Campylobacter bacteriophage DA10: an excised temperate bacteriophage targeted by CRISPR-cas.
CRISPR-mediated immunity
Campylobacter bacteriophages
Campylobacters
Evolution
Lytic phage
Prophage
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
12 Jun 2020
12 Jun 2020
Historique:
received:
06
12
2019
accepted:
05
06
2020
entrez:
14
6
2020
pubmed:
14
6
2020
medline:
9
3
2021
Statut:
epublish
Résumé
Lytic bacteriophages that infect Campylobacter spp. have been utilized to develop therapeutic/decontamination techniques. However, the association of Campylobacter spp. and bacteriophages has been the focus of several strands of research aimed at understanding the complex relationships that have developed between predators and prey over evolutionary time. The activities of endogenous temperate bacteriophages have been used to evaluate genomic rearrangements and differential protein expression in host cells, and mechanisms of resistance to bacteriophage infection in campylobacters such as phase variation and CRISPR-mediated immunity. Temperate bacteriophage DA10 represents a novel excised and infective virus capable of replication in a restricted set of C. jejuni and C. coli hosts. Whole genome sequencing reveals that DA10 (35,379 bp) forms part of a novel group of temperate bacteriophages that have limited distribution among database host genome sequences. Analysis of potential host genomes reveals a robust response against DA10 and DA10-like bacteriophages is driven by CRISPR-mediated immunity with 75% of DA10 ORFs represented as ~ 30 bp spacer sequences in numerous Campylobacter Type II-C CRISPR arrays. Several DA10-like homologues have been identified in a small sub-set of C. jejuni and C. coli genome sequences (ranging from near complete integrated prophage sequences to fragments recognisable in the sequence read archive). A complete intact DA10-like prophage in C. jejuni CJ677CC520 provides evidence that the associations between host and DA10-like bacteriophages are long-standing in evolutionary timescales. Extensive nucleotide substitution and loss can be observed in the integrated DA10-like prophage of CJ677CC520 compared to other relatives as observed through pairwise genome comparisons. Examining factors that have limited the population expansion of the prophage, while others appear to have thrived and prospered (Mu-like, CJIE-like, and lytic Campylobacter bacteriophages) will assist in identifying the underlying evolutionary processes in the natural environment.
Sections du résumé
BACKGROUND
BACKGROUND
Lytic bacteriophages that infect Campylobacter spp. have been utilized to develop therapeutic/decontamination techniques. However, the association of Campylobacter spp. and bacteriophages has been the focus of several strands of research aimed at understanding the complex relationships that have developed between predators and prey over evolutionary time. The activities of endogenous temperate bacteriophages have been used to evaluate genomic rearrangements and differential protein expression in host cells, and mechanisms of resistance to bacteriophage infection in campylobacters such as phase variation and CRISPR-mediated immunity.
RESULTS
RESULTS
Temperate bacteriophage DA10 represents a novel excised and infective virus capable of replication in a restricted set of C. jejuni and C. coli hosts. Whole genome sequencing reveals that DA10 (35,379 bp) forms part of a novel group of temperate bacteriophages that have limited distribution among database host genome sequences. Analysis of potential host genomes reveals a robust response against DA10 and DA10-like bacteriophages is driven by CRISPR-mediated immunity with 75% of DA10 ORFs represented as ~ 30 bp spacer sequences in numerous Campylobacter Type II-C CRISPR arrays. Several DA10-like homologues have been identified in a small sub-set of C. jejuni and C. coli genome sequences (ranging from near complete integrated prophage sequences to fragments recognisable in the sequence read archive).
CONCLUSIONS
CONCLUSIONS
A complete intact DA10-like prophage in C. jejuni CJ677CC520 provides evidence that the associations between host and DA10-like bacteriophages are long-standing in evolutionary timescales. Extensive nucleotide substitution and loss can be observed in the integrated DA10-like prophage of CJ677CC520 compared to other relatives as observed through pairwise genome comparisons. Examining factors that have limited the population expansion of the prophage, while others appear to have thrived and prospered (Mu-like, CJIE-like, and lytic Campylobacter bacteriophages) will assist in identifying the underlying evolutionary processes in the natural environment.
Identifiants
pubmed: 32532247
doi: 10.1186/s12864-020-06808-3
pii: 10.1186/s12864-020-06808-3
pmc: PMC7291426
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
400Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : [grant number BB/P02355X/1]
Pays : United Kingdom
Références
Genome Announc. 2016 May 26;4(3):
pubmed: 27231378
Nature. 2016 Apr 21;532(7599):385-8
pubmed: 27074511
J Mol Biol. 2018 Jul 20;430(15):2237-2243
pubmed: 29258817
BMC Microbiol. 2012 Nov 20;12:269
pubmed: 23167543
Nat Struct Mol Biol. 2014 Jun;21(6):528-34
pubmed: 24793649
Nucleic Acids Res. 2018 Jul 2;46(W1):W246-W251
pubmed: 29790974
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W52-7
pubmed: 17537822
J Bacteriol. 2010 Feb;192(4):936-41
pubmed: 20023031
BMC Genomics. 2008 Feb 08;9:75
pubmed: 18261238
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100
pubmed: 2172928
Genome Biol Evol. 2015 Sep 02;7(9):2663-79
pubmed: 26338188
Front Microbiol. 2018 Feb 02;9:82
pubmed: 29467727
PLoS One. 2014 Mar 27;9(3):e92798
pubmed: 24676150
J Mol Biol. 1990 Oct 5;215(3):403-10
pubmed: 2231712
J Med Microbiol. 1998 Feb;47(2):123-8
pubmed: 9879954
Genome Biol Evol. 2014 Sep 04;6(9):2424-38
pubmed: 25193305
Front Microbiol. 2016 Mar 23;7:355
pubmed: 27047470
Appl Environ Microbiol. 2003 Aug;69(8):4511-8
pubmed: 12902236
J Virol. 1970 Jul;6(1):94-9
pubmed: 4097234
mBio. 2018 Nov 13;9(6):
pubmed: 30425154
Int J Med Microbiol. 2017 Jun;307(4-5):233-240
pubmed: 28408091
J Clin Microbiol. 2017 May;55(5):1269-1275
pubmed: 28249998
Sci Rep. 2015 Nov 25;5:17300
pubmed: 26603914
BMC Microbiol. 2014 Mar 19;14:70
pubmed: 24641125
Clin Microbiol Rev. 2019 Jul 3;32(4):
pubmed: 31270126
Mol Microbiol. 2001 Jan;39(2):260-71
pubmed: 11136448
Front Microbiol. 2017 Mar 27;8:513
pubmed: 28396658
Front Cell Infect Microbiol. 2018 Jun 12;8:195
pubmed: 29951376
Front Microbiol. 2015 Jan 05;5:744
pubmed: 25601859
Microbiol Mol Biol Rev. 2004 Sep;68(3):560-602, table of contents
pubmed: 15353570
Front Microbiol. 2015 Jul 10;6:699
pubmed: 26217328
Nucleic Acids Res. 2016 Jul 8;44(W1):W16-21
pubmed: 27141966
PLoS Pathog. 2007 Aug 24;3(8):e119
pubmed: 17722979
Appl Environ Microbiol. 2019 Mar 22;85(7):
pubmed: 30709824
BMC Microbiol. 2008 Mar 20;8:49
pubmed: 18366706
Genome Res. 2004 Jun;14(6):1188-90
pubmed: 15173120
PLoS Biol. 2005 Jan;3(1):e15
pubmed: 15660156
Arch Virol. 2014 Jan;159(1):181-90
pubmed: 23881082
Emerg Infect Dis. 2013 Oct;19(10):1653-5
pubmed: 24047729
J Clin Microbiol. 2006 Nov;44(11):4125-35
pubmed: 16943349
Clin Microbiol Rev. 2015 Jul;28(3):687-720
pubmed: 26062576
J Bacteriol. 2009 Apr;191(7):2296-306
pubmed: 19151136
Front Microbiol. 2016 Nov 29;7:1908
pubmed: 27965643
Appl Microbiol. 1973 Sep;26(3):404-9
pubmed: 4201644
Am J Vet Res. 1968 Nov;29(11):2229-35
pubmed: 5693467