Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features

Wenjing Wei, Shuai Zhang, Joy Fleming, Ying Chen, Zihui Li, Shanghua Fan, Yi Liu, Wei Wang, Ting Wang, Ying Liu, Baiguang Ren, Ming Wang, Jianjian Jiao, Yuanyuan Chen, Ying Zhou, Yafeng Zhou, Shoujin Gu, Xiaoli Zhang, Li Wan, Tao Chen & 6 others Lin Zhou, Yong Chen, Xian En Zhang, Chuanyou Li, Hongtai Zhang, Lijun Bi

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems are prokaryotic adaptive immune systems against invading nucleic acids. CRISPR locus variability has been exploited in evolutionary and epidemiological studies of Mycobacterium tuberculosis, the causative agent of tuberculosis, for over 20 yr, yet the biological function of this type III-A system is largely unexplored. Here, using cell biology and biochemical, mutagenic, and RNA-seq approaches, we show it is active in invader defense and has features atypical of type III-A systems: mature CRISPR RNA (crRNA) in its crRNA-CRISPR/Cas protein complex are of uniform length (∼71 nt) and appear not to be subject to 39-end processing after Cas6 cleavage of repeat RNA 8 nt from its 39 end. crRNAs generated resemble mature crRNA in type I systems, having both 59 (8 nt) and 39 (28 nt) repeat tags. Cas6 cleavage of repeat RNA is ion dependent, and accurate cleavage depends on the presence of a 39 hairpin in the repeat RNA and the sequence of its stem base nucleotides. This study unveils further diversity among CRISPR/Cas systems and provides insight into the crRNA recognition mechanism in M. tuberculosis, providing a foundation for investigating the potential of a type III-A-based genome editing system.

Original languageEnglish (US)
Pages (from-to)1496-1509
Number of pages14
JournalFASEB Journal
Volume33
Issue number1
DOIs
StatePublished - Jan 1 2019
Externally publishedYes

Fingerprint

CRISPR-Associated Proteins
Clustered Regularly Interspaced Short Palindromic Repeats
Mycobacterium tuberculosis
RNA
RNA Cleavage
Cytology
Immune system
Nucleic Acids
Cell Biology

Keywords

  • Cas6
  • Hairpin
  • Mature crRNA
  • Metal ion dependence

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Genetics

Cite this

Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features. / Wei, Wenjing; Zhang, Shuai; Fleming, Joy; Chen, Ying; Li, Zihui; Fan, Shanghua; Liu, Yi; Wang, Wei; Wang, Ting; Liu, Ying; Ren, Baiguang; Wang, Ming; Jiao, Jianjian; Chen, Yuanyuan; Zhou, Ying; Zhou, Yafeng; Gu, Shoujin; Zhang, Xiaoli; Wan, Li; Chen, Tao; Zhou, Lin; Chen, Yong; Zhang, Xian En; Li, Chuanyou; Zhang, Hongtai; Bi, Lijun.

In: FASEB Journal, Vol. 33, No. 1, 01.01.2019, p. 1496-1509.

Research output: Contribution to journalArticle

Wei, W, Zhang, S, Fleming, J, Chen, Y, Li, Z, Fan, S, Liu, Y, Wang, W, Wang, T, Liu, Y, Ren, B, Wang, M, Jiao, J, Chen, Y, Zhou, Y, Zhou, Y, Gu, S, Zhang, X, Wan, L, Chen, T, Zhou, L, Chen, Y, Zhang, XE, Li, C, Zhang, H & Bi, L 2019, 'Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features', FASEB Journal, vol. 33, no. 1, pp. 1496-1509. https://doi.org/10.1096/fj.201800557RR
Wei, Wenjing ; Zhang, Shuai ; Fleming, Joy ; Chen, Ying ; Li, Zihui ; Fan, Shanghua ; Liu, Yi ; Wang, Wei ; Wang, Ting ; Liu, Ying ; Ren, Baiguang ; Wang, Ming ; Jiao, Jianjian ; Chen, Yuanyuan ; Zhou, Ying ; Zhou, Yafeng ; Gu, Shoujin ; Zhang, Xiaoli ; Wan, Li ; Chen, Tao ; Zhou, Lin ; Chen, Yong ; Zhang, Xian En ; Li, Chuanyou ; Zhang, Hongtai ; Bi, Lijun. / Mycobacterium tuberculosis type III-A CRISPR/Cas system crRNA and its maturation have atypical features. In: FASEB Journal. 2019 ; Vol. 33, No. 1. pp. 1496-1509.
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AU - Zhang, Shuai

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AU - Fan, Shanghua

AU - Liu, Yi

AU - Wang, Wei

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AU - Jiao, Jianjian

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AU - Zhou, Ying

AU - Zhou, Yafeng

AU - Gu, Shoujin

AU - Zhang, Xiaoli

AU - Wan, Li

AU - Chen, Tao

AU - Zhou, Lin

AU - Chen, Yong

AU - Zhang, Xian En

AU - Li, Chuanyou

AU - Zhang, Hongtai

AU - Bi, Lijun

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N2 - Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems are prokaryotic adaptive immune systems against invading nucleic acids. CRISPR locus variability has been exploited in evolutionary and epidemiological studies of Mycobacterium tuberculosis, the causative agent of tuberculosis, for over 20 yr, yet the biological function of this type III-A system is largely unexplored. Here, using cell biology and biochemical, mutagenic, and RNA-seq approaches, we show it is active in invader defense and has features atypical of type III-A systems: mature CRISPR RNA (crRNA) in its crRNA-CRISPR/Cas protein complex are of uniform length (∼71 nt) and appear not to be subject to 39-end processing after Cas6 cleavage of repeat RNA 8 nt from its 39 end. crRNAs generated resemble mature crRNA in type I systems, having both 59 (8 nt) and 39 (28 nt) repeat tags. Cas6 cleavage of repeat RNA is ion dependent, and accurate cleavage depends on the presence of a 39 hairpin in the repeat RNA and the sequence of its stem base nucleotides. This study unveils further diversity among CRISPR/Cas systems and provides insight into the crRNA recognition mechanism in M. tuberculosis, providing a foundation for investigating the potential of a type III-A-based genome editing system.

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