11
|
Klyczek KK, Bonilla JA, Jacobs-Sera D, Adair TL, Afram P, Allen KG, Archambault ML, Aziz RM, Bagnasco FG, Ball SL, Barrett NA, Benjamin RC, Blasi CJ, Borst K, Braun MA, Broomell H, Brown CB, Brynell ZS, Bue AB, Burke SO, Casazza W, Cautela JA, Chen K, Chimalakonda NS, Chudoff D, Connor JA, Cross TS, Curtis KN, Dahlke JA, Deaton BM, Degroote SJ, DeNigris DM, DeRuff KC, Dolan M, Dunbar D, Egan MS, Evans DR, Fahnestock AK, Farooq A, Finn G, Fratus CR, Gaffney BL, Garlena RA, Garrigan KE, Gibbon BC, Goedde MA, Guerrero Bustamante CA, Harrison M, Hartwell MC, Heckman EL, Huang J, Hughes LE, Hyduchak KM, Jacob AE, Kaku M, Karstens AW, Kenna MA, Khetarpal S, King RA, Kobokovich AL, Kolev H, Konde SA, Kriese E, Lamey ME, Lantz CN, Lapin JS, Lawson TO, Lee IY, Lee SM, Lee-Soety JY, Lehmann EM, London SC, Lopez AJ, Lynch KC, Mageeney CM, Martynyuk T, Mathew KJ, Mavrich TN, McDaniel CM, McDonald H, McManus CJ, Medrano JE, Mele FE, Menninger JE, Miller SN, Minick JE, Nabua CT, Napoli CK, Nkangabwa M, Oates EA, Ott CT, Pellerino SK, Pinamont WJ, Pirnie RT, Pizzorno MC, Plautz EJ, Pope WH, Pruett KM, Rickstrew G, Rimple PA, Rinehart CA, Robinson KM, Rose VA, Russell DA, Schick AM, Schlossman J, Schneider VM, Sells CA, Sieker JW, Silva MP, Silvi MM, Simon SE, Staples AK, Steed IL, Stowe EL, Stueven NA, Swartz PT, Sweet EA, Sweetman AT, Tender C, Terry K, Thomas C, Thomas DS, Thompson AR, Vanderveen L, Varma R, Vaught HL, Vo QD, Vonberg ZT, Ware VC, Warrad YM, Wathen KE, Weinstein JL, Wyper JF, Yankauskas JR, Zhang C, Hatfull GF. Tales of diversity: Genomic and morphological characteristics of forty-six Arthrobacter phages. PLoS One 2017; 12:e0180517. [PMID: 28715480 PMCID: PMC5513430 DOI: 10.1371/journal.pone.0180517] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/17/2017] [Indexed: 11/19/2022] Open
Abstract
The vast bacteriophage population harbors an immense reservoir of genetic information. Almost 2000 phage genomes have been sequenced from phages infecting hosts in the phylum Actinobacteria, and analysis of these genomes reveals substantial diversity, pervasive mosaicism, and novel mechanisms for phage replication and lysogeny. Here, we describe the isolation and genomic characterization of 46 phages from environmental samples at various geographic locations in the U.S. infecting a single Arthrobacter sp. strain. These phages include representatives of all three virion morphologies, and Jasmine is the first sequenced podovirus of an actinobacterial host. The phages also span considerable sequence diversity, and can be grouped into 10 clusters according to their nucleotide diversity, and two singletons each with no close relatives. However, the clusters/singletons appear to be genomically well separated from each other, and relatively few genes are shared between clusters. Genome size varies from among the smallest of siphoviral phages (15,319 bp) to over 70 kbp, and G+C contents range from 45-68%, compared to 63.4% for the host genome. Although temperate phages are common among other actinobacterial hosts, these Arthrobacter phages are primarily lytic, and only the singleton Galaxy is likely temperate.
Collapse
Affiliation(s)
- Karen K. Klyczek
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - J. Alfred Bonilla
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tamarah L. Adair
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Patricia Afram
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Katherine G. Allen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Megan L. Archambault
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Rahat M. Aziz
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Filippa G. Bagnasco
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah L. Ball
- Center for Life Sciences Education, The Ohio State University, Columbus, Ohio, United States of America
| | - Natalie A. Barrett
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Robert C. Benjamin
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Christopher J. Blasi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Katherine Borst
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Mary A. Braun
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Haley Broomell
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Conner B. Brown
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Zachary S. Brynell
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Ashley B. Bue
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Sydney O. Burke
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - William Casazza
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Julia A. Cautela
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin Chen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Dylan Chudoff
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Jade A. Connor
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Trevor S. Cross
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Kyra N. Curtis
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jessica A. Dahlke
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Bethany M. Deaton
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Sarah J. Degroote
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Danielle M. DeNigris
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Katherine C. DeRuff
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Milan Dolan
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - David Dunbar
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Marisa S. Egan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Daniel R. Evans
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Abby K. Fahnestock
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Amal Farooq
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Garrett Finn
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | | | - Bobby L. Gaffney
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Rebecca A. Garlena
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kelly E. Garrigan
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Bryan C. Gibbon
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Michael A. Goedde
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | | | - Melinda Harrison
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Megan C. Hartwell
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily L. Heckman
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Jennifer Huang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lee E. Hughes
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Kathryn M. Hyduchak
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Aswathi E. Jacob
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Machika Kaku
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Allen W. Karstens
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Margaret A. Kenna
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Susheel Khetarpal
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rodney A. King
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Amanda L. Kobokovich
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Hannah Kolev
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Sai A. Konde
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Elizabeth Kriese
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Morgan E. Lamey
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Carter N. Lantz
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jonathan S. Lapin
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Temiloluwa O. Lawson
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - In Young Lee
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Scott M. Lee
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Y. Lee-Soety
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Emily M. Lehmann
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Shawn C. London
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - A. Javier Lopez
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Kelly C. Lynch
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Catherine M. Mageeney
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Tetyana Martynyuk
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Kevin J. Mathew
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Travis N. Mavrich
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Christopher M. McDaniel
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Hannah McDonald
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - C. Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jessica E. Medrano
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Francis E. Mele
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jennifer E. Menninger
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Sierra N. Miller
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Josephine E. Minick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Courtney T. Nabua
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Caroline K. Napoli
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Martha Nkangabwa
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Elizabeth A. Oates
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Cassandra T. Ott
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Sarah K. Pellerino
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - William J. Pinamont
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Ross T. Pirnie
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Marie C. Pizzorno
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Emilee J. Plautz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Welkin H. Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katelyn M. Pruett
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Gabbi Rickstrew
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Patrick A. Rimple
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Claire A. Rinehart
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Kayla M. Robinson
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Victoria A. Rose
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Daniel A. Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amelia M. Schick
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Julia Schlossman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Victoria M. Schneider
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chloe A. Sells
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jeremy W. Sieker
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Morgan P. Silva
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Marissa M. Silvi
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Stephanie E. Simon
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Amanda K. Staples
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Isabelle L. Steed
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emily L. Stowe
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Noah A. Stueven
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Porter T. Swartz
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Emma A. Sweet
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Abigail T. Sweetman
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Corrina Tender
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Katrina Terry
- Department of Science, Cabrini University, Radnor, Pennsylvania, United States of America
| | - Chrystal Thomas
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Daniel S. Thomas
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Allison R. Thompson
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Lorianna Vanderveen
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rohan Varma
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Hannah L. Vaught
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Quynh D. Vo
- Department of Biological Sciences, University of North Texas, Denton, Texas, United States of America
| | - Zachary T. Vonberg
- Biology Department, University of Wisconsin-River Falls, River Falls, Wisconsin, United States of America
| | - Vassie C. Ware
- Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Yasmene M. Warrad
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Kaitlyn E. Wathen
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, United States of America
| | - Jonathan L. Weinstein
- Biology Department, Saint Joseph’s University, Philadelphia, Pennsylvania, United States of America
| | - Jacqueline F. Wyper
- Department of Biology, Baylor University, Waco, Texas, United States of America
| | - Jakob R. Yankauskas
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Christine Zhang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|