细菌整合性接合元件SXT/R391传播和进化的基因组分析

Integrative and conjugative elements (ICEs) have recently been shown to be the most abundant conjugative elements in practically all prokaryotic clades. ICEs are self-transmissible mobile genetic elements able to confer multidrug resistance and other adaptive features to bacterial hosts. As such, ICEs are a major driving force of bacterial genome evolution allowing rapid acquisition of a variety of new traits and adaptive functions such as virulence, metabolic pathways and resistance to antimicrobial compounds, heavy metals or bacteriophage infection. To date, various types of ICEs have been identified in both Gram negative and Gram positive bacteria. The SXT/R391 family is one of the largest, diverse and well-studied set of ICEs among Gram-negative bacteria. ICEs of the SXT/R391 family have been recognized as key drivers of antibiotic resistance dissemination in the seventh-pandemic lineage of Vibrio cholerae. SXT/R391 ICEs propagate by conjugation and integrate site-specifically into the chromosome of a wide range of environmental and clinical bacteria..In recent years, SXT/R391 ICEs have been the subject of extensive study and while there is growing understanding of their prevalence, diversity, and molecular aspects. However, our understanding of ICE evolution is only beginning to be unraveled. The knowledge of evolutionary origin, migration patterns, and corresponding demography history of SXT/R391 ICEs is poor. Increasing such knowledge would help us better prevent and control the spreading of SXT/R391 element. .In this study, aiming to access the spreading mechanism and evolution of SXT/R391 ICEs in global source, many bioinformatic studies will be performed with all SXT/R391 ICE genome sequences available, including sequences retrieved from publicly sequence databases and intact SXT sequences from the genome sequenced V. cholerae strains in this project. First, comparative ICE genomic and pan-genomic analysis will be performed to explore the evolutionary relationship. Second, Bayesian phylogeography framework would be applied to determine the source, migration patterns, and corresponding demography history of the SXT/R391 ICEs that circulated in all bacteria. Third, the relationship between the host range of an ICE and the genetic content of the permissive (or nonpermissive) hosts will be well understood. Finally, the temporal dynamics of SXT-R391 ICE origin and spread will be reconstructed and all evolutionary events generating significant diversity in ICEs will be identified..These results will be helpful for better understanding of the evolution profile and spreading mechanism of bacterial SXT/R391 ICEs. This study will provide useful information for prevention and control of the transferring of SXT/R391 element.

SXT/R391整合性接合元件是近年来在细菌中发现的一种可移动的基因元件，它位于染色体上，可通过接合转移的方式介导细菌间基因的水平转移。许多SXT/R391元件包含耐药基因，这些元件的扩散加速了耐药基因在同种及不同种属之间的传播，造成细菌多重耐药问题日益严重。携带SXT/R391 的细菌在临床和环境中出现的频率逐渐增高。SXT/R391 元件的进化能造成其扩散能力的增强。目前有关SXT/R391 元件的进化的知识很匮乏。本项目在充分利用现有的SXT/R391 ICEs基因组数据的基础上，结合我们测定的SXT序列，利用泛基因组模型、系统发生地理学、溯祖分析等技术，拟从全基因组角度探讨SXT/R391元件之间的进化关系，并结合适应性进化分析，揭示SXT/R391元件在扩散传播经历的微进化特征，以还原SXT/R391基因组的动力学过程，重构这个移动遗传因子家族的起源、传播经历的进化历程的全貌。

整合性接合元件(ICEs)是近年来在细菌中发现的一种可移动的基因元件，它位于染色体上，可通过接合方式介导细菌间基因的水平转移。SXT/R391 ICEs目前已知ICEs中命名最早、多样性最丰富以及研究最详细的一个家族。项目通过文献萃取、数据库检索、生物信息学预测等手段，共收集和整理了83个具有全基因组序列的SXT/R391元件。本项目在此基础上针对SXT/R391元件的进化规律和变异特征，展开了一系列研究。.首先，通过泛基因组模型分析发现，SXT/R391元件可能存在一个封闭的泛基因组。之后对核心基因树和基因含量树的分析比较，发现SXT/R391元件的基因获得/丢失等基因流动事件非常频繁。通过对核心基因的进化发现，SXT/R391元件核心区的进化非常复杂，不同功能模块之间可能会发生频繁重组，核心基因会经历基因复制、基因融合/裂解等进化事件。.其次，我们发现重组和正选择在SXT/R391元件核心基因的进化过程中发挥了重要作用。另外通过SXT/R391元件各个不同核心功能模块基因的系统地理发生学系谱树和传播网络图，发现了SXT/R391 ICE不同模块的进化特征和传播模式完全不同，四个必需功能模块都有自己的独立的起源时间、产生地点和传播线路。通过对SXT/R391 ICE的各模块起源时间的分析结果表明，SXT/R391元件起源是近期事件，这与文献推测SXT/R391 ICE是近期起源的观点是一致的。.第三，本项目还发现SXT/R391元件的毒素抗毒素基因经历的进化历程差异显著，二者之间并不存在协同进化，这与细菌典型的毒素抗毒素系统的进化规律不一致。另外，SXT/R391元件的毒素抗毒素系统未检测到正选择和重组信号，毒素抗毒素系统基因的适应性进化特征不明显。.通过对75 株霍乱弧菌菌株的基因组序列分析，我们发现，影响霍乱弧菌捕获SXT元件的遗传决定因素应该位于菌株染色体2的一个区域。.本项目对SXT/R391元件的基因组、系统发生、分子进化、系统地理传播、遗传背景等各个方面做了系统的探究，揭示了目前已知的SXT/R391元件的进化特征和扩散规律，为进一步研究细菌基因组的耐药扩散、水平基因转移、系统分类等奠定了基础。