An archaeal virus-encoded anti-CRISPR protein inhibits type III-B immunity by inhibiting Cas RNP complex turnover

CRISPR-Cas systems are widespread in prokaryotes and provide adaptive immune against viral infection. Viruses encode a type of proteins called anti-CRISPR to evade the immunity. Here, we identify an archaeal virus-encoded anti-CRISPR protein, AcrIIIB2, that inhibits Type III-B immunity. We find that AcrIIIB2 inhibits Type III-B CRISPR-Cas immunity in vivo regardless of viral early or middle-/late-expressed genes to be targeted. We also demonstrate that AcrIIIB2 interacts with Cmr4 alpha subunit, forming a complex with target RNA and Cmr-alpha ribonucleoprotein complex (RNP). Furtherly, we discover that AcrIIIB2 inhibits the RNase activity, ssDNase activity and cOA synthesis activity of Cmr-alpha RNP in vitro under a higher target RNA-to-Cmr-alpha RNP ratio and has no effect on Cmr-alpha activities at the target RNA-to-Cmr-alpha RNP ratio of 1. Our results suggest that once the target RNA is cleaved by Cmr-alpha RNP, AcrIIIB2 probably inhibits the disassociation of cleaved target RNA, therefore blocking the access of other target RNA substrates. Together, our findings highlight the multiple functions of a novel anti-CRISPR protein on inhibition of the most complicated CRISPR-Cas system targeting the genes involved in the whole life cycle of viruses.

Automated summary

In this study, a viral-encoded anti-CRISPR protein, AcrIIIB2, was identified to inhibit Type III-B CRISPR-Cas immunity. The interaction between AcrIIIB2 and Cmr4 alpha subunit and the mechanism by which AcrIIIB2 inhibits the activity of Cmr-alpha ribonucleoprotein complex were elucidated.