Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue 22, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv1259
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Funding
- Iowa State University College of Liberal Arts and Sciences
- Roy J. Carver Charitable Trust
- National Institutes of Health [GM10407]
- Russian Science Foundation [14-14-00988]
- Ministry of Education and Science of Russian Federation [14.B25.31.0004]
- Nertherlands Organisation for Scientific Research NWO VIDI [864.11.005]
- European Research Council [639707]
- European Research Council (ERC) [639707] Funding Source: European Research Council (ERC)
- Russian Science Foundation [14-14-00988] Funding Source: Russian Science Foundation
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CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid 'primed' adaptation. Here, we use multiple spacer sequences to re-examine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR-Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed 'naive' adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection.
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