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Esser, S. P.*; Rahlff, J.*; Zhao, W.*; Predl, M.*; Plewka, J.*; Sures, K.*; Wimmer, F.*; Lee, J.*; Adam, P. S.*; McGonigle, J.*; et al.
Nature Microbiology (Internet), 8(9), p.1619 - 1633, 2023/09
被引用回数：2 パーセンタイル：75.4(Microbiology)CRISPR-Cas systems defend prokaryotic cells from viruses, plasmids, and other mobile genetic elements. Capitalizing on multi-omics approaches, we show here that the CRISPR-Cas systems of uncultivated archaea also play an integral role in mitigating potentially detrimental interactions with episymbionts. A comprehensive analysis of CRISPR-Cas-based infection histories revealed that uncultivated deep-subsurface archaeal primary-producers defend themselves from archaeal episymbionts of the DPANN superphylum of archaea, some of which are known to fuse their membranes with their host. We show that host cells counter these attacks by deploying one of two CRISPR-Cas systems (type I-B and type III-A) to target and disrupt essential genes in the episymbiont. However, genome-scale modeling of metabolic interactions between two deep subsurface host-symbiont systems revealed that host cells also benefit from the symbionts via metabolic complementation. We speculate that populations of these uncultivated archaeal episymbionts are currently transitioning from a parasitic lifestyle to one of mutualism, as must have occurred in countless mutualistic systems known today. By expanding our analysis to thousands of archaeal genomes, we conclude that CRISPR-Cas mediated resistance to archaeal episymbiosis evolved independently in various archaeal lineages and may be a wide-spread evolutionary phenomenon.
archaeaSchoelmerich, M. C.*; Oubouter, H. T.*; Sachdeva, R.*; Penev, P. I.*; 天野 由記; West-Roberts, J.*; Welte, C. U.*; Banfield, J. F.*
Nature Communications (Internet), 13, p.7085_1 - 7085_11, 2022/11
被引用回数：6 パーセンタイル：70.43(Multidisciplinary Sciences)Anaerobic methanotrophic archaea (ANME) make energy from the breakdown of methane, an important driver of global warming, yet the extrachromosomal genetic elements that impact the activities of ANME are little understood. Here we describe large plasmids associated with ANME of the Methanoperedens Genus. These have been maintained in two enrichment bioreactors that are highly dominated by different species and associate with species in other anaerobic environments. By manual curation we show that two of the plasmids are large (155,607 bp and 191,912 bp), circular, and replicate bidirectionally. The group of species that carry these plasmids is related to 
,
and 
and the plasmids occur in the same copy number as the main chromosome. The larger plasmid encodes transporters that potentially enhance access to Ni, which is required for the MCR complex, Co required for the cobalamin cofactor needed for methyltransferases tied to central processes and amino acid uptake. We show that many plasmid genes are actively transcribed, including genes involved in plasmid chromosome maintenance and segregation, a Co
/Ni transporter and cell protective proteins. Notably, plasmid-borne genes for a ribosomal protein uL16 and adjacent elongation factor eEF2 are highly expressed. These are not encoded in the host genome, indicating an obligate interdependence between this plasmid and its host. The finding of plasmids of opens the way for the development of genetic vectors that could be used to probe little understood aspects of physiology. Ultimately, this may provide a route to introduce or alter genes that may enhance growth and overall metabolism to accelerate methane oxidation rates.
福田 健二; 渡辺 勇輔; 村上 裕晃; 天野 由記; 青才 大介*; 原 直広*
JAEA-Data/Code 2020-012, 80 Pages, 2020/10
JAEA-Data-Code-2020-012.pdf:3.55MB
日本原子力研究開発機構は岐阜県瑞浪市で進めている超深地層研究所計画において、研究坑道の掘削・維持管理が周辺の地下水の地球化学特性に与える影響の把握を目的とした調査研究を行っている。本データ集は、超深地層研究所計画において、2019年度に実施した地下水の採水調査によって得られた地球化学データおよび微生物データを取りまとめたものである。データの追跡性を確保するため、試料採取場所, 試料採取時間, 採取方法および分析方法などを示し、あわせてデータの品質管理方法について示した。
