Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system.
CRISPR-Cas systems provide bacteria with adaptive immunity against foreign nucleic acids by acquiring short, invader-derived sequences called spacers. Here, we use high-throughput sequencing to analyse millions of spacer acquisition events in wild-type populations of Pectobacterium atrosepticum. Plasmids not previously encountered, or plasmids that had escaped CRISPR-Cas targeting via point mutation, are used to provoke naive or primed spacer acquisition, respectively. The origin, location and order of spacer acquisition show that spacer selection through priming initiates near the site of CRISPR-Cas recognition (the protospacer), but on the displaced strand, and is consistent with 3'-5' translocation of the Cas1:Cas2-3 acquisition machinery. Newly acquired spacers determine the location and strand specificity of subsequent spacers and demonstrate that interference-driven spacer acquisition ('targeted acquisition') is a major contributor to adaptation in type I-F CRISPR-Cas systems. Finally, we show that acquisition of self-targeting spacers is occurring at a constant rate in wild-type cells and can be triggered by foreign DNA with similarity to the bacterial chromosome.
Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
Raymond H J
RH
Staals
Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
Simon A
SA
Jackson
Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
Ambarish
A
Biswas
Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
Stan J J
SJ
Brouns
Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand.|Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
Chris M
CM
Brown
Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.|Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand.|Bio-Protection Research Centre, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
Peter C
PC
Fineran
D000222:Adaptation, Physiological; D064130:CRISPR-Associated Proteins / Q000235:genetics; D064113:CRISPR-Cas Systems; D002876:Chromosomes, Bacterial / Q000648:ultrastructure; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D009154:Mutation; D044043:Pectobacterium / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D017354:Point Mutation; D013941:Thymine / Q000737:chemistry
D064130:CRISPR-Associated Proteins; D004269:DNA, Bacterial; D013941:Thymine
Nat Commun. 2013;4:1430
23385575
Nature. 1974 Sep 27;251(5473):337-40
4610399
RNA Biol. 2011 May-Jun;8(3):517-28
21519197
Nature. 2000 May 18;405(6784):299-304
10830951
Nat Biotechnol. 2014 Nov;32(11):1146-50
25282355
PLoS One. 2012;7(4):e35888
22558257
J Bacteriol. 2008 Feb;190(4):1390-400
18065545
Mol Cell. 2015 Apr 2;58(1):60-70
25752578
Curr Biol. 2015 Apr 20;25(8):1043-9
25772450
J Biol Chem. 2013 Aug 2;288(31):22184-92
23760266
Nat Rev Microbiol. 2015 Nov;13(11):722-36
26411297
Nat Biotechnol. 2014 Nov;32(11):1141-5
25240928
Bioinformatics. 2012 Dec 1;28(23):3150-2
23060610
Nucleic Acids Res. 2014 Jun;42(11):7226-35
24803673
Nat Rev Microbiol. 2016 Feb;14(2):67-76
26751509
Nat Struct Mol Biol. 2014 Jun;21(6):528-34
24793649
Nat Rev Microbiol. 2014 Jul;12(7):479-92
24909109
Genes Dev. 2015 Feb 15;29(4):356-61
25691466
Mol Microbiol. 2014 Jul;93(1):1-9
24806524
Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10098-103
21646539
BMC Genomics. 2016 May 17;17:356
27184979
Nature. 2015 Mar 12;519(7542):199-202
25707807
Nature. 2013 Jan 17;493(7432):429-32
23242138
Nature. 2015 Nov 26;527(7579):535-8
26503043
Nat Commun. 2012 Jul 10;3:945
22781758
PLoS One. 2012;7(12):e49549
23226499
Cell Rep. 2015 Mar 3;:null
25753419
RNA Biol. 2013 May;10(5):770-8
23406879
Mol Microbiol. 2013 Nov;90(3):457-71
23957692
Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1629-38
24711427
Microbiology. 2009 Mar;155(Pt 3):733-40
19246744
Nature. 2015 Mar 12;519(7542):193-8
25707795
MBio. 2014 Jan 28;5(1):e00928-13
24473129
Nucleic Acids Res. 2015 Dec 15;43(22):10848-60
26586803
Elife. 2015 Aug 18;4:null
26284603
RNA Biol. 2013 May;10(5):817-27
23492433
Mol Microbiol. 2011 Jan;79(2):484-502
21219465
Nature. 2016 Feb 25;530(7591):499-503
26863189
Science. 2007 Mar 23;315(5819):1709-12
17379808
Nature. 2015 Apr 23;520(7548):505-10
25874675
Virology. 2012 Dec 20;434(2):202-9
23123013
Nucleic Acids Res. 2015 Feb 18;43(3):1749-58
25589547
Proc Natl Acad Sci U S A. 2013 Aug 27;110(35):14396-401
23940313
Nucleic Acids Res. 2014 Feb;42(4):2483-92
24265226
Cell. 2015 Nov 5;163(4):840-53
26478180
Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11105-10
15263089
Trends Genet. 2010 Aug;26(8):335-40
20598393
Nucleic Acids Res. 2015 Dec 15;43(22):10831-47
26586800
Nucleic Acids Res. 2012 Jul;40(12):5569-76
22402487
Bioinformatics. 2014 Jul 1;30(13):1805-13
24578404
Mol Cell. 2016 Apr 7;62(1):137-47
27041224
Science. 2008 Aug 15;321(5891):960-4
18703739
RNA Biol. 2013 May;10(5):792-802
23445770
PLoS Genet. 2013 Apr;9(4):e1003454
23637624
Nature. 2015 Oct 1;526(7571):55-61
26432244
Microbiology. 2005 Mar;151(Pt 3):653-63
15758212
Curr Opin Struct Biol. 2014 Feb;24:106-14
24480304
Microbiol Mol Biol Rev. 1998 Jun;62(2):434-64
9618448
J Mol Evol. 2005 Feb;60(2):174-82
15791728
PLoS One. 2012;7(7):e40102
22792219
Annu Rev Microbiol. 2001;55:709-42
11544372
Cell. 2015 Nov 5;163(4):854-65
26522594
Nucleic Acids Res. 2014 May;42(9):5907-16
24728991
RNA Biol. 2013 May;10(5):716-25
23619643
Nat Microbiol. 2016 Jun 13;1(8):16085
27573108
Nucleic Acids Res. 2015 Dec 15;43(22):10821-30
26578567
Biochem J. 2016 Apr 15;473(8):1063-72
26929403
Mol Cell. 2012 Jun 8;46(5):595-605
22521689
Nucleic Acids Res. 2014 Jul;42(13):8516-26
24990370
EMBO J. 2011 Apr 6;30(7):1335-42
21343909