Complex prokaryotic genome structure: rapid evolution of chromosome II

Abstract

Although many bacteria with two chromosomes have been sequenced, the roles of such complex genome structuring are still unclear. To uncover levels of chromosome I (CI) and chromosome II (CII) sequence divergence, Mauve 2.2.0 was used to align the CI- and CII-specific sequences of bacteria with complex genome structuring in two sets of comparisons: the first set was conducted among the CI and CII of bacterial strains of the same species, while the second set was conducted among the CI and CII of species in Alphaproteobacteria that possess two chromosomes. The analyses revealed a rapid evolution of CII-specific DNA sequences compared with CI-specific sequences in a majority of organisms. In addition, levels of protein divergence between CI-specific and CII-specific genes were determined using phylogenetic analyses and confirmed the DNA alignment findings. Analysis of synonymous and nonsynonymous substitutions revealed that the structural and functional constraints on CI and CII genes are not significantly different. Also, horizontal gene transfer estimates in selected organisms demonstrated that CII in many species has acquired higher levels of horizontally transferred segments than CI. In summary, rapid evolution of CII may perform particular roles for organisms such as aiding in adapting to specialized niches.

Variation in genomic islands contribute to genome plasticity in Cupriavidus metallidurans

“…These results are in agreement with the study of Bavishi and colleagues [34], which indicated that chromosome 2 evolves faster than chromosome 1, leading to different conservation on inter- and intraspecies level. This global comparison also indicated that strain CH34 is more closely related to strains isolated from Congo than with the two other strains (CH42 and CH79) isolated in Belgium.…”

The Novel Sigma Factor-Like Regulator RpoQ Controls Luminescence, Chitinase Activity, and Motility in Vibrio fischeri

“…Interestingly, rpoQ and its A. salmonicida homologue, VSAL_II0319 , are found on the smaller, second chromosomes of V. fischeri and A. salmonicida , respectively, where many paralogs and nonessential genes are also located (43). Such a position would be consistent with our hypothesis that rpoQ is a recently duplicated gene and diverged in the Vibrionaceae (44, 45). …”

Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1

“…Although it is not immediately clear which predominates, it is probably a combination of both situations. As hypothesized before [26], it is likely then that relaxed structural constraints on the CII of bacteria significantly contributes to their increased evolution and divergence compared to CI, although the findings of the current study may stand in contrast to that idea.…”

“…In R. sphaeroides 2.4.1, CII has been shown to be rapidly evolving [25,26]. For this reason, the second hypothesis was that gene paralogs on different replicons might have experienced different selective pressures within R. sphaeroides and specifically that paralogs between CI and CII might have experienced different levels of selection from those contained strictly within CI, within CII, or within plasmids.…”

“…Therefore, the first hypothesis was that in-paralogs have experienced varying levels of selective constraints. Second, it was expected that gene paralogs on different chromosomes (CI and CII) have experienced different selective pressures, since CII sequences evolve more rapidly than the CI sequences in R. sphaeroides [25,26]. Third, since protein size is an indicator of gene complexity in eukaryotes [27], it is hypothesized that gene-pairs encoding larger proteins in complex prokaryotic genomes like R. sphaeroides are maintained by stronger selection than gene-pairs encoding smaller proteins.…”