Dai Zehan, Wu Tianzhi, Xu Shuangbin, Zhou Lang, Tang Wenli, Hu Erqian, Zhan Li, Chen Meijun, Yu Guangchuang
Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
Front Microbiol. 2022 Aug 16;13:951774. doi: 10.3389/fmicb.2022.951774. eCollection 2022.
The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in , as one of the bacterial species with ARGs, have not yet been completely demonstrated. In this study, we explored the TA systems from the public genomic sequencing data and genome sequences. A small scale of genomic sequencing data in 281 isolates was selected from the NCBI SRA database, reassembling the genomes of these isolates led to the findings of abundant TA homologs. Furthermore, remapping these identified TA modules on 5,437 genome/draft genomes uncovers a great diversity of TA modules in . Moreover, manual inspection revealed several TA systems that were not yet reported in including the , , , , and . Additional annotation revealed that a large number of MGEs were closely distributed with TA. Also, 16% of ARGs are located relatively close to TA. Our work confirmed a wealth of TA genes in the unexplored pan-genomes, expanded the knowledge on , and provided methodological tips on large-scale data mining for future studies. The co-occurrence of MGE, ARG, and TA may indicate a potential interaction in their dissemination.
毒素-抗毒素（TA）系统是一组广泛分布的遗传模块，在原核生物生命活动中发挥重要作用，移动遗传元件（MGEs）促进了抗生素抗性基因（ARG）的传播。作为具有ARG的细菌物种之一，[具体细菌名称未给出]中TA系统的多样性和丰富性尚未得到充分证明。在本研究中，我们从公开的基因组测序数据和基因组序列中探索TA系统。从NCBI SRA数据库中选取了281个分离株的小规模基因组测序数据，对这些分离株的基因组进行重新组装，发现了大量TA同源物。此外，将这些鉴定出的TA模块重新映射到5437个基因组/草图基因组上，揭示了[具体细菌名称未给出]中TA模块的巨大多样性。此外，人工检查发现了一些在[具体细菌名称未给出]中尚未报道的TA系统，包括[具体系统名称未给出]、[具体系统名称未给出]、[具体系统名称未给出]、[具体系统名称未给出]和[具体系统名称未给出]。进一步注释显示，大量MGEs与TA紧密分布。此外，16%的ARG相对靠近TA定位。我们的工作证实了未探索的[具体细菌名称未给出]泛基因组中存在丰富的TA基因，扩展了对[具体细菌名称未给出]的认识，并为未来研究提供了大规模数据挖掘的方法提示。MGE、ARG和TA的共现可能表明它们在传播过程中存在潜在相互作用。
