van Belkum A, Soriaga LB, LaFave MC, Akella S, Veyrieras JB, Barbu EM, et al. Phylogenetic distribution of CRISPR-Cas systems in antibiotic-resistant Pseudomonas aeruginosa. MBio. 2015;6:e01796–15.
Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJ, et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol. 2019;18:1–17.
Portillo MC, Gonzalez JM. CRISPR elements in the Thermococcales: evidence for associated horizontal gene transfer in Pyrococcus furiosus. J Appl Genet. 2009;50:421–30.
Watson BN, Staals RH, Fineran, PC. CRISPR-Cas-mediated phage resistance enhances horizontal gene transfer by transduction. MBio. 2018;9:e02406–17.
Varble A, Meaden S, Barrangou R, Westra ER, Marraffini LA. Recombination between phages and CRISPR-cas loci facilitates horizontal gene transfer in staphylococci. Nat Microbiol. 2019;4:956–63.
Levin BR. Nasty viruses, costly plasmids, population dynamics, and the conditions for establishing and maintaining CRISPR-mediated adaptive immunity in bacteria. PLoS Genet. 2010;6:e1001171.
van Houte S, Buckling A, Westra ER. Evolutionary ecology of prokaryotic immune mechanisms. Microbiol Mol Biol Rev. 2016;80:745–63.
Rollie C, Chevallereau A, Watson BN, Chyou TY, Fradet O, McLeod I, et al. Targeting of temperate phages drives loss of type I CRISPR-Cas systems. Nature. 2020;578:149–53.
Westra ER, van Houte S, Oyesiku-Blakemore S, Makin B, Broniewski JM, Best A, et al. Parasite exposure drives selective evolution of constitutive versus inducible defense. Curr Biol. 2015;25:1043–9.
Vale PF, Lafforgue G, Gatchitch F, Gardan R, Moineau S, Gandon S. Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus. Proc R Soc B: Biol Sci. 2015;282:20151270.
van Houte S, Ekroth AK, Broniewski JM, Chabas H, Ashby B, Bondy-Denomy J, et al. The diversity-generating benefits of a prokaryotic adaptive immune system. Nature. 2016;532:385–8.
Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. Self-targeting by CRISPR: gene regulation or autoimmunity? Trends Genet. 2010;26:335–40.
Levy A, Goren MG, Yosef I, Auster O, Manor M, Amitai G, et al. CRISPR adaptation biases explain preference for acquisition of foreign DNA. Nature. 2015;520:505–10.
Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS, et al. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet. 2013;9:e1003454.
Staals RH, Jackson SA, Biswas A, Brouns SJ, Brown CM, Fineran PC. Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR–Cas system. Nat Commun. 2016;7:1–13.
Weissman JL, Stoltzfus A, Westra ER, Johnson PL. Avoidance of Self during CRISPR immunization. Trends Microbiol. 2020;28:543–53.
Koonin EV. Open questions: CRISPR biology. BMC Biol. 2018;16:1–3.
Patterson AG, Yevstigneyeva MS, Fineran PC. Regulation of CRISPR–Cas adaptive immune systems. Curr Opin Microbiol. 2017;37:1–7.
Quax TE, Voet M, Sismeiro O, Dillies MA, Jagla B, Coppee JY, et al. Massive activation of archaeal defense genes during viral infection. J Virol. 2013;87:8419–28.
Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, et al. Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PloS ONE. 2012;7:e38077.
Agari Y, Sakamoto K, Tamakoshi M, Oshima T, Kuramitsu S, Shinkai A. Transcription profile of Thermus thermophilus CRISPR systems after phage infection. J Mol Biol. 2010;395:270–81.
Chabas H, van Houte S, Høyland-Kroghsbo NM, Buckling A, Westra ER. Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies. Proc R Soc B: Biol Sci. 2016;283:20160721.
Pawluk A, Staals RH, Taylor C, Watson BN, Saha S, Fineran PC, et al. Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nat Microbiol. 2016;1:1–6.
Bondy-Denomy J, Garcia B, Strum S, Du M, Rollins MF, Hidalgo-Reyes Y, et al. Multiple mechanisms for CRISPR-Cas inhibition by anti-CRISPR proteins. Nature. 2015;526:136–9.
Stanley SY, Borges AL, Chen KH, Swaney DL, Krogan NJ, Bondy-Denomy J, et al. Anti-CRISPR-associated proteins are crucial repressors of anti-CRISPR transcription. Cell. 2019;178:1452–64.
Cady KC, Bondy-Denomy J, Heussler GE, Davidson AR, O’Toole GA. The CRISPR/Cas adaptive immune system of Pseudomonas aeruginosa mediates resistance to naturally occurring and engineered phages. J Bacteriol. 2012;194:5728–38.
Chevallereau A, Meaden S, Fradet O, Landsberger M, Maestri A, Biswas A, et al. Exploitation of the cooperative behaviors of anti-CRISPR phages. Cell Host Microbe. 2020;27:189–98.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17:10–12.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Zhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics. 2014;30:614–20.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ. 2015;3:e1420.
Chao A. Nonparametric estimation of the number of classes in a population. Scand J Stat. 1984;11:265–70.
Biswas A, Staals RH, Morales SE, Fineran PC, Brown CM. CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genom. 2016;17:1–14.
Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 2013;10:817–27.
Joshi N. & Fass J. Sickle: A sliding-window, adaptive, quality-based trimming tool for fastQ files (version 1.33) [software]. 2011. https://github.com/najoshi/sickle.
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25:1754–60.
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Galili T. dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering. Bioinformatics. 2015;31:3718–20.
Richter C, Dy RL, McKenzie RE, Watson BN, Taylor C, Chang JT, et al. Priming in the Type IF CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Res. 2014;42:8516–26.
Fineran PC, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, et al. Degenerate target sites mediate rapid primed CRISPR adaptation. Proc Natl Acad Sci USA. 2014;111:E1629–38.
Xue C, Seetharam AS, Musharova O, Severinov K, Brouns J, Severin SJ, et al. CRISPR interference and priming varies with individual spacer sequences. Nucleic Acids Res. 2015;43:10831–47.
Wortham BW, Oliveira MA, Patel CN. Polyamines in bacteria: pleiotropic effects yet specific mechanisms. In: (eds Perry RD, Fetherston JD). The genus Yersinia. New York, NY: Springer; 2007. p. 106–15.
Bru JL, Rawson B, Trinh C, Whiteson K, Høyland-Kroghsbo NM, Siryaporn A. PQS produced by the Pseudomonas aeruginosa stress response repels swarms away from bacteriophage and antibiotics. J Bacteriol. 2019;201:e00383–19.
Doron S, Fedida A, Hernández-Prieto MA, Sabehi G, Karunker I, Stazic D, et al. Transcriptome dynamics of a broad host-range cyanophage and its hosts. ISME J. 2016;10:1437–55.
Landsberger M, Gandon S, Meaden S, Rollie C, Chevallereau A, Chabas H, et al. Anti-CRISPR phages cooperate to overcome CRISPR-Cas immunity. Cell. 2018;174:908–16.
Wei Y, Terns RM, Terns MP. Cas9 function and host genome sampling in Type II-A CRISPR-Cas adaptation. Genes Dev. 2015;29:356–61.
Fokine A, Rossmann MG. Common evolutionary origin of procapsid proteases, phage tail tubes, and tubes of bacterial type VI secretion systems. Structure. 2016;24:1928–35.
Modell JW, Jiang W, Marraffini LA. CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity. Nature. 2017;544:101–4.
van Sluijs L, van Houte S, van Der Oost J, Brouns SJ, Buckling A, Westra ER. Addiction systems antagonize bacterial adaptive immunity. FEMS Microbiol Lett. 2019;366:fnz047.
Wagemans J, Blasdel BG, Van den Bossche A, Uytterhoeven B, De Smet J, Paeshuyse J, et al. Functional elucidation of antibacterial phage ORFans targeting Pseudomonas aeruginosa. Cell Microbiol. 2014;16:1822–35.
van Houte S, Ros VI, van Oers MM. Walking with insects: molecular mechanisms behind parasitic manipulation of host behaviour. Mol Ecol. 2013;22:3458–75.
Taylor TB, Buckling A. Bacterial motility confers fitness advantage in the presence of phages. J Evolut Biol. 2013;26:2154–60.
Heussler GE, Cady KC, Koeppen K, Bhuju S, Stanton BA, O’Toole GA. Clustered regularly interspaced short palindromic repeat-dependent, biofilm-specific death of Pseudomonas aeruginosa mediated by increased expression of phage-related genes. MBio. 2015;6:e00129–15.
Hernandez CA, Koskella B. Phage resistance evolution in vitro is not reflective of in vivo outcome in a plant‐bacteria‐phage system. Evolution. 2019;73:2461–75.
Alseth EO, Pursey E, Luján AM, McLeod I, Rollie C, Westra ER. Bacterial biodiversity drives the evolution of CRISPR-based phage resistance. Nature. 2019;574:549–52.
Westra E, Levin BR. How important is CRISPR-Cas for protecting natural populations of bacteria against infections with badass DNAs? BioRxiv. 2020. https://www.biorxiv.org/content/10.1101/2020.02.05.935965v2.
Source: Ecology - nature.com
