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首页> 美国卫生研究院文献>AMB Express >In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2
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In silico genome analysis reveals the metabolic versatility and biotechnology potential of a halotorelant phthalic acid esters degrading Gordonia alkanivorans strain YC-RL2

机译：在计算机基因组分析中揭示了卤代邻苯二甲酸邻苯二甲酸酯降解Gordonia alkanivorans菌株YC-RL2的代谢多功能性和生物技术潜力

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Members of genus Gordonia are known to degrade various xenobitics and produce secondary metabolites. The genome of a halotorelant phthalic acid ester (PAEs) degrading actinobacterium Gordonia alkanivorans strain YC-RL2 was sequenced using Biosciences RS II platform and Single Molecular Real-Time (SMRT) technology. The reads were assembled de novo by hierarchical genome assembly process (HGAP) algorithm version 2. Genes were annotated by NCBI Prokaryotic Genome Annotation Pipeline. The generated genome sequence was 4,979,656 bp with an average G+C content of 67.45%. Calculation of ANI confirmed previous classification that strain YC-RL2 is G. alkanivorans. The sequences were searched against KEGG and COG databases; 3132 CDSs were assigned to COG families and 1808 CDSs were predicted to be involved in 111 pathways. 95 of the KEGG annotated genes were predicted to be involved in the degradation of xenobiotics. A phthalate degradation operon could not be identified in the genome indicating that strain YC-RL2 possesses a novel way of phthalate degradation. A total of 203 and 22 CDSs were annotated as esterase/hydrolase and dioxygenase genes respectively. A total of 53 biosynthetic gene clusters (BGCs) were predicted by antiSMASH (antibiotics & Secondary Metabolite Analysis Shell) bacterial version 4.0. The genome also contained putative genes for heavy metal metabolism. The strain could tolerate 1 mM of Cd2+, Co2+, Cu2+, Ni2+, Zn2+, Mn2+ and Pb2+ ions. These results show that strain YC-RL2 has a great potential to degrade various xenobiotics in different environments and will provide a rich genetic resource for further biotechnological and remediation studies.Electronic supplementary materialThe online version of this article (10.1186/s13568-019-0733-5) contains supplementary material, which is available to authorized users.
机译：已知Gordonia属的成员会降解各种异种物质并产生次级代谢产物。使用Biosciences RS II平台和Single Molecular Real-Time（SMRT）技术对降解卤代放线菌的放线菌戈登尼亚链霉菌YC-RL2的基因组进行测序。这些读物是通过层次基因组组装过程（HGAP）算法版本2从头组装的。基因由NCBI原核基因组注释管道注释。产生的基因组序列为4,979,656 bp，平均G + C含量为67.45％。 ANI的计算证实了先前的分类，即菌株YC-RL2是链霉菌。在KEGG和COG数据库中搜索序列； 3132个CDS被分配给COG家族，预计1808个CDS参与111条途径。预测有KEGG注释的基因中有95个与异源生物降解有关。不能在基因组中鉴定邻苯二甲酸酯降解操纵子，这表明菌株YC​​-RL2具有新型的邻苯二甲酸酯降解方式。共有203个和22个CDS分别标注为酯酶/水解酶和双加氧酶基因。 antiSMASH（抗生素和次生代谢产物分析壳）细菌4.0版预测总共有53个生物合成基因簇（BGC）。该基因组还包含重金属代谢的推定基因。该菌株可耐受1mM的Cd 2 + ，Co 2 + ，Cu 2 + ，Ni 2 + ，Zn 2 + ，Mn 2 + 和Pb 2 + 离子。这些结果表明，YC-RL2菌株具有在不同环境中降解各种异种生物的巨大潜力，并将为进一步的生物技术和修复研究提供丰富的遗传资源。电子补充材料本文的在线版本（10.1186 / s13568-019-0733- 5）包含补充材料，授权用户可以使用。

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