Defying Muller's Ratchet: Ancient Heritable Endobacteria Escape Extinction through Retention of Recombination and Genome Plasticity

Abstract

Heritable endobacteria, which are transmitted from one host generation to the next, are subjected to evolutionary forces that are different from those experienced by free-living bacteria. In particular, they suffer consequences of Muller's ratchet, a mechanism that leads to extinction of small asexual populations due to fixation of slightly deleterious mutations combined with the random loss of the most-fit genotypes, which cannot be recreated without recombination. Mycoplasma-related endobacteria (MRE) are heritable symbionts of fungi from two ancient lineages, Glomeromycota (arbuscular mycorrhizal fungi) and Mucoromycotina Previous studies revealed that MRE maintain unusually diverse populations inside their hosts and may have been associated with fungi already in the early Paleozoic. Here we show that MRE are vulnerable to genomic degeneration and propose that they defy Muller's ratchet thanks to retention of recombination and genome plasticity. We suggest that other endobacteria may be capable of raising similar defenses against Muller's ratchet.

FIG 1

Bayesian phylogeny of MRE reconstructed based on the concatenated nucleotide sequences of the following genes: dnaG, infC, nusA, rplA, rplB, rplC, rplE, rplF, rplM, rplN, rplP, rplT, rpmA, rpsB, rpsC, rpsE, rpsJ, rpsS, and smpB. MRE were sampled from Dentiscutata heterogama (MRE-DH), Racocetra verrucosa (MRE-RV), and Rhizophagus clarus (MRE-RC). Bayesian posterior probabilities greater than 0.90 are shown at nodes; Bayesian analyses were conducted using MrBayes v.3.2 (64) under the nucleotide substitution model GTR + Γ + I with 1,000,000 generations and a 250,000 burn-in. The numbers above branches are the estimates of dN/dS ratios obtained using the codeml module of PAML v.4.8 (65), assuming a two-ratio model. The thickened branch leading to MRE indicates that, according to the likelihood ratio model testing conducted in codeml, the dN/dS ratio along it is significantly different from the background dN/dS ratio for all other branches (χ² = 36.12, P < 0.001). Taxa in boldface were subjected to Tajima 1D relative rate tests (26) (Table 1).

FIG 2

Loss and retention of select genes involved in DNA replication (black), repair (red), and recombination (blue). The four populations of the obligate endobacteria MRE are compared with free-living bacteria and other endobacteria, categorized as nonessential, essential, and antagonistic symbionts. Colored squares indicate the presence of the gene, and white squares indicate loss of the gene. The non-MRE bacterial strains used (with GenBank accession numbers in parentheses) are Escherichia coli O157:H7 strain Sakai (BA000007.2), Lactobacillus salivarius UCC118 (CP000233.1), “Candidatus Glomeribacter gigasporarum” BEG34 (CAFB00000000.1), “Candidatus Hamiltonella defensa” 5AT (CP001277.1), “Candidatus Regiella insecticola” LSR1 (ACYF00000000.1), Serratia symbiotica SAp (AENX00000000.1), Wolbachia pipientis endosymbiont of Drosophila melanogaster wDm (AE017196.1), Buchnera aphidicola APS (BA000003.2), “Candidatus Portiera aleyrodidarum” BT-QVLC (CP003867.1), “Candidatus Tremblaya princeps” PCVAL (CP002918.1), Serratia symbiotica SCc (CP002295.1), Wolbachia pipientis endosymbiont of Brugia malayi WBM (AE017321.1), Mycoplasma agalactiae PG2 (CU179680.1), Mycoplasma gallisepticum S6 (CP006916.2), Mycoplasma genitalium 6282 (CP003771.1), and Mycoplasma mobile 163K (AE017308.1).

FIG 3

MRE transmission and Muller’s ratchet progression compared to theoretical predictions for heritable endobacteria. Due to transmission bottlenecks and fixation of slightly deleterious mutations, heritable endobacteria are expected to degenerately progress to a relatively homogeneous population of unfit individuals. MRE escape Muller’s ratchet by retention of recombination and genome plasticity to purge some of the slightly deleterious mutations and maintain a genetically diverse population. Intrahost selection is expected to eliminate low-fitness genotypes generated by recombination. Black outlined rectangles represent host cells, with red arrows indicating transmission bottlenecks. Endobacteria are represented as small circles, with darker shading depicting the most-fit individuals to lighter shading depicting the least-fit individuals. Circles with two-tone color depict recombination events in MRE.