title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process.
abstract: The clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system mediates adaptive immunity against foreign nucleic acids in prokaryotes. However, efficient adaptation of a native CRISPR to purified viruses has only been observed for the type II-A system from a Streptococcus thermophilus industry strain, and rarely reported for laboratory strains. Here, we provide a second native system showing efficient adaptation. Infected by a newly isolated virus HHPV-2, Haloarcula hispanica type I-B CRISPR system acquired spacers discriminatively from viral sequences. Unexpectedly, in addition to Cas1, Cas2 and Cas4, this process also requires Cas3 and at least partial Cascade proteins, which are involved in interference and/or CRISPR RNA maturation. Intriguingly, a preexisting spacer partially matching a viral sequence is also required, and spacer acquisition from upstream and downstream sequences of its target sequence (i.e. priming protospacer) shows different strand bias. These evidences strongly indicate that adaptation in this system strictly requires a priming process. This requirement, if validated also true for other CRISPR systems as implied by our bioinformatic analysis, may help to explain failures to observe efficient adaptation to purified viruses in many laboratory strains, and the discrimination mechanism at the adaptation level that has confused scientists for years.
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and University of Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Rui
authors.initials: R
authors.lastname: Wang
authors.forename: Dahe
authors.initials: D
authors.lastname: Zhao
authors.forename: Hua
authors.initials: H
authors.lastname: Xiang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D023641:Archaeal Viruses / Q000235:genetics* / Q000302:isolation & purification; D064130:CRISPR-Associated Proteins / Q000235:genetics; D064113:CRISPR-Cas Systems; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004267:DNA Viruses / Q000235:genetics / Q000302:isolation & purification; D004279:DNA, Viral / Q000737:chemistry; D016679:Genome, Viral; D019613:Haloarcula / Q000235:genetics* / Q000821:virology; D008969:Molecular Sequence Data; D048249:Streptococcus thermophilus / Q000235:genetics
chemical_list: D064130:CRISPR-Associated Proteins; D004279:DNA, Viral