title: CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3.
abstract: The prokaryotic CRISPR/Cas immune system is based on genomic loci that contain incorporated sequence tags from viruses and plasmids. Using small guide RNA molecules, these sequences act as a memory to reject returning invaders. Both the Cascade ribonucleoprotein complex and the Cas3 nuclease/helicase are required for CRISPR interference in Escherichia coli, but it is unknown how natural target DNA molecules are recognized and neutralized by their combined action. Here we show that Cascade efficiently locates target sequences in negatively supercoiled DNA, but only if these are flanked by a protospacer-adjacent motif (PAM). PAM recognition by Cascade exclusively involves the crRNA-complementary DNA strand. After Cascade-mediated R loop formation, the Cse1 subunit recruits Cas3, which catalyzes nicking of target DNA through its HD-nuclease domain. The target is then progressively unwound and cleaved by the joint ATP-dependent helicase activity and Mg(2+)-dependent HD-nuclease activity of Cas3, leading to complete target DNA degradation and invader neutralization.
authors.affiliation: Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands.
authors.forename: Edze R
authors.initials: ER
authors.lastname: Westra
authors.forename: Paul B G
authors.initials: PB
authors.lastname: van Erp
authors.forename: Tim
authors.initials: T
authors.lastname: Künne
authors.forename: Shi Pey
authors.initials: SP
authors.lastname: Wong
authors.forename: Raymond H J
authors.initials: RH
authors.lastname: Staals
authors.forename: Christel L C
authors.initials: CL
authors.lastname: Seegers
authors.forename: Sander
authors.initials: S
authors.lastname: Bollen
authors.forename: Matthijs M
authors.initials: MM
authors.lastname: Jore
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Semenova
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.forename: Remus T
authors.initials: RT
authors.lastname: Dame
authors.forename: Renko
authors.initials: R
authors.lastname: de Vries
authors.forename: Stan J J
authors.initials: SJ
authors.lastname: Brouns
authors.forename: John
authors.initials: J
authors.lastname: van der Oost
mesh_terms: D064130:CRISPR-Associated Proteins; D004265:DNA Helicases / Q000235:genetics / Q000502:physiology*; D004278:DNA, Superhelical / Q000378:metabolism*; D048168:Escherichia coli K12 / Q000235:genetics / Q000276:immunology* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D018448:Models, Immunological; D009690:Nucleic Acid Conformation
chemical_list: D064130:CRISPR-Associated Proteins; D004278:DNA, Superhelical; D029968:Escherichia coli Proteins; D004265:DNA Helicases; C574631:ygcB protein, E coli