title: 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. This work allowed the identification of putative enzyme candidates with promising features from metagenomes, providing a suitable starting point for further developments.
authors.affiliation: Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut U9120ACD, Argentina. musumeci@cenpat-conicet.gob.ar.
authors.forename: Matías A
authors.initials: MA
authors.lastname: Musumeci
authors.affiliation: Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut U9120ACD, Argentina. lozada@cenpat-conicet.gob.ar.
authors.forename: Mariana
authors.initials: M
authors.lastname: Lozada
authors.affiliation: Área Biología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531 S2002LRK Rosario, Argentina. drial@fbioyf.unr.edu.ar.
authors.forename: Daniela V
authors.initials: DV
authors.lastname: Rial
authors.affiliation: Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires C1010AAZ, Argentina. wmac@ffyb.uba.ar.|Instituto de Nanobiotecnología (NANOBIOTEC), CONICET-Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1113AAD, Argentina. wmac@ffyb.uba.ar.
authors.forename: Walter P
authors.initials: WP
authors.lastname: Mac Cormack
authors.affiliation: Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA. janet.jansson@pnnl.gov.
authors.forename: Janet K
authors.initials: JK
authors.lastname: Jansson
authors.affiliation: School of Natural Sciences and Environmental Studies, Södertörn University, 141 89 Huddinge, Sweden. sara.sjoling@sh.se.
authors.forename: Sara
authors.initials: S
authors.lastname: Sjöling
authors.affiliation: Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, NO-9296 Tromsø, Norway. jolynn.carroll@akvaplan.niva.no.|ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037 Tromsø, Norway. jolynn.carroll@akvaplan.niva.no.
authors.forename: JoLynn
authors.initials: J
authors.lastname: Carroll
authors.affiliation: Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut U9120ACD, Argentina. hdionisi@cenpat-conicet.gob.ar.
authors.forename: Hebe M
authors.initials: HM
authors.lastname: Dionisi
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000235:genetics; D055162:Biocatalysis; D001709:Biotechnology / Q000379:methods; D003080:Cold Temperature; D003577:Cytochrome P-450 Enzyme System / Q000235:genetics; D007700:Kinetics; D054892:Metagenome / Q000235:genetics*; D006899:Mixed Function Oxygenases / Q000235:genetics*; D010084:Oxidation-Reduction; D010802:Phylogeny; D016415:Sequence Alignment; D013379:Substrate Specificity / Q000235:genetics
chemical_list: D003577:Cytochrome P-450 Enzyme System; D006899:Mixed Function Oxygenases; C435228:cytochrome P-450 CYP153 (Acinetobacter)
keywords: Baeyer–Villiger monooxygenases; bacterial cytochrome P450; bioprospecting biocatalysts; molecular modeling; phylogenetic analysis