Type-III-A structure of mycobacteria CRISPR-Csm complexes involving atypical crRNAs

Hongtai Zhang; Mingmin Shi; Xiaoli Ma; Mengxi Liu; Nenhan Wang; Qiuhua Lu; Zekai Li; Yanfeng Zhao; Hongshen Zhao; Hong Chen; Huizhi Zhang; Tao Jiang; Songying Ouyang; Yangao Huo; Lijun Bi

doi:10.1016/j.ijbiomac.2024.129331

Type-III-A structure of mycobacteria CRISPR-Csm complexes involving atypical crRNAs

Int J Biol Macromol. 2024 Mar;260(Pt 2):129331. doi: 10.1016/j.ijbiomac.2024.129331. Epub 2024 Jan 11.

Authors

Hongtai Zhang¹, Mingmin Shi², Xiaoli Ma², Mengxi Liu³, Nenhan Wang⁴, Qiuhua Lu³, Zekai Li³, Yanfeng Zhao⁴, Hongshen Zhao², Hong Chen², Huizhi Zhang², Tao Jiang⁵, Songying Ouyang⁶, Yangao Huo⁷, Lijun Bi⁸

Affiliations

¹ National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Center for Disease Prevention and Control, Beijing 100013, China.
² National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
³ Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
⁴ Beijing Center for Disease Prevention and Control, Beijing 100013, China.
⁵ National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing, China. Electronic address: tjiang@ibp.ac.cn.
⁶ Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: ouyangsy@fjnu.edu.cn.
⁷ National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: huoyangao@ibp.ac.cn.
⁸ National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Guangzhou National Laboratory, Guangzhou, 510005, China. Electronic address: blj@sun5.ibp.ac.cn.

PMID: 38218299
DOI: 10.1016/j.ijbiomac.2024.129331

Abstract

Tuberculosis (TB), a leading cause of mortality globally, is a chronic infectious disease caused by Mycobacterium tuberculosis that primarily infiltrates the lung. The mature crRNAs in M. tuberculosis transcribed from the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus exhibit an atypical structure featured with 5' and 3' repeat tags at both ends of the intact crRNA, in contrast to typical Type-III-A crRNAs that possess 5' repeat tags and partial crRNA sequences. However, this structural peculiarity particularly concerning the specific binding characteristics of the 3' repeat end within the mature crRNA within the Csm complex, has not been comprehensively elucidated. Here, our Mycobacteria CRISPR-Csm complexes structure represents the largest Csm complex reported to date. It incorporates an atypical Type-III-A CRISPR RNA (crRNA) (46 nt) with 5' 8-nt and 3' 4-nt repeat sequences in the stoichiometry of Mycobacteria Csm1₁2₅3₆4₁5_1. The PAM-independent single-stranded RNAs (ssRNAs) are the most suitable substrate for the Csm complex. The 3'-repeat end trimming of mature crRNA was not necessary for its cleavage activity in Type-III-A Csm complex. Our work broadens our understanding of the Type-III-A Csm complex and identifies another mature crRNA processing mechanism in the Type-III-A CRISPR-Cas system based on structural biology.

Keywords: CRISPR-Cas system; Csm complex; Mature crRNA; Mycobacteria; RNase activity; Type-III-A.

MeSH terms

CRISPR-Cas Systems / genetics
Humans
Mycobacterium tuberculosis* / genetics
Mycobacterium tuberculosis* / metabolism
RNA, Bacterial / genetics
RNA, Guide, CRISPR-Cas Systems
Tuberculosis* / genetics

Substances

RNA, Guide, CRISPR-Cas Systems
RNA, Bacterial