Phages and their satellites encode hotspots of antiviral systems.
abortive infection
bacterial immunity
genetic diversity
inter-viral competition
mobile genetic elements
phage defense
phage satellite
Journal
Cell host & microbe
ISSN: 1934-6069
Titre abrégé: Cell Host Microbe
Pays: United States
ID NLM: 101302316
Informations de publication
Date de publication:
11 05 2022
11 05 2022
Historique:
received:
03
02
2021
revised:
27
01
2022
accepted:
23
02
2022
pubmed:
23
3
2022
medline:
18
5
2022
entrez:
22
3
2022
Statut:
ppublish
Résumé
Bacteria carry diverse genetic systems to defend against viral infection, some of which are found within prophages where they inhibit competing viruses. Phage satellites pose additional pressures on phages by hijacking key viral elements to their own benefit. Here, we show that E. coli P2-like phages and their parasitic P4-like satellites carry hotspots of genetic variation containing reservoirs of anti-phage systems. We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein. Antiviral hotspots participate in inter-viral competition and shape dynamics between the bacterial host, P2-like phages, and P4-like satellites. Notably, the anti-phage activity of satellites can benefit the helper phage during competition with virulent phages, turning a parasitic relationship into a mutualistic one. Anti-phage hotspots are present across distant species and constitute a substantial source of systems that participate in the competition between mobile genetic elements.
Identifiants
pubmed: 35316646
pii: S1931-3128(22)00104-4
doi: 10.1016/j.chom.2022.02.018
pmc: PMC9122126
pii:
doi:
Substances chimiques
Antiviral Agents
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
740-753.e5Informations de copyright
Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests D.B. is a founder of Eligo Bioscience and a member of its scientific advisory board.
Références
mBio. 2019 Mar 19;10(2):
pubmed: 30890601
Science. 2018 Mar 2;359(6379):
pubmed: 29371424
Nat Commun. 2020 Nov 6;11(1):5652
pubmed: 33159058
Proc Natl Acad Sci U S A. 1978 Jan;75(1):400-4
pubmed: 272656
PLoS Genet. 2022 Feb 14;18(2):e1010065
pubmed: 35157704
Nucleic Acids Res. 2019 Jan 8;47(D1):D427-D432
pubmed: 30357350
Nucleic Acids Res. 2020 Jun 4;48(10):5397-5406
pubmed: 32338761
Trends Microbiol. 2005 Aug;13(8):381-8
pubmed: 15994078
Cell. 2007 Sep 7;130(5):824-36
pubmed: 17803906
PLoS One. 2014 Oct 17;9(10):e110726
pubmed: 25330359
Bacteriophage. 2016 Feb 18;6(1):e1145782
pubmed: 27144088
PLoS Biol. 2022 Jan 13;20(1):e3001514
pubmed: 35025885
Mol Cell. 2013 Apr 11;50(1):136-48
pubmed: 23478446
Nucleic Acids Res. 2022 Mar 21;50(5):e29
pubmed: 34904653
J Mol Biol. 2018 Jul 20;430(15):2237-2243
pubmed: 29258817
ISME J. 2016 Dec;10(12):2854-2866
pubmed: 27258950
Nat Microbiol. 2021 Mar;6(3):301-312
pubmed: 33462433
Cell Host Microbe. 2016 Oct 12;20(4):471-481
pubmed: 27667697
BMC Bioinformatics. 2019 Sep 14;20(1):473
pubmed: 31521110
Nucleic Acids Res. 2020 Jun 19;48(11):e64
pubmed: 32352514
Nat Biotechnol. 2017 Nov;35(11):1026-1028
pubmed: 29035372
Science. 2020 Aug 28;369(6507):1077-1084
pubmed: 32855333
Nature. 2020 Nov;587(7835):632-637
pubmed: 32731256
Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8
pubmed: 34597593
J Crohns Colitis. 2017 Jul 01;11(7):840-847
pubmed: 28130329
Gene. 1990 Nov 30;96(1):9-15
pubmed: 2265763
mBio. 2014 Dec 16;5(6):
pubmed: 25516616
J Bacteriol. 2002 Dec;184(23):6592-601
pubmed: 12426348
PLoS Pathog. 2015 Dec 04;11(12):e1005317
pubmed: 26636713
J Virol. 1990 Jan;64(1):24-36
pubmed: 2403440
Nat Microbiol. 2017 Jan 09;2:16251
pubmed: 28067906
Genome Res. 2012 Apr;22(4):802-9
pubmed: 22300632
Nat Microbiol. 2020 Dec;5(12):1608-1615
pubmed: 32839535
Nature. 2020 Oct;586(7829):429-433
pubmed: 32877915
Nucleic Acids Res. 2013 Apr;41(8):4360-77
pubmed: 23470997
Bioinformatics. 2021 Jan 18;:
pubmed: 33459763
PLoS Genet. 2017 Jun 8;13(6):e1006838
pubmed: 28594826
J Bacteriol. 2006 Feb;188(4):1643-7
pubmed: 16452449
J Mol Biol. 1989 Jun 20;207(4):675-93
pubmed: 2760929
J Mol Biol. 2007 Aug 3;371(1):25-33
pubmed: 17544443
Nature. 2018 Dec;564(7735):283-286
pubmed: 30518855
Annu Rev Virol. 2020 Sep 29;7(1):371-384
pubmed: 32559405
Nucleic Acids Res. 2021 May 21;49(9):5216-5229
pubmed: 33885789
Nature. 1999 Nov 4;402(6757):86-90
pubmed: 10573422
Nature. 2021 Dec;600(7887):116-120
pubmed: 34853457
J Biol Chem. 2014 Sep 26;289(39):27046-27054
pubmed: 25118281
Bacteriophage. 2012 Oct 1;2(4):225-228
pubmed: 23739268
Nat Rev Microbiol. 2020 Feb;18(2):113-119
pubmed: 31695182
Curr Opin Microbiol. 2014 Dec;22:22-9
pubmed: 25305534
J Mol Biol. 2004 Oct 8;343(1):1-28
pubmed: 15381417
J Mol Biol. 1975 May 15;94(2):283-95
pubmed: 1095770
Environ Microbiol. 2012 Aug;14(8):1844-54
pubmed: 22118225
Cell. 2020 Dec 10;183(6):1551-1561.e12
pubmed: 33157039
Mol Microbiol. 1995 Feb;15(3):415-20
pubmed: 7540246
J Bacteriol. 2011 Nov;193(21):6039-56
pubmed: 21908672
Nucleic Acids Res. 2020 Mar 18;48(5):2762-2776
pubmed: 32009148
Mol Microbiol. 2011 Nov;82(3):567-77
pubmed: 21985444
Nat Commun. 2017 Oct 10;8(1):841
pubmed: 29018197
Nat Microbiol. 2018 Jan;3(1):90-98
pubmed: 29085076
Nucleic Acids Res. 2014 Apr;42(7):4590-605
pubmed: 24465005
J Bacteriol. 1953 Feb;65(2):113-21
pubmed: 13034700
J Bacteriol. 1995 Feb;177(3):497-501
pubmed: 7836278
Mol Cell. 2021 Dec 16;81(24):5039-5051.e5
pubmed: 34784509
PLoS One. 2008;3(11):e3647
pubmed: 18985154
EMBO J. 2015 Jan 13;34(2):169-83
pubmed: 25452498
Proc Natl Acad Sci U S A. 1978 May;75(5):2200-4
pubmed: 276860
Nat Rev Genet. 2020 Feb;21(2):119-131
pubmed: 31611667
Mol Microbiol. 2002 Jan;43(2):509-20
pubmed: 11985726
Nat Microbiol. 2020 Jul;5(7):917-928
pubmed: 32251370
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
J Bacteriol. 1999 Nov;181(21):6822-7
pubmed: 10542186
Nature. 2021 Jan;589(7840):120-124
pubmed: 32937646
Biol Direct. 2013 Jun 15;8:15
pubmed: 23768067
Front Genet. 2014 Apr 30;5:102
pubmed: 24817877
Nucleic Acids Res. 2019 Jan 8;47(D1):D666-D677
pubmed: 30289528
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W429-32
pubmed: 17483518
Environ Microbiol. 2016 Jul;18(7):2237-45
pubmed: 26971586
Nucleic Acids Res. 2019 Sep 26;47(17):9448-9463
pubmed: 31400118
J Mol Biol. 1995 Jun 23;249(5):857-68
pubmed: 7791212
Microbiol Rev. 1993 Sep;57(3):683-702
pubmed: 8246844
Int Immunol. 2005 Jan;17(1):1-14
pubmed: 15585605
Science. 2021 Jul 30;373(6554):
pubmed: 34326207
Nucleic Acids Res. 2017 Jan 4;45(D1):D482-D490
pubmed: 27899678
Mol Biol Evol. 2004 Jan;21(1):1-13
pubmed: 12949155
Nature. 2019 Oct;574(7780):691-695
pubmed: 31533127
Microb Pathog. 1988 Feb;4(2):103-13
pubmed: 2849027
Science. 1991 May 17;252(5008):969-71
pubmed: 1709758
Virology. 2004 Nov 24;329(2):425-33
pubmed: 15518820
mBio. 2014 Apr 15;5(2):e00896
pubmed: 24736222
PLoS One. 2014 Nov 25;9(11):e114083
pubmed: 25423096
Mol Biol (Mosk). 2014 Jan-Feb;48(1):176-84
pubmed: 25842838
Virology. 2008 Mar 30;373(1):25-9
pubmed: 18096197
Curr Opin Microbiol. 2020 Aug;56:52-58
pubmed: 32653777
Nat Commun. 2018 May 15;9(1):1912
pubmed: 29765036
Science. 2021 Oct 22;374(6566):488-492
pubmed: 34672730
Nat Methods. 2009 May;6(5):343-5
pubmed: 19363495
Methods Enzymol. 2013;529:329-36
pubmed: 24011059
Nat Commun. 2022 May 10;13(1):2561
pubmed: 35538097
Cell. 2021 Nov 11;184(23):5728-5739.e16
pubmed: 34644530
Nucleic Acids Res. 2020 Dec 16;48(22):12632-12647
pubmed: 33275130
Methods Mol Biol. 2014;1151:165-88
pubmed: 24838886
Philos Trans R Soc Lond B Biol Sci. 2022 Jan 17;377(1842):20200475
pubmed: 34839713