Classification and nomenclature of CRISPR-Cas systems: where from here?

KS Makarova, YI Wolf, EV Koonin - The CRISPR journal, 2018 - liebertpub.com
As befits an immune mechanism, CRISPR-Cas systems are highly variable with respect to
Cas protein sequences, gene composition, and organization of the genomic loci. Optimal …

Revenge of the phages: defeating bacterial defences

JE Samson, AH Magadán, M Sabri… - Nature Reviews …, 2013 - nature.com
Bacteria and their viral predators (bacteriophages) are locked in a constant battle. In order to
proliferate in phage-rich environments, bacteria have an impressive arsenal of defence …

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

RJ Roberts, T Vincze, J Posfai… - Nucleic acids research, 2015 - academic.oup.com
REBASE is a comprehensive and fully curated database of information about the
components of restriction-modification (RM) systems. It contains fully referenced information …

DISARM is a widespread bacterial defence system with broad anti-phage activities

G Ofir, S Melamed, H Sberro, Z Mukamel… - Nature …, 2018 - nature.com
The evolutionary pressure imposed by phage predation on bacteria and archaea has
resulted in the development of effective anti-phage defence mechanisms, including …

Evolutionary genomics of defense systems in archaea and bacteria

EV Koonin, KS Makarova, YI Wolf - Annual review of …, 2017 - annualreviews.org
Evolution of bacteria and archaea involves an incessant arms race against an enormous
diversity of genetic parasites. Accordingly, a substantial fraction of the genes in most …

[HTML][HTML] The epigenomic landscape of prokaryotes

MJ Blow, TA Clark, CG Daum, AM Deutschbauer… - PLoS …, 2016 - journals.plos.org
DNA methylation acts in concert with restriction enzymes to protect the integrity of
prokaryotic genomes. Studies in a limited number of organisms suggest that methylation …

Diverse functions of restriction-modification systems in addition to cellular defense

K Vasu, V Nagaraja - Microbiology and molecular biology reviews, 2013 - Am Soc Microbiol
Restriction-modification (RM) systems are ubiquitous and are often considered primitive
immune systems in bacteria. Their diversity and prevalence across the prokaryotic kingdom …

Comparative genomics of defense systems in archaea and bacteria

KS Makarova, YI Wolf, EV Koonin - Nucleic acids research, 2013 - academic.oup.com
Our knowledge of prokaryotic defense systems has vastly expanded as the result of
comparative genomic analysis, followed by experimental validation. This expansion is both …

The phage‐host arms race: shaping the evolution of microbes

A Stern, R Sorek - Bioessays, 2011 - Wiley Online Library
Bacteria, the most abundant organisms on the planet, are outnumbered by a factor of 10 to 1
by phages that infect them. Faced with the rapid evolution and turnover of phage particles …

The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

PH Oliveira, M Touchon, EPC Rocha - Nucleic acids research, 2014 - academic.oup.com
The roles of restriction-modification (RM) systems in providing immunity against horizontal
gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much …