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Thousands of small, novel genes predicted in global phage genomes

2022; Cell Press; Volume: 39; Issue: 12 Linguagem: Inglês

10.1016/j.celrep.2022.110984

2639-1856

Brayon J. Fremin, Ami S. Bhatt, Nikos C. Kyrpides, Aditi Sengupta, Alexander Sczyrba, Aline Maria da Silva, Alison Buchan, Amélie C. M. Gaudin, Andreas Brune, Ann M. Hirsch, Anthony P. Neumann, Ashley Shade, Axel Visel, Barbara J. Campbell, Brett J. Baker, Brian P. Hedlund, Byron C. Crump, Cameron R. Currie, Charlene N. Kelly, Chris Craft, Christina Hazard, Christopher Francis, Christopher W. Schadt, Colin Averill, Courtney Mobilian, D. H. Buckley, Dana E. Hunt, Daniel R. Noguera, David A. C. Beck, David L. Valentine, David A. Walsh, D. Y. Sumner, Despoina S. Lymperopoulou, Devaki Bhaya, Donald A. Bryant, Elise S. Morrison, Eoin Brodie, Erica B. Young, Erik A. Lilleskov, Eva Högfors‐Rönnholm, Feng Chen, Frank J. Stewart, Graeme W. Nicol, Hanno Teeling, Harry R. Beller, Hebe M. Dionisi, Hui-Ling Liao, J. Michael Beman, James Stegen, James M. Tiedje, Janet Jansson, Jean S. VanderGheynst, Jeanette M. Norton, Jeff Dangl, Jeffrey L. Blanchard, Jennifer L. Bowen, Jennifer L. Macalady, Jennifer Pett‐Ridge, Jeremy N. Rich, Jérôme P. Payet, John Gladden, Jonathan D. Raff, Jonathan L. Klassen, Jonathan Tarn, Josh D. Neufeld, Kelly Gravuer, Kirsten Hofmockel, Ko‐Hsuan Chen, Konstantinos T. Konstantinidis, Kristen M. DeAngelis, Laila P. Partida‐Martínez, Laura Meredith, Ludmila Chistoserdova, Mary Ann Moran, Matthew J. Scarborough, Matthew Schrenk, Matthew B. Sullivan, Maude M. David, Michelle O’Malley, Mónica Medina, Mussie Y. Habteselassie, Nicholas Ward, Nicole Pietrasiak, Olivia U. Mason, Patrick O. Sorensen, Paulina Estrada‐de los Santos, Petr Baldrián, R. Michael L. McKay, Rachel L. Simister, Ramūnas Stepanauskas, Rebecca B. Neumann, Rex R. Malmstrom, Ricardo Cavicchioli, Robert M. Kelly, Roland Hatzenpichler, Roman Stocker, Rose Ann Cattolico, Ryan Ziels, Rytas Vilgalys, Sara E. Blumer‐Schuette, Sean A. Crowe, Simon Roux, Steven Hallam, Steven E. Lindow, Susan H. Brawley, Susannah G. Tringe, Tanja Woyke, Thea Whitman, Thomas S. Bianchi, Thomas Möck, Timothy J. Donohue, Timothy Y. James, Udaya C. Kalluri, Ulaş Karaöz, Vincent J. Denef, Wen‐Tso Liu, William B. Whitman, Yang Ouyang,

RNA and protein synthesis mechanisms

Small genes ( 40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.