserved head-on genes accumulate amino acid-changing mutations at a higher rate compared with codirectional genes (12). Furthermore, based on experimental evidence, we proposed that the differential rate of mutagenesis for the genes in the two orientations is due to the two types of replication-transcription collisions.…”

“…Although head-on transcription is demonstrably more detrimental to the cell, the fundamental mechanism that underlies orientationdependent severity remains a mystery. Additionally, in Bacillus subtilis (and other bacteria), a significant number of highly conserved genes (17%) and some essential genes (6%) remain on the lagging strand (12) and thus are transcribed head-on with respect to replication. Whether there are biological reasons for the headon orientation of these genes is unclear.…”

The rpoS Gene Is Predominantly Inactivated during Laboratory Storage and Undergoes Source-Sink Evolution in Escherichia coli Species

“…In nature, a wide continuum of phenotypes is observed in isolates from individual patients suffering from severe E. coli extraintestinal infections due to a tradeoff between self-preservation and nutritional competence as a consequence of variable levels of RpoS (22). Interestingly, the rpoS gene is located on the lagging strand, where the rate of point mutations is higher than on the leading strand, probably due to conflicts between replication and transcription (3). rpoS is also located close to the MR gene mutS, in a region that has high genomic variability as a result of horizontal gene transfer (23,24).…”

“…Some regions of bacterial chromosomes are more prone to mutation (1)(2)(3)(4) or recombination (5) than other regions, due to physical or physiological constraints. Then, selection can favor diversification, for example, that of cell surface proteins such as beta barrel porins (6), and recombination events, which can restore particular functions, as in the case of the mismatch repair (MR) genes (7,8).…”