A predicted CRISPR-mediated symbiosis between uncultivated archaea.

Autor: Esser SP; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., Rahlff J; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany.; Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden., Zhao W; Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA.; Shanghai Jiao Tong University, School of Life Sciences and Biotechnology, International Center for Deep Life Investigation (IC-DLI), Shanghai Jiao Tong University, Shanghai, China., Predl M; Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.; Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria., Plewka J; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., Sures K; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., Wimmer F; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany., Lee J; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Adam PS; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., McGonigle J; School of Biological Sciences, University of Utah, Salt Lake City, UT, USA., Turzynski V; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., Banas I; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., Schwank K; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany.; University of Regensburg, Biochemistry III, Regensburg, Germany., Krupovic M; Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France., Bornemann TLV; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., Figueroa-Gonzalez PA; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany., Jarett J; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Rattei T; Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.; Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria., Amano Y; Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai, Japan., Blaby IK; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Cheng JF; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Brazelton WJ; School of Biological Sciences, University of Utah, Salt Lake City, UT, USA., Beisel CL; Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Centre for Infection Research (HZI), Würzburg, Germany.; Medical faculty, University of Würzburg, Würzburg, Germany., Woyke T; DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA., Zhang Y; Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA., Probst AJ; Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.; Group for Aquatic Microbial Ecology, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.; Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.; Centre of Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2023 Sep; Vol. 8 (9), pp. 1619-1633. Date of Electronic Publication: 2023 Jul 27.
DOI: 10.1038/s41564-023-01439-2
Abstrakt: CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.
(© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)
Databáze: MEDLINE
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