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功能宏基因组学揭示了煤宏基因组中的腈水解酶。

Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome.

作者信息

Achudhan Arunmozhi Bharathi, Kannan Priya, Saleena Lilly M

机构信息

Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India.

出版信息

Front Mol Biosci. 2023 Mar 17;10:1123902. doi: 10.3389/fmolb.2023.1123902. eCollection 2023.

Abstract

Nitriles are the most toxic compounds that can lead to serious human illness through inhalation and consumption due to environmental pollution. Nitrilases can highly degrade nitriles isolated from the natural ecosystem. In the current study, we focused on the discovery of novel nitrilases from a coal metagenome using mining. Coal metagenomic DNA was isolated and sequenced on the Illumina platform. Quality reads were assembled using MEGAHIT, and statistics were checked using QUAST. Annotation was performed using the automated tool SqueezeMeta. The annotated amino acid sequences were mined for nitrilase from the unclassified organism. Sequence alignment and phylogenetic analyses were carried out using ClustalW and MEGA11. Conserved regions of the amino acid sequences were identified using InterProScan and NCBI-CDD servers. The physicochemical properties of the amino acids were measured using ExPASy's ProtParam. Furthermore, NetSurfP was used for 2D structure prediction, while AlphaFold2 in Chimera X 1.4 was used for 3D structure prediction. To check the solvation of the predicted protein, a dynamic simulation was conducted on the WebGRO server. Ligands were extracted from the Protein Data Bank (PDB) for molecular docking upon active site prediction using the CASTp server. mining of annotated metagenomic data revealed nitrilase from unclassified . By using the artificial intelligence program AlphaFold2, the 3D structure was predicted with a per-residue confidence statistic score of about 95.8%, and the stability of the predicted model was verified with molecular dynamics for a 100-ns simulation. Molecular docking analysis determined the binding affinity of a novel nitrilase with nitriles. The binding scores produced by the novel nitrilase were approximately similar to those of the other prokaryotic nitrilase crystal structures, with a deviation of ±0.5.

摘要

腈类是毒性最强的化合物,由于环境污染,可通过吸入和食用导致严重的人类疾病。腈水解酶能够高效降解从自然生态系统中分离出的腈类。在本研究中,我们专注于通过挖掘从煤炭宏基因组中发现新型腈水解酶。从煤炭中分离宏基因组DNA,并在Illumina平台上进行测序。使用MEGAHIT组装高质量读段,并使用QUAST检查统计数据。使用自动化工具SqueezeMeta进行注释。从未分类生物的注释氨基酸序列中挖掘腈水解酶。使用ClustalW和MEGA11进行序列比对和系统发育分析。使用InterProScan和NCBI - CDD服务器鉴定氨基酸序列的保守区域。使用ExPASy的ProtParam测量氨基酸的物理化学性质。此外,使用NetSurfP进行二维结构预测,而在Chimera X 1.4中使用AlphaFold2进行三维结构预测。为了检查预测蛋白质的溶剂化情况,在WebGRO服务器上进行了动态模拟。使用CASTp服务器预测活性位点后,从蛋白质数据库(PDB)中提取配体进行分子对接。对注释的宏基因组数据进行挖掘,发现了来自未分类生物的腈水解酶。通过使用人工智能程序AlphaFold2,预测的三维结构的每个残基置信统计得分约为95.8%,并通过100纳秒模拟的分子动力学验证了预测模型的稳定性。分子对接分析确定了新型腈水解酶与腈类的结合亲和力。新型腈水解酶产生的结合分数与其他原核腈水解酶晶体结构的结合分数大致相似,偏差为±0.5。

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