单链DNA退火蛋白介导细菌基因组同源重组的机制及应用研究进展

doi:10.13560/j.cnki.biotech.bull.1985.2024-0457

生物技术通报 ›› 2025, Vol. 41 ›› Issue (1): 39-48.doi: 10.13560/j.cnki.biotech.bull.1985.2024-0457

单链DNA退火蛋白介导细菌基因组同源重组的机制及应用研究进展

尹号¹^,²(), 尤留超¹^,², 韩瑞¹^,², 高鹏程¹^,², 付磊¹^,²(), 储岳峰¹^,²()

1.中国农业科学院兰州兽医研究所兰州大学动物医学与生物安全学院动物疫病防控全国重点实验室，兰州 730000
2.甘肃省病原生物学基础学科研究中心，兰州 730046

收稿日期:2024-05-16 出版日期:2025-01-26 发布日期:2025-01-22
通讯作者: 付磊，男，博士，助理研究员，研究方向：病原学及分子生物学；E-mail: fulei@caas.cn；
储岳峰，男，博士，研究员，研究方向：草食动物细菌病防控技术及其基础研究；E-mail: chuyuefeng@caas.cn
作者简介:尹号，男，硕士研究生，研究方向：分子生物学；E-mail: qubaobaozz@163.com
基金资助:
国家自然科学基金面上项目(32373019);中国农业科学院兰州兽医研究所重点项目(CAAS-ASTIP-JBGS-20210701);甘肃省重点人才项目(2021RCXM047);甘肃省陇原青年创新创业人才（个人）项目(2023LQGR55);中国农业科学院兰州兽医研究所基本业务费-科研业务费项目(110231160042012)

Mechanisms and Application Research Progress of Bacterial Genomic Homologous Recombination Mediated by Single-stranded DNA Annealing Protein

YIN Hao¹^,²(), YOU Liu-chao¹^,², HAN Rui¹^,², GAO Peng-cheng¹^,², FU Lei¹^,²(), CHU Yue-feng¹^,²()

1. State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000
2. Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046

Received:2024-05-16 Published:2025-01-26 Online:2025-01-22

摘要/Abstract

摘要：

基因组编辑技术是研究细菌等微生物在基因功能、耐药机制及致病机制等方面的重要工具，而同源重组是细菌基因组编辑的重要方式之一，传统的细菌内源性重组途径存在效率低下的问题，而一种来自噬菌体的单链DNA退火蛋白（SSAP）表现出了远超内源性重组途径的基因组编辑效率，该蛋白具有单链DNA结合活性、介导基因组定向重组的特点，使其成为目前极具潜力的基因组编辑工具。本文主要对同源重组基本原理、噬菌体源SSAP介导的同源重组途径的基本元件、重组机制模型以及应用策略展开概述，旨在为进一步解析单链DNA退火蛋白介导的同源重组过程提供帮助，为研究更多细菌基因功能、致病机制以及开发工程菌株提供技术支撑，也为缺乏基因编辑方法的细菌提供技术参考。

关键词: 细菌, 单链DNA退火蛋白, 同源重组, 机制, 应用

Abstract:

Genome editing technology is an important tool for studying the gene function, drug resistance mechanism, and pathogenic mechanism of bacteria and other microorganisms. Homologous recombination is one of the key methods for bacterial genome editing. The conventional endogenous pathways in bacteria suffer from low efficiency. However, a single-stranded DNA annealing protein（SSAP）from bacteriophages, which has shown gene editing efficiencies far surpassing those of endogenous pathways. This protein has the characteristics of single-stranded DNA binding activity and mediates genome directed recombination, making it an extremely promising tool for genome editing. This article provides an overview of the basic principles of homologous recombination, the fundamental components of the SSAP-mediated homologous recombination pathway from phages, recombination mechanism models, and application strategies. The aim is to assist in further elucidating the process of homologous recombination mediated by SSAP to provide technical support for studying the functions and pathogenic mechanisms of more bacterial genes, and to develop engineering strains. It also provides technical support for bacteria lacking gene editing methods.

Key words: bacteria, single-stranded DNA annealing protein, homologous recombination, mechanism, application

尹号, 尤留超, 韩瑞, 高鹏程, 付磊, 储岳峰. 单链DNA退火蛋白介导细菌基因组同源重组的机制及应用研究进展[J]. 生物技术通报, 2025, 41(1): 39-48.

YIN Hao, YOU Liu-chao, HAN Rui, GAO Peng-cheng, FU Lei, CHU Yue-feng. Mechanisms and Application Research Progress of Bacterial Genomic Homologous Recombination Mediated by Single-stranded DNA Annealing Protein[J]. Biotechnology Bulletin, 2025, 41(1): 39-48.

图/表 2

图1 RecA介导ssDNA的重组模型及SSAP的链退火模型 RecA具有ssDNA结合活性，SSAP具有ssDNA退火活性，Exo具有靶向dsDNA的5'-3'端核酸外切酶活性。RecA介导的同源重组过程以链入侵为主要途径，SSAP介导的同源重组过程以链退火为主要途径。a：RecA结合ssDNA形成RecA-DNA复合物，携带ssDNA入侵至基因组的同源序列处，形成D环结构，从而完成重组过程；b：SSAP可直接结合ssDNA，将其以冈崎片段的形式退火至复制叉上，dsDNA则通过Exo处理成ssDNA后，以相同的方式完成重组

Fig. 1 Model of RecA-mediated recombination of ssDNA and the strand annealing model of SSAP RecA possesses ssDNA-binding activity, SSAP has ssDNA annealing activity, and Exo has 5'-3' exonuclease activity targeting dsDNA. The homologous recombination process mediated by RecA is primarily involved in strand invasion, while the homologous recombination process mediated by SSAP primarily in strand annealing. a: RecA binds to ssDNA to form a RecA-DNA complex, which carries the ssDNA to invade the homologous sequence in the genome, forming a D-loop structure, thereby completing the recombination process. b: SSAP can directly bind to ssDNA, annealing it to the replication fork in the form of Okazaki fragments. dsDNA is processed into ssDNA by Exo and then completes recombination in the same manner

图2 SSAP介导的重组过程示意图 SSAP为ssDNA退火活性，Exo为靶向dsDNA的5'-3'端核酸外切酶活性。a：SSAP介导ssDNA退火过程，以冈崎片段的形式退火至滞后链上；b：dsDNA会被Exo处理成其中一条链完全降解的ssDNA或暴露出两端3'悬垂的重组中间体；c：一般认为的SSAP介导ssDNA重组策略的复制叉模型：d：协同工作模型，即Exo降解dsDNA的其中一条链，另一条链则同时被SSAP退火到复制叉中

Fig. 2 Schematic diagram of the recombination process mediated by SSAP SSAP possesses ssDNA annealing activity, while Exo exhibits a 5'-3' exonuclease activity targeted at dsDNA. a: SSAP mediates the annealing of ssDNA, annealing it to the lagging strand in the form of Okazaki fragments. b: dsDNA is processed by Exo into either a completely degraded single strand of ssDNA or a recombination intermediate exposing 3' overhangs at both ends. c: The generally accepted model of SSAP-mediated ssDNA recombination strategy at the replication fork. d: A cooperative working model where Exo degrades one strand of the dsDNA while the other strand is simultaneously annealed by SSAP into the replication fork

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单链DNA退火蛋白介导细菌基因组同源重组的机制及应用研究进展

Mechanisms and Application Research Progress of Bacterial Genomic Homologous Recombination Mediated by Single-stranded DNA Annealing Protein

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