Abstract
A detailed functional analysis of the CRISPR-associated
Thermus thermophilus
Cas5d protein identifies it as a sequence-specific pre-crRNA processing endonuclease. High-resolution X-ray structural studies of a second Cas5d ortholog highlight similarities with previously characterized CRISPR processing enzymes. A combination of structural and functional analyses based on these results allow a modeling of the interaction of Cas5d with its RNA substrate and suggest that it is a member of a larger conserved family of CRISPR RNA endonucleases.
Small RNAs derived from clustered, regularly interspaced, short palindromic repeat (CRISPR) loci in bacteria and archaea are involved in an adaptable and heritable gene-silencing pathway. Resistance to invasive genetic material is conferred by the incorporation of short DNA sequences derived from this material into the genome as CRISPR spacer elements separated by short repeat sequences. Processing of long primary transcripts (pre-crRNAs) containing these repeats by a CRISPR-associated (Cas) RNA endonuclease generates the mature effector RNAs that target foreign nucleic acid for degradation. Here we describe functional studies of a Cas5d ortholog, and high-resolution structural studies of a second Cas5d family member, demonstrating that Cas5d is a sequence-specific RNA endonuclease that cleaves CRISPR repeats and is thus responsible for processing of pre-crRNA. Analysis of the structural homology of Cas5d with the previously characterized Cse3 protein allows us to model the interaction of Cas5d with its RNA substrate and conclude that it is a member of a larger family of CRISPR RNA endonucleases.