Clades of huge phages from across Earth’s ecosystems

Basem Al-Shayeb, Rohan Sachdeva, Lin-Xing Chen, Fred Ward, Patrick Munk, Audra Devoto, Cindy J. Castelle, Matthew R. Olm, Keith Bouma-Gregson, Yuki Amano, Christine He, Raphaël Méheust, Brandon Brooks, Alex Thomas, Adi Lavy, Paula Matheus-Carnevali, Christine Sun, Daniela S. A. Goltsman, Mikayla A. Borton, Allison Sharrar, Alexander L. Jaffe, Tara C. Nelson, Rose Kantor, Ray Keren, Katherine R. Lane, Ibrahim F. Farag, Shufei Lei, Kari Finstad, Ronald Amundson, Karthik Anantharaman, Jinglie Zhou, Alexander J. Probst, Mary E. Power, Susannah G. Tringe, Wen-Jun Li, Kelly Wrighton, Sue Harrison, Michael Morowitz, David A. Relman, Jennifer A. Doudna, Anne-Catherine Lehours, Lesley Warren, Jamie H. D. Cate, Joanne M. Santini and Jillian F. Banfield ()
Additional contact information
Basem Al-Shayeb: University of California Berkeley
Rohan Sachdeva: University of California Berkeley
Lin-Xing Chen: University of California Berkeley
Fred Ward: University of California Berkeley
Patrick Munk: Technical University of Denmark
Audra Devoto: University of California Berkeley
Cindy J. Castelle: University of California Berkeley
Matthew R. Olm: University of California Berkeley
Keith Bouma-Gregson: University of California Berkeley
Yuki Amano: Japan Atomic Energy Agency
Christine He: University of California Berkeley
Raphaël Méheust: University of California Berkeley
Brandon Brooks: University of California Berkeley
Alex Thomas: University of California Berkeley
Adi Lavy: University of California Berkeley
Paula Matheus-Carnevali: University of California Berkeley
Christine Sun: Stanford University
Daniela S. A. Goltsman: Stanford University
Mikayla A. Borton: Colorado State University
Allison Sharrar: University of California Berkeley
Alexander L. Jaffe: University of California Berkeley
Tara C. Nelson: University of Toronto
Rose Kantor: University of California Berkeley
Ray Keren: University of California Berkeley
Katherine R. Lane: University of California Berkeley
Ibrahim F. Farag: University of California Berkeley
Shufei Lei: University of California Berkeley
Kari Finstad: University of California Berkeley
Ronald Amundson: University of California Berkeley
Karthik Anantharaman: University of California Berkeley
Jinglie Zhou: DOE Joint Genome Institute
Alexander J. Probst: University of California Berkeley
Mary E. Power: University of California Berkeley
Susannah G. Tringe: DOE Joint Genome Institute
Wen-Jun Li: Sun Yat-Sen University
Kelly Wrighton: Colorado State University
Sue Harrison: University of Cape Town
Michael Morowitz: University of Pittsburgh School of Medicine
David A. Relman: Stanford University
Jennifer A. Doudna: University of California Berkeley
Anne-Catherine Lehours: Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS
Lesley Warren: University of Toronto
Jamie H. D. Cate: University of California Berkeley
Joanne M. Santini: University College London
Jillian F. Banfield: University of California Berkeley

Nature, 2020, vol. 578, issue 7795, 425-431

Abstract: Abstract Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is—to our knowledge—the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR–Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR–Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR–Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth’s ecosystems.

Date: 2020
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Citations: View citations in EconPapers (9)

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DOI: 10.1038/s41586-020-2007-4

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