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Phylum-level studies of bacterial cutinases for unravelling enzymatic specificity toward PET degradation: an in silico approach

  • Environmental and Biodiversity - Research Paper
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Abstract

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.

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Acknowledgements

The authors greatly acknowledge the support of Gautam Buddha University (Greater Noida) and Jawaharlal Nehru University for writing this manuscript.

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This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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Authors and Affiliations

  1. School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India

    Shubham Kumar & Barkha Singhal

  2. School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India

    Bhupendra Chaudhary

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Contributions

Barkha Singhal conceptualized the idea and wrote the manuscript. Shubham Kumar has performed in silico studies using various computational software to study bacterial cutinases' structural and functional aspects. Bhupendra Chaudhary performed a detailed analysis of the phylogenetic relationship of bacterial cutinases.

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Correspondence to Barkha Singhal.

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Supplementary information

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42770_2024_1362_MOESM1_ESM.docx

Supplementary file1 (DOCX 122 KB) Table S1 A preliminary data of 196 sequences of cutinase retrieved from 43 different bacterial phyla.

42770_2024_1362_MOESM2_ESM.pdf

Supplementary file2 (PDF 227 KB) Fig. S1 Multiple sequence alignment of selected 196 bacterial cutinase enzyme sequences

42770_2024_1362_MOESM3_ESM.tif

Supplementary file3 (TIF 397 KB) Fig. S2 Interaction of 14 cutinase sequences out of 17 selected sequences with ligand PET through molecular docking

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Kumar, S., Chaudhary, B. & Singhal, B. Phylum-level studies of bacterial cutinases for unravelling enzymatic specificity toward PET degradation: an in silico approach. Braz J Microbiol (2024). https://doi.org/10.1007/s42770-024-01362-6

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