铜绿假单胞菌降解烃类污染物的泛基因组分析  

Functional pan-genome analyses of hydrocarbon biodegradation by diverse Pseudomonas aeruginosa

作　　者：潘金程 李艳冰 李晶 马艳玲[1] PAN Jincheng;LI Yanbing;LI Jing;MA Yanling(College of Life Science,Northwest University,Xi’an 710069,China;Xi’an Rege Biotechnology Co.Ltd.,Xi’an 710065,China)

机构地区：[1]西北大学生命科学学院,西安710069 [2]西安瑞捷生物科技有限公司,西安710065

出　　处：《应用与环境生物学报》2021年第5期1281-1288,共8页Chinese Journal of Applied and Environmental Biology

基　　金：国家自然科学基金青年项目(31000069);陕西省重点研发计划重点项目(2018ZDXM-NY-065)资助。

摘　　要：铜绿假单胞菌是一种常见的烃类降解菌,在环境污染治理中具有广阔的应用前景.利用泛基因组对10株铜绿假单胞菌进行分析以深入了解其泛基因组特征、生物降解潜力及芳香族化合物降解中心途径.结果显示,铜绿假单胞菌的核心基因组大约包含4923个基因,占泛基因组的56.2%.泛基因组分析表明其泛基因组即将闭合,说明分析的铜绿假单胞菌通过HGT获得新基因的能力较弱.核心基因组包含了大量ABC转运蛋白和双组分调节系统相关基因,氨基酸代谢(合成和降解)、鞭毛组装和生物膜相关基因也是核心基因组的一部分.核心基因的KEGG注释表明,铜绿假单胞菌主要通过4条中心途径来降解芳香族化合物:β-酮己二酸酯、高儿茶酸、尿黑酸和龙胆酸途径,同时还具有相对完整的烷烃羟化酶系统.根据GC含量及侧翼转座酶和整合酶可以得出结论,铜绿假单胞菌可通过HGT获得芳香族化合物降解相关因.本文对10株菌的泛基因组分析表明铜绿假单胞菌虽然通过横向转移获得新基因的频率较低,但是已拥有完整的烃类降解系统.该分析结果有助于了解铜绿假单胞菌群体的基因组成及基因组分特征,提供对其生物修复潜力及降解机制更进一步的认识.As a versatile degrader,Pseudomonas aeruginosa has promising applications in removing both saturated aliphatic and aromatic hydrocarbons.To present bacterial genomic characteristics,functional genomic analysis of 10 P.aeruginosa strains was employed to interpret the core genome and pan-genome,the potential of hydrocarbon biodegradation,and the central pathway of aromatic compound degradation.Most of the homologous genes constituted the core genome that contained 4923 genes accounting for 56.2%of the pangenome,with a tiny portion of unique types of genomic evidence in these strains.The open pan-genome was about to close momentarily with its growing number of genomes,implying that the ability to exchange genetic information with the external condition by HGT was feeble among the selected strains of P.aeruginosa.The most abundant genes within the core genome were those that encode nutrient transporters and a two-component system.Genes that encode amino acid metabolism(synthesis and degradation),biofilm formation,and flagella assembly were all part of the core genome.Moreover,the KEGG annotation of the core genes demonstrated thatβ-ketoadipate,homoprotocatechuate,homogentisate,and gentisate pathways were the main catabolic processes of aromatic compounds in the P.aeruginosa strains,which concurrently possessed a relatively complete alkane hydroxylase system.Based on the GC content,flanked transposase,and integrase coding genes,it could be concluded that the aromatic compound degradation gene clusters in P.aeruginosa could be obtained through horizontal gene transfer.Functional pan-genome analysis of these 10 strains showed that the frequency of HGT in P.aeruginosa to obtain new genes from the outside world was relatively weak and had a complete system to degrade hydrocarbons.The results would be beneficial for better understanding the genomic composition and characteristics and providing useful information on the potential and mechanism of degradation of P.aeruginosa.

关 键 词：铜绿假单胞菌 泛基因组 核心基因 独特基因 生物降解 

分 类 号：X172[环境科学与工程—环境科学]