支原体整合性接合元件基因组分析

Genomic analysis of integrating conjugative elements of Mycoplasma

目的 探讨支原体整合性接合元件(MICE)的传播特征及其为宿主支原体带来的影响,从基因组水平全面分析其结构、功能、进化、传播和泛基因组学、系统发生关系以及遗传差异的分子基础。方法 收集MICE序列共21条,利用OrthoFinder程序构建其直系同源基因/蛋白质组,并通过比对分析其结构与功能特征,充分利用MICE的基因组数据并综合多个现有基因注释数据库对收集到的MICE所包含的基因进行注释,使用PanGP构建MICE的泛基因组模型,基因含量法构建泛基因组的系统发生树,RDP4对MICE基因组进行重组事件分析,Datamonkey识别MICE基因组中正选择位点,I-TASSER预测蛋白的三维结构,从全基因组角度探讨MICE的进化关系。结果 在收集到的MICE原件419个蛋白中,对其中386个进行了注释,并识别了其核心模块的关键基因:T4SS四型分泌系统、SSB单链结合蛋白和TraE蛋白;对MICE的整合与剪切模块、复制模块、分泌模块进行了定义,使对同类MICE的结构功能进化等分析时更加有迹可循;发现其中有9个MICE携带毒力基因;MICE的泛基因组表现出封闭模式;核心基因树与泛基因树的拓扑结构差异显著;识别了8个直系同源基因组的重组信号,5个直系同源蛋白质组的正选择位点,蛋白质结构预测结果显示这些正选择位点与元件的转移运输相关。结论 普遍将MICE视作一类整合性接合元件(ICE)进行描述可能并不合适,而在泛基因组分析中无核心基因,在核心模块及骨架分析中也明显展示出数种模式。

Objective To investigate the way Mycoplasma integrating conjugative elements(MICEs)are transmitted and their impact on host Mycoplasma,and to analyze their structure,function,evolution,pangenomics,phylogenetic relationships and the molecular basis of genetic differences at the genomic level.Methods A total of 21 MICE sequences were collected,whose structural and functional characteristics were analyzed by constructing their immediate homologous gene/proteome using OrthoFinder.The genomic data of MICEs was utilized and several existing gene annotation databases were integrated to annotate the genes contained in the collected MICEs.The phylogenetic tree of the pan-genome was constructed using PanGP.The recombination events of the MICE genome were analyzed using RDP4.The positive selection sites in the MICE genome were identified using Datamonkey,the three-dimensional structure of the protein was predicted using I-TASSER,and the evolutionary relationships of MICEs were explored from a genome-wide perspective.Results Of the 419 proteins collected in the original MICEs,386 were annotated and the key genes of their core modules were identified:T4SS typeⅣsecretion system,SSB single chain binding protein and TraE protein.The integrated shearing module,replication module and secretion module of MICEs were also defined to make more traceable the analysis of the structure-function evolution of similar MICEs.The pan-genome of MICE exhibited a closed pattern.The topology of the core gene tree and the pangenetic tree differed significantly.Eight immediate homologous genomic recombination signals and five immediate homologous proteomic positive selection sites were identified.Results of protein structure prediction showed that these positive selection sites were associated with translocation transport of elements.Conclusion It may be inappropriate to generally describe MICEa as a class of ICEs.Our results show that the structure of MICEs not only has no core genes in the pan-genomic analysis,but also clearly exhibits several patterns in the core module and backbone analysis.