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Sørensen T, Petersen C, Muurmann AT, Christiansen JV, Brundtø ML, Overgaard CK, Boysen AT, Wollenberg RD, Larsen TO, Sørensen JL, Nielsen KL, Sondergaard TE. Apiospora arundinis, a panoply of carbohydrate-active enzymes and secondary metabolites. IMA Fungus 2024; 15:10. [PMID: 38582937 PMCID: PMC10999098 DOI: 10.1186/s43008-024-00141-0] [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: 10/04/2023] [Accepted: 03/16/2024] [Indexed: 04/08/2024] Open
Abstract
The Apiospora genus comprises filamentous fungi with promising potential, though its full capabilities remain undiscovered. In this study, we present the first genome assembly of an Apiospora arundinis isolate, demonstrating a highly complete and contiguous assembly estimated to 48.8 Mb, with an N99 of 3.0 Mb. Our analysis predicted a total of 15,725 genes, with functional annotations for 13,619 of them, revealing a fungus capable of producing very high amounts of carbohydrate-active enzymes (CAZymes) and secondary metabolites. Through transcriptomic analysis, we observed differential gene expression in response to varying growth media, with several genes related to carbohydrate metabolism showing significant upregulation when the fungus was cultivated on a hay-based medium. Finally, our metabolomic analysis unveiled a fungus capable of producing a diverse array of metabolites.
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Affiliation(s)
- Trine Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark
| | - Celine Petersen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark
| | - Asmus T Muurmann
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark
| | - Johan V Christiansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kongens Lyngby, 2800, Denmark
| | - Mathias L Brundtø
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark
| | - Christina K Overgaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark
| | - Anders T Boysen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark
| | - Rasmus D Wollenberg
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark
| | - Thomas O Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kongens Lyngby, 2800, Denmark
| | - Jens L Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Niels-Bohrs Vej 8, Esbjerg, 6700, Denmark
| | - Kåre L Nielsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark.
| | - Teis E Sondergaard
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, 9220, Denmark.
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Yu X, Zhao Y, Yu J, Wang L. Recent advances in the efficient degradation of lignocellulosic metabolic networks by lytic polysaccharide monooxygenase. Acta Biochim Biophys Sin (Shanghai) 2023; 55:529-539. [PMID: 37036250 DOI: 10.3724/abbs.2023059] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023] Open
Abstract
Along with long-term evolution, the plant cell wall generates lignocellulose and other anti-degradation barriers to confront hydrolysis by fungi. Lytic polysaccharide monooxygenase (LPMO) is a newly defined oxidase in lignocellulosic degradation systems that significantly fuels hydrolysis. LPMO accepts electrons from wide sources, such as cellobiose dehydrogenase (CDH), glucose-methanol-choline (GMC) oxidoreductases, and small phenols. In addition, the extracellular cometabolic network formed by cosubstrates improves the degradation efficiency, forming a stable and efficient lignocellulose degradation system. In recent years, using structural proteomics to explore the internal structure and the complex redox system of LPMOs has become a research hotspot. In this review, the diversity of LPMOs, catalytic domains, carbohydrate binding modules, direct electron transfer with CDH, cosubstrates, and degradation networks of LPMOs are explored, which can provide a systematic reference for the application of lignocellulosic degradation systems in industrial approaches.
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Affiliation(s)
- Xinran Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Yue Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Junhong Yu
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao 266035, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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Tessaro APG, de Araujo LG, Silva TT, Coelho E, Corrêa B, Rolindo NC, Vicente R. Prospects for fungal bioremediation of unburied waste packages from the Goiânia radiological accident. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:41045-41059. [PMID: 36627427 DOI: 10.1007/s11356-023-25247-7] [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: 05/18/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
Goiânia, the Goiás State capital, starred in 1987, where one of the largest radiological accidents in the world happened. A teletherapy machine was subtracted from a derelict radiotherapy clinic and disassembled by scavengers who distributed fragments of the 50 TBq 137CsCl source among relatives and acquaintances, enchanted by the blue shine of the substance. During the 15 days before the accident was acknowledged, contaminated recycling materials were delivered to recycling factories in four cities in the state of São Paulo, Brazil, in the form of recycling paper bales. The contaminated bales were spotted, collected, and stored in fifty 1.6 m3 steel boxes at the interim storage facility of the Nuclear and Energy Research Institute (IPEN). In 2017, a check of the content was performed in a few boxes and the presence of high moisture content was observed even though the bales were dry when conditioned and the packages were kept sealed since then. The main objective of this work was to report the fungi found in the radioactive waste after they evolved for 30 years in isolation inside the waste boxes and their role in the decay of the waste. Examination of the microbiome showed the presence of nematodes and fungal communities. The fungi species isolated were Aspergillus quadricinctus, Fusarium oxysporum, Lecanicillium coprophilumi, Scedosporium boydii, Scytalidium lignicola, Xenoacremonium recifei, and Pleurostoma richardsiae. These microorganisms showed a significant capacity to digest cellulose in our trials, which could be one of the ways they survive in such a harsh environment, reducing the volume of radioactive paper waste. These metabolic abilities give us a future perspective of using these fungi in biotechnology to remediate radioactively contaminated materials, particularly cellulose-based waste.
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Affiliation(s)
- Ana Paula Gimenes Tessaro
- Instituto de Pesquisas Energéticas E Nucleares, IPEN/CNEN, Av. Prof. Lineu Prestes, 2242, São Paulo, SP, 05508-000, Brazil
| | - Leandro Goulart de Araujo
- Instituto de Pesquisas Energéticas E Nucleares, IPEN/CNEN, Av. Prof. Lineu Prestes, 2242, São Paulo, SP, 05508-000, Brazil.
- Current Affiliation, Université de Lorraine, CNRS, 88000, Epinal, IJL, France.
| | - Thalita Tieko Silva
- Instituto de Pesquisas Energéticas E Nucleares, IPEN/CNEN, Av. Prof. Lineu Prestes, 2242, São Paulo, SP, 05508-000, Brazil
| | - Ednei Coelho
- Microbiology Department, University of Sao Paulo, Av. Professor Lineu Prestes, São Paulo, 1374, Brazil
| | - Benedito Corrêa
- Microbiology Department, University of Sao Paulo, Av. Professor Lineu Prestes, São Paulo, 1374, Brazil
| | - Natalie Costa Rolindo
- Instituto de Pesquisas Energéticas E Nucleares, IPEN/CNEN, Av. Prof. Lineu Prestes, 2242, São Paulo, SP, 05508-000, Brazil
| | - Roberto Vicente
- Instituto de Pesquisas Energéticas E Nucleares, IPEN/CNEN, Av. Prof. Lineu Prestes, 2242, São Paulo, SP, 05508-000, Brazil
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Sagarika MS, Parameswaran C, Senapati A, Barala J, Mitra D, Prabhukarthikeyan SR, Kumar A, Nayak AK, Panneerselvam P. Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150451. [PMID: 34607097 DOI: 10.1016/j.scitotenv.2021.150451] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.
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Affiliation(s)
- Mahapatra Smruthi Sagarika
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India; Indira Gandhi Agricultural University, Raipur, Chhattisgarh 492012, India
| | | | - Ansuman Senapati
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Jatiprasad Barala
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Debasis Mitra
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | | | - Anjani Kumar
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
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Tokin R, Frandsen KEH, Ipsen JØ, Lo Leggio L, Poojary MM, Berrin JG, Grisel S, Brander S, Jensen PE, Johansen KS. Inhibition of lytic polysaccharide monooxygenase by natural plant extracts. THE NEW PHYTOLOGIST 2021; 232:1337-1349. [PMID: 34389999 DOI: 10.1111/nph.17676] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes of industrial and biological importance. In particular, LPMOs play important roles in fungal lifestyle. No inhibitors of LPMOs have yet been reported. In this study, a diverse library of 100 plant extracts was screened for LPMO activity-modulating effects. By employing protein crystallography and LC-MS, we successfully identified a natural LPMO inhibitor. Extract screening revealed a significant LPMO inhibition by methanolic extract of Cinnamomum cassia (cinnamon), which inhibited LsAA9A LPMO from Lentinus similis in a concentration-dependent manner. With a notable exception, other microbial LPMOs from families AA9 and AA10 were also inhibited by this cinnamon extract. The polyphenol cinnamtannin B1 was identified as the inhibitory component by crystallography. Cinnamtannin B1 was bound to the surface of LsAA9A at two distinct binding sites: one close to the active site and another at a pocket on the opposite side of the protein. Independent characterization of cinnamon extract by LC-MS and subsequent activity measurements confirmed that the compound inhibiting LsAA9A was cinnamtannin B1. The results of this study show that specific natural LPMO inhibitors of plant origin exist in nature, providing the opportunity for future exploitation of such compounds within various biotechnological contexts.
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Affiliation(s)
- Radina Tokin
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Kristian E H Frandsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Johan Ørskov Ipsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, 1871, Denmark
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Copenhagen Ø, 2100, Denmark
| | - Mahesha M Poojary
- Department of Food Science, University of Copenhagen, Frederiksberg C, 1958, Denmark
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Université, Biodiversité et Biotechnologie Fongiques (BBF), Marseille, 13009, France
| | - Sacha Grisel
- INRAE, Aix Marseille Université, Biodiversité et Biotechnologie Fongiques (BBF), Marseille, 13009, France
| | - Søren Brander
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, 1958, Denmark
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Frederiksberg C, 1958, Denmark
| | - Katja Salomon Johansen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Frederiksberg C, 1958, Denmark
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6
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Mazurkewich S, Seveso A, Hüttner S, Brändén G, Larsbrink J. Structure of a C1/C4-oxidizing AA9 lytic polysaccharide monooxygenase from the thermophilic fungus Malbranchea cinnamomea. Acta Crystallogr D Struct Biol 2021; 77:1019-1026. [PMID: 34342275 PMCID: PMC8329866 DOI: 10.1107/s2059798321006628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/25/2021] [Indexed: 11/20/2022] Open
Abstract
The thermophilic fungus Malbranchea cinnamomea contains a host of enzymes that enable its ability as an efficient degrader of plant biomass and that could be mined for industrial applications. This thermophilic fungus has been studied and found to encode eight lytic polysaccharide monooxygenases (LPMOs) from auxiliary activity family 9 (AA9), which collectively possess different substrate specificities for a range of plant cell-wall-related polysaccharides and oligosaccharides. To gain greater insight into the molecular determinants defining the different specificities, structural studies were pursued and the structure of McAA9F was determined. The enzyme contains the immunoglobulin-like fold typical of previously solved AA9 LPMO structures, but contains prominent differences in the loop regions found on the surface of the substrate-binding site. Most significantly, McAA9F has a broad substrate specificity, with activity on both crystalline and soluble polysaccharides. Moreover, it contains a small loop in a region where a large loop has been proposed to govern specificity towards oligosaccharides. The presence of the small loop leads to a considerably flatter and more open surface that is likely to enable the broad specificity of the enzyme. The enzyme contains a succinimide residue substitution, arising from intramolecular cyclization of Asp10, at a position where several homologous members contain an equivalent residue but cyclization has not previously been observed. This first structure of an AA9 LPMO from M. cinnamomea aids both the understanding of this family of enzymes and the exploration of the repertoire of industrially relevant lignocellulolytic enzymes from this fungus.
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Affiliation(s)
- Scott Mazurkewich
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Andrea Seveso
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Silvia Hüttner
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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C-type cytochrome-initiated reduction of bacterial lytic polysaccharide monooxygenases. Biochem J 2021; 478:2927-2944. [PMID: 34240737 PMCID: PMC8981238 DOI: 10.1042/bcj20210376] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
The release of glucose from lignocellulosic waste for subsequent fermentation into biofuels holds promise for securing humankind's future energy needs. The discovery of a set of copper-dependent enzymes known as lytic polysaccharide monooxygenases (LPMOs) has galvanised new research in this area. LPMOs act by oxidatively introducing chain breaks into cellulose and other polysaccharides, boosting the ability of cellulases to act on the substrate. Although several proteins have been implicated as electron sources in fungal LPMO biochemistry, no equivalent bacterial LPMO electron donors have been previously identified, although the proteins Cbp2D and E from Cellvibrio japonicus have been implicated as potential candidates. Here we analyse a small c-type cytochrome (CjX183) present in Cellvibrio japonicus Cbp2D, and show that it can initiate bacterial CuII/I LPMO reduction and also activate LPMO-catalyzed cellulose-degradation. In the absence of cellulose, CjX183-driven reduction of the LPMO results in less H2O2 production from O2, and correspondingly less oxidative damage to the enzyme than when ascorbate is used as the reducing agent. Significantly, using CjX183 as the activator maintained similar cellulase boosting levels relative to the use of an equivalent amount of ascorbate. Our results therefore add further evidence to the impact that the choice of electron source can have on LPMO action. Furthermore, the study of Cbp2D and other similar proteins may yet reveal new insight into the redox processes governing polysaccharide degradation in bacteria.
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Jagadeeswaran G, Veale L, Mort AJ. Do Lytic Polysaccharide Monooxygenases Aid in Plant Pathogenesis and Herbivory? TRENDS IN PLANT SCIENCE 2021; 26:142-155. [PMID: 33097402 DOI: 10.1016/j.tplants.2020.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/07/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs), copper-dependent enzymes mainly found in fungi, bacteria, and viruses, are responsible for enabling plant infection and degradation processes. Since their discovery 10 years ago, significant progress has been made in understanding the major role these enzymes play in biomass conversion. The recent discovery of additional LPMO families in fungi and oomycetes (AA16) as well as insects (AA15) strongly suggests that LPMOs might also be involved in biological processes such as overcoming plant defenses. In this review, we aim to give a comprehensive overview of the potential role of different LPMO families from the perspective of plant defense and their multiple implications in devising new strategies for achieving crop protection from plant pathogens and insect pests.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Lawrie Veale
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Andrew J Mort
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA.
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9
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Sahu N, Merényi Z, Bálint B, Kiss B, Sipos G, Owens RA, Nagy LG. Hallmarks of Basidiomycete Soft- and White-Rot in Wood-Decay -Omics Data of Two Armillaria Species. Microorganisms 2021; 9:149. [PMID: 33440901 PMCID: PMC7827401 DOI: 10.3390/microorganisms9010149] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/01/2021] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Wood-decaying Basidiomycetes are among the most efficient degraders of plant cell walls, making them key players in forest ecosystems, global carbon cycle, and in bio-based industries. Recent insights from -omics data revealed a high functional diversity of wood-decay strategies, especially among the traditional white-rot and brown-rot dichotomy. We examined the mechanistic bases of wood-decay in the conifer-specialists Armillaria ostoyae and Armillaria cepistipes using transcriptomic and proteomic approaches. Armillaria spp. (Fungi, Basidiomycota) include devastating pathogens of temperate forests and saprotrophs that decay wood. They have been discussed as white-rot species, though their response to wood deviates from typical white-rotters. While we observed an upregulation of a diverse suite of plant cell wall degrading enzymes, unlike white-rotters, they possess and express an atypical wood-decay repertoire in which pectinases and expansins are enriched, whereas lignin-decaying enzymes (LDEs) are generally downregulated. This combination of wood decay genes resembles the soft-rot of Ascomycota and appears widespread among Basidiomycota that produce a superficial white rot-like decay. These observations are consistent with ancestral soft-rot decay machinery conserved across asco- and Basidiomycota, a gain of efficient lignin-degrading ability in white-rot fungi and repeated, complete, or partial losses of LDE encoding gene repertoires in brown- and secondarily soft-rot fungi.
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Affiliation(s)
- Neha Sahu
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, 6726 Szeged, Hungary
| | - Zsolt Merényi
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - Balázs Bálint
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - Brigitta Kiss
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
| | - György Sipos
- Research Center for Forestry and Wood Industry, Functional Genomics and Bioinformatics Group, University of Sopron, 9400 Sopron, Hungary;
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Rebecca A. Owens
- Department of Biology, Maynooth University, W23 F2H6 Kildare, Ireland;
| | - László G. Nagy
- Biological Research Center, Synthetic and Systems Biology Unit, 6726 Szeged, Hungary; (N.S.); (Z.M.); (B.B.); (B.K.)
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary
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Bunterngsook B, Mhuantong W, Kanokratana P, Iseki Y, Watanabe T, Champreda V. Identification and characterization of a novel AA9-type lytic polysaccharide monooxygenase from a bagasse metagenome. Appl Microbiol Biotechnol 2020; 105:197-210. [PMID: 33230603 DOI: 10.1007/s00253-020-11002-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/20/2020] [Accepted: 11/03/2020] [Indexed: 11/25/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are auxiliary enzymes catalyzing oxidative cleavages of cellulose chains in crystalline regions, resulting in their increasing accessibility to the hydrolytic enzyme counterparts and hence higher released sugars from biomass saccharification. In this study, a novel auxiliary protein family 9 LPMO (BgAA9) was identified from a metagenomic library derived from a thermophilic microbial community in bagasse collection site where diverse AA9 and AA10 putative sequences were annotated. The enzyme showed highest similarity to a glycoside hydrolase family 61 from Chaetomium thermophilum. Recombinant BgAA9 expressed in Pichia pastoris cleaved cellohexaose (DP6) into shorter cellooligosaccharides (DP2, DP3, and DP4). Supplementation BgAA9 to a commercial cellulase, Accellerase® 1500 showed strong synergistic effect on saccharification of Avicel® PH101, decrystallized cellulose, filter paper, and alkaline-pretreated sugarcane bagasse, resulting in 63-93% increase in the total reducing sugar yield after incubation at 50 °C for 72 h. Strong synergism was shown between BgAA9 and the cellulase with the highest total fermentable sugar yield obtained from 75:25% of Accellerase®1500:BgAA9 which released 39 mg glucose/FPU (filter paper unit) equivalent to 38.7% higher than Accellerase®1500 alone at the same total protein dosage of 5 mg/g substrate according to the mixture design study. The enzyme represented the first characterized LPMO from environmental metagenome and a potent auxiliary component for biomass saccharification. KEY POINTS: • BgAA9 represents the first characterized LPMO from metagenome. • 12 AA families were annotated in thermophilic bagasse fosmid library by NGS. • BgAA9 showed homology to Cel61 in Chaetomium thermophilum. • BgAA9 oxidized cellohexaose and PASC to DP2, DP4, and DP6. • BgAA9 showed strong synergism to Accellerase on bagasse hydrolysis.
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Affiliation(s)
- Benjarat Bunterngsook
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Wuttichai Mhuantong
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Pattanop Kanokratana
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand
| | - Yu Iseki
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Watanabe
- Laboratory of Biomass Conversion, Research Institute for Sustainable Humanosphere (RISH), Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Verawat Champreda
- Enzyme Technology Laboratory, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathumthani, 12120, Thailand.
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11
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Østby H, Hansen LD, Horn SJ, Eijsink VGH, Várnai A. Enzymatic processing of lignocellulosic biomass: principles, recent advances and perspectives. J Ind Microbiol Biotechnol 2020; 47:623-657. [PMID: 32840713 PMCID: PMC7658087 DOI: 10.1007/s10295-020-02301-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
Efficient saccharification of lignocellulosic biomass requires concerted development of a pretreatment method, an enzyme cocktail and an enzymatic process, all of which are adapted to the feedstock. Recent years have shown great progress in most aspects of the overall process. In particular, increased insights into the contributions of a wide variety of cellulolytic and hemicellulolytic enzymes have improved the enzymatic processing step and brought down costs. Here, we review major pretreatment technologies and different enzyme process setups and present an in-depth discussion of the various enzyme types that are currently in use. We pay ample attention to the role of the recently discovered lytic polysaccharide monooxygenases (LPMOs), which have led to renewed interest in the role of redox enzyme systems in lignocellulose processing. Better understanding of the interplay between the various enzyme types, as they may occur in a commercial enzyme cocktail, is likely key to further process improvements.
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Affiliation(s)
- Heidi Østby
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Line Degn Hansen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Svein J Horn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), P.O. Box 5003, 1432, Aas, Norway.
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12
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Dadwal A, Sharma S, Satyanarayana T. Progress in Ameliorating Beneficial Characteristics of Microbial Cellulases by Genetic Engineering Approaches for Cellulose Saccharification. Front Microbiol 2020; 11:1387. [PMID: 32670240 PMCID: PMC7327088 DOI: 10.3389/fmicb.2020.01387] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/29/2020] [Indexed: 12/15/2022] Open
Abstract
Lignocellulosic biomass is a renewable and sustainable energy source. Cellulases are the enzymes that cleave β-1, 4-glycosidic linkages in cellulose to liberate sugars that can be fermented to ethanol, butanol, and other products. Low enzyme activity and yield, and thermostability are, however, some of the limitations posing hurdles in saccharification of lignocellulosic residues. Recent advancements in synthetic and systems biology have generated immense interest in metabolic and genetic engineering that has led to the development of sustainable technology for saccharification of lignocellulosics in the last couple of decades. There have been several attempts in applying genetic engineering in the production of a repertoire of cellulases at a low cost with a high biomass saccharification. A diverse range of cellulases are produced by different microbes, some of which are being engineered to evolve robust cellulases. This review summarizes various successful genetic engineering strategies employed for improving cellulase kinetics and cellulolytic efficiency.
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Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, New Delhi, India
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13
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Wang BT, Hu S, Yu XY, Jin L, Zhu YJ, Jin FJ. Studies of Cellulose and Starch Utilization and the Regulatory Mechanisms of Related Enzymes in Fungi. Polymers (Basel) 2020; 12:polym12030530. [PMID: 32121667 PMCID: PMC7182937 DOI: 10.3390/polym12030530] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 12/24/2022] Open
Abstract
Polysaccharides are biopolymers made up of a large number of monosaccharides joined together by glycosidic bonds. Polysaccharides are widely distributed in nature: Some, such as peptidoglycan and cellulose, are the components that make up the cell walls of bacteria and plants, and some, such as starch and glycogen, are used as carbohydrate storage in plants and animals. Fungi exist in a variety of natural environments and can exploit a wide range of carbon sources. They play a crucial role in the global carbon cycle because of their ability to break down plant biomass, which is composed primarily of cell wall polysaccharides, including cellulose, hemicellulose, and pectin. Fungi produce a variety of enzymes that in combination degrade cell wall polysaccharides into different monosaccharides. Starch, the main component of grain, is also a polysaccharide that can be broken down into monosaccharides by fungi. These monosaccharides can be used for energy or as precursors for the biosynthesis of biomolecules through a series of enzymatic reactions. Industrial fermentation by microbes has been widely used to produce traditional foods, beverages, and biofuels from starch and to a lesser extent plant biomass. This review focuses on the degradation and utilization of plant homopolysaccharides, cellulose and starch; summarizes the activities of the enzymes involved and the regulation of the induction of the enzymes in well-studied filamentous fungi.
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14
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Srivastava PA, Hegg EL, Fox BG, Yennamalli RM. PreDSLpmo: A neural network-based prediction tool for functional annotation of lytic polysaccharide monooxygenases. J Biotechnol 2020; 308:148-155. [DOI: 10.1016/j.jbiotec.2019.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/25/2019] [Accepted: 12/08/2019] [Indexed: 11/30/2022]
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15
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Zhang W, Corwin JA, Copeland DH, Feusier J, Eshbaugh R, Cook DE, Atwell S, Kliebenstein DJ. Plant-necrotroph co-transcriptome networks illuminate a metabolic battlefield. eLife 2019; 8:e44279. [PMID: 31081752 PMCID: PMC6557632 DOI: 10.7554/elife.44279] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/08/2019] [Indexed: 12/27/2022] Open
Abstract
A central goal of studying host-pathogen interaction is to understand how host and pathogen manipulate each other to promote their own fitness in a pathosystem. Co-transcriptomic approaches can simultaneously analyze dual transcriptomes during infection and provide a systematic map of the cross-kingdom communication between two species. Here we used the Arabidopsis-B. cinerea pathosystem to test how plant host and fungal pathogen interact at the transcriptomic level. We assessed the impact of genetic diversity in pathogen and host by utilization of a collection of 96 isolates infection on Arabidopsis wild-type and two mutants with jasmonate or salicylic acid compromised immunities. We identified ten B. cinereagene co-expression networks (GCNs) that encode known or novel virulence mechanisms. Construction of a dual interaction network by combining four host- and ten pathogen-GCNs revealed potential connections between the fungal and plant GCNs. These co-transcriptome data shed lights on the potential mechanisms underlying host-pathogen interaction.
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Affiliation(s)
- Wei Zhang
- Department of Plant PathologyKansas State UniversityManhattanUnited States
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Jason A Corwin
- Department of Ecology and Evolution BiologyUniversity of ColoradoBoulderUnited States
| | | | - Julie Feusier
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Robert Eshbaugh
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - David E Cook
- Department of Plant PathologyKansas State UniversityManhattanUnited States
| | - Suzi Atwell
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
| | - Daniel J Kliebenstein
- Department of Plant SciencesUniversity of California, DavisDavisUnited States
- DynaMo Center of ExcellenceUniversity of CopenhagenFrederiksbergDenmark
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16
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Basotra N, Dhiman SS, Agrawal D, Sani RK, Tsang A, Chadha BS. Characterization of a novel Lytic Polysaccharide Monooxygenase from Malbranchea cinnamomea exhibiting dual catalytic behavior. Carbohydr Res 2019; 478:46-53. [DOI: 10.1016/j.carres.2019.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/27/2019] [Accepted: 04/23/2019] [Indexed: 10/26/2022]
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17
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A Lytic Polysaccharide Monooxygenase from a White-Rot Fungus Drives the Degradation of Lignin by a Versatile Peroxidase. Appl Environ Microbiol 2019; 85:AEM.02803-18. [PMID: 30824433 DOI: 10.1128/aem.02803-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs), a class of copper-dependent enzymes, play a crucial role in boosting the enzymatic decomposition of polysaccharides. Here, we reveal that LPMOs might be associated with a lignin degradation pathway. An LPMO from white-rot fungus Pleurotus ostreatus, LPMO9A (PoLPMO9A), was shown to be able to efficiently drive the activity of class II lignin-degrading peroxidases in vitro through H2O2 production regardless of the presence or absence of a cellulose substrate. An LPMO-driven peroxidase reaction can degrade β-O-4 and 5-5' types of lignin dimer with 46.5% and 37.7% degradation, respectively, as well as alter the structure of natural lignin and kraft lignin. H2O2 generated by PoLPMO9A was preferentially utilized for the peroxidase from Physisporinus sp. strain P18 (PsVP) reaction rather than cellulose oxidation, indicating that white-rot fungi may have a strategy for preferential degradation of resistant lignin. This discovery shows that LPMOs may be involved in lignin oxidation as auxiliary enzymes of lignin-degrading peroxidases during the white-rot fungal decay process.IMPORTANCE The enzymatic biodegradation of structural polysaccharides is affected by the degree of delignification of lignocellulose during the white-rot fungal decay process. The lignin matrix decreases accessibility to the substrates for LPMOs. H2O2 has been studied as a cosubstrate for LPMOs, but the formation and utilization of H2O2 in the reactions still represent an intriguing focus of current research. Lignin-degrading peroxidases and LPMOs usually coexist during fungal decay, and therefore, the relationship between H2O2-dependent lignin-degrading peroxidases and LPMOs should be considered during the wood decay process. The current study revealed that white-rot fungal LPMOs may be involved in the degradation of lignin through driving a versatile form of peroxidase activity in vitro and that H2O2 generated by PoLPMO9A was preferentially used for lignin oxidation by lignin-degrading peroxidase (PsVP). These findings reveal a potential relationship between LPMOs and lignin degradation, which will be of great significance for further understanding the contribution of LPMOs to the white-rot fungal decay process.
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18
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Analytical Enzymatic Saccharification of Lignocellulosic Biomass for Conversion to Biofuels and Bio-Based Chemicals. ENERGIES 2018. [DOI: 10.3390/en11112936] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lignocellulosic feedstocks are an important resource for biorefining of renewables to bio-based fuels, chemicals, and materials. Relevant feedstocks include energy crops, residues from agriculture and forestry, and agro-industrial and forest-industrial residues. The feedstocks differ with respect to their recalcitrance to bioconversion through pretreatment and enzymatic saccharification, which will produce sugars that can be further converted to advanced biofuels and other products through microbial fermentation processes. In analytical enzymatic saccharification, the susceptibility of lignocellulosic samples to pretreatment and enzymatic saccharification is assessed in analytical scale using high-throughput or semi-automated techniques. This type of analysis is particularly relevant for screening of large collections of natural or transgenic varieties of plants that are dedicated to production of biofuels or other bio-based chemicals. In combination with studies of plant physiology and cell wall chemistry, analytical enzymatic saccharification can provide information about the fundamental reasons behind lignocellulose recalcitrance as well as about the potential of collections of plants or different fractions of plants for industrial biorefining. This review is focused on techniques used by researchers for screening the susceptibility of plants to pretreatment and enzymatic saccharification, and advantages and disadvantages that are associated with different approaches.
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19
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Balabanova L, Slepchenko L, Son O, Tekutyeva L. Biotechnology Potential of Marine Fungi Degrading Plant and Algae Polymeric Substrates. Front Microbiol 2018; 9:1527. [PMID: 30050513 PMCID: PMC6052901 DOI: 10.3389/fmicb.2018.01527] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022] Open
Abstract
Filamentous fungi possess the metabolic capacity to degrade environment organic matter, much of which is the plant and algae material enriched with the cell wall carbohydrates and polyphenol complexes that frequently can be assimilated by only marine fungi. As the most renewable energy feedstock on the Earth, the plant or algae polymeric substrates induce an expression of microbial extracellular enzymes that catalyze their cleaving up to the component sugars. However, the question of what the marine fungi contributes to the plant and algae material biotransformation processes has yet to be highlighted sufficiently. In this review, we summarized the potential of marine fungi alternatively to terrestrial fungi to produce the biotechnologically valuable extracellular enzymes in response to the plant and macroalgae polymeric substrates as sources of carbon for their bioconversion used for industries and bioremediation.
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Affiliation(s)
- Larissa Balabanova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Lubov Slepchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Oksana Son
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
| | - Liudmila Tekutyeva
- Innovative Technology Center, Far Eastern Federal University, Vladivostok, Russia
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20
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The effect of a lytic polysaccharide monooxygenase and a xylanase from Gloeophyllum trabeum on the enzymatic hydrolysis of lignocellulosic residues using a commercial cellulase. Enzyme Microb Technol 2018; 113:75-82. [DOI: 10.1016/j.enzmictec.2017.11.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 12/16/2022]
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21
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Liu B, Kognole AA, Wu M, Westereng B, Crowley MF, Kim S, Dimarogona M, Payne CM, Sandgren M. Structural and molecular dynamics studies of a C1‐oxidizing lytic polysaccharide monooxygenase from
Heterobasidion irregulare
reveal amino acids important for substrate recognition. FEBS J 2018; 285:2225-2242. [DOI: 10.1111/febs.14472] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/28/2018] [Accepted: 04/09/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Bing Liu
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - Abhishek A. Kognole
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
| | - Miao Wu
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
| | - Bjørge Westereng
- Department of Chemistry, Biotechnology, and Food Science Norwegian University of Life Sciences Ås Norway
| | | | - Seonah Kim
- Biosciences Center National Renewable Energy Laboratory Golden CO USA
| | - Maria Dimarogona
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
- Department of Chemical Engineering University of Patras Greece
| | - Christina M. Payne
- Department of Chemical and Materials Engineering University of Kentucky Lexington KY USA
- Directorate of Engineering Division of Chemical, Bioengineering, Environmental, and Transport Systems National Science Foundation Alexandria VA USA
| | - Mats Sandgren
- Department of Molecular Sciences Swedish University of Agricultural Sciences Uppsala Sweden
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22
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Production and spectroscopic characterization of lytic polysaccharide monooxygenases. Methods Enzymol 2018; 613:63-90. [DOI: 10.1016/bs.mie.2018.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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23
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Construction of a cellulose-metabolizing Komagataella phaffii (Pichia pastoris) by co-expressing glucanases and β-glucosidase. Appl Microbiol Biotechnol 2017; 102:1297-1306. [DOI: 10.1007/s00253-017-8656-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/12/2017] [Accepted: 11/14/2017] [Indexed: 12/22/2022]
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24
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Bomble YJ, Lin CY, Amore A, Wei H, Holwerda EK, Ciesielski PN, Donohoe BS, Decker SR, Lynd LR, Himmel ME. Lignocellulose deconstruction in the biosphere. Curr Opin Chem Biol 2017; 41:61-70. [DOI: 10.1016/j.cbpa.2017.10.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/18/2022]
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25
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Druzhinina IS, Kubicek CP. Genetic engineering of Trichoderma reesei cellulases and their production. Microb Biotechnol 2017; 10:1485-1499. [PMID: 28557371 PMCID: PMC5658622 DOI: 10.1111/1751-7915.12726] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/11/2017] [Accepted: 04/11/2017] [Indexed: 11/26/2022] Open
Abstract
Lignocellulosic biomass, which mainly consists of cellulose, hemicellulose and lignin, is the most abundant renewable source for production of biofuel and biorefinery products. The industrial use of plant biomass involves mechanical milling or chipping, followed by chemical or physicochemical pretreatment steps to make the material more susceptible to enzymatic hydrolysis. Thereby the cost of enzyme production still presents the major bottleneck, mostly because some of the produced enzymes have low catalytic activity under industrial conditions and/or because the rate of hydrolysis of some enzymes in the secreted enzyme mixture is limiting. Almost all of the lignocellulolytic enzyme cocktails needed for the hydrolysis step are produced by fermentation of the ascomycete Trichoderma reesei (Hypocreales). For this reason, the structure and mechanism of the enzymes involved, the regulation of their expression and the pathways of their formation and secretion have been investigated in T. reesei in considerable details. Several of the findings thereby obtained have been used to improve the formation of the T. reesei cellulases and their properties. In this article, we will review the achievements that have already been made and also show promising fields for further progress.
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Affiliation(s)
- Irina S. Druzhinina
- Microbiology GroupResearch Area Biochemical TechnologyInstitute of Chemical, Environmental and Biological EngineeringTU WienViennaAustria
| | - Christian P. Kubicek
- Microbiology GroupResearch Area Biochemical TechnologyInstitute of Chemical, Environmental and Biological EngineeringTU WienViennaAustria
- Present address:
Steinschötelgasse 7Wien1100Austria
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26
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Abstract
ABSTRACT
The fungal lineage is one of the three large eukaryotic lineages that dominate terrestrial ecosystems. They share a common ancestor with animals in the eukaryotic supergroup Opisthokonta and have a deeper common ancestry with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among all living organisms. This article provides an overview of some of the most important fungal traits, how they evolve, and what major genes and gene families contribute to their development. The traits highlighted here represent just a sample of the characteristics that have evolved in fungi, including polarized multicellular growth, fruiting body development, dimorphism, secondary metabolism, wood decay, and mycorrhizae. However, a great number of other important traits also underlie the evolution of the taxonomically and phenotypically hyperdiverse fungal kingdom, which could fill up a volume on its own. After reviewing the evolution of these six well-studied traits in fungi, we discuss how the recurrent evolution of phenotypic similarity, that is, convergent evolution in the broad sense, has shaped their phylogenetic distribution in extant species.
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27
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Nelson CE, Rogowski A, Morland C, Wilhide JA, Gilbert HJ, Gardner JG. Systems analysis in Cellvibrio japonicus resolves predicted redundancy of β-glucosidases and determines essential physiological functions. Mol Microbiol 2017; 104:294-305. [PMID: 28118504 DOI: 10.1111/mmi.13625] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2017] [Indexed: 12/29/2022]
Abstract
Degradation of polysaccharides forms an essential arc in the carbon cycle, provides a percentage of our daily caloric intake, and is a major driver in the renewable chemical industry. Microorganisms proficient at degrading insoluble polysaccharides possess large numbers of carbohydrate active enzymes (CAZymes), many of which have been categorized as functionally redundant. Here we present data that suggests that CAZymes that have overlapping enzymatic activities can have unique, non-overlapping biological functions in the cell. Our comprehensive study to understand cellodextrin utilization in the soil saprophyte Cellvibrio japonicus found that only one of four predicted β-glucosidases is required in a physiological context. Gene deletion analysis indicated that only the cel3B gene product is essential for efficient cellodextrin utilization in C. japonicus and is constitutively expressed at high levels. Interestingly, expression of individual β-glucosidases in Escherichia coli K-12 enabled this non-cellulolytic bacterium to be fully capable of using cellobiose as a sole carbon source. Furthermore, enzyme kinetic studies indicated that the Cel3A enzyme is significantly more active than the Cel3B enzyme on the oligosaccharides but not disaccharides. Our approach for parsing related CAZymes to determine actual physiological roles in the cell can be applied to other polysaccharide-degradation systems.
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Affiliation(s)
- Cassandra E Nelson
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
| | - Artur Rogowski
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Carl Morland
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Joshua A Wilhide
- Molecular Characterization and Analysis Complex, University of Maryland - Baltimore County, Maryland, USA
| | - Harry J Gilbert
- Molecular Characterization and Analysis Complex, University of Maryland - Baltimore County, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
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28
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Development of a novel compound microbial agent for degradation of kitchen waste. Braz J Microbiol 2017; 48:442-450. [PMID: 28279600 PMCID: PMC5498451 DOI: 10.1016/j.bjm.2016.12.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 11/04/2016] [Accepted: 12/26/2016] [Indexed: 11/20/2022] Open
Abstract
Large quantities of kitchen waste are produced in modern society and its disposal poses serious environmental and social problems. The aim of this study was to isolate degradative strains from kitchen waste and to develop a novel and effective microbial agent. One hundred and four strains were isolated from kitchen waste and the 84 dominant strains were used to inoculate protein-, starch-, fat- and cellulose-containing media for detecting their degradability. Twelve dominant strains of various species with high degradability (eight bacteria, one actinomycetes and three fungi) were selected to develop a compound microbial agent “YH” and five strains of these species including H7 (Brevibacterium epidermidis), A3 (Paenibacillus polymyxa), E3 (Aspergillus japonicus), F9 (Aspergillus versicolor) and A5 (Penicillium digitatum), were new for kitchen waste degradation. YH was compared with three commercial microbial agents—“Tiangeng” (TG), “Yilezai” (YLZ) and Effective Microorganisms (EM), by their effects on reduction, maturity and deodorization. The results showed that YH exerted the greatest efficacy on mass loss which decreased about 65.87% after 14 days. The agent inhibited NH3 and H2S emissions significantly during composting process. The concentration of NH3 decreased from 7.1 to 3.2 ppm and that of H2S reduced from 0.7 to 0.2 ppm. Moreover, E4/E6 (Extinction value460nm/Extinction value665nm) of YH decreased from 2.51 to 1.31, which meant YH had an obvious maturity effect. These results highlighted the potential application of YH in composting kitchen waste.
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29
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Looi HK, Toh YF, Yew SM, Na SL, Tan YC, Chong PS, Khoo JS, Yee WY, Ng KP, Kuan CS. Genomic insight into pathogenicity of dematiaceous fungus Corynespora cassiicola. PeerJ 2017; 5:e2841. [PMID: 28149676 PMCID: PMC5274520 DOI: 10.7717/peerj.2841] [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: 06/07/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023] Open
Abstract
Corynespora cassiicola is a common plant pathogen that causes leaf spot disease in a broad range of crop, and it heavily affect rubber trees in Malaysia (Hsueh, 2011; Nghia et al., 2008). The isolation of UM 591 from a patient's contact lens indicates the pathogenic potential of this dematiaceous fungus in human. However, the underlying factors that contribute to the opportunistic cross-infection have not been fully studied. We employed genome sequencing and gene homology annotations in attempt to identify these factors in UM 591 using data obtained from publicly available bioinformatics databases. The assembly size of UM 591 genome is 41.8 Mbp, and a total of 13,531 (≥99 bp) genes have been predicted. UM 591 is enriched with genes that encode for glycoside hydrolases, carbohydrate esterases, auxiliary activity enzymes and cell wall degrading enzymes. Virulent genes comprising of CAZymes, peptidases, and hypervirulence-associated cutinases were found to be present in the fungal genome. Comparative analysis result shows that UM 591 possesses higher number of carbohydrate esterases family 10 (CE10) CAZymes compared to other species of fungi in this study, and these enzymes hydrolyses wide range of carbohydrate and non-carbohydrate substrates. Putative melanin, siderophore, ent-kaurene, and lycopene biosynthesis gene clusters are predicted, and these gene clusters denote that UM 591 are capable of protecting itself from the UV and chemical stresses, allowing it to adapt to different environment. Putative sterigmatocystin, HC-toxin, cercosporin, and gliotoxin biosynthesis gene cluster are predicted. This finding have highlighted the necrotrophic and invasive nature of UM 591.
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Affiliation(s)
- Hong Keat Looi
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Yue Fen Toh
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Su Mei Yew
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Shiang Ling Na
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Yung-Chie Tan
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Pei-Sin Chong
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Jia-Shiun Khoo
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Wai-Yan Yee
- Department of Science and Technology, Codon Genomics SB, Seri Kembangan, Selangor, Malaysia
| | - Kee Peng Ng
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Chee Sian Kuan
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
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Schuerg T, Prahl JP, Gabriel R, Harth S, Tachea F, Chen CS, Miller M, Masson F, He Q, Brown S, Mirshiaghi M, Liang L, Tom LM, Tanjore D, Sun N, Pray TR, Singer SW. Xylose induces cellulase production in Thermoascus aurantiacus. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:271. [PMID: 29167701 PMCID: PMC5688616 DOI: 10.1186/s13068-017-0965-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/07/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Lignocellulosic biomass is an important resource for renewable production of biofuels and bioproducts. Enzymes that deconstruct this biomass are critical for the viability of biomass-based biofuel production processes. Current commercial enzyme mixtures have limited thermotolerance. Thermophilic fungi may provide enzyme mixtures with greater thermal stability leading to more robust processes. Understanding the induction of biomass-deconstructing enzymes in thermophilic fungi will provide the foundation for strategies to construct hyper-production strains. RESULTS Induction of cellulases using xylan was demonstrated during cultivation of the thermophilic fungus Thermoascus aurantiacus. Simulated fed-batch conditions with xylose induced comparable levels of cellulases. These fed-batch conditions were adapted to produce enzymes in 2 and 19 L bioreactors using xylose and xylose-rich hydrolysate from dilute acid pretreatment of corn stover. Enzymes from T. aurantiacus that were produced in the xylose-fed bioreactor demonstrated comparable performance in the saccharification of deacetylated, dilute acid-pretreated corn stover when compared to a commercial enzyme mixture at 50 °C. The T. aurantiacus enzymes retained this activity at of 60 °C while the commercial enzyme mixture was largely inactivated. CONCLUSIONS Xylose induces both cellulase and xylanase production in T. aurantiacus and was used to produce enzymes at up to the 19 L bioreactor scale. The demonstration of induction by xylose-rich hydrolysate and saccharification of deacetylated, dilute acid-pretreated corn stover suggests a scenario to couple biomass pretreatment with onsite enzyme production in a biorefinery. This work further demonstrates the potential for T. aurantiacus as a thermophilic platform for cellulase development.
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Affiliation(s)
- Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Chyi-Shin Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Matthew Miller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Fabrice Masson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Qian He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Sarah Brown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Mona Mirshiaghi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ling Liang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Lauren M. Tom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Ning Sun
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Todd R. Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
- Advanced Biofuels Process Development Unit, Emeryville, CA USA
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608 USA
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Kubicek CP, Kubicek EM. Enzymatic deconstruction of plant biomass by fungal enzymes. Curr Opin Chem Biol 2016; 35:51-57. [DOI: 10.1016/j.cbpa.2016.08.028] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
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Abstract
Complex carbohydrates are ubiquitous in all kingdoms of life. As major components of the plant cell wall they constitute both a rich renewable carbon source for biotechnological transformation into fuels, chemicals and materials, and also form an important energy source as part of a healthy human diet. In both contexts, there has been significant, sustained interest in understanding how microbes transform these substrates. Classical perspectives of microbial polysaccharide degradation are currently being augmented by recent advances in the discovery of lytic polysaccharide monooxygenases (LPMOs) and polysaccharide utilization loci (PULs). Fundamental discoveries in carbohydrate enzymology are both advancing biological understanding, as well as informing applications in industrial biomass conversion and modulation of the human gut microbiota to mediate health benefits.
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Corrêa TLR, dos Santos LV, Pereira GAG. AA9 and AA10: from enigmatic to essential enzymes. Appl Microbiol Biotechnol 2016; 100:9-16. [PMID: 26476647 DOI: 10.1007/s00253-015-7040-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 12/15/2022]
Abstract
The lignocellulosic biomass, comprised mainly of cellulose, hemicellulose, and lignin, is a strong competitor for petroleum to obtain fuels and other products because of its renewable nature, low cost, and non-competitiveness with food production when obtained from agricultural waste. Due to its recalcitrance, lignocellulosic material requires an arsenal of enzymes for its deconstruction and the consequent release of fermentable sugars. In this context, enzymes currently classified as auxiliary activity 9 (AA9/formerly GH61) and 10 (AA10/formerly CBM 33) or lytic polysaccharide monooxygenases (LPMO) have emerged as cellulase boosting enzymes. AA9 and AA10 are the new paradigm for deconstruction of lignocellulosic biomass by enhancing the activity and decreasing the loading of classical enzymes to the reaction and, consequently, reducing costs of the hydrolysis step in the second-generation ethanol production chain. In view of that disclosed above, the goal of this work is to review experimental data that supports the relevance of AA9 and AA10 for the biomass deconstruction field.
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Shida Y, Furukawa T, Ogasawara W. Deciphering the molecular mechanisms behind cellulase production in Trichoderma reesei, the hyper-cellulolytic filamentous fungus. Biosci Biotechnol Biochem 2016; 80:1712-29. [DOI: 10.1080/09168451.2016.1171701] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Abstract
The filamentous fungus Trichoderma reesei is a potent cellulase producer and the best-studied cellulolytic fungus. A lot of investigations not only on glycoside hydrolases produced by T. reesei, but also on the machinery controlling gene expression of these enzyme have made this fungus a model organism for cellulolytic fungi. We have investigated the T. reesei strain including mutants developed in Japan in detail to understand the molecular mechanisms that control the cellulase gene expression, the biochemical and morphological aspects that could favor this phenotype, and have attempted to generate novel strains that may be appropriate for industrial use. Subsequently, we developed recombinant strains by combination of these insights and the heterologous-efficient saccharifing enzymes. Resulting enzyme preparations were highly effective for saccharification of various biomass. In this review, we present some of the salient findings from the recent biochemical, morphological, and molecular analyses of this remarkable cellulase hyper-producing fungus.
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Affiliation(s)
- Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Takanori Furukawa
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
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Activating Intrinsic Carbohydrate-Active Enzymes of the Smut Fungus Ustilago maydis for the Degradation of Plant Cell Wall Components. Appl Environ Microbiol 2016; 82:5174-85. [PMID: 27316952 DOI: 10.1128/aem.00713-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/10/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The microbial conversion of plant biomass to valuable products in a consolidated bioprocess could greatly increase the ecologic and economic impact of a biorefinery. Current strategies for hydrolyzing plant material mostly rely on the external application of carbohydrate-active enzymes (CAZymes). Alternatively, production organisms can be engineered to secrete CAZymes to reduce the reliance on externally added enzymes. Plant-pathogenic fungi have a vast repertoire of hydrolytic enzymes to sustain their lifestyle, but expression of the corresponding genes is usually highly regulated and restricted to the pathogenic phase. Here, we present a new strategy in using the biotrophic smut fungus Ustilago maydis for the degradation of plant cell wall components by activating its intrinsic enzyme potential during axenic growth. This fungal model organism is fully equipped with hydrolytic enzymes, and moreover, it naturally produces value-added substances, such as organic acids and biosurfactants. To achieve the deregulated expression of hydrolytic enzymes during the industrially relevant yeast-like growth in axenic culture, the native promoters of the respective genes were replaced by constitutively active synthetic promoters. This led to an enhanced conversion of xylan, cellobiose, and carboxymethyl cellulose to fermentable sugars. Moreover, a combination of strains with activated endoglucanase and β-glucanase increased the release of glucose from carboxymethyl cellulose and regenerated amorphous cellulose, suggesting that mixed cultivations could be a means for degrading more complex substrates in the future. In summary, this proof of principle demonstrates the potential applicability of activating the expression of native CAZymes from phytopathogens in a biocatalytic process. IMPORTANCE This study describes basic experiments that aim at the degradation of plant cell wall components by the smut fungus Ustilago maydis As a plant pathogen, this fungus contains a set of lignocellulose-degrading enzymes that may be suited for biomass degradation. However, its hydrolytic enzymes are specifically expressed only during plant infection. Here, we provide the proof of principle that these intrinsic enzymes can be synthetically activated during the industrially relevant yeast-like growth. The fungus is known to naturally synthesize valuable compounds, such as itaconate or glycolipids. Therefore, it could be suited for use in a consolidated bioprocess in which more complex and natural substrates are simultaneously converted to fermentable sugars and to value-added compounds in the future.
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Gupta VK, Kubicek CP, Berrin JG, Wilson DW, Couturier M, Berlin A, Filho EXF, Ezeji T. Fungal Enzymes for Bio-Products from Sustainable and Waste Biomass. Trends Biochem Sci 2016; 41:633-645. [PMID: 27211037 DOI: 10.1016/j.tibs.2016.04.006] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/13/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Lignocellulose, the most abundant renewable carbon source on earth, is the logical candidate to replace fossil carbon as the major biofuel raw material. Nevertheless, the technologies needed to convert lignocellulose into soluble products that can then be utilized by the chemical or fuel industries face several challenges. Enzymatic hydrolysis is of major importance, and we review the progress made in fungal enzyme technology over the past few years with major emphasis on (i) the enzymes needed for the conversion of polysaccharides (cellulose and hemicellulose) into soluble products, (ii) the potential uses of lignin degradation products, and (iii) current progress and bottlenecks for the use of the soluble lignocellulose derivatives in emerging biorefineries.
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Affiliation(s)
- Vijai K Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, National University of Ireland Galway, Galway City, Ireland.
| | - Christian P Kubicek
- Biotechnology and Microbiology, Institute of Chemical Engineering, Technische Universität Wien, Gumpendorferstrasse, 1060 Wien, Austria
| | - Jean-Guy Berrin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1163-Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France; Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France
| | - David W Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Marie Couturier
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche (UMR) 1163-Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France; Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Avenue de Luminy, 13288 Marseille, France
| | - Alex Berlin
- Novozymes, Inc., 1445 Drew Ave, Davis CA 95618 USA
| | - Edivaldo X F Filho
- Laboratory of Enzymology, Department of Cell Biology, University of Brasilia, Asa Norte, 70910-900 Brasilia, DF Brazil
| | - Thaddeus Ezeji
- Biotechnology and Fermentation Group, Department of Animal Sciences, Ohio State University and Ohio Agricultural Research and Development Center (OARDC), Madison Avenue, Wooster, OH 44691, USA
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Patyshakuliyeva A, Arentshorst M, Allijn IE, Ram AFJ, de Vries RP, Gelber IB. Improving cellulase production by Aspergillus niger using adaptive evolution. Biotechnol Lett 2016; 38:969-74. [PMID: 26879082 PMCID: PMC4853455 DOI: 10.1007/s10529-016-2060-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/03/2016] [Indexed: 11/29/2022]
Abstract
Objectives To evaluate the potential of adaptive evolution as a tool in generating strains with an improved production of plant biomass degrading enzymes. Results An Aspergillus niger cellulase mutant was obtained by adaptive evolution. Physiological properties of this mutant revealed a five times higher cellulose production than the parental strain. Transcriptomic analysis revealed that the expression of noxR, encoding the regulatory subunit of the NADPH oxidase complex, was reduced in the mutant compared to the parental strain. Subsequent analysis of a noxR knockout strain showed the same phenotypic effect as observed for the evolution mutant, confirming the role of NoxR in cellulose degradation. Conclusions Adaptive evolution is an efficient approach to modify a strain and activate genes involved in polysaccharide degradation.
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Affiliation(s)
| | - Mark Arentshorst
- Molecular Microbiology and Biotechnology, Leiden University, Leiden, The Netherlands
| | - Iris E Allijn
- Fungal Molecular Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Utrecht, The Netherlands
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Leiden University, Leiden, The Netherlands
| | - Ronald P de Vries
- Fungal Molecular Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Utrecht, The Netherlands
| | - Isabelle Benoit Gelber
- Fungal Molecular Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Utrecht, The Netherlands.
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The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Moses V, Hatherley R, Tastan Bishop Ö. Bioinformatic characterization of type-specific sequence and structural features in auxiliary activity family 9 proteins. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:239. [PMID: 27833654 PMCID: PMC5101804 DOI: 10.1186/s13068-016-0655-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/25/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Due to the impending depletion of fossil fuels, it has become important to identify alternative energy sources. The biofuel industry has proven to be a promising alternative. However, owing to the complex nature of plant biomass, hence the degradation, biofuel production remains a challenge. The copper-dependent Auxiliary Activity family 9 (AA9) proteins have been found to act synergistically with other cellulose-degrading enzymes resulting in an increased rate of cellulose breakdown. AA9 proteins are lytic polysaccharide monooxygenase (LPMO) enzymes, otherwise known as polysaccharide monooxygenases (PMOs). They are further classified as Type 1, 2 or 3 PMOs, depending on the different cleavage products formed. As AA9 proteins are known to exhibit low sequence conservation, the analysis of unique features of AA9 domains of these enzymes should provide insights for the better understanding of how different AA9 PMO types function. RESULTS Bioinformatics approaches were used to identify features specific to the catalytic AA9 domains of each type of AA9 PMO. Sequence analysis showed the N terminus to be highly variable with type-specific inserts evident in this region. Phylogenetic analysis was performed to cluster AA9 domains based on their types. Motif analysis enabled the identification of sub-groups within each AA9 PMO type with the majority of these motifs occurring within the highly variable N terminus of AA9 domains. AA9 domain structures were manually docked to crystalline cellulose and used to analyze both the type-specific inserts and motifs at a structural level. The results indicated that these regions influence the AA9 domain active site topology and may contribute to the regioselectivity displayed by different AA9 PMO types. Physicochemical property analysis was performed and detected significant differences in aromaticity, isoelectric point and instability index between certain AA9 PMO types. CONCLUSIONS In this study, a type-specific characterisation of AA9 domains was performed using various bioinformatics approaches. These highly variable proteins were found to have a greater degree of conservation within their respective types. Type-specific features were identified for AA9 domains, which could be observed at a sequence, structural and physicochemical level. This provides a basis under which to identify and group new AA9 LPMOs in future.
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Affiliation(s)
- Vuyani Moses
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
| | - Rowan Hatherley
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140 South Africa
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Mahajan C, Basotra N, Singh S, Di Falco M, Tsang A, Chadha BS. Malbranchea cinnamomea: A thermophilic fungal source of catalytically efficient lignocellulolytic glycosyl hydrolases and metal dependent enzymes. BIORESOURCE TECHNOLOGY 2016; 200:55-63. [PMID: 26476165 DOI: 10.1016/j.biortech.2015.09.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 05/11/2023]
Abstract
This study reports thermophilic fungus Malbranchea cinnamomea as an important source of lignocellulolytic enzymes. The secretome analysis using LC-MS/MS orbitrap showed that fungus produced a spectrum of glycosyl hydrolases (cellulase/hemicellulase), polysaccharide lyases (PL) and carbohydrate esterases (CE) in addition to cellobiose dehydrogenase (CDH) indicating the presence of functional classical and oxidative cellulolytic mechanisms. The protein fractions in the secretome resolved by ion exchange chromatography were analyzed for ability to hydrolyze alkali treated carrot grass (ATCG) in the presence of Mn(2+)/Cu(2+). This strategy in tandem with peptide mass fingerprinting led to identification of metal dependent protein hydrolases with no apparent hydrolytic activity, however, showed 5.7 folds higher saccharification in presence of Mn(2+). Furthermore, adding different protein fractions to commercial cellulase (Novozymes: Cellic CTec2) resulted in enhanced hydrolysis of ATCG ranging between 1.57 and 3.43 folds indicating the enzymes from M. cinnamomea as catalytically efficient.
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Affiliation(s)
- Chhavi Mahajan
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
| | - Neha Basotra
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
| | - Surender Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Marcos Di Falco
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - B S Chadha
- Department of Microbiology, Guru Nanak Dev University, Amritsar 143005, Punjab, India.
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Shida Y, Yamaguchi K, Nitta M, Nakamura A, Takahashi M, Kidokoro SI, Mori K, Tashiro K, Kuhara S, Matsuzawa T, Yaoi K, Sakamoto Y, Tanaka N, Morikawa Y, Ogasawara W. The impact of a single-nucleotide mutation of bgl2 on cellulase induction in a Trichoderma reesei mutant. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:230. [PMID: 26719764 PMCID: PMC4696228 DOI: 10.1186/s13068-015-0420-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/15/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina) produces increased cellulase expression when grown on cellulose or its derivatives as a sole carbon source. It has been believed that β-glucosidases of T. reesei not only metabolize cellobiose but also contribute in the production of inducers of cellulase gene expression by their transglycosylation activity. The cellulase hyper-producing mutant PC-3-7 developed in Japan has enhanced cellulase production ability when cellobiose is used as the inducer. The comparative genomics analysis of PC-3-7 and its parent revealed a single-nucleotide mutation within the bgl2 gene encoding intracellular β-glucosidase II (BGLII/Cel1a), giving rise to an amino acid substitution in PC-3-7, which could potentially account for the enhanced cellulase expression when these strains are cultivated on cellulose and cellobiose. RESULTS To analyze the effects of the BGLII mutation in cellulase induction, we constructed both a bgl2 revertant and a disruptant. Enzymatic analysis of the transformant lysates showed that the strain expressing mutant BGLII exhibited weakened cellobiose hydrolytic activity, but produced some transglycosylation products, suggesting that the SNP in bgl2 strongly diminished cellobiase activity, but did not result in complete loss of function of BGLII. The analysis of the recombinant BGLII revealed that transglycosylation products might be oligosaccharides, composed probably of glucose linked β-1,4, β-1,3, or a mixture of both. PC-3-7 revertants of bgl2 exhibited reduced expression and inducibility of cellulase during growth on cellulose and cellobiose substrates. Furthermore, the effect of this bgl2 mutation was reproduced in the common strain QM9414 in which the transformants showed cellulase production comparable to that of PC-3-7. CONCLUSION We conclude that BGLII plays an important role in cellulase induction in T. reesei and that the bgl2 mutation in PC-3-7 brought about enhanced cellulase expression on cellobiose. The results of the investigation using PC-3-7 suggested that other mutation(s) in PC-3-7 could also contribute to cellulase induction. Further investigation is essential to unravel the mechanism responsible for cellulase induction in T. reesei.
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Affiliation(s)
- Yosuke Shida
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kaori Yamaguchi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Mikiko Nitta
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
- />Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 Japan
| | - Ayana Nakamura
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Machiko Takahashi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Shun-ichi Kidokoro
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kazuki Mori
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Kosuke Tashiro
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Satoru Kuhara
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Tomohiko Matsuzawa
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Katsuro Yaoi
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Yasumitsu Sakamoto
- />School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694 Japan
| | - Nobutada Tanaka
- />School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555 Japan
| | - Yasushi Morikawa
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Wataru Ogasawara
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
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Nagy LG, Riley R, Tritt A, Adam C, Daum C, Floudas D, Sun H, Yadav JS, Pangilinan J, Larsson KH, Matsuura K, Barry K, Labutti K, Kuo R, Ohm RA, Bhattacharya SS, Shirouzu T, Yoshinaga Y, Martin FM, Grigoriev IV, Hibbett DS. Comparative Genomics of Early-Diverging Mushroom-Forming Fungi Provides Insights into the Origins of Lignocellulose Decay Capabilities. Mol Biol Evol 2015; 33:959-70. [DOI: 10.1093/molbev/msv337] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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Lytic Polysaccharide Monooxygenases in Biomass Conversion. Trends Biotechnol 2015; 33:747-761. [DOI: 10.1016/j.tibtech.2015.09.006] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/28/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
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Jung S, Song Y, Kim HM, Bae HJ. Enhanced lignocellulosic biomass hydrolysis by oxidative lytic polysaccharide monooxygenases (LPMOs) GH61 from Gloeophyllum trabeum. Enzyme Microb Technol 2015; 77:38-45. [DOI: 10.1016/j.enzmictec.2015.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 01/13/2023]
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Borisova AS, Isaksen T, Dimarogona M, Kognole AA, Mathiesen G, Várnai A, Røhr ÅK, Payne CM, Sørlie M, Sandgren M, Eijsink VGH. Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity. J Biol Chem 2015; 290:22955-69. [PMID: 26178376 DOI: 10.1074/jbc.m115.660183] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 01/02/2023] Open
Abstract
The recently discovered lytic polysaccharide monooxygenases (LPMOs) carry out oxidative cleavage of polysaccharides and are of major importance for efficient processing of biomass. NcLPMO9C from Neurospora crassa acts both on cellulose and on non-cellulose β-glucans, including cellodextrins and xyloglucan. The crystal structure of the catalytic domain of NcLPMO9C revealed an extended, highly polar substrate-binding surface well suited to interact with a variety of sugar substrates. The ability of NcLPMO9C to act on soluble substrates was exploited to study enzyme-substrate interactions. EPR studies demonstrated that the Cu(2+) center environment is altered upon substrate binding, whereas isothermal titration calorimetry studies revealed binding affinities in the low micromolar range for polymeric substrates that are due in part to the presence of a carbohydrate-binding module (CBM1). Importantly, the novel structure of NcLPMO9C enabled a comparative study, revealing that the oxidative regioselectivity of LPMO9s (C1, C4, or both) correlates with distinct structural features of the copper coordination sphere. In strictly C1-oxidizing LPMO9s, access to the solvent-facing axial coordination position is restricted by a conserved tyrosine residue, whereas access to this same position seems unrestricted in C4-oxidizing LPMO9s. LPMO9s known to produce a mixture of C1- and C4-oxidized products show an intermediate situation.
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Affiliation(s)
- Anna S Borisova
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Trine Isaksen
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Maria Dimarogona
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
| | - Abhishek A Kognole
- the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Geir Mathiesen
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Anikó Várnai
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Åsmund K Røhr
- the Department of Biosciences, University of Oslo, N-0316 Oslo, Norway, and
| | - Christina M Payne
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden, the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506
| | - Morten Sørlie
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway
| | - Mats Sandgren
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden,
| | - Vincent G H Eijsink
- the Department of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences, N-1432 Ås, Norway,
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Lo Leggio L, Simmons TJ, Poulsen JCN, Frandsen KEH, Hemsworth GR, Stringer MA, von Freiesleben P, Tovborg M, Johansen KS, De Maria L, Harris PV, Soong CL, Dupree P, Tryfona T, Lenfant N, Henrissat B, Davies GJ, Walton PH. Structure and boosting activity of a starch-degrading lytic polysaccharide monooxygenase. Nat Commun 2015; 6:5961. [PMID: 25608804 PMCID: PMC4338556 DOI: 10.1038/ncomms6961] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 11/25/2014] [Indexed: 12/23/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are recently discovered enzymes that oxidatively deconstruct polysaccharides. LPMOs are fundamental in the effective utilization of these substrates by bacteria and fungi; moreover, the enzymes have significant industrial importance. We report here the activity, spectroscopy and three-dimensional structure of a starch-active LPMO, a representative of the new CAZy AA13 family. We demonstrate that these enzymes generate aldonic acid-terminated malto-oligosaccharides from retrograded starch and boost significantly the conversion of this recalcitrant substrate to maltose by β-amylase. The detailed structure of the enzyme's active site yields insights into the mechanism of action of this important class of enzymes.
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Affiliation(s)
- Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Thomas J. Simmons
- Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | | | - Kristian E. H. Frandsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | | | | | | | | | | | | | - Paul V. Harris
- Novozymes, Inc., 1445 Drew Avenue, Davis, California 95618, USA
| | - Chee-Leong Soong
- Novozymes North America Inc., 77 Perrys Chapel Church Road, Franklinton, North Carolina 27525, USA
| | - Paul Dupree
- Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Theodora Tryfona
- Department of Biochemistry, University Of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
| | - Nicolas Lenfant
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Paul H. Walton
- Department of Chemistry, University of York, York YO10 5DD, UK
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Dollhofer V, Podmirseg SM, Callaghan TM, Griffith GW, Fliegerová K. Anaerobic Fungi and Their Potential for Biogas Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 151:41-61. [PMID: 26337843 DOI: 10.1007/978-3-319-21993-6_2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Plant biomass is the largest reservoir of environmentally friendly renewable energy on earth. However, the complex and recalcitrant structure of these lignocellulose-rich substrates is a severe limitation for biogas production. Microbial pro-ventricular anaerobic digestion of ruminants can serve as a model for improvement of converting lignocellulosic biomass into energy. Anaerobic fungi are key players in the digestive system of various animals, they produce a plethora of plant carbohydrate hydrolysing enzymes. Combined with the invasive growth of their rhizoid system their contribution to cell wall polysaccharide decomposition may greatly exceed that of bacteria. The cellulolytic arsenal of anaerobic fungi consists of both secreted enzymes, as well as extracellular multi-enzyme complexes called cellulosomes. These complexes are extremely active, can degrade both amorphous and crystalline cellulose and are probably the main reason of cellulolytic efficiency of anaerobic fungi. The synergistic use of mechanical and enzymatic degradation makes anaerobic fungi promising candidates to improve biogas production from recalcitrant biomass. This chapter presents an overview about their biology and their potential for implementation in the biogas process.
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Affiliation(s)
- Veronika Dollhofer
- Bavarian State Research Center for Agriculture, Central Department for Quality Assurance and Analytics, Micro- and Molecular Biology, Lange Point 6, 85354, Freising, Germany,
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Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:220. [PMID: 26697109 PMCID: PMC4687162 DOI: 10.1186/s13068-015-0402-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/30/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. RESULTS CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. CONCLUSION We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Taichi E. Takasuka
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Kai Deng
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Sandia National Laboratories, Livermore, CA 94551 USA
| | - Christopher M. Bianchetti
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, WI 54901 USA
| | - Hannah S. Udell
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ben M. Prom
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hyunkee Kim
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Paul D. Adams
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- />Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Trent R. Northen
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Brian G. Fox
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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49
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Bennati-Granier C, Garajova S, Champion C, Grisel S, Haon M, Zhou S, Fanuel M, Ropartz D, Rogniaux H, Gimbert I, Record E, Berrin JG. Substrate specificity and regioselectivity of fungal AA9 lytic polysaccharide monooxygenases secreted by Podospora anserina. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:90. [PMID: 26136828 PMCID: PMC4487207 DOI: 10.1186/s13068-015-0274-3] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/12/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND The understanding of enzymatic polysaccharide degradation has progressed intensely in the past few years with the identification of a new class of fungal-secreted enzymes, the lytic polysaccharide monooxygenases (LPMOs) that enhance cellulose conversion. In the fungal kingdom, saprotrophic fungi display a high number of genes encoding LPMOs from family AA9 but the functional relevance of this redundancy is not fully understood. RESULTS In this study, we investigated a set of AA9 LPMOs identified in the secretomes of the coprophilous ascomycete Podospora anserina, a biomass degrader of recalcitrant substrates. Their activity was assayed on cellulose in synergy with the cellobiose dehydrogenase from the same organism. We showed that the total release of oxidized oligosaccharides from cellulose was higher for PaLPMO9A, PaLPMO9E, and PaLPMO9H that harbored a carbohydrate-binding module from the family CBM1. Investigation of their regioselective mode of action revealed that PaLPMO9A and PaLPMO9H oxidatively cleaved at both C1 and C4 positions while PaLPMO9E released only C1-oxidized products. Rapid cleavage of cellulose was observed using PaLPMO9H that was the most versatile in terms of substrate specificity as it also displayed activity on cello-oligosaccharides and β-(1,4)-linked hemicellulose polysaccharides (e.g., xyloglucan, glucomannan). CONCLUSIONS This study provides insights into the mode of cleavage and substrate specificities of fungal AA9 LPMOs that will facilitate their application for the development of future biorefineries.
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Affiliation(s)
- Chloé Bennati-Granier
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Sona Garajova
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
- />Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Charlotte Champion
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Sacha Grisel
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Mireille Haon
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Simeng Zhou
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Mathieu Fanuel
- />INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - David Ropartz
- />INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - Hélène Rogniaux
- />INRA, Plateforme BIBS, Unité de Recherche Biopolymères, Interactions, Assemblages, 44316 Nantes, France
| | - Isabelle Gimbert
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Eric Record
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
| | - Jean-Guy Berrin
- />INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Faculté des Sciences de Luminy, ESIL Polytech, F-13288 Marseille, France
- />Polytech Marseille, Aix Marseille Université, F-13288 Marseille, France
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Affiliation(s)
- Adrian Tsang
- Centre for Structural and Functional Genomics Concordia University 7141 Sherbrooke Street West Montreal, Quebec H4B1R6 Canada
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