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Cochereau B, Le Strat Y, Ji Q, Pawtowski A, Delage L, Weill A, Mazéas L, Hervé C, Burgaud G, Gunde-Cimerman N, Pouchus YF, Demont-Caulet N, Roullier C, Meslet-Cladiere L. Heterologous Expression and Biochemical Characterization of a New Chloroperoxidase Isolated from the Deep-Sea Hydrothermal Vent Black Yeast Hortaea werneckii UBOCC-A-208029. Mar Biotechnol (NY) 2023; 25:519-536. [PMID: 37354383 PMCID: PMC10427571 DOI: 10.1007/s10126-023-10222-7] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/04/2023] [Indexed: 06/26/2023]
Abstract
The initiation of this study relies on a targeted genome-mining approach to highlight the presence of a putative vanadium-dependent haloperoxidase-encoding gene in the deep-sea hydrothermal vent fungus Hortaea werneckii UBOCC-A-208029. To date, only three fungal vanadium-dependent haloperoxidases have been described, one from the terrestrial species Curvularia inaequalis, one from the fungal plant pathogen Botrytis cinerea, and one from a marine derived isolate identified as Alternaria didymospora. In this study, we describe a new vanadium chloroperoxidase from the black yeast H. werneckii, successfully cloned and overexpressed in a bacterial host, which possesses higher affinity for bromide (Km = 26 µM) than chloride (Km = 237 mM). The enzyme was biochemically characterized, and we have evaluated its potential for biocatalysis by determining its stability and tolerance in organic solvents. We also describe its potential three-dimensional structure by building a model using the AlphaFold 2 artificial intelligence tool. This model shows some conservation of the 3D structure of the active site compared to the vanadium chloroperoxidase from C. inaequalis but it also highlights some differences in the active site entrance and the volume of the active site pocket, underlining its originality.
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Affiliation(s)
- Bastien Cochereau
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Yoran Le Strat
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Qiaolin Ji
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Audrey Pawtowski
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Ludovic Delage
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Amélie Weill
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Univ Brest, UBO Culture Collection (UBOCC), F-29280, Plouzané, France
| | - Lisa Mazéas
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Cécile Hervé
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Gaëtan Burgaud
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Nina Gunde-Cimerman
- Molecular Genetics and Biology of Microorganisms, Dept. Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Nathalie Demont-Caulet
- INRAE, University of Paris, UMR ECOSYS, INRAE, Université Paris-Saclay, 78026, Versailles, AgroParisTech, France
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France.
| | - Laurence Meslet-Cladiere
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
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Mazéas L, Yonamine R, Barbeyron T, Henrissat B, Drula E, Terrapon N, Nagasato C, Hervé C. Assembly and synthesis of the extracellular matrix in brown algae. Semin Cell Dev Biol 2023; 134:112-124. [PMID: 35307283 DOI: 10.1016/j.semcdb.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/03/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022]
Abstract
In brown algae, the extracellular matrix (ECM) and its constitutive polymers play crucial roles in specialized functions, including algal growth and development. In this review we offer an integrative view of ECM construction in brown algae. We briefly report the chemical composition of its main constituents, and how these are interlinked in a structural model. We examine the ECM assembly at the tissue and cell level, with consideration on its structure in vivo and on the putative subcellular sites for the synthesis of its main constituents. We further discuss the biosynthetic pathways of two major polysaccharides, alginates and sulfated fucans, and the progress made beyond the candidate genes with the biochemical validation of encoded proteins. Key enzymes involved in the elongation of the glycan chains are still unknown and predictions have been made at the gene level. Here, we offer a re-examination of some glycosyltransferases and sulfotransferases from published genomes. Overall, our analysis suggests novel investigations to be performed at both the cellular and biochemical levels. First, to depict the location of polysaccharide structures in tissues. Secondly, to identify putative actors in the ECM synthesis to be functionally studied in the future.
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Affiliation(s)
- Lisa Mazéas
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Rina Yonamine
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Japan
| | - Tristan Barbeyron
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Bernard Henrissat
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; Technical University of Denmark, DTU Bioengineering, DK-2800 Kgs., Lyngby, Denmark
| | - Elodie Drula
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France
| | - Nicolas Terrapon
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Japan
| | - Cécile Hervé
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
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Hao LP, Mazéas L, Lü F, Grossin-Debattista J, He PJ, Bouchez T. Effect of ammonia on methane production pathways and reaction rates in acetate-fed biogas processes. Water Sci Technol 2017; 75:1839-1848. [PMID: 28452776 DOI: 10.2166/wst.2017.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In order to understand the correlation between ammonia and methanogenesis metabolism, methane production pathways and their specific rates were studied at total ammonium nitrogen (TAN) concentrations of 0.14-9 g/L in three methanogenic sludges fed with acetate, at both mesophilic and thermophilic conditions. Results showed that high levels of TAN had significant inhibition on methanogenesis; this could, however, be recovered via syntrophic acetate oxidation (SAO) coupled with Hydrogenotrophic Methanogenesis (HM) performed by acetate oxidizing syntrophs or through Acetoclastic Methanogenesis (AM) catalyzed by Methanosarcinaceae, after a long lag phase >50 d. Free ammonia (NH3) was the active component for this inhibition, of which 200 mg/L is suggested as the threshold for the pathway shift from AM to SAO-HM. Methane production rate via SAO-HM at TAN of 7-9 g/L was about 5-9-fold lower than that of AM at TAN of 0.14 g/L, which was also lower than the rate of AM pathway recovered at TAN of 7 g/L in the incubations with a French mesophilic inoculum. Thermophilic condition favored the establishment of the SAO-catalyzing microbial community, as indicated by the higher reaction rate and shorter lag phase. The operational strategy is thus suggested to be adjusted when NH3 exceeds 200 mg/L.
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Affiliation(s)
- L P Hao
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark; Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, Antony 92761, France E-mail:
| | - L Mazéas
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, Antony 92761, France E-mail:
| | - F Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China
| | | | - P J He
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China
| | - T Bouchez
- Irstea, UR HBAN, 1 rue Pierre-Gilles de Gennes, Antony 92761, France E-mail:
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Qu X, Vavilin VA, Mazéas L, Lemunier M, Duquennoi C, He PJ, Bouchez T. Anaerobic biodegradation of cellulosic material: batch experiments and modelling based on isotopic data and focusing on aceticlastic and non-aceticlastic methanogenesis. Waste Manag 2009; 29:1828-1837. [PMID: 19157832 DOI: 10.1016/j.wasman.2008.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2008] [Revised: 11/30/2008] [Accepted: 12/04/2008] [Indexed: 05/27/2023]
Abstract
Utilizing stable carbon isotope data to account for aceticlastic and non-aceticlastic pathways of methane generation, a model was created to describe laboratory batch anaerobic decomposition of cellulosic materials (office paper and cardboard). The total organic and inorganic carbon concentrations, methane production volume, and methane and CO(2) partial pressure values were used for the model calibration and validation. According to the fluorescent in situ hybridization observations, three groups of methanogens including strictly hydrogenotrophic methanogens, strictly aceticlastic methanogens (Methanosaeta sp.) and Methanosarcina sp., consuming both acetate and H(2)/H(2)CO(3) as well as acetate-oxidizing syntrophs, were considered. It was shown that temporary inhibition of aceticlastic methanogens by non-ionized volatile fatty acids or acidic pH was responsible for two-step methane production from office paper at 35 degrees C where during the first and second steps methane was generated mostly from H(2)/H(2)CO(3) and acetate, respectively. Water saturated and unsaturated cases were tested. According to the model, at the intermediate moisture (150%), much lower methane production occurred because of full-time inhibition of aceticlastic methanogens. At the lowest moisture, methane production was very low because most likely hydrolysis was seriously inhibited. Simulations showed that during cardboard and office paper biodegradation at 55 degrees C, non-aceticlastic syntrophic oxidation by acetate-oxidizing syntrophs and hydrogenotrophic methanogens were the dominant methanogenic pathways.
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Affiliation(s)
- X Qu
- Tongji University, Shanghai 200092, China
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Vavilin VA, Qu X, Qu X, Mazéas L, Lemunier M, Duquennoi C, Mouchel JM, He P, Bouchez T. Similar evolution in delta 13CH4 and model-predicted relative rate of aceticlastic methanogenesis during mesophilic methanization of municipal solid wastes. Water Sci Technol 2009; 60:3173-3179. [PMID: 19955641 DOI: 10.2166/wst.2009.724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Similar evolution was obtained for the stable carbon isotope signatures delta (13)CH(4) and the model-predicted relative rate of aceticlastic methanogenesis during mesophilic methanization of municipal solid wastes. In batch incubations, the importance of aceticlastic and hydrogenotrophic methanogenesis changes in time. Initially, hydrogenotrophic methanogenesis dominated, but increasing population of Methanosarcina sp. enhances aceticlastic methanogenesis. Later, hydrogenotrophic methanogenesis intensified again. A mathematical model was developed to evaluate the relative contribution of hydrogenotrophic and aceticlastic pathways of methane generation during mesophilic batch anaerobic biodegradation of the French and the Chinese Municipal Solid Wastes (FMSW and CMSW). Taking into account molecular biology analysis reported earlier three groups of methanogens including strictly hydrogenotrophic methanogens, strictly aceticlastic methanogens (Methanosaeta sp.) and Methanosarcina sp., consuming both acetate and H(2)/H(2)CO(3) were considered in the model. The total organic and inorganic carbon concentrations, methane production volume, methane and carbon dioxide partial pressures values were used for the model calibration and validation. Methane isotopic composition (delta (13)CH(4)) evolution during the incubations was used to independently validate the model results. The model demonstrated that only the putrescible solid waste was totally converted to methane.
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Affiliation(s)
- V A Vavilin
- Cemagref, UR-HBAN, Parc de Tourvoie, Antony cedex F-92163, France
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