{"title":"细菌角质酶的门级研究,以揭示 PET 降解酶的特异性:一种硅学方法。","authors":"Shubham Kumar, Bhupendra Chaudhary, Barkha Singhal","doi":"10.1007/s42770-024-01362-6","DOIUrl":null,"url":null,"abstract":"<p><p>The overwhelming use of PET plastic in various day-to-day activities led to the voluminous increase in PET waste and growing environmental hazards. A plethora of methods have been used that are associated with secondary pollutants. Therefore, microbial degradation of PET provides a sustainable approach due to its versatile metabolic diversity and capacity. The present work highlights the cutinase enzyme's role in PET degradation. This study focuses on the bacterial cutinases homologs screened from 43 reported phylum of bacteria. The reported bacterial cutinases for plastic degradation have been chosen as reference sequences, and 917 sequences have shown homology across the bacterial phyla. The dienelactone hydrolase (DLH) domain was identified for attaining specificity towards PET binding in 196 of 917 sequences. Various computational tools have been used for the physicochemical characterization of 196 sequences. The analysis revealed that most selected sequences are hydrophilic, extracellular, and thermally stable. Based on this analysis, 17 sequences have been further pursued for three-dimensional structure prediction and validation. The molecular docking studies of 17 selected sequences revealed efficient PET binding with the three sequences derived from the phylum Bacteroidota, the lowest binding energy of -5.9 kcal/mol, Armatimonadota, and Nitrososphaerota with -5.8 kcal/mol. The two enzyme sequences retrieved from the phylum Bacteroidota and Armatimonadota are metagenomically derived. Therefore, the present studies concluded that there is a high probability of finding cutinase homologs in various environmental resources that can be further explored for PET degradation.</p>","PeriodicalId":9090,"journal":{"name":"Brazilian Journal of Microbiology","volume":" ","pages":"2385-2400"},"PeriodicalIF":2.1000,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11405750/pdf/","citationCount":"0","resultStr":"{\"title\":\"Phylum-level studies of bacterial cutinases for unravelling enzymatic specificity toward PET degradation: an in silico approach.\",\"authors\":\"Shubham Kumar, Bhupendra Chaudhary, Barkha Singhal\",\"doi\":\"10.1007/s42770-024-01362-6\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The overwhelming use of PET plastic in various day-to-day activities led to the voluminous increase in PET waste and growing environmental hazards. A plethora of methods have been used that are associated with secondary pollutants. Therefore, microbial degradation of PET provides a sustainable approach due to its versatile metabolic diversity and capacity. The present work highlights the cutinase enzyme's role in PET degradation. This study focuses on the bacterial cutinases homologs screened from 43 reported phylum of bacteria. The reported bacterial cutinases for plastic degradation have been chosen as reference sequences, and 917 sequences have shown homology across the bacterial phyla. The dienelactone hydrolase (DLH) domain was identified for attaining specificity towards PET binding in 196 of 917 sequences. Various computational tools have been used for the physicochemical characterization of 196 sequences. The analysis revealed that most selected sequences are hydrophilic, extracellular, and thermally stable. Based on this analysis, 17 sequences have been further pursued for three-dimensional structure prediction and validation. The molecular docking studies of 17 selected sequences revealed efficient PET binding with the three sequences derived from the phylum Bacteroidota, the lowest binding energy of -5.9 kcal/mol, Armatimonadota, and Nitrososphaerota with -5.8 kcal/mol. The two enzyme sequences retrieved from the phylum Bacteroidota and Armatimonadota are metagenomically derived. 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引用次数: 0
摘要
在各种日常活动中大量使用 PET 塑料,导致 PET 废弃物大量增加,环境危害日益严重。人们使用了大量与二次污染物有关的方法。因此,由于微生物代谢的多样性和能力,微生物降解 PET 提供了一种可持续的方法。本研究强调了角叉菜酶在 PET 降解中的作用。本研究的重点是从 43 个已报道的细菌门中筛选出的细菌角质酶同源物。研究选择了已报道的用于塑料降解的细菌角叉菜胶酶作为参考序列,917 个序列在各细菌门中显示出同源性。在 917 个序列中的 196 个序列中,二烯丙基内酯水解酶(DLH)结构域被确定为具有 PET 结合的特异性。对 196 个序列的物理化学特征采用了各种计算工具。分析表明,所选序列大多具有亲水性、细胞外性和热稳定性。在此分析基础上,进一步对 17 个序列进行了三维结构预测和验证。对 17 个选定序列进行的分子对接研究显示,PET 与来自细菌门的三个序列的结合能最低,为-5.9 kcal/mol,与 Armatimonadota 和 Nitrososphaerota 的结合能最低,为-5.8 kcal/mol。从类菌门和亚门检索到的两种酶序列均来自元基因组。因此,本研究得出结论,在各种环境资源中发现角叉菜胶酶同源物的可能性很大,可以进一步开发用于 PET 降解的酶。
Phylum-level studies of bacterial cutinases for unravelling enzymatic specificity toward PET degradation: an in silico approach.
The overwhelming use of PET plastic in various day-to-day activities led to the voluminous increase in PET waste and growing environmental hazards. A plethora of methods have been used that are associated with secondary pollutants. Therefore, microbial degradation of PET provides a sustainable approach due to its versatile metabolic diversity and capacity. The present work highlights the cutinase enzyme's role in PET degradation. This study focuses on the bacterial cutinases homologs screened from 43 reported phylum of bacteria. The reported bacterial cutinases for plastic degradation have been chosen as reference sequences, and 917 sequences have shown homology across the bacterial phyla. The dienelactone hydrolase (DLH) domain was identified for attaining specificity towards PET binding in 196 of 917 sequences. Various computational tools have been used for the physicochemical characterization of 196 sequences. The analysis revealed that most selected sequences are hydrophilic, extracellular, and thermally stable. Based on this analysis, 17 sequences have been further pursued for three-dimensional structure prediction and validation. The molecular docking studies of 17 selected sequences revealed efficient PET binding with the three sequences derived from the phylum Bacteroidota, the lowest binding energy of -5.9 kcal/mol, Armatimonadota, and Nitrososphaerota with -5.8 kcal/mol. The two enzyme sequences retrieved from the phylum Bacteroidota and Armatimonadota are metagenomically derived. Therefore, the present studies concluded that there is a high probability of finding cutinase homologs in various environmental resources that can be further explored for PET degradation.
期刊介绍:
The Brazilian Journal of Microbiology is an international peer reviewed journal that covers a wide-range of research on fundamental and applied aspects of microbiology.
The journal considers for publication original research articles, short communications, reviews, and letters to the editor, that may be submitted to the following sections: Biotechnology and Industrial Microbiology, Food Microbiology, Bacterial and Fungal Pathogenesis, Clinical Microbiology, Environmental Microbiology, Veterinary Microbiology, Fungal and Bacterial Physiology, Bacterial, Fungal and Virus Molecular Biology, Education in Microbiology. For more details on each section, please check out the instructions for authors.
The journal is the official publication of the Brazilian Society of Microbiology and currently publishes 4 issues per year.