CRISPR-mediated host genomic DNA damage is efficiently repaired through microhomology-mediated end joining in Zymomonas mobilis |
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| Authors: | Xiaojie Wang Bo Wu Xin Sui Zhufeng Zhang Tao Liu Yingjun Li Guoquan Hu Mingxiong He Nan Peng |
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| Affiliation: | 1. State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China;2. Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu, Sichuan 610041, China;1. Eye Center of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;2. The Institute of Translational Medicine, Zhejiang University, Hangzhou 310058, China;3. Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China;4. Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan;5. Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou 310058, China;6. MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China;1. Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA;2. Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA;1. School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China;2. Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;3. Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;4. Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221002, China;5. Department of Radiation and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC 27599-7461, USA;6. Shenzhen Graduate School of Harbin Institute of Technology, Shenzhen 518055, China;1. National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China;2. University of the Chinese Academy of Sciences, Beijing 100049, China;3. School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China |
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| Abstract: | CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against mobile genetic elements(MGEs) through uptake of invader-derived spacers. De novo adaptation samples spacers from both invaders and hosts, whereas primed adaptation shows higher specificity to sample spacers from invaders in many model systems as well as in the subtype I-F system of Zymomonas mobilis. Self-derived spacers will lead to CRISPR self-interference. However, our in vivo study demonstrated that this species used the microhomology-mediated end joining(MMEJ) pathway to efficiently repair subtype I-F CRISPR-Cas system-mediated DNA breaks guided by the self-targeting spacers. MMEJ repair of DNA breaks requires direct microhomologous sequences flanking the protospacers and leads to DNA deletions covering the protospacers. Importantly, CRISPR-mediated genomic DNA breaks failed to be repaired via MMEJ pathway in presence of higher copies of short homologous DNA. Moreover, CRISPR-cleaved exogenous plasmid DNA was failed to be repaired through MMEJ pathway, probably due to the inhibition of MMEJ by the presence of higher copies of the plasmid DNA in Z. mobilis. Our results infer that MMEJ pathway discriminates DNA damages between in the host chromosome versus mobile genetic element(MGE) DNA, and maintains genome stability post CRISPR immunity in Z. mobilis. |
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| Keywords: | CRISPR-Cas CRISPR adaptation Self-interference Microhomology-mediated end joining |
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