Emergence of networks of shared restriction-modification systems in phage–bacteria ecosystems

Arber W 1965 Host-controlled modification of bacteriophage. Annu. Rev. Microbiol. 19 365–378

CAS  Article  Google Scholar 

Bar-On YM, Phillips R and Milo R 2018 The biomass distribution on Earth. Proc. Natl. Acad. Sci. USA 115 6506–6511

CAS  Article  Google Scholar 

Berngruber TW, Lion S and Gandon S 2013 Evolution of suicide as a defence strategy against pathogens in a spatially structured environment. Ecol. Lett. 16 446–453

Article  Google Scholar 

De Paepe M and Taddei F 2006 Viruses’ life history: Towards a mechanistic basis of a trade-off between survival and reproduction among phages. PLoS Biol. 4 e193

Article  Google Scholar 

Dupuis MÈ , Villion M, Magadán AH and Moineau S 2013 CRISPR-Cas and restriction-modification systems are compatible and increase phage resistance. Nat. Commun 4 2087

Article  Google Scholar 

Eriksen RS and Krishna S 2020 Data from: Defense versus growth in a hostile world - Lessons from phage and bacteria. Zenodo online repository. https://doi.org/10.5281/zenodo.3842682

Eriksen RS and Krishna S 2020 Defence versus growth in a hostile world: lessons from phage and bacteria. R. Soc. Open Sci. 7 201118

Article  Google Scholar 

Eriksen RS, Malhotra N, Seshasayee ASN, Sneppen K and Krishna S 2021 Data from: Emergence of networks of shared restriction-modification systems in phage–bacteria ecosystems. Zenodo online repository. https://doi.org/10.5281/zenodo.6210319

Forterre P and Prangishvili D 2009 The Great Billion-year War between ribosome- and capsid-encoding organisms (cells and viruses) as the major source of evolutionary novelties. Ann. NY Acad. Sci. 1178 65–77

CAS  Article  Google Scholar 

Frank SA 1994 Polymorphism of bacterial restriction-modification systems: the advantage of diversity. Evolution 48 1470–1477

PubMed  Google Scholar 

Fullmer MS, Ouellette M, Louyakis AS, Papke RT and Gogarten JP 2019 The patchy distribution of restriction-modification system genes and the conservation of orphan methyltransferases in Halobacteria. Genes 10 233

CAS  Article  Google Scholar 

Knowles B, Silveira CB, Bailey BA, et al. 2016 Lytic to temperate switching of viral communities. Nature 531 466–470

CAS  Article  Google Scholar 

Koonin EV and Wolf YI 2012 Evolution of microbes and viruses: a paradigm shift in evolutionary biology? Front. Cell. Infect. Microbiol. 2 119

Article  Google Scholar 

Koskella B and Meaden S 2013 Understanding bacteriophage specificity in natural microbial communities. Viruses 5 806–823

Article  Google Scholar 

Makarova KS, Wolf YI and Koonin EV 2013 Comparative genomics of defense systems in archaea and bacteria. Nucleic Acids Res. 41 4360–4377

CAS  Article  Google Scholar 

Moineau S, Pandian S and Klaenhammer TR 1993 Restriction/modification systems and restriction endonucleases are more effective on lactococcal bacteriophages that have emerged recently in the dairy industry. Appl. Environ. Microbiol. 59 197–202

CAS  Article  Google Scholar 

O’Leary NA, Wright MW, Brister JR, et al. 2016 Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44 D733– D745

Article  Google Scholar 

Pagie L 2000 Individual- and population-based diversity in restriction-modification systems. Bull. Math. Biol. 62 759–774

CAS  Article  Google Scholar 

Pavlopoulos GA, Kontou PI, Pavlopoulou A, et al. 2018 Bipartite graphs in systems biology and medicine: a survey of methods and applications. GigaScience 7 1–31

Article  Google Scholar 

Payne P, Geyrhofer L, Barton NH and Bollback JP 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife 7 1–33

Pleška M, Qian L, Okura R, et al. 2016 Bacterial autoimmunity due to a restriction-modification system. Curr. Biol. 26 404–409

Article  Google Scholar 

Roberts RJ, Vincze T, Posfai J and Macelis D 2015 REBASE-a database for DNA restriction and modification: Enzymes, genes and genomes. Nucleic Acids Res. 43 D298–D299

CAS  Article  Google Scholar 

Roer L, Hendriksen RS, Leekitcharoenphon P, et al. 2016 Is the Evolution of Salmonella enterica subsp. enterica linked to restriction- modification systems? mSystems 1 e00009–e00016

Seshasayee ASN, Singh P and Krishna S 2012 Context-dependent conservation of DNA methyltransferases in bacteria. Nucleic Acids Res. 40 7066–7073

CAS  Article  Google Scholar 

Sneppen K, Semsey S, Seshasayee AS and Krishna S 2015 Restriction modification systems as engines of diversity. Front. Microbiol. 6 528

Article  Google Scholar 

Stern A and Sorek R 2011 The phage-host arms race: Shaping the evolution of microbes. BioEssays 33 43–51

CAS  Article  Google Scholar 

Suttle CA 2007 Marine viruses - Major players in the global ecosystem. Nat. Rev. Microbiol. 5 801–812

CAS  Article  Google Scholar 

Vasu K and Nagaraja V 2013 Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol. Mol. Biol. Rev. 77 53–72

CAS  Article  Google Scholar 

留言 (0)

沒有登入
gif