An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli

Abstract

BackgroundThere are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation.ResultsHierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (p<0.001). This is further supported by a linear association between strain-wise dS and dN values (β = 26.94 ± 0.44, R2~0.98, p<0.001). The non-core part of the genome was also significantly more AT-rich (p<0.001) than the core genome and E. coli genome size correlated with estimated HGT size (p<0.001). In addition, genome size (p<0.001), AT content (p<0.001) as well as estimated HGT size (p<0.005) were all associated with the presence of virulence factors, suggesting that pathogenicity traits in E. coli are largely attained through HGT. No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98).ConclusionsOn a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-882) contains supplementary material, which is available to authorized users.

More than 18,000 effectors in the Legionella genus genome provide multiple, independent combinations for replication in human cells

“…These T4ASSs [classified as T4SSF, -G, -I, and -T (17)] are present in each strain to varying degrees, indicating that they circulate among the different Legionella strains (SI Appendix, Table S2) and therefore drive genome dynamics and diversification. It has been suggested that the incorporation of foreign DNA via horizontal gene transfer (HGT) is responsible for an increase in the AT content and the increase in genome size (18). Indeed, we found a negative correlation between the genome size and the GC content for the Legionella genomes, which also suggests frequent HGT ( Fig.…”

Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai–Tibet plateau of China

“…30 Phylogroup A is known to have diverged the latest among the phylogroups. 40, 43 By virulence gene content, phylogroup A contained the least number of virulence factors. 12 Indeed the well-known commensal E. coli strains in phylogroup A, HS, K-12 and BL21, contained none, one ( aslA ) and three ( aslA, kpsD and shiA ) of the 22 virulence genes, respectively.…”

The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes

“…Accessory genes, on the other hand, may increase fitness due to a particular environmental niche or short-term exposure such as antibiotic challenge [ 39 ]. It is presumed that core genomes are subjected to stronger purifying selection than the accessory genome, since they have been retained in all strains of a species [ 5 , 38 , 40 – 44 ]. Hence, analyzing the intragenic nucleotide composition in microbial core and accessory genomes could reveal how selective pressures, as well as putative selectively neutral processes such as gBGC and amelioration, affect base composition.…”