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

“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 Trichonymph...

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Autores principales: Izawa, Kazuki, Kuwahara, Hirokazu, Kihara, Kumiko, Yuki, Masahiro, Lo, Nathan, Itoh, Takehiko, Ohkuma, Moriya, Hongoh, Yuichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174739/
https://www.ncbi.nlm.nih.gov/pubmed/27635050
http://dx.doi.org/10.1093/gbe/evw227
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author Izawa, Kazuki
Kuwahara, Hirokazu
Kihara, Kumiko
Yuki, Masahiro
Lo, Nathan
Itoh, Takehiko
Ohkuma, Moriya
Hongoh, Yuichi
author_facet Izawa, Kazuki
Kuwahara, Hirokazu
Kihara, Kumiko
Yuki, Masahiro
Lo, Nathan
Itoh, Takehiko
Ohkuma, Moriya
Hongoh, Yuichi
author_sort Izawa, Kazuki
collection PubMed
description “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.
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spelling pubmed-51747392016-12-27 Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA Izawa, Kazuki Kuwahara, Hirokazu Kihara, Kumiko Yuki, Masahiro Lo, Nathan Itoh, Takehiko Ohkuma, Moriya Hongoh, Yuichi Genome Biol Evol Letter “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. Oxford University Press 2016-09-15 /pmc/articles/PMC5174739/ /pubmed/27635050 http://dx.doi.org/10.1093/gbe/evw227 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Letter
Izawa, Kazuki
Kuwahara, Hirokazu
Kihara, Kumiko
Yuki, Masahiro
Lo, Nathan
Itoh, Takehiko
Ohkuma, Moriya
Hongoh, Yuichi
Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA
title Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA
title_full Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA
title_fullStr Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA
title_full_unstemmed Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA
title_short Comparison of Intracellular “Ca. Endomicrobium Trichonymphae” Genomovars Illuminates the Requirement and Decay of Defense Systems against Foreign DNA
title_sort comparison of intracellular “ca. endomicrobium trichonymphae” genomovars illuminates the requirement and decay of defense systems against foreign dna
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5174739/
https://www.ncbi.nlm.nih.gov/pubmed/27635050
http://dx.doi.org/10.1093/gbe/evw227
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