Genomic diversity of bacteriophages infecting Microbacterium spp.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2020
2020
Historique:
received:
10
04
2020
accepted:
29
05
2020
entrez:
20
6
2020
pubmed:
20
6
2020
medline:
1
9
2020
Statut:
epublish
Résumé
The bacteriophage population is vast, dynamic, old, and genetically diverse. The genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, and replete with genes of unknown function. To further explore this broad group of bacteriophages, we describe here the isolation and genomic characterization of 116 phages that infect Microbacterium spp. Most of the phages are lytic, and can be grouped into twelve clusters according to their overall relatedness; seven of the phages are singletons with no close relatives. Genome sizes vary from 17.3 kbp to 97.7 kbp, and their G+C% content ranges from 51.4% to 71.4%, compared to ~67% for their Microbacterium hosts. The phages were isolated on five different Microbacterium species, but typically do not efficiently infect strains beyond the one on which they were isolated. These Microbacterium phages contain many novel features, including very large viral genes (13.5 kbp) and unusual fusions of structural proteins, including a fusion of VIP2 toxin and a MuF-like protein into a single gene. These phages and their genetic components such as integration systems, recombineering tools, and phage-mediated delivery systems, will be useful resources for advancing Microbacterium genetics.
Identifiants
pubmed: 32555720
doi: 10.1371/journal.pone.0234636
pii: PONE-D-20-10367
pmc: PMC7302621
doi:
Substances chimiques
DNA, Viral
0
Viral Fusion Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0234636Subventions
Organisme : NIGMS NIH HHS
ID : R01 GM116884
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM131729
Pays : United States
Organisme : Howard Hughes Medical Institute
ID : GT12053
Pays : United States
Organisme : Howard Hughes Medical Institute
ID : 54308198
Pays : United States
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Curr Protoc Bioinformatics. 2011 Sep;Chapter 4:Unit 4.5.1-17
pubmed: 21901741
J Mol Biol. 2010 Mar 19;397(1):119-43
pubmed: 20064525
BMC Bioinformatics. 2007 May 23;8:172
pubmed: 17521438
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Bioinformatics. 2019 Oct 26;:
pubmed: 31665271
Methods Mol Biol. 2018;1681:109-125
pubmed: 29134591
Nucleic Acids Res. 2004 Jan 02;32(1):11-6
pubmed: 14704338
Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11030-5
pubmed: 15258291
J Bacteriol. 2012 Sep;194(17):4785
pubmed: 22887680
J Clin Microbiol. 2003 May;41(5):2242-6
pubmed: 12734292
Gene. 1990 Jul 2;91(1):95-100
pubmed: 2401411
Gene. 1996 Jun 12;172(1):41-6
pubmed: 8654988
Cell. 2003 Apr 18;113(2):171-82
pubmed: 12705866
Int J Syst Evol Microbiol. 2002 Jul;52(Pt 4):1229-1234
pubmed: 12148633
PLoS One. 2017 Jul 17;12(7):e0180517
pubmed: 28715480
Nature. 2016 Mar 24;531(7595):466-70
pubmed: 26982729
Bioinformatics. 2007 Mar 15;23(6):673-9
pubmed: 17237039
Commun Integr Biol. 2017 Feb 23;10(2):e1296614
pubmed: 28451057
J Hazard Mater. 2019 May 15;370:225-231
pubmed: 29429846
Nat Microbiol. 2017 Jul 10;2:17112
pubmed: 28692019
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8
pubmed: 15980461
Res Microbiol. 2007 Sep;158(7):582-90
pubmed: 17869067
Int J Syst Evol Microbiol. 2007 Oct;57(Pt 10):2355-2359
pubmed: 17911310
Genome Announc. 2017 Jan 5;5(1):
pubmed: 28057748
Mol Cell. 2004 Oct 8;16(1):11-21
pubmed: 15469818
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
BMC Microbiol. 2018 Mar 1;18(1):19
pubmed: 29490612
Elife. 2015 Apr 28;4:e06416
pubmed: 25919952
Perit Dial Int. 2018 Jan-Feb;38(1):9-13
pubmed: 29311193
Methods Enzymol. 2003;370:83-94
pubmed: 14712636
Int J Syst Evol Microbiol. 2006 Sep;56(Pt 9):2113-2117
pubmed: 16957107
BMC Bioinformatics. 2011 Oct 12;12:395
pubmed: 21991981
Int J Syst Evol Microbiol. 2001 Jul;51(Pt 4):1267-1276
pubmed: 11491322
Mol Biol Evol. 1987 Jul;4(4):406-25
pubmed: 3447015
Virology. 2012 Dec 20;434(2):187-201
pubmed: 23084079
PLoS One. 2011 Jan 27;6(1):e16329
pubmed: 21298013
Methods Mol Biol. 1998;101:145-73
pubmed: 9921476
J Biol Chem. 2011 Mar 11;286(10):7727-31
pubmed: 21224389
JMM Case Rep. 2018 Oct 31;5(11):e005169
pubmed: 30619613
J Bacteriol. 1953 Apr;65(4):428-33
pubmed: 13069397
BMC Microbiol. 2013 May 03;13:97
pubmed: 23642186
mBio. 2012 Sep 25;3(5):
pubmed: 23015740
PLoS One. 2015 Mar 05;10(3):e0118725
pubmed: 25742016
J Infect Chemother. 2019 Oct;25(10):806-810
pubmed: 30982728
Arch Virol. 2014 Sep;159(9):2537-40
pubmed: 24777828
J Virol. 2012 Jan;86(1):358-63
pubmed: 22013058
Microbiol Spectr. 2014 Mar 7;2(2):1-36
pubmed: 25328854
mBio. 2017 Aug 15;8(4):
pubmed: 28811342
PLoS Genet. 2006 Jun;2(6):e92
pubmed: 16789831
Bioinformatics. 1998;14(1):68-73
pubmed: 9520503
J Gen Appl Microbiol. 2007 Feb;53(1):1-5
pubmed: 17429156
Adv Virus Res. 2012;82:179-288
pubmed: 22420855
Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):13531-13536
pubmed: 29208718
Int J Syst Evol Microbiol. 2005 Mar;55(Pt 2):661-665
pubmed: 15774640
Microbiol Resour Announc. 2019 Jan 31;8(5):
pubmed: 30714032
mBio. 2014 Dec 02;5(6):e02145
pubmed: 25467442
Bioinformatics. 1998;14(4):378-9
pubmed: 9632836
Microb Ecol. 2006 Apr;51(3):375-93
pubmed: 16598639
Bioinformatics. 2007 Apr 15;23(8):1026-8
pubmed: 17309896
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904
Methods Mol Biol. 2018;1681:217-229
pubmed: 29134598
Bioinformatics. 2017 Mar 1;33(5):784-786
pubmed: 28365761
Sci Rep. 2020 Jan 24;10(1):1116
pubmed: 31980664
Microbiol Spectr. 2018 Oct;6(5):
pubmed: 30291704
PLoS One. 2011;6(10):e26750
pubmed: 22053209
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
pubmed: 19458158
J Microbiol Immunol Infect. 2016 Jun;49(3):464-5
pubmed: 24856423