title: 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.
authors.affiliation: Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Izawa
authors.affiliation: Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Hirokazu
authors.initials: H
authors.lastname: Kuwahara
authors.affiliation: Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan Department of Biological and Chemical Systems Engineering, National Institute of Technology Kumamoto College, Yatsushiro, Japan.
authors.forename: Kumiko
authors.initials: K
authors.lastname: Kihara
authors.affiliation: Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Yuki
authors.affiliation: School of Biological Sciences, University of Sydney, Sydney, NSW, Australia.
authors.forename: Nathan
authors.initials: N
authors.lastname: Lo
authors.affiliation: Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan.
authors.forename: Takehiko
authors.initials: T
authors.lastname: Itoh
authors.affiliation: Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science, Tsukuba, Japan Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan.
authors.forename: Moriya
authors.initials: M
authors.lastname: Ohkuma
authors.affiliation: Department of Biological Sciences, Tokyo Institute of Technology, Tokyo, Japan Japan Collection of Microorganisms, RIKEN BioResource Center, Tsukuba, Japan yhongo@bio.titech.ac.jp.
authors.forename: Yuichi
authors.initials: Y
authors.lastname: Hongoh
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics* / Q000472:pathogenicity; D064113:CRISPR-Cas Systems; D015280:DNA Restriction-Modification Enzymes; D016680:Genome, Bacterial; D056952:Hypermastigia / Q000382:microbiology* / Q000472:pathogenicity; D020049:Isoptera / Q000469:parasitology; D016366:Open Reading Frames; D011544:Pseudogenes; D012641:Selection, Genetic; D013559:Symbiosis / Q000235:genetics*; D014774:Virulence / Q000235:genetics
chemical_list: D015280:DNA Restriction-Modification Enzymes
keywords: CRISPR; endosymbiosis; gut bacteria; insect; restriction–modification system; termite