Research News
Dr. Keqiong Ye's laboratory reveals structural mechanism of how CRISPR-Cas systems cleave RNA
On Dec 24, 2014, Dr. Keqiong Ye's laboratory published an article titled "Cmr4 is the slicer in the RNA-targeting Cmr CRISPR complex" in Nucleic Acids Research. This paper studies the biochemical and structural mechanism of how the Cmr complex from III-B CRISPR-Cas systems cleaves RNA.
CRISPR-Cas system is an adaptive and inheritable immune system that is wildly distributed in prokaryotes, including bacteria and archaea, and protects hosts from mobile genetic elements, such as bacteriophages and conjugative plasmids. It is composed of arrays of clustered, regularly interspaced, short palindromic repeats (CRISPRs) and CRISPR-associated (cas) genes. This system works in three phases. In the first adaptation stage, hosts select and integrate short fragments of foreign nucleic acids into CRISPR loci in a polarized manner. In the second expression stage, the CRISPR locus is transcribed into a long pre-crRNA that is subsequently processed into mature crRNAs. In the last interference stage, the crRNA assembles with Cas proteins to form the effector complex and guide the effector complex to degrade specific DNA or RNA using its base-pairing potential. Recently, the system is classified into three major types (I, II and III) and ten sub-types. The Cmr complex is the effector complex in type III-B CRISPR-Cas systems and consists of six protein subunits Cmr1-6 and one crRNA. Previous study has proposed that the Cmr complex cleaves the substrate at a single specific site that is determined by the distance to the 3'-end of the crRNA.
To understand the structure and function of the Cmr complex, the Ye laboratory has determined the structure of Cmr2 in previous studies (FEBS Letter 2012). In this paper, the authors showed that the Cmr complex of Pyrococcus furiosus cleaves the substrate RNA at multiple sites that are 6 nucleotides apart and are positioned relative to the 5'-end of the crRNA, revising the previous conclusion. The authors identified Cmr4 as the slicer and determined its crystal structure at 2.8 Å resolution. In the crystal, Cmr4 forms a helical filament that most likely reflects its structural organization in the Cmr complex. The putative active site is located at the inner surface of the filament where the guide and substrate RNA are thought to bind. The filament structure of Cmr4 accounts for multiple periodic cleavage sites on the substrate. This study provides new insights into the structure and mechanism of the RNA-targeting Cmr complex.
Xing Zhu, a previous NIBS graduate student, is the first author of this paper. Dr. Keqiong Ye is the corresponding author. The study was supported by Ministry of Science and Technology of China, National Natural Science Foundation of China, Chinese Academy of Sciences and Beijing Municipal Government and conducted at NIBS.
