Comparison of Intracellular “Ca.Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA

Abstract

“Candidatus Endomicrobium trichonymphae” (Bacteria; Elusimicrobia) is an obligate intracellular symbiont of the cellulolytic protist genus Trichonympha in the termite gut. A previous genome analysis of “Ca. Endomicrobium trichonymphae” phylotype Rs-D17 (genomovar Ri2008), obtained from a Trichonympha agilis cell in the gut of the termite Reticulitermes speratus, revealed that its genome is small (1.1 Mb) and contains many pseudogenes; it is in the course of reductive genome evolution. Here we report the complete genome sequence of another Rs-D17 genomovar, Ti2015, obtained from a different T. agilis cell present in an R. speratus gut. These two genomovars share most intact protein-coding genes and pseudogenes, showing 98.6% chromosome sequence similarity. However, characteristic differences were found in their defense systems, which comprised restriction-modification and CRISPR/Cas systems. The repertoire of intact restriction-modification systems differed between the genomovars, and two of the three CRISPR/Cas loci in genomovar Ri2008 are pseudogenized or missing in genomovar Ti2015. These results suggest relaxed selection pressure for maintaining these defense systems. Nevertheless, the remaining CRISPR/Cas system in each genomovar appears to be active; none of the “spacer” sequences (112 in Ri2008 and 128 in Ti2015) were shared whereas the “repeat” sequences were identical. Furthermore, we obtained draft genomes of three additional endosymbiotic Endomicrobium phylotypes from different host protist species, and discovered multiple, intact CRISPR/Cas systems in each genome. Collectively, unlike bacteriome endosymbionts in insects, the Endomicrobium endosymbionts of termite-gut protists appear to require defense against foreign DNA, although the required level of defense has likely been reduced during their intracellular lives.

Genome analyses of uncultured TG2/ZB3 bacteria in ‘Margulisbacteria’ specifically attached to ectosymbiotic spirochetes of protists in the termite gut

“…The NkOx7-01 and NkOx7-02 genomes encoded CRISPR-Cas systems. CRISPR loci have been found in the genomes of several other bacterial species from the termite gut [43,[65][66][67], and we also found CRISPR-Cas systems widely in other known genomes of 'Margulisbacteria' (data not shown). The absence of cytochrome oxidase, catalase and superoxide dismutase indicated that they are strict anaerobes, and the presence of rubrerythrin and rubredoxin may facilitate the survival of these bacteria during oxidative stress [68].…”

Genome Analysis of Endomicrobium proavitum Suggests Loss and Gain of Relevant Functions during the Evolution of Intracellular Symbionts

“…Nevertheless, the presence of defense systems against foreign DNA in "Ca. Endomicrobium trichonymphae" (32) suggests that endosymbionts of termite gut flagellates, unlike the obligately intracellular bacteria colonizing insect tissues (2), are not entirely cut off from gene flow in their intracellular habitat.…”

Discovery of ectosymbiotic Endomicrobium lineages associated with protists in the gut of stolotermitid termites

“…The complete genome sequences of ‘ Candidatus Endomicrobium trichonymphae’ phylotype Rs‐D17 were obtained from bacterial populations within the cells of the protist Trichonympha agilis from the gut of the termite Reticulitermes speratus (Hongoh et al ., ; Izawa et al ., ). Genome analyses suggested that the endosymbionts are specialized to synthesize amino acids and cofactors and may provide nitrogenous compounds to the host protist and termite (Hongoh et al ., ; Izawa et al ., ). Considering the abundance and ubiquity of Endomicrobium endosymbionts in the gut of lower termites, they may play important roles in the termite gut symbiotic system.…”