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Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference

You, Lilan, Ma, Jun, Wang, Jiuyu, Artamonova, Daria, Wang, Min, Liu, Liang, Xiang, Hua, Severinov, Konstantin, Zhang, Xinzheng, Wang, Yanli
Cell 2019 v.176 no.1-2 pp. 239-253.e16
DNA damage, RNA, deoxyribonucleases, enzyme activity, gene editing, ribonucleases
Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, the structural features allowing target RNA-binding-dependent activation of DNA cleavage and cOA generation remain unknown. Here, we report the structure of Csm in complex with crRNA together with structures of cognate or non-cognate target RNA bound Csm complexes. We show that depending on complementarity with the 5′ tag of crRNA, the 3′ anti-tag region of target RNA binds at two distinct sites of the Csm complex. Importantly, the interaction between the non-complementary anti-tag region of cognate target RNA and Csm1 induces a conformational change at the Csm1 subunit that allosterically activates DNA cleavage and cOA generation. Together, our structural studies provide crucial insights into the mechanistic processes required for crRNA-meditated sequence-specific RNA cleavage, RNA target-dependent non-specific DNA cleavage, and cOA generation.