51
|
Qu MB, Guo XX, Kong L, Hou LJ, Yang Q. A midgut-specific lytic polysaccharide monooxygenase of Locusta migratoria is indispensable for the deconstruction of the peritrophic matrix. INSECT SCIENCE 2022; 29:1287-1298. [PMID: 35150068 DOI: 10.1111/1744-7917.13016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are important enzymes that boost the hydrolysis of recalcitrant polysaccharides, such as chitin. They are found extensively in different insect species and are classified as auxiliary activities family 15 (AA15) LPMOs (LPMO15). Some of them were identified from the insect midgut and proven to act on chitin. However, knowledge about their physiological roles during insect growth and development remains limited. Here, we found that midgut-specific LPMO15s are widely distributed in different insect orders, such as the orthopteran Locusta migratoria and the lepidopteran Bombyx mori. Using L. migratoria as a model insect, the function of midgut-specific LmLPMO15-3 during development was investigated. Double-stranded RNA-mediated downregulation of LmLPMO15-3 expression at the 4th or 5th instar nymph stage severely decreased the survival rate and resulted in lethal phenotypes. Hematoxylin and eosin staining results indicated that the deficient individuals exhibited incompletely digested peritrophic matrix (PM), which suggested that LmLPMO15-3 is essential for the deconstruction of the PM during molting. This study provides direct evidence of the physiological importance of a midgut-specific LPMO15 during insect development. As L. migratoria is one of the most destructive agricultural pests, LmLPMO15-3 is a potential target for pest management.
Collapse
Affiliation(s)
- Ming-Bo Qu
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning Province, China
| | - Xiao-Xi Guo
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning Province, China
| | - Lin Kong
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning Province, China
| | - Ling-Jie Hou
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning Province, China
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning Province, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| |
Collapse
|
52
|
Ngo ST, Phan HN, Luu CX, Le CN, Ho GT, Ngo NTC, Le LQ, Mai BK, Phung HTT, Nguyen HD, Vu KB, Vu VV. Distal Hydrophobic Loop Modulates the Copper Active Site and Reaction of AA13 Polysaccharide Monooxygenases. J Phys Chem B 2022; 126:7567-7578. [PMID: 36137238 DOI: 10.1021/acs.jpcb.2c04215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polysaccharide monooxygenases (PMOs) use a type-2 copper center to activate O2 for the selective hydroxylation of one of the two C-H bonds of glycosidic linkages. Our electron paramagnetic resonance (EPR) analysis and molecular dynamics (MD) simulations suggest the unprecedented dynamic roles of the loop containing the residue G89 (G89 loop) on the active site structure and reaction cycle of starch-active PMOs (AA13 PMOs). In the Cu(II) state, the G89 loop could switch between an "open" and "closed" conformation, which is associated with the binding and dissociation of an aqueous ligand in the distal site, respectively. The conformation of the G89 loop influences the positioning of the copper center on the preferred substrate of AA13 PMOs. The dissociation of the distal ligand results in the bending of the T-shaped core of the Cu(II) active site, which could help facilitate its reduction to the active Cu(I) state. In the Cu(I) state, the G89 loop is in the "closed" conformation with a confined copper center, which could allow for efficient O2 binding. In addition, the G89 loop remains in the "closed" conformation in the Cu(II)-superoxo intermediate, which could prevent off-pathway superoxide release via exchange with the distal aqueous ligand. Finally, at the end of the reaction cycle, aqueous ligand binding to the distal site could switch the G89 loop to the "open" conformation and facilitate product release.
Collapse
Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam.,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | - Han N Phan
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam
| | - Cuong X Luu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam
| | - Chinh N Le
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam
| | - Giap T Ho
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam
| | - Nhung T C Ngo
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam
| | - Loan Q Le
- Institute of Tropical Biology, Vietnam Academy of Science and Technology, 9/621 Hanoi Highway, Thu Duc District, Ho Chi Minh City 700000, Vietnam
| | - Binh Khanh Mai
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Huong T T Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam
| | - Hoang-Dung Nguyen
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam.,Institute of Tropical Biology, Vietnam Academy of Science and Technology, 9/621 Hanoi Highway, Thu Duc District, Ho Chi Minh City 700000, Vietnam
| | - Khanh B Vu
- Department of Chemical Engineering, School of Biotechnology, International University, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 700000, Vietnam.,Vietnam National University, Quarter 6, Linh Trung Ward, Thu Duc District, Ho Chi Minh City 700000, Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, District 4, Ho Chi Minh City 700000, Vietnam
| |
Collapse
|
53
|
Moon M, Lee JP, Park GW, Lee JS, Park HJ, Min K. Lytic polysaccharide monooxygenase (LPMO)-derived saccharification of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2022; 359:127501. [PMID: 35753567 DOI: 10.1016/j.biortech.2022.127501] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Given that traditional biorefineries have been based on microbial fermentation to produce useful fuels, materials, and chemicals as metabolites, saccharification is an important step to obtain fermentable sugars from biomass. It is well-known that glycosidic hydrolases (GHs) are responsible for the saccharification of recalcitrant polysaccharides through hydrolysis, but the discovery of lytic polysaccharide monooxygenase (LPMO), which is a kind of oxidative enzyme involved in cleaving polysaccharides and boosting GH performance, has profoundly changed the understanding of enzyme-based saccharification. This review briefly introduces the classification, structural information, and catalytic mechanism of LPMOs. In addition to recombinant expression strategies, synergistic effects with GH are comprehensively discussed. Challenges and perspectives for LPMO-based saccharification on a large scale are also briefly mentioned. Ultimately, this review can provide insights for constructing an economically viable lignocellulose-based biorefinery system and a closed-carbon loop to cope with climate change.
Collapse
Affiliation(s)
- Myounghoon Moon
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Joon-Pyo Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Gwon Woo Park
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Jin-Suk Lee
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea
| | - Hyun June Park
- Department of Biotechnology, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Kyoungseon Min
- Gwangju Bio/Energy R&D Center, Korea Institute of Energy Research (KIER), Gwangju 61003, Republic of Korea.
| |
Collapse
|
54
|
Detomasi TC, Rico-Ramírez AM, Sayler RI, Gonçalves AP, Marletta MA, Glass NL. A moonlighting function of a chitin polysaccharide monooxygenase, CWR-1, in Neurospora crassa allorecognition. eLife 2022; 11:e80459. [PMID: 36040303 PMCID: PMC9550227 DOI: 10.7554/elife.80459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Organisms require the ability to differentiate themselves from organisms of different or even the same species. Allorecognition processes in filamentous fungi are essential to ensure identity of an interconnected syncytial colony to protect it from exploitation and disease. Neurospora crassa has three cell fusion checkpoints controlling formation of an interconnected mycelial network. The locus that controls the second checkpoint, which allows for cell wall dissolution and subsequent fusion between cells/hyphae, cwr (cell wall remodeling), encodes two linked genes, cwr-1 and cwr-2. Previously, it was shown that cwr-1 and cwr-2 show severe linkage disequilibrium with six different haplogroups present in N. crassa populations. Isolates from an identical cwr haplogroup show robust fusion, while somatic cell fusion between isolates of different haplogroups is significantly blocked in cell wall dissolution. The cwr-1 gene encodes a putative polysaccharide monooxygenase (PMO). Herein we confirm that CWR-1 is a C1-oxidizing chitin PMO. We show that the catalytic (PMO) domain of CWR-1 was sufficient for checkpoint function and cell fusion blockage; however, through analysis of active-site, histidine-brace mutants, the catalytic activity of CWR-1 was ruled out as a major factor for allorecognition. Swapping a portion of the PMO domain (V86 to T130) did not switch cwr haplogroup specificity, but rather cells containing this chimera exhibited a novel haplogroup specificity. Allorecognition to mediate cell fusion blockage is likely occurring through a protein-protein interaction between CWR-1 with CWR-2. These data highlight a moonlighting role in allorecognition of the CWR-1 PMO domain.
Collapse
Affiliation(s)
- Tyler C Detomasi
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Adriana M Rico-Ramírez
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Richard I Sayler
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
| | - A Pedro Gonçalves
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Michael A Marletta
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| |
Collapse
|
55
|
Zheng B, Yu S, Chen Z, Huo YX. A consolidated review of commercial-scale high-value products from lignocellulosic biomass. Front Microbiol 2022; 13:933882. [PMID: 36081794 PMCID: PMC9445815 DOI: 10.3389/fmicb.2022.933882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
For decades, lignocellulosic biomass has been introduced to the public as the most important raw material for the environmentally and economically sustainable production of high-valued bioproducts by microorganisms. However, due to the strong recalcitrant structure, the lignocellulosic materials have major limitations to obtain fermentable sugars for transformation into value-added products, e.g., bioethanol, biobutanol, biohydrogen, etc. In this review, we analyzed the recent trends in bioenergy production from pretreated lignocellulose, with special attention to the new strategies for overcoming pretreatment barriers. In addition, persistent challenges in developing for low-cost advanced processing technologies are also pointed out, illustrating new approaches to addressing the global energy crisis and climate change caused by the use of fossil fuels. The insights given in this study will enable a better understanding of current processes and facilitate further development on lignocellulosic bioenergy production.
Collapse
Affiliation(s)
- Bo Zheng
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| |
Collapse
|
56
|
Chitin-Active Lytic Polysaccharide Monooxygenases Are Rare in Cellulomonas Species. Appl Environ Microbiol 2022; 88:e0096822. [PMID: 35862679 PMCID: PMC9361826 DOI: 10.1128/aem.00968-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cellulomonas flavigena is a saprotrophic bacterium that encodes, within its genome, four predicted lytic polysaccharide monooxygenases (LPMOs) from Auxiliary Activity family 10 (AA10). We showed previously that three of these cleave the plant polysaccharide cellulose by oxidation at carbon-1 (J. Li, L. Solhi, E.D. Goddard-Borger, Y. Mattieu et al., Biotechnol Biofuels 14:29, 2021, https://doi.org/10.1186/s13068-020-01860-3). Here, we present the biochemical characterization of the fourth C. flavigena AA10 member (CflaLPMO10D) as a chitin-active LPMO. Both the full-length CflaLPMO10D-Carbohydrate-Binding Module family 2 (CBM2) and catalytic module-only proteins were produced in Escherichia coli using the native general secretory (Sec) signal peptide. To quantify chitinolytic activity, we developed a high-performance anion-exchange chromatography-pulsed amperometric detection (HPAEC-PAD) method as an alternative to the established hydrophilic interaction liquid ion chromatography coupled with UV detection (HILIC-UV) method for separation and detection of released oxidized chito-oligosaccharides. Using this method, we demonstrated that CflaLPMO10D is strictly active on the β-allomorph of chitin, with optimal activity at pH 5 to 6 and a preference for ascorbic acid as the reducing agent. We also demonstrated the importance of the CBM2 member for both mediating enzyme localization to substrates and prolonging LPMO activity. Together with previous work, the present study defines the distinct substrate specificities of the suite of C. flavigena AA10 members. Notably, a cross-genome survey of AA10 members indicated that chitinolytic LPMOs are, in fact, rare among Cellulomonas bacteria. IMPORTANCE Species from the genus Cellulomonas have a long history of study due to their roles in biomass recycling in nature and corresponding potential as sources of enzymes for biotechnological applications. Although Cellulomonas species are more commonly associated with the cleavage and utilization of plant cell wall polysaccharides, here, we show that C. flavigena produces a unique lytic polysaccharide monooxygenase with activity on β-chitin, which is found, for example, in arthropods. The limited distribution of orthologous chitinolytic LPMOs suggests adaptation of individual cellulomonads to specific nutrient niches present in soil ecosystems. This research provides new insight into the biochemical specificity of LPMOs in Cellulomonas species and related bacteria, and it raises new questions about the physiological function of these enzymes.
Collapse
|
57
|
Franco Cairo JPL, Mandelli F, Tramontina R, Cannella D, Paradisi A, Ciano L, Ferreira MR, Liberato MV, Brenelli LB, Gonçalves TA, Rodrigues GN, Alvarez TM, Mofatto LS, Carazzolle MF, Pradella JGC, Paes Leme AF, Costa-Leonardo AM, Oliveira-Neto M, Damasio A, Davies GJ, Felby C, Walton PH, Squina FM. Oxidative cleavage of polysaccharides by a termite-derived superoxide dismutase boosts the degradation of biomass by glycoside hydrolases. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2022; 24:4845-4858. [PMID: 35813357 PMCID: PMC9208272 DOI: 10.1039/d1gc04519a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/07/2022] [Indexed: 05/31/2023]
Abstract
Wood-feeding termites effectively degrade plant biomass through enzymatic degradation. Despite their high efficiencies, however, individual glycoside hydrolases isolated from termites and their symbionts exhibit anomalously low effectiveness in lignocellulose degradation, suggesting hereto unknown enzymatic activities in their digestome. Herein, we demonstrate that an ancient redox-active enzyme encoded by the lower termite Coptotermes gestroi, a Cu/Zn superoxide dismutase (CgSOD-1), plays a previously unknown role in plant biomass degradation. We show that CgSOD-1 transcripts and peptides are up-regulated in response to an increased level of lignocellulose recalcitrance and that CgSOD-1 localizes in the lumen of the fore- and midguts of C. gestroi together with termite main cellulase, CgEG-1-GH9. CgSOD-1 boosts the saccharification of polysaccharides by CgEG-1-GH9. We show that the boosting effect of CgSOD-1 involves an oxidative mechanism of action in which CgSOD-1 generates reactive oxygen species that subsequently cleave the polysaccharide. SOD-type enzymes constitute a new addition to the growing family of oxidases, ones which are up-regulated when exposed to recalcitrant polysaccharides, and that are used by Nature for biomass degradation.
Collapse
Affiliation(s)
- João Paulo L Franco Cairo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP) Campinas São Paulo Brazil
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
- Department of Chemistry, University of York York YO10 5DD UK
| | - Fernanda Mandelli
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Robson Tramontina
- Programa de Processos Tecnológicos e Ambientais da Universidade de Sorocaba (UNISO) Sorocaba SP Brazil
| | - David Cannella
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
| | | | - Luisa Ciano
- Department of Chemistry, University of York York YO10 5DD UK
| | - Marcel R Ferreira
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP Botucatu São Paulo Brasil
| | - Marcelo V Liberato
- Programa de Processos Tecnológicos e Ambientais da Universidade de Sorocaba (UNISO) Sorocaba SP Brazil
| | - Lívia B Brenelli
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Thiago A Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP) Campinas São Paulo Brazil
| | - Gisele N Rodrigues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Thabata M Alvarez
- Programa de Mestrado e Doutorado em Biotecnologia Industrial, Universidade Positivo Curitiba PR Brasil
| | - Luciana S Mofatto
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade de Campinas, UNICAMP Campinas São Paulo Brasil
| | - Marcelo F Carazzolle
- Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade de Campinas, UNICAMP Campinas São Paulo Brasil
| | - José G C Pradella
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials Campinas São Paulo Brazil
| | - Adriana F Paes Leme
- Laboratório Nacional de Biociências (LNBio) do Centro Nacional de Pesquisa em Energia e Materiais (CNPEM) Campinas São Paulo Brasil
| | - Ana M Costa-Leonardo
- Laboratório de Cupins, Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista, UNESP Rio Claro São Paulo Brasil
| | - Mário Oliveira-Neto
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista, UNESP Botucatu São Paulo Brasil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP) Campinas São Paulo Brazil
| | - Gideon J Davies
- Department of Chemistry, University of York York YO10 5DD UK
| | - Claus Felby
- Department of Geosciences and Natural Resource Management, Faculty of Science, University of Copenhagen Rolighedsvej 23 DK-1958 Frederiksberg C Denmark
| | - Paul H Walton
- Department of Chemistry, University of York York YO10 5DD UK
| | - Fabio M Squina
- Programa de Processos Tecnológicos e Ambientais da Universidade de Sorocaba (UNISO) Sorocaba SP Brazil
| |
Collapse
|
58
|
Wang K, Gao P, Geng L, Liu C, Zhang J, Shu C. Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line. MICROBIOME 2022; 10:90. [PMID: 35698170 PMCID: PMC9195238 DOI: 10.1186/s40168-022-01291-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study. RESULTS Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively. CONCLUSIONS This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.
Collapse
Affiliation(s)
- Kui Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Peiwen Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lili Geng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Chunqin Liu
- Hebei Key Laboratory of Soil Entomology, Cangzhou Academy of Agricultural and Forestry Sciences, Cangzhou, 061001 China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| |
Collapse
|
59
|
Li F, Liu Y, Liu Y, Li Y, Yu H. Heterologous expression and characterization of a novel lytic polysaccharide monooxygenase from Natrialbaceae archaeon and its application for chitin biodegradation. BIORESOURCE TECHNOLOGY 2022; 354:127174. [PMID: 35436543 DOI: 10.1016/j.biortech.2022.127174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Lytic polysaccharide monooxygenases could enhance the enzymatic conversion of recalcitrant polysaccharides by glycoside hydrolases. This study reports the expression and identification of a novel AA10 LPMO from Natrialbaceae archaeon, named NaLPMO10A, as a C1 oxidizer of chitin. The optimal temperature and pH for NaLPMO10A activity were 40 °C and 9.0, respectively, and NaLPMO10A exhibited high thermostability and pH stability under alkaline conditions. NaLPMO10A was also highly tolerant and stable when treated with high concentration of metal ions (1 M). Moreover, metal ions (Na+, K+, Ca2+ and Mg2+) significantly promoted NaLPMO10A activity and improved the saccharification efficiency of chitin by 22.6%, 45.9%, 36.7% and 53.9%, respectively, compared to commercial chitinase alone. Together, the findings of this study fill a gap in archaeal LPMO research, and for the first time demonstrate that archaeal NaLPMO10A could be a promising enzyme for improving saccharification under extreme condition, with potential applications in biorefineries.
Collapse
Affiliation(s)
- Fei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yuxin Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yang Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yanjun Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hongbo Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| |
Collapse
|
60
|
Qu M, Guo X, Tian S, Yang Q, Kim M, Mun S, Noh MY, Kramer KJ, Muthukrishnan S, Arakane Y. AA15 lytic polysaccharide monooxygenase is required for efficient chitinous cuticle turnover during insect molting. Commun Biol 2022; 5:518. [PMID: 35641660 PMCID: PMC9156745 DOI: 10.1038/s42003-022-03469-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of crystalline polysaccharides including chitin and cellulose. The discovery of a large assortment of LPMO-like proteins widely distributed in insect genomes suggests that they could be involved in assisting chitin degradation in the exoskeleton, tracheae and peritrophic matrix during development. However, the physiological functions of insect LPMO-like proteins are still undetermined. To investigate the functions of insect LPMO15 subgroup I-like proteins (LPMO15-1s), two evolutionarily distant species, Tribolium castaneum and Locusta migratoria, were chosen. Depletion by RNAi of T. castaneum TcLPMO15-1 caused molting arrest at all developmental stages, whereas depletion of the L. migratoria LmLPMO15-1, prevented only adult eclosion. In both species, LPMO15-1-deficient animals were unable to shed their exuviae and died. TEM analysis revealed failure of turnover of the chitinous cuticle, which is critical for completion of molting. Purified recombinant LPMO15-1-like protein from Ostrinia furnacalis (rOfLPMO15-1) exhibited oxidative cleavage activity and substrate preference for chitin. These results reveal the physiological importance of catalytically active LPMO15-1-like proteins from distant insect species and provide new insight into the enzymatic mechanism of cuticular chitin turnover during molting.
Collapse
Affiliation(s)
- Mingbo Qu
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
| | - Xiaoxi Guo
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
| | - Shuang Tian
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China
| | - Qing Yang
- School of Bioengineering, Dalian University of Technology, 116024, Dalian, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
| | - Myeongjin Kim
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Seulgi Mun
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea
| | - Mi Young Noh
- Department of Forest Resources, AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, 61186, South Korea
| | - Karl J Kramer
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Subbaratnam Muthukrishnan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Yasuyuki Arakane
- Department of Applied Biology, Chonnam National University, Gwangju, 61186, South Korea.
| |
Collapse
|
61
|
Wilkens C, Vuillemin M, Pilgaard B, Polikarpov I, Morth JP. A GH115 α-glucuronidase structure reveals dimerization-mediated substrate binding and a proton wire potentially important for catalysis. Acta Crystallogr D Struct Biol 2022; 78:658-668. [PMID: 35503213 PMCID: PMC9063842 DOI: 10.1107/s2059798322003527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/28/2022] [Indexed: 11/25/2022] Open
Abstract
The crystal structure of a GH115 α-glucuronidase obtained in complex with xylohexaose and Ca2+ reveals that the two molecules constituting the homodimer cooperatively bind the substrate and that a divalent ion is involved in formation of the Michaelis–Menten complex and is likely to contribute to the formation of a protein wire that is essential for catalysis. Xylan is a major constituent of plant cell walls and is a potential source of biomaterials, and the derived oligosaccharides have been shown to have prebiotic effects. Xylans can be highly substituted with different sugar moieties, which pose steric hindrance to the xylanases that catalyse the hydrolysis of the xylan backbone. One such substituent is α-d-glucuronic acid, which is linked to the O2′ position of the β-1,4 d-xylopyranoses composing the main chain of xylans. The xylan-specific α-glucuronidases from glycoside hydrolase family 115 (GH115) specifically catalyse the removal of α-d-glucuronic acid (GlcA) or methylated GlcA (MeGlcA). Here, the molecular basis by which the bacterial GH115 member wtsAgu115A interacts with the main chain of xylan and the indirect involvement of divalent ions in the formation of the Michaelis–Menten complex are described. A crystal structure at 2.65 Å resolution of wtsAgu115A originating from a metagenome from an anaerobic digester fed with wastewater treatment sludge was determined in complex with xylohexaose, and Asp303 was identified as the likely general acid. The residue acting as the general base could not be identified. However, a proton wire connecting the active site to the metal site was observed and hence a previous hypothesis suggesting a Grotthuss-like mechanism cannot be rejected. Only a single molecule was found in the asymmetric unit. However, wtsAgu115A forms a dimer with a symmetry-related molecule in the crystal lattice. The xylohexaose moieties of the xylohexaose are recognized by residues from both protomers, thus creating a xylohexaose recognition site at the dimer interface. The dimer was confirmed by analytical size-exclusion chromatography in solution. Kinetic analysis with aldouronic acids resulted in a Hill coefficient of greater than 2, suggesting cooperativity between the two binding sites. Three Ca2+ ions were identified in the wtsAgu115A structures. One Ca2+ ion is of particular interest as it is coordinated by the residues of the loops that also interact with the substrate. Activity studies showed that the presence of Mg2+ or Mn2+ resulted in a higher activity towards aldouronic acids, while the less restrictive coordination geometry of Ca2+ resulted in a decrease in activity.
Collapse
|
62
|
Whole-Genome Sequence and Comparative Analysis of Trichoderma asperellum ND-1 Reveal Its Unique Enzymatic System for Efficient Biomass Degradation. Catalysts 2022. [DOI: 10.3390/catal12040437] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The lignocellulosic enzymes of Trichoderma asperellum have been intensely investigated toward efficient conversion of biomass into high-value chemicals/industrial products. However, lack of genome data is a remarkable hurdle for hydrolase systems studies. The secretory enzymes of newly isolated T. asperellum ND-1 during lignocellulose degradation are currently poorly known. Herein, a high-quality genomic sequence of ND-1, obtained by both Illumina HiSeq 2000 sequencing platforms and PacBio single-molecule real-time, has an assembly size of 35.75 Mb comprising 10,541 predicted genes. Secretome analysis showed that 895 proteins were detected, with 211 proteins associated with carbohydrate-active enzymes (CAZymes) responsible for biomass hydrolysis. Additionally, T. asperellum ND-1, T. atroviride IMI 206040, and T. virens Gv-298 shared 801 orthologues that were not identified in T. reesei QM6a, indicating that ND-1 may play critical roles in biological-control. In-depth analysis suggested that, compared with QM6a, the genome of ND-1 encoded a unique enzymatic system, especially hemicellulases and chitinases. Moreover, after comparative analysis of lignocellulase activities of ND-1 and other fungi, we found that ND-1 displayed higher hemicellulases (particularly xylanases) and comparable cellulases activities. Our analysis, combined with the whole-genome sequence information, offers a platform for designing advanced T. asperellum ND-1 strains for industrial utilizations, such as bioenergy production.
Collapse
|
63
|
Stepnov AA, Eijsink VGH, Forsberg Z. Enhanced in situ H 2O 2 production explains synergy between an LPMO with a cellulose-binding domain and a single-domain LPMO. Sci Rep 2022; 12:6129. [PMID: 35414104 PMCID: PMC9005612 DOI: 10.1038/s41598-022-10096-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/29/2022] [Indexed: 02/02/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that catalyze oxidative depolymerization of recalcitrant substrates such as chitin or cellulose. Recent work has shown that LPMOs catalyze fast peroxygenase reactions and that, under commonly used reaction set-ups, access to in situ generated H2O2 likely limits catalysis. Based on a hypothesis that the impact of a cellulose-binding module (CBM) on LPMO activity could relate to changes in in situ H2O2 production, we have assessed the interplay between CBM-containing ScLPMO10C and its truncated form comprising the catalytic domain only (ScLPMO10CTR). The results show that truncation of the linker and CBM leads to elevated H2O2 production and decreased enzyme stability. Most interestingly, combining the two enzyme forms yields strong synergistic effects, which are due to the combination of high H2O2 generation by ScLPMO10CTR and efficient productive use of H2O2 by the full-length enzyme. Thus, cellulose degradation becomes faster, while enzyme inactivation due to off-pathway reactions with excess H2O2 is reduced. These results underpin the complexity of ascorbic acid-driven LPMO reactions and reveal a potential mechanism for how LPMOs may interact synergistically during cellulose degradation.
Collapse
Affiliation(s)
- Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432, Ås, Norway.
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, 1432, Ås, Norway.
| |
Collapse
|
64
|
Mattila H, Österman-Udd J, Mali T, Lundell T. Basidiomycota Fungi and ROS: Genomic Perspective on Key Enzymes Involved in Generation and Mitigation of Reactive Oxygen Species. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:837605. [PMID: 37746164 PMCID: PMC10512322 DOI: 10.3389/ffunb.2022.837605] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/21/2022] [Indexed: 09/26/2023]
Abstract
Our review includes a genomic survey of a multitude of reactive oxygen species (ROS) related intra- and extracellular enzymes and proteins among fungi of Basidiomycota, following their taxonomic classification within the systematic classes and orders, and focusing on different fungal lifestyles (saprobic, symbiotic, pathogenic). Intra- and extracellular ROS metabolism-involved enzymes (49 different protein families, summing 4170 protein models) were searched as protein encoding genes among 63 genomes selected according to current taxonomy. Extracellular and intracellular ROS metabolism and mechanisms in Basidiomycota are illustrated in detail. In brief, it may be concluded that differences between the set of extracellular enzymes activated by ROS, especially by H2O2, and involved in generation of H2O2, follow the differences in fungal lifestyles. The wood and plant biomass degrading white-rot fungi and the litter-decomposing species of Agaricomycetes contain the highest counts for genes encoding various extracellular peroxidases, mono- and peroxygenases, and oxidases. These findings further confirm the necessity of the multigene families of various extracellular oxidoreductases for efficient and complete degradation of wood lignocelluloses by fungi. High variations in the sizes of the extracellular ROS-involved gene families were found, however, among species with mycorrhizal symbiotic lifestyle. In addition, there are some differences among the sets of intracellular thiol-mediation involving proteins, and existence of enzyme mechanisms for quenching of intracellular H2O2 and ROS. In animal- and plant-pathogenic species, extracellular ROS enzymes are absent or rare. In these fungi, intracellular peroxidases are seemingly in minor role than in the independent saprobic, filamentous species of Basidiomycota. Noteworthy is that our genomic survey and review of the literature point to that there are differences both in generation of extracellular ROS as well as in mechanisms of response to oxidative stress and mitigation of ROS between fungi of Basidiomycota and Ascomycota.
Collapse
Affiliation(s)
| | | | | | - Taina Lundell
- Department of Microbiology, Faculty of Agriculture and Forestry, Viikki Campus, University of Helsinki, Helsinki, Finland
| |
Collapse
|
65
|
Verschoor JA, Kusumawardhani H, Ram AFJ, de Winde JH. Toward Microbial Recycling and Upcycling of Plastics: Prospects and Challenges. Front Microbiol 2022; 13:821629. [PMID: 35401461 PMCID: PMC8985596 DOI: 10.3389/fmicb.2022.821629] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
Annually, 400 Mt of plastics are produced of which roughly 40% is discarded within a year. Current plastic waste management approaches focus on applying physical, thermal, and chemical treatments of plastic polymers. However, these methods have severe limitations leading to the loss of valuable materials and resources. Another major drawback is the rapid accumulation of plastics into the environment causing one of the biggest environmental threats of the twenty-first century. Therefore, to complement current plastic management approaches novel routes toward plastic degradation and upcycling need to be developed. Enzymatic degradation and conversion of plastics present a promising approach toward sustainable recycling of plastics and plastics building blocks. However, the quest for novel enzymes that efficiently operate in cost-effective, large-scale plastics degradation poses many challenges. To date, a wide range of experimental set-ups has been reported, in many cases lacking a detailed investigation of microbial species exhibiting plastics degrading properties as well as of their corresponding plastics degrading enzymes. The apparent lack of consistent approaches compromises the necessary discovery of a wide range of novel enzymes. In this review, we discuss prospects and possibilities for efficient enzymatic degradation, recycling, and upcycling of plastics, in correlation with their wide diversity and broad utilization. Current methods for the identification and optimization of plastics degrading enzymes are compared and discussed. We present a framework for a standardized workflow, allowing transparent discovery and optimization of novel enzymes for efficient and sustainable plastics degradation in the future.
Collapse
Affiliation(s)
- Jo-Anne Verschoor
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | | | - Arthur F. J. Ram
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Johannes H. de Winde
- Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| |
Collapse
|
66
|
Mechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion. Nat Commun 2022; 13:1449. [PMID: 35304453 PMCID: PMC8933493 DOI: 10.1038/s41467-022-28938-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 02/11/2022] [Indexed: 12/02/2022] Open
Abstract
Glucuronoyl esterases (GEs) are α/β serine hydrolases and a relatively new addition in the toolbox to reduce the recalcitrance of lignocellulose, the biggest obstacle in cost-effective utilization of this important renewable resource. While biochemical and structural characterization of GEs have progressed greatly recently, there have yet been no mechanistic studies shedding light onto the rate-limiting steps relevant for biomass conversion. The bacterial GE OtCE15A possesses a classical yet distinctive catalytic machinery, with easily identifiable catalytic Ser/His completed by two acidic residues (Glu and Asp) rather than one as in the classical triad, and an Arg side chain participating in the oxyanion hole. By QM/MM calculations, we identified deacylation as the decisive step in catalysis, and quantified the role of Asp, Glu and Arg, showing the latter to be particularly important. The results agree well with experimental and structural data. We further calculated the free-energy barrier of post-catalysis dissociation from a complex natural substrate, suggesting that in industrial settings non-catalytic processes may constitute the rate-limiting step, and pointing to future directions for enzyme engineering in biomass utilization. Zong and coworkers combine computational and experimental methods to decipher in detail the mechanism of action of glucuronoyl esterases, enzymes with significant biotechnological potential for decoupling lignin from polysaccharides in biomass.
Collapse
|
67
|
Serra I, Piccinini D, Paradisi A, Ciano L, Bellei M, Bortolotti CA, Battistuzzi G, Sola M, Walton PH, Di Rocco G. Activity and substrate specificity of lytic polysaccharide monooxygenases: An ATR FTIR-based sensitive assay tested on a novel species from Pseudomonas putida. Protein Sci 2022; 31:591-601. [PMID: 34897841 PMCID: PMC8862430 DOI: 10.1002/pro.4255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 11/06/2022]
Abstract
Pseudomonas putida W619 is a soil Gram-negative bacterium commonly used in environmental studies thanks to its ability in degrading many aromatic compounds. Its genome contains several putative carbohydrate-active enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases (PMOs). In this study, we have heterologously produced in Escherichia coli and characterized a new enzyme belonging to the AA10 family, named PpAA10 (Uniprot: B1J2U9), which contains a chitin-binding type-4 module and showed activity toward β-chitin. The active form of the enzyme was produced in E. coli exploiting the addition of a cleavable N-terminal His tag which ensured the presence of the copper-coordinating His as the first residue. Electron paramagnetic resonance spectroscopy showed signal signatures similar to those observed for the copper-binding site of chitin-cleaving PMOs. The protein was used to develop a versatile, highly sensitive, cost-effective and easy-to-apply method to detect PMO's activity exploiting attenuated total reflection-Fourier transform infrared spectroscopy and able to easily discriminate between different substrates.
Collapse
Affiliation(s)
- Ilenia Serra
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly,Present address:
BIMEF Laboratory, Department of ChemistryUniversity of AntwerpAntwerpBelgium
| | - Daniele Piccinini
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly
| | - Alessandro Paradisi
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly,Department of ChemistryUniversity of YorkYorkUK
| | - Luisa Ciano
- Department of Chemistry and GeologyUniversity of Modena and Reggio EmiliaModenaItaly,Present address:
School of ChemistryUniversity of NottinghamNottinghamUK
| | - Marzia Bellei
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly
| | | | | | - Marco Sola
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly
| | | | - Giulia Di Rocco
- Department of Life SciencesUniversity of Modena and Reggio EmiliaModenaItaly
| |
Collapse
|
68
|
Vandhana TM, Reyre JL, Sushmaa D, Berrin JG, Bissaro B, Madhuprakash J. On the expansion of biological functions of lytic polysaccharide monooxygenases. THE NEW PHYTOLOGIST 2022; 233:2380-2396. [PMID: 34918344 DOI: 10.1111/nph.17921] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/19/2021] [Indexed: 05/21/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) constitute an enigmatic class of enzymes, the discovery of which has opened up a new arena of riveting research. LPMOs can oxidatively cleave the glycosidic bonds found in carbohydrate polymers enabling the depolymerisation of recalcitrant biomasses, such as cellulose or chitin. While most studies have so far mainly explored the role of LPMOs in a (plant) biomass conversion context, alternative roles and paradigms begin to emerge. In the present review, we propose a historical perspective of LPMO research providing a succinct overview of the major achievements of LPMO research over the past decade. This journey through LPMOs landscape leads us to dive into the emerging biological functions of LPMOs and LPMO-like proteins. We notably highlight roles in fungal and oomycete plant pathogenesis (e.g. potato late blight), but also in mutualistic/commensalism symbiosis (e.g. ectomycorrhizae). We further present the potential importance of LPMOs in other microbial pathogenesis including diseases caused by bacteria (e.g. pneumonia), fungi (e.g. human meningitis), oomycetes and viruses (e.g. entomopox), as well as in (micro)organism development (including several plant pests). Our assessment of the literature leads to the formulation of outstanding questions, promising for the coming years exciting research and discoveries on these moonlighting proteins.
Collapse
Affiliation(s)
- Theruvothu Madathil Vandhana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Jean-Lou Reyre
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Dangudubiyyam Sushmaa
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Jean-Guy Berrin
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
| | - Bastien Bissaro
- INRAE, UMR1163 Biodiversité et Biotechnologie Fongiques, Aix Marseille University, 13009, Marseille, France
| | - Jogi Madhuprakash
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| |
Collapse
|
69
|
Morgan T, Tavares MP, Ladeira-Ázar RI, de Oliveira Mendes TA, Guimarães VM. The lytic polysaccharide monooxigenases secreted by the fungus Chrysoporthe cubensis: Genomic analysis and impact on sugarcane bagasse saccharification. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
70
|
Yang Z, Hu X, Zhang F, Durrani S, Zhang J, Pang AP, Gao Y, Wu FG, Lin F. Chitosan-modified fluorescent dye for simple, fast, and in-situ measurement of fungal cell growth in the presence of insoluble compounds. FEMS Microbiol Lett 2022; 369:6884137. [PMID: 36481926 DOI: 10.1093/femsle/fnac118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/24/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The measurement of fungal cell growth in submerged culture systems containing insoluble compounds is essential yet difficult due to the interferences from the insoluble compounds like biopolymers. Here, we developed a fluorescent strategy based on chitosan-modified fluorescein isothiocyanate (GC-FITC) to monitor the cell growth of lignocellulosic fungi cultivated on biopolymers. GC-FITC could stain only lignocellulosic fungi (Tricoderma reesei, Penicillium oxalicum, Aspergillus nidulans, and Neurospora crassa), but not biopolymers (cellulose, xylan, pectin, or lignin), excluding the interferences from these insoluble biopolymer. Moreover, a linear relationship was observed between the fluorescence intensity of GC-FITC absorbed by lignocellulosic fungi and the biomass of lignocellulosic fungi. Therefore, GC-FITC was leveraged to monitor the cell growth of lignocellulosic fungi when using biopolymers like cellulose as the carbon sources, which is faster, more convenient, time-saving, and cost-effective than the existing methods using protein/DNA content measurement. GC-FITC offers a powerful tool to detect fungal growth in culture systems with insoluble materials.
Collapse
Affiliation(s)
- Zihuayuan Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xin Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Funing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Samran Durrani
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jie Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Ai-Ping Pang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yichen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| |
Collapse
|
71
|
Lindley PJ, Parkin A, Davies GJ, Walton PH. Mapping the protonation states of the histidine brace in an AA10 lytic polysaccharide monooxygenase using CW-EPR spectroscopy and DFT calculations. Faraday Discuss 2022; 234:336-348. [PMID: 35171174 DOI: 10.1039/d1fd00068c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The active site of the polysaccharide-degrading lytic polysaccharide monooxygenase (LPMO) enzyme features a single copper ion coordinated by a histidine brace. The primary coordination sphere of the copper contains several ligating atoms which are bonded to ionisable protons (e.g. OH2, NH2), the pKas of which are unknown. Using a combination of CW-EPR X-band spectroscopy over a range of pH values and DFT calculations, we show that the active site of a chitin-active AA10 LPMO can exist in three different protonation states (pKa1 = 8.7, pKa2 ∼ 11.5), representing the ionisation of the coordinating groups. The middle pH species (fully formed at pH ∼ 10.5) is proposed to be Cu(II)(His)2(OH)2 (N2O2 coordination) with a decoordinated R-NH3+ group at the amino terminus. This species also sees a rotation of the SOMO equatorial plane from the canonical histidine brace plane, whereby the nominal Cu d(x2 - y2)-orbital has rotated some 45° along the His-Cu(II)-His axis, driven by the elongation and decoordination of the amino group. The highest pH species (>12) is proposed to exist as a Cu(II)-azanide, in which the NH2 of the amino terminus has been deprotonated. The high pH means that this species is unlikely to be biologically relevant in the catalytic cycle of AA10 LPMOs.
Collapse
Affiliation(s)
- Peter J Lindley
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Alison Parkin
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Gideon J Davies
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| |
Collapse
|
72
|
Karnaouri A, Chorozian K, Zouraris D, Karantonis A, Topakas E, Rova U, Christakopoulos P. Lytic polysaccharide monooxygenases as powerful tools in enzymatically assisted preparation of nano-scaled cellulose from lignocellulose: A review. BIORESOURCE TECHNOLOGY 2022; 345:126491. [PMID: 34871721 DOI: 10.1016/j.biortech.2021.126491] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 06/13/2023]
Abstract
Nanocellulose, either in the form of fibers or crystals, constitutes a renewable, biobased, biocompatible material with advantageous mechanical properties that can be isolated from lignocellulosic biomass. Enzyme-assisted isolation of nanocellulose is an attractive, environmentally friendly approach that leads to products of higher quality compared to their chemically prepared counterparts. Lytic polysaccharide monooxygenases (LPMOs) are enzymes that oxidatively cleave the β-1,4-glycosidic bond of polysaccharides upon activation of O2 or H2O2 and presence of an electron donor. Their use for treatment of cellulose fibers towards the preparation of nano-scaled cellulose is related to the ability of LPMOs to create nicking points on the fiber surface, thus facilitating fiber disruption and separation. The aim of this review is to describe the mode of action of LPMOs on cellulose fibers towards the isolation of nanostructures, thus highlighting their great potential for the production of nanocellulose as a novel value added product from lignocellulose.
Collapse
Affiliation(s)
- Anthi Karnaouri
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Lab, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece; Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
| | - Koar Chorozian
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Lab, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Dimitrios Zouraris
- Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, Zografou, 15780 Athens, Greece
| | - Antonis Karantonis
- Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, Zografou, 15780 Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Lab, School of Chemical Engineering, National Technical University of Athens, 9 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Ulrika Rova
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| |
Collapse
|
73
|
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.
Collapse
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
| | | | | |
Collapse
|
74
|
Tomé LMR, da Silva FF, Fonseca PLC, Mendes-Pereira T, Azevedo VADC, Brenig B, Badotti F, Góes-Neto A. Hybrid Assembly Improves Genome Quality and Completeness of Trametes villosa CCMB561 and Reveals a Huge Potential for Lignocellulose Breakdown. J Fungi (Basel) 2022; 8:jof8020142. [PMID: 35205897 PMCID: PMC8876698 DOI: 10.3390/jof8020142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Trametes villosa is a wood-decaying fungus with great potential to be used in the bioconversion of agro-industrial residues and to obtain high-value-added products, such as biofuels. Nonetheless, the lack of high-quality genomic data hampers studies investigating genetic mechanisms and metabolic pathways in T. villosa, hindering its application in industry. Herein, applying a hybrid assembly pipeline using short reads (Illumina HiSeq) and long reads (Oxford Nanopore MinION), we obtained a high-quality genome for the T. villosa CCMB561 and investigated its genetic potential for lignocellulose breakdown. The new genome possesses 143 contigs, N50 of 1,009,271 bp, a total length of 46,748,415 bp, 14,540 protein-coding genes, 22 secondary metabolite gene clusters, and 426 genes encoding Carbohydrate-Active enzymes. Our CAZome annotation and comparative genomic analyses of nine Trametes spp. genomes revealed T. villosa CCMB561 as the species with the highest number of genes encoding lignin-modifying enzymes and a wide array of genes encoding proteins for the breakdown of cellulose, hemicellulose, and pectin. These results bring to light the potential of this isolate to be applied in the bioconversion of lignocellulose and will support future studies on the expression, regulation, and evolution of genes, proteins, and metabolic pathways regarding the bioconversion of lignocellulosic residues.
Collapse
Affiliation(s)
- Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Felipe Ferreira da Silva
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Paula Luize Camargos Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Thairine Mendes-Pereira
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil;
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073 Göttingen, Germany;
| | - Fernanda Badotti
- Department of Chemistry, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte 30421-169, MG, Brazil;
| | - Aristóteles Góes-Neto
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil; (L.M.R.T.); (F.F.d.S.); (T.M.-P.)
- Correspondence: ; Tel.: +55-31-994130996
| |
Collapse
|
75
|
Comparison of six lytic polysaccharide monooxygenases from Thermothielavioides terrestris shows that functional variation underlies the multiplicity of LPMO genes in filamentous fungi. Appl Environ Microbiol 2022; 88:e0009622. [PMID: 35080911 PMCID: PMC8939357 DOI: 10.1128/aem.00096-22] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are mono-copper enzymes that oxidatively degrade various polysaccharides. Genes encoding LPMOs in the AA9 family are abundant in filamentous fungi while their multiplicity remains elusive. We describe a detailed functional characterization of six AA9 LPMOs from the ascomycetous fungus Thermothielavioides terrestris LPH172 (syn. Thielavia terrestris). These six LPMOs were shown to be upregulated during growth on different lignocellulosic substrates in our previous study. Here, we produced them heterologously in Pichia pastoris and tested their activity on various model and native plant cell wall substrates. All six T. terrestris AA9 (TtAA9) LPMOs produced hydrogen peroxide in the absence of polysaccharide substrate and displayed peroxidase-like activity on a model substrate, yet only five of them were active on selected cellulosic substrates. TtLPMO9A and TtLPMO9E were also active on birch acetylated glucuronoxylan, but only when the xylan was combined with phosphoric acid-swollen cellulose (PASC). Another of the six AA9s, TtLPMO9G, was active on spruce arabinoglucuronoxylan mixed with PASC. TtLPMO9A, TtLPMO9E, TtLPMO9G, and TtLPMO9T could degrade tamarind xyloglucan and, with the exception of TtLPMO9T, beechwood xylan when combined with PASC. Interestingly, none of the tested enzymes were active on wheat arabinoxylan, konjac glucomannan, acetylated spruce galactoglucomannan, or cellopentaose. Overall, these functional analyses support the hypothesis that the multiplicity of the fungal LPMO genes assessed in this study relates to the complex and recalcitrant structure of lignocellulosic biomass. Our study also highlights the importance of using native substrates in functional characterization of LPMOs, as we were able to demonstrate distinct, previously unreported xylan-degrading activities of AA9 LPMOs using such substrates. IMPORTANCE The discovery of LPMOs in 2010 has revolutionized the industrial biotechnology field, mainly by increasing the efficiency of cellulolytic enzyme cocktails. Nonetheless, the biological purpose of the multiplicity of LPMO-encoding genes in filamentous fungi has remained an open question. Here, we address this point by showing that six AA9 LPMOs from a single fungal strain have various substrate preferences and activities on tested cellulosic and hemicellulosic substrates, including several native xylan substrates. Importantly, several of these activities could only be detected when using copolymeric substrates that likely resemble plant cell walls more than single fractionated polysaccharides do. Our results suggest that LPMOs have evolved to contribute to the degradation of different complex structures in plant cell walls where different biomass polymers are closely associated. This knowledge together with the elucidated novel xylanolytic activities could aid in further optimization of enzymatic cocktails for efficient degradation of lignocellulosic substrates and more.
Collapse
|
76
|
Wang Y, Hu J, Li Y, Liu Z. Rare earth ion Nd3+ promotes production of cellulose ethanol by Clostridium thermocellum ATCC 27405. Polyhedron 2022. [DOI: 10.1016/j.poly.2021.115555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
77
|
Stepnov AA, Christensen IA, Forsberg Z, Aachmann FL, Courtade G, Eijsink VGH. The impact of reductants on the catalytic efficiency of a lytic polysaccharide monooxygenase and the special role of dehydroascorbic acid. FEBS Lett 2022; 596:53-70. [PMID: 34845720 DOI: 10.1002/1873-3468.14246] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 12/13/2022]
Abstract
Monocopper lytic polysaccharide monooxygenases (LPMOs) catalyse oxidative cleavage of glycosidic bonds in a reductant-dependent reaction. Recent studies indicate that LPMOs, rather than being O2 -dependent monooxygenases, are H2 O2 -dependent peroxygenases. Here, we describe SscLPMO10B, a novel LPMO from the phytopathogenic bacterium Streptomyces scabies and address links between this enzyme's catalytic rate and in situ hydrogen peroxide production in the presence of ascorbic acid, gallic acid and l-cysteine. Studies of Avicel degradation showed a clear correlation between the catalytic rate of SscLPMO10B and the rate of H2 O2 generation in the reaction mixture. We also assessed the impact of oxidised ascorbic acid, dehydroascorbic acid (DHA), on LPMO activity, since DHA, which is not considered a reductant, was recently reported to drive LPMO reactions. Kinetic studies, combined with NMR analysis, showed that DHA is unstable and converts into multiple derivatives, some of which are redox active and can fuel the LPMO reaction by reducing the active site copper and promoting H2 O2 production. These results show that the apparent monooxygenase activity observed in SscLPMO10B reactions without exogenously added H2 O2 reflects a peroxygenase reaction.
Collapse
Affiliation(s)
- Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Idd A Christensen
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| | - Finn L Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Gaston Courtade
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Sciences, Ås, Norway
| |
Collapse
|
78
|
Li X, Dilokpimol A, Kabel MA, de Vries RP. Fungal xylanolytic enzymes: Diversity and applications. BIORESOURCE TECHNOLOGY 2022; 344:126290. [PMID: 34748977 DOI: 10.1016/j.biortech.2021.126290] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 05/26/2023]
Abstract
As important polysaccharide degraders in nature, fungi can diversify their extensive set of carbohydrate-active enzymes to survive in ecological habitats of various composition. Among these enzymes, xylanolytic ones can efficiently and sustainably degrade xylans into (fermentable) monosaccharides to produce valuable chemicals or fuels from, for example relevant for upgrading agro-food industrial side streams. Moreover, xylanolytic enzymes are being used in various industrial applications beyond biomass saccharification, e.g. food, animal feed, biofuel, pulp and paper. As a reference for researchers working in related areas, this review summarized the current knowledge on substrate specificity of xylanolytic enzymes from different families of the Carbohydrate-Active enZyme database. Additionally, the diversity of enzyme sets in fungi were discussed by comparing the number of genes encoding xylanolytic enzymes in selected fungal genomes. Finally, to support bio-economy, the current applications of fungal xylanolytic enzymes in industry were reviewed.
Collapse
Affiliation(s)
- Xinxin Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
| |
Collapse
|
79
|
Zerva A, Pentari C, Ferousi C, Nikolaivits E, Karnaouri A, Topakas E. Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2021; 342:126058. [PMID: 34597805 DOI: 10.1016/j.biortech.2021.126058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The field of enzymatic degradation of lignocellulose is actively growing and the recent updates of the last few years indicate that there is still much to learn. The growing number of protein sequences with unknown function in microbial genomes indicates that there is still much to learn on the mechanisms of lignocellulose degradation. In this review, a summary of the progress in the field is presented, including recent discoveries on the nature of the structural polysaccharides, new technologies for the discovery and functional annotation of gene sequences including omics technologies, and the novel lignocellulose-acting enzymes described. Novel enzymatic activities and enzyme families as well as accessory enzymes and their synergistic relationships regarding biomass breakdown are described. Moreover, it is shown that all the valuable knowledge of the enzymatic decomposition of plant biomass polymers can be employed towards the decomposition and upgrading of synthetic polymers, such as plastics.
Collapse
Affiliation(s)
- Anastasia Zerva
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Pentari
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Ferousi
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Anthi Karnaouri
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece; Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
| |
Collapse
|
80
|
Quantifying Oxidation of Cellulose-Associated Glucuronoxylan by Two Lytic Polysaccharide Monooxygenases from Neurospora crassa. Appl Environ Microbiol 2021; 87:e0165221. [PMID: 34613755 PMCID: PMC8612270 DOI: 10.1128/aem.01652-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Family AA9 lytic polysaccharide monooxygenases (LPMOs) are abundant in fungi, where they catalyze oxidative depolymerization of recalcitrant plant biomass. These AA9 LPMOs cleave cellulose and some also act on hemicelluloses, primarily other (substituted) β-(1→4)-glucans. Oxidative cleavage of xylan has been shown for only a few AA9 LPMOs, and it remains unclear whether this activity is a minor side reaction or primary function. Here, we show that Neurospora crassa LPMO9F (NcLPMO9F) and the phylogenetically related, hitherto uncharacterized NcLPMO9L from N. crassa are active on both cellulose and cellulose-associated glucuronoxylan but not on glucuronoxylan alone. A newly developed method for simultaneous quantification of xylan-derived and cellulose-derived oxidized products showed that NcLPMO9F preferentially cleaves xylan when acting on a cellulose–beechwood glucuronoxylan mixture, yielding about three times more xylan-derived than cellulose-derived oxidized products. Interestingly, under similar conditions, NcLPMO9L and the previously characterized McLPMO9H, from Malbranchea cinnamomea, showed different xylan-to-cellulose preferences, giving oxidized product ratios of about 0.5:1 and 1:1, respectively, indicative of functional variation among xylan-active LPMOs. Phylogenetic and structural analysis of xylan-active AA9 LPMOs led to the identification of characteristic structural features, including unique features that do not occur in phylogenetically remote AA9 LPMOs, such as four AA9 LPMOs whose lack of activity toward glucuronoxylan was demonstrated in the present study. Taken together, the results provide a path toward discovery of additional xylan-active LPMOs and show that the huge family of AA9 LPMOs has members that preferentially act on xylan. These findings shed new light on the biological role and industrial potential of these fascinating enzymes. IMPORTANCE Plant cell wall polysaccharides are highly resilient to depolymerization by hydrolytic enzymes, partly due to cellulose chains being tightly packed in microfibrils that are covered by hemicelluloses. Lytic polysaccharide monooxygenases (LPMOs) seem well suited to attack these resilient copolymeric structures, but the occurrence and importance of hemicellulolytic activity among LPMOs remain unclear. Here, we show that certain AA9 LPMOs preferentially cleave xylan when acting on a cellulose–glucuronoxylan mixture, and that this ability is the result of protein evolution that has resulted in a clade of AA9 LPMOs with specific structural features. Our findings strengthen the notion that the vast arsenal of AA9 LPMOs in certain fungal species provides functional versatility and that AA9 LPMOs may have evolved to promote oxidative depolymerization of a wide variety of recalcitrant, copolymeric plant polysaccharide structures. These findings have implications for understanding the biological roles and industrial potential of LPMOs.
Collapse
|
81
|
Chromatographic analysis of oxidized cello-oligomers generated by lytic polysaccharide monooxygenases using dual electrolytic eluent generation. J Chromatogr A 2021; 1662:462691. [PMID: 34894418 DOI: 10.1016/j.chroma.2021.462691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 11/20/2022]
Abstract
Research on oligosaccharides, including the complicated product mixtures generated by lytic polysaccharide monooxygenases (LPMOs), is growing at a rapid pace. LPMOs are gaining major interest, and the ability to efficiently and accurately separate and quantify their native and oxidized products chromatographically is essential in furthering our understanding of these oxidative enzymes. Here we present a novel set of methods based on dual electrolytic eluent generation, where the conventional sodium acetate/sodium hydroxide (NaOAc/NaOH) eluents in high-performance anion-exchange chromatography (HPAEC) are replaced by electrolytically-generated potassium methane sulfonate/potassium hydroxide (KMSA/KOH). The new methods separate all compounds of interest within 24-45 min and with high sensitivity; limits of detection and quantification were in the range of 0.0001-0.0032 mM and 0.0002-0.0096 mM, respectively. In addition, an average of 3.5 times improvement in analytical CV was obtained. This chromatographic platform overcomes drawbacks associated with manual preparation of eluents and offers simplified operation and rapid method optimization, with increased precision for less abundant LPMO-derived products.
Collapse
|
82
|
Filiatrault-Chastel C, Heiss-Blanquet S, Margeot A, Berrin JG. From fungal secretomes to enzymes cocktails: The path forward to bioeconomy. Biotechnol Adv 2021; 52:107833. [PMID: 34481893 DOI: 10.1016/j.biotechadv.2021.107833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/17/2022]
Abstract
Bioeconomy is seen as a way to mitigate the carbon footprint of human activities by reducing at least part of the fossil resources-based economy. In this new paradigm of sustainable development, the use of enzymes as biocatalysts will play an increasing role to provide services and goods. In industry, most of multicomponent enzyme cocktails are of fungal origin. Filamentous fungi secrete complex enzyme sets called "secretomes" that can be utilized as enzyme cocktails to valorize different types of bioresources. In this review, we highlight recent advances in the study of fungal secretomes using improved computational and experimental secretomics methods, the progress in the understanding of industrially important fungi, and the discovery of new enzymatic mechanisms and interplays to degrade renewable resources rich in polysaccharides (e.g. cellulose). We review current biotechnological applications focusing on the benefits and challenges of fungal secretomes for industrial applications with some examples of commercial cocktails of fungal origin containing carbohydrate-active enzymes (CAZymes) and we discuss future trends.
Collapse
Affiliation(s)
- Camille Filiatrault-Chastel
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France; IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Senta Heiss-Blanquet
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Antoine Margeot
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison, France.
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Univ., Biodiversité et Biotechnologie Fongiques, UMR1163, Marseille, France.
| |
Collapse
|
83
|
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.
Collapse
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
| |
Collapse
|
84
|
Dai L, Qu Y, Hu Y, Min J, Yu X, Chen CC, Huang JW, Guo RT. Catalytically inactive lytic polysaccharide monooxygenase PcAA14A enhances the enzyme-mediated hydrolysis of polyethylene terephthalate. Int J Biol Macromol 2021; 190:456-462. [PMID: 34499955 DOI: 10.1016/j.ijbiomac.2021.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 10/20/2022]
Abstract
The massive accumulation of polyethylene terephthalate (PET) in the global ecosystem is a growing environmental crisis. Development of environmental friendly strategies to achieve enzyme-catalyzed PET degradation has attracted tremendous attention. In this study, we demonstrated the synergistic effects of combining a specific PET-degrading enzyme IsPETaseEHA variant from PET-assimilating bacterium Ideonella sakaiensis and a lytic polysaccharide monooxygenase from a white-rot fungus Pycnoporus coccineus (PcAA14A) in PET degradation. We found that the presence of PcAA14A alone did not result in PET hydrolysis, but its presence could stimulate IsPETaseEHA-mediated hydrolytic efficiency by up to 1.3-fold. Notably, the stimulatory effects of PcAA14A on IsPETaseEHA-catalyzed PET hydrolysis were found to be independent of monooxygenase activity. Dose-effects of IsPETaseEHA and PcAA14A on PET hydrolysis were observed, with the optimal concentrations being determined to 25 μg/mL and 0.25 μg/mL, respectively. In the 5-day PET hydrolysis experiment, 1097 μM hydrolysis products were produced by adding the optimized concentrations of IsPETaseEHA and PcAA14A, which was 27.7% higher than those were produced by IsPETaseEHA alone. Our study reports the first time that PcAA14A could stimulate the IsPETaseEHA-mediated PET hydrolysis through a monooxygenase activity independent manner.
Collapse
Affiliation(s)
- Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yingying Qu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yumei Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Xuejing Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Chun-Chi Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, School of Life Sciences, Hubei University, Wuhan, 430062, PR China.
| |
Collapse
|
85
|
Franco Cairo JPL, Almeida DV, Damasio A, Garcia W, Squina FM. The periplasmic expression and purification of AA15 lytic polysaccharide monooxygenases from insect species in Escherichia coli. Protein Expr Purif 2021; 190:105994. [PMID: 34655732 DOI: 10.1016/j.pep.2021.105994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are metalloenzymes that cleave structural polysaccharides through an oxidative mechanism. The enzymatic activity of LPMOs relies on the presence of a Cu2+ histidine-brace motif in their flat catalytic surface. Upon reduction by an external electron donor and in the presence of its co-substrates, O2 or H2O2, LPMOs can generate reactive oxygen species to oxidize the substrates. Fungal and bacterial LPMOs are involved in the catabolism of polysaccharides, such as chitin, cellulose, and hemicelluloses, and virulence mechanisms. Based on the reports on the discovery of LPMOs from the family AA15 in termites, firebrats, and flies, the functional role of the LPMO in the biosphere could expand, as these enzymes may be correlated with chitin remodeling and molting in insects. However, there is limited knowledge of AA15 LPMOs due to difficulties in recombinant expression of soluble proteins and purification protocols. In this study, we describe a protocol for the cloning, expression, and purification of insect AA15 LPMOs from Arthropoda, mainly from termites, followed by the expression and purification of an AA15 LPMO from the silkworm Bombyx mori, which contains a relatively high number of disulfide bonds. We also report the recombinant expression and purification of a protein with homology to AA15 family from the western European honeybee Apis mellifera, an LPMO-like enzyme lacking the canonical histidine brace. Therefore, this work can support future studies concerning the role of LPMOs in the biology of insects and inspire molecular entomologists and insect biochemists in conducting activities in this field.
Collapse
Affiliation(s)
- João Paulo L Franco Cairo
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Programa de Processos Tecnológicos da Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil
| | - Dnane V Almeida
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fabio M Squina
- Programa de Processos Tecnológicos da Universidade de Sorocaba (UNISO), Sorocaba, São Paulo, Brazil.
| |
Collapse
|
86
|
Kuusk S, Väljamäe P. Kinetics of H 2O 2-driven catalysis by a lytic polysaccharide monooxygenase from the fungus Trichoderma reesei. J Biol Chem 2021; 297:101256. [PMID: 34597668 PMCID: PMC8528726 DOI: 10.1016/j.jbc.2021.101256] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 01/17/2023] Open
Abstract
Owing to their ability to break glycosidic bonds in recalcitrant crystalline polysaccharides such as cellulose, the catalysis effected by lytic polysaccharide monooxygenases (LPMOs) is of major interest. Kinetics of these reductant-dependent, monocopper enzymes is complicated by the insoluble nature of the cellulose substrate and parallel, enzyme-dependent, and enzyme-independent side reactions between the reductant and oxygen-containing cosubstrates. Here, we provide kinetic characterization of cellulose peroxygenase (oxidative cleavage of glycosidic bonds in cellulose) and reductant peroxidase (oxidation of the reductant) activities of the LPMO TrAA9A of the cellulose-degrading model fungus Trichoderma reesei. The catalytic efficiency (kcat/Km(H2O2)) of the cellulose peroxygenase reaction (kcat = 8.5 s−1, and Km(H2O2)=30μM) was an order of magnitude higher than that of the reductant (ascorbic acid) peroxidase reaction. The turnover of H2O2 in the ascorbic acid peroxidase reaction followed the ping-pong mechanism and led to irreversible inactivation of the enzyme with a probability of 0.0072. Using theoretical analysis, we suggest a relationship between the half-life of LPMO, the values of kinetic parameters, and the concentrations of the reactants.
Collapse
Affiliation(s)
- Silja Kuusk
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Priit Väljamäe
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
| |
Collapse
|
87
|
Rani Singhania R, Dixit P, Kumar Patel A, Shekher Giri B, Kuo CH, Chen CW, Di Dong C. Role and significance of lytic polysaccharide monooxygenases (LPMOs) in lignocellulose deconstruction. BIORESOURCE TECHNOLOGY 2021; 335:125261. [PMID: 34000697 DOI: 10.1016/j.biortech.2021.125261] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) emerged a decade ago and have been described as biomass deconstruction boosters as they play an extremely important role in unravelling the enzymatic biomass hydrolysis scheme. These are oxidative enzymes requiring partners to donate electrons during catalytic action on cellulose backbone. Commercial cellulase preparations are mostly from the robust fungal sources, hence LPMOs from fungi (AA9) have been discussed. Characterisation of LPMOs suffers due to multiple complications which has been discussed and challenges in detection of LPMOs in secretomes has also been highlighted. This review focuses on the significance of LPMOs on biomass hydrolysis due to which it has become a key component of cellulolytic cocktail available commercially for biomass deconstruction and its routine analysis challenge has also been discussed. It has also outlined a few key points that help in expressing catalytic active recombinant AA9 LPMOs.
Collapse
Affiliation(s)
- Reeta Rani Singhania
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Pooja Dixit
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | - Anil Kumar Patel
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Balendu Shekher Giri
- Department of Chemical Engineering, Indian Institute of Technology, Guwahati 781039 India
| | - Chia-Hung Kuo
- Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Chiu-Wen Chen
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan
| | - Cheng Di Dong
- Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan.
| |
Collapse
|
88
|
Calderaro F, Bevers LE, van den Berg MA. Oxidative Power: Tools for Assessing LPMO Activity on Cellulose. Biomolecules 2021; 11:biom11081098. [PMID: 34439765 PMCID: PMC8391687 DOI: 10.3390/biom11081098] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have sparked a lot of research regarding their fascinating mode-of-action. Particularly, their boosting effect on top of the well-known cellulolytic enzymes in lignocellulosic hydrolysis makes them industrially relevant targets. As more characteristics of LPMO and its key role have been elucidated, the need for fast and reliable methods to assess its activity have become clear. Several aspects such as its co-substrates, electron donors, inhibiting factors, and the inhomogeneity of lignocellulose had to be considered during experimental design and data interpretation, as they can impact and often hamper outcomes. This review provides an overview of the currently available methods to measure LPMO activity, including their potential and limitations, and it is illustrated with practical examples.
Collapse
Affiliation(s)
- Federica Calderaro
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands; (L.E.B.); (M.A.v.d.B.)
- Molecular Enzymolog y Group, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
- Correspondence: ; Tel.: +31-6-36028569
| | - Loes E. Bevers
- DSM Biotechnology Center, 2613 AX Delft, The Netherlands; (L.E.B.); (M.A.v.d.B.)
| | | |
Collapse
|
89
|
Vuong TV, Master ER. Enzymatic upgrading of heteroxylans for added-value chemicals and polymers. Curr Opin Biotechnol 2021; 73:51-60. [PMID: 34311175 DOI: 10.1016/j.copbio.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/27/2021] [Accepted: 07/02/2021] [Indexed: 02/06/2023]
Abstract
Xylan is one of the most abundant, natural polysaccharides, and much recent interest focuses on upgrading heteroxylan to make use of its unique structures and chemistries. Significant progress has been made in the discovery and application of novel enzymes for debranching and modifying heteroxylans. Debranching enzymes include acetylxylan esterases, α-l-arabinofuranosidases and α-dglucuronidases that release side groups from the xylan backbone to recover both biochemicals and less substituted xylans for polymer applications in food packaging or drug delivery systems. Besides esterases and hydrolases, many oxidoreductases including carbohydrate oxidases, lytic polysaccharide monooxygenases, laccases and peroxidases have been also applied to alter different types of xylans for improved physical and chemical properties. This review will highlight the recent discovery and application of enzymes for upgrading xylans for use as added-value chemicals and in functional polymers.
Collapse
Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada; Department of Bioproducts and Biosystems, Aalto University, Espoo, Finland.
| |
Collapse
|
90
|
Ruiz-Dueñas FJ, Barrasa JM, Sánchez-García M, Camarero S, Miyauchi S, Serrano A, Linde D, Babiker R, Drula E, Ayuso-Fernández I, Pacheco R, Padilla G, Ferreira P, Barriuso J, Kellner H, Castanera R, Alfaro M, Ramírez L, Pisabarro AG, Riley R, Kuo A, Andreopoulos W, LaButti K, Pangilinan J, Tritt A, Lipzen A, He G, Yan M, Ng V, Grigoriev IV, Cullen D, Martin F, Rosso MN, Henrissat B, Hibbett D, Martínez AT. Genomic Analysis Enlightens Agaricales Lifestyle Evolution and Increasing Peroxidase Diversity. Mol Biol Evol 2021; 38:1428-1446. [PMID: 33211093 PMCID: PMC8480192 DOI: 10.1093/molbev/msaa301] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
As actors of global carbon cycle, Agaricomycetes (Basidiomycota) have developed complex enzymatic machineries that allow them to decompose all plant polymers, including lignin. Among them, saprotrophic Agaricales are characterized by an unparalleled diversity of habitats and lifestyles. Comparative analysis of 52 Agaricomycetes genomes (14 of them sequenced de novo) reveals that Agaricales possess a large diversity of hydrolytic and oxidative enzymes for lignocellulose decay. Based on the gene families with the predicted highest evolutionary rates—namely cellulose-binding CBM1, glycoside hydrolase GH43, lytic polysaccharide monooxygenase AA9, class-II peroxidases, glucose–methanol–choline oxidase/dehydrogenases, laccases, and unspecific peroxygenases—we reconstructed the lifestyles of the ancestors that led to the extant lignocellulose-decomposing Agaricomycetes. The changes in the enzymatic toolkit of ancestral Agaricales are correlated with the evolution of their ability to grow not only on wood but also on leaf litter and decayed wood, with grass-litter decomposers as the most recent eco-physiological group. In this context, the above families were analyzed in detail in connection with lifestyle diversity. Peroxidases appear as a central component of the enzymatic toolkit of saprotrophic Agaricomycetes, consistent with their essential role in lignin degradation and high evolutionary rates. This includes not only expansions/losses in peroxidase genes common to other basidiomycetes but also the widespread presence in Agaricales (and Russulales) of new peroxidases types not found in wood-rotting Polyporales, and other Agaricomycetes orders. Therefore, we analyzed the peroxidase evolution in Agaricomycetes by ancestral-sequence reconstruction revealing several major evolutionary pathways and mapped the appearance of the different enzyme types in a time-calibrated species tree.
Collapse
Affiliation(s)
| | - José M Barrasa
- Life Sciences Department, Alcalá University, Alcalá de Henares, Spain
| | | | - Susana Camarero
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | | | - Ana Serrano
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Rashid Babiker
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France
| | | | - Remedios Pacheco
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Guillermo Padilla
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Patricia Ferreira
- Biochemistry and Molecular and Cellular Biology Department and BIFI, Zaragoza University, Zaragoza, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| | - Harald Kellner
- International Institute Zittau, Technische Universität Dresden, Zittau, Germany
| | - Raúl Castanera
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Manuel Alfaro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Lucía Ramírez
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Antonio G Pisabarro
- Institute for Multidisciplinary Research in Applied Biology, IMAB-UPNA, Pamplona, Spain
| | - Robert Riley
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Alan Kuo
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - William Andreopoulos
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Kurt LaButti
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Andrew Tritt
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Guifen He
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Mi Yan
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Vivian Ng
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Lab, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Cullen
- Forest Products Laboratory, US Department of Agriculture, Madison, WI, USA
| | - Francis Martin
- INRAE, Laboratory of Excellence ARBRE, Champenoux, France
| | - Marie-Noëlle Rosso
- INRAE, Biodiversité et Biotechnologie Fongiques, Aix-Marseille University, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS/Aix-Marseille University, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David Hibbett
- Biology Department, Clark University, Worcester, MA, USA
| | - Angel T Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid, Spain
| |
Collapse
|
91
|
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.
Collapse
|
92
|
Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
Collapse
Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
| |
Collapse
|
93
|
Manavalan T, Stepnov AA, Hegnar OA, Eijsink VGH. Sugar oxidoreductases and LPMOs - two sides of the same polysaccharide degradation story? Carbohydr Res 2021; 505:108350. [PMID: 34049079 DOI: 10.1016/j.carres.2021.108350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) catalyze the oxidative cleavage of glycosidic bonds in recalcitrant polysaccharides such as chitin and cellulose and their discovery has revolutionized our understanding of enzymatic biomass conversion. The discovery of LPMOs raises interesting new questions regarding the roles of other oxidoreductases and abiotic redox processes in biomass conversion. LPMOs need reducing power and an oxygen co-substrate and biomass degrading ecosystems contain a multitude of redox enzymes that affect the availability of both. For example, biomass degrading fungi produce multiple sugar oxidoreductases whose biological functions so far have remained somewhat enigmatic. It is now conceivable that these redox enzymes, in particular H2O2-producing sugar oxidases, could play a role in fueling and controlling LPMO reactions. Here, we shortly review contemporary issues in the LPMO field, paying particular attention to the possible roles of sugar oxidoreductases.
Collapse
Affiliation(s)
- Tamilvendan Manavalan
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Anton A Stepnov
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Olav A Hegnar
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU - Norwegian University of Life Science, N-1432, Ås, Norway.
| |
Collapse
|
94
|
Li F, Zhao H, Shao R, Zhang X, Yu H. Enhanced Fenton Reaction for Xenobiotic Compounds and Lignin Degradation Fueled by Quinone Redox Cycling by Lytic Polysaccharide Monooxygenases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7104-7114. [PMID: 34130454 DOI: 10.1021/acs.jafc.1c01684] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The Fenton reaction is considered to be of great significance in the initial attack of lignocellulose in wood-decaying fungi. Quinone redox cycling is the main way to induce the Fenton reaction in fungi. We show that lytic polysaccharide monooxygenases (LPMOs), through LPMO-catalyzed oxidation of hydroquinone, can efficiently cooperate with glucose dehydrogenase (GDH) to achieve quinone redox cycling. The LPMO/GDH system can enhance Fe3+-reducing activity, H2O2 production, and hydroxyl radical generation, resulting in a fueled Fenton reaction. The system-generated hydroxyl radicals exhibited a strong capacity to decolorize different synthetic dyes and degrade lignin. Our results reveal a potentially critical connection between LPMOs and the Fenton reaction, suggesting that LPMOs could be involved in xenobiotic compound and lignin degradation in fungi. This new role of LPMOs may be exploited for application in biorefineries.
Collapse
Affiliation(s)
- Fei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Honglu Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ruijian Shao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaoyu Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hongbo Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
95
|
Tõlgo M, Hüttner S, Rugbjerg P, Thuy NT, Thanh VN, Larsbrink J, Olsson L. Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:131. [PMID: 34082802 PMCID: PMC8176577 DOI: 10.1186/s13068-021-01975-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Biomass-degrading enzymes with improved activity and stability can increase substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate low pH and high temperatures. Here, we aimed to illuminate the lignocellulose-degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail. RESULTS We sequenced and analyzed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. 10,128 predicted genes were found in total, which included 411 CAZy domains. Compared to other fungi, auxiliary activity (AA) domains were particularly enriched. A higher GC content was found in coding sequences compared to the overall genome, as well as a high GC3 content, which is hypothesized to contribute to thermophilicity. Primarily auxiliary activity (AA) family 9 lytic polysaccharide monooxygenase (LPMO) and glycoside hydrolase (GH) family 7 glucanase encoding genes were upregulated when LPH172 was cultivated on cellulosic substrates. Conventional hemicellulose encoding genes (GH10, GH11 and various CEs), as well as AA9 LPMOs, were upregulated when LPH172 was cultivated on xylan. The observed co-expression and co-upregulation of genes encoding AA9 LPMOs, other AA CAZymes, and (hemi)cellulases point to a complex and nuanced degradation strategy. CONCLUSIONS Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal that the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterization of potential new enzymes for industrial biomass saccharification.
Collapse
Affiliation(s)
- Monika Tõlgo
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Silvia Hüttner
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Peter Rugbjerg
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Nguyen Thanh Thuy
- Center for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Hanoi, Vietnam
| | - Vu Nguyen Thanh
- Center for Industrial Microbiology, Food Industries Research Institute, Thanh Xuan, Hanoi, Vietnam
| | - Johan Larsbrink
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Wallenberg Wood Science Centre, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
- Division of Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.
| |
Collapse
|
96
|
A Multiomic Approach to Understand How Pleurotus eryngii Transforms Non-Woody Lignocellulosic Material. J Fungi (Basel) 2021; 7:jof7060426. [PMID: 34071235 PMCID: PMC8227661 DOI: 10.3390/jof7060426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Pleurotus eryngii is a grassland-inhabiting fungus of biotechnological interest due to its ability to colonize non-woody lignocellulosic material. Genomic, transcriptomic, exoproteomic, and metabolomic analyses were combined to explain the enzymatic aspects underlaying wheat–straw transformation. Up-regulated and constitutive glycoside–hydrolases, polysaccharide–lyases, and carbohydrate–esterases active on polysaccharides, laccases active on lignin, and a surprisingly high amount of constitutive/inducible aryl–alcohol oxidases (AAOs) constituted the suite of extracellular enzymes at early fungal growth. Higher enzyme diversity and abundance characterized the longer-term growth, with an array of oxidoreductases involved in depolymerization of both cellulose and lignin, which were often up-regulated since initial growth. These oxidative enzymes included lytic polysaccharide monooxygenases (LPMOs) acting on crystalline polysaccharides, cellobiose dehydrogenase involved in LPMO activation, and ligninolytic peroxidases (mainly manganese-oxidizing peroxidases), together with highly abundant H2O2-producing AAOs. Interestingly, some of the most relevant enzymes acting on polysaccharides were appended to a cellulose-binding module. This is potentially related to the non-woody habitat of P. eryngii (in contrast to the wood habitat of many basidiomycetes). Additionally, insights into the intracellular catabolism of aromatic compounds, which is a neglected area of study in lignin degradation by basidiomycetes, were also provided. The multiomic approach reveals that although non-woody decay does not result in dramatic modifications, as revealed by detailed 2D-NMR and other analyses, it implies activation of the complete set of hydrolytic and oxidative enzymes characterizing lignocellulose-decaying basidiomycetes.
Collapse
|
97
|
Miyauchi S, Hage H, Drula E, Lesage-Meessen L, Berrin JG, Navarro D, Favel A, Chaduli D, Grisel S, Haon M, Piumi F, Levasseur A, Lomascolo A, Ahrendt S, Barry K, LaButti KM, Chevret D, Daum C, Mariette J, Klopp C, Cullen D, de Vries RP, Gathman AC, Hainaut M, Henrissat B, Hildén KS, Kües U, Lilly W, Lipzen A, Mäkelä MR, Martinez AT, Morel-Rouhier M, Morin E, Pangilinan J, Ram AFJ, Wösten HAB, Ruiz-Dueñas FJ, Riley R, Record E, Grigoriev IV, Rosso MN. Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus. DNA Res 2021; 27:5856740. [PMID: 32531032 PMCID: PMC7406137 DOI: 10.1093/dnares/dsaa011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H2O2-producing enzymes with H2O2-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.
Collapse
Affiliation(s)
- Shingo Miyauchi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Hayat Hage
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Elodie Drula
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Laurence Lesage-Meessen
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Jean-Guy Berrin
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - David Navarro
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Anne Favel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Delphine Chaduli
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France.,INRAE, CIRM-CF, UMR1163, Aix Marseille University, Marseille, France
| | - Sacha Grisel
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Mireille Haon
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - François Piumi
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | | | - Anne Lomascolo
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Steven Ahrendt
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Kurt M LaButti
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Didier Chevret
- INRAE, UMR1319, Micalis, Plateforme d'Analyse Protéomique de Paris Sud-Ouest, Jouy-en-Josas, France
| | - Chris Daum
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Jérôme Mariette
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Christophe Klopp
- INRAE, Genotoul Bioinfo, UR875, Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | | | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands.,Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Allen C Gathman
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Matthieu Hainaut
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS, UMR7257, AFMB, Aix Marseille University, Marseille, France.,INRAE, USC1408, AFMB, Marseille, France
| | | | - Ursula Kües
- Department of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, Georg-August-University Göttingen, Göttingen, Germany.,Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Walt Lilly
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MI, USA
| | - Anna Lipzen
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | | | - Mélanie Morel-Rouhier
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Emmanuelle Morin
- INRAE, UMR1136, Interactions Arbres/Microorganismes, Université de Lorraine, Nancy, France
| | - Jasmyn Pangilinan
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Arthur F J Ram
- Molecular Microbiology and Biotechnology, Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Han A B Wösten
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | | | - Robert Riley
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - Eric Record
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| | - Igor V Grigoriev
- US Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Marie-Noëlle Rosso
- INRAE, UMR1163, Biodiversity and Biotechnology of Fungi, Aix Marseille University, 13009 Marseille, France
| |
Collapse
|
98
|
From lignocellulose to plastics: Knowledge transfer on the degradation approaches by fungi. Biotechnol Adv 2021; 50:107770. [PMID: 33989704 DOI: 10.1016/j.biotechadv.2021.107770] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/04/2021] [Accepted: 05/08/2021] [Indexed: 01/21/2023]
Abstract
In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation.
Collapse
|
99
|
Polonio Á, Fernández‐Ortuño D, de Vicente A, Pérez‐García A. A haustorial-expressed lytic polysaccharide monooxygenase from the cucurbit powdery mildew pathogen Podosphaera xanthii contributes to the suppression of chitin-triggered immunity. MOLECULAR PLANT PATHOLOGY 2021; 22:580-601. [PMID: 33742545 PMCID: PMC8035642 DOI: 10.1111/mpp.13045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 05/06/2023]
Abstract
Podosphaera xanthii is the main causal agent of cucurbit powdery mildew and a limiting factor of crop productivity. The lifestyle of this fungus is determined by the development of specialized parasitic structures inside epidermal cells, termed haustoria, that are responsible for the acquisition of nutrients and the release of effectors. A typical function of fungal effectors is the manipulation of host immunity, for example the suppression of pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI). Chitin is a major component of fungal cell walls, and chitin oligosaccharides are well-known PAMP elicitors. In this work, we examined the role of PHEC27213, the most highly expressed, haustorium-specific effector candidate of P. xanthii. According to different computational predictions, the protein folding of PHEC27213 was similar to that of lytic polysaccharide monooxygenases (LPMOs) and included a conserved histidine brace; however, PHEC27213 had low sequence similarity with LPMO proteins and displayed a putative chitin-binding domain that was different from the canonical carbohydrate-binding module. Binding and enzymatic assays demonstrated that PHEC27213 was able to bind and catalyse colloidal chitin, as well as chitooligosaccharides, acting as an LPMO. Furthermore, RNAi silencing experiments showed the potential of this protein to prevent the activation of chitin-triggered immunity. Moreover, proteins with similar features were found in other haustorium-forming fungal pathogens. Our results suggest that this protein is a new fungal LPMO that catalyses chitooligosaccharides, thus contributing to the suppression of plant immunity during haustorium development. To our knowledge, this is the first mechanism identified in the haustorium to suppress chitin signalling.
Collapse
Affiliation(s)
- Álvaro Polonio
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
| | - Dolores Fernández‐Ortuño
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
| | - Antonio de Vicente
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
| | - Alejandro Pérez‐García
- Departamento de MicrobiologíaFacultad de CienciasUniversidad de MálagaMálagaSpain
- Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de MálagaConsejo Superior de Investigaciones Científicas (IHSM−UMA−CSIC)MálagaSpain
| |
Collapse
|
100
|
de Figueiredo FL, de Oliveira ACP, Terrasan CRF, Gonçalves TA, Gerhardt JA, Tomazetto G, Persinoti GF, Rubio MV, Peña JAT, Araújo MF, de Carvalho Silvello MA, Franco TT, Rabelo SC, Goldbeck R, Squina FM, Damasio A. Multi-omics analysis provides insights into lignocellulosic biomass degradation by Laetiporus sulphureus ATCC 52600. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:96. [PMID: 33865436 PMCID: PMC8052766 DOI: 10.1186/s13068-021-01945-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 04/01/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Wood-decay basidiomycetes are effective for the degradation of highly lignified and recalcitrant plant substrates. The degradation of lignocellulosic materials by brown-rot strains is carried out by carbohydrate-active enzymes and non-enzymatic Fenton mechanism. Differences in the lignocellulose catabolism among closely related brown rots are not completely understood. Here, a multi-omics approach provided a global understanding of the strategies employed by L. sulphureus ATCC 52600 for lignocellulose degradation. RESULTS The genome of Laetiporus sulphureus ATCC 52600 was sequenced and phylogenomic analysis supported monophyletic clades for the Order Polyporales and classification of this species within the family Laetiporaceae. Additionally, the plasticity of its metabolism was revealed in growth analysis on mono- and disaccharides, and polysaccharides such as cellulose, hemicelluloses, and polygalacturonic acid. The response of this fungus to the presence of lignocellulosic substrates was analyzed by transcriptomics and proteomics and evidenced the occurrence of an integrated oxidative-hydrolytic metabolism. The transcriptomic profile in response to a short cultivation period on sugarcane bagasse revealed 125 upregulated transcripts, which included CAZymes (redox enzymes and hemicellulases) as well as non-CAZy redox enzymes and genes related to the synthesis of low-molecular-weight compounds. The exoproteome produced in response to extended cultivation time on Avicel, and steam-exploded sugarcane bagasse, sugarcane straw, and Eucalyptus revealed 112 proteins. Contrasting with the mainly oxidative profile observed in the transcriptome, the secretomes showed a diverse hydrolytic repertoire including constitutive cellulases and hemicellulases, in addition to 19 upregulated CAZymes. The secretome induced for 7 days on sugarcane bagasse, representative of the late response, was applied in the saccharification of hydrothermally pretreated grass (sugarcane straw) and softwood (pine) by supplementing a commercial cocktail. CONCLUSION This study shows the singularity of L. sulphureus ATCC 52600 compared to other Polyporales brown rots, regarding the presence of cellobiohydrolase and peroxidase class II. The multi-omics analysis reinforces the oxidative-hydrolytic metabolism involved in lignocellulose deconstruction, providing insights into the overall mechanisms as well as specific proteins of each step.
Collapse
Affiliation(s)
- Fernanda Lopes de Figueiredo
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Ana Carolina Piva de Oliveira
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Brazilian Biorenewables National Laboratory (LNBr), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Cesar Rafael Fanchini Terrasan
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Thiago Augusto Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
- Department of Technological and Environmental Processes, University of Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Jaqueline Aline Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Geizecler Tomazetto
- Department of Biological and Chemical Engineering (BCE), Aarhus University, 8200, Aarhus, Denmark
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory (LNBr), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Marcelo Ventura Rubio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | | | | | - Telma Teixeira Franco
- Interdisciplinary Center of Energy Planning (NIPE), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Sarita Cândida Rabelo
- Department of Bioprocess and Biotechnology, College of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Rosana Goldbeck
- Department of Food Engineering, Faculty of Food Engineering, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Department of Technological and Environmental Processes, University of Sorocaba (UNISO), Sorocaba, SP, Brazil.
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, SP, Brazil.
- São Paulo Fungal Group, São Paulo, Brazil.
| |
Collapse
|