Recombination in Bacterial Genomes: Evolutionary Trends

Abstract

Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.

Recombine and succeed: a story of Cry toxins to expand the host range

“…Recombination is considered one of the key evolutionary forces in the bacterial world. Apart from maintaining genomic diversity, this phenomenon increases environmental fitness thereby enabling organisms to thrive in novel niches during ecological diversification and the establishment of symbiotic/pathogenic relationships [50]. Although this phenomenon is mostly viewed as the replacement of the entire genes, recent studies show that intra-genic recombination causing domain swapping often occurs in loci encoding bacterial toxins, e.g., in Clostridium botulinum [51] or Streptococcus salivarius [52], being essential for the evolution of pathogenicity determinants (Supplementary text).…”

Diversity, Distribution, and Chromosomal Rearrangements of TRIP1 Repeat Sequences in Escherichia coli

“…In the E. coli genomes, a few TRIP1 repeats were found at the junction of flanking genes from two separate loci. This is a typical result of intra-chromosomal rearrangement caused by repeat sequences [6,43,44]. To determine the frequency and influence of chromosomal arrangement caused by TRIP1 repeats, we scanned all genomes for the relative position of the 10 flanking genes from the five loci.…”