Recombination between elongation factor 1α genes from distantly related archaeal lineages

Abstract

Homologous recombination (HR) and lateral gene transfer are major processes in genome evolution. The combination of the two processes, HR between genes in different species, has been documented but is thought to be restricted to very similar sequences in relatively closely related organisms. Here we report two cases of interspecific HR in the gene encoding the core translational protein translation elongation factor 1␣ (EF-1␣) between distantly related archaeal groups. Maximum-likelihood sliding window analyses indicate that a fragment of the EF-1␣ gene from the archaeal lineage represented by Methanopyrus kandleri was recombined into the orthologous gene in a common ancestor of the Thermococcales. A second recombination event appears to have occurred between the EF-1␣ gene of the genus Methanothermobacter and its ortholog in a common ancestor of the Methanosarcinales, a distantly related euryarchaeal lineage. These findings suggest that HR occurs across a much larger evolutionary distance than generally accepted and affects highly conserved essential ''informational'' genes. Although difficult to detect by standard whole-gene phylogenetic analyses, interspecific HR in highly conserved genes may occur at an appreciable frequency, potentially confounding deep phylogenetic inference and hypothesis testing.hypothesis testing ͉ lateral gene transfer ͉ maximum likelihood ͉ sliding window analysis

Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code

“…To our knowledge, previously published reconstructions of ancient protein families have not been impacted by known partial HGT events. While it has been shown that partial HGT events have occurred within the EF-1a sequences of some archaeal lineages (Inagaki et al 2006), these groups were not included in the published ancestral reconstruction of homologous bacterial EF-Tu proteins (Gaucher et al 2003).…”

Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes

“…Second, the generally low rates of point mutation (8,9) and the relatively high degree of sequence conservation of chloroplast and plant mitochondrial genes increase the probability that these genes might at least occasionally recombine with one another. Third, although the frequency of homologous recombination correlates positively and tightly with DNA sequence similarity and decreases sharply with the level of relatedness between donor and recipient (10,11), several cases have nonetheless been reported in recent years of recombination between sequences that are distantly related in time and/or sequence (5,(12)(13)(14)(15). Finally, 2 cases are now known of plant mitochondrial housekeeping genes that have a clear history of chimerism, through recombination between native mitochondrial genes and foreign copies acquired via horizontal gene transfer from other, distantly related angiosperms (16,17).…”

Lateral Transfer of Genes and Gene Fragments in Staphylococcus Extends beyond Mobile Elements

“…It has been shown, how-ever, that genetic material integrated via LGT can constitute an entire gene (41,104), a partial (fragmentary) gene (10,49,75), or multiple (entire or fragmentary) adjacent genes, including multigene operons (34,48,81). We recently examined the transfer of genes and gene fragments among 144 prokaryote genomes (15,18), demonstrating that studies focusing entirely on whole-gene transfer are likely to underestimate the extent of LGT.…”