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Vieira MM, Valadares FL, Velasco J, da Silva SS, Segato F, Chandel AK. Analysis of Aureobasidium pullulans LB83 secretome reveals distinct carbohydrate active enzymes for biomass saccharification. Prep Biochem Biotechnol 2024; 54:729-735. [PMID: 37966162 DOI: 10.1080/10826068.2023.2279109] [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] [Indexed: 11/16/2023]
Abstract
Aureobasidium pullulans LB83 is a versatile biocatalyst that produces a plethora of bioactive products thriving on a variety of feedstocks under the varying culture conditions. In our last study using this microorganism, we found cellulase activity (FPase, 2.27 U/ml; CMCase, 7.42 U/ml) and other plant cell wall degrading enzyme activities grown on sugarcane bagasse and soybean meal as carbon source and nitrogen, respectively. In the present study, we provide insights on the secretome analysis of this enzymatic cocktail. The secretome analysis of A. pullulans LB83 by Liquid Chromatography coupled to Mass Spectroscopy (LC-MS/MS) revealed 38 classes of Carbohydrate Active enZymes (CAZymes) of a total of 464 identified proteins. These CAZymes consisted of 21 glycoside hydrolases (55.26%), 12 glycoside hydrolases harboring carbohydrate-binding module (31.58%), 4 carbohydrate esterases (10.53%) and one glycosyl transferase (2.63%). To the best of our knowledge, this is the first report on the secretome analysis of A. pullulans LB83.
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Affiliation(s)
- Matheus Maitan Vieira
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Fernanda Lima Valadares
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Josman Velasco
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Silvio S da Silva
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Fernando Segato
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
| | - Anuj K Chandel
- Department of Biotechnology, Engineering School of Lorena- University of São Paulo, Lorena, Brazil
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2
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Structural and functional insights of the catalytic GH5 and Calx-β domains from the metagenome-derived endoglucanase CelE2. Enzyme Microb Technol 2023; 165:110206. [PMID: 36758494 DOI: 10.1016/j.enzmictec.2023.110206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/14/2023] [Accepted: 01/23/2023] [Indexed: 01/29/2023]
Abstract
Cellulose is the most abundant natural polymer on Earth, representing an attractive feedstock for bioproducts and biofuel production. Cellulases promote the depolymerization of cellulose, generating short oligosaccharides and glucose, which are useful in biotechnological applications. Among the classical cellulases, those from glycoside hydrolase family 5 (GH5) are one of the most abundant in Nature, displaying several modular architectures with other accessory domains attached to its catalytic core, such as carbohydrate-binding modules (CBMs), Ig-like, FN3-like, and Calx-β domains, which can influence the enzyme activity. The metagenome-derived endoglucanase CelE2 has in its modular architecture an N-terminal domain belonging to the GH5 family and a C-terminal domain with a high identity to the Calx-β domain. In this study, the GH5 and the Calx-β domains were subcloned and heterologously expressed in E. coli, to evaluate the structural and functional properties of the individualized domains of CelE2. Thermostability analysis by circular dichroism (CD) revealed a decrease in the denaturation temperature values around 4.6 °C for the catalytic domain (CelE21-381) compared to CelE2 full-length. The CD analyses revealed that the Calx-β domain (CelE2382-477) was unfolded, suggesting that this domain requires to be attached to the catalytic core to become structurally stable. The three-dimensional structure of the catalytic domain CelE21-381 was determined at 2.1 Å resolution, showing a typical (α/β)8-barrel fold and a narrow active site compared to other cellulases from the same family. The biochemical characterization showed that the deletion of the Calx-β domain increased more than 3-fold the activity of the catalytic domain CelE21-381 towards the insoluble substrate Avicel. The main functional properties of CelE2, such as substrate specificity, optimal pH and temperature, thermal stability, and activation by CaCl2, were not altered after the deletion of the accessory domain. Furthermore, the Small Angle X-ray Scattering (SAXS) analyses showed that the addition of CaCl2 was beneficial CelE21-381 protein solvency. This work contributed to fundamental concepts about the structure and function of cellulases, which are useful in applications involving lignocellulosic materials degradation into food and feedstuffs and biofuel production.
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3
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Analysis of carbohydrate-active enzymes and sugar transporters in Penicillium echinulatum: A genome-wide comparative study of the fungal lignocellulolytic system. Gene 2022; 822:146345. [PMID: 35189252 DOI: 10.1016/j.gene.2022.146345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/09/2022] [Accepted: 02/15/2022] [Indexed: 02/06/2023]
Abstract
Penicillium echinulatum 2HH is an ascomycete well known for its production of cellulolytic enzymes. Understanding lignocellulolytic and sugar uptake systems is essential to obtain efficient fungi strains for the production of bioethanol. In this study we performed a genome-wide functional annotation of carbohydrate-active enzymes and sugar transporters involved in the lignocellulolytic system of P. echinulatum 2HH and S1M29 strains (wildtype and mutant, respectively) and eleven related fungi. Additionally, signal peptide and orthology prediction were carried out. We encountered a diverse assortment of cellulolytic enzymes in P. echinulatum, especially in terms of β-glucosidases and endoglucanases. Other enzymes required for the breakdown of cellulosic biomass were also found, including cellobiohydrolases, lytic cellulose monooxygenases and cellobiose dehydrogenases. The S1M29 mutant, which is known to produce an increased cellulase activity, and the 2HH wild type strain of P. echinulatum did not show significant differences between their enzymatic repertoire. Nevertheless, we unveiled an amino acid substitution for a predicted intracellular β-glucosidase of the mutant, which might contribute to hyperexpression of cellulases through a cellodextrin induction pathway. Most of the P. echinulatum enzymes presented orthologs in P. oxalicum 114-2, supporting the presence of highly similar cellulolytic mechanisms and a close phylogenetic relationship between these fungi. A phylogenetic analysis of intracellular β-glucosidases and sugar transporters allowed us to identify several proteins potentially involved in the accumulation of intracellular cellodextrins. These may prove valuable targets in the genetic engineering of P. echinulatum focused on industrial cellulases production. Our study marks an important step in characterizing and understanding the molecular mechanisms employed by P. echinulatum in the enzymatic hydrolysis of lignocellulosic biomass.
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Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
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Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
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5
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Velasco J, Oliva B, Mulinari EJ, Quintero LP, da Silva Lima A, Gonçalves AL, Gonçalves TA, Damasio A, Squina FM, Ferreira Milagres AM, Abdella A, Wilkins MR, Segato F. Heterologous expression and functional characterization of a GH10 endoxylanase from Aspergillus fumigatus var. niveus with potential biotechnological application. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 24:e00382. [PMID: 31799141 PMCID: PMC6881608 DOI: 10.1016/j.btre.2019.e00382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/26/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Xylanases decrease the xylan content in pretreated biomass releasing it from hemicellulose, thus improving the accessibility of cellulose for cellulases. In this work, an endo-β-1,4-xylanase from Aspergillus fumigatus var. niveus (AFUMN-GH10) was successfully expressed. The structural analysis and biochemical characterization showed this AFUMN-GH10 does not contain a carbohydrate-binding module. The enzyme retained its activity in a pH range from 4.5 to 7.0, with an optimal temperature at 60 °C. AFUMN-GH10 showed the highest activity in beechwood xylan. The mode of action of AFUMN-GH10 was investigated by hydrolysis of APTS-labeled xylohexaose, which resulted in xylotriose and xylobiose as the main products. AFUMN-GH10 released 27% of residual xylan from hydrothermally-pretreated corn stover and 14% of residual xylan from hydrothermally-pretreated sugarcane bagasse. The results showed that environmentally friendly pretreatment followed by enzymatic hydrolysis with AFUMN-GH10 in low concentration is a suitable method to remove part of residual and recalcitrant hemicellulose from biomass.
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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
| | - Evandro José Mulinari
- Department of Physics and Applied Sciences, São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Leidy Patricia Quintero
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Awana da Silva Lima
- 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
| | - Thiago Augusto Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | | | - Asmaa Abdella
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Mark R. Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
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Matrix Discriminant Analysis Evidenced Surface-Lithium as an Important Factor to Increase the Hydrolytic Saccharification of Sugarcane Bagasse. Molecules 2019; 24:molecules24193614. [PMID: 31597244 PMCID: PMC6804010 DOI: 10.3390/molecules24193614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/10/2019] [Accepted: 09/20/2019] [Indexed: 11/17/2022] Open
Abstract
Statistical evidence pointing to the very soft change in the ionic composition on the surface of the sugar cane bagasse is crucial to improve yields of sugars by hydrolytic saccharification. Removal of Li+ by pretreatments exposing -OH sites was the most important factor related to the increase of saccharification yields using enzyme cocktails. Steam Explosion and Microwave:H2SO4 pretreatments produced unrelated structural changes, but similar ionic distribution patterns. Both increased the saccharification yield 1.74-fold. NaOH produced structural changes related to Steam Explosion, but released surface-bounded Li+ obtaining 2.04-fold more reducing sugars than the control. In turn, the higher amounts in relative concentration and periodic structures of Li+ on the surface observed in the control or after the pretreatment with Ethanol:DMSO:Ammonium Oxalate, blocked -OH and O- available for ionic sputtering. These changes correlated to 1.90-fold decrease in saccharification yields. Li+ was an activator in solution, but its presence and distribution pattern on the substrate was prejudicial to the saccharification. Apparently, it acts as a phase-dependent modulator of enzyme activity. Therefore, no correlations were found between structural changes and the efficiency of the enzymatic cocktail used. However, there were correlations between the Li+ distribution patterns and the enzymatic activities that should to be shown.
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Berto GL, Velasco J, Tasso Cabos Ribeiro C, Zanphorlin LM, Noronha Domingues M, Tyago Murakami M, Polikarpov I, de Oliveira LC, Ferraz A, Segato F. Functional characterization and comparative analysis of two heterologous endoglucanases from diverging subfamilies of glycosyl hydrolase family 45. Enzyme Microb Technol 2019; 120:23-35. [DOI: 10.1016/j.enzmictec.2018.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/26/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022]
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8
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Zubieta MP, Contesini FJ, Rubio MV, Gonçalves AEDSS, Gerhardt JA, Prade RA, Damasio ARDL. Protein profile in Aspergillus nidulans recombinant strains overproducing heterologous enzymes. Microb Biotechnol 2018; 11:346-358. [PMID: 29316319 PMCID: PMC5812239 DOI: 10.1111/1751-7915.13027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/23/2017] [Accepted: 10/26/2017] [Indexed: 01/01/2023] Open
Abstract
Filamentous fungi are robust cell factories and have been used for the production of large quantities of industrially relevant enzymes. However, the production levels of heterologous proteins still need to be improved. Therefore, this article aimed to investigate the global proteome profiling of Aspergillus nidulans recombinant strains in order to understand the bottlenecks of heterologous enzymes production. About 250, 441 and 424 intracellular proteins were identified in the control strain Anid_pEXPYR and in the recombinant strains Anid_AbfA and Anid_Cbhl respectively. In this context, the most enriched processes in recombinant strains were energy pathway, amino acid metabolism, ribosome biogenesis, translation, endoplasmic reticulum and oxidative stress, and repression under secretion stress (RESS). The global protein profile of the recombinant strains Anid_AbfA and Anid_Cbhl was similar, although the latter strain secreted more recombinant enzyme than the former. These findings provide insights into the bottlenecks involved in the secretion of recombinant proteins in A. nidulans, as well as in regard to the rational manipulation of target genes for engineering fungal strains as microbial cell factories.
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Affiliation(s)
- Mariane Paludetti Zubieta
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Fabiano Jares Contesini
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Marcelo Ventura Rubio
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | | | - Jaqueline Aline Gerhardt
- Department of Biochemistry and Tissue BiologyInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSPBrazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOKUSA
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9
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Fonseca-Maldonado R, Meleiro LP, Mendes LFS, Alves LF, Carli S, Morero LD, Basso LGM, Costa-Filho AJ, Ward RJ. Lignocellulose binding of a Cel5A-RtCBM11 chimera with enhanced β-glucanase activity monitored by electron paramagnetic resonance. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:269. [PMID: 29163671 PMCID: PMC5686792 DOI: 10.1186/s13068-017-0964-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/07/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The Bacillus subtilis endo-β-1,4-glucanase (BsCel5A) hydrolyzes β-1,3-1,4-linked glucan, and the enzyme includes a family 3 carbohydrate-binding module (CBM3) that binds β-1,4-linked glucan. METHODS Here we investigate the BsCel5A β-1,3-1,4 glucanase activity after exchanging the CBM3 domain for the family 11 CBM from Ruminiclostridium thermocellum celH (RtCBM11) having β-1,3-1,4 glucan affinity. RESULTS The BsCel5A-RtCBM11 presents a 50.4% increase in Vmax, a 10% reduction in K0.5, and a 2.1-fold increase in catalytic efficiency. Enzyme mobility and binding to barley β-1,3-1,4 glucan and pre-treated sugarcane bagasse were investigated using Electron Paramagnetic Resonance (EPR) with Site-Directed Spin Labeling (SDSL) of the binding site regions of the CBM3 and RtCBM11 domains in the BsCel5A-CBM3 and BsCel5A-RtCBM11, respectively. Although higher mobility than the RtCBM11 was shown, no interaction of the spin-labeled CBM3 with β-1,3-1,4 glucan was observed. In contrast, a Ka value of 0.22 mg/mL was estimated from titration of the BsCel5A-RtCBM11 with β-1,3-1,4 glucan. Enzyme binding as inferred from altered EPR spectra of the BsCel5A-RtCBM11 was observed only after xylan or lignin extraction from sugarcane bagasse. Binding to xylan- or lignin-free lignocellulose was correlated with a 4.5- to 5-fold increase in total reducing sugar release as compared to the milled intact sugarcane bagasse, suggesting that xylan impedes enzyme access to the β-1,3-1,4 glucan. CONCLUSIONS These results show that the non-specific binding of the BsCel5A-RtCBM11 to the lignin component of the cell wall is minimal, and represent the first reported use of EPR to directly study the interaction of glycoside hydrolyse enzymes with natural insoluble substrates.
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Affiliation(s)
- Raquel Fonseca-Maldonado
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
- Departamento de Gestão, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo/IFSP Campus Jacareí, Jacareí, São Paulo Brazil
| | - Luana P. Meleiro
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
| | - Luís F. S. Mendes
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Luana F. Alves
- Departamento de Bioquímica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Sibeli Carli
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
| | - Lucas D. Morero
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Luis G. M. Basso
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Antonio J. Costa-Filho
- Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo Brazil
| | - Richard J. Ward
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, São Paulo Brazil
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Damasio ARDL, Rubio MV, Gonçalves TA, Persinoti GF, Segato F, Prade RA, Contesini FJ, de Souza AP, Buckeridge MS, Squina FM. Xyloglucan breakdown by endo-xyloglucanase family 74 from Aspergillus fumigatus. Appl Microbiol Biotechnol 2016; 101:2893-2903. [PMID: 28013403 DOI: 10.1007/s00253-016-8014-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 11/09/2016] [Accepted: 11/12/2016] [Indexed: 12/30/2022]
Abstract
Xyloglucan is the most abundant hemicellulose in primary walls of spermatophytes except for grasses. Xyloglucan-degrading enzymes are important in lignocellulosic biomass hydrolysis because they remove xyloglucan, which is abundant in monocot-derived biomass. Fungal genomes encode numerous xyloglucanase genes, belonging to at least six glycoside hydrolase (GH) families. GH74 endo-xyloglucanases cleave xyloglucan backbones with unsubstituted glucose at the -1 subsite or prefer xylosyl-substituted residues in the -1 subsite. In this work, 137 GH74-related genes were detected by examining 293 Eurotiomycete genomes and Ascomycete fungi contained one or no GH74 xyloglucanase gene per genome. Another interesting feature is that the triad of tryptophan residues along the catalytic cleft was found to be widely conserved among Ascomycetes. The GH74 from Aspergillus fumigatus (AfXEG74) was chosen as an example to conduct comprehensive biochemical studies to determine the catalytic mechanism. AfXEG74 has no CBM and cleaves the xyloglucan backbone between the unsubstituted glucose and xylose-substituted glucose at specific positions, along the XX motif when linked to regions deprived of galactosyl branches. It resembles an endo-processive activity, which after initial random hydrolysis releases xyloglucan-oligosaccharides as major reaction products. This work provides insights on phylogenetic diversity and catalytic mechanism of GH74 xyloglucanases from Ascomycete fungi.
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Affiliation(s)
- André Ricardo de Lima Damasio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Marcelo Ventura Rubio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Thiago Augusto Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas, Campinas, SP, Brazil
| | - Gabriela Felix Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Fernando Segato
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.,Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, SP, Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Fabiano Jares Contesini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Amanda Pereira de Souza
- Laboratório de Fisiologia e Ecologia de Plantas (LAFIECO), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Marcos Silveira Buckeridge
- Laboratório de Fisiologia e Ecologia de Plantas (LAFIECO), Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), São Paulo, SP, Brazil
| | - Fabio Marcio Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil.
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11
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dos Santos HB, Bezerra TMS, Pradella JGC, Delabona P, Lima D, Gomes E, Hartson SD, Rogers J, Couger B, Prade R. Myceliophthora thermophila M77 utilizes hydrolytic and oxidative mechanisms to deconstruct biomass. AMB Express 2016; 6:103. [PMID: 27807811 PMCID: PMC5093097 DOI: 10.1186/s13568-016-0276-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/27/2016] [Indexed: 12/23/2022] Open
Abstract
Biomass is abundant, renewable and useful for biofuel production as well as chemical priming for plastics and composites. Deconstruction of biomass by enzymes is perceived as recalcitrant while an inclusive breakdown mechanism remains to be discovered. Fungi such as Myceliophthora thermophila M77 appear to decompose natural biomass sources quite well. This work reports on this fungus fermentation property while producing cellulolytic enzymes using natural biomass substrates. Little hydrolytic activity was detected, insufficient to explain the large amount of biomass depleted in the process. Furthermore, this work makes a comprehensive account of extracellular proteins and describes how secretomes redirect their qualitative protein content based on the nature and chemistry of the nutritional source. Fungus grown on purified cellulose or on natural biomass produced secretomes constituted by: cellobiohydrolases, cellobiose dehydrogenase, β-1,3 glucanase, β-glucosidases, aldose epimerase, glyoxal oxidase, GH74 xyloglucanase, galactosidase, aldolactonase and polysaccharide monooxygenases. Fungus grown on a mixture of purified hemicellulose fractions (xylans, arabinans and arabinoxylans) produced many enzymes, some of which are listed here: xylosidase, mixed β-1,3(4) glucanase, β-1,3 glucanases, β-glucosidases, β-mannosidase, β-glucosidases, galactosidase, chitinases, polysaccharide lyase, endo β-1,6 galactanase and aldose epimerase. Secretomes produced on natural biomass displayed a comprehensive set of enzymes involved in hydrolysis and oxidation of cellulose, hemicellulose-pectin and lignin. The participation of oxidation reactions coupled to lignin decomposition in the breakdown of natural biomass may explain the discrepancy observed for cellulose decomposition in relation to natural biomass fermentation experiments.
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Affiliation(s)
- Hévila Brognaro dos Santos
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
| | - Thaís Milena Souza Bezerra
- Laboratório de Enzimologia, Instituto de Química, UNESP, Araraquara, São Paulo Brazil
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
| | - José G. C. Pradella
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
| | - Priscila Delabona
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
| | - Deise Lima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Rua Giuseppe Máximo Scolfaro, 10.000, Bairro Guará, Campinas, SP CEP 13083-970 Brazil
| | - Eleni Gomes
- Laboratório de Microbiologia e Bioquímica Aplicada, Departamento de Biologia, IBILCE/UNESP, Rua Cristovão Colombo, 2265 Bairro Jd. Nazareth, São José do Rio Preto, SP CEP 15054-000 Brazil
| | - Steve D. Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078 USA
| | - Brian Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
| | - Rolf Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
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Gomes E, de Souza AR, Orjuela GL, Da Silva R, de Oliveira TB, Rodrigues A. Applications and Benefits of Thermophilic Microorganisms and Their Enzymes for Industrial Biotechnology. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_21] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Peng X, Su H, Mi S, Han Y. A multifunctional thermophilic glycoside hydrolase from Caldicellulosiruptor owensensis with potential applications in production of biofuels and biochemicals. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:98. [PMID: 27141233 PMCID: PMC4852416 DOI: 10.1186/s13068-016-0509-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/14/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Thermophilic enzymes have attracted much attention for their advantages of high reaction velocity, exceptional thermostability, and decreased risk of contamination. Exploring efficient thermophilic glycoside hydrolases will accelerate the industrialization of biofuels and biochemicals. RESULTS A multifunctional glycoside hydrolase (GH) CoGH1A, belonging to GH1 family with high activities of β-d-glucosidase, exoglucanase, β-d-xylosidase, β-d-galactosidase, and transgalactosylation, was cloned and expressed from the extremely thermophilic bacterium Caldicellulosiruptor owensensis. The enzyme exerts excellent thermostability by retaining 100 % activity after 12-h incubation at 75 °C. The catalytic coefficients (k cat/K m) of the enzyme against pNP-β-D-galactopyranoside, pNP-β-D-glucopyranoside, pNP-β-D-cellobioside, pNP-β-D-xylopyranoside, and cellobiose were, respectively, 7450.0, 2467.5, 1085.4, 90.9, and 137.3 mM(-1) s(-1). When CoGH1A was supplemented at the dosage of 20 Ucellobiose g(-1) biomass for hydrolysis of the pretreated corn stover, comparing with the control, the glucose and xylose yields were, respectively, increased 37.9 and 42.1 %, indicating that the enzyme contributed not only for glucose but also for xylose release. The efficiencies of lactose decomposition and synthesis of galactooligosaccharides (GalOS) by CoGH1A were investigated at low (40 g L(-1)) and high (500 g L(-1)) initial lactose concentrations. At low lactose concentration, the time for decomposition of 83 % lactose was 10 min, which is much shorter than the reported 2-10 h for reaching such a decomposition rate. At high lactose concentration, after 50-min catalysis, the GalOS concentration reached 221 g L(-1) with a productivity of 265.2 g L(-1) h(-1). This productivity is at least 12-fold higher than those reported in literature. CONCLUSIONS The multifunctional glycoside hydrolase CoGH1A has high capabilities in saccharification of lignocellulosic biomass, decomposition of lactose, and synthesis of galactooligosaccharides. It is a promising enzyme to be used for bioconversion of carbohydrates in industrial scale. In addition, the results of this study indicate that the extremely thermophilic bacteria are potential resources for screening highly efficient glycoside hydrolases for the production of biofuels and biochemicals.
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Affiliation(s)
- Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Hong Su
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Shuofu Mi
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
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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.
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15
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Segato F, Berto GL, Ares de Araújo E, Muniz JR, Polikarpov I. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-β-1,4-glucanase from glycoside hydrolase family 12. Acta Crystallogr F Struct Biol Commun 2014; 70:267-70. [PMID: 24637772 PMCID: PMC3936441 DOI: 10.1107/s2053230x13034936] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Endoglucanases are important enzymes that are involved in the modification and degradation of cellulose. Filamentous fungi such as Aspergillus terreus are effective biomass degraders in nature owing to their capacity to produce an enzymatic arsenal of glycoside hydrolases, including endoglucanase from glycoside hydrolase family 12 (GH12). The A. terreus GH12 endoglucanase was cloned and overexpressed in A. nidulans, purified and crystallized. A single crystal was obtained from a solution consisting of 2 M ammonium sulfate, 5%(v/v) 2-propanol. X-ray diffraction data were collected to a resolution of 1.85 Å using synchrotron radiation and a preliminary molecular-replacement solution was obtained in the trigonal space group P3(2)21. The unit-cell parameters were a = b = 103.24, c = 48.96 Å.
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Affiliation(s)
- Fernando Segato
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Gabriela L. Berto
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Evandro Ares de Araújo
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - João Renato Muniz
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador Saocarlense 400, 13566-590 São Carlos-SP, Brazil
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Várnai A, Siika-aho M, Viikari L. Carbohydrate-binding modules (CBMs) revisited: reduced amount of water counterbalances the need for CBMs. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:30. [PMID: 23442543 PMCID: PMC3599012 DOI: 10.1186/1754-6834-6-30] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/04/2013] [Indexed: 05/07/2023]
Abstract
BACKGROUND A vast number of organisms are known to produce structurally diversified cellulases capable of degrading cellulose, the most abundant biopolymer on earth. The generally accepted paradigm is that the carbohydrate-binding modules (CBMs) of cellulases are required for efficient saccharification of insoluble substrates. Based on sequence data, surprisingly more than 60% of the cellulases identified lack carbohydrate-binding modules or alternative protein structures linked to cellulases (dockerins). This finding poses the question about the role of the CBMs: why would most cellulases lack CBMs, if they are necessary for the efficient hydrolysis of cellulose? RESULTS The advantage of CBMs, which increase the affinity of cellulases to substrates, was found to be diminished by reducing the amount of water in the hydrolytic system, which increases the probability of enzyme-substrate interaction. At low substrate concentration (1% w/w), CBMs were found to be more important in the catalytic performance of the cellobiohydrolases TrCel7A and TrCel6A of Trichoderma reesei as compared to that of the endoglucanases TrCel5A and TrCel7B. Increasing the substrate concentration while maintaining the enzyme-to-substrate ratio enhanced adsorption of TrCel7A, independent of the presence of the CBM. At 20% (w/w) substrate concentration, the hydrolytic performance of cellulases without CBMs caught up with that of cellulases with CBMs. This phenomenon was more noticeable on the lignin-containing pretreated wheat straw as compared to the cellulosic Avicel, presumably due to unproductive adsorption of enzymes to lignin. CONCLUSIONS Here we propose that the water content in the natural environments of carbohydrate-degrading organisms might have led to the evolution of various substrate-binding structures. In addition, some well recognized problems of economical saccharification such as unproductive binding of cellulases, which reduces the hydrolysis rate and prevents recycling of enzymes, could be partially overcome by omitting CBMs. This finding could help solve bottlenecks of enzymatic hydrolysis of lignocelluloses and speed up commercialization of second generation bioethanol.
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Affiliation(s)
- Anikó Várnai
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
| | - Matti Siika-aho
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Espoo, Finland
| | - Liisa Viikari
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
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