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Liberato MV, Paixao DAA, Tomazetto G, Ndeh D, Bolam DN, Squina FM. Discovery, structural characterization, and functional insights into a novel apiosidase from the GH140 family, isolated from a lignocellulolytic-enriched mangrove microbial community. Biotechnol Lett 2024; 46:201-211. [PMID: 38280177 DOI: 10.1007/s10529-023-03460-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/29/2024]
Abstract
OBJECTIVES Apiosidases are enzymes that cleave the glycosidic bond between the monosaccharides linked to apiose, a branched chain furanose found in the cell walls of vascular plants and aquatic monocots. There is biotechnological interest in this enzyme group because apiose is the flavor-active compound of grapes, fruit juice, and wine, and the monosaccharide is found to be a plant secondary metabolite with pharmaceutical properties. However, functional and structural studies of this enzyme family are scarce. Recently, a glycoside hydrolase family member GH140 was isolated from Bacteroides thetaiotaomicron and identified as an endo-apiosidase. RESULTS The structural characterization and functional identification of a second GH140 family enzyme, termed MmApi, discovered through mangrove soil metagenomic approach, are described. Among the various substrates tested, MmApi exhibited activity on an apiose-containing oligosaccharide derived from the pectic polysaccharide rhamnogalacturonan-II. While the crystallographic model of MmApi was similar to the endo-apiosidase from Bacteroides thetaiotaomicron, differences in the shape of the binding sites indicated that MmApi could cleave apioses within oligosaccharides of different compositions. CONCLUSION This enzyme represents a novel tool for researchers interested in studying the physiology and structure of plant cell walls and developing biocatalytic strategies for drug and flavor production.
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Affiliation(s)
- Marcelo Vizona Liberato
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, England
| | - Douglas Antonio Alvaredo Paixao
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Geizecler Tomazetto
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, United States
| | - Didier Ndeh
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, Scotland
| | - David N Bolam
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, England
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil.
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2
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Tramontina R, Ciancaglini I, Roman EKB, Chacón MG, Corrêa TLR, Dixon N, Bugg TDH, Squina FM. Sustainable biosynthetic pathways to value-added bioproducts from hydroxycinnamic acids. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12571-8. [PMID: 37212882 DOI: 10.1007/s00253-023-12571-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 05/23/2023]
Abstract
The biorefinery concept, in which biomass is utilized for the production of fuels and chemicals, emerges as an eco-friendly, cost-effective, and renewable alternative to petrochemical-based production. The hydroxycinnamic acid fraction of lignocellulosic biomass represents an untapped source of aromatic molecules that can be converted to numerous high-value products with industrial applications, including in the flavor and fragrance sector and pharmaceuticals. This review describes several biochemical pathways useful in the development of a biorefinery concept based on the biocatalytic conversion of the hydroxycinnamic acids ferulic, caffeic, and p-coumaric acid into high-value molecules. KEY POINTS: • The phenylpropanoids bioconversion pathways in the context of biorefineries • Description of pathways from hydroxycinnamic acids to high-value compounds • Metabolic engineering and synthetic biology advance hydroxycinnamic acid-based biorefineries.
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Affiliation(s)
- Robson Tramontina
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Programa de Processos Tecnológicos E Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil
| | - Iara Ciancaglini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Ellen K B Roman
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Micaela G Chacón
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Thamy L R Corrêa
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Neil Dixon
- Manchester Institute of Biotechnology (MIB), Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos E Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil.
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3
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Structural and functional insights of the catalytic GH5 and Calx-β domains from the metagenome-derived endoglucanase CelE2. Enzyme Microb Technol 2023; 165:110206. [PMID: 36758494 DOI: 10.1016/j.enzmictec.2023.110206] [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: 11/16/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 01/29/2023]
Abstract
Cellulose is the most abundant natural polymer on Earth, representing an attractive feedstock for bioproducts and biofuel production. Cellulases promote the depolymerization of cellulose, generating short oligosaccharides and glucose, which are useful in biotechnological applications. Among the classical cellulases, those from glycoside hydrolase family 5 (GH5) are one of the most abundant in Nature, displaying several modular architectures with other accessory domains attached to its catalytic core, such as carbohydrate-binding modules (CBMs), Ig-like, FN3-like, and Calx-β domains, which can influence the enzyme activity. The metagenome-derived endoglucanase CelE2 has in its modular architecture an N-terminal domain belonging to the GH5 family and a C-terminal domain with a high identity to the Calx-β domain. In this study, the GH5 and the Calx-β domains were subcloned and heterologously expressed in E. coli, to evaluate the structural and functional properties of the individualized domains of CelE2. Thermostability analysis by circular dichroism (CD) revealed a decrease in the denaturation temperature values around 4.6 °C for the catalytic domain (CelE21-381) compared to CelE2 full-length. The CD analyses revealed that the Calx-β domain (CelE2382-477) was unfolded, suggesting that this domain requires to be attached to the catalytic core to become structurally stable. The three-dimensional structure of the catalytic domain CelE21-381 was determined at 2.1 Å resolution, showing a typical (α/β)8-barrel fold and a narrow active site compared to other cellulases from the same family. The biochemical characterization showed that the deletion of the Calx-β domain increased more than 3-fold the activity of the catalytic domain CelE21-381 towards the insoluble substrate Avicel. The main functional properties of CelE2, such as substrate specificity, optimal pH and temperature, thermal stability, and activation by CaCl2, were not altered after the deletion of the accessory domain. Furthermore, the Small Angle X-ray Scattering (SAXS) analyses showed that the addition of CaCl2 was beneficial CelE21-381 protein solvency. This work contributed to fundamental concepts about the structure and function of cellulases, which are useful in applications involving lignocellulosic materials degradation into food and feedstuffs and biofuel production.
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4
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Chen J, Hao X, Chi Y, Ma L. Metabolic regulation mechanism of Trametes gibbosa CB_1 on lignin. Int J Biol Macromol 2023; 240:124189. [PMID: 36990410 DOI: 10.1016/j.ijbiomac.2023.124189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
White rot fungi can degrade lignin and play a significant role in the recycling of carbon resources for environmental protection. Trametes gibbosa is the main white rot fungus in Northeast China. The main acids produced by T. gibbosa degradation, include long-chain fatty acids, lactic acid, succinic acid, and some small molecular compounds for example benzaldehyde. A variety of proteins respond to lignin stress and play an important role in xenobiotics metabolism, metal ion transport, and redox. Coordinated regulation and detoxification activation of H2O2 produced in oxidative stress by peroxidase coenzyme system and Fenton reaction. The Dioxygenase cleavage pathway and β-ketoadipic acid pathway are the main oxidation pathways of lignin degradation, which mediate the entry of "COA" into the TCA cycle. In the joint action of hydrolase and coenzyme, cellulose, hemicellulose, and other polysaccharides are degraded and finally converted to glucose to participate in energy metabolism. The expression of the laccase (Lcc_1) protein was verified by E. coli. Also, the Lcc_1 overexpression mutant was established. The morphology of mycelium was dense and the lignin degradation rate was improved. We completed the first non-directional mutation of in T. gibbosa. It also improved the mechanism of T. gibbosa in response to lignin stress.
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Mahajan R, Hudson BS, Sharma D, Kolte V, Sharma G, Goel G. Transcriptome Analysis of Podoscypha petalodes Strain GGF6 Reveals the Diversity of Proteins Involved in Lignocellulose Degradation and Ligninolytic Function. Indian J Microbiol 2022; 62:569-582. [PMID: 36458217 PMCID: PMC9705691 DOI: 10.1007/s12088-022-01037-6] [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: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 11/05/2022] Open
Abstract
The present study reports transcriptomic profiling of a Basidiomycota fungus, Podoscypha petalodes strain GGF6 belonging to the family Podoscyphaceae, isolated from the North-Western Himalayan ranges in Himachal Pradesh, India. Podoscypha petalodes strain GGF6 possesses significant biotechnological potential as it has been reported for endocellulase, laccase, and other lignocellulolytic enzymes under submerged fermentation conditions. The present study attempts to enhance our knowledge of its lignocellulolytic potential as no previous omics-based analysis is available for this white-rot fungus. The transcriptomic analysis of P. petalodes GGF6 reveals the presence of 280 CAZy proteins. Furthermore, bioprospecting transcriptome signatures in the fungi revealed a diverse array of proteins associated with cellulose, hemicellulose, pectin, and lignin degradation. Interestingly, two copper-dependent lytic polysaccharide monooxygenases (AA14) and one pyrroloquinolinequinone-dependent oxidoreductase (AA12) were also identified, which are known to help in the lignocellulosic plant biomass degradation. Overall, this transcriptome profiling-based study provides deeper molecular-level insights into this Basidiomycota fungi, P. petalodes, for its potential application in diverse biotechnological applications, not only in the biofuel industry but also in the environmental biodegradation of recalcitrant molecules. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-022-01037-6.
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Affiliation(s)
- Rishi Mahajan
- Department of Microbiology, College of Basic Sciences, CSK Himachal Pradesh Krishi Vishvavidyalaya, Palampur, 176062 India
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234 India
| | - B. Shenu Hudson
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka India
| | - Deepak Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234 India
| | - Vaishnavi Kolte
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka India
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, Karnataka India
| | - Gunjan Goel
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, 173234 India
- Department of Microbiology, School of Interdisciplinary and Applied Sciences (SIAS), Central University of Haryana, Mahendergarh, Haryana India
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6
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Franco Cairo JPL, Mandelli F, Tramontina R, Cannella D, Paradisi A, Ciano L, Ferreira MR, Liberato MV, Brenelli LB, Gonçalves TA, Rodrigues GN, Alvarez TM, Mofatto LS, Carazzolle MF, Pradella JGC, Paes Leme AF, Costa-Leonardo AM, Oliveira-Neto M, Damasio A, Davies GJ, Felby C, Walton PH, Squina FM. Oxidative cleavage of polysaccharides by a termite-derived superoxide dismutase boosts the degradation of biomass by glycoside hydrolases. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2022; 24:4845-4858. [PMID: 35813357 PMCID: PMC9208272 DOI: 10.1039/d1gc04519a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/07/2022] [Indexed: 05/31/2023]
Abstract
Wood-feeding termites effectively degrade plant biomass through enzymatic degradation. Despite their high efficiencies, however, individual glycoside hydrolases isolated from termites and their symbionts exhibit anomalously low effectiveness in lignocellulose degradation, suggesting hereto unknown enzymatic activities in their digestome. Herein, we demonstrate that an ancient redox-active enzyme encoded by the lower termite Coptotermes gestroi, a Cu/Zn superoxide dismutase (CgSOD-1), plays a previously unknown role in plant biomass degradation. We show that CgSOD-1 transcripts and peptides are up-regulated in response to an increased level of lignocellulose recalcitrance and that CgSOD-1 localizes in the lumen of the fore- and midguts of C. gestroi together with termite main cellulase, CgEG-1-GH9. CgSOD-1 boosts the saccharification of polysaccharides by CgEG-1-GH9. We show that the boosting effect of CgSOD-1 involves an oxidative mechanism of action in which CgSOD-1 generates reactive oxygen species that subsequently cleave the polysaccharide. SOD-type enzymes constitute a new addition to the growing family of oxidases, ones which are up-regulated when exposed to recalcitrant polysaccharides, and that are used by Nature for biomass degradation.
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Affiliation(s)
- João Paulo L Franco Cairo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP) Campinas São Paulo Brazil
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
- Department of Chemistry, University of York York YO10 5DD UK
| | - Fernanda Mandelli
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Robson Tramontina
- Programa de Processos Tecnológicos e Ambientais da Universidade de Sorocaba (UNISO) Sorocaba SP Brazil
| | - David Cannella
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
| | | | - Luisa Ciano
- Department of Chemistry, University of York York YO10 5DD UK
| | - Marcel R Ferreira
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP Botucatu São Paulo Brasil
| | - Marcelo V Liberato
- Programa de Processos Tecnológicos e Ambientais da Universidade de Sorocaba (UNISO) Sorocaba SP Brazil
| | - Lívia B Brenelli
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Thiago A Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP) Campinas São Paulo Brazil
| | - Gisele N Rodrigues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Thabata M Alvarez
- Programa de Mestrado e Doutorado em Biotecnologia Industrial, Universidade Positivo Curitiba PR Brasil
| | - Luciana S Mofatto
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade de Campinas, UNICAMP Campinas São Paulo Brasil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade de Campinas, UNICAMP Campinas São Paulo Brasil
| | - José G C Pradella
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Adriana F Paes Leme
- Laboratório Nacional de Biociências (LNBio) do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas São Paulo Brasil
| | - Ana M Costa-Leonardo
- Laboratório de Cupins, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista, UNESP Rio Claro São Paulo Brasil
| | - Mário Oliveira-Neto
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP Botucatu São Paulo Brasil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP) Campinas São Paulo Brazil
| | - Gideon J Davies
- Department of Chemistry, University of York York YO10 5DD UK
| | - Claus Felby
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
| | - Paul H Walton
- Department of Chemistry, University of York York YO10 5DD UK
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais da Universidade de Sorocaba (UNISO) Sorocaba SP Brazil
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7
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Paixão DAA, Tomazetto G, Sodré VR, Gonçalves TA, Uchima CA, Büchli F, Alvarez TM, Persinoti GF, da Silva MJ, Bragatto J, Liberato MV, Franco Cairo JPL, Leme AFP, Squina FM. Microbial enrichment and meta-omics analysis identify CAZymes from mangrove sediments with unique properties. Enzyme Microb Technol 2021; 148:109820. [PMID: 34116762 DOI: 10.1016/j.enzmictec.2021.109820] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 12/19/2022]
Abstract
Although lignocellulose is the most abundant and renewable natural resource for biofuel production, its use remains under exploration because of its highly recalcitrant structure. Its deconstruction into sugar monomers is mainly driven by carbohydrate-active enzymes (CAZymes). To develop highly efficient and fast strategies to discover biomass-degrading enzymes for biorefinery applications, an enrichment process combined with integrative omics approaches was used to identify new CAZymes. The lignocellulolytic-enriched mangrove microbial community (LignoManG) established on sugarcane bagasse (SB) was enriched with lignocellulolytic bacteria and fungi such as Proteobacteria, Bacteroidetes, Basidiomycota, and Ascomycota. These microbial communities were able to degrade up to 55 % of the total SB, indicating the production of lignocellulolytic enzymes. Metagenomic analysis revealed that the LignoManG harbors 18.042 CAZyme sequences such as of cellulases, hemicellulases, carbohydrate esterases, and lytic polysaccharide monooxygenase. Similarly, our metaproteomic analysis depicted several enzymes from distinct families of different CAZy families. Based on the LignoManG data, a xylanase (coldXynZ) was selected, amplified, cloned, expressed, and biochemically characterized. The enzyme displayed psicrofilic properties, with the highest activity at 15 °C, retaining 77 % of its activity when incubated at 0 °C. Moreover, molecular modeling in silico indicated that coldXynZ is composed of a TIM barrel, which is a typical folding found in the GH10 family, and displayed similar structural features related to cold-adapted enzymes. Collectively, the data generated in this study represent a valuable resource for lignocellulolytic enzymes with potential biotechnological applications.
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Affiliation(s)
| | - Geizecler Tomazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, 8200, Aarhus, Denmark
| | - Victoria Ramos Sodré
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Thiago A Gonçalves
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fernanda Büchli
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Thabata Maria Alvarez
- Graduate Programme in Industrial Biotechnology, Universidade Positivo, Curitiba, Brazil
| | - Gabriela Felix Persinoti
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Márcio José da Silva
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Juliano Bragatto
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Marcelo Vizoná Liberato
- Laboratório Nacional de Biorenováveis, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - João Paulo L Franco Cairo
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazi; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
| | - Adriana Franco Paes Leme
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil.
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8
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Scharf ME, Peterson BF. A Century of Synergy in Termite Symbiosis Research: Linking the Past with New Genomic Insights. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:23-43. [PMID: 33417825 DOI: 10.1146/annurev-ento-022420-074746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Termites have long been studied for their symbiotic associations with gut microbes. In the late nineteenth century, this relationship was poorly understood and captured the interest of parasitologists such as Joseph Leidy; this research led to that of twentieth-century biologists and entomologists including Cleveland, Hungate, Trager, and Lüscher. Early insights came via microscopy, organismal, and defaunation studies, which led to descriptions of microbes present, descriptions of the roles of symbionts in lignocellulose digestion, and early insights into energy gas utilization by the host termite. Focus then progressed to culture-dependent microbiology and biochemical studies of host-symbiont complementarity, which revealed specific microhabitat requirements for symbionts and noncellulosic mechanisms of symbiosis (e.g., N2 fixation). Today, knowledge on termite symbiosis has accrued exponentially thanks to omic technologies that reveal symbiont identities, functions, and interdependence, as well as intricacies of host-symbiont complementarity. Moving forward, the merging of classical twentieth-century approaches with evolving omic tools should provide even deeper insights into host-symbiont interplay.
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Affiliation(s)
- Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Brittany F Peterson
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, Illinois 62026, USA;
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9
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Franco Cairo JPL, Cannella D, Oliveira LC, Gonçalves TA, Rubio MV, Terrasan CRF, Tramontina R, Mofatto LS, Carazzolle MF, Garcia W, Felby C, Damasio A, Walton PH, Squina F. On the roles of AA15 lytic polysaccharide monooxygenases derived from the termite Coptotermes gestroi. J Inorg Biochem 2020; 216:111316. [PMID: 33421883 DOI: 10.1016/j.jinorgbio.2020.111316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/02/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes which catalyze the oxidative cleavage of polysaccharides. LPMOs belonging to family 15 in the Auxiliary Activity (AA) class from the Carbohydrate-Active Enzyme database are found widespread across the Tree of Life, including viruses, algae, oomycetes and animals. Recently, two AA15s from the firebrat Thermobia domestica were reported to have oxidative activity, one towards cellulose or chitin and the other towards chitin, signalling that AA15 LPMOs from insects potentially have different biochemical functions. Herein, we report the identification and characterization of two family AA15 members from the lower termite Coptotermes gestroi. Addition of Cu(II) to CgAA15a or CgAA15b had a thermostabilizing effect on both. Using ascorbate and O2 as co-substrates, CgAA15a and CgAA15b were able to oxidize chitin, but showed no activity on celluloses, xylan, xyloglucan and starch. Structural models indicate that the LPMOs from C. gestroi (CgAA15a/CgAA15b) have a similar fold but exhibit key differences in the catalytic site residues when compared to the cellulose/chitin-active LPMO from T. domestica (TdAA15a), especially the presence of a non-coordinating phenylalanine nearby the Cu ion in CgAA15a/b, which appears as a tyrosine in the active site of TdAA15a. Despite the overall similarity in protein folds, however, mutation of the active site phenylalanine in CgAA15a to a tyrosine did not expanded the enzymatic specificity from chitin to cellulose. Our data show that CgAA15a/b enzymes are likely not involved in lignocellulose digestion but might play a role in termite developmental processes as well as on chitin and nitrogen metabolisms.
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Affiliation(s)
- João Paulo L Franco Cairo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil; Department of Chemistry, University of York, Heslington, York, United Kingdom; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba - UNISO, Sorocaba, SP, Brazil
| | - David Cannella
- PhotoBioCatalysis Unit, Crop Production and Biocatalysis - CPBL, Biomass Transformation lab - BTL, Interfaculty School of Bioengineers, Université Libre de Bruxelles, Belgium
| | - Leandro C Oliveira
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Thiago A Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil; Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba - UNISO, Sorocaba, SP, Brazil
| | - Marcelo V Rubio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Cesar R F Terrasan
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Robson Tramontina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba - UNISO, Sorocaba, SP, Brazil
| | - Luciana S Mofatto
- Department of Genetic, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Marcelo F Carazzolle
- Department of Genetic, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Claus Felby
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil; São Paulo Fungal Group, Brazil
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, York, United Kingdom.
| | - Fabio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba - UNISO, Sorocaba, SP, Brazil.
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10
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Scharf ME. Challenges and physiological implications of wood feeding in termites. CURRENT OPINION IN INSECT SCIENCE 2020; 41:79-85. [PMID: 32823202 DOI: 10.1016/j.cois.2020.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Termites are fascinating insects for a number of reasons, one of which being their specialization on diets of wood lignocellulose. The goal of this review is to consider stress-inducing characteristics of wood and apparent molecular-physiological adaptations in termite guts to overcome these stressors. Defensive factors present in wood include extractive secondary plant metabolites, lignin and related phenolics, crystalline cellulose, and low nitrogen content. Molecular-physiological adaptations of the termite gut to deal with these factors include robust detoxification and antioxidant machinery, the production of a peritrophic matrix and a wide range of cellulases from host and symbiotic sources, and creation of niches available to nitrogen-fixing bacterial symbionts. Considering termite gut physiology and symbioses in the context of stress-response has applied implications. These outcomes can include development of efficient biomass breakdown strategies, protection of microbes during industrial processing applications, and safeguarding wooden structures from termite damage.
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Affiliation(s)
- Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.
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11
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Tramontina R, Brenelli LB, Sodré V, Franco Cairo JP, Travália BM, Egawa VY, Goldbeck R, Squina FM. Enzymatic removal of inhibitory compounds from lignocellulosic hydrolysates for biomass to bioproducts applications. World J Microbiol Biotechnol 2020; 36:166. [PMID: 33000321 DOI: 10.1007/s11274-020-02942-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/25/2020] [Indexed: 01/04/2023]
Abstract
The physicochemical pretreatment is an important step to reduce biomass recalcitrance and facilitate further processing of plant lignocellulose into bioproducts. This process results in soluble and insoluble biomass fractions, and both may contain by-products that inhibit enzymatic biocatalysts and microbial fermentation. These fermentation inhibitory compounds (ICs) are produced during the degradation of lignin and sugars, resulting in phenolic and furanic compounds, and carboxylic acids. Therefore, detoxification steps may be required to improve lignocellulose conversion by microoganisms. Several physical and chemical methods, such as neutralization, use of activated charcoal and organic solvents, have been developed and recommended for removal of ICs. However, biological processes, especially enzyme-based, have been shown to efficiently remove ICs with the advantage of minimizing environmental issues since they are biogenic catalysts and used in low quantities. This review focuses on describing several enzymatic approaches to promote detoxification of lignocellulosic hydrolysates and improve the performance of microbial fermentation for the generation of bioproducts. Novel strategies using classical carbohydrate active enzymes (CAZymes), such as laccases (AA1) and peroxidases (AA2), as well as more advanced strategies using prooxidant, antioxidant and detoxification enzymes (dubbed as PADs), i.e. superoxide dismutases, are discussed as perspectives in the field.
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Affiliation(s)
- Robson Tramontina
- Programa de Pós-Graduação em Biociências e Tecnologia de Produtos Bioativos (BTPB), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
- School of Food Engineering, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lívia Beatriz Brenelli
- Interdisciplinary Center of Energy Planning (NIPE), State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Victoria Sodré
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil
- Programa de Pós-Graduação em Biologia Funcional e Molecular (BFM), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - João Paulo Franco Cairo
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil
| | | | - Viviane Yoshimi Egawa
- School of Agriculture, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Rosana Goldbeck
- School of Food Engineering, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil.
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12
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Tramontina R, Brenelli LB, Sousa A, Alves R, Zetty Arenas AM, Nascimento VM, Rabelo SC, Freitas S, Ruller R, Squina FM. Designing a cocktail containing redox enzymes to improve hemicellulosic hydrolysate fermentability by microorganisms. Enzyme Microb Technol 2019; 135:109490. [PMID: 32146936 DOI: 10.1016/j.enzmictec.2019.109490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/07/2019] [Accepted: 12/09/2019] [Indexed: 12/22/2022]
Abstract
Bioproducts production using monomeric sugars derived from lignocellulosic biomass presents several challenges, such as to require a physicochemical pretreatment to improve its conversion yields. Hydrothermal lignocellulose pretreatment has several advantages and results in solid and liquid streams. The former is called hemicellulosic hydrolysate (HH), which contains inhibitory phenolic compounds and sugar degradation products that hinder microbial fermentation products from pentose sugars. Here, we developed and applied a novel enzyme process to detoxify HH. Initially, the design of experiments with different redox activities enzymes was carried out. The enzyme mixture containing the peroxidase (from Armoracia rusticana) together with superoxide dismutase (from Coptotermes gestroi) are the most effective to detoxify HH derived from sugarcane bagasse. Butanol fermentation by the bacteria Clostridium saccharoperbutylacetonicum and ethanol production by the yeast Scheffersomyces stipitis increased by 24.0× and 2.4×, respectively, relative to the untreated hemicellulosic hydrolysates. Detoxified HH was analyzed by chromatographic and spectrometric methods elucidating the mechanisms of phenolic compound modifications by enzymatic treatment. The enzyme mixture degraded and reduced the hydroxyphenyl- and feruloyl-derived units and polymerized the lignin fragments. This strategy uses biocatalysts under environmentally friendly conditions and could be applied in the fuel, food, and chemical industries.
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Affiliation(s)
- Robson Tramontina
- Laboratório Nacional de Biorrenováveis (LNBR) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil; Programa em Biociências e Tecnologia de Produtos Bioativos (BTPB), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Lívia Beatriz Brenelli
- Laboratório Nacional de Biorrenováveis (LNBR) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Amanda Sousa
- Laboratório Nacional de Biorrenováveis (LNBR) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | | | - Ana Maria Zetty Arenas
- Laboratório Nacional de Biorrenováveis (LNBR) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil; Programa em Bioenergia, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, (UNICAMP), Campinas, SP, Brazil
| | - Viviane Marcos Nascimento
- Laboratório Nacional de Biorrenováveis (LNBR) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Sarita Cândida Rabelo
- Departamento de Bioprocessos e Biotecnologia, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, São Paulo, Brazil
| | - Sindélia Freitas
- Laboratório Nacional de Biorrenováveis (LNBR) Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil; Programa em Bioenergia, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, (UNICAMP), Campinas, SP, Brazil; Faculdade de Engenharia Química (FEQ), Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Roberto Ruller
- Laboratório de Bioquimica Geral e de Microorganismos, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil; Instituto de Biociências, Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista, São José do Rio Preto, SP, Brazil
| | - Fabio Marcio Squina
- Programa em Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil.
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13
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Crystal Structure and Biophysical Analysis of Furfural-Detoxifying Aldehyde Reductase from Clostridium beijerinckii. Appl Environ Microbiol 2019; 85:AEM.00978-19. [PMID: 31101612 DOI: 10.1128/aem.00978-19] [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: 04/30/2019] [Accepted: 05/07/2019] [Indexed: 11/20/2022] Open
Abstract
Many aldehydes, such as furfural, are present in high quantities in lignocellulose lysates and are fermentation inhibitors, which makes biofuel production from this abundant carbon source extremely challenging. Cbei_3974 has recently been identified as an aldo-keto reductase responsible for partial furfural resistance in Clostridium beijerinckii Rational engineering of this enzyme could enhance the furfural tolerance of this organism, thereby improving biofuel yields. We report an extensive characterization of Cbei_3974 and a single-crystal X-ray structure of Cbei_3974 in complex with NADPH at a resolution of 1.75 Å. Docking studies identified residues involved in substrate binding, and an activity screen revealed the substrate tolerance of the enzyme. Hydride transfer, which is partially rate limiting under physiological conditions, occurs from the pro-R hydrogen of NADPH. Enzyme isotope labeling revealed a temperature-independent enzyme isotope effect of unity, indicating that the enzyme does not use dynamic coupling for catalysis and suggesting that the active site of the enzyme is optimally configured for catalysis with the substrate tested.IMPORTANCE Here we report the crystal structure and biophysical properties of an aldehyde reductase that can detoxify furfural, a common inhibitor of biofuel fermentation found in lignocellulose lysates. The data contained here will serve as a guide for protein engineers to develop improved enzyme variants that would impart furfural resistance to the microorganisms used in biofuel production and thus lead to enhanced biofuel yields from this sustainable resource.
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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Kumar M, Verma S, Gazara RK, Kumar M, Pandey A, Verma PK, Thakur IS. Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:154. [PMID: 29991962 PMCID: PMC5987411 DOI: 10.1186/s13068-018-1148-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/17/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Lignin is a major component of plant biomass and is recalcitrant to degradation due to its complex and heterogeneous aromatic structure. The biomass-based research mainly focuses on polysaccharides component of biomass and lignin is discarded as waste with very limited usage. The sustainability and success of plant polysaccharide-based biorefinery can be possible if lignin is utilized in improved ways and with minimal waste generation. Discovering new microbial strains and understanding their enzyme system for lignin degradation are necessary for its conversion into fuel and chemicals. The Pandoraea sp. ISTKB was previously characterized for lignin degradation and successfully applied for pretreatment of sugarcane bagasse and polyhydroxyalkanoate (PHA) production. In this study, genomic analysis and proteomics on aromatic polymer kraft lignin and vanillic acid are performed to find the important enzymes for polymer utilization. RESULTS Genomic analysis of Pandoraea sp. ISTKB revealed the presence of strong lignin degradation machinery and identified various candidate genes responsible for lignin degradation and PHA production. We also applied label-free quantitative proteomic approach to identify the expression profile on monoaromatic compound vanillic acid (VA) and polyaromatic kraft lignin (KL). Genomic and proteomic analysis simultaneously discovered Dyp-type peroxidase, peroxidases, glycolate oxidase, aldehyde oxidase, GMC oxidoreductase, laccases, quinone oxidoreductase, dioxygenases, monooxygenases, glutathione-dependent etherases, dehydrogenases, reductases, and methyltransferases and various other recently reported enzyme systems such as superoxide dismutases or catalase-peroxidase for lignin degradation. A strong stress response and detoxification mechanism was discovered. The two important gene clusters for lignin degradation and three PHA polymerase spanning gene clusters were identified and all the clusters were functionally active on KL-VA. CONCLUSIONS The unusual aerobic '-CoA'-mediated degradation pathway of phenylacetate and benzoate (reported only in 16 and 4-5% of total sequenced bacterial genomes), peroxidase-accessory enzyme system, and fenton chemistry based are the major pathways observed for lignin degradation. Both ortho and meta ring cleavage pathways for aromatic compound degradation were observed in expression profile. Genomic and proteomic approaches provided validation to this strain's robust machinery for the metabolism of recalcitrant compounds and PHA production and provide an opportunity to target important enzymes for lignin valorization in future.
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Affiliation(s)
- Madan Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sandhya Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Rajesh Kumar Gazara
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Manish Kumar
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ashok Pandey
- CSIR-Indian Institute of Toxicology Research, 31 MG Marg, Lucknow, 226 001 India
| | - Praveen Kumar Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Indu Shekhar Thakur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Gene expression metadata analysis reveals molecular mechanisms employed by Phanerochaete chrysosporium during lignin degradation and detoxification of plant extractives. Curr Genet 2017; 63:877-894. [PMID: 28275822 DOI: 10.1007/s00294-017-0686-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 10/20/2022]
Abstract
Lignin, most complex and abundant biopolymer on the earth's surface, attains its stability from intricate polyphenolic units and non-phenolic bonds, making it difficult to depolymerize or separate from other units of biomass. Eccentric lignin degrading ability and availability of annotated genome make Phanerochaete chrysosporium ideal for studying lignin degrading mechanisms. Decoding and understanding the molecular mechanisms underlying the process of lignin degradation will significantly aid the progressing biofuel industries and lead to the production of commercially vital platform chemicals. In this study, we have performed a large-scale metadata analysis to understand the common gene expression patterns of P. chrysosporium during lignin degradation. Gene expression datasets were retrieved from NCBI GEO database and analyzed using GEO2R and Bioconductor packages. Commonly expressed statistically significant genes among different datasets were further considered to understand their involvement in lignin degradation and detoxification mechanisms. We have observed three sets of enzymes commonly expressed during ligninolytic conditions which were later classified into primary ligninolytic, aromatic compound-degrading and other necessary enzymes. Similarly, we have observed three sets of genes coding for detoxification and stress-responsive, phase I and phase II metabolic enzymes. Results obtained in this study indicate the coordinated action of enzymes involved in lignin depolymerization and detoxification-stress responses under ligninolytic conditions. We have developed tentative network of genes and enzymes involved in lignin degradation and detoxification mechanisms by P. chrysosporium based on the literature and results obtained in this study. However, ambiguity raised due to higher expression of several uncharacterized proteins necessitates for further proteomic studies in P. chrysosporium.
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