AI-driven discovery of host thioredoxin as a CRISPR enhancer of phage-encoded miniature Cas12 hacker nuclease

doi:10.1101/2025.01.20.633832

	AI-driven discovery of host thioredoxin as a CRISPR enhancer of phage-encoded miniature Cas12 hacker nuclease
	Wang, Zhipeng1,2 ; Wang, Yujue1,2 ; Gao, Hui1,2 ; Dai, Jiani1,2 ; Tang, Na 1,2; Wang, Yannan1,2 ; Ji, Quanjiang1,2,3,4
	2025-01-21
状态	已发表
摘要	The evolutionary arms race between bacteriophages and their bacterial hosts has driven the evolution of sophisticated adaptive immune systems, such as CRISPR-Cas, as a crucial defense mechanism. While bacteriophages have developed various anti-CRISPR strategies to counteract these immune systems, the role of bacterial host factors in enhancing CRISPR-Cas functions has been relatively unexplored. In this study, we employ an artificial intelligence (AI)-driven approach to systematically analyze potential interactions between Escherichia coli (E. coli) proteins and fifteen previously uncharacterized Cas12 proteins, generating 65,715 predicted binary complex structures. Our findings reveal a previously unknown dimension of CRISPR immunity, demonstrating that the host’s ubiquitous redox enzyme, thioredoxin (TrxA), significantly enhances the DNA cleavage efficiency of a phage-encoded, miniature Cas12 nuclease (termed ‘Cas12 hacker’). This synergistic relationship represents a strategic inversion, where a bacteriophage hijacks a host protein to reinforce its own genome degradation machinery, possibly targeting rival nucleic acids. Through comprehensive biochemical characterizations, structural analyses of the Cas12 hacker-TrxA-sgRNA-dsDNA quaternary complex, and in vivo bacterial defense assays, we uncover an intricate association in which thioredoxin binds to and activates the Cas12 hacker nuclease, intensifying its DNA cleavage capacity and bolstering CRISPR immunity. Our findings expand the understanding of the molecular interactions underlying host-phage conflicts and highlight the potential for harnessing endogenous host factors to enhance the capabilities of CRISPR-based genetic engineering tools.
语种	英语
DOI	10.1101/2025.01.20.633832
相关网址	查看原文
出处	bioRxiv
收录类别	PPRN.PPRN
WOS记录号	PPRN:120844402
WOS类目	Microbiology
资助项目	Postdoctoral Fellowship Program of CPSF[GZC20231672] ; China Postdoctoral Science Foundation["2023M742367","2024M752064"] ; National Key R&D Program of China["2022YFC3403400","2023YFC3400200"] ; National Natural Science Foundation of China["22277078","22077083"] ; Shanghai Committee of Science and Technology, China["22ZR1480100","23HC1400800"]
文献类型	预印本
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/503595
专题	物质科学与技术学院生命科学与技术学院物质科学与技术学院_PI研究组_季泉江组生命科学与技术学院_博士生物质科学与技术学院_博士生
通讯作者	Ji, Quanjiang
作者单位	1.shanghaitech University 2.ShanghaiTech Univ, Sch Phys Sci & Technol, Shanghai 201210, Peoples R China 3.ShanghaiTech Univ, State Key Lab Adv Med Mat & Devices, Shanghai 201210, Peoples R China 4.ShanghaiTech Univ, Gene Editing Ctr, Sch Life Sci & Technol, Shanghai 201210, Peoples R China 5.Shanghai Clin Res & Trial Ctr, Shanghai 201210, Peoples R China
推荐引用方式 GB/T 7714	Wang, Zhipeng,Wang, Yujue,Gao, Hui,et al. AI-driven discovery of host thioredoxin as a CRISPR enhancer of phage-encoded miniature Cas12 hacker nuclease. 2025.