Liu Guitian, Li Xiaobin, Guan Jiahao, Tai Cui, Weng Yuqing, Chen Xiaohua, Ou Hong-Yu
Department of Infectious Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China.
State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Nucleic Acids Res. 2025 Jan 6;53(D1):D163-D168. doi: 10.1093/nar/gkae869.
Conjugation and mobilization are two important pathways of horizontal transfer of bacterial mobile genetic elements (MGEs). The origin-of-transfer (oriT) region is crucial for this process, serving as a recognition site for relaxase and containing the DNA nicking site (nic site), which initiates the conjugation or mobilization. Here, we present a database of the origin-of-transfer regions of bacterial MGEs, oriTDB (https://bioinfo-mml.sjtu.edu.cn/oriTDB2/). Incorporating data from text mining and genome analysis, oriTDB comprises 122 experimentally validated and 22 927 predicted oriTs within bacterial plasmids, Integrative and Conjugative Elements, and Integrative and Mobilizable Elements. Additionally, oriTDB includes details about associated relaxases, auxiliary proteins, type IV coupling proteins, and a gene cluster encoding the type IV secretion system. The database also provides predicted secondary structures of oriT sequences, dissects oriT regions into pairs of inverted repeats, nic sites, and their flanking conserved sequences, and offers an interactive visual representation. Furthermore, oriTDB includes an enhanced oriT prediction pipeline, oriTfinder2, which integrates a functional annotation module for cargo genes in bacterial MGEs. This resource is intended to support research on bacterial conjugative or mobilizable elements and promote an understanding of their cargo gene functions.
接合作用和转移作用是细菌可移动遗传元件（MGEs）水平转移的两个重要途径。转移起始（oriT）区域对于这一过程至关重要，它作为解旋酶的识别位点，并包含DNA切口位点（nic位点），该位点启动接合作用或转移作用。在此，我们展示了一个细菌MGEs转移起始区域的数据库oriTDB（https://bioinfo-mml.sjtu.edu.cn/oriTDB2/）。oriTDB整合了文本挖掘和基因组分析的数据，包含细菌质粒、整合性接合元件和整合性可移动元件中122个经过实验验证的oriT和22927个预测的oriT。此外，oriTDB还包括有关相关解旋酶、辅助蛋白、IV型偶联蛋白以及编码IV型分泌系统的基因簇的详细信息。该数据库还提供oriT序列的预测二级结构，将oriT区域解析为反向重复序列对、nic位点及其侧翼保守序列，并提供交互式可视化表示。此外，oriTDB包括一个增强的oriT预测管道oriTfinder2，它整合了细菌MGEs中货物基因的功能注释模块。该资源旨在支持对细菌接合或可移动元件的研究，并促进对其货物基因功能的理解。
