DOCSLIB.ORG

Characterizing Xylan-Degrading Enzymes from a Putative Xylan Utilization System Derived from Termite Gut Metagenome Haiyang Wu

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterizing Xylan-Degrading Enzymes from a Putative Xylan Utilization System Derived from Termite Gut Metagenome Haiyang Wu Characterizing xylan-degrading enzymes from a putative Xylan Utilization System derived from termite gut metagenome Haiyang Wu To cite this version: Haiyang Wu. Characterizing xylan-degrading enzymes from a putative Xylan Utilization System derived from termite gut metagenome. Biomolecules [q-bio.BM]. INSA de Toulouse, 2018. English. NNT : 2018ISAT0039. tel-02918134 HAL Id: tel-02918134 https://tel.archives-ouvertes.fr/tel-02918134 Submitted on 20 Aug 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. 5)µ4& &OWVFEFMPCUFOUJPOEV %0$503"5%&-6/*7&34*5²%&506-064& %ÏMJWSÏQBS Institut National des Sciences Appliquées de Toulouse (INSA de Toulouse) 1SÏTFOUÏFFUTPVUFOVFQBS Haiyang WU le vendredi 23 mars 2018 5JUSF Characterizing xylan-degrading enzymes from a putative Xylan Utilization System derived from termite gut metagenome Caractérisation des enzymes xylanolytiques d'un locus d'utilisation du xylane issu d'un métagénome de termite ²DPMF EPDUPSBMF et discipline ou spécialité ED SEVAB : Ingénieries microbienne et enzymatique 6OJUÏEFSFDIFSDIF Laboratoire d’Ingénierie des Système Biologiques et des Procédés (UMR INRA 792 et CNRS 5504) %JSFDUFVSUSJDF T EFʾÒTF Claire DUMON - Chargée de recherche - INRA de Toulouse Michael J. O’DONOHUE - Directeur de Recherche - INRA de Toulouse Jury : Evelyne FORANO - Directrice de recherche - INRA, Saint-Genès-Champanelle - Rapporteur Harry J. GILBERT - Professeur - Université de Newcastle upon Tyne - Rapporteur Bernard HENRISSAT - Directeur de recherche - CNRS, Aix-Marseille Université - Examinateur NOM : WU Prénom: Haiyang Titre: Caractérisation des enzymes xylanolytiques d'un locus d'utilisation du xylane issu d'un métagénome de termite Spécialité: Sciences Ecologique, Vétérinaires, Agronomiques et Bioingénieries, Filière: Ingénieries microbienne et enzymatique Année: 2018 Lieu: INSA de Toulouse RESUME Dans le contexte de la bioéconomie, la découverte et la caractérisation des enzymes capables de dégrader la paroi végétale est particulièrement intéressante pour l’utilisation de la biomasse lignocellulosique dans l’industrie. A cet égard, la métagénomique fonctionnelle est un outil puissant pour découvrir de nouvelles enzymes à partir d’écosystèmes microbiens variés, comme l’illustrent les travaux sur le tube digestif du termite Pseudacanthotermes militaris. Cette étude a fourni une mine d’informations et identifié un hypothétique locus d’utilisation du xylane (XUS), codant pour cinq glycosides hydrolases (GH) et une carbohydrate esterase (CE) de Bacteroidales. Le XUS du métagénome de Pseudacanthotermes militaris contient une xylanase de la famille GH10 qui possède une organisation modulaire complexe dans laquelle la séquence du domaine GH10 est interrompue par une insertion de deux carbohydrate binding modules (CBM). Des travaux préliminaires ont montré que cette enzyme modulaire, désignée Pm25, est active sur xylane. Par conséquent, un des objectifs de cette étude a été la caractérisation détaillée des propriétés biochimiques et catalytiques de Pm25. Le rôle des CBM a également été examiné en quantifiant les interactions protéines-sucres et permettant ainsi une meilleure compréhension du rôle spécifique de ces modules, les résultats obtenus permettent de cerner l’impact de la modularité de Pm25 sur ses propriétés fonctionnelles. Dans une deuxième partie de l’étude, nous avons entrepris d’étudier la fonction de Pm25 dans le contexte du cluster XUS. Pour ce faire, nous avons étudié les enzymes adjacentes à Pm25 sur le locus, une autre GH10, une GH11, une GH115 et une GH43. La comparaison des paramètres cinétiques et une étude détaillée des produits d’hydrolyse ont été analysés par spectrométrie de masse et ont révélé que la GH10 et la GH11 étaient les enzymes clefs de la dépolymérisation en étant 20 fois plus efficaces que Pm25. En parallèle, nous avons développé un protocole pour l’utilisation de la micro-thermophorèse (MST) pour quantifier les interactions CBM-sucres, une approche intéressante qui nécessite peut d’échantillon et de ligand contrairement à d’autres méthodes biophysiques. Dans l’ensemble, cette étude a révélé le rôle important de Pm25 et ses homologues dans les locus d’utilisation des xylanes chez les Bacteroidetes et a permis d’identifié le sens de cette architecture particulière. Mots clefs: Xylanase, GH10, CBM, MST, XUS, Biomasse lignocellulosique, Bacteroidetes, métagénomique, bioeconomie Ecole doctorale : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Unité de recherche : Laboratoire d’Ingénierie des Système Biologiques et des Procédés (UMR CNRS 5504, UMR INRA 792) de l’INSA de Toulouse I Last Name: WU First Name: Haiyang Title: Characterizing xylan-degrading enzymes from a putative Xylan Utilization System derived from termite gut metagenome. Speciality: Ecological, Veterinary, Agronomic Sciences and Bioengineering; Field: Enzymatic and Microbial engineering Year: 2018 Place: INSA de Toulouse SUMMARY In the context of bioeconomy, the discovery and study of plant-cell wall degrading enzymes is particularly relevant for the use of lignocellulosic biomass for industrial purposes. In this respect, functional metagenomics has proven to be a powerful tool to discover new enzymes from a variety of microbial ecosystems, as exemplified by work performed on the gut of the termite Pseudacanthotermes militaris. This study provided a wealth of information and identified an interesting hypothetical xylan utilization system, encoding five glycoside hydrolases (GH) and one carbohydrate esterase (CE) annotated from bacteroidales. The Pseudacanthotermes militaris-derived putative XUS cluster contains a GH10 xylanase that displays a quite complex modular arrangement wherein the GH10 catalytic module contains two insertional carbohydrate binding modules (CBM). During the preliminary work, this modular enzyme, designated Pm25, was shown to be active on xylan, thus in the present research we set out to more thoroughly characterize its biochemical and catalytic properties. The role of the CBM was also investigated, quantifying protein-carbohydrate interactions and thus providing better insight into the specific role of the modules. Taken together, the results obtained provide insight into how Pm25 modularity translates into functional properties. In second part of our study, we set out investigate the function of Pm25 in the context of the XUS cluster. To achieve this we studied a xylan utilization system, which is constituted by another GH10, GH11, GH115 and GH43. The comparison of kinetic parameters and a detailed end product analysis by mass spectrometry showed that GH10 and GH11 outweigh over 20 fold Pm25 catalytic efficiency. In parallel, we developed the use of MicroScale Thermophoresis (MST) to quantify CBM - carbohydrates interactions, an interesting approach requiring smaller concentration of proteins and ligands compared to other biophysical methods. Overall this study highlighted the important role of Pm25 homologs in the xylan utilization system in Bacteroidetes, and pinpointed the meaning of its unusual architecture. Keywords: Xylanase, GH10, CBM, MST, XUS, lignocellulosic biomass, Bacteroidetes, metagenomic, bioeconomy Doctoral school : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) Research unit : Laboratoire d’Ingénierie des Système Biologiques et des Procédés (UMR CNRS 5504, UMR INRA 792) de l’INSA de Toulouse III PUBLICATIONS Published Wu H., Montanier C.Y., Dumon C. (2017) Quantifying CBM Carbohydrate Interactions Using Microscale Thermophoresis. In: Abbott D., Lammerts van Bueren A. (eds) Protein- Carbohydrate Interactions. Methods in Molecular Biology, vol 1588. Humana Press, New York, NY To be submitted Wu H., Ioannou E, Montanier C.Y., O’Donohue M., Dumon C. Understanding the multimodularity of a Xyn10C-like protein found in termite gut. Wu H., Montanier C.Y., O’Donohue M., Dumon C. Investigation of the function of a putative xylan utilization locus from termite gut microbiome. COMMUNICATIONS ORALES 1. INRA-Séminaire BILI (BIoraffinerie des LIgnocelluloses), March 11, 2016, Paris, France. Oral presentation on topic Characterization of an unusual GH10 xylanase from termite gut. 2. INSA-CIMEs (Catalysis and Enzyme Molecular Engineering Team) meeting, February 2nd, 2017, Toulouse, France. Oral presentation on topic Characterization of a multi-modular xylanase belonging to a potential microbial xylan utilization system. 3. 12th Carbohydrate Bioengineering Meeting, April 23-26, 2017, Vienna, Austria. Oral presentation on topic Characterization of an unusual GH10 xylanase from termite gut. COMMUNICATIONS PAR POSTERS 1. Characterization of an unusual GH10 xylanase from termite gut. Wu H., Ioannou E, Montanier C., Arnal G., Fernandez-Fuentes N., O’Donohue M., Dumon C. ; Summer Course Glycosciences (14th European Training Course on Carbohydrates) , 12-16 June 2016, Groningen, The Netherlands. 2. Characterization of an unusual multimodular GH10 xylanase Ioannou E, Wu H., Cioci G., Guyez B., Arnal G., Dumon C, Bryant D, Fernandez- Fuentes
Load more

Recommended publications
  • Structure and Dynamics of the Microbial Communities Underlying the Carboxylate Platform for Biofuel Production
    Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production E.B. Hollister 1, A.K. Forrest 2, H.H. Wilkinson 3, D.J. Ebbole 3, S.A. Malfatti 4, S.G. Tringe 4, M.T. Holtzapple 2, T.J. Gentry 1 1 Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA 77843-2474 2 Department of Chemical Engineering, Texas A&M University, College Station, TX, USA 77843-3122 3 Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX USA 77843-2132 4 DOE Joint Genome Institute, Walnut Creek, CA, USA 94598 July 31, 2010 ACKNOWLEDGMENT The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 DISCLAIMER This document was prepared as an account of work sponsored by the United States Government. While this document is believed to contain correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California.
    [Show full text]
  • A Study of the Impact of Mazie SBE I on the [Alpha]-Polyglucan Produced in Synechocystis Sp
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 2007 A study of the impact of mazie SBE I on the [alpha]- polyglucan produced in Synechocystis sp. strain PCC 6803 Shayani Deborah Nesaranjani Pieris Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Plant Biology Commons Recommended Citation Pieris, Shayani Deborah Nesaranjani, "A study of the impact of mazie SBE I on the [alpha]-polyglucan produced in Synechocystis sp. strain PCC 6803" (2007). Retrospective Theses and Dissertations. 15850. https://lib.dr.iastate.edu/rtd/15850 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. A study of the impact of mazie SBE I on the -polyglucan produced in Synechocystis sp. strain PCC 6803 by Shayani Deborah Nesaranjani Pieris A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Plant Physiology Program of Study Committee: Martin H. Spalding, Major Professor Madan K. Bhattacharyya Jay -lin Jane David J. Oliver Paul M. Scott Iowa State University Ames, Iowa 200 7 Copyright © Shayani Deborah Nesara njani Pieris , 200 7. All right s reserved. UMI Number: 3294976 UMI Microform 3294976 Copyright 2008 by ProQuest Information and Learning Company. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code.
    [Show full text]
  • Supplementary Materials
    SUPPLEMENTARY MATERIALS Table S1. Chemical characteristics of the two digestate forms (SD and WD). Values quoted are expressed as % of air-dry digestate (means followed by standard error in brackets). References for the employed methods used for determination of each chemical characteristic is also reported. SD WD Reference Org C % 44.4 (0.33) 1.1 (0.01) [81] Tot N % 1.4 (0.01) 0.4 (0.01) [82] C/N 31.4 (0.17) 3.1 (0.04) NH4-N % n.d 0.2 (0.00) [83] K % 1.7 (0.00) n.d. [84] P % 0.9 (0.01) n.d. [84] S % 0.23 (0.02) n.d. [85] SD = solid digestate; WD = whole digestate. Table S2. Soil physical and chemical characteristics at the beginning of trial (t0) (means from 9 observations followed by standard errors in brackets). Clay (%) 41.9 (1.22) Silt (%) 47.8 (2.13) Moisture (%) 24.46 (1.24) Bulk density (g cm-3) 1.39 (0.04) pH 8.3 (0) CaCO3 (%) 11.4 (0.7) TOC (g kg-1) 12.8 (0.3) TN (g kg-1) 1.4 (0) C/N 9.4 (0.3) CEC (cmol(+) kg-1) 21.0 (0.7) Exchangeable Bases (mg kg-1) K 278.7 (8.0) Na 22.0 (3.0) Mg 201.7 (25.6) Ca 3718.6 (176.3) Available Microelements (mg kg-1) Cu 28.0 (5.0) Zn 1.7 (0.2) Fe 15.4 (0.5) Mn 16.3 (0.5) TOC = total organic C; TN = total N; CEC = cation exchange capacity Table S3.
    [Show full text]
  • Microbial Diversity in Raw Milk and Sayram Ketteki from Southern of Xinjiang, China
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.15.435442; this version posted March 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Microbial diversity in raw milk and Sayram Ketteki from southern of Xinjiang, China DongLa Gao1,2，Weihua Wang1,2*，ZhanJiang Han1,3，Qian Xi1,2, ，RuiCheng Guo1,2，PengCheng Kuang1,2，DongLiang Li1,2 1 College of Life Science, Tarim University, Alaer, Xinjiang , China 2 Xinjiang Production and Construction Corps Key Laboratory of Deep Processing of Agricultural Products in South Xinjiang, Alar, Xinjiang ,China 3 Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Alar, Xinjiang , China *Corresponding author E-mail: [email protected]（Weihua Wang） bioRxiv preprint doi: https://doi.org/10.1101/2021.03.15.435442; this version posted March 15, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Raw milk and fermented milk are rich in microbial resources, which are essential for the formation of texture, flavor and taste. In order to gain a deeper knowledge of the bacterial and fungal community diversity in local raw milk and home-made yogurts
    [Show full text]
  • Agency Response Letter GRAS Notice No. GRN 000675
    . Janet Oesterling Novozymes North America, Inc. 77 Perry Chapel Church Road Franklinton, NC 27525 Re: GRAS Notice No. GRN 000675 Dear Ms. Oesterling: The Food and Drug Administration (FDA, we) completed our evaluation of GRN 000675. We received the notice, dated October 10, 2016, that you submitted in accordance with the agency’s proposed regulation, proposed 21 CFR 170.36 (62 FR 18938; April 17, 1997; Substances Generally Recognized as Safe (GRAS); the GRAS proposal) on July 17, 2016, and filed it on October 14, 2016. We received amendments containing clarifying information on February, 22, 2017 and March 09, 2017. FDA published the GRAS final rule on August 17, 2016 (81 FR 54960), with an effective date of October 17, 2016. As GRN 000675 was pending on the effective date of the GRAS final rule, we requested some additional information consistent with the format and requirements of the final rule. We received an amendment responding to this request on October 24, 2016. The subject of the notice is xylanase enzyme preparation produced by Trichoderma reesei carrying a xylanase gene from Talaromyces leycettanus (xylanase enzyme preparation). The notice informs us of the view of Novozymes North America, Inc. (Novozymes) that xylanase enzyme preparation is GRAS, through scientific procedures, for use as an enzyme at levels up to 48.33 mg Total Organic Solids (TOS) per kg raw material in brewing, cereal beverage processing, baking, and processing of cereal grains such as corn, wheat, barley, and oats. Commercial enzyme preparations that are used in food processing typically contain an enzyme component that catalyzes the chemical reaction as well as substances used as stabilizers, preservatives, or diluents.
    [Show full text]
  • Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications
    Hindawi Publishing Corporation Enzyme Research Volume 2012, Article ID 921362, 14 pages doi:10.1155/2012/921362 Review Article Pullulanase: Role in Starch Hydrolysis and Potential Industrial Applications Siew Ling Hii,1 Joo Shun Tan,2 Tau Chuan Ling,3 and Arbakariya Bin Ariff4 1 Department of Chemical Engineering, Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, 53300 Kuala Lumpur, Malaysia 2 Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia 3 Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia 4 Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia Correspondence should be addressed to Arbakariya Bin Ariff, [email protected] Received 26 March 2012; Revised 12 June 2012; Accepted 12 June 2012 Academic Editor: Joaquim Cabral Copyright © 2012 Siew Ling Hii et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The use of pullulanase (EC 3.2.1.41) has recently been the subject of increased applications in starch-based industries especially those aimed for glucose production. Pullulanase, an important debranching enzyme, has been widely utilised to hydrolyse the α-1,6 glucosidic linkages in starch, amylopectin, pullulan, and related oligosaccharides, which enables a complete and efficient conversion of the branched polysaccharides into small fermentable sugars during saccharification process. The industrial manufacturing of glucose involves two successive enzymatic steps: liquefaction, carried out after gelatinisation by the action of α- amylase; saccharification, which results in further transformation of maltodextrins into glucose.
    [Show full text]
  • 1 Recurrent Loss of Abaa, a Master Regulator of Asexual Development in Filamentous Fungi
    bioRxiv preprint doi: https://doi.org/10.1101/829465; this version posted November 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, 2 correlates with changes in genomic and morphological traits 3 4 Matthew E. Meada,*, Alexander T. Borowskya,b,*, Bastian Joehnkc, Jacob L. Steenwyka, Xing- 5 Xing Shena, Anita Silc, and Antonis Rokasa,# 6 7 aDepartment of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA 8 bCurrent Address: Department of Botany and Plant Sciences, University of California Riverside, 9 Riverside, California, USA 10 cDepartment of Microbiology and Immunology, University of California San Francisco, San 11 Francisco, California, USA 12 13 Short Title: Recurrent loss of abaA across Eurotiomycetes 14 #Address correspondence to Antonis Rokas, [email protected] 15 16 *These authors contributed equally to this work 17 18 19 Keywords: Fungal asexual development, abaA, evolution, developmental evolution, 20 morphology, binding site, Histoplasma capsulatum, regulatory rewiring, gene regulatory 21 network, evo-devo 22 1 bioRxiv preprint doi: https://doi.org/10.1101/829465; this version posted November 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 23 Abstract 24 Gene regulatory networks (GRNs) drive developmental and cellular differentiation, and variation 25 in their architectures gives rise to morphological diversity.
    [Show full text]
  • Novel Xylan Degrading Enzymes from Polysaccharide Utilizing Loci of Prevotella Copri DSM18205
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419226; this version posted December 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Novel xylan degrading enzymes from polysaccharide utilizing loci of Prevotella copri DSM18205 Javier A. Linares-Pastén1*, Johan Sebastian Hero2, José Horacio Pisa2, Cristina Teixeira1, Margareta Nyman3, Patrick Adlercreutz1, M. Alejandra Martinez2,4, Eva Nordberg Karlsson1** 1Biotechnology, Dept of Chemistry, Lund University, P.O.Box 124, 221 00 Lund, Sweden. 2Planta Piloto de Procesos Industriales Microbiológicos PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, San Miguel de Tucumán, Argentina. 3 Dept Food Technology, Engineering and Nutrition, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden. 4Facultad de Ciencias Exactas y Tecnología, UNT. Av. Independencia 1800, San Miguel de Tucumán, 4000, Argentina. Corresponding authors: *e-mail: [email protected] ** e-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.12.10.419226; this version posted December 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Prevotella copri DSM18205 is a bacterium, classified under Bacteroidetes that can be found in the human gastrointestinal tract (GIT). The role of P. copri in the GIT is unclear, and elevated numbers of the microbe have been reported both in dietary fiber- induced improvement in glucose metabolism but also in conjunction with certain inflammatory conditions.
    [Show full text]
  • Exogenous Enzymes As Zootechnical Additives in Animal Feed: a Review
    catalysts Review Exogenous Enzymes as Zootechnical Additives in Animal Feed: A Review Brianda Susana Velázquez-De Lucio 1, Edna María Hernández-Domínguez 1, Matilde Villa-García 1, Gerardo Díaz-Godínez 2, Virginia Mandujano-Gonzalez 3, Bethsua Mendoza-Mendoza 4 and Jorge Álvarez-Cervantes 1,* 1 Cuerpo Académico Manejo de Sistemas Agrobiotecnológicos Sustentables, Posgrado Biotecnología, Universidad Politécnica de Pachuca, Zempoala 43830, Hidalgo, Mexico; [email protected] (B.S.V.-D.L.); [email protected] (E.M.H.-D.); [email protected] (M.V.-G.) 2 Centro de Investigación en Ciencias Biológicas, Laboratorio de Biotecnología, Universidad Autónoma de Tlaxcala, Tlaxcala 90000, Tlaxcala, Mexico; [email protected] 3 Ingeniería en Biotecnología, Laboratorio Biotecnología, Universidad Tecnológica de Corregidora, Santiago de Querétaro 76900, Querétaro, Mexico; [email protected] 4 Instituto Tecnológico Superior del Oriente del Estado de Hidalgo, Apan 43900, Hidalgo, Mexico; [email protected] * Correspondence: [email protected]; Tel.: +52-771-5477510 Abstract: Enzymes are widely used in the food industry. Their use as a supplement to the raw Citation: Velázquez-De Lucio, B.S.; material for animal feed is a current research topic. Although there are several studies on the Hernández-Domínguez, E.M.; application of enzyme additives in the animal feed industry, it is necessary to search for new Villa-García, M.; Díaz-Godínez, G.; enzymes, as well as to utilize bioinformatics tools for the design of specific enzymes that work in Mandujano-Gonzalez, V.; certain environmental conditions and substrates. This will allow the improvement of the productive Mendoza-Mendoza, B.; Álvarez-Cervantes, J.
    [Show full text]
  • Function and Structure Studies of GH Family 31 and 97 \Alpha
    110610 (RV-17) Biosci. Biotechnol. Biochem., 75 (12), 110610-1–9, 2011 Award Review Function and Structure Studies of GH Family 31 and 97 -Glycosidases Masayuki OKUYAMA Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo 060-8589, Japan Online Publication, December 7, 2011 [doi:10.1271/bbb.110610] A huge number of glycoside hydrolases are classified an evolutionary relationship of proteins in the family, into the glycoside hydrolase family (GH family) based from which it is often possible to extract information on on their amino-acid sequence similarity. The glycoside function and structure.3) Classification in a GH family hydrolases acting on -glucosidic linkage are in GH has, accordingly, become indispensable for research on family 4, 13, 15, 31, 63, 97, and 122. This review deals glycoside hydrolases. Glycoside hydrolases are also mainly with findings on GH family 31 and 97 enzymes. divided into two mechanistic classes, inverting and Research on two GH family 31 enzymes is described: retaining enzymes: with inversion or net retention of clarification of the substrate recognition of Escherichia anomeric configuration during the catalytic reaction.4) coli -xylosidase, and glycosynthase derived from Schiz- The stereochemical outcome is generally conserved in a osaccharomyces pombe -glucosidase. GH family 97 is GH family. The inverting mechanism proceeds via a an aberrant GH family, containing inverting and simple single displacement. Two functional groups, retainingAdvance glycoside hydrolases. The inverting View enzyme usually carboxyl groups, act as general acid and general in GH family 97 displays significant similarity to base catalysts. The general acid catalyst donates a proton retaining -glycosidases, including GH family 97 retain- to the departure aglycon, and the general base catalyst ing -glycosidase, but the inverting enzyme has no simultaneously deprotonates the incoming water mole- catalytic nucleophile residue.
    [Show full text]
  • Thermophilic Fungi: Taxonomy and Biogeography
    Journal of Agricultural Technology Thermophilic Fungi: Taxonomy and Biogeography Raj Kumar Salar1* and K.R. Aneja2 1Department of Biotechnology, Chaudhary Devi Lal University, Sirsa – 125 055, India 2Department of Microbiology, Kurukshetra University, Kurukshetra – 136 119, India Salar, R. K. and Aneja, K.R. (2007) Thermophilic Fungi: Taxonomy and Biogeography. Journal of Agricultural Technology 3(1): 77-107. A critical reappraisal of taxonomic status of known thermophilic fungi indicating their natural occurrence and methods of isolation and culture was undertaken. Altogether forty-two species of thermophilic fungi viz., five belonging to Zygomycetes, twenty-three to Ascomycetes and fourteen to Deuteromycetes (Anamorphic Fungi) are described. The taxa delt with are those most commonly cited in the literature of fundamental and applied work. Latest legal valid names for all the taxa have been used. A key for the identification of thermophilic fungi is given. Data on geographical distribution and habitat for each isolate is also provided. The specimens deposited at IMI bear IMI number/s. The document is a sound footing for future work of indentification and nomenclatural interests. To solve residual problems related to nomenclatural status, further taxonomic work is however needed. Key Words: Biodiversity, ecology, identification key, taxonomic description, status, thermophile Introduction Thermophilic fungi are a small assemblage in eukaryota that have a unique mechanism of growing at elevated temperature extending up to 60 to 62°C. During the last four decades many species of thermophilic fungi sporulating at 45oC have been reported. The species included in this account are only those which are thermophilic in the sense of Cooney and Emerson (1964).
    [Show full text]
  • The Phylogeny of Plant and Animal Pathogens in the Ascomycota
    Physiological and Molecular Plant Pathology (2001) 59, 165±187 doi:10.1006/pmpp.2001.0355, available online at http://www.idealibrary.com on MINI-REVIEW The phylogeny of plant and animal pathogens in the Ascomycota MARY L. BERBEE* Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada (Accepted for publication August 2001) What makes a fungus pathogenic? In this review, phylogenetic inference is used to speculate on the evolution of plant and animal pathogens in the fungal Phylum Ascomycota. A phylogeny is presented using 297 18S ribosomal DNA sequences from GenBank and it is shown that most known plant pathogens are concentrated in four classes in the Ascomycota. Animal pathogens are also concentrated, but in two ascomycete classes that contain few, if any, plant pathogens. Rather than appearing as a constant character of a class, the ability to cause disease in plants and animals was gained and lost repeatedly. The genes that code for some traits involved in pathogenicity or virulence have been cloned and characterized, and so the evolutionary relationships of a few of the genes for enzymes and toxins known to play roles in diseases were explored. In general, these genes are too narrowly distributed and too recent in origin to explain the broad patterns of origin of pathogens. Co-evolution could potentially be part of an explanation for phylogenetic patterns of pathogenesis. Robust phylogenies not only of the fungi, but also of host plants and animals are becoming available, allowing for critical analysis of the nature of co-evolutionary warfare. Host animals, particularly human hosts have had little obvious eect on fungal evolution and most cases of fungal disease in humans appear to represent an evolutionary dead end for the fungus.
    [Show full text]