Evolution of genetic diversity of repetitive extragenic palindromic elements (REPs): A comparative study

Jaroslav Nunvář

IBT, Prague

Repetitive extragenic palindromic elements (REPs) constitute a group of bacterial genomic repeats known for their high abundance and several functions of importance for host cells´ physiology. We analyzed the phylogenetic distribution of particular classes of REP elements in genomic sequences of sixty-three bacterial strains belonging to the Pseudomonas fluorescens species complex and ten strains of Stenotrophomonas sp., in order to assess intraspecific REP diversity and to gain insight into long-term REP evolution.

Based on proximity to RAYT (REP-associated tyrosine transposase) genes, twenty-two and thirteen unique REP classes were determined in fluorescent pseudomonads and stenotrophomonads, respectively. REPs were generally occurring in hundreds or even over a thousand of perfect copies of particular REP class per genome. REP sequences showed highly heterogenous distribution. The abundances of REP classes roughly followed host strains´ phylogeny, differing markedly among phylogenetic clades. High abundances of particular REP classes appeared to depend on the presence of cognate RAYT gene, and deviations from this state could be attributed to recent or ancient mutations of rayt-flanking REPs, or RAYT loss. RAYTs of both studied bacterial groups are monophyletic, and their cognate REPs show species-specific characteristics, suggesting shared evolutionary history of REPs, RAYTs and their hosts.

Our results show that REP elements constitute intriguingly dynamic components of genomes of fluorescent pseudomonads and stenotrophomonads, and indicate that REP diversification and proliferation are ongoing processes. High numbers of REPs have apparently been retained during the entire evolutionary time since the establishment of these two bacterial lineages, probably because of their beneficial effect on host long-term fitness. REP elements in these bacteria represent suitable platform to study interplay between repeated elements, their mobilizers and host bacterial cells.