Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System

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dc.contributor.author Hoikkala, Ville
dc.contributor.author Ravantti, Janne
dc.contributor.author Diez-Villasenor, Cesar
dc.contributor.author Tiirola, Marja
dc.contributor.author Conrad, Rachel A.
dc.contributor.author McBride, Mark J.
dc.contributor.author Moineau, Sylvain
dc.contributor.author Sundberg, Lotta-Riina
dc.date.accessioned 2021-05-20T15:40:01Z
dc.date.available 2021-05-20T15:40:01Z
dc.date.issued 2021
dc.identifier.citation Hoikkala , V , Ravantti , J , Diez-Villasenor , C , Tiirola , M , Conrad , R A , McBride , M J , Moineau , S & Sundberg , L-R 2021 , ' Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System ' , mBio , vol. 12 , no. 2 , ARTN e03338-20 . https://doi.org/10.1128/mBio.03338-20
dc.identifier.other PURE: 163849437
dc.identifier.other PURE UUID: a6b0d93f-19c2-43a6-8bad-f230f6ac1a0e
dc.identifier.other WOS: 000643733900008
dc.identifier.other ORCID: /0000-0002-8578-7230/work/94194364
dc.identifier.uri http://hdl.handle.net/10138/330148
dc.description.abstract CRISPR-Cas immune systems adapt to new threats by acquiring new spacers from invading nucleic acids such as phage genomes. However, some CRISPR-Cas loci lack genes necessary for spacer acquisition despite variation in spacer content between microbial strains. It has been suggested that such loci may use acquisition machinery from cooccurring CRISPR-Cas systems within the same strain. Here, following infection by a virulent phage with a double-stranded DNA (dsDNA) genome, we observed spacer acquisition in the native host Flavobacterium columnare that carries an acquisition-deficient CRISPR-Cas subtype VI-B system and a complete subtype II-C system. We show that the VI-B locus acquires spacers from both the bacterial and phage genomes, while the newly acquired II-C spacers mainly target the viral genome. Both loci preferably target the terminal end of the phage genome, with priming-like patterns around a preexisting II-C protospacer. Through gene deletion, we show that the RNA-cleaving VI-B system acquires spacers in trans using acquisition machinery from the DNA-cleaving II-C system. Our observations support the concept of cross talk between CRISPR-Cas systems and raise further questions regarding the plasticity of adaptation modules. IMPORTANCE CRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader's genome. These fragments, called spacers, are integrated into a memory bank on the bacterial genome called the CRISPR array. The spacers allow for the recognition of the same invader upon subsequent infection. Most CRISPR-Cas systems target DNA, but recently, systems that exclusively target RNA have been discovered. RNA-targeting CRISPR-Cas systems often lack genes necessary for spacer acquisition, and it is thus unknown how new spacers are acquired and if they can be acquired from DNA phages. Here, we show that an RNA-targeting system "borrows" acquisition machinery from another CRISPR-Cas locus in the genome. Most new spacers in this locus are unable to target phage mRNA and are therefore likely redundant. Our results reveal collaboration between distinct CRISPR-Cas types and raise further questions on how other CRISPR-Cas loci may cooperate. en
dc.format.extent 18
dc.language.iso eng
dc.relation.ispartof mBio
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject CRISPR
dc.subject adaptation
dc.subject bacteriophages
dc.subject coevolution
dc.subject spacer acquisition
dc.subject type II
dc.subject type VI
dc.subject 1184 Genetics, developmental biology, physiology
dc.title Cooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting System en
dc.type Article
dc.contributor.organization Molecular and Integrative Biosciences Research Programme
dc.contributor.organization Biosciences
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1128/mBio.03338-20
dc.relation.issn 2150-7511
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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