title: The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity.
abstract: All organisms need to continuously adapt to changes in their environment. Through horizontal gene transfer, bacteria and archaea can rapidly acquire new traits that may contribute to their survival. However, because new DNA may also cause damage, removal of imported DNA and protection against selfish invading DNA elements are also important. Hence, there should be a delicate balance between DNA uptake and DNA degradation. Here, we describe prokaryotic antiviral defense systems, such as receptor masking or mutagenesis, blocking of phage DNA injection, restriction/modification, and abortive infection. The main focus of this review is on CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated), a prokaryotic adaptive immune system. Since its recent discovery, our biochemical understanding of this defense system has made a major leap forward. Three highly diverse CRISPR/Cas types exist that display major structural and functional differences in their mode of generating resistance against invading nucleic acids. Because several excellent recent reviews cover all CRISPR subtypes, we mainly focus on a detailed description of the type I-E CRISPR/Cas system of the model bacterium Escherichia coli K12.
authors.affiliation: Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB Wageningen, The Netherlands. edze.westra@wur.nl
authors.forename: Edze R
authors.initials: ER
authors.lastname: Westra
authors.forename: Daan C
authors.initials: DC
authors.lastname: Swarts
authors.forename: Raymond H J
authors.initials: RH
authors.lastname: Staals
authors.forename: Matthijs M
authors.initials: MM
authors.lastname: Jore
authors.forename: Stan J J
authors.initials: SJ
authors.lastname: Brouns
authors.forename: John
authors.initials: J
authors.lastname: van der Oost
mesh_terms: D020816:Amino Acid Motifs; D001435:Bacteriophages / Q000235:genetics / Q000276:immunology / Q000472:pathogenicity; D064130:CRISPR-Associated Proteins; D004265:DNA Helicases / Q000235:genetics / Q000378:metabolism*; D004279:DNA, Viral / Q000235:genetics / Q000378:metabolism; D015253:Deoxyribonucleases, Type I Site-Specific / Q000235:genetics / Q000378:metabolism; D004706:Endodeoxyribonucleases / Q000235:genetics / Q000378:metabolism*; D048168:Escherichia coli K12 / Q000235:genetics / Q000276:immunology* / Q000378:metabolism / Q000821:virology; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D008242:Lysogeny; D039002:Prophages / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D053586:Virus Internalization
chemical_list: D064130:CRISPR-Associated Proteins; D004279:DNA, Viral; D029968:Escherichia coli Proteins; D004706:Endodeoxyribonucleases; C557650:YgbT protein, E coli; D015253:Deoxyribonucleases, Type I Site-Specific; C109830:HsdR protein, E coli; D004265:DNA Helicases; C574631:ygcB protein, E coli