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Fernandez-Lopez L, Sanchez-Carrillo S, García-Moyano A, Borchert E, Almendral D, Alonso S, Cea-Rama I, Miguez N, Larsen Ø, Werner J, Makarova KS, Plou FJ, Dahlgren TG, Sanz-Aparicio J, Hentschel U, Bjerga GEK, Ferrer M. The bone-degrading enzyme machinery: From multi-component understanding to the treatment of residues from the meat industry. Comput Struct Biotechnol J 2021; 19:6328-6342. [PMID: 34938409 PMCID: PMC8645421 DOI: 10.1016/j.csbj.2021.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 11/19/2022] Open
Abstract
Characterization of enzymes from bone-degrading marine microbiomes. Enzymes degrade sialo/glyco-proteins at multiple conditions of pH and temperatures. Enzyme cocktails are useful for valorising bone residues in biorefinery industry.
Many microorganisms feed on the tissue and recalcitrant bone materials from dead animals, however little is known about the collaborative effort and characteristics of their enzymes. In this study, microbial metagenomes from symbionts of the marine bone-dwelling worm Osedax mucofloris, and from microbial biofilms growing on experimentally deployed bone surfaces were screened for specialized bone-degrading enzymes. A total of 2,043 taxonomically (closest match within 40 phyla) and functionally (1 proteolytic and 9 glycohydrolytic activities) diverse and non-redundant sequences (median pairwise identity of 23.6%) encoding such enzymes were retrieved. The taxonomic assignation and the median identity of 72.2% to homologous proteins reflect microbial and functional novelty associated to a specialized bone-degrading marine community. Binning suggests that only one generalist hosting all ten targeted activities, working in synergy with multiple specialists hosting a few or individual activities. Collagenases were the most abundant enzyme class, representing 48% of the total hits. A total of 47 diverse enzymes, representing 8 hydrolytic activities, were produced in Escherichia coli, whereof 13 were soluble and active. The biochemical analyses revealed a wide range of optimal pH (4.0–7.0), optimal temperature (5–65 °C), and of accepted substrates, specific to each microbial enzyme. This versatility may contribute to a high environmental plasticity of bone-degrading marine consortia that can be confronted to diverse habitats and bone materials. Through bone-meal degradation tests, we further demonstrated that some of these enzymes, particularly those from Flavobacteriaceae and Marinifilaceae, may be an asset for development of new value chains in the biorefinery industry.
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Key Words
- Bone degradation
- Bone microbiome
- COLL, collagenases (peptidases families U32 and M9)
- Collagenase
- DNS, dinitrosalicylic acid
- FALGPA, N-[3-(2-furyl)acryloyl]-L-leucyl-glycyl-L-prolyl-L-alanine
- Glycosidase
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- HMM, Hidden Markov Models
- HPAEC-PAD, High performance anion-exchange chromatography with pulsed amperometric detection
- MAG, Metagenome Assembled Genome
- Metagenomics
- Neu5Ac-GM2, N-acetyl-galactose-β-1,4-[N-acetylneuraminidate-α-2,3-]-galactose-β-1,4-glucose-α-ceramide
- Neu5Ac-GM3, Neu5Acα2-3Galβ1-4Glcβ1-ceramide
- Ni-NTA, nickel-nitrilotriacetic acid
- Osedax mucofloris
- PEPT, peptidase (families S1, S8, S53, M61)
- RHAM, α-rhamnosidases
- SIAL, sialidases
- pNP-NAβGal, pNP-N-acetyl-β-galactosaminide
- pNP-NAβGlu, pNP-N-acetyl-β-glucosaminide
- pNP-Neu5Ac, 2-O-(p-nitrophenyl)-α-acetylneuraminic acid
- pNP-sugars, p-nitrophenyl-sugars
- pNP-αAFur, pNP-α-arabinofuranoside
- pNP-αAPyr, pNP-α-arabinopyranoside
- pNP-αFuc, pNP-α-fucopyranoside
- pNP-αGal, pNP-α-galactopyranoside
- pNP-αGlu, pNP-α-glucopyranoside
- pNP-αMal, pNP-α-maltoside
- pNP-αMan, pNP-α-mannopyranoside
- pNP-αRham, pNP-α-rhamnopyranoside
- pNP-αXyl, pNP-α-xylopyranoside
- pNP-βAPyr, pNP-β-arabinopyranoside
- pNP-βCel, pNP-β-cellobioside
- pNP-βFuc, pNP-β-fucopyranoside
- pNP-βGal, pNP-β-galactopyranoside
- pNP-βGlu, pNP-β-glucopyranoside
- pNP-βGlucur, pNP-β-glucuronide
- pNP-βLac, pNP-β-lactoside
- pNP-βMan, pNP-β-mannopyranoside
- pNP-βXyl, pNP-β-xylopyranoside
- αFUC, α-fucosidases
- αGAL, α-galactosidases
- αMAN, α-mannosidases
- αNAG, α-N-acetyl-hexosaminidases
- βGAL, β-galactosidases
- βGLU, β-glucosidases
- βNAG, β-N-acetyl-hexosaminidases
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Affiliation(s)
| | | | | | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, Germany
- Corresponding authors at: GEOMAR Helmholtz Centre for Ocean Research, Wischhofstraße 1-3, 24148 Kiel, Germany (E. Borchert). Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain (M. Ferrer).
| | | | | | - Isabel Cea-Rama
- Institute of Physical Chemistry “Rocasolano”, CSIC, 28006 Madrid, Spain
| | - Noa Miguez
- CSIC, Institute of Catalysis, 28049 Madrid, Spain
| | - Øivind Larsen
- NORCE Norwegian Research Centre, P.O. Box 22 Nygårdstangen, 5838 Bergen, Norway
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, 72074 Tübingen, Germany
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, 20892 MD, USA
| | | | - Thomas G. Dahlgren
- NORCE Norwegian Research Centre, P.O. Box 22 Nygårdstangen, 5838 Bergen, Norway
| | | | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, 24148 Kiel, Germany
- Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | | | - Manuel Ferrer
- CSIC, Institute of Catalysis, 28049 Madrid, Spain
- Corresponding authors at: GEOMAR Helmholtz Centre for Ocean Research, Wischhofstraße 1-3, 24148 Kiel, Germany (E. Borchert). Institute of Catalysis, CSIC, Marie Curie 2, 28049 Madrid, Spain (M. Ferrer).
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