Rates of Lateral Gene Transfer in Prokaryotes: High but Why?

Abstract

Lateral gene transfer is of fundamental importance to the evolution of prokaryote genomes and has important practical consequences, as evidenced by the rapid dissemination of antibiotic resistance and virulence determinants. Relatively little effort has so far been devoted to explicitly quantifying the rate at which accessory genes are taken up and lost, but it is possible that the combined rate of lateral gene transfer and gene loss is higher than that of point mutation. What evolutionary forces underlie the rate of lateral gene transfer are not well understood. We here use theory developed to explain the evolution of mutation rates to address this question and explore its consequences for the study of prokaryote evolution.

Prokaryote genome fluidity is dependent on effective population size

“…This finding supports the emerging view that changes in gene content occur at high rates relative to mutation in bacteria (Touchon et al , 2009; Nowell et al , 2014; Vos et al , 2015; Wielgoss et al , 2016). The uptake and loss of accessory genes is in part mediated via recombination of flanking homologous sequences (Polz et al , 2013).…”

Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica

“…On the other hand, 13 IS elements were found in the ATH-43 genome sequence using the IS finder tool (www-is.biotoul.fr), along with 21 transposases and 17 integrases (not shown), all elements routinely associated with horizontal gene transfer providing advantage in metal and antibiotic resistance, general stress tolerance, and aromatic compound degradation, among others (Vos et al, 2015; Koonin, 2016). As with tRNA genes, the genome of ATH-43 displays a higher number of genetic determinants involved in metal, antibiotic, and oxidative stress resistance as compared with other reference P. putida genomes (Wu et al, 2011), which may be a reflect of the dramatic selective pressure occurring in the Antarctic continent.…”

Why prokaryotes have pangenomes

“…Evolutionary theory tells us that the fate of a new allele in a population is dependent on the long-term effective population size of the species and the fitness effect of the new allele 25 . A truly neutral new allele in a population of size N will have an initial frequency of 1/N.…”

“…However, while HGT can have these costs, if HGT were always deleterious, or even usually deleterious it could not result in pangenomes. Additionally the knock-on effect would be to promote the evolution of lower HGT rates 25 . It is clear that HGT rates, at least in some organisms, are quite high 30 , suggesting that HGT is not always deleterious.…”