Volume 33, No 10, Oct 2023

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 33 Issue 10, October 2023: 762-774   |  Open Access

ORIGINAL ARTICLES

Structural insights into mechanisms of Argonaute protein-associated NADase activation in bacterial immunity

Xiaoshen Wang^1,† , Xuzichao Li^1,† , Guimei Yu^1,† , Lingling Zhang^1,† , Chendi Zhang^2,† , Yong Wang^3,4,† , Fumeng Liao¹ , Yanan Wen¹ , Hang Yin⁵ , Xiang Liu⁶ , Yong Wei⁷ , Zhuang Li^2,* , Zengqin Deng^3,8,* , Heng Zhang^1,*

¹National key laboratory of blood science, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Haihe Laboratory of Cell Ecosystem, Tianjin Institute of Immunology, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
²State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, China
³Center for Antiviral Research, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
⁴University of Chinese Academy of Sciences, Beijing, China
⁵Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
⁶State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
⁷The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
⁸Hubei Jiangxia Laboratory, Wuhan, Hubei, China
^†These authors contributed equally: Xiaoshen Wang, Xuzichao Li, Guimei Yu, Lingling Zhang, Chendi Zhang, Yong Wang
Correspondence: Zhuang Li(zhuangli@hubu.edu.cn)Zengqin Deng(dengzengqin@wh.iov.cn)Heng Zhang(zhangheng134@gmail.com)

Nicotinamide adenine dinucleotide (NAD+) is a central metabolite in cellular processes. Depletion of NAD+ has been demonstrated to be a prevalent theme in both prokaryotic and eukaryotic immune responses. Short prokaryotic Argonaute proteins (Agos) are associated with NADase domain-containing proteins (TIR-APAZ or SIR2-APAZ) encoded in the same operon. They confer immunity against mobile genetic elements, such as bacteriophages and plasmids, by inducing NAD+ depletion upon recognition of target nucleic acids. However, the molecular mechanisms underlying the activation of such prokaryotic NADase/Ago immune systems remain unknown. Here, we report multiple cryo-EM structures of NADase/Ago complexes from two distinct systems (TIR-APAZ/Ago and SIR2-APAZ/Ago). Target DNA binding triggers tetramerization of the TIR-APAZ/Ago complex by a cooperative self-assembly mechanism, while the heterodimeric SIR2-APAZ/Ago complex does not assemble into higher-order oligomers upon target DNA binding. However, the NADase activities of these two systems are unleashed via a similar closed-to-open transition of the catalytic pocket, albeit by different mechanisms. Furthermore, a functionally conserved sensor loop is employed to inspect the guide RNA–target DNA base pairing and facilitate the conformational rearrangement of Ago proteins required for the activation of these two systems. Overall, our study reveals the mechanistic diversity and similarity of Ago protein-associated NADase systems in prokaryotic immune response.

https://doi.org/10.1038/s41422-023-00839-7

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