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Flores-Almaraz VS, Truong C, Hernández-Oaxaca D, Reyes-Galindo V, Mastretta-Yanes A, Jaramillo-Correa JP, Salas-Lizana R. Foliar mycobiome remains unaltered under urban air-pollution but differentially express stress-related genes. MICROBIAL ECOLOGY 2024; 87:72. [PMID: 38755460 PMCID: PMC11098924 DOI: 10.1007/s00248-024-02387-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/29/2024] [Indexed: 05/18/2024]
Abstract
Air pollution caused by tropospheric ozone contributes to the decline of forest ecosystems; for instance, sacred fir, Abies religiosa (Kunth) Schltdl. & Cham. forests in the peri-urban region of Mexico City. Individual trees within these forests exhibit variation in their response to ozone exposure, including the severity of visible symptoms in needles. Using RNA-Seq metatranscriptomic data and ITS2 metabarcoding, we investigated whether symptom variation correlates with the taxonomic and functional composition of fungal mycobiomes from needles collected in this highly polluted area in the surroundings of Mexico City. Our findings indicate that ozone-related symptoms do not significantly correlate with changes in the taxonomic composition of fungal mycobiomes. However, genes coding for 30 putative proteins were differentially expressed in the mycobiome of asymptomatic needles, including eight genes previously associated with resistance to oxidative stress. These results suggest that fungal communities likely play a role in mitigating the oxidative burst caused by tropospheric ozone in sacred fir. Our study illustrates the feasibility of using RNA-Seq data, accessible from global sequence repositories, for the characterization of fungal communities associated with plant tissues, including their gene expression.
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Affiliation(s)
- Valeria Stephany Flores-Almaraz
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, C.P. 04510, Distrito Federal, México
- Instituto de Biología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Camille Truong
- Royal Botanic Gardens Victoria, Birdwood Ave, Melbourne, VIC 3004, Australia.
| | - Diana Hernández-Oaxaca
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad S/N, 62210, Cuernavaca, Morelos, México
| | - Verónica Reyes-Galindo
- Depto. de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Alicia Mastretta-Yanes
- Consejo Nacional de Humanidades Ciencias y Tecnología (CONAHCYT), Avenida Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Ciudad de México, 03940, México.
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico.
| | - Juan Pablo Jaramillo-Correa
- Depto. de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Ciudad de México, Mexico
| | - Rodolfo Salas-Lizana
- Laboratorios de Micología. Depto. de Biología Comparada, Facultad de Ciencias., Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México.
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Chatterjee S, Nochebuena J, Cisneros GA. Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity. J Am Chem Soc 2024; 146:13247-13257. [PMID: 38701006 DOI: 10.1021/jacs.4c01100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) at neutral pH. However, the atomistic details remain elusive. In the enzymatic landscape of HRP, compound II (Cpd II) plays a key role and involves a histidine (H42) residue. Cpd II exists as oxoferryl (2a) or hydroxoferryl (2b(FeIV)) forms, where 2a is the predominantly observed form in experimental studies. Intriguingly, the ferric 2b(FeIII) form seen in synthetic complexes has not been observed in HRP. Here, we have investigated the structure and dynamics of HRP in pure water and aqueous [EMIm][EtSO4] (0.26 M), as well as the reaction mechanism of 2a to 2b conversion using polarizable molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations. When HRP is solvated in aq [EMIm][EtSO4], the catalytic water displaces, and H42 directly orients over the ferryl moiety, allowing a direct proton transfer (PT) with a significant energy barrier reduction. Conversely, in neat water, the reaction of 2a to 2b follows the previously reported mechanism. We further investigated the deprotonated form of H42. Analysis of the electric fields at the active site indicates that the aq [EMIm][EtSO4] medium facilitates the reaction by providing a more favorable environment compared with the system solvated in neat water. Overall, the atomic level supports the previous experimental observations and underscores the importance of favorable electric fields in the active site to promote catalysis.
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Affiliation(s)
- Shubham Chatterjee
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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Perkins AK, Rose AL, Grossart HP, Schulz KG, Neubauer D, Tonge MP, Rosentreter JA, Eyre BD, Rojas-Jimenez K, Deschaseaux E, Oakes JM. Fungi increases kelp (Ecklonia radiata) remineralisation and dissolved organic carbon, alkalinity, and dimethylsulfoniopropionate (DMSP) production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166957. [PMID: 37704140 DOI: 10.1016/j.scitotenv.2023.166957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Fungi are key players in terrestrial organic matter (OM) degradation, but little is known about their role in marine environments. Here we compared the degradation of kelp (Ecklonia radiata) in mesocosms with and without fungicides over 45 days. The aim was to improve our understanding of the vital role of fungal OM degradation and remineralisation and its relevance to marine biogeochemical cycles (e.g., carbon, nitrogen, sulfur, or volatile sulfur). In the presence of fungi, 68 % of the kelp detritus degraded over 45 days, resulting in the production of 0.6 mol of dissolved organic carbon (DOC), 0.16 mol of dissolved inorganic carbon (DIC), 0.23 mol of total alkalinity (TA), and 0.076 mol of CO2, which was subsequently emitted to the atmosphere. Conversely, when fungi were inhibited, the bacterial community diversity was reduced, and only 25 % of the kelp detritus degraded over 45 days. The application of fungicides resulted in the generation of an excess amount of 1.5 mol of DOC, but we observed only 0.02 mol of DIC, and 0.04 mol of TA per one mole of kelp detritus, accompanied by a CO2 emission of 0.081 mol. In contrast, without fungi, remineralisation of kelp detritus to DIC, TA, dimethyl sulfide (DMS), dimethylsulfoniopropionate (DMSP) and methanethiol (MeSH) was significantly reduced. Fungal kelp remineralisation led to a remarkable 100,000 % increase in DMSP production. The observed substantial changes in sediment chemistry when fungi are inhibited highlight the important biogeochemical role of fungal remineralisation, which likely plays a crucial role in defining coastal biogeochemical cycling, blue carbon sequestration, and thus climate regulation.
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Affiliation(s)
- Anita K Perkins
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia.
| | - Andrew L Rose
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia; Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Hans-Peter Grossart
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Kai G Schulz
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Darshan Neubauer
- Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB), Experimental Limnology, 16775 Neuglobsow, Germany; University of Potsdam, Institute of Biochemistry and Biology, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Matthew P Tonge
- Southern Cross Geoscience, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Judith A Rosentreter
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Bradley D Eyre
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | | | - Elisabeth Deschaseaux
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
| | - Joanne M Oakes
- Centre for Coastal Biogeochemistry, Faculty of Science and Engineering, Southern Cross University, Lismore, 2480, NSW, Australia
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Gómez D, Acosta J, López-Sandoval H, Torres-Palma RA, Ávila-Torres Y. Enantioselective Biomimetic Structures Inspired by Oxi-Dase-Type Metalloenzymes, Utilizing Polynuclear Compounds Containing Copper (II) and Manganese (II) Ions as Building Blocks. Biomimetics (Basel) 2023; 8:423. [PMID: 37754174 PMCID: PMC10527443 DOI: 10.3390/biomimetics8050423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
This study focuses on developing and evaluating two novel enantioselective biomimetic models for the active centers of oxidases (ascorbate oxidase and catalase). These models aim to serve as alternatives to enzymes, which often have limited action and a delicate nature. For the ascorbate oxidase (AO) model (compound 1), two enantiomers, S,S(+)cpse and R,R(-)cpse, were combined in a crystalline structure, resulting in a racemic compound. The analysis of their magnetic properties and electrochemical behavior revealed electronic transfer between six metal centers. Compound 1 effectively catalyzed the oxidation of ascorbic to dehydroascorbic acid, showing a 45.5% yield for the racemic form. This was notably higher than the enantiopure compounds synthesized previously and tested in the current report, which exhibited yields of 32% and 28% for the S,S(+)cpse and R,R(-)cpse enantiomers, respectively. This outcome highlights the influence of electronic interactions between metal ions in the racemic compound compared to pure enantiomers. On the other hand, for the catalase model (compound 2), both the compound and its enantiomer displayed polymeric properties and dimeric behavior in the solid and solution states, respectively. Compound 2 proved to be effective in catalyzing the oxidation of hydrogen peroxide to oxygen with a yield of 64.7%. In contrast, its enantiomer (with R,R(-)cpse) achieved only a 27% yield. This further validates the functional nature of the prepared biomimetic models for oxidases. This research underscores the importance of understanding and designing biomimetic models of metalloenzyme active centers for both biological and industrial applications. These models show promising potential as viable alternatives to natural enzymes in various processes.
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Affiliation(s)
- Didier Gómez
- Facultad de Tecnologías, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (D.G.); (J.A.)
| | - Jorge Acosta
- Facultad de Tecnologías, Universidad Tecnológica de Pereira, Pereira 660003, Colombia; (D.G.); (J.A.)
| | - Horacio López-Sandoval
- Departamento de Química Inorgánica, Facultad de Química, Universidad Nacional Autónoma de México, C.U., Coyoacán, México City 04510, Mexico;
| | - Ricardo A. Torres-Palma
- Grupo de Investigación en Remediación Ambiental y Biocatálisis (GIRAB), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 50010, Colombia;
| | - Yenny Ávila-Torres
- Grupo de Investigación en Remediación Ambiental y Biocatálisis (GIRAB), Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín 50010, Colombia;
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Fleurat-Lessard P, Luini E, La Camera S, Thibault F, Roblin G, Berjeaud JM. Fungal wood-degrading enzymes in esca-diseased grapevine and effects of carbohydrate environment on fungal development. Arch Microbiol 2023; 205:194. [PMID: 37061655 DOI: 10.1007/s00203-023-03544-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023]
Abstract
In esca disease affecting grapevines, Phaeomoniella chlamydospora and Phaeoacremonium minimum colonize the woody parts of the trunks and arms, where they obtain nutrition from xylem sap and, potentially, from residues resulting from the enzymatic breakdown of lignified cell walls, particularly osidic residues. We quantified the secretion of lignin peroxidase, manganese peroxidase and laccase by these fungi in woody tissues of selectively infected cuttings using immunolabeling and transmission electron microscopy. Our results indicated that the detection of these enzymes was generally higher in tissues infected with Phaeoacremonium minimum. These data were confirmed through immunodetection of enzymes secreted by hyphae of fungi grown in vitro. Additionally, we observed that the supply of various carbohydrates (mono, di, tri and tetrasaccharides and polymers) differentially influenced fungal growth and polypeptide secretion. Since some secreted polypeptides display detrimental effects on grapevine cells, these results raise the question of whether the carbohydrate environment could be a factor affecting the aggressiveness of these pathogens.
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Affiliation(s)
- Pierrette Fleurat-Lessard
- Laboratoire EBI (Ecologie et Biologie des Interactions), UMR CNRS 7267, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Estelle Luini
- Laboratoire EBI (Ecologie et Biologie des Interactions), UMR CNRS 7267, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Sylvain La Camera
- Laboratoire EBI (Ecologie et Biologie des Interactions), UMR CNRS 7267, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Florence Thibault
- Laboratoire EBI (Ecologie et Biologie des Interactions), UMR CNRS 7267, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Gabriel Roblin
- Laboratoire EBI (Ecologie et Biologie des Interactions), UMR CNRS 7267, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Jean-Marc Berjeaud
- Laboratoire EBI (Ecologie et Biologie des Interactions), UMR CNRS 7267, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, 86073, Poitiers Cedex 9, France.
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Phenylalanine Ammonia-Lyase: A Key Gene for Color Discrimination of Edible Mushroom Flammulina velutipes. J Fungi (Basel) 2023; 9:jof9030339. [PMID: 36983507 PMCID: PMC10053379 DOI: 10.3390/jof9030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
In nature; Flammulina velutipes, also known as winter mushrooms, vary in the color of their fruiting bodies, from black, yellow, pale yellow, or beige to white. The purpose of this study was to compare the genome sequences of different colored strains of F. velutipes and to identify variations in the genes associated with fruiting body color. Comparative genomics of six F. velutipes strains revealed 70 white-strain-specific variations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), in the genome sequences. Among them, 36 variations were located in the open reading frames, and only one variation was identified as a mutation with a disruptive in-frame deletion (ΔGCGCAC) within the annotated gene phenylalanine ammonia-lyase 1 (Fvpal1). This mutation was found to cause a deletion, without a frameshift, of two amino acids at positions 112 and 113 (arginine and threonine, respectively) in the Fvpal1 gene of the white strain. Specific primers to detect this mutation were designed, and amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) was performed to evaluate whether the mutation is color specific for the F. velutipes fruiting body. PCR analysis of a total of 95 F. velutipes strains revealed that this mutation was present only in white strains. In addition, monospores of the heterozygous mutant were isolated, and whether this mutation was related to the color of the fruiting body was evaluated by a mating assay. In the mating analysis of monospores with mutations in Fvpal1, it was found that this mutation plays an important role in determining the color of the fruiting body. Furthermore, the deletion (Δ112RT113) in Fvpal1 is located between motifs that play a key role in the catalytic function of FvPAL1. These results suggest that this mutation can be used as an effective marker for the color-specific breeding of F. velutipes, a representative edible mushroom.
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Gan J, Bilal M, Li X, Hussain Shah SZ, Mohamed BA, Hadibarata T, Cheng H. Peroxidases-based enticing biotechnological platforms for biodegradation and biotransformation of emerging contaminants. CHEMOSPHERE 2022; 307:136035. [PMID: 35973503 DOI: 10.1016/j.chemosphere.2022.136035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/27/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Rampant industrial boom, urbanization, and exponential population growth resulted in widespread environmental pollution, with water being one of the leading affected resources. All kinds of pollutants, including phenols, industrial dyes, antibiotics, pharmaceutically active residues, and persistent/volatile organic compounds, have a paramount effect, either directly or indirectly, on human health and aquatic entities. Strategies for affordable and efficient decontamination of these emerging pollutants have become the prime focus of academic researchers, industry, and government to constitute a sustainable human society. Classical treatment techniques for environmental contaminants are associated with several limitations, such as inefficiency, complex pretreatments, overall high process cost, high sludge generation, and highly toxic side-products formation. Enzymatic remediation is considered a green and ecologically friendlier method that holds considerable potential to mitigate any kinds of contaminating agents. Exploiting the potential of various peroxidases for pollution abatement is an emerging research area and has considerable advantages, such as efficiency and ease of handling, over other methods. This work is designed to provide recent progress in deploying peroxidases as green and versatile biocatalytic tools for the degradation and transformation of a spectrum of potentially hazardous environmental pollutants to broaden their scope for biotechnological and environmental purposes. More studies are required to explicate the degradation mechanisms, assess the toxicology levels of bio-transformed metabolites, and standardize the treatment strategies for economic viability.
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Affiliation(s)
- JianSong Gan
- School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou, 221094, China; School of Food and Drug, Jiangsu Vocational College of Finance & Economics, Huaian, 223003, China.
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China
| | - XiaoBing Li
- School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou, 221094, China.
| | | | - Badr A Mohamed
- Department of Agricultural Engineering, Cairo University, El-Gamma Street, Giza, Egypt
| | - Tony Hadibarata
- Environmental Engineering Program, Faculty of Engineering and Science, Curtin University Malaysia, CDT 250, Miri, 98009, Malaysia
| | - Hairong Cheng
- Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Wang S, Wang X, Penttinen L, Luo H, Zhang Y, Liu B, Yao B, Hakulinen N, Zhang W, Su X. Patulin Detoxification by Recombinant Manganese Peroxidase from Moniliophthora roreri Expressed by Pichia pastoris. Toxins (Basel) 2022; 14:toxins14070440. [PMID: 35878178 PMCID: PMC9324453 DOI: 10.3390/toxins14070440] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023] Open
Abstract
The fungal secondary metabolite patulin is a mycotoxin widespread in foods and beverages which poses a serious threat to human health. However, no enzyme was known to be able to degrade this mycotoxin. For the first time, we discovered that a manganese peroxidase (MrMnP) from Moniliophthora roreri can efficiently degrade patulin. The MrMnP gene was cloned into pPICZα(A) and then the recombinant plasmid was transformed into Pichia pastoris X-33. The recombinant strain produced extracellular manganese peroxidase with an activity of up to 3659.5 U/L. The manganese peroxidase MrMnP was able to rapidly degrade patulin, with hydroascladiol appearing as a main degradation product. Five mg/L of pure patulin were completely degraded within 5 h. Moreover, up to 95% of the toxin was eliminated in a simulated patulin-contaminated apple juice after 24 h. Using Escherichia coli as a model, it was demonstrated that the deconstruction of patulin led to detoxification. Collectively, these traits make MrMnP an intriguing candidate useful in enzymatic detoxification of patulin in foods and beverages.
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Affiliation(s)
- Shuai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (Y.Z.); (B.L.)
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.W.); (H.L.); (B.Y.)
| | - Leena Penttinen
- Department of Chemistry, Joensuu Campus, University of Eastern Finland, FIN-80101 Joensuu, Finland; (L.P.); (N.H.)
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.W.); (H.L.); (B.Y.)
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (Y.Z.); (B.L.)
| | - Bo Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (Y.Z.); (B.L.)
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.W.); (H.L.); (B.Y.)
| | - Nina Hakulinen
- Department of Chemistry, Joensuu Campus, University of Eastern Finland, FIN-80101 Joensuu, Finland; (L.P.); (N.H.)
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (S.W.); (Y.Z.); (B.L.)
- Correspondence: (W.Z.); (X.S.)
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.W.); (H.L.); (B.Y.)
- Correspondence: (W.Z.); (X.S.)
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Temporiti MEE, Nicola L, Nielsen E, Tosi S. Fungal Enzymes Involved in Plastics Biodegradation. Microorganisms 2022; 10:1180. [PMID: 35744698 PMCID: PMC9230134 DOI: 10.3390/microorganisms10061180] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 12/04/2022] Open
Abstract
Plastic pollution is a growing environmental problem, in part due to the extremely stable and durable nature of this polymer. As recycling does not provide a complete solution, research has been focusing on alternative ways of degrading plastic. Fungi provide a wide array of enzymes specialized in the degradation of recalcitrant substances and are very promising candidates in the field of plastic degradation. This review examines the present literature for different fungal enzymes involved in plastic degradation, describing their characteristics, efficacy and biotechnological applications. Fungal laccases and peroxidases, generally used by fungi to degrade lignin, show good results in degrading polyethylene (PE) and polyvinyl chloride (PVC), while esterases such as cutinases and lipases were successfully used to degrade polyethylene terephthalate (PET) and polyurethane (PUR). Good results were also obtained on PUR by fungal proteases and ureases. All these enzymes were isolated from many different fungi, from both Basidiomycetes and Ascomycetes, and have shown remarkable efficiency in plastic biodegradation under laboratory conditions. Therefore, future research should focus on the interactions between the genes, proteins, metabolites and environmental conditions involved in the processes. Further steps such as the improvement in catalytic efficiency and genetic engineering could lead these enzymes to become biotechnological applications in the field of plastic degradation.
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Affiliation(s)
- Marta Elisabetta Eleonora Temporiti
- Laboratory of Mycology, Department of Earth and Environmental Sciences, Università degli Studi di Pavia, Via S. Epifanio 14, 27100 Pavia, Italy; (L.N.); (S.T.)
| | - Lidia Nicola
- Laboratory of Mycology, Department of Earth and Environmental Sciences, Università degli Studi di Pavia, Via S. Epifanio 14, 27100 Pavia, Italy; (L.N.); (S.T.)
| | - Erik Nielsen
- Department of Biology and Biotechnology, Università degli Studi di Pavia, Via Ferrata 9, 27100 Pavia, Italy;
| | - Solveig Tosi
- Laboratory of Mycology, Department of Earth and Environmental Sciences, Università degli Studi di Pavia, Via S. Epifanio 14, 27100 Pavia, Italy; (L.N.); (S.T.)
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Pavlović J, Bosch-Roig P, Rusková M, Planý M, Pangallo D, Sanmartín P. Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel. Appl Microbiol Biotechnol 2022; 106:4297-4314. [PMID: 35596787 PMCID: PMC9200699 DOI: 10.1007/s00253-022-11961-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/14/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO4) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO3)2 and Mg(NO3)2) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out. KEY POINTS : • Poorly (CaSO4) and highly (Ca(NO3)2, Mg(NO3)2) soluble salts were detected • Halophilic and mineral weathering microorganisms reveal ecological impacts of salts • Microbial communities involved in nitrate and sulfate cycles were detected.
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Affiliation(s)
- Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Pilar Bosch-Roig
- Instituto Universitario de Restauración del Patrimonio, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Magdalena Rusková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Matej Planý
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
- Caravella, s.r.o., Tupolevova 2, 851 01, Bratislava, Slovakia
| | - Patricia Sanmartín
- Departamento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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11
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Cochereau B, Meslet-Cladière L, Pouchus YF, Grovel O, Roullier C. Halogenation in Fungi: What Do We Know and What Remains to Be Discovered? Molecules 2022; 27:3157. [PMID: 35630634 PMCID: PMC9144378 DOI: 10.3390/molecules27103157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.
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Affiliation(s)
- Bastien Cochereau
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Laurence Meslet-Cladière
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Olivier Grovel
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
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12
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Gao Y, Shah K, Kwok I, Wang M, Rome LH, Mahendra S. Immobilized fungal enzymes: Innovations and potential applications in biodegradation and biosynthesis. Biotechnol Adv 2022; 57:107936. [PMID: 35276253 DOI: 10.1016/j.biotechadv.2022.107936] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 01/10/2023]
Abstract
Microbial enzymes catalyze various reactions inside and outside living cells. Among the widely studied enzymes, fungal enzymes have been used for some of the most diverse purposes, especially in bioremediation, biosynthesis, and many nature-inspired commercial applications. To improve their stability and catalytic ability, fungal enzymes are often immobilized on assorted materials, conventional as well as nanoscale. Recent advances in fungal enzyme immobilization provide effective and sustainable approaches to achieve improved environmental and commercial outcomes. This review aims to provide a comprehensive overview of commonly studied fungal enzymes and immobilization technologies. It also summarizes recent advances involving immobilized fungal enzymes for the degradation or assembly of compounds used in the manufacture of products, such as detergents, food additives, and fossil fuel alternatives. Furthermore, challenges and future directions are highlighted to offer new perspectives on improving existing technologies and addressing unexplored fields of applications.
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Affiliation(s)
- Yifan Gao
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Kshitjia Shah
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Ivy Kwok
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States
| | - Meng Wang
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Leonard H Rome
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, United States; California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA 90095, United States; California NanoSystems Institute, University of California, Los Angeles, CA 90095, United States.
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13
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Sellami K, Couvert A, Nasrallah N, Maachi R, Abouseoud M, Amrane A. Peroxidase enzymes as green catalysts for bioremediation and biotechnological applications: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150500. [PMID: 34852426 DOI: 10.1016/j.scitotenv.2021.150500] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 05/16/2023]
Abstract
The fast-growing consumer demand drives industrial process intensification, which subsequently creates a significant amount of waste. These products are discharged into the environment and can affect the quality of air, degrade water streams, and alter soil characteristics. Waste materials may contain polluting agents that are especially harmful to human health and the ecosystem, such as the synthetic dyes, phenolic agents, polycyclic aromatic hydrocarbons, volatile organic compounds, polychlorinated biphenyls, pesticides and drug substances. Peroxidases are a class oxidoreductases capable of performing a wide variety of oxidation reactions, ranging from reactions driven by radical mechanisms, to oxygen insertion into CH bonds, and two-electron substrate oxidation. This versatility in the mode of action presents peroxidases as an interesting alternative in cleaning the environment. Herein, an effort has been made to describe mechanisms governing biochemical process of peroxidase enzymes while referring to H2O2/substrate stoichiometry and metabolite products. Plant peroxidases including horseradish peroxidase (HRP), soybean peroxidase (SBP), turnip and bitter gourd peroxidases have revealed notable biocatalytic potentialities in the degradation of toxic products. On the other hand, an introduction on the role played by ligninolytic enzymes such as manganese peroxidase (MnP) and lignin peroxidase (LiP) in the valorization of lignocellulosic materials is addressed. Moreover, sensitivity and selectivity of peroxidase-based biosensors found use in the quantitation of constituents and the development of diagnostic kits. The general merits of peroxidases and some key prospective applications have been outlined as concluding remarks.
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Affiliation(s)
- Kheireddine Sellami
- Laboratoire de Génie de la Réaction, Faculté de Génie Mécanique et Génie des Procédés, Université des Sciences et de la Technologie Houari Boumediene, Bab Ezzouar, Alger 16111, Algeria; Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France.
| | - Annabelle Couvert
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
| | - Noureddine Nasrallah
- Laboratoire de Génie de la Réaction, Faculté de Génie Mécanique et Génie des Procédés, Université des Sciences et de la Technologie Houari Boumediene, Bab Ezzouar, Alger 16111, Algeria
| | - Rachida Maachi
- Laboratoire de Génie de la Réaction, Faculté de Génie Mécanique et Génie des Procédés, Université des Sciences et de la Technologie Houari Boumediene, Bab Ezzouar, Alger 16111, Algeria
| | - Mahmoud Abouseoud
- Laboratoire de Génie de la Réaction, Faculté de Génie Mécanique et Génie des Procédés, Université des Sciences et de la Technologie Houari Boumediene, Bab Ezzouar, Alger 16111, Algeria; Laboratoire de Biomatériaux et Phénomènes de Transport, Faculté des Sciences et de la Technologie, Université Yahia Fares de Médéa, Pôle Universitaire, RN1, Médéa 26000, Algeria
| | - Abdeltif Amrane
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
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14
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Characterization of Two Hydrogen Peroxide Resistant Peroxidases from Rhodococcus opacus 1CP. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11177941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dye-decolorizing peroxidases (DyP) are a family of heme-dependent enzymes present on a broad spectrum of microorganisms. While the natural function of these enzymes is not fully understood, their capacity to degrade highly contaminant pigments such as azo dyes or anthraquinones make them excellent candidates for applications in bioremediation and organic synthesis. In this work, two novel DyP peroxidases from the organism Rhodococcus opacus 1CP (DypA and DypB) were cloned and expressed in Escherichia coli. The enzymes were purified and biochemically characterized. The activities of the two DyPs via 2,2′-azino-bis [3-ethylbenzthiazoline-6-sulphonic acid] (ABTS) assay and against Reactive Blue 5 were assessed and optimized. Results showed varying trends for DypA and DypB. Remarkably, these enzymes presented a particularly high tolerance towards H2O2, retaining its activities at about 10 mM H2O2 for DypA and about 4.9 mM H2O2 for DypB.
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15
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Dahdouh A, Kati DE, Bachir-Bey M, Aksas A, Rezgui F. Deployment of response surface methodology to optimize microencapsulation of peroxidases from turnip roots (Brassica rapa L.) by double emulsion in PLA polymer. J Food Sci 2021; 86:1893-1906. [PMID: 33895995 DOI: 10.1111/1750-3841.15721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 03/05/2021] [Accepted: 03/13/2021] [Indexed: 11/27/2022]
Abstract
In order to improve the preservation conditions and stability of peroxidase catalytic properties, a number of immobilization techniques have been widely developed. In this context, we set as objective, the optimization of synthesis and stability of microcapsules of peroxidases (POD) from turnip using polylactic acid (PLA) polymer with the double emulsion technique. The surfactant, polymer, and peroxidase concentrations were the optimized parameters. According to the results obtained using the Box-Behnken design, the optimal parameters found were 1.55% of PVA, 55 mg/mL of peroxidases, and 30 mg/mL of PLA polymer with an encapsulation efficiency of 57.29%. The scanning electron microscopy morphological characterization of the optimized microcapsules showed a regular spherical structure. Fourier transform infrared spectroscopy identified the specific functional groups and chemical bonds before and after microencapsulation. The elaborated microcapsules were characterized by an average size of 200 µm (mainly from 150 to 500 µm) with a low residual moisture content (2.26%) and the encapsulated peroxidases showed better thermal stability. The in vitro release of peroxidases confirmed that the microcapsules have an excellent sustained release in simulated gastric digestion. Encapsulated peroxidases' storage under 25 and 4 °C displays a good residual POD activity with about 60% of initial activities during 80 days of storage, whereas free POD losses its initial activity within 15 and 30 days, respectively. The obtained results are promising for the development of effective therapeutic treatment of some intestinal troubles due to oxidative stress. PRACTICAL APPLICATION: Brassica rapa L. root is well known for its richness on peroxidases and thus presents an interesting potential for developing high added value products. In order to preserve the activity of extracted peroxidases (POD) from turnip roots, microencapsulation was optimized using a polylactic acid polymer. The encapsulated POD showed the maintenance of its activity under the effect of different storage conditions (time and temperature) and demonstrated resistance to gastric acidity. According to the obtained results, the encapsulation of peroxidases opens up medicine and pharmaceutical applications such as intestinal and colic protection against inflammations.
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Affiliation(s)
- Amel Dahdouh
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Djamel Edine Kati
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Mostapha Bachir-Bey
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Ali Aksas
- Laboratoire de Biotechnologies Végétales et Ethnobotanique, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Farouk Rezgui
- Laboratoire des Matériaux organiques, Département de Génie des Procèdes, Faculté de Technologie, Université de Bejaia, Bejaia, Algeria
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16
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Bilal M, Bagheri AR, Vilar DS, Aramesh N, Eguiluz KIB, Ferreira LFR, Ashraf SS, Iqbal HMN. Oxidoreductases as a versatile biocatalytic tool to tackle pollutants for clean environment – a review. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY 2021. [DOI: 10.1002/jctb.6743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering Huaiyin Institute of Technology Huaian 223003 China
| | | | - Débora S Vilar
- Graduate Program in Process Engineering Tiradentes University (UNIT) Av. Murilo Dantas, 300, Farolândia Aracaju‐Sergipe 49032‐490 Brazil
| | - Nahal Aramesh
- Department of Chemistry Yasouj University Yasouj Iran
| | - Katlin Ivon Barrios Eguiluz
- Graduate Program in Process Engineering Tiradentes University (UNIT) Av. Murilo Dantas, 300, Farolândia Aracaju‐Sergipe 49032‐490 Brazil
| | - Luiz Fernando Romanholo Ferreira
- Waste and Effluent Treatment Laboratory, Institute of Technology and Research (ITP) Tiradentes University (UNIT) Av. Murilo Dantas, 300, Farolândia Aracaju‐Sergipe 49032‐490 Brazil
| | - Syed Salman Ashraf
- Department of Chemistry College of Arts and Sciences, Khalifa University Abu Dhabi United Arab Emirates
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey School of Engineering and Sciences Monterrey 64849 Mexico
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17
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Ferreira DDSS, de Santana CS, Santana IB, Araújo JSC, Souza BCD, Leite FHA, Kato RB, Benevides RG, Góes-Neto A. Functional annotation and comparative modeling of ligninolytic enzymes from Trametes villosa (SW.) Kreisel for biotechnological applications. J Biomol Struct Dyn 2021; 40:6330-6339. [PMID: 33554764 DOI: 10.1080/07391102.2021.1883479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Functional annotation of Trametes villosa genome was performed to search Class II peroxidase proteins in this white-rot fungus, which can be valuable for several biotechnological processes. After sequence identification and manual curation, five proteins were selected to build 3 D models by comparative modeling. Analysis of sequential and structural sequences from selected targets revealed the presence of two putative Lignin Peroxidase and three putative Manganese Peroxidase on this fungal genome. All 3 D models had a similar folding pattern from selected 3 D structure templates. After minimization and validation steps, the best 3 D models were subjected to docking studies and molecular dynamics to identify structural requirements and the interactions required for molecular recognition. Two reliable 3 D models of Class II peroxidases, with typical catalytic site and architecture, and its protein sequences are indicated to recombinant production in biotechnological applications, such as bioenergy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Isis Bugia Santana
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana (UEFS), Bahia, Brazil
| | | | - Bruno Cruz de Souza
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana (UEFS), Bahia, Brazil
| | | | - Rodrigo Bentes Kato
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | | | - Aristóteles Góes-Neto
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
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18
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Degradation of low-rank coal excavated from coal-mine Záhorie by filamentous fungi. ACTA CHIMICA SLOVACA 2021. [DOI: 10.2478/acs-2020-0019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The ability of Trichoderma strains isolated from lignite and of Earth surface-derived strains to attack (solubilise) lignite, peat and wood was compared using glutamate as a carbon source. The results showed that lignite-derived microorganisms solubilise lignite to similar extent as Trichoderma strains isolated from the Earth surface. Solubilisation processes involve the action of enzymes and alkaline pH. The solubilisation of lignite was accompanied by a small increase of conidia-bound laccase, whereas that of peat was accompanied by (secretion) activity of cellulase, laminarinase, laccase, and lignin-peroxidase-like enzyme. In addition, data were obtained which show that bacteria contained in the lignite are able of lignite solubilisation and utilisation.
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19
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Musengi A, Durrell K, Prins A, Khan N, Agunbiade M, Kudanga T, Kirby-McCullough B, Pletschke BI, Burton SG, Le Roes-Hill M. Production and characterisation of a novel actinobacterial DyP-type peroxidase and its application in coupling of phenolic monomers. Enzyme Microb Technol 2020; 141:109654. [PMID: 33051013 DOI: 10.1016/j.enzmictec.2020.109654] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/06/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
The extracellular peroxidase from Streptomyces albidoflavus BSII#1 was purified to near homogeneity using sequential steps of acid and acetone precipitation, followed by ultrafiltration. The purified peroxidase was characterised and tested for the ability to catalyse coupling reactions between selected phenolic monomer pairs. A 46-fold purification of the peroxidase was achieved, and it was shown to be a 46 kDa haem peroxidase. Unlike other actinobacteria-derived peroxidases, it was only inhibited (27 % inhibition) by relatively high concentrations of sodium azide (5 mM) and was capable of oxidising eleven (2,4-dichlorophenol, 2,6-dimethoxyphenol, 4-tert-butylcatechol, ABTS, caffeic acid, catechol, guaiacol, l-DOPA, o-aminophenol, phenol, pyrogallol) of the seventeen substrates tested. The peroxidase remained stable at temperatures of up to 80 °C for 60 min and retained >50 % activity after 24 h between pH 5.0-9.0, but was most sensitive to incubation with hydrogen peroxide (H2O2; 0.01 mM), l-cysteine (0.02 mM) and ascorbate (0.05 mM) for one hour. It was significantly inhibited by all organic solvents tested (p ≤ 0.05). The Km and Vmax values of the partially purified peroxidase with the substrate 2,4-DCP were 0.95 mM and 0.12 mmol min-1, respectively. The dyes reactive blue 4, reactive black 5, and Azure B, were all decolourised to a certain extent: approximately 30 % decolourisation was observed after 24 h (1 μM dye). The peroxidase successfully catalysed coupling reactions between several phenolic monomer pairs including catechin-caffeic acid, catechin-catechol, catechin-guaiacol and guaiacol-syringaldazine under the non-optimised conditions used in this study. Genome sequencing confirmed the identity of strain BSII#1 as a S. albidoflavus strain. In addition, the genome sequence revealed the presence of one peroxidase gene that includes the twin arginine translocation signal sequence of extracellular proteins. Functional studies confirmed that the peroxidase produced by S. albidoflavus BSII#1 is part of the dye-decolourising peroxidase (DyP-type) family.
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Affiliation(s)
- Amos Musengi
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa; Biotechnology Department, Harare Institute of Technology, P. O. Box BE 277, Belvedere, Harare, Zimbabwe
| | - Kim Durrell
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Alaric Prins
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa; Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Nuraan Khan
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Mayowa Agunbiade
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa
| | - Tukayi Kudanga
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa; Department of Biotechnology and Food Technology, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Bronwyn Kirby-McCullough
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, 7535, South Africa
| | - Brett I Pletschke
- Department of Biochemistry and Microbiology, Rhodes University, PO Box 94, Makhanda (Grahamstown), 6140, South Africa
| | - Stephanie G Burton
- Vice-Principal: Research and Postgraduate Education and Department of Biochemistry, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Marilize Le Roes-Hill
- Applied Microbiology and Health Biotechnology Institute, Cape Peninsula University of Technology, PO Box 1906, Bellville, 7535, South Africa.
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Ram C, Rani P, Gebru KA, Mariam Abrha MG. Pulp and paper industry wastewater treatment: use of microbes and their enzymes. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2019-0050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractPulp and paper industry is coming under one of the most water polluting industries, and generated wastewater is highly toxic in nature. The paper mill requires huge quantity (~50–60 m3 of water to produce one ton of paper) of water, and accordingly huge quantity of chemical contaminated wastewater is discharged. The paper mill effluents have identified 240–250 chemicals in different stages of paper making. Various chemical constituents such as high chemical oxygen demand, biochemical oxygen demand, AOX, chlorinated compounds, color, suspended materials, lignin and their derivatives are released in the wastewater. The present review study is focused on the paper mill processes, wastewater generation and its effective treatment by microorganisms. The biological treatment has been identified as cost-effective and eco-friendly methods for the degradation of xenobiotic compounds for paper mill wastewater. Various studies have been performed so far to investigate the complex nature of wastewater by the application of bacteria, fungi and their enzymes at industrial scale. Therefore, the article discussed the importance of biological method as an effective technique for the degradation of paper mill wastewater.
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Affiliation(s)
- Chhotu Ram
- Department of Chemical Engineering, Adigrat University College of Engineering, Adigrat, Tigray7040, Ethiopia
| | - Pushpa Rani
- Department of Environmental Science & Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, India
| | - Kibrom Alebel Gebru
- Department of Chemical Engineering, Adigrat University College of Engineering, Adigrat, Tigray7040, Ethiopia
| | - Mebrhit G Mariam Abrha
- Department of Chemical Engineering, Adigrat University College of Engineering, Adigrat, Tigray7040, Ethiopia
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21
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Morsi R, Bilal M, Iqbal HMN, Ashraf SS. Laccases and peroxidases: The smart, greener and futuristic biocatalytic tools to mitigate recalcitrant emerging pollutants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 714:136572. [PMID: 31986384 DOI: 10.1016/j.scitotenv.2020.136572] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/05/2020] [Accepted: 01/05/2020] [Indexed: 02/08/2023]
Abstract
Various organic pollutants so-called emerging pollutants (EPs), including active residues from pharmaceuticals, pesticides, surfactants, hormones, and personal care products, are increasingly being detected in numerous environmental matrices including water. The persistence of these EPs can cause adverse ecological and human health effects even at very small concentrations in the range of micrograms per liter or lower, hence called micropollutants (MPs). The existence of EPs/MPs tends to be challenging to mitigate from the environment effectively. Unfortunately, most of them are not removed during the present-day treatment plants. So far, a range of treatment processes and degradation methods have been introduced and deployed against various EPs and/or MPs, such as ultrafiltration, nanofiltration, advanced oxidation processes (AOPs) and enzyme-based treatments coupled with membrane filtrations. To further strengthen the treatment processes and to overcome the EPs/MPs effective removal dilemma, numerous studies have revealed the applicability and notable biocatalytic potentialities of laccases and peroxidases to degrade different classes of organic pollutants. Exquisite selectivity and unique catalytic properties make these enzymes powerful biocatalytic candidates for bio-transforming an array of toxic contaminants to harmless entities. This review focuses on the use of laccases and peroxidases, such as soybean peroxidase (SBP), horseradish peroxidase (HRP), lignin peroxidase (LiP), manganese peroxidase (MnP), and chloroperoxidase (CPO) as a greener oxidation route towards efficient and effective removal or degradation of EPs/MPs.
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Affiliation(s)
- Rana Morsi
- Department of Chemistry, College of Science, UAE University, Al Ain, United Arab Emirates.
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Science, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, NL CP 64849, Mexico.
| | - S Salman Ashraf
- Department of Chemistry, College of Arts and Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.
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Functional Expression and One-Step Protein Purification of Manganese Peroxidase 1 (rMnP1) from Phanerochaete chrysosporium Using the E. coli-Expression System. Int J Mol Sci 2020; 21:ijms21020416. [PMID: 31936493 PMCID: PMC7013543 DOI: 10.3390/ijms21020416] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/14/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022] Open
Abstract
Manganese peroxidases (MnP) from the white-rot fungi Phanerochaete chrysosporium catalyse the oxidation of Mn2+ to Mn3+, a strong oxidizer able to oxidize a wide variety of organic compounds. Different approaches have been used to unravel the enzymatic properties and potential applications of MnP. However, these efforts have been hampered by the limited production of native MnP by fungi. Heterologous expression of MnP has been achieved in both eukaryotic and prokaryotic expression systems, although with limited production and many disadvantages in the process. Here we described a novel molecular approach for the expression and purification of manganese peroxidase isoform 1 (MnP1) from P. chrysosporium using an E. coli-expression system. The proposed strategy involved the codon optimization and chemical synthesis of the MnP1 gene for optimised expression in the E. coli T7 shuffle host. Recombinant MnP1 (rMnP1) was expressed as a fusion protein, which was recovered from solubilised inclusion bodies. rMnP1 was purified from the fusion protein using intein-based protein purification techniques and a one-step affinity chromatography. The designated strategy allowed production of an active enzyme able to oxidize guaiacol or Mn2+.
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Aptitude of Oxidative Enzymes for Treatment of Wastewater Pollutants: A Laccase Perspective. Molecules 2019; 24:molecules24112064. [PMID: 31151229 PMCID: PMC6600482 DOI: 10.3390/molecules24112064] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/19/2019] [Accepted: 04/27/2019] [Indexed: 01/28/2023] Open
Abstract
Natural water sources are very often contaminated by municipal wastewater discharges which contain either of xenobiotic pollutants and their sometimes more toxic degradation products, or both, which frustrates the universal millenium development goal of provision of the relatively scarce pristine freshwater to water-scarce and -stressed communities, in order to augment their socioeconomic well-being. Seeing that both regulatory measures, as regards the discharge limits of wastewater, and the query for efficient treatment methods remain unanswered, partially, the prospects of enzymatic treatment of wastewater is advisable. Therefore, a reconsideration was assigned to the possible capacity of oxidative enzymes and the respective challenges encountered during their applications in wastewater treatment, and ultimately, the prospects of laccase, a polyphenol oxidase that oxidizes aromatic and inorganic substrates with electron-donating groups in treatment aromatic contaminants of wastewater, in real wastewater situations, since it is assumed to be a vehicle for a greener community. Furthermore, the importance of laccase-driven catalysis toward maintaining mass-energy balance, hence minimizing environmental waste, was comprehensibly elucidated, as well the strategic positioning of laccase in a model wastewater treatment facility for effective treatment of wastewater contaminants.
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Bilal M, Rasheed T, Iqbal HMN, Yan Y. Peroxidases-assisted removal of environmentally-related hazardous pollutants with reference to the reaction mechanisms of industrial dyes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1-13. [PMID: 29980079 DOI: 10.1016/j.scitotenv.2018.06.274] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/07/2018] [Accepted: 06/22/2018] [Indexed: 02/05/2023]
Abstract
Environmental protection is one of the most important challenges for the humankind. Increasing number of emerging pollutants resulting from industrial/human-made activities represents a serious menace to the ecological and environmental equilibrium. Industrial dyes, endocrine disrupters, pesticides, phenols and halogenated phenols, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, and other xenobiotics are among the top priority environmental pollutants. Some classical remediation approaches including physical, chemical and biological are being employed, but are ineffective in cleaning the environment. Enzyme-catalyzed transformation reactions are gearing accelerating attention in this context as potential alternatives to classical chemical methods. Peroxidases are catalysts able to decontaminate an array of toxic compounds by a free radical mechanism resulting in oxidized or depolymerized products along with a significant toxicity reduction. Admittedly, enzymatic catalysis offers the hallmark of high chemo-, regio-, and enantioselectivity and superior catalytic efficiency under given reaction environment. Moreover, enzymes are considered more benign, socially acceptable and greener production routes since derived from the renewable and sustainable feedstock. Regardless of their versatility and potential use in environmental processes, several limitations, such as heterologous production, catalytic stability, and redox potential should be overcome to implement peroxidases at large-scale transformation and bio-elimination of recalcitrant pollutants. In this article, a critical review of the transformation of different types of hazardous pollutants by peroxidases, with special reference to the proposed reaction mechanisms of several dyes is presented. Following that major challenges for industrial and environmental applications of peroxidases are also discussed. Towards the end, the information is also given on miscellaneous applications of peroxidases, concluding remarks and outlook.
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Affiliation(s)
- Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Tahir Rasheed
- The School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, NL CP 64849, Mexico.
| | - Yunjun Yan
- Key Lab of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, China.
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Pourfakhraei E, Badraghi J, Mamashli F, Nazari M, Saboury AA. Biodegradation of asphaltene and petroleum compounds by a highly potent Daedaleopsis sp. J Basic Microbiol 2018; 58:609-622. [PMID: 29775208 DOI: 10.1002/jobm.201800080] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/15/2018] [Accepted: 04/22/2018] [Indexed: 11/11/2022]
Abstract
Petroleum, as the major energy source, is indispensable from our lives. Presence of compounds resistant to degradation can pose risks for human health and environment. Basidiomycetes have been considered as powerful candidates in biodegradation of petroleum compounds via secreting ligninolytic enzymes. In this study a wood-decaying fungus was isolated by significant degradation ability that was identified as Daedaleopsis sp. by morphological and molecular identification methods. According to GC/MS studies, incubation of heavy crude oil with Daedaleopsis sp. resulted in increased amounts of <C24 hydrocarbons and decreased amounts of >C24 compounds. Degradation of asphaltene, anthracene, and dibenzofuran by the identified fungal strain was determined to evaluate its potential in biodegradation. After 14 days of incubation, Daedaleopsis sp. could degrade 93.7% and 91.2% of anthracene and dibenzofuran, respectively, in pH 5 and 40 °C in optimized medium, as revealed by GC/FID. Notably, analysis of saturates, aromatics, resins, and asphaltenes showed a reduction of 88.7% and 38% in asphaletene and aromatic fractions. Laccase, lignin peroxidase, and manganese peroxidase activities were enhanced from 51.3, 145.2, 214.5 U ml-1 in the absence to 121.5, 231.4, and 352.5 U ml-1 in the presence of heavy crude oil, respectively. This is the first report that Daedaleopsis sp. can degrade asphaltene and dibenzofuran. Moreover, compared to the reported results of asphaltene biodegradation, this strain was the most successful. Thus, Daedaleopsis sp. could be a promising candidate for biotransformation of heavy crude oil and biodegradation of recalcitrant toxic compounds.
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Affiliation(s)
- Elaheh Pourfakhraei
- Research Institute of Applied Sciences, Academic Center of Education, Culture and Research (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Jalil Badraghi
- Research Institute of Applied Sciences, Academic Center of Education, Culture and Research (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Fatemeh Mamashli
- Research Institute of Applied Sciences, Academic Center of Education, Culture and Research (ACECR), Shahid Beheshti University, Tehran, Iran
| | - Mahboobeh Nazari
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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Mogilnaya O, Ronzhin N, Artemenko K, Bondar V. Nanodiamonds as an effective adsorbent for immobilization of extracellular peroxidases from luminous fungus Neonothopanus nambi to construct a phenol detection system. BIOCATAL BIOTRANSFOR 2018. [DOI: 10.1080/10242422.2018.1472586] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Olga Mogilnaya
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
| | - Nikita Ronzhin
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
| | - Karina Artemenko
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
| | - Vladimir Bondar
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
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Chiu PC, Li YJ, Chiou RYY. Peroxidase characterization isolated from germinated peanut embryos (GPE) and application of the freeze-dried GPE powder as enzyme source for biomimetic production of δ-viniferin. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Raveendran S, Parameswaran B, Ummalyma SB, Abraham A, Mathew AK, Madhavan A, Rebello S, Pandey A. Applications of Microbial Enzymes in Food Industry. Food Technol Biotechnol 2018; 56:16-30. [PMID: 29795993 DOI: 10.17113/ftb.56.01.18.5491] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The use of enzymes or microorganisms in food preparations is an age-old process. With the advancement of technology, novel enzymes with wide range of applications and specificity have been developed and new application areas are still being explored. Microorganisms such as bacteria, yeast and fungi and their enzymes are widely used in several food preparations for improving the taste and texture and they offer huge economic benefits to industries. Microbial enzymes are the preferred source to plants or animals due to several advantages such as easy, cost-effective and consistent production. The present review discusses the recent advancement in enzyme technology for food industries. A comprehensive list of enzymes used in food processing, the microbial source of these enzymes and the wide range of their application are discussed.
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Affiliation(s)
- Sindhu Raveendran
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Binod Parameswaran
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Sabeela Beevi Ummalyma
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India.,Institute of Bioresources and Sustainable Development, 795001 Imphal, India
| | - Amith Abraham
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | - Anil Kuruvilla Mathew
- Centre for Biofuels, National Institute for Interdisciplinary Science and Technology, CSIR, 695019 Trivandrum, India
| | | | - Sharrel Rebello
- Communicable Disease Research Laboratory, St. Joseph's College, 680121 Irinjalakuda, India
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research (CSIR-IITR), 226001 Lucknow, India
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Wasak A, Drozd R, Struk Ł, Grygorcewicz B. Entrapment of DyP-type peroxidase from Pseudomonas fluorescens Pf-5 into Ca-alginate magnetic beads. Biotechnol Appl Biochem 2017; 65:238-245. [PMID: 28326617 DOI: 10.1002/bab.1562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/15/2017] [Indexed: 11/10/2022]
Abstract
The aim of this study was to investigate the optimal conditions for the immobilization and stabilization of DyP1B dye decolorizing peroxidases type B (DyP1B) from Pseudomonas fluorescens Pf-5 immobilized in Ca-alginate ferromagnetic beads. The immobilized DyP1B was used in the degradation of the Reactive Blue 5 (RB5) synthetic dye. The enzyme was successfully entrapped in a Ca-alginate matrix and showed an encapsulation efficiency of 94%. The concentration of DyP1B (0.8 mg mL-1 ), 2% of alginate and magnetite (10.0 mg mL-1 ) was optimal for immobilization. The immobilized DyP1B showed optimum activity at pH 7.0 and 40 °C compared with pH 5.5 and 30 °C for free peroxidase. Reusability studies showed that after five cycles, the immobilized DyP1B system retained more than 58% of its initial activity. The immobilized DyP1B was able to decolorize RB5 at concentrations of 0.1, 0.05, and 0.01% (w v-1 ) with efficiency rates of about 20, 29, and 45%, respectively. The immobilization of DyP1B in alginate beads with the addition of Fe3 O4 increased its catalytic and applicative potential.
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Affiliation(s)
- Agata Wasak
- Department of Immunology, Microbiology and Physiological Chemistry, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology, Szczecin, Poland
| | - Radosław Drozd
- Department of Immunology, Microbiology and Physiological Chemistry, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology, Szczecin, Poland
| | - Łukasz Struk
- Department of Organic and Physical Chemistry, Faculty of Chemical Technology and Engineering, West Pomeranian University of Technology, Szczecin, Poland
| | - Bartłomiej Grygorcewicz
- Department of Immunology, Microbiology and Physiological Chemistry, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology, Szczecin, Poland
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Casciello C, Tonin F, Berini F, Fasoli E, Marinelli F, Pollegioni L, Rosini E. A valuable peroxidase activity from the novel species Nonomuraea gerenzanensis growing on alkali lignin. ACTA ACUST UNITED AC 2017; 13:49-57. [PMID: 28352563 PMCID: PMC5361131 DOI: 10.1016/j.btre.2016.12.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/07/2016] [Accepted: 12/21/2016] [Indexed: 11/22/2022]
Abstract
Actinomycetes represent an attractive source of ligninolytic enzymes. 43 actinomycetes were screened for laccase and peroxidase activities. The novel species N. gerenzanensis produces a valuable bacterial peroxidase activity. The dye-decolorizing activity paves the way for an industrial use of this peroxidase.
Degradation of lignin constitutes a key step in processing biomass to become useful monomers but it remains challenging. Compared to fungi, bacteria are much less characterized with respect to their lignin metabolism, although it is reported that many soil bacteria, especially actinomycetes, attack and solubilize lignin. In this work, we screened 43 filamentous actinomycetes by assaying their activity on chemically different substrates including a soluble and semi-degraded lignin derivative (known as alkali lignin or Kraft lignin), and we discovered a novel and valuable peroxidase activity produced by the recently classified actinomycete Nonomuraea gerenzanensis. Compared to known fungal manganese and versatile peroxidases, the stability of N. gerenzanensis peroxidase activity at alkaline pHs and its thermostability are significantly higher. From a kinetic point of view, N. gerenzanensis peroxidase activity shows a Km for H2O2 similar to that of Phanerochaete chrysosporium and Bjerkandera enzymes and a lower affinity for Mn2+, whereas it differs from the six Pleurotus ostreatus manganese peroxidase isoenzymes described in the literature. Additionally, N. gerenzanensis peroxidase shows a remarkable dye-decolorizing activity that expands its substrate range and paves the way for an industrial use of this enzyme. These results confirm that by exploring new bacterial diversity, we may be able to discover and exploit alternative biological tools putatively involved in lignin modification and degradation.
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Key Words
- 2,4-DCP, 2,4-dichlorophenol
- 2,6-DMP, 2,6-dimethoxyphenol
- ABTS, 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid)
- Alkali lignin
- DyP, dye decolorizing peroxidase
- Filamentous actinomycetes
- Kraft lignin
- LiP, lignin peroxidase
- MAM, mannitol agar medium
- MM-L, minimal salt medium plus lignin
- MnP, manganese peroxidase
- Nonomuraea gerenzanensis
- Peroxidases
- RB5, reactive black 5
- RBBR, remazol brilliant blue R
- VP, versatile peroxidase
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Affiliation(s)
- Carmine Casciello
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Fabio Tonin
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Elisa Fasoli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico of Milano, via Mancinelli 7, 20131, Milano, Italy
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy; The Protein Factory Research Center, Politecnico of Milano and University of Insubria, via Mancinelli 7, 20131 Milano, Italy
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Zafra G, Taylor TD, Absalón AE, Cortés-Espinosa DV. Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium. JOURNAL OF HAZARDOUS MATERIALS 2016; 318:702-710. [PMID: 27484946 DOI: 10.1016/j.jhazmat.2016.07.060] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/29/2016] [Accepted: 07/25/2016] [Indexed: 05/02/2023]
Abstract
In this study, we used a taxonomic and functional metagenomic approach to analyze some of the effects (e.g. displacement, permanence, disappearance) produced between native microbiota and a previously constructed Polycyclic Aromatic Hydrocarbon (PAH)-degrading microbial consortium during the bioremediation process of a soil polluted with PAHs. Bioaugmentation with a fungal-bacterial consortium and biostimulation of native microbiota using corn stover as texturizer produced appreciable changes in the microbial diversity of polluted soils, shifting native microbial communities in favor of degrading specific populations. Functional metagenomics showed changes in gene abundance suggesting a bias towards aromatic hydrocarbon and intermediary degradation pathways, which greatly favored PAH mineralization. In contrast, pathways favoring the formation of toxic intermediates such as cytochrome P450-mediated reactions were found to be significantly reduced in bioaugmented soils. PAH biodegradation in soil using the microbial consortium was faster and reached higher degradation values (84% after 30 d) as a result of an increased co-metabolic degradation when compared with other mixed microbial consortia. The main differences between inoculated and non-inoculated soils were observed in aromatic ring-hydroxylating dioxygenases, laccase, protocatechuate, salicylate and benzoate-degrading enzyme genes. Based on our results, we propose that several concurrent metabolic pathways are taking place in soils during PAH degradation.
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Affiliation(s)
- German Zafra
- Instituto Politécnico Nacional, CIBA-Tlaxcala, Carretera Estatal San Inés Tecuexcomac-Tepetitla Km 1.5, Tepetitla, Tlaxcala. 90700, Mexico
| | - Todd D Taylor
- RIKEN Center for Integrative Medical Sciences, Laboratory for Integrated Bioinformatics, Tsurumi-ku 230-0045, Yokohama, Kanagawa, Japan
| | - Angel E Absalón
- Instituto Politécnico Nacional, CIBA-Tlaxcala, Carretera Estatal San Inés Tecuexcomac-Tepetitla Km 1.5, Tepetitla, Tlaxcala. 90700, Mexico.
| | - Diana V Cortés-Espinosa
- Instituto Politécnico Nacional, CIBA-Tlaxcala, Carretera Estatal San Inés Tecuexcomac-Tepetitla Km 1.5, Tepetitla, Tlaxcala. 90700, Mexico.
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Oszajca M, Brindell M, Orzeł Ł, Dąbrowski JM, Śpiewak K, Łabuz P, Pacia M, Stochel-Gaudyn A, Macyk W, van Eldik R, Stochel G. Mechanistic studies on versatile metal-assisted hydrogen peroxide activation processes for biomedical and environmental incentives. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.05.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Wang Q, Gong J, Chisti Y, Sirisansaneeyakul S. Production of theabrownins using a crude fungal enzyme concentrate. J Biotechnol 2016; 231:250-259. [DOI: 10.1016/j.jbiotec.2016.06.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 11/16/2022]
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Ngo ACR, Devanadera MKP, Dedeles GR. Decolorization of Selected Synthetic Textile Dyes by Yeasts from Leaves and Fruit Peels. J Health Pollut 2016; 6:42-55. [PMID: 30524784 PMCID: PMC6236547 DOI: 10.5696/2156-9614-6-10.42] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND Discharge of textile dyes into the environment poses a significant threat. They are poorly biodegradable and toxic due to their complex composition and aromatic structures. In the search for alternatives to physical and chemical treatments, biodegradation of synthetic dyes by various microbes is emerging as an effective and promising approach. OBJECTIVES The decolorization of synthetic dyes by yeast co-cultures and consortia from leaves and fruit peels was assessed at a 50 μg/mL dye concentration. METHODS Yeasts isolates from leaves and fruit peels were screened for potential decolorization of synthetic dyes at 25-50 μg/mL. Decolorization parameters were optimized for synergistic properties and development of yeast co-cultures and consortium. Possible decolorization reactions were initially assessed by cell immobilization, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and Fourier transform infrared spectroscopy (FTIR) analysis. RESULTS A total of 16 organisms were isolated from rose, mango, and pineapple leaves and pineapple fruit peels. Only 4 organisms showed high decolorization of four synthetic dyes: Direct Pink B, Disperse Yellow 5G, Direct Fast Orange S, and Reactive Turquoise Blue G. The optimum condition for best decolorizers of selected dyes at 50 μg/mL were Candida guilliermondii (Y011) for Direct Pink B at pH 9, 37°C; C. dubliniensis (Y014) for Disperse Yellow 5G at pH 4, 25°C; C. guilliermondii (Y004) for Direct Fast Orange S at pH 7, 25°C, and C. famata (Y003) for Reactive Turquoise Blue G at pH 4, 35°C. None of the 4 yeast isolates showed any antagonistic activity when subjected to the lawn-spotting method for the formation of co-cultures and consortium. The best co-cultures obtained 61% decolorization of Direct Pink B, 65% decolorization of Disperse Yellow 5G, 41% decolorization of Direct Fast Orange S, and 50-51% decolorization of Reactive Turquoise Blue G. Immobilized yeast cells were active in decolorizing the dyes and SDS-PAGE analysis confirmed the presence of an extracellular protein. The results of FTIR also showed changes in the functional group of Direct Pink B, but minimal changes in the functional groups of Reactive Turquoise Blue G, indicating a different decolorization pathway. CONCLUSIONS Yeasts in co-cultures and consortia can decolorize toxic synthetic dyes through different decolorization pathways such as enzyme degradation and bioaccumulation. This technique may have a use in the treatment of wastewater systems.
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Affiliation(s)
- Anna Christina R. Ngo
- The Graduate School, University of Santo Tomas
- Research Center for the Natural and Applied Sciences, University of Santo Tomas
| | - Mark Kevin P. Devanadera
- The Graduate School, University of Santo Tomas
- Research Center for the Natural and Applied Sciences, University of Santo Tomas
| | - Gina R. Dedeles
- The Graduate School, University of Santo Tomas
- Research Center for the Natural and Applied Sciences, University of Santo Tomas
- Department of Biological Sciences, College of Science, University of Santo Tomas, España, Manila, 1015 Philippines
- Corresponding Author: Gina Rio Dedeles, Laboratory of Pure and Applied Microbiology, Research Center for the Natural and Applied Sciences, Thomas Aquinas Research Complex University of Santo Tomas, Manila, 1008 Philippines, Tel. +63-(2)-4061611 loc. 8297,
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36
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Comparative analysis of lignin peroxidase and manganese peroxidase activity on coniferous and deciduous wood using ToF-SIMS. Appl Microbiol Biotechnol 2016; 100:8013-20. [DOI: 10.1007/s00253-016-7560-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/10/2016] [Accepted: 04/16/2016] [Indexed: 11/30/2022]
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37
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Homologous and Heterologous Expression of Basidiomycete Genes Related to Plant Biomass Degradation. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mogil’naya OA, Ronzhin NO, Medvedeva SE, Bondar’ VS. Total peroxidase and catalase activity of luminous basidiomycetes Armillaria borealis and Neonothopanus nambi in comparison with the level of light emission. APPL BIOCHEM MICRO+ 2015. [DOI: 10.1134/s0003683815040110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Sherwood P, Villari C, Capretti P, Bonello P. Mechanisms of induced susceptibility to Diplodia tip blight in drought-stressed Austrian pine. TREE PHYSIOLOGY 2015; 35:549-62. [PMID: 25900028 DOI: 10.1093/treephys/tpv026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/08/2015] [Indexed: 05/11/2023]
Abstract
Plants experiencing drought stress are frequently more susceptible to pathogens, likely via alterations in physiology that create favorable conditions for pathogens. Common plant responses to drought include the production of reactive oxygen species (ROS) and the accumulation of free amino acids (AAs), particularly proline. These same phenomena also frequently occur during pathogenic attack. Therefore, drought-induced perturbations in AA and ROS metabolism could potentially contribute to the observed enhanced susceptibility. Furthermore, nitrogen (N) availability can influence AA accumulation and affect plant resistance, but its contributions to drought-induced susceptibility are largely unexplored. Here we show that drought induces accumulation of hydrogen peroxide (H2O2) in Austrian pine (Pinus nigra Arnold) shoots, but that shoot infection by the blight and canker pathogen Diplodia sapinea (Fr.) Fuckel leads to large reductions in H2O2 levels in droughted plants. In in vitro assays, H2O2 was toxic to D. sapinea, and the fungus responded to this oxidative stress by increasing catalase and peroxidase activities, resulting in substantial H2O2 degradation. Proline increased in response to drought and infection when examined independently, but unlike all other AAs, proline further increased in infected shoots of droughted trees. In the same tissues, the proline precursor, glutamate, decreased significantly. Proline was found to protect D. sapinea from H2O2 damage, while also serving as a preferred N source in vitro. Fertilization increased constitutive and drought-induced levels of some AAs, but did not affect plant resistance. A new model integrating interactions of proline and H2O2 metabolism with drought and fungal infection of plants is proposed.
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Affiliation(s)
- Patrick Sherwood
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210 , USA
| | - Caterina Villari
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210 , USA
| | - Paolo Capretti
- Dipartimento di Scienze Produzioni Agroalimentari e dell'Ambiente, Università degli Studi di Firenze, Firenze 50144, Italy
| | - Pierluigi Bonello
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210 , USA
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Gautério G, Fernandes S, Molon F, Figueira F, Buffon J, Kalil S. Purification of Peroxidase from Rice Bran Using Expanded-Bed Ion-Exchange Chromatography. ADSORPT SCI TECHNOL 2015. [DOI: 10.1260/0263-6174.33.2.153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- G.V. Gautério
- Food and Chemistry School, Campus Carreiros, Federal University of Rio Grande, Avenida Itália km 8 s/n, Rio Grande (RS), CEP 96203-900, Brazil
| | - S.S. Fernandes
- Food and Chemistry School, Campus Carreiros, Federal University of Rio Grande, Avenida Itália km 8 s/n, Rio Grande (RS), CEP 96203-900, Brazil
| | - F.O. Molon
- Food and Chemistry School, Campus Carreiros, Federal University of Rio Grande, Avenida Itália km 8 s/n, Rio Grande (RS), CEP 96203-900, Brazil
| | - F.S. Figueira
- Food and Chemistry School, Campus Carreiros, Federal University of Rio Grande, Avenida Itália km 8 s/n, Rio Grande (RS), CEP 96203-900, Brazil
| | - J.G. Buffon
- Food and Chemistry School, Campus Carreiros, Federal University of Rio Grande, Avenida Itália km 8 s/n, Rio Grande (RS), CEP 96203-900, Brazil
| | - S.J. Kalil
- Food and Chemistry School, Campus Carreiros, Federal University of Rio Grande, Avenida Itália km 8 s/n, Rio Grande (RS), CEP 96203-900, Brazil
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42
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Sheridan KJ, Dolan SK, Doyle S. Endogenous cross-talk of fungal metabolites. Front Microbiol 2015; 5:732. [PMID: 25601857 PMCID: PMC4283610 DOI: 10.3389/fmicb.2014.00732] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/04/2014] [Indexed: 12/21/2022] Open
Abstract
Non-ribosomal peptide (NRP) synthesis in fungi requires a ready supply of proteogenic and non-proteogenic amino acids which are subsequently incorporated into the nascent NRP via a thiotemplate mechanism catalyzed by NRP synthetases. Substrate amino acids can be modified prior to or during incorporation into the NRP, or following incorporation into an early stage amino acid-containing biosynthetic intermediate. These post-incorporation modifications involve a range of additional enzymatic activities including but not exclusively, monooxygenases, methyltransferases, epimerases, oxidoreductases, and glutathione S-transferases which are essential to effect biosynthesis of the final NRP. Likewise, polyketide biosynthesis is directly by polyketide synthase megaenzymes and cluster-encoded ancillary decorating enzymes. Additionally, a suite of additional primary metabolites, for example: coenzyme A (CoA), acetyl CoA, S-adenosylmethionine, glutathione (GSH), NADPH, malonyl CoA, and molecular oxygen, amongst others are required for NRP and polyketide synthesis (PKS). Clearly these processes must involve exquisite orchestration to facilitate the simultaneous biosynthesis of different types of NRPs, polyketides, and related metabolites requiring identical or similar biosynthetic precursors or co-factors. Moreover, the near identical structures of many natural products within a given family (e.g., ergot alkaloids), along with localization to similar regions within fungi (e.g., conidia) suggests that cross-talk may exist, in terms of biosynthesis and functionality. Finally, we speculate if certain biosynthetic steps involved in NRP and PKS play a role in cellular protection or environmental adaptation, and wonder if these enzymatic reactions are of equivalent importance to the actual biosynthesis of the final metabolite.
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Affiliation(s)
| | - Stephen K Dolan
- Department of Biology, Maynooth University Maynooth, Ireland
| | - Sean Doyle
- Department of Biology, Maynooth University Maynooth, Ireland
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van Kuijk S, Sonnenberg A, Baars J, Hendriks W, Cone J. Fungal treated lignocellulosic biomass as ruminant feed ingredient: A review. Biotechnol Adv 2015; 33:191-202. [DOI: 10.1016/j.biotechadv.2014.10.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 09/23/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
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Zelena K, Eisele N, Berger RG. Escherichia coli as a production host for novel enzymes from basidiomycota. Biotechnol Adv 2014; 32:1382-95. [DOI: 10.1016/j.biotechadv.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/14/2014] [Accepted: 08/25/2014] [Indexed: 01/14/2023]
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45
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Microbial enzyme systems for lignin degradation and their transcriptional regulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1336-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Zhou LW, Wei YL, Dai YC. Phylogenetic analysis of ligninolytic peroxidases: preliminary insights into the alternation of white-rot and brown-rot fungi in their lineage. Mycology 2014; 5:29-42. [PMID: 24772372 PMCID: PMC3979444 DOI: 10.1080/21501203.2014.895784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 02/14/2014] [Indexed: 11/04/2022] Open
Abstract
White-rot and brown-rot fungi employ different mechanisms to degrade lignocellulose. These fungi are not monophyletic and even alternate in their common lineage. To explore the reason for this, seventy-six ligninolytic peroxidases (LPs), including 14 sequences newly identified from available basidiomycetous whole-genome and EST databases in this study, were utilized for phylogenetic and selective pressure analyses. We demonstrate that LPs were subjected to the mixed process of concerted and birth-and-death evolution. After the duplication events of original LPs, various LP types may originate from mutation events of several key residues driven by positive selection, which may change LP types and even rot types in a small fraction of wood-decaying fungi. Our findings provide preliminary insights into the cause for the alternation of the two fungal rot types within the same lineage.
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Affiliation(s)
- Li-Wei Zhou
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China
| | - Yu-Lian Wei
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China
| | - Yu-Cheng Dai
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China
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Balasubramanian M, Boopathy R. Purification and characterization of peroxidases from liquid endosperm of Cocos nucifera (L.): Biotransformation. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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48
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Si J, Cui BK. A new fungal peroxidase with alkaline-tolerant, chloride-enhancing activity and dye decolorization capacity. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Affiliation(s)
- Étienne Delannoy
- Unité “Résistance des plantes”, IRD (Institut de recherche pour le développement), UMR DGPC, 911 avenue Agropolis, B.P. 64501, F-34394, Montpellier cedex
| | - Philippe Marmey
- Unité “Résistance des plantes”, IRD (Institut de recherche pour le développement), UMR DGPC, 911 avenue Agropolis, B.P. 64501, F-34394, Montpellier cedex
| | - Claude Penel
- Laboratoire de Physiologie végétale, Université de Genève, Quai Ernest-Ansermet 30, CH-1211, Genève 4
| | - Michel Nicole
- Unité “Résistance des plantes”, IRD (Institut de recherche pour le développement), UMR DGPC, 911 avenue Agropolis, B.P. 64501, F-34394, Montpellier cedex
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50
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Singh R, Grigg JC, Qin W, Kadla JF, Murphy MEP, Eltis LD. Improved manganese-oxidizing activity of DypB, a peroxidase from a lignolytic bacterium. ACS Chem Biol 2013; 8:700-6. [PMID: 23305326 DOI: 10.1021/cb300608x] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DypB, a dye-decolorizing peroxidase from the lignolytic soil bacterium Rhodococcus jostii RHA1, catalyzes the peroxide-dependent oxidation of divalent manganese (Mn(2+)), albeit less efficiently than fungal manganese peroxidases. Substitution of Asn246, a distal heme residue, with alanine increased the enzyme's apparent k(cat) and k(cat)/K(m) values for Mn(2+) by 80- and 15-fold, respectively. A 2.2 Å resolution X-ray crystal structure of the N246A variant revealed the Mn(2+) to be bound within a pocket of acidic residues at the heme edge, reminiscent of the binding site in fungal manganese peroxidase and very different from that of another bacterial Mn(2+)-oxidizing peroxidase. The first coordination sphere was entirely composed of solvent, consistent with the variant's high K(m) for Mn(2+) (17 ± 2 mM). N246A catalyzed the manganese-dependent transformation of hard wood kraft lignin and its solvent-extracted fractions. Two of the major degradation products were identified as 2,6-dimethoxybenzoquinone and 4-hydroxy-3,5-dimethoxybenzaldehyde, respectively. These results highlight the potential of bacterial enzymes as biocatalysts to transform lignin.
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Affiliation(s)
- Rahul Singh
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Jason C. Grigg
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Wei Qin
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - John F. Kadla
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Michael E. P. Murphy
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
| | - Lindsay D. Eltis
- Department
of Microbiology and Immunology and ‡Advanced Biomaterials Chemistry Laboratory, University of British Columbia, Vancouver,
British Columbia, Canada
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