Signs of neutralization in a redundant gene involved in homologous recombination in Wolbachia endosymbionts

Abstract

Genomic reduction in bacterial endosymbionts occurs through large genomic deletions and long-term accumulation of mutations. The latter process involves successive steps including gene neutralization, pseudogenization, and gradual erosion until complete loss. Although many examples of pseudogenes at various levels of degradation have been reported, neutralization cases are scarce because of the transient nature of the process. Gene neutralization may occur due to relaxation of selection in nonessential genes, for example, those involved in redundant functions. Here, we report an example of gene neutralization in the homologous recombination (HR) pathway of Wolbachia, a bacterial endosymbiont of arthropods and nematodes. The HR pathway is often depleted in endosymbiont genomes, but it is apparently intact in some Wolbachia strains. Analysis of 12 major HR genes showed that they have been globally under strong purifying selection during the evolution of Wolbachia strains hosted by arthropods, supporting the evolutionary importance of the HR pathway for these Wolbachia genomes. However, we detected signs of recent neutralization of the ruvA gene in a subset of Wolbachia strains, which might be related to an ancestral, clade-specific amino acid change that impaired DNA-binding activity. Strikingly, RuvA is part of the RuvAB complex involved in branch migration, whose function overlaps with the RecG helicase. Although ruvA is experiencing neutralization, recG is under strong purifying selection. Thus, our high phylogenetic resolution suggests that we identified a rare example of targeted neutralization of a gene involved in a redundant function in an endosymbiont genome.

Keywords: endosymbiosis; gene loss; genomic reduction; molecular evolution; nonorthologous gene displacement; selection relaxation.

Fig. 1.—

Gene loss through pseudogenization. Starting from a functional gene under selection (a) relaxation of selective pressures leads to accumulation of slightly deleterious mutations and neutralization of the gene (b) until the gene is effectively inactivated and pseudogenized (c). A bias in favor of deletions (yellow bars) relative to insertions (blue bars) leads to gradual erosion of the pseudogene (d) until its complete loss (e).

Fig. 2.—

Schematic representation of the HR pathway. Repair of DNA single- and double-strand breaks is initiated by RecJ/RecFOR and AddAB, respectively. The initiation step promotes the recruitment of RecA filament that catalyzes strand exchange. Then, branch migration and resolution of Holliday junction is completed by the RuvABC complex or RecG helicase. Repair of DNA double-strand breaks is finally completed with PriA which mediates primosome assembly for replication.

Fig. 3.—

Maximum-likelihood phylogenetic tree of the 12 concatenated HR genes, based on the GTR+G model (gamma = 5) and 85% partial deletion. Bootstrap scores (%) are shown on branches (based on 1,000 replicates). The phylogenetic tree reveals three highly supported monophyletic groups, each composed of six Wolbachia strains including: Strains from supergroup A, from supergroup B hosted by insects and from supergroup B hosted by isopods. Intragroup mean distances are noted besides each group. Intergroup mean distances are: 10.2% between A and B from insects, 9.3% between A and B from isopods, and 5.9% between B from insects and B from isopods.