1TBRC, University of the Ryukyus, 2Okinawa Institute of Advanced Sciences, 3Department of Liberal Arts, The Open University of Japan, 4Bioproduction Research Institute, AIST
An anaerobic ciliate, Trimyema compressum is known to harbor two types of prokaryotic cells in its cytoplasm. One of them is methanogenic archaeum that is expected to contribute to host anaerobic metabolism as an H2-scavenger (TS1), whereas the other one is a conspicuous firmicutes whose function is unknown (TC1). TC1 symbiont is essential for vigorous growth of host ciliate, but its physiological role in the host cell and evolutional history of their partnership remain unclear. In the present study, to uncover the physiology and structural details of this unique intracellular resident, the endosymbiotic cells were collected and its genome sequence was analyzed. Approximately two micro-g of symbiont genome was subjected to shotgun sequencing by PacBio RSII sequencer with 20 kb insert size library. The resulting 5.64 Gb sequence reads successfully reconstructed a circular TC1 genome with 839-fold sequence coverage. The complete genome size was 1,586,452 bp. The GC content of entire genome was 32.8% indicating that TC1 genome is influenced by strict AT-bias in intracellular habitat. The genome also contained 207 pairs of homologous sequences with longer than 1 kb, which might be a cause of unsuccessful genome completion as other sequencing platforms were used. As the results of gene annotation, 2,297 CDSs were found in its genome, but nearly a half of them was suspected to be pseudogenes. The survey of key enzymes responsible for energy yielding processes showed that fermentative metabolism of reductive compounds such as pyruvate is most likely to happen. On the other hand, most of major cofactors and vitamins are unlikely to be synthesized in TC1 cells judging from the soundness of the pathways. The genome features of TC1 symbiont suggested that they are in the middle of genome reduction process, which implicated strict interdependency between T. compressum and TC1 symbiont and their relatively long-term partnership.