Cell Reports (May 2023)
Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY
- Amy Prichard,
- Jina Lee,
- Thomas G. Laughlin,
- Amber Lee,
- Kyle P. Thomas,
- Annika E. Sy,
- Tara Spencer,
- Aileen Asavavimol,
- Allison Cafferata,
- Mia Cameron,
- Nicholas Chiu,
- Demyan Davydov,
- Isha Desai,
- Gabriel Diaz,
- Melissa Guereca,
- Kiley Hearst,
- Leyi Huang,
- Emily Jacobs,
- Annika Johnson,
- Samuel Kahn,
- Ryan Koch,
- Adamari Martinez,
- Meliné Norquist,
- Tyler Pau,
- Gino Prasad,
- Katrina Saam,
- Milan Sandhu,
- Angel Jose Sarabia,
- Siena Schumaker,
- Aaron Sonin,
- Ariya Uyeno,
- Alison Zhao,
- Kevin D. Corbett,
- Kit Pogliano,
- Justin Meyer,
- Julianne H. Grose,
- Elizabeth Villa,
- Rachel Dutton,
- Joe Pogliano
Affiliations
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Thomas G. Laughlin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Amber Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Kyle P. Thomas
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Annika E. Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Tara Spencer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Aileen Asavavimol
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Allison Cafferata
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Mia Cameron
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Nicholas Chiu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Demyan Davydov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Isha Desai
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Gabriel Diaz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Melissa Guereca
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Kiley Hearst
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Leyi Huang
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Emily Jacobs
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Annika Johnson
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Samuel Kahn
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Ryan Koch
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Adamari Martinez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Meliné Norquist
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Tyler Pau
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Gino Prasad
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Katrina Saam
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Milan Sandhu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Angel Jose Sarabia
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Siena Schumaker
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Aaron Sonin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Ariya Uyeno
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Alison Zhao
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Kevin D. Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Julianne H. Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
- Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
- Rachel Dutton
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Corresponding author
- Journal volume & issue
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Vol. 42,
no. 5
p. 112432
Abstract
Summary: We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
