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胶质芽孢杆菌K02的全基因组序列及比较基因组分析

Complete genome sequence and comparative genome analysis of the Paenibacillus mucilaginosus K02.

作者信息

Xiao Bo, Sun Yu-Fang, Lian Bin, Chen Tian-Ming

机构信息

Key Laboratory for Ecology and Pollution Control of Coastal Wetlands, School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng 224051, China; Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China.

Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China.

出版信息

Microb Pathog. 2016 Apr;93:194-203. doi: 10.1016/j.micpath.2016.01.016. Epub 2016 Jan 21.

Abstract

AIM

Paenibacillus mucilaginosus (P. mucilaginosus) K02 is implicated in mineral weathering. However, relevant molecular mechanisms remain obscure. The study aims to uncover the bacterium's physiological processes using genomic approaches.

METHODS AND RESULTS

Genomic DNA from P. mucilaginosus K02 was sequenced using high-throughput Solexa sequencing technology and then conducted for Clusters of Orthologous Group (COG) annotation. Thereafter, genome sequences of K02 were compared with two strains, 3016 and KNP414. Mummer was applied for collinearity analysis of three P. mucilaginosus genomes. BLAST was used to identify pan and core genes in these strains. Finally, a phylogenetic tree was constructed using the maximum likelihood method by TreeBeST. Complete genome sequence of P. mucilaginosus K02 indicated the strain comprises one circular chromosome with 8,819,200 bases containing 58.3% GC content and 84.75% coding regions. A total of 7299 predicted ORFs were identified in the genome, among them, several genes were related to carbonic anhydrase (CA), and exopolysaccharide biosynthesis and secretion. Moreover, proteins of the predicted genes were annotated in COG categories such as "Carbohydrate transport and metabolism" and "Inorganic ion transport and metabolism." In comparison with KNP414 and 3016, K02 exhibited chromosomal recombination or transposition. A total of 6662 core genes were identified among three P. mucilaginosus strains. The phylogenomic study indicated that P. mucilaginosus K02 was clustered with P. mucilaginosus strains 3016 and KNP414.

CONCLUSIONS

In P. mucilaginosus K02, genes related to CA and exopolysaccharide biosynthesis and secretion, and that involved in metabolism-related processes might play significant roles in mineral weathering.

摘要

目的

胶质芽孢杆菌(P. mucilaginosus)K02与矿物风化有关。然而,相关分子机制仍不清楚。本研究旨在利用基因组方法揭示该细菌的生理过程。

方法与结果

使用高通量Solexa测序技术对胶质芽孢杆菌K02的基因组DNA进行测序,然后进行直系同源簇(COG)注释。此后,将K02的基因组序列与3016和KNP414两个菌株进行比较。利用Mummer对三个胶质芽孢杆菌基因组进行共线性分析。使用BLAST鉴定这些菌株中的泛基因和核心基因。最后,通过TreeBeST使用最大似然法构建系统发育树。胶质芽孢杆菌K02的完整基因组序列表明,该菌株包含一条环状染色体,有8,819,200个碱基,GC含量为58.3%,编码区为84.75%。基因组中总共鉴定出7299个预测的开放阅读框(ORF),其中一些基因与碳酸酐酶(CA)、胞外多糖生物合成和分泌有关。此外,预测基因的蛋白质被注释到COG类别中,如“碳水化合物转运和代谢”和“无机离子转运和代谢”。与KNP414和3016相比,K02表现出染色体重组或转座。在三个胶质芽孢杆菌菌株中总共鉴定出6662个核心基因。系统发育基因组学研究表明,胶质芽孢杆菌K02与胶质芽孢杆菌菌株3016和KNP414聚类在一起。

结论

在胶质芽孢杆菌K02中,与CA、胞外多糖生物合成和分泌相关的基因以及参与代谢相关过程的基因可能在矿物风化中发挥重要作用。

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