A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins
Abstract There are significant environmental and health concerns associated with the current inefficient plastic recycling process. This study presents the first integrated reference catalog of plastic-contaminated environments obtained using an insilico workflow that could play a significant role i...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-43042-9 |
| _version_ | 1797452974978498560 |
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| author | Donya Afshar Jahanshahi Shohreh Ariaeenejad Kaveh Kavousi |
| author_facet | Donya Afshar Jahanshahi Shohreh Ariaeenejad Kaveh Kavousi |
| author_sort | Donya Afshar Jahanshahi |
| collection | DOAJ |
| description | Abstract There are significant environmental and health concerns associated with the current inefficient plastic recycling process. This study presents the first integrated reference catalog of plastic-contaminated environments obtained using an insilico workflow that could play a significant role in discovering new plastizymes. Here, we combined 66 whole metagenomic data from plastic-contaminated environment samples from four previously collected metagenome data with our new sample. In this study, an integrated plastic-contaminated environment gene, protein, taxa, and plastic degrading enzyme catalog (PDEC) was constructed. These catalogs contain 53,300,583 non-redundant genes and proteins, 691 metagenome-assembled genomes, and 136,654 plastizymes. Based on KEGG and eggNOG annotations, 42% of recognized genes lack annotations, indicating their functions remain elusive and warrant further investigation. Additionally, the PDEC catalog highlights hydrolases, peroxidases, and cutinases as the prevailing plastizymes. Ultimately, following multiple validation procedures, our effort focused on pinpointing enzymes that exhibited the highest similarity to the introduced plastizymes in terms of both sequence and three-dimensional structural aspects. This encompassed evaluating the linear composition of constituent units as well as the complex spatial conformation of the molecule. The resulting catalog is expected to improve the resolution of future multi-omics studies, providing new insights into plastic-pollution related research. |
| first_indexed | 2024-03-09T15:17:04Z |
| format | Article |
| id | doaj.art-e112095da97c4096bd1ca3c0fb6b2b57 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-09T15:17:04Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-e112095da97c4096bd1ca3c0fb6b2b572023-11-26T13:04:36ZengNature PortfolioScientific Reports2045-23222023-09-0113111410.1038/s41598-023-43042-9A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteinsDonya Afshar Jahanshahi0Shohreh Ariaeenejad1Kaveh Kavousi2Department of Bioinformatics, Kish International Campus University of TehranDepartment of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO)Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of TehranAbstract There are significant environmental and health concerns associated with the current inefficient plastic recycling process. This study presents the first integrated reference catalog of plastic-contaminated environments obtained using an insilico workflow that could play a significant role in discovering new plastizymes. Here, we combined 66 whole metagenomic data from plastic-contaminated environment samples from four previously collected metagenome data with our new sample. In this study, an integrated plastic-contaminated environment gene, protein, taxa, and plastic degrading enzyme catalog (PDEC) was constructed. These catalogs contain 53,300,583 non-redundant genes and proteins, 691 metagenome-assembled genomes, and 136,654 plastizymes. Based on KEGG and eggNOG annotations, 42% of recognized genes lack annotations, indicating their functions remain elusive and warrant further investigation. Additionally, the PDEC catalog highlights hydrolases, peroxidases, and cutinases as the prevailing plastizymes. Ultimately, following multiple validation procedures, our effort focused on pinpointing enzymes that exhibited the highest similarity to the introduced plastizymes in terms of both sequence and three-dimensional structural aspects. This encompassed evaluating the linear composition of constituent units as well as the complex spatial conformation of the molecule. The resulting catalog is expected to improve the resolution of future multi-omics studies, providing new insights into plastic-pollution related research.https://doi.org/10.1038/s41598-023-43042-9 |
| spellingShingle | Donya Afshar Jahanshahi Shohreh Ariaeenejad Kaveh Kavousi A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins Scientific Reports |
| title | A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins |
| title_full | A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins |
| title_fullStr | A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins |
| title_full_unstemmed | A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins |
| title_short | A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins |
| title_sort | metagenomic catalog for exploring the plastizymes landscape covering taxa genes and proteins |
| url | https://doi.org/10.1038/s41598-023-43042-9 |
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