Abstract

Temperate phages are common, and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses that infect mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages revealed at least five distinct prophage-expressed viral defence systems that interfere with the infection of lytic and temperate phages that are either closely related (homotypic defence) or unrelated (heterotypic defence) to the prophage. Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defence systems include a single-subunit restriction system, a heterotypic exclusion system and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, which acts as a highly effective counter-defence system. Prophage-mediated viral defence offers an efficient mechanism for bacterial success in host–virus dynamics, and counter-defence promotes phage co-evolution.

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Acknowledgements

The authors thank the many students in the SEA-PHAGES programme that contributed to the isolation, annotation and characterization of the phages described here. Specific contributions are noted at http://phagesdb.org. The authors thank J. Schiebel, A. Jonas, T. Stoner, D. Green, R. Rush and L. Lin for help with escape mutant isolation, C.-C. Ko for help with plasmid construction and D. Asai, V. Sivanathan, K. Bradley and L. Barker for support of the SEA-PHAGES programme. This work was supported by grants from the National Institutes of Health (GM116884) and the Howard Hughes Medical Institute (54308198) to G.F.H. and a National Science Foundation pre-doctoral fellowship to T.N.M. (no. 1247842).

Author information

Author notes

    • Rebekah M. Dedrick
    •  & Deborah Jacobs-Sera

    These authors contributed equally to this work.

Affiliations

  1. Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA

    • Rebekah M. Dedrick
    • , Deborah Jacobs-Sera
    • , Carlos A. Guerrero Bustamante
    • , Rebecca A. Garlena
    • , Travis N. Mavrich
    • , Welkin H. Pope
    • , Juan C. Cervantes Reyes
    • , Daniel A. Russell
    • , Bryony R. Brown
    • , Cory F. Hayes
    • , Matthew T. Montgomery
    •  & Graham F. Hatfull
  2. Department of Biology, Baylor University, Waco, Texas 76798, USA

    • Tamarah Adair
  3. Biology Department, Illinois-Wesleyan University, Bloomington, Illinois 61702, USA

    • Richard Alvey
  4. Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin 54016, USA

    • J. Alfred Bonilla
    •  & Karen K. Klyczek
  5. Biology Department, Nebraska-Wesleyan University, Lincoln, Nebraska 68504, USA

    • Jerald S. Bricker
  6. Biology Department, Carthage College, Kenosha, Wisconsin 53140, USA

    • Deanna Byrnes
  7. Biology Department, James Madison University, Harrisonburg, Virginia 22807, USA

    • Steven G. Cresawn
  8. School of Molecular Biosciences, Washington State University Pullman, Washington 99164, USA

    • William B. Davis
  9. Department of Biology, Howard University, Washington, Washington DC 20059, USA

    • Leon A. Dickson
    •  & Courtney J. Robinson
  10. Biology Department, Southern Connecticut State University, New Haven, Connecticut 06515, USA

    • Nicholas P. Edgington
  11. Biology, School of Sciences, University of Louisiana at Monroe, Monroe, Louisiana 71209, USA

    • Ann M. Findley
  12. Biological Sciences and Geology, Queensborough Community College, Bayside, New York 11364, USA

    • Urszula Golebiewska
  13. Biology Department, Brigham Young University, Provo, Utah 84602, USA

    • Julianne H. Grose
  14. Biological Sciences, University of North Texas, Denton, Texas 76203, USA

    • Lee E. Hughes
  15. Molecular and Biomedical Sciences, University of Maine, Honors College, Orono, Maine 04469, USA

    • Keith W. Hutchison
    •  & Sally D. Molloy
  16. Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA

    • Sharon Isern
    •  & Scott F. Michael
  17. Biology Department, Virginia Commonwealth University, Richmond, Virginia 23284, USA

    • Allison A. Johnson
  18. Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, USA

    • Margaret A. Kenna
    • , Catherine M. Mageeney
    • , Joseph N. Teyim
    •  & Vassie C. Ware
  19. Biology Department, The Evergreen State College, Olympia, Washington 98502, USA

    • James Neitzel
  20. Division of Environmental and Biological Sciences, University of Maine-Machias, Machias, Maine 04654, USA

    • Shallee T. Page
  21. Biology Department, Bucknell University, Lewisburg, Pennsylvania 17837, USA

    • Marie C. Pizzorno
  22. Biology Department, Gonzaga University, Spokane, Washington 99258, USA

    • Marianne K. Poxleitner
  23. Biology Department, Western Kentucky University, Bowling Green, Kentucky 42101, USA

    • Claire A. Rinehart
  24. Biology Department, University of Puerto Rico-Cayey, Cayey, Puerto Rico 00736, USA

    • Michael R. Rubin
    •  & Edwin Vazquez
  25. Department of Biology and Chemistry, Nyack College, Nyack, New York 10960, USA

    • Jacqueline Washington

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Contributions

R.M.D., D.J.-S., C.A.G.B., T.N.M., W.H.P., V.C.W., J.W. and G.F.H. conceived and designed the experiments. R.M.D., D.J.-S., C.A.G.B., R.A.G., W.H.P., J.C.C.R., D.A.R., B.R.B., C.F.H., C.M.M., M.T.M. and J.N.T. performed the experiments. R.M.D., D.J.-S., C.A.G.B., R.A.G., T.N.M., W.H.P., B.R.B., J.C.C.R., D.A.R., T.A., R.A., J.A.B., J.S.B., D.B., S.G.C., W.B.D., L.A.D., N.P.E., A.M.F., U.G., J.H.G., C.F.H., L.E.H., K.W.H., S.I., A.A.J., M.A.K., K.K.K., C.M.M., S.F.M., S.D.M., M.T.M., J.N., S.T.P., M.C.P., M.K.P., C.A.R., C.J.R., M.R.R., J.N.T., E.V., V.C.W., J.W. and G.F.H. analysed the data. S.G.C. contributed material/analysis tools. R.M.D., D.J.-S., T.N.M., W.H.P., D.A.R., T.A., R.A., J.A.B., J.S.B., D.B., S.G.C., W.B.D., L.A.D., N.P.E., A.M.F., U.G., J.H.G., L.E.H., K.W.H., S.I., A.A.J., M.A.K., K.K.K., C.M.M., S.F.M., S.D.M., J.N., S.T.P., M.C.P., M.K.P., C.A.R., C.J.R., M.R.R., E.V., V.C.W., J.W. and G.F.H. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Graham F. Hatfull.

Supplementary information

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    Supplementary information

    Supplementary Discussion; Supplementary References; Supplementary Tables 1–4; Supplementary Figures 1–22

Excel files

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    Supplementary Table 5

    Oligonucleotides used in this study