Ecology and molecular targets of hypermutation in the global microbiome

Simon Roux (), Blair G. Paul, Sarah C. Bagby, Stephen Nayfach, Michelle A. Allen, Graeme Attwood, Ricardo Cavicchioli, Ludmila Chistoserdova, Robert J. Gruninger, Steven J. Hallam, Maria E. Hernandez, Matthias Hess, Wen-Tso Liu, Tim A. McAllister, Michelle A. O’Malley, Xuefeng Peng, Virginia I. Rich, Scott R. Saleska and Emiley A. Eloe-Fadrosh ()
Additional contact information
Simon Roux: Lawrence Berkeley National Laboratory
Blair G. Paul: Marine Biological Laboratory
Sarah C. Bagby: Case Western Reserve University
Stephen Nayfach: Lawrence Berkeley National Laboratory
Michelle A. Allen: The University of New South Wales
Graeme Attwood: AgResearch Limited, Grasslands Research Centre
Ricardo Cavicchioli: The University of New South Wales
Ludmila Chistoserdova: University of Washington
Robert J. Gruninger: Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada
Steven J. Hallam: University of British Columbia
Maria E. Hernandez: Instituto de Ecología A.C. Red de Manejo Biotechnológico de Recursos. Xalapa
Matthias Hess: University of California Davis
Wen-Tso Liu: University of Illinois at Urbana-Champaign
Tim A. McAllister: Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada
Michelle A. O’Malley: University of California Santa Barbara
Xuefeng Peng: Marine Science Institute, University of California Santa Barbara
Virginia I. Rich: Ohio State University
Scott R. Saleska: University of Arizona
Emiley A. Eloe-Fadrosh: Lawrence Berkeley National Laboratory

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract Changes in the sequence of an organism’s genome, i.e., mutations, are the raw material of evolution. The frequency and location of mutations can be constrained by specific molecular mechanisms, such as diversity-generating retroelements (DGRs). DGRs have been characterized from cultivated bacteria and bacteriophages, and perform error-prone reverse transcription leading to mutations being introduced in specific target genes. DGR loci were also identified in several metagenomes, but the ecological roles and evolutionary drivers of these DGRs remain poorly understood. Here, we analyze a dataset of >30,000 DGRs from public metagenomes, establish six major lineages of DGRs including three primarily encoded by phages and seemingly used to diversify host attachment proteins, and demonstrate that DGRs are broadly active and responsible for >10% of all amino acid changes in some organisms. Overall, these results highlight the constraints under which DGRs evolve, and elucidate several distinct roles these elements play in natural communities.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-23402-7

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DOI: 10.1038/s41467-021-23402-7

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