Comprehensive in silico studies on the microbial enzymes capable of degrading organophosphorus pesticide

IF 4.1 2区 环境科学与生态学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Priyanka Raul , Yasmin Begum , Sandipa Tripathi , Monalisha Karmakar , Kartik Chandra Guchhait , Subhamoy Dey , Suparna Majumder , Sunil Kanti Mondal , Amiya Kumar Panda , Chandradipa Ghosh
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Abstract

Phorate, an organophosphorus compound is known to have applications against pests. However, its hazardous nature is a matter of concern. Microbial biodegradation is a potent method that can eliminate pesticides from the environment by enzymatic reactions. As toxicity and binding specificity are inherently correlated to each other, this study was focussed on finding out binding sites for ensuing biodegradation. Brevibacterium frigoritolerans GD44 and Enterobacter cloacae subsp. cloacae ATCC 13047 were included in the study for genomic and structural analyses as alkaline phosphatase from Brevibacterium frigoritolerans GD44 and endonuclease/exonuclease/phosphatase from Enterobacter cloacae subsp. cloacae ATCC 13047 were found to degrade phorate. It was apparent from the present findings that alkaline phosphatase containing homologous bacterial species are AT-rich, while the phosphatase containing bacteria are GC-rich. Bacterial species having phosphatase enzyme contain more aromatic amino acids that stabilize the protein structure than alkaline phosphatase containing bacteria. Variation of relative synonymous codon usage (RSCU) value was found to be very little and natural selection pressure was preferred over mutational pressure in determining codon usage pattern. High level of codon adaptation index (CAI) found in both the bacterial species indicates higher level of codon usage bias and gene expression in them. Furthermore, docking results suggest that alkaline phosphatase has higher binding affinity to phorate than phosphatase that might be considered effective in bioremediation. The results obtained are considered to shed further light in the experimental biodegradation of organophosphorus pesticides by the bacteria.

Abstract Image

对能够降解有机磷农药的微生物酶进行全面的硅学研究
众所周知,甲拌磷是一种有机磷化合物,可用于防治害虫。然而,它的危险性令人担忧。微生物生物降解是一种有效的方法,可以通过酶促反应消除环境中的杀虫剂。由于毒性和结合特异性在本质上是相互关联的,因此本研究的重点是寻找结合位点,以实现生物降解。本研究将弗氏乳杆菌(Brevibacterium frigoritolerans GD44)和泄殖腔肠杆菌亚种(Enterobacter cloacae subsp.cloacae ATCC 13047)纳入基因组和结构分析,因为发现弗氏乳杆菌(Brevibacterium frigoritolerans GD44)的碱性磷酸酶和泄殖腔肠杆菌亚种(Enterobacter cloacae subsp.cloacae ATCC 13047)的内切酶/外切酶/磷酸酶可降解甲拌磷。本研究结果表明,含有碱性磷酸酶的同源细菌物种富含 AT,而含有磷酸酶的细菌富含 GC。与含有碱性磷酸酶的细菌相比,含有磷酸酶的细菌种类含有更多的芳香族氨基酸,可稳定蛋白质结构。研究发现,相对同义密码子使用(RSCU)值的变化非常小,在决定密码子使用模式时,自然选择压力比突变压力更重要。在这两种细菌中发现的高水平密码子适应指数(CAI)表明,它们的密码子使用偏差和基因表达水平较高。此外,对接结果表明,碱性磷酸酶与甲拌磷的结合亲和力高于磷酸酶,而磷酸酶在生物修复中可能被认为是有效的。这些结果将进一步揭示细菌对有机磷农药的生物降解实验。
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来源期刊
CiteScore
9.60
自引率
10.40%
发文量
107
审稿时长
21 days
期刊介绍: International Biodeterioration and Biodegradation publishes original research papers and reviews on the biological causes of deterioration or degradation.
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