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Jury: Prof. dr. ir. Walter Steurbaut (chairman) Prof. dr. ir. Erick Vandamme (promotor) Prof. dr. ir. Wim Soetaert (promotor) Prof. dr. ir. Nico Boon Prof. dr. ir. Monica Höfte Prof. dr. Els Van Damme Dr. Roel Bovenberg Dr. Thierry Dauvrin Promotors: Prof. dr. ir. Erick VANDAMME Prof. dr. ir. Wim SOETAERT Laboratory of Industrial Microbiology and Biocatalysis Department of Biochemical and Microbial Technology Ghent University Dean: Prof. dr. ir. Herman VAN LANGENHOVE Rector: Prof. dr. Paul VAN CAUWENBERGE S. De Maeseneire was supported by a fellowship of the Flemish Institute for the Promotion of Scientific and Technological Research in the Industry (IWT-Vlaanderen). The research was conducted at the Laboratory of Industrial Microbiology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University. ir. Sofie De Maeseneire MYROTHECIUM GRAMINEUM AS A NOVEL FUNGAL EXPRESSION HOST Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences Cell and Gene Biotechnology Titel van het doctoraatsproefschrift in het Nederlands: Myrothecium gramineum als een nieuwe fungale expressie-gastheer Cover illustration: ‘ Myrothecium gramineum’ by Sofie De Maeseneire (June 2007) To refer to this thesis: De Maeseneire, S. L. (2007) Myrothecium gramineum as a novel fungal expression host. PhD-thesis, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium, 308 p. ISBN-number: 978-90-5989-176-0 The author and the promotors give the authorisation to consult and to copy parts of this work for personal use only. Every other use is subject to copy right laws. Permission to reproduce any material contained in this work should be obtained from the author. -
Identification and Phylogeny of Ascomycetous Yeasts from Analysis
Antonie van Leeuwenhoek 73: 331–371, 1998. 331 © 1998 Kluwer Academic Publishers. Printed in the Netherlands. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences Cletus P. Kurtzman∗ & Christie J. Robnett Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Ser- vice, U.S. Department of Agriculture, Peoria, Illinois 61604, USA (∗ author for correspondence) E-mail: [email protected] Received 19 June 1998; accepted 19 June 1998 Key words: Ascomycetous yeasts, phylogeny, ribosomal DNA, systematics Abstract Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported. Introduction lesser ranges of nDNA relatedness than those found among heterothallic species. Disadvantages of nDNA reassociation studies in- Procedures commonly used for yeast identification clude the need for pairwise comparisons of all isolates rely on the appearance of cellular morphology and dis- under study and that resolution is limited to the ge- tinctive reactions on a standardized set of fermentation netic distance of sister species, i.e., closely related and assimilation tests. -
Phylogenetic Circumscription of Saccharomyces, Kluyveromyces
FEMS Yeast Research 4 (2003) 233^245 www.fems-microbiology.org Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora Cletus P. Kurtzman à Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University Street, Peoria, IL 61604, USA Received 22 April 2003; received in revised form 23 June 2003; accepted 25 June 2003 First published online Abstract Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417^432] resolved the family Saccharomycetaceae into 11 well-supported clades. In the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. ß 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. Keywords: Saccharomyces; Kluyveromyces; New ascosporic yeast genera; Molecular systematics; Multigene phylogeny 1. Introduction support the maintenance of three distinct genera. Yarrow [8^10] revived the concept of three genera and separated The name Saccharomyces was proposed for bread and Torulaspora and Zygosaccharomyces from Saccharomyces, beer yeasts by Meyen in 1838 [1], but it was Reess in 1870 although species assignments were often di⁄cult. -
Oxylipin Distribution in Eremothecium
1 Oxylipin distribution in Eremothecium by Ntsoaki Joyce Leeuw Submitted in accordance with the requirements for the degree Magister Scientiae in the Department of Microbial, Biochemical and Food Biotechnology Faculty of Natural and Agricultural Sciences University of the Free State Bloemfontein South Africa Supervisor: Prof J.L.F. Kock Co- supervisors: Dr C.H. Pohl Prof P.W.J. Van Wyk November 2006 2 This dissertation is dedicated to the following people: My mother (Nkotseng Leeuw) My brother (Kabelo Leeuw) My cousins (Bafokeng, Lebohang, Mami, Thabang and Rorisang) Mr. Eugean Malebo 3 ACKNOWLEDGEMENTS I wish to thank and acknowledge the following: ) God, to You be the glory for the things You have done in my life. ) My family (especially my mom) – for always being there for me when I’m in need. ) Prof. J.L.F Kock for his patience, constructive criticisms and guidance during the course of this study. ) Dr. C.H. Pohl for her encouragement and assistance in the writing up of this dissertation. ) Mr. P.J. Botes for assistance with the GC-MS. ) Prof. P.W.J. Van Wyk and Miss B. Janecke for assistance with the CLSM and SEM. ) My fellow colleagues (especially Chantel and Desmond) for their assistance, support and encouragement. ) Mr. Eugean Malebo for always being there when I needed you. 4 CONTENTS Page Title page I Acknowledgements II Contents III CHAPTER 1 Introduction 1.1 Motivation 2 1.2 Definition and classification of yeasts 3 1.3 Classification of Eremothecium and related genera 5 1.4 Pathogenicity 12 1.5 Oxylipins 13 1.5.1 Definition -
Phylogenetic Circumscription of Saccharomyces, Kluyveromyces
FEMS Yeast Research 4 (2003) 233^245 www.fems-microbiology.org Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora Downloaded from https://academic.oup.com/femsyr/article-abstract/4/3/233/562841 by guest on 29 May 2020 Cletus P. Kurtzman à Microbial Genomics and Bioprocessing Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 N. University Street, Peoria, IL 61604, USA Received 22 April 2003; received in revised form 23 June 2003; accepted 25 June 2003 First published online Abstract Genera currently assigned to the Saccharomycetaceae have been defined from phenotype, but this classification does not fully correspond with species groupings determined from phylogenetic analysis of gene sequences. The multigene sequence analysis of Kurtzman and Robnett [FEMS Yeast Res. 3 (2003) 417^432] resolved the family Saccharomycetaceae into 11 well-supported clades. In the present study, the taxonomy of the Saccharomyctaceae is evaluated from the perspective of the multigene sequence analysis, which has resulted in reassignment of some species among currently accepted genera, and the proposal of the following five new genera: Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. ß 2003 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved. Keywords: Saccharomyces; Kluyveromyces; New ascosporic yeast genera; Molecular systematics; Multigene phylogeny 1. Introduction support the maintenance of three distinct genera. Yarrow [8^10] revived the concept of three genera and separated The name Saccharomyces was proposed for bread and Torulaspora and Zygosaccharomyces from Saccharomyces, beer yeasts by Meyen in 1838 [1], but it was Reess in 1870 although species assignments were often di⁄cult. -
Ashbya Gossypii Beyond Industrial Riboflavin Production
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Universidade do Minho: RepositoriUM JBA-06974; No of Pages 13 Biotechnology Advances xxx (2015) xxx–xxx Contents lists available at ScienceDirect Biotechnology Advances journal homepage: www.elsevier.com/locate/biotechadv Research review paper Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications Tatiana Q. Aguiar 1,RuiSilva1, Lucília Domingues ⁎ CEB − Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal article info abstract Article history: The filamentous fungus Ashbya gossypii has been safely and successfully used for more than two decades in the Received 28 May 2015 commercial production of riboflavin (vitamin B2). Its industrial relevance combined with its high genetic similar- Received in revised form 28 September 2015 ity with Saccharomyces cerevisiae together promoted the accumulation of fundamental knowledge that has been Accepted 4 October 2015 efficiently converted into a significant molecular and in silico toolbox for its genetic engineering. This synergy has Available online xxxx enabled a directed and sustained exploitation of A. gossypii as an industrial riboflavin producer. Although there is fl Keywords: still room for optimizing ribo avin production, the recent years have seen an abundant advance in the explora- Ashbya gossypii tion of A. gossypii for other biotechnological applications, such as the production of recombinant proteins, single Physiology cell oil and flavour compounds. Here, we will address the biotechnological potential of A. gossypii beyond ribofla- Metabolism vin production by presenting (a) a physiological and metabolic perspective over this fungus; (b) the molecular Genetic engineering toolbox available for its manipulation; and (c) commercial and emerging biotechnological applications for this Riboflavin industrially important fungus, together with the approaches adopted for its engineering. -
Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two
(topsheet) Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113. Fieldiana, Botany H. Thorsten Lumbsch Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7881 fax: 312-665-7158 e-mail: [email protected] Sabine M. Huhndorf Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7855 fax: 312-665-7158 e-mail: [email protected] 1 (cover page) FIELDIANA Botany NEW SERIES NO 00 Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 H. Thorsten Lumbsch Sabine M. Huhndorf [Date] Publication 0000 PUBLISHED BY THE FIELD MUSEUM OF NATURAL HISTORY 2 Table of Contents Abstract Part One. Outline of Ascomycota - 2009 Introduction Literature Cited Index to Ascomycota Subphylum Taphrinomycotina Class Neolectomycetes Class Pneumocystidomycetes Class Schizosaccharomycetes Class Taphrinomycetes Subphylum Saccharomycotina Class Saccharomycetes Subphylum Pezizomycotina Class Arthoniomycetes Class Dothideomycetes Subclass Dothideomycetidae Subclass Pleosporomycetidae Dothideomycetes incertae sedis: orders, families, genera Class Eurotiomycetes Subclass Chaetothyriomycetidae Subclass Eurotiomycetidae Subclass Mycocaliciomycetidae Class Geoglossomycetes Class Laboulbeniomycetes Class Lecanoromycetes Subclass Acarosporomycetidae Subclass Lecanoromycetidae Subclass Ostropomycetidae 3 Lecanoromycetes incertae sedis: orders, genera Class Leotiomycetes Leotiomycetes incertae sedis: families, genera Class Lichinomycetes Class Orbiliomycetes Class Pezizomycetes Class Sordariomycetes Subclass Hypocreomycetidae Subclass Sordariomycetidae Subclass Xylariomycetidae Sordariomycetes incertae sedis: orders, families, genera Pezizomycotina incertae sedis: orders, families Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 Introduction Literature Cited 4 Abstract Part One presents the current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota. -
7.5 X 11.5.Doubleline.P65
Cambridge University Press 978-0-521-01483-0 - Introduction to Fungi, Third Edition John Webster and Roland Weber Table of Contents More information Contents Preface to the first edition page xiii Preface to the second edition xv Preface to the third edition xvii Acknowledgements xix Chapter 1 Introduction 1 1.1 What are fungi? 1 1.2 Physiology of the growing hypha 3 1.3 Hyphal aggregates 14 1.4 Spores of fungi 22 1.5 Taxonomy of fungi 32 Chapter 2 Protozoa: Myxomycota (slime moulds) 40 2.1 Introduction 40 2.2 Acrasiomycetes: acrasid cellular slime moulds 40 2.3 Dictyosteliomycetes: dictyostelid slime moulds 41 2.4 Protosteliomycetes: protostelid plasmodial slime moulds 45 2.5 Myxomycetes: true (plasmodial) slime moulds 47 Chapter 3 Protozoa: Plasmodiophoromycota 54 3.1 Introduction 54 3.2 Plasmodiophorales 54 3.3 Control of diseases caused by Plasmodiophorales 62 3.4 Haptoglossa (Haptoglossales) 64 Chapter 4 Straminipila: minor fungal phyla 67 4.1 Introduction 67 4.2 The straminipilous flagellum 68 4.3 Hyphochytriomycota 70 4.4 Labyrinthulomycota 71 Chapter 5 Straminipila: Oomycota 75 5.1 Introduction 75 5.2 Saprolegniales 79 5.3 Pythiales 95 5.4 Peronosporales 115 5.5 Sclerosporaceae 125 © Cambridge University Press www.cambridge.org Cambridge University Press 978-0-521-01483-0 - Introduction to Fungi, Third Edition John Webster and Roland Weber Table of Contents More information viii CONTENTS Chapter 6 Chytridiomycota 127 6.1 Introduction 127 6.2 Chytridiales 134 6.3 Spizellomycetales 145 6.4 Neocallimastigales (rumen fungi) 150 6.5 -
The Yeast Handbook Carlos Rosa, Gábor Péter (Eds.)
The Yeast Handbook Carlos Rosa, Gábor Péter (Eds.) Biodiversity and Ecophysiology of Yeasts With 40 Figures and 43 Tables Dr. Gábor Péter Professor Carlos Rosa Budapest University of Economic Departmento de Microbiologia Sciences and Public Administration ICB, CP 486 Faculty of Food Sciences Universidade Federal de Minas Gerais National Collection of Agricultural and Belo Horizonte, MG Industrial Microorganisms 31270-901 Somloi út 14-16 Brazil H-1118 Budapest Hungary Cover pictures by courtesy of: Vincent Robert, Centraalbureau voor Schimmelcultures (CBS), The Netherlands Carlos Rosa, Universidade Federal de Minas Gerais, Brazil ISBN-10 3-540-26100-1 Springer Berlin Heidelberg New York ISBN-13 978-3-540-26100-1 Springer Berlin Heidelberg New York Library of Congress Control Number: 2005930628 This work is subject to copyright. All rights are reserved, whether the whole or part of the mate- rial is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recita- tion, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. Springer-Verlag is a part of Springer Science+Business Media springeronline.com © Springer-Verlag Berlin Heidelberg 2006 Printed in Germany The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. -
Ashbya Gossypii Beyond Industrial Riboflavin Production
JBA-06974; No of Pages 13 Biotechnology Advances xxx (2015) xxx–xxx Contents lists available at ScienceDirect Biotechnology Advances journal homepage: www.elsevier.com/locate/biotechadv Research review paper Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications Tatiana Q. Aguiar 1,RuiSilva1, Lucília Domingues ⁎ CEB − Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal article info abstract Article history: The filamentous fungus Ashbya gossypii has been safely and successfully used for more than two decades in the Received 28 May 2015 commercial production of riboflavin (vitamin B2). Its industrial relevance combined with its high genetic similar- Received in revised form 28 September 2015 ity with Saccharomyces cerevisiae together promoted the accumulation of fundamental knowledge that has been Accepted 4 October 2015 efficiently converted into a significant molecular and in silico toolbox for its genetic engineering. This synergy has Available online xxxx enabled a directed and sustained exploitation of A. gossypii as an industrial riboflavin producer. Although there is fl Keywords: still room for optimizing ribo avin production, the recent years have seen an abundant advance in the explora- Ashbya gossypii tion of A. gossypii for other biotechnological applications, such as the production of recombinant proteins, single Physiology cell oil and flavour compounds. Here, we will address the biotechnological potential of A. gossypii beyond ribofla- Metabolism vin production by presenting (a) a physiological and metabolic perspective over this fungus; (b) the molecular Genetic engineering toolbox available for its manipulation; and (c) commercial and emerging biotechnological applications for this Riboflavin industrially important fungus, together with the approaches adopted for its engineering. -
Outline of Ascomycota - 2007
ISSN 1403-1418 VOLUME 13 DECEMBER 31, 2007 Outline of Ascomycota - 2007 H. Thorsten Lumbsch and Sabine M. Huhndorf (eds.) The Field Museum, Department of Botany, Chicago, USA Abstract Lumbsch, H. T. and S.M. Huhndorf (ed.) 2007. Outline of Ascomycota – 2007. Myconet 13: 1 - 58. The present classification contains all accepted genera and higher taxa above the generic level in phylum Ascomycota. Introduction The present classification is based in part on earlier versions published in Systema Ascomycetum and Myconet (see http://www.fieldmuseum.org/myconet/) and reflects the numerous changes made in the Deep Hypha issue of Mycologia (Spatafora et al. 2006), in Hibbett et al. (2007) and those listed in Myconet Notes Nos. 4408-4750 (Lumbsch & Huhndorf 2007). It includes all accepted genera and higher taxa of Ascomycota. New synonymous generic names are included in the outline. In future outlines attempts will be made to incorporate all synonymous generic names (for a list of synonymous generic names, see Eriksson & Hawksworth 1998). A question mark (?) indicates that the position of the taxon is uncertain. Eriksson O.E. & Hawksworth D.L. 1998. Outline of the ascomycetes - 1998. - Systema Ascomycetum 16: 83-296. Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M., Lucking, R., Lumbsch, H.T., Lutzoni, F., Matheny, P.B., McLaughlin, D.J., Powell, M.J., Redhead, S., Schoch, C.L., Spatafora, J.W., Stalpers, J.A., Vilgalys, R., Aime, M.C., Aptroot, A., Bauer, R., Begerow, D., -
7.5 X 11.5.Doubleline.P65
Cambridge University Press 978-0-521-80739-5 - Introduction to Fungi, Third Edition John Webster and Roland Weber Table of Contents More information Contents Preface to the first edition page xiii Preface to the second edition xv Preface to the third edition xvii Acknowledgements xix Chapter 1 Introduction 1 1.1 What are fungi? 1 1.2 Physiology of the growing hypha 3 1.3 Hyphal aggregates 14 1.4 Spores of fungi 22 1.5 Taxonomy of fungi 32 Chapter 2 Protozoa: Myxomycota (slime moulds) 40 2.1 Introduction 40 2.2 Acrasiomycetes: acrasid cellular slime moulds 40 2.3 Dictyosteliomycetes: dictyostelid slime moulds 41 2.4 Protosteliomycetes: protostelid plasmodial slime moulds 45 2.5 Myxomycetes: true (plasmodial) slime moulds 47 Chapter 3 Protozoa: Plasmodiophoromycota 54 3.1 Introduction 54 3.2 Plasmodiophorales 54 3.3 Control of diseases caused by Plasmodiophorales 62 3.4 Haptoglossa (Haptoglossales) 64 Chapter 4 Straminipila: minor fungal phyla 67 4.1 Introduction 67 4.2 The straminipilous flagellum 68 4.3 Hyphochytriomycota 70 4.4 Labyrinthulomycota 71 Chapter 5 Straminipila: Oomycota 75 5.1 Introduction 75 5.2 Saprolegniales 79 5.3 Pythiales 95 5.4 Peronosporales 115 5.5 Sclerosporaceae 125 © Cambridge University Press www.cambridge.org Cambridge University Press 978-0-521-80739-5 - Introduction to Fungi, Third Edition John Webster and Roland Weber Table of Contents More information viii CONTENTS Chapter 6 Chytridiomycota 127 6.1 Introduction 127 6.2 Chytridiales 134 6.3 Spizellomycetales 145 6.4 Neocallimastigales (rumen fungi) 150 6.5