Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach
Abstract
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. As a result, this work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable startingmore »
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1420452
- Alternate Identifier(s):
- OSTI ID: 1356489
- Report Number(s):
- PNNL-SA-124674
Journal ID: ISSN 1660-3397; MDARE6; PII: md15040114
- Grant/Contract Number:
- AC05-76RLO1830; AC05-76RL01830
- Resource Type:
- Published Article
- Journal Name:
- Marine Drugs
- Additional Journal Information:
- Journal Name: Marine Drugs Journal Volume: 15 Journal Issue: 4; Journal ID: ISSN 1660-3397
- Publisher:
- MDPI AG
- Country of Publication:
- Switzerland
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; bacterial cyochrome P450; Baeyer-Villiger Monooxygenases; Bioprospecting; biocatalysts; phylogenetic; analysis; molecular modeling
Citation Formats
Musumeci, Matías, Lozada, Mariana, Rial, Daniela, Mac Cormack, Walter, Jansson, Janet, Sjöling, Sara, Carroll, JoLynn, and Dionisi, Hebe. Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach. Switzerland: N. p., 2017.
Web. doi:10.3390/md15040114.
Musumeci, Matías, Lozada, Mariana, Rial, Daniela, Mac Cormack, Walter, Jansson, Janet, Sjöling, Sara, Carroll, JoLynn, & Dionisi, Hebe. Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach. Switzerland. https://doi.org/10.3390/md15040114
Musumeci, Matías, Lozada, Mariana, Rial, Daniela, Mac Cormack, Walter, Jansson, Janet, Sjöling, Sara, Carroll, JoLynn, and Dionisi, Hebe. Sun .
"Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach". Switzerland. https://doi.org/10.3390/md15040114.
@article{osti_1420452,
title = {Prospecting Biotechnologically-Relevant Monooxygenases from Cold Sediment Metagenomes: An In Silico Approach},
author = {Musumeci, Matías and Lozada, Mariana and Rial, Daniela and Mac Cormack, Walter and Jansson, Janet and Sjöling, Sara and Carroll, JoLynn and Dionisi, Hebe},
abstractNote = {The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis. Phylogenetic analyses were used to select the most divergent sequences affiliated to these enzyme families among the 264 putative monooxygenases recovered from the ~14 million protein-coding sequences in the assembled metagenome dataset. Three-dimensional structure modeling and docking analysis suggested features useful in biotechnological applications in five metagenomic sequences, such as wide substrate range, novel substrate specificity or regioselectivity. Further analysis revealed structural features associated with psychrophilic enzymes, such as broader substrate accessibility, larger catalytic pockets or low domain interactions, suggesting that they could be applied in biooxidations at room or low temperatures, saving costs inherent to energy consumption. As a result, this work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.},
doi = {10.3390/md15040114},
journal = {Marine Drugs},
number = 4,
volume = 15,
place = {Switzerland},
year = {Sun Apr 09 00:00:00 EDT 2017},
month = {Sun Apr 09 00:00:00 EDT 2017}
}
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Works referencing / citing this record:
In-Silico Bioprospecting: Finding Better Enzymes
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