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Rodríguez-Sanz A, Fuciños C, Soares C, Torrado AM, Lima N, Rúa ML. A comprehensive method for the sequential separation of extracellular xylanases and β-xylosidases/arabinofuranosidases from a new Fusarium species. Int J Biol Macromol 2024; 272:132722. [PMID: 38821304 DOI: 10.1016/j.ijbiomac.2024.132722] [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: 12/22/2023] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Several fungal species produce diverse carbohydrate-active enzymes useful for the xylooligosaccharide biorefinery. These enzymes can be isolated by different purification methods, but fungi usually produce other several compounds which interfere in the purification process. So, the present work has three interconnected aims: (i) compare β-xylosidase production by Fusarium pernambucanum MUM 18.62 with other crop pathogens; (ii) optimise F. pernambucanum xylanolytic enzymes expression focusing on the pre-inoculum media composition; and (iii) design a downstream strategy to eliminate interfering substances and sequentially isolate β-xylosidases, arabinofuranosidases and endo-xylanases from the extracellular media. F. pernambucanum showed the highest β-xylosidase activity among all the evaluated species. It also produced endo-xylanase and arabinofuranosidase. The growth and β-xylosidase expression were not influenced by the pre-inoculum source, contrary to endo-xylanase activity, which was higher with xylan-enriched agar. Using a sequential strategy involving ammonium sulfate precipitation of the extracellular interferences, and several chromatographic steps of the supernatant (hydrophobic chromatography, size exclusion chromatography, and anion exchange chromatography), we were able to isolate different enzyme pools: four partially purified β-xylosidase/arabinofuranoside; FpXylEAB trifunctional GH10 endo-xylanase/β-xylosidase/arabinofuranoside enzyme (39.8 kDa) and FpXynE GH11 endo-xylanase with molecular mass (18.0 kDa). FpXylEAB and FpXynE enzymes were highly active at pH 5-6 and 60-50 °C.
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Affiliation(s)
- Andrea Rodríguez-Sanz
- Biochemistry Laboratory, Department of Analytical and Food Chemistry, University of Vigo, Ourense, Spain
| | - Clara Fuciños
- Biochemistry Laboratory, Department of Analytical and Food Chemistry, University of Vigo, Ourense, Spain
| | - Célia Soares
- CEB-Biological Engineering Centre, University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS-Associate Laboratory, Braga, Guimarães, Portugal
| | - Ana M Torrado
- Biochemistry Laboratory, Department of Analytical and Food Chemistry, University of Vigo, Ourense, Spain
| | - Nelson Lima
- CEB-Biological Engineering Centre, University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS-Associate Laboratory, Braga, Guimarães, Portugal
| | - María L Rúa
- Biochemistry Laboratory, Department of Analytical and Food Chemistry, University of Vigo, Ourense, Spain.
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2
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Coconi Linares N, Li X, Dilokpimol A, de Vries RP. Comparative characterization of nine novel GH51, GH54 and GH62 α-l-arabinofuranosidases from Penicillium subrubescens. FEBS Lett 2022; 596:360-368. [PMID: 35014696 DOI: 10.1002/1873-3468.14278] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 11/07/2022]
Abstract
α-l-Arabinofuranosidases (ABFs) are important enzymes in plant biomass degradation with a wide range of applications. The ascomycete fungus Penicillium subrubescens has more α-l-arabinofuranosidase-encoding genes in its genome compared to other Penicillia. We characterized nine ABFs from glycoside hydrolase (GH) families GH51, GH54 and GH62 from this fungus and demonstrated that they have highly diverse specificity and activity levels, indicating that the expansion was accompanied by diversification of the enzymes. Comparison of the substrate preference of the enzymes to the expression of the corresponding genes when the fungus was grown on either of two plant biomass substrates did not show a clear correlation, suggesting a more complex regulatory system governing l-arabinose release from plant biomass by P. subrubescens.
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Affiliation(s)
- Nancy Coconi Linares
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Xinxin Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, The Netherlands
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3
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McGregor NGS, Turkenburg JP, Mørkeberg Krogh KBR, Nielsen JE, Artola M, Stubbs KA, Overkleeft HS, Davies GJ. Structure of a GH51 α-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi. Acta Crystallogr D Struct Biol 2020; 76:1124-1133. [PMID: 33135683 PMCID: PMC7604909 DOI: 10.1107/s205979832001253x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/14/2020] [Indexed: 03/17/2023] Open
Abstract
α-L-Arabinofuranosidases from glycoside hydrolase family 51 use a stereochemically retaining hydrolytic mechanism to liberate nonreducing terminal α-L-arabinofuranose residues from plant polysaccharides such as arabinoxylan and arabinan. To date, more than ten fungal GH51 α-L-arabinofuranosidases have been functionally characterized, yet no structure of a fungal GH51 enzyme has been solved. In contrast, seven bacterial GH51 enzyme structures, with low sequence similarity to the fungal GH51 enzymes, have been determined. Here, the crystallization and structural characterization of MgGH51, an industrially relevant GH51 α-L-arabinofuranosidase cloned from Meripilus giganteus, are reported. Three crystal forms were grown in different crystallization conditions. The unliganded structure was solved using sulfur SAD data collected from a single crystal using the I23 in vacuo diffraction beamline at Diamond Light Source. Crystal soaks with arabinose, 1,4-dideoxy-1,4-imino-L-arabinitol and two cyclophellitol-derived arabinose mimics reveal a conserved catalytic site and conformational itinerary between fungal and bacterial GH51 α-L-arabinofuranosidases.
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Affiliation(s)
- Nicholas G. S. McGregor
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
| | | | - Jens Erik Nielsen
- Protein Biochemistry and Stability, Novozymes A/S, Krogshøjvej 36, 2880 Bagsvaerd, Denmark
| | - Marta Artola
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Keith A. Stubbs
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands
| | - Gideon J. Davies
- York Structural Biology Laboratory, University of York, Heslington, York YO10 5DD, United Kingdom
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Sunkar B, Kannoju B, Bhukya B. Optimized Production of Xylanase by Penicillium purpurogenum and Ultrasound Impact on Enzyme Kinetics for the Production of Monomeric Sugars From Pretreated Corn Cobs. Front Microbiol 2020; 11:772. [PMID: 32390996 PMCID: PMC7193903 DOI: 10.3389/fmicb.2020.00772] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Corn cob is an abundant organic source with significant potential in sustainable energy development. For the effective conversion of the feedstocks to valued commodities, effective biocatalysts are highly desired. The present study aims at optimizing the critical parameters required for xylanase production by Penicillium purpurogenum isolated from rotten wood sample using the Taguchi orthogonal array layout of L25 (5∧6). The optimized conditions like temperature 40°C, pH 3, size of inoculum 1.2 × 108 spores/ml, moisture 70%, peptone 0.8%, and 5 days of incubation resulted in 1,097 ± 6.76 U/gram dry substrate (gds) xylanase which was 65.72% more when compared to un-optimized production of xylanase. The xylanase thus produced, effectively carried out pretreated corn cob saccharification and the reaction was further improved with ultrasound assistance which has increased the saccharification yield to 12.02% along with significant reduction in reaction time. The saccharification efficiency of pretreated corn cob was found to be 80.29% more compared to the raw corn cob, reflecting its recalcitrance to digestion. Indeed, xylan being the second most abundant polymer in lignocellulosic biomass, considerable attention is being paid for its effective conversion to valued products.
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Affiliation(s)
- Bindu Sunkar
- Centre for Microbial and Fermentation Technology, Department of Microbiology, University College of Science, Osmania University, Hyderabad, India
| | - Balakrishna Kannoju
- Centre for Microbial and Fermentation Technology, Department of Microbiology, University College of Science, Osmania University, Hyderabad, India
| | - Bhima Bhukya
- Centre for Microbial and Fermentation Technology, Department of Microbiology, University College of Science, Osmania University, Hyderabad, India
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Poria V, Saini JK, Singh S, Nain L, Kuhad RC. Arabinofuranosidases: Characteristics, microbial production, and potential in waste valorization and industrial applications. BIORESOURCE TECHNOLOGY 2020; 304:123019. [PMID: 32089440 DOI: 10.1016/j.biortech.2020.123019] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 05/15/2023]
Abstract
Alpha-L-arabinofuranoside arabinofuranohydrolase (ARA), more commonly known as alpha-L-arabinofuranosidase (E.C. number 3.2.1.55), is a hydrolytic enzyme, catalyzing the cleavage of alpha-L-arabinose by acting on the non-reducing ends of alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linked arabinoxylans and arabinogalactans. ARA functions as debranching enzyme removing arabinose substituents from arabinoxylan and arabinoxylooligomers, thereby, boosting the hydrolysis of arabinoxylan fraction of hemicellulose and improving bioconversion of lignocellulosic biomass. Previously, comprehensive information on this enzyme has not been reviewed thoroughly. Therefore, the main aim of this review is to highlight the important properties of this interesting enzyme, microorganisms used for its production, and enhanced production using genetic engineering approach. An account on synergism with other biomass hydrolyzing enzymes and various industrial applications of this enzyme has also been provided along with an outlook on further research and development.
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Affiliation(s)
- Vikram Poria
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Jitendra Kumar Saini
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India
| | - Surender Singh
- Department of Microbiology, Central University of Haryana, Mahendergarh, Haryana PIN-123031, India; Division of Microbiology, Indian Agricultural Research Institute, New Delhi PIN-110012, India.
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi PIN-110012, India
| | - Ramesh Chander Kuhad
- Central University of Haryana, Mahendergarh, Haryana PIN-123031, India; Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, New Delhi PIN-110021, India
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6
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Cann I, Pereira GV, Abdel-Hamid AM, Kim H, Wefers D, Kayang BB, Kanai T, Sato T, Bernardi RC, Atomi H, Mackie RI. Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products. Appl Environ Microbiol 2020; 86:e02296-19. [PMID: 31980431 PMCID: PMC7082577 DOI: 10.1128/aem.02296-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.
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Affiliation(s)
- Isaac Cann
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Gabriel V Pereira
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ahmed M Abdel-Hamid
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel Wefers
- Karlsruhe Institute of Technology, Institute of Applied Biosciences, Department of Food Chemistry and Phytochemistry, Karlsruhe, Germany
| | - Boniface B Kayang
- Department of Animal Science, School of Agriculture, University of Ghana, Legon, Ghana
| | - Tamotsu Kanai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
| | - Takaaki Sato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haruyuki Atomi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
- JST, CREST, Tokyo, Japan
| | - Roderick I Mackie
- Department of Animal Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Energy Biosciences Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Tu T, Li X, Meng K, Bai Y, Wang Y, Wang Z, Yao B, Luo H. A GH51 α-L-arabinofuranosidase from Talaromyces leycettanus strain JCM12802 that selectively drives synergistic lignocellulose hydrolysis. Microb Cell Fact 2019; 18:138. [PMID: 31426823 PMCID: PMC6699109 DOI: 10.1186/s12934-019-1192-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/10/2019] [Indexed: 12/29/2022] Open
Abstract
Background The development of sustainable technologies for plant cell wall degradation greatly depends on enzymes with hydrolytic activities against carbohydrates. The waste by-products of agricultural cereals are important biomass sources because they contain large amounts of saccharides. Achieving efficient debranching and depolymerization are two important objectives for increasing the utilization of such renewable bioresources. GH51 α-l-arabinofuranosidases are important in biomass pretreatment because they act synergistically with other enzymes during hemicellulose hydrolysis. Results A GH51 α-l-arabinofuranosidase from Talaromyces leycettanus JCM12802 was heterologously expressed in Pichia pastoris GS115 and characterized. The recombinant α-l-arabinofuranosidase, TlAbf51, showed an optimum temperature and pH of 55–60 °C and 3.5–4.0, respectively, and remained stable at 50 °C and pH 3.0–9.0. TlAbf51 showed a higher catalytic efficiency (5712 mM−1 s−1) than most fungal α-l-arabinofuranosidases towards the substrate 4-nitrophenyl-α-l-arabinofuranoside. Moreover, TlAbf51 preferentially removed 1,2- or 1,3-linked arabinofuranose residues from arabinoxylan and acted synergistically with the bifunctional xylanase/cellulase TcXyn10A at an activity ratio of 5:1. The highest yields of arabinose and xylooligosaccharides were obtained when TlAbf51 was added after TcXyn10A or when both enzymes were added simultaneously. High-performance anion-exchange chromatography analyses showed that (i) arabinose and xylooligosaccharides with low degrees of polymerization (DP1–DP5) and (ii) arabinose and xylooligosaccharides (DP1–DP3) were the major hydrolysates obtained during the hydrolysis of sodium hydroxide-pretreated cornstalk and corn bran, respectively. Conclusions In contrast to other fungal GH51 α-l-arabinofuranosidases, recombinant TlAbf51 showed excellent stability over a broad pH range and high catalytic efficiency. Moreover, TlAbf51 acted synergistically with another hemicellulase to digest arabino-polysaccharides. These favorable enzymatic properties make TlAbf51 attractive for biomass pretreatment and biofuel production. Electronic supplementary material The online version of this article (10.1186/s12934-019-1192-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
| | - Xiaoli Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Zhenxing Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081, People's Republic of China.
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Mardones W, Callegari E, Eyzaguirre J. Corncob and sugar beet pulp induce specific sets of lignocellulolytic enzymes in Penicillium purpurogenum. Mycology 2019; 10:118-125. [PMID: 31069125 PMCID: PMC6493289 DOI: 10.1080/21501203.2018.1517830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/26/2018] [Indexed: 01/19/2023] Open
Abstract
Penicillium purpurogenum is a filamentous fungus, which grows on a variety of natural carbon sources and secretes a large number of enzymes involved in cellulose, hemicelluloses and pectin biodegradation. The purpose of this work has been to identify potential lignocellulolytic enzymes and to compare the secreted enzymes produced when the fungus is grown on sugar beet pulp (rich in cellulose and pectin) and corn cob (rich in cellulose and xylan). Culture supernatants were subjected to two-dimensional nano-liquid chromatography/tandem mass spectrometry. Using MASCOT and a genome-derived protein database, the proteins present in the supernatant were identified. The putative function in the degradation of the polysaccharides was determined using dbCAN software. The results show that there is a good correlation between the polysaccharide composition of the carbon sources and the function of the secreted enzymes: both cultures are rich in cellulases, while sugar beet pulp induces pectinases and corncob, xylanases. The eventual biochemical characterisation of these enzymes will be of value for a better understanding of the biodegradation process performed by the fungus and increase the availability of enzymes for biotechnological methods associated with this process.
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Affiliation(s)
- Wladimir Mardones
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Eduardo Callegari
- BRIN-USDSSOM Proteomics Facility, University of South Dakota, Vermillion, SD, USA
| | - Jaime Eyzaguirre
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
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Fortune B, Mhlongo S, van Zyl LJ, Huddy R, Smart M, Trindade M. Characterisation of three novel α-L-arabinofuranosidases from a compost metagenome. BMC Biotechnol 2019; 19:22. [PMID: 30999885 PMCID: PMC6472066 DOI: 10.1186/s12896-019-0510-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/13/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The importance of the accessory enzymes such as α-L-arabinofuranosidases (AFases) in synergistic interactions within cellulolytic mixtures has introduced a paradigm shift in the search for hydrolytic enzymes. The aim of this study was to characterize novel AFase genes encoding enzymes with differing temperature optima and thermostabilities for use in hydrolytic cocktails. RESULTS Three fosmids, pFos-H4, E3 and D3 were selected from the cloned metagenome of high temperature compost, expressed in Escherichia coli and subsequently purified to homogeneity from cell lysate. All the AFases were clustered within the GH51 AFase family and shared a homo-hexameric structure. Both AFase-E3 and H4 showed optimal activity at 60 °C while AFase-D3 had unique properties as it showed optimal activity at 25 °C as well as the ability to maintain substantial activity at temperatures as high as 90 °C. However, AFase-E3 was the most thermostable amongst the three AFases showing full activity even at 70 °C. The maximum activity was observed at a pH profile between pH 4.0-6.0 for all three AFases with optimal activity for AFase H4, D3 and E3 at pH 5.0, 4.5 and 4.0, respectively. All the AFases showed KM range between 0.31 mM and 0.43 mM, Kcat range between 131 s- 1 and 219 s- 1 and the specific activity for AFase-H4, AFases-E3 and was 143, 228 and 175 U/mg, respectively. AFases-E3 and D3 displayed activities against pNP-β-L-arabinopyranoside and pNP-β-L-mannopyranoside respectively, and both hydrolysed pNP-β-D-glucopyranoside. CONCLUSION All three AFases displayed different biochemical characteristics despite all showing conserved overall structural similarity with typical domains of AFases belonging to GH51 family. The hydrolysis of cellobiose by a GH51 family AFase is demonstrated for the first time in this study.
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Affiliation(s)
- Brent Fortune
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Sizwe Mhlongo
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa
| | - Robert Huddy
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Mariette Smart
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.,Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Bellville, South Africa.
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10
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dos Santos CR, de Giuseppe PO, de Souza FHM, Zanphorlin LM, Domingues MN, Pirolla RAS, Honorato RV, Tonoli CCC, de Morais MAB, de Matos Martins VP, Fonseca LM, Büchli F, de Oliveira PSL, Gozzo FC, Murakami MT. The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:223. [PMID: 30127853 PMCID: PMC6087011 DOI: 10.1186/s13068-018-1212-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/23/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Arabinoxylan is an abundant polysaccharide in industrially relevant biomasses such as sugarcane, corn stover and grasses. However, the arabinofuranosyl di-substitutions that decorate the xylan backbone are recalcitrant to most known arabinofuranosidases (Abfs). RESULTS In this work, we identified a novel GH51 Abf (XacAbf51) that forms trimers in solution and can cope efficiently with both mono- and di-substitutions at terminal or internal xylopyranosyl units of arabinoxylan. Using mass spectrometry, the kinetic parameters of the hydrolysis of 33-α-l-arabinofuranosyl-xylotetraose and 23,33-di-α-l-arabinofuranosyl-xylotetraose by XacAbf51 were determined, demonstrating the capacity of this enzyme to cleave arabinofuranosyl linkages of internal mono- and di-substituted xylopyranosyl units. Complementation studies of fungal enzyme cocktails with XacAbf51 revealed an increase of up to 20% in the release of reducing sugars from pretreated sugarcane bagasse, showing the biotechnological potential of a generalist GH51 in biomass saccharification. To elucidate the structural basis for the recognition of internal di-substitutions, the crystal structure of XacAbf51 was determined unveiling the existence of a pocket strategically arranged near to the - 1 subsite that can accommodate a second arabinofuranosyl decoration, a feature not described for any other GH51 Abf structurally characterized so far. CONCLUSIONS In summary, this study reports the first kinetic characterization of internal di-substitution release by a GH51 Abf, provides the structural basis for this activity and reveals a promising candidate for industrial processes involving plant cell wall depolymerization.
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Affiliation(s)
- Camila Ramos dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Priscila Oliveira de Giuseppe
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Flávio Henrique Moreira de Souza
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Letícia Maria Zanphorlin
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Mariane Noronha Domingues
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Renan Augusto Siqueira Pirolla
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Rodrigo Vargas Honorato
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Celisa Caldana Costa Tonoli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Mariana Abrahão Bueno de Morais
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Vanesa Peixoto de Matos Martins
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Lucas Miranda Fonseca
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Fernanda Büchli
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Paulo Sergio Lopes de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
| | - Fábio Cesar Gozzo
- Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, Sao Paulo 13083-861 Brazil
| | - Mário Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-970 Brazil
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11
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Mardones W, Di Genova A, Cortés MP, Travisany D, Maass A, Eyzaguirre J. The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. Mycology 2018; 9:59-69. [PMID: 30123662 PMCID: PMC6059080 DOI: 10.1080/21501203.2017.1419995] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 12/18/2017] [Indexed: 01/18/2023] Open
Abstract
The high lignocellulolytic activity displayed by the soft-rot fungus Penicillium purpurogenum has made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2 Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and Core Eukaryotic Genes Mapping Approach (CEGMA) analysis reveals that our assembly captures almost all protein-coding genes. RNA-seq was performed and 93.1% of the reads aligned to the assembled genome. These data, plus the independent sequencing of a set of genes of lignocellulose-degrading enzymes, validate the quality of the genome sequence. P. purpurogenum shows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequenced Penicillia. These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.
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Affiliation(s)
- Wladimir Mardones
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
| | - Alex Di Genova
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,Erable Team, INRIA Grenoble, Montbonno, France.,Center for Mathematical Modeling, University of Chile, Santiago, Chile.,Center for Genome Regulation, University of Chile, Santiago, Chile
| | - María Paz Cortés
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,Center for Mathematical Modeling, University of Chile, Santiago, Chile.,Center for Genome Regulation, University of Chile, Santiago, Chile
| | - Dante Travisany
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, Santiago, Chile.,Center for Mathematical Modeling, University of Chile, Santiago, Chile.,Center for Genome Regulation, University of Chile, Santiago, Chile
| | - Alejandro Maass
- Center for Mathematical Modeling, University of Chile, Santiago, Chile.,Center for Genome Regulation, University of Chile, Santiago, Chile.,Department of Mathematical Engineering, University of Chile, Santiago, Chile
| | - Jaime Eyzaguirre
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile
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12
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Yang W, Bai Y, Yang P, Luo H, Huang H, Meng K, Shi P, Wang Y, Yao B. A novel bifunctional GH51 exo-α-l-arabinofuranosidase/endo-xylanase from Alicyclobacillus sp. A4 with significant biomass-degrading capacity. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:197. [PMID: 26628911 PMCID: PMC4666033 DOI: 10.1186/s13068-015-0366-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 10/27/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Improving the hydrolytic performance of xylanolytic enzymes on arabinoxylan is of importance in the ethanol fermentation industry. Supplementation of debranching (arabinofuranosidase) and depolymerizing (xylanase) enzymes is a way to address the problem. In the present study, we identified a bifunctional α-l-arabinofuranosidase/endo-xylanase (Ac-Abf51A) of glycoside hydrolase family 51 in Alicyclobacillus sp. strain A4. Its biochemical stability and great hydrolysis efficiency against complex biomass make it a potential candidate for the production of biofuels. RESULTS The gene encoding Ac-Abf51A was cloned. The comparison of its sequence with reference proteins having resolved 3D-structures revealed nine key residues involved in catalysis and substrate-binding interaction. Recombinant Ac-Abf51A produced in Escherichia coli showed optimal activity at pH 6.0 and 60 °C with 4-nitrophenyl-α-l-arabinofuranoside as the substrate. The enzyme exhibited an exo-type mode of action on polyarabinosides by catalyzing the cleavage of α-1,2- and α-1,3-linked arabinofuranose side chains in sugar beet arabinan and water-soluble wheat arabinoxylan and α-1,5-linked arabinofuranosidic bonds in debranched sugar beet arabinan. Surprisingly, it had capacity to release xylobiose and xylotriose from wheat arabinoxylan and was active on xylooligosaccharides (xylohexaose 1.2/mM/min, xylopentaose 6.9/mM/min, and xylotetraose 19.7/mM/min), however a lower level of activity. Moreover, Ac-Abf51A showed greater synergistic effect in combination with xylanase (2.92-fold) on wheat arabinoxylan degradation than other reported enzymes, for the amounts of arabinose, xylose, and xylobiose were all increased in comparison to that by the enzymes acting individually. CONCLUSIONS This study for the first time reports a GH51 enzyme with both exo-α-l-arabinofuranosidase and endo-xylanase activities. It was stable over a broad pH range and at high temperature, and showed greater synergistic effect with xylanase on the degradation of wheat arabinoxylan than other counterparts. The distinguished synergy might be ascribed to its bifunctional α-l-arabinofuranosidase/xylanase activity, which may represent a possible way to degrade biomass at lower enzyme loadings.
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Affiliation(s)
- Wenxia Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Peilong Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Yaru Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
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13
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Heterologous expression and characterization of α-l-arabinofuranosidase 4 from Penicillium purpurogenum and comparison with the other isoenzymes produced by the fungus. Fungal Biol 2015; 119:641-7. [DOI: 10.1016/j.funbio.2015.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/23/2015] [Accepted: 04/02/2015] [Indexed: 11/18/2022]
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14
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Yang Y, Zhang L, Guo M, Sun J, Matsukawa S, Xie J, Wei D. Novel α-L-arabinofuranosidase from Cellulomonas fimi ATCC 484 and its substrate-specificity analysis with the aid of computer. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3725-33. [PMID: 25797391 DOI: 10.1021/jf5059683] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In the process of gene mining for novel α-L-arabinofuranosidases (AFs), the gene Celf_3321 from Cellulomonas fimi ATCC 484 encodes an AF, termed as AbfCelf, with potent activity, 19.4 U/mg under the optimum condition, pH 6.0 and 40 °C. AbfCelf can hydrolyze α-1,5-linked oligosaccharides, sugar beet arabinan, linear 1,5-α-arabinan, and wheat flour arabinoxylan, which is partly different from some previously well-characterized GH 51 AFs. The traditional substrate-specificity analysis for AFs is labor-consuming and money costing, because the substrates include over 30 kinds of various 4-nitrophenol (PNP)-glycosides, oligosaccharides, and polysaccharides. Hence, a preliminary structure and mechanism based method was applied for substrate-specificity analysis. The binding energy (ΔG, kcal/mol) obtained by docking suggested the reaction possibility and coincided with the experimental results. AbfA crystal 1QW9 was used to test the rationality of docking method in simulating the interaction between enzyme and substrate, as well the credibility of the substrate-specificity analysis method in silico.
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Affiliation(s)
- Ying Yang
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Lujia Zhang
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Mingrong Guo
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Jiaqi Sun
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Shingo Matsukawa
- §Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Jingli Xie
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- ‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China
| | - Dongzhi Wei
- †State Key Laboratory of Bioreactor Engineering, Department of Food Science and Technology, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, People's Republic of China
- ‡Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, People's Republic of China
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15
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Ravanal MC, Alegría-Arcos M, Gonzalez-Nilo FD, Eyzaguirre J. Penicillium purpurogenum produces two GH family 43 enzymes with β-xylosidase activity, one monofunctional and the other bifunctional: Biochemical and structural analyses explain the difference. Arch Biochem Biophys 2013; 540:117-24. [DOI: 10.1016/j.abb.2013.10.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/08/2013] [Accepted: 10/21/2013] [Indexed: 11/24/2022]
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16
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β-xylosidases and α-L-arabinofuranosidases: accessory enzymes for arabinoxylan degradation. Biotechnol Adv 2013; 32:316-32. [PMID: 24239877 DOI: 10.1016/j.biotechadv.2013.11.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/28/2013] [Accepted: 11/09/2013] [Indexed: 11/22/2022]
Abstract
Arabinoxylan (AX) is among the most abundant hemicelluloses on earth and one of the major components of feedstocks that are currently investigated as a source for advanced biofuels. As global research into these sustainable biofuels is increasing, scientific knowledge about the enzymatic breakdown of AX advanced significantly over the last decade. This review focuses on the exo-acting AX hydrolases, such as α-arabinofuranosidases and β-xylosidases. It aims to provide a comprehensive overview of the diverse substrate specificities and corresponding structural features found in the different glycoside hydrolase families. A careful review of the available literature reveals a marked difference in activity between synthetically labeled and naturally occurring substrates, often leading to erroneous enzymatic annotations. Therefore, special attention is given to enzymes with experimental evidence on the hydrolysis of natural polymers.
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17
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Ohta K, Fujii S, Higashida C. Characterization of a glycoside hydrolase family-51 α-l-arabinofuranosidase gene from Aureobasidium pullulans ATCC 20524 and its encoded product. J Biosci Bioeng 2013; 116:287-92. [DOI: 10.1016/j.jbiosc.2013.03.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 03/05/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
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18
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Sakamoto T, Inui M, Yasui K, Hosokawa S, Ihara H. Substrate specificity and gene expression of two Penicillium chrysogenum α-l-arabinofuranosidases (AFQ1 and AFS1) belonging to glycoside hydrolase families 51 and 54. Appl Microbiol Biotechnol 2012; 97:1121-30. [DOI: 10.1007/s00253-012-3978-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 02/13/2012] [Accepted: 02/15/2012] [Indexed: 11/29/2022]
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19
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Ravanal MC, Rosa L, Eyzaguirre J. Α-L-arabinofuranosidase 3 from Penicillium purpurogenum (ABF3): potential application in the enhancement of wine flavour and heterologous expression of the enzyme. Food Chem 2012; 134:888-93. [PMID: 23107704 DOI: 10.1016/j.foodchem.2012.02.200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/11/2012] [Accepted: 02/28/2012] [Indexed: 11/30/2022]
Abstract
An α-l-arabinofuranosidase (ABF3) from Penicillium purpurogenum was purified and its possible biotechnological application in the enhancement of wine flavour combined with P. purpurogenum β-glucosidase was studied. A must from Muscat of Alexandria was used to isolate the glycosides. The total monosaccharide (glucose, arabinose and xylose) levels in the glycosides were determined after acid hydrolysis, and were compared with the result of enzymatic hydrolysis. These results were analogous to those obtained in similar experiments using a commercial preparation, thus suggesting that the enzyme from P. purpurogenum may prove useful in this particular application. This prompted us to express the enzyme heterologously. The abf3 gene was thus expressed in Pichia pastoris. The recombinant enzyme was purified and it shows the same properties of the native ABF3 (substrate specificity, kinetic constants, pH and temperature optima and antibody cross-reactivity).
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Affiliation(s)
- Maria Cristina Ravanal
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, República 217, Santiago, Chile
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20
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Yan Q, Tang L, Yang S, Zhou P, Zhang S, Jiang Z. Purification and characterization of a novel thermostable α-l-arabinofuranosidase (α-l-AFase) from Chaetomium sp. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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21
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Navarrete M, Callegari E, Eyzaguirre J. The effect of acetylated xylan and sugar beet pulp on the expression and secretion of enzymes by Penicillium purpurogenum. Appl Microbiol Biotechnol 2011; 93:723-41. [DOI: 10.1007/s00253-011-3744-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 11/02/2011] [Accepted: 11/16/2011] [Indexed: 01/26/2023]
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22
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Podospora anserina hemicellulases potentiate the Trichoderma reesei secretome for saccharification of lignocellulosic biomass. Appl Environ Microbiol 2010; 77:237-46. [PMID: 21037302 DOI: 10.1128/aem.01761-10] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To improve the enzymatic hydrolysis (saccharification) of lignocellulosic biomass by Trichoderma reesei, a set of genes encoding putative polysaccharide-degrading enzymes were selected from the coprophilic fungus Podospora anserina using comparative genomics. Five hemicellulase-encoding genes were successfully cloned and expressed as secreted functional proteins in the yeast Pichia pastoris. These novel fungal CAZymes belonging to different glycoside hydrolase families (PaMan5A and PaMan26A mannanases, PaXyn11A xylanase, and PaAbf51A and PaAbf62A arabinofuranosidases) were able to break down their predicted cognate substrates. Although PaMan5A and PaMan26A displayed similar specificities toward a range of mannan substrates, they differed in their end products, suggesting differences in substrate binding. The N-terminal CBM35 module of PaMan26A displayed dual binding specificity toward xylan and mannan. PaXyn11A harboring a C-terminal CBM1 module efficiently degraded wheat arabinoxylan, releasing mainly xylobiose as end product. PaAbf51A and PaAbf62A arabinose-debranching enzymes exhibited differences in activity toward arabinose-containing substrates. Further investigation of the contribution made by each P. anserina auxiliary enzyme to the saccharification of wheat straw and spruce demonstrated that the endo-acting hemicellulases (PaXyn11A, PaMan5A, and PaMan26A) individually supplemented the secretome of the industrial T. reesei CL847 strain. The most striking effect was obtained with PaMan5A that improved the release of total sugars by 28% and of glucose by 18%, using spruce as lignocellulosic substrate.
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Gonzalez-Vogel A, Eyzaguirre J, Oleas G, Callegari E, Navarrete M. Proteomic analysis in non-denaturing condition of the secretome reveals the presence of multienzyme complexes in Penicillium purpurogenum. Appl Microbiol Biotechnol 2010; 89:145-55. [PMID: 20972675 DOI: 10.1007/s00253-010-2953-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/05/2010] [Accepted: 10/12/2010] [Indexed: 01/23/2023]
Abstract
Proteins secreted by filamentous fungi play key roles in different aspects of their biology. The fungus Penicillium purpurogenum, used as a model organism, is able to degrade hemicelluloses and pectins by secreting a variety of enzymes to the culture medium. This work shows that these enzymes interact with each other to form high molecular weight, catalytically active complexes. By using a proteomics approach, we were able to identify several protein complexes in the secretome of this fungus. The expression and assembly of these complexes depend on the carbon source used and display molecular masses ranging from 300 to 700 kDa. These complexes are composed of a variety of enzymes, including arabinofuranosidases, acetyl xylan esterases, feruloyl esterases, β-glucosidases and xylanases. The protein-protein interactions in these multienzyme complexes were confirmed by coimmunoprecipitation assays. One of the complexes was purified from sugar beet pulp cultures and the subunits identified by tandem mass spectrometry. A better understanding of the biological significance of these kinds of interactions will help in the comprehension of the degradation mechanisms used by fungi and may be of special interest to the biotechnology industry.
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Affiliation(s)
- Alvaro Gonzalez-Vogel
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
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24
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Ravanal MC, Callegari E, Eyzaguirre J. Novel bifunctional alpha-L-arabinofuranosidase/xylobiohydrolase (ABF3) from Penicillium purpurogenum. Appl Environ Microbiol 2010; 76:5247-53. [PMID: 20562284 PMCID: PMC2916492 DOI: 10.1128/aem.00214-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 06/09/2010] [Indexed: 11/20/2022] Open
Abstract
The soft rot fungus Penicillium purpurogenum grows on a variety of natural substrates and secretes various isoforms of xylanolytic enzymes, including three arabinofuranosidases. This work describes the biochemical properties as well as the nucleotide and amino acid sequences of arabinofuranosidase 3 (ABF3). This enzyme has been purified to homogeneity. It is a glycosylated monomer with a molecular weight of 50,700 and can bind cellulose. The enzyme is active with p-nitrophenyl alpha-L-arabinofuranoside and p-nitrophenyl beta-D-xylopyranoside with a K(m) of 0.65 mM and 12 mM, respectively. The enzyme is active on xylooligosaccharides, yielding products of shorter length, including xylose. However, it does not hydrolyze arabinooligosaccharides. When assayed with polymeric substrates, little arabinose is liberated from arabinan and debranched arabinan; however, it hydrolyzes arabinose and releases xylooligosaccharides from arabinoxylan. Sequencing both ABF3 cDNA and genomic DNA reveals that this gene does not contain introns and that the open reading frame is 1,380 nucleotides in length. The deduced mature protein is composed of 433 amino acids residues and has a calculated molecular weight of 47,305. The deduced amino acid sequence has been validated by mass spectrometry analysis of peptides from purified ABF3. A total of 482 bp of the promoter were sequenced; putative binding sites for transcription factors such as CreA (four), XlnR (one), and AreA (three) and two CCAAT boxes were found. The enzyme has two domains, one similar to proteins of glycosyl hydrolase family 43 at the amino-terminal end and a family 6 carbohydrate binding module at the carboxyl end. ABF3 is the first described modular family 43 enzyme from a fungal source, having both alpha-L-arabinofuranosidase and xylobiohydrolase functionalities.
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Affiliation(s)
- María Cristina Ravanal
- Departamento de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile, BRIN-USDSSOM Proteomics Facility, University of South Dakota, Vermillion, South Dakota
| | - Eduardo Callegari
- Departamento de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile, BRIN-USDSSOM Proteomics Facility, University of South Dakota, Vermillion, South Dakota
| | - Jaime Eyzaguirre
- Departamento de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile, BRIN-USDSSOM Proteomics Facility, University of South Dakota, Vermillion, South Dakota
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Guais O, Tourrasse O, Dourdoigne M, Parrou JL, Francois JM. Characterization of the family GH54 α-l-arabinofuranosidases in Penicillium funiculosum, including a novel protein bearing a cellulose-binding domain. Appl Microbiol Biotechnol 2010; 87:1007-21. [DOI: 10.1007/s00253-010-2532-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 02/26/2010] [Accepted: 02/28/2010] [Indexed: 11/29/2022]
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Gene Cloning, Expression, and Characterization of a Family 51 α-l-Arabinofuranosidase from Streptomyces sp. S9. Appl Biochem Biotechnol 2009; 162:707-18. [DOI: 10.1007/s12010-009-8816-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 10/08/2009] [Indexed: 11/26/2022]
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