1
|
Ernst P, Wirtz A, Wynands B, Wierckx N. Establishing an itaconic acid production process with Ustilago species on the low-cost substrate starch. FEMS Yeast Res 2024; 24:foae023. [PMID: 39038994 PMCID: PMC11312366 DOI: 10.1093/femsyr/foae023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/15/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Ustilago maydis and Ustilago cynodontis are natural producers of a broad range of valuable molecules including itaconate, malate, glycolipids, and triacylglycerols. Both Ustilago species are insensitive toward medium impurities, and have previously been engineered for efficient itaconate production and stabilized yeast-like growth. Due to these features, these strains were already successfully used for the production of itaconate from different alternative feedstocks such as molasses, thick juice, and crude glycerol. Here, we analyzed the amylolytic capabilities of Ustilago species for metabolization of starch, a highly abundant and low-cost polymeric carbohydrate widely utilized as a substrate in several biotechnological processes. Ustilago cynodontis was found to utilize gelatinized potato starch for both growth and itaconate production, confirming the presence of extracellular amylolytic enzymes in Ustilago species. Starch was rapidly degraded by U. cynodontis, even though no α-amylase was detected. Further experiments indicate that starch hydrolysis is caused by the synergistic action of glucoamylase and α-glucosidase enzymes. The enzymes showed a maximum activity of around 0.5 U ml-1 at the fifth day after inoculation, and also released glucose from additional substrates, highlighting potential broader applications. In contrast to U. cynodontis, U. maydis showed no growth on starch accompanied with no detectable amylolytic activity.
Collapse
Affiliation(s)
- Philipp Ernst
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Astrid Wirtz
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| |
Collapse
|
2
|
Liu Y, Angelov A, Feiler W, Baudrexl M, Zverlov V, Liebl W, Vanderhaeghen S. Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:121. [PMID: 36371193 PMCID: PMC9655821 DOI: 10.1186/s13068-022-02216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited. RESULTS In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-L-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan). CONCLUSIONS We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.
Collapse
Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Werner Feiler
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Sonja Vanderhaeghen
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: IMGM Laboratories, Lochhamer Straße 29a, 82152 Planegg, Germany
| |
Collapse
|
3
|
Biochemical characterization of a thermophilic exo-arabinanase from the filamentous fungus Rasamsonia emersonii. J Biosci Bioeng 2022; 133:316-322. [PMID: 35031213 DOI: 10.1016/j.jbiosc.2021.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022]
Abstract
Arabinan in plant cell wall constitutes a major source of arabinose and arabino-oligosaccharides in nature. Exo-α-l-1,5-arabinanases release arabinose or arabino-oligosaccharides from arabinan in an exo-acting manner and therefore contribute to arabinan degradation. In this study, an exo-α-l-1,5-arabinanase belonging to GH93 family was identified from the thermophilic filamentous fungus Rasamsonia emersonii. The corresponding encoding gene (Reabn93) was cloned from the R. emersonii genome and heterologously expressed in Pichia pastoris. The purified recombinant ReAbn93 exhibited the maximum activity at 70 °C and retained 70% of its activity after incubation at 70 °C for 3 h ReAbn93 had an acidic pH optimum (pH 4.0) but remained stable over a broad pH range (pH 3-9). The specific activity of ReAbn93 toward linear arabinan under optimal conditions was 466.08 U mg-1. Similar to the few other reported GH93 members, ReAbn93 degrades linear arabinan or arabino-oligosaccharides in an exo-acting manner with arabinobiose as the only hydrolytic product. Of note, ReAbn93 possessed remarkably better thermostability and higher specific activity compared to the only reported thermophilic counterpart in GH93, and therefore holds potential in relevant biotechnological applications.
Collapse
|
4
|
de Freitas EN, Salgado JCS, Alnoch RC, Contato AG, Habermann E, Michelin M, Martínez CA, Polizeli MDLTM. Challenges of Biomass Utilization for Bioenergy in a Climate Change Scenario. BIOLOGY 2021; 10:1277. [PMID: 34943192 PMCID: PMC8698859 DOI: 10.3390/biology10121277] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 12/01/2022]
Abstract
The climate changes expected for the next decades will expose plants to increasing occurrences of combined abiotic stresses, including drought, higher temperatures, and elevated CO2 atmospheric concentrations. These abiotic stresses have significant consequences on photosynthesis and other plants' physiological processes and can lead to tolerance mechanisms that impact metabolism dynamics and limit plant productivity. Furthermore, due to the high carbohydrate content on the cell wall, plants represent a an essential source of lignocellulosic biomass for biofuels production. Thus, it is necessary to estimate their potential as feedstock for renewable energy production in future climate conditions since the synthesis of cell wall components seems to be affected by abiotic stresses. This review provides a brief overview of plant responses and the tolerance mechanisms applied in climate change scenarios that could impact its use as lignocellulosic biomass for bioenergy purposes. Important steps of biofuel production, which might influence the effects of climate change, besides biomass pretreatments and enzymatic biochemical conversions, are also discussed. We believe that this study may improve our understanding of the plant biological adaptations to combined abiotic stress and assist in the decision-making for selecting key agronomic crops that can be efficiently adapted to climate changes and applied in bioenergy production.
Collapse
Affiliation(s)
- Emanuelle Neiverth de Freitas
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (E.N.d.F.); (A.G.C.)
| | - José Carlos Santos Salgado
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil;
| | - Robson Carlos Alnoch
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
| | - Alex Graça Contato
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (E.N.d.F.); (A.G.C.)
| | - Eduardo Habermann
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
| | - Michele Michelin
- Centre of Biological Engineering (CEB), Gualtar Campus, University of Minho, 4710-057 Braga, Portugal;
| | - Carlos Alberto Martínez
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
| | - Maria de Lourdes T. M. Polizeli
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto 14049-900, São Paulo, Brazil; (E.N.d.F.); (A.G.C.)
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), University of São Paulo, Ribeirão Preto 14040-901, São Paulo, Brazil; (R.C.A.); (E.H.); (C.A.M.)
| |
Collapse
|
5
|
Strictosidine synthase, an indispensable enzyme involved in the biosynthesis of terpenoid indole and β-carboline alkaloids. Chin J Nat Med 2021; 19:591-607. [PMID: 34419259 DOI: 10.1016/s1875-5364(21)60059-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Indexed: 11/21/2022]
Abstract
Terpenoid indole (TIAs) and β-carboline alkaloids (BCAs), such as suppressant reserpine, vasodilatory yohimbine, and antimalarial quinine, are natural compounds derived from strictosidine. These compounds can exert powerful pharmacological effects but be obtained from limited source in nature. the whole biosynthetic pathway of TIAs and BCAs, The Pictet-Spengler reaction catalyzed by strictosidine synthase (STR; EC: 4.3.3.2) is the rate-limiting step. Therefore, it is necessary to investigate their biosynthesis pathways, especially the role of STR, and related findings will support the biosynthetic generation of natural and unnatural compounds. This review summarizes the latest studies concerning the function of STR in TIA and BCA biosynthesis, and illustrates the compounds derived from strictosidine. The substrate specificity of STR based on its structure is also summarized. Proteins that contain six-bladed four-stranded β-propeller folds in many organisms, other than plants, are listed. The presence of these folds may lead to similar functions among organisms. The expression of STR gene can greatly influence the production of many compounds. STR is mainly applied to product various valuable drugs in plant cell suspension culture and biosynthesis in other carriers.
Collapse
|
6
|
Formela-Luboińska M, Remlein-Starosta D, Waśkiewicz A, Karolewski Z, Bocianowski J, Stępień Ł, Labudda M, Jeandet P, Morkunas I. The Role of Saccharides in the Mechanisms of Pathogenicity of Fusarium oxysporum f. sp. lupini in Yellow Lupine ( Lupinus luteus L.). Int J Mol Sci 2020; 21:ijms21197258. [PMID: 33019571 PMCID: PMC7582877 DOI: 10.3390/ijms21197258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/21/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
The primary aim of this study was to determine the relationship between soluble sugar levels (sucrose, glucose, or fructose) in yellow lupine embryo axes and the pathogenicity of the hemibiotrophic fungus Fusarium oxysporum f. sp. Schlecht lupini. The first step of this study was to determine the effect of exogenous saccharides on the growth and sporulation of F. oxysporum. The second one focused on estimating the levels of ergosterol as a fungal growth indicator in infected embryo axes cultured in vitro on sugar containing-medium or without it. The third aim of this study was to record the levels of the mycotoxin moniliformin as the most characteristic secondary metabolite of F. oxysporum in the infected embryo axes with the high sugar medium and without it. Additionally, morphometric measurements, i.e., the length and fresh weight of embryo axes, were done. The levels of ergosterol were the highest in infected embryo axes with a sugar deficit. At the same time, significant accumulation of the mycotoxin moniliformin was recorded in those tissues. Furthermore, it was found that the presence of sugars in water agar medium inhibited the sporulation of the pathogenic fungus F. oxysporum in relation to the control (sporulation of the pathogen on medium without sugar), the strongest inhibiting effect was observed in the case of glucose. Infection caused by F. oxysporum significantly limited the growth of embryo axes, but this effect was more visible on infected axes cultured under sugar deficiency than on the ones cultured with soluble sugars. The obtained results thus showed that high sugar levels may lead to reduced production of mycotoxins by F. oxysporum, limiting infection development and fusariosis.
Collapse
Affiliation(s)
- Magda Formela-Luboińska
- Department of Plant Physiology, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland;
| | - Dorota Remlein-Starosta
- Department of Ecology and Environmental Protection, Institute of Plant Protection—National Research Institute, Władysława Węgorka 20, 60-318 Poznań, Poland
| | - Agnieszka Waśkiewicz
- Department of Chemistry, Poznań University of Life Sciences, Wojska Polskiego 75, 60-625 Poznań, Poland;
| | - Zbigniew Karolewski
- Department of Phytopathology, Seed Science and Technology, Poznań University of Life Sciences, Dąbrowskiego 159, 60-594 Poznań, Poland;
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland;
| | - Łukasz Stępień
- Department of Pathogen Genetics and Plant Resistance, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | - Mateusz Labudda
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland;
| | - Philippe Jeandet
- Research Unit “Induced Resistance and Plant Bioprotection”, UPRES EA 4707, Department of Biology and Biochemistry, Faculty of Sciences, University of Reims, P.O. Box 1039, CEDEX 02, 51687 Reims, France;
| | - Iwona Morkunas
- Department of Plant Physiology, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland;
- Correspondence: or ; Tel.: +48-61-8466040
| |
Collapse
|
7
|
Velasco J, Oliva B, Gonçalves AL, Lima AS, Ferreira G, França BA, Mulinari EJ, Gonçalves TA, Squina FM, Kadowaki MAS, Maiorano A, Polikarpov I, Oliveira LCD, Segato F. Functional characterization of a novel thermophilic exo-arabinanase from Thermothielavioides terrestris. Appl Microbiol Biotechnol 2020; 104:8309-8326. [PMID: 32813063 DOI: 10.1007/s00253-020-10806-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/06/2020] [Accepted: 08/02/2020] [Indexed: 10/23/2022]
Abstract
Arabinanases from glycoside hydrolase family GH93 are enzymes with exo-activity that hydrolyze the α-1,5 bonds between arabinose residues present on arabinan. Currently, several initiatives aiming to use byproducts rich in arabinan such as pectin and sugar beet pulp as raw material to produce various compounds of interest are being developed. However, it is necessary to use robust enzymes that have an optimal performance under pH and temperature conditions used in the industrial processes. In this work, the first GH93 from the thermophilic fungus Thermothielavioides terrestris (Abn93T) was heterologously expressed in Aspergillus nidulans, purified and biochemically characterized. The enzyme is a thermophilic glycoprotein (optimum activity at 70 °C) with prolonged stability in acid pHs (4.0 to 6.5). The presence of glycosylation affected slightly the hydrolytic capacity of the enzyme, which was further increased by 34% in the presence of 1 mM CoCl2. Small-angle X-ray scattering results show that Abn93T is a globular-like-shaped protein with a slight bulge at one end. The hydrolytic mechanism of the enzyme was elucidated using capillary zone electrophoresis and molecular docking calculations. Abn93T has an ability to produce (in synergism with arabinofuranosidases) arabinose and arabinobiose from sugar beet arabinan, which can be explored as fermentable sugars and prebiotics. KEY POINTS: • Thermophilic exo-arabinanase from family GH93 • Molecular basis of arabinan depolymerization.
Collapse
Affiliation(s)
- Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Aline Larissa Gonçalves
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Awana Silva Lima
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Gislene Ferreira
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bruno Alves França
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Evandro José Mulinari
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Thiago Augusto Gonçalves
- Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.,Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Fábio Márcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - Marco Antonio Seiki Kadowaki
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Alfredo Maiorano
- Instituto de Pesquisas Tecnológicas do Estado de São Paulo, Diretoria de Operações e Negócios, Núcleo de Bionanomanufatura, São Paulo, SP, Brazil
| | - Igor Polikarpov
- Departamento de Física e Ciências Aplicadas, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil.
| |
Collapse
|
8
|
Nester K, Plazinski W. Deciphering the conformational preferences of furanosides. A molecular dynamics study. J Biomol Struct Dyn 2020; 38:3359-3370. [DOI: 10.1080/07391102.2019.1656670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| |
Collapse
|
9
|
Hao G, McCormick S, Vaughan MM, Naumann TA, Kim HS, Proctor R, Kelly A, Ward TJ. Fusarium graminearum arabinanase (Arb93B) Enhances Wheat Head Blight Susceptibility by Suppressing Plant Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:888-898. [PMID: 30759350 DOI: 10.1094/mpmi-06-18-0170-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Fusarium head blight (FHB) of wheat and barley caused by the fungus Fusarium graminearum reduces crop yield and contaminates grain with mycotoxins. In this study, we investigated two exo-1,5-α-L-arabinanases (Arb93A and Arb93B) secreted by F. graminearum and their effect on wheat head blight development. Arabinan is an important component of plant cell walls but it was not known whether these arabinanases play a role in FHB. Both ARB93A and ARB93B were induced during the early stages of infection. arb93A mutants did not exhibit a detectable change in ability to cause FHB, whereas arb93B mutants caused lower levels of FHB symptoms and deoxynivalenol contamination compared with the wild type. Furthermore, virulence and deoxynivalenol contamination were restored to wild-type levels in ARB93B complemented mutants. Fusion proteins of green fluorescent protein (GFP) with the predicted chloroplast peptide or the mature protein of Arb93B were not observed in the chloroplast. Reactive oxygen species (ROS) production was reduced in the infiltrated zones of Nicotiana benthamiana leaves expressing ARB93B-GFP. Coexpression of ARB93B-GFP and Bax in N. benthamiana leaves significantly suppressed Bax-programmed cell death. Our results indicate that Arb93B enhances plant disease susceptibility by suppressing ROS-associated plant defense responses.
Collapse
Affiliation(s)
- Guixia Hao
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| | - Susan McCormick
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| | - Martha M Vaughan
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| | - Todd A Naumann
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| | - Hye-Seon Kim
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| | - Robert Proctor
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| | - Amy Kelly
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| | - Todd J Ward
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, United States Department of Agriculture-Agricultural Research Service, Peoria, IL, U.S.A
| |
Collapse
|
10
|
Nester K, Gaweda K, Plazinski W. A GROMOS Force Field for Furanose-Based Carbohydrates. J Chem Theory Comput 2019; 15:1168-1186. [DOI: 10.1021/acs.jctc.8b00838] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| |
Collapse
|
11
|
α-l-Arabinofuranosidase: A Potential Enzyme for the Food Industry. ENERGY, ENVIRONMENT, AND SUSTAINABILITY 2019. [DOI: 10.1007/978-981-13-3263-0_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
12
|
Gao J, Zhao Y, Zhang G, Li Y, Li Q. Production optimization, purification, expression, and characterization of a novel α-l-arabinofuranosidase from Paenibacillus polymyxa. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|
13
|
Affiliation(s)
- Csaba Fehér
- Department of Applied Biotechnology and Food Science, Biorefinery Research Group, Budapest University of Technology and Economics, Budapest, Hungary
| |
Collapse
|
14
|
Pedrogo DAM, Jensen MD, Van Dyke CT, Murray JA, Woods JA, Chen J, Kashyap PC, Nehra V. Gut Microbial Carbohydrate Metabolism Hinders Weight Loss in Overweight Adults Undergoing Lifestyle Intervention With a Volumetric Diet. Mayo Clin Proc 2018; 93:1104-1110. [PMID: 30077203 PMCID: PMC6107068 DOI: 10.1016/j.mayocp.2018.02.019] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/09/2018] [Accepted: 02/23/2018] [Indexed: 01/31/2023]
Abstract
The rising incidence of obesity requires the reevaluation of our current therapeutic strategies to optimize patient outcomes. The objective of this study was to determine whether compositional and functional characteristics of the gut microbiota in adults predict responses to a comprehensive lifestyle intervention program in overweight and obese adults. We recruited 26 participants from the Mayo Clinic Obesity Treatment Research Program between August 6, 2013, and September 12, 2013, to participate in a lifestyle intervention program for weight loss. Adults aged 18 to 65 years with a body mass index of 27 to 39.9 kg/m2 and able to provide informed consent were included in the study. Fecal stool samples were obtained at baseline and after 3 months. Loss of at least 5% of baseline weight after 3 months was defined as success. Clinical characteristics and gut microbial composition and function were compared between those who achieved at least 5% and those who achieved less than 5% weight loss. After 3 months, 9 of 26 participants lost at least 5% of their weight. The mean weight loss was 7.89 kg (95% CI, 6.46-9.32 kg) in the success group and 1.51 kg (95% CI, 0.52-2.49 kg) in the less than 5% weight loss group. An increased abundance of Phascolarctobacterium was associated with success. In contrast, an increased abundance of Dialister and of genes encoding gut microbial carbohydrate-active enzymes was associated with failure to lose 5% body weight. A gut microbiota with increased capability for carbohydrate metabolism appears to be associated with decreased weight loss in overweight and obese patients undergoing a lifestyle intervention program.
Collapse
Affiliation(s)
- David A. Muñiz Pedrogo
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN
- University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Michael D. Jensen
- Division of Endocrinology, Diabetes, Metabolism, and Nutrition, Mayo Clinic, Rochester, MN
| | - Carol T. Van Dyke
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Joseph A. Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | - Jeffrey A. Woods
- Professor of Kinesiology and Community Health; Director, Center on Health, Aging and Disability. University of Illinois at Urbana-Champaign, Champaign, IL
| | - Jun Chen
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Purna C. Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
- Corresponding authors: Purna Kashyap, MBBS, Assistant Professor of Medicine, Vandana Nehra, MD, Assistant professor of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN. 55905, and
| | - Vandana Nehra
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
- Corresponding authors: Purna Kashyap, MBBS, Assistant Professor of Medicine, Vandana Nehra, MD, Assistant professor of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN. 55905, and
| |
Collapse
|
15
|
Investigation of the indigenous fungal community populating barley grains: Secretomes and xylanolytic potential. J Proteomics 2017; 169:153-164. [DOI: 10.1016/j.jprot.2017.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/03/2017] [Accepted: 03/13/2017] [Indexed: 11/23/2022]
|
16
|
Coyle T, Debowski AW, Varrot A, Stubbs KA. Exploiting sp 2 -Hybridisation in the Development of Potent 1,5-α-l-Arabinanase Inhibitors. Chembiochem 2017; 18:974-978. [PMID: 28266777 DOI: 10.1002/cbic.201700073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Indexed: 11/07/2022]
Abstract
The synthesis of potent inhibitors of GH93 arabinanases as well as a synthesis of a chromogenic substrate to measure GH93 arabinanase activity are described. An insight into the reasons behind the potency of the inhibitors was gained through X-ray crystallographic analysis of the arabinanase Arb93A from Fusarium graminearum. These compounds lay a foundation for future inhibitor development as well as for the use of the chromogenic substrate in biochemical studies of GH93 arabinanases.
Collapse
Affiliation(s)
- Travis Coyle
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Present address: School of Chemistry, University College Dublin, Stillorgan Road, Belfield, Dublin, 4, Ireland
| | - Aleksandra W Debowski
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Annabelle Varrot
- CERMAV, Université Grenoble Alpes, CNRS, 38000, Grenoble, France
| | - Keith A Stubbs
- School of Molecular Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| |
Collapse
|
17
|
Wang X, Woods RJ. Insights into furanose solution conformations: beyond the two-state model. JOURNAL OF BIOMOLECULAR NMR 2016; 64:291-305. [PMID: 26968894 PMCID: PMC5115177 DOI: 10.1007/s10858-016-0028-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/08/2016] [Indexed: 05/15/2023]
Abstract
A two-state model is commonly used for interpreting ring conformations of furanoses based on NMR scalar (3) J-coupling constants, with the ring populating relatively narrow distributions in the North and the South of the pseudorotation itinerary. The validity of this simple approach has been questioned, and is examined here in detail employing molecular dynamics (MD) simulations with a new GLYCAM force field parameter set for furanoses. Theoretical (3) J-coupling constants derived from unrestrained MD simulations with the new furanose-specific parameters agreed with the experimental coupling constants to within 1 Hz on average. The results confirm that a two state model is a reasonable description for the ring conformation in the majority of methyl furanosides. However, in the case of methyl α-D-arabinofuranoside the ring populates a continuum of states from North to South via the eastern side of the pseudorotational itinerary. Two key properties are responsible for these differences. Firstly, East and West regions in β- and α-anomers, respectively, are destabilized by the absence of the anomeric effect. And, secondly, East or West conformations can be further destabilized by repulsive interactions among vicinal hydroxyl groups and ring oxygen atoms when the vicinal hydroxyl groups are in syn-configurations (such as in ribose and lyxose) more so than when in anti (arabinose, xylose).
Collapse
Affiliation(s)
- Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
18
|
Mardones W, Callegari E, Eyzaguirre J. Heterologous expression of a Penicillium purpurogenum exo-arabinanase in Pichia pastoris and its biochemical characterization. Fungal Biol 2015; 119:1267-1278. [DOI: 10.1016/j.funbio.2015.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 11/27/2022]
|
19
|
Abstract
SUMMARY Biomass is constructed of dense recalcitrant polymeric materials: proteins, lignin, and holocellulose, a fraction constituting fibrous cellulose wrapped in hemicellulose-pectin. Bacteria and fungi are abundant in soil and forest floors, actively recycling biomass mainly by extracting sugars from holocellulose degradation. Here we review the genome-wide contents of seven Aspergillus species and unravel hundreds of gene models encoding holocellulose-degrading enzymes. Numerous apparent gene duplications followed functional evolution, grouping similar genes into smaller coherent functional families according to specialized structural features, domain organization, biochemical activity, and genus genome distribution. Aspergilli contain about 37 cellulase gene models, clustered in two mechanistic categories: 27 hydrolyze and 10 oxidize glycosidic bonds. Within the oxidative enzymes, we found two cellobiose dehydrogenases that produce oxygen radicals utilized by eight lytic polysaccharide monooxygenases that oxidize glycosidic linkages, breaking crystalline cellulose chains and making them accessible to hydrolytic enzymes. Among the hydrolases, six cellobiohydrolases with a tunnel-like structural fold embrace single crystalline cellulose chains and cooperate at nonreducing or reducing end termini, splitting off cellobiose. Five endoglucanases group into four structural families and interact randomly and internally with cellulose through an open cleft catalytic domain, and finally, seven extracellular β-glucosidases cleave cellobiose and related oligomers into glucose. Aspergilli contain, on average, 30 hemicellulase and 7 accessory gene models, distributed among 9 distinct functional categories: the backbone-attacking enzymes xylanase, mannosidase, arabinase, and xyloglucanase, the short-side-chain-removing enzymes xylan α-1,2-glucuronidase, arabinofuranosidase, and xylosidase, and the accessory enzymes acetyl xylan and feruloyl esterases.
Collapse
|
20
|
Babbar N, Dejonghe W, Gatti M, Sforza S, Elst K. Pectic oligosaccharides from agricultural by-products: production, characterization and health benefits. Crit Rev Biotechnol 2015; 36:594-606. [DOI: 10.3109/07388551.2014.996732] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Neha Babbar
- Separation & Conversion Technology, VITO-Flemish Institute for Technological Research, Boeretang, Mol, Belgium and
- Department of Food Science, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Winnie Dejonghe
- Separation & Conversion Technology, VITO-Flemish Institute for Technological Research, Boeretang, Mol, Belgium and
| | - Monica Gatti
- Department of Food Science, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Stefano Sforza
- Department of Food Science, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Kathy Elst
- Separation & Conversion Technology, VITO-Flemish Institute for Technological Research, Boeretang, Mol, Belgium and
| |
Collapse
|
21
|
Investigating the function of an arabinan utilization locus isolated from a termite gut community. Appl Environ Microbiol 2014; 81:31-9. [PMID: 25304507 DOI: 10.1128/aem.02257-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biocatalysts are essential for the development of bioprocesses efficient for plant biomass degradation. Previously, a metagenomic clone containing DNA from termite gut microbiota was pinpointed in a functional screening that revealed the presence of arabinofuranosidase activity. Subsequent genetic and bioinformatic analysis revealed that the DNA fragment belonged to a member of the genus Bacteroides and encoded 19 open reading frames (ORFs), and annotation suggested the presence of hypothetical transporter and regulator proteins and others involved in the catabolism of pentose sugar. In this respect and considering the phenotype of the metagenomic clone, it was noted that among the ORFs, there are four putative arabinose-specific glycoside hydrolases, two from family GH43 and two from GH51. In this study, a thorough bioinformatics analysis of the metagenomic clone gene cluster has been performed and the four aforementioned glycoside hydrolases have been characterized. Together, the results provide evidence that the gene cluster is a polysaccharide utilization locus dedicated to the breakdown of the arabinan component in pectin and related substrates. Characterization of the two GH43 and the two GH51 glycoside hydrolases has revealed that each of these enzymes displays specific catalytic capabilities and that when these are combined the enzymes act synergistically, increasing the efficiency of arabinan degradation.
Collapse
|
22
|
Elucidation of the molecular basis for arabinoxylan-debranching activity of a thermostable family GH62 α-l-arabinofuranosidase from Streptomyces thermoviolaceus. Appl Environ Microbiol 2014; 80:5317-29. [PMID: 24951792 DOI: 10.1128/aem.00685-14] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Xylan-debranching enzymes facilitate the complete hydrolysis of xylan and can be used to alter xylan chemistry. Here, the family GH62 α-l-arabinofuranosidase from Streptomyces thermoviolaceus (SthAbf62A) was shown to have a half-life of 60 min at 60°C and the ability to cleave α-1,3 l-arabinofuranose (l-Araf) from singly substituted xylopyranosyl (Xylp) backbone residues in wheat arabinoxylan; low levels of activity on arabinan as well as 4-nitrophenyl α-l-arabinofuranoside were also detected. After selective removal of α-1,3 l-Araf substituents from disubstituted Xylp residues present in wheat arabinoxylan, SthAbf62A could also cleave the remaining α-1,2 l-Araf substituents, confirming the ability of SthAbf62A to remove α-l-Araf residues that are (1→2) and (1→3) linked to monosubstituted β-d-Xylp sugars. Three-dimensional structures of SthAbf62A and its complex with xylotetraose and l-arabinose confirmed a five-bladed β-propeller fold and revealed a molecular Velcro in blade V between the β1 and β21 strands, a disulfide bond between Cys27 and Cys297, and a calcium ion coordinated in the central channel of the fold. The enzyme-arabinose complex structure further revealed a narrow and seemingly rigid l-arabinose binding pocket situated at the center of one side of the β propeller, which stabilized the arabinofuranosyl substituent through several hydrogen-bonding and hydrophobic interactions. The predicted catalytic amino acids were oriented toward this binding pocket, and the catalytic essentiality of Asp53 and Glu213 was confirmed by site-specific mutagenesis. Complex structures with xylotetraose revealed a shallow cleft for xylan backbone binding that is open at both ends and comprises multiple binding subsites above and flanking the l-arabinose binding pocket.
Collapse
|
23
|
Shi H, Ding H, Huang Y, Wang L, Zhang Y, Li X, Wang F. Expression and characterization of a GH43 endo-arabinanase from Thermotoga thermarum. BMC Biotechnol 2014; 14:35. [PMID: 24886412 PMCID: PMC4021227 DOI: 10.1186/1472-6750-14-35] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 04/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Arabinan is an important plant polysaccharide degraded mainly by two hydrolytic enzymes, endo-arabinanase and α-L-arabinofuranosidase. In this study, the characterization and application in arabinan degradation of an endo-arabinanase from Thermotoga thermarum were investigated. RESULTS The recombinant endo-arabinanase was expressed in Escherichia coli BL21 (DE3) and purified by heat treatment followed by purification on a nickel affinity column chromatography. The purified endo-arabinanase exhibited optimal activity at pH 6.5 and 75°C and its residual activity retained more than 80% of its initial activity after being incubated at 80°C for 2 h. The results showed that the endo-arabinanase was very effective for arabinan degradation at higher temperature. When linear arabinan was used as the substrate, the apparent K(m) and V(max) values were determined to be 12.3 ± 0.15 mg ml⁻¹ and 1,052.1 ± 12.7 μmol ml⁻¹ min⁻¹, respectively (at pH 6.5, 75°C), and the calculated kcat value was 349.3 ± 4.2 s⁻¹. CONCLUSIONS This work provides a useful endo-arabinanase with high thermostability andcatalytic efficiency, and these characteristics exhibit a great potential for enzymatic conversion of arabinan.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Fei Wang
- College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
24
|
Multiple rewards from a treasure trove of novel glycoside hydrolase and polysaccharide lyase structures: new folds, mechanistic details, and evolutionary relationships. Curr Opin Struct Biol 2013; 23:652-9. [DOI: 10.1016/j.sbi.2013.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/04/2013] [Accepted: 06/04/2013] [Indexed: 11/18/2022]
|
25
|
Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| |
Collapse
|
26
|
Benoit I, Coutinho PM, Schols HA, Gerlach JP, Henrissat B, de Vries RP. Degradation of different pectins by fungi: correlations and contrasts between the pectinolytic enzyme sets identified in genomes and the growth on pectins of different origin. BMC Genomics 2012; 13:321. [PMID: 22812459 PMCID: PMC3460790 DOI: 10.1186/1471-2164-13-321] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 07/07/2012] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Pectins are diverse and very complex biomolecules and their structure depends on the plant species and tissue. It was previously shown that derivatives of pectic polymers and oligosaccharides from pectins have positive effects on human health. To obtain specific pectic oligosaccharides, highly defined enzymatic mixes are required. Filamentous fungi are specialized in plant cell wall degradation and some produce a broad range of pectinases. They may therefore shed light on the enzyme mixes needed for partial hydrolysis. RESULTS The growth profiles of 12 fungi on four pectins and four structural elements of pectins show that the presence/absence of pectinolytic genes in the fungal genome clearly correlates with their ability to degrade pectins. However, this correlation is less clear when we zoom in to the pectic structural elements. CONCLUSIONS This study highlights the complexity of the mechanisms involved in fungal degradation of complex carbon sources such as pectins. Mining genomes and comparative genomics are promising first steps towards the production of specific pectinolytic fractions.
Collapse
Affiliation(s)
- Isabelle Benoit
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, Case 932, 163 Av de Luminy, Marseille cedex 9, 13288, France
| | - Henk A Schols
- Laboratory of Food Chemistry, Wageningen University, Bomenweg 2, Wageningen, 6703HD, The Netherlands
| | - Jan P Gerlach
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, CNRS UMR 7257, Case 932, 163 Av de Luminy, Marseille cedex 9, 13288, France
| | - Ronald P de Vries
- Microbiology & Kluyver Centre for Genomics of Industrial Fermentations, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Fungal Physiology, CBS-KNAW, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| |
Collapse
|
27
|
Yang F, Jensen JD, Svensson B, Jørgensen HJL, Collinge DB, Finnie C. Secretomics identifies Fusarium graminearum proteins involved in the interaction with barley and wheat. MOLECULAR PLANT PATHOLOGY 2012; 13:445-53. [PMID: 22044785 PMCID: PMC6638632 DOI: 10.1111/j.1364-3703.2011.00759.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Fusarium graminearum is a phytopathogenic fungus primarily infecting small grain cereals, including barley and wheat. Secreted enzymes play important roles in the pathogenicity of many fungi. In order to access the secretome of F. graminearum, the fungus was grown in liquid culture with barley or wheat flour as the sole nutrient source to mimic the host-pathogen interaction. A gel-based proteomics approach was employed to identify the proteins secreted into the culture medium. Sixty-nine unique fungal proteins were identified in 154 protein spots, including enzymes involved in the degradation of cell walls, starch and proteins. Of these proteins, 35% had not been identified in previous in planta or in vitro studies, 70% were predicted to contain signal peptides and a further 16% may be secreted in a nonclassical manner. Proteins identified in the 72 spots showing differential appearance between wheat and barley flour medium were mainly involved in fungal cell wall remodelling and the degradation of plant cell walls, starch and proteins. The in planta expression of corresponding F. graminearum genes was confirmed by quantitative reverse transcriptase-polymerase chain reaction in barley and wheat spikelets harvested at 2-6 days after inoculation. In addition, a clear difference in the accumulation of fungal biomass and the extent of fungal-induced proteolysis of plant β-amylase was observed in barley and wheat. The present study considerably expands the current database of F. graminearum secreted proteins which may be involved in Fusarium head blight.
Collapse
Affiliation(s)
- Fen Yang
- Department of Systems Biology, Enzyme and Protein Chemistry, Technical University of Denmark, 2800-Kongens Lyngby, Denmark
| | | | | | | | | | | |
Collapse
|
28
|
Chlubnova I, Legentil L, Dureau R, Pennec A, Almendros M, Daniellou R, Nugier-Chauvin C, Ferrières V. Specific and non-specific enzymes for furanosyl-containing conjugates: biosynthesis, metabolism, and chemo-enzymatic synthesis. Carbohydr Res 2012; 356:44-61. [PMID: 22554502 DOI: 10.1016/j.carres.2012.04.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/02/2012] [Accepted: 04/03/2012] [Indexed: 11/27/2022]
Abstract
There is no doubt now that the synthesis of compounds of varying complexity such as saccharides and derivatives thereof continuously grows with enzymatic methods. This review focuses on recent basic knowledge on enzymes specifically involved in the biosynthesis and degradation of furanosyl-containing polysaccharides and conjugates. Moreover, and when possible, biocatalyzed approaches, alternative to standard synthesis, will be detailed in order to strengthen the high potential of these biocatalysts to go further with the preparation of rare furanosides. Interesting results will be also proposed with chemo-enzymatic processes based on nonfuranosyl-specific enzymes.
Collapse
Affiliation(s)
- Ilona Chlubnova
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, UMR 6226, Avenue du Général Leclerc, CS 50837, 35708 Rennes Cedex 7, France
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Islam SM, Richards MR, Taha HA, Byrns SC, Lowary TL, Roy PN. Conformational Analysis of Oligoarabinofuranosides: Overcoming Torsional Barriers with Umbrella Sampling. J Chem Theory Comput 2011; 7:2989-3000. [DOI: 10.1021/ct200333p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Shahidul M. Islam
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| | - Michele R. Richards
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Hashem A. Taha
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Simon C. Byrns
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Department of Chemistry and Alberta Ingenuity Centre for Carbohydrate Science, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada N2L 3G1
| |
Collapse
|
30
|
Sogabe Y, Kitatani T, Yamaguchi A, Kinoshita T, Adachi H, Takano K, Inoue T, Mori Y, Matsumura H, Sakamoto T, Tada T. High-resolution structure of exo-arabinanase fromPenicillium chrysogenum. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:415-22. [DOI: 10.1107/s0907444911006299] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 02/19/2011] [Indexed: 11/11/2022]
|
31
|
Seiboth B, Metz B. Fungal arabinan and L-arabinose metabolism. Appl Microbiol Biotechnol 2011; 89:1665-73. [PMID: 21212945 PMCID: PMC3044236 DOI: 10.1007/s00253-010-3071-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 12/04/2022]
Abstract
l-Arabinose is the second most abundant pentose beside d-xylose and is found in the plant polysaccharides, hemicellulose and pectin. The need to find renewable carbon and energy sources has accelerated research to investigate the potential of l-arabinose for the development and production of biofuels and other bioproducts. Fungi produce a number of extracellular arabinanases, including α-l-arabinofuranosidases and endo-arabinanases, to specifically release l-arabinose from the plant polymers. Following uptake of l-arabinose, its intracellular catabolism follows a four-step alternating reduction and oxidation path, which is concluded by a phosphorylation, resulting in d-xylulose 5-phosphate, an intermediate of the pentose phosphate pathway. The genes and encoding enzymes l-arabinose reductase, l-arabinitol dehydrogenase, l-xylulose reductase, xylitol dehydrogenase, and xylulokinase of this pathway were mainly characterized in the two biotechnological important fungi Aspergillus niger and Trichoderma reesei. Analysis of the components of the l-arabinose pathway revealed a number of specific adaptations in the enzymatic and regulatory machinery towards the utilization of l-arabinose. Further genetic and biochemical analysis provided evidence that l-arabinose and the interconnected d-xylose pathway are also involved in the oxidoreductive degradation of the hexose d-galactose.
Collapse
Affiliation(s)
- Bernhard Seiboth
- Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Wien, Austria.
| | | |
Collapse
|
32
|
Goddard-Borger ED, Carapito R, Jeltsch JM, Phalip V, Stick RV, Varrot A. α-l-Arabinofuranosylated pyrrolidines as arabinanase inhibitors. Chem Commun (Camb) 2011; 47:9684-6. [DOI: 10.1039/c1cc13675e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
33
|
Kühnel S, Westphal Y, Hinz SWA, Schols HA, Gruppen H. Mode of action of Chrysosporium lucknowense C1 α-l-arabinohydrolases. BIORESOURCE TECHNOLOGY 2011; 102:1636-1643. [PMID: 20933404 DOI: 10.1016/j.biortech.2010.09.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 09/07/2010] [Accepted: 09/08/2010] [Indexed: 05/30/2023]
Abstract
The mode of action of four Chrysosporium lucknowense C1 α-L-arabinohydrolases was determined to enable controlled and effective degradation of arabinan. The active site of endoarabinanase Abn1 has at least six subsites, of which the subsites -1 to +2 have to be occupied for hydrolysis. Abn1 was able to hydrolyze a branched arabinohexaose with a double substituted arabinose at subsite -2. The exo acting enzymes Abn2, Abn4 and Abf3 release arabinobiose (Abn2) and arabinose (Abn4 and Abf3) from the non-reducing end of reduced arabinose oligomers. Abn2 binds the two arabinose units only at the subsites -1 and -2. Abf3 prefers small oligomers over large oligomers. It is able to hydrolyze all linkages present in beet arabinan, including the linkages of double substituted residues. Abn4 is more active towards polymeric substrate and releases arabinose monomers from single substituted arabinose residues. Depending on the combination of the enzymes, the C1 arabinohydrolases can be used to effectively release branched arabinose oligomers and/or arabinose monomers.
Collapse
Affiliation(s)
- S Kühnel
- Laboratory of Food Chemistry, Wageningen University, Bomenweg 2, 6703 HD Wageningen, The Netherlands
| | | | | | | | | |
Collapse
|
34
|
Vuong TV, Wilson DB. Glycoside hydrolases: catalytic base/nucleophile diversity. Biotechnol Bioeng 2010; 107:195-205. [PMID: 20552664 DOI: 10.1002/bit.22838] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent studies have shown that a number of glycoside hydrolase families do not follow the classical catalytic mechanisms, as they lack a typical catalytic base/nucleophile. A variety of mechanisms are used to replace this function, including substrate-assisted catalysis, a network of several residues, and the use of non-carboxylate residues or exogenous nucleophiles. Removal of the catalytic base/nucleophile by mutation can have a profound impact on substrate specificity, producing enzymes with completely new functions.
Collapse
Affiliation(s)
- Thu V Vuong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | | |
Collapse
|
35
|
Crystal structure of an inverting GH 43 1,5-α-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate. Biochem J 2009; 422:73-82. [DOI: 10.1042/bj20090180] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Arabinanases are glycosidases that hydrolyse α-(1→5)- arabinofuranosidic linkages found in the backbone of the pectic polysaccharide arabinan. Here we describe the biochemical characterization and the enzyme–substrate crystal structure of an inverting family 43 arabinanase from Geobacillus stearothermophilus T-6 (AbnB). Based on viscosity and reducing power measurements, and based on product analysis for the hydrolysis of linear arabinan by AbnB, the enzyme works in an endo mode of action. Isothermal titration calorimetry studies of a catalytic mutant with various arabino-oligosaccharides suggested that the enzyme active site can accommodate at least five arabinose units. The crystal structure of AbnB was determined at 1.06 Å (1 Å=0.1 nm) resolution, revealing a single five-bladed-β-propeller fold domain. Co-crystallization of catalytic mutants of the enzyme with different substrates allowed us to obtain complex structures of AbnBE201A with arabinotriose and AbnBD147A with arabinobiose. Based on the crystal structures of AbnB together with its substrates, the position of the three catalytic carboxylates: Asp27, the general base; Glu201, the general acid; and Asp147, the pKa modulator, is in agreement with their putative catalytic roles. In the complex structure of AbnBE201A with arabinotriose, a single water molecule is located 2.8 Å from Asp27 and 3.7 Å from the anomeric carbon. The position of this water molecule is kept via hydrogen bonding with a conserved tyrosine (Tyr229) that is 2.6 Å distant from it. The location of this molecule suggests that it can function as the catalytic water molecule in the hydrolysis reaction, resulting in the inversion of the anomeric configuration of the product.
Collapse
|