New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics
Bioremediation, the degradation of environmental pollutants by living organisms, has immense potential to lead to a greener planet. Bioinformatics analysis can contribute to the identification of novel microorganisms, which biodegrade contaminants, or of participating proteins and enzymes, and the e...
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MDPI AG
2024-10-01
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| Series: | Bacteria |
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| Online Access: | https://www.mdpi.com/2674-1334/3/4/21 |
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| author | Marina Giannakara Vassiliki Lila Koumandou |
| author_facet | Marina Giannakara Vassiliki Lila Koumandou |
| author_sort | Marina Giannakara |
| collection | DOAJ |
| description | Bioremediation, the degradation of environmental pollutants by living organisms, has immense potential to lead to a greener planet. Bioinformatics analysis can contribute to the identification of novel microorganisms, which biodegrade contaminants, or of participating proteins and enzymes, and the elucidation of the complex metabolic pathways involved. In this study, we focus on C-P lyase and glyphosate oxidoreductase (Gox), two enzymes which degrade glyphosate, a widely used pesticide. Amino acid sequences of the two enzymes were collected from a broad range of microorganisms using the KEGG database and BLAST. Based on this, we identified additional lineages, with putative glyphosate-degrading activity, for which no glyphosate-degrading species have been reported yet. The conserved residues in each enzyme were identified via multiple alignments and mapped onto the 3D structures of the enzymes, using PyMOL, leading to novel insights into their function. As the experimental structure of Gox is still unknown, we created structural models based on three different programs and compared the results. This approach can be used to yield insights into the characteristics of potential glyphosate-degrading enzymes. Given the limited information available, such a step is important to gain further knowledge about them, which can contribute to their application in bioremediation in the future. |
| format | Article |
| id | doaj-art-47088d3c7a44444ea34e2e757ed39aed |
| institution | OA Journals |
| issn | 2674-1334 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | MDPI AG |
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| series | Bacteria |
| spelling | doaj-art-47088d3c7a44444ea34e2e757ed39aed2025-08-20T02:01:00ZengMDPI AGBacteria2674-13342024-10-013431432910.3390/bacteria3040021New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on BioinformaticsMarina Giannakara0Vassiliki Lila Koumandou1Genetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, GreeceGenetics Laboratory, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, 11855 Athens, GreeceBioremediation, the degradation of environmental pollutants by living organisms, has immense potential to lead to a greener planet. Bioinformatics analysis can contribute to the identification of novel microorganisms, which biodegrade contaminants, or of participating proteins and enzymes, and the elucidation of the complex metabolic pathways involved. In this study, we focus on C-P lyase and glyphosate oxidoreductase (Gox), two enzymes which degrade glyphosate, a widely used pesticide. Amino acid sequences of the two enzymes were collected from a broad range of microorganisms using the KEGG database and BLAST. Based on this, we identified additional lineages, with putative glyphosate-degrading activity, for which no glyphosate-degrading species have been reported yet. The conserved residues in each enzyme were identified via multiple alignments and mapped onto the 3D structures of the enzymes, using PyMOL, leading to novel insights into their function. As the experimental structure of Gox is still unknown, we created structural models based on three different programs and compared the results. This approach can be used to yield insights into the characteristics of potential glyphosate-degrading enzymes. Given the limited information available, such a step is important to gain further knowledge about them, which can contribute to their application in bioremediation in the future.https://www.mdpi.com/2674-1334/3/4/21glyphosateC-P lyaseglyphosate oxidoreductasebiodegradationbioinformaticsphylogenetics |
| spellingShingle | Marina Giannakara Vassiliki Lila Koumandou New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics Bacteria glyphosate C-P lyase glyphosate oxidoreductase biodegradation bioinformatics phylogenetics |
| title | New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics |
| title_full | New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics |
| title_fullStr | New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics |
| title_full_unstemmed | New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics |
| title_short | New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics |
| title_sort | new insights on the glyphosate degrading enzymes c p lyase and glyphosate oxidoreductase based on bioinformatics |
| topic | glyphosate C-P lyase glyphosate oxidoreductase biodegradation bioinformatics phylogenetics |
| url | https://www.mdpi.com/2674-1334/3/4/21 |
| work_keys_str_mv | AT marinagiannakara newinsightsontheglyphosatedegradingenzymescplyaseandglyphosateoxidoreductasebasedonbioinformatics AT vassilikililakoumandou newinsightsontheglyphosatedegradingenzymescplyaseandglyphosateoxidoreductasebasedonbioinformatics |