Ashbya Gossypii Beyond Industrial Riboflavin Production
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Final 130607
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. -
Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)
| YEASTBOOK GENOME ORGANIZATION AND INTEGRITY Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina) Bernard A. Dujon*,†,1 and Edward J. Louis‡,§ *Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France, †University Pierre and Marie Curie UFR927, 75005 Paris, France, ‡Centre for Genetic Architecture of Complex Traits, and xDepartment of Genetics, University of Leicester, LE1 7RH, United Kingdom ORCID ID: 0000-0003-1157-3608 (E.J.L.) ABSTRACT Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. -
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 -
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. -
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. -
Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases LÁSZLÓ G
Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases LÁSZLÓ G. NAGY,1 RENÁTA TÓTH,2 ENIKŐ KISS,1 JASON SLOT,3 ATTILA GÁCSER,2 and GÁBOR M. KOVÁCS4,5 1Synthetic and Systems Biology Unit, Institute of Biochemistry, HAS, Szeged, Hungary; 2Department of Microbiology, University of Szeged, Szeged, Hungary; 3Department of Plant Pathology, Ohio State University, Columbus, OH 43210; 4Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary; 5Plant Protection Institute, Center for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary ABSTRACT The fungal lineage is one of the three large provides an overview of some of the most important eukaryotic lineages that dominate terrestrial ecosystems. fungal traits, how they evolve, and what major genes They share a common ancestor with animals in the eukaryotic and gene families contribute to their development. The supergroup Opisthokonta and have a deeper common ancestry traits highlighted here represent just a sample of the with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among characteristics that have evolved in fungi, including po- all living organisms. This article provides an overview of some of larized multicellular growth, fruiting body development, the most important fungal traits, how they evolve, and what dimorphism, secondary metabolism, wood decay, and major genes and gene families contribute to their development. mycorrhizae. However, a great deal of other important The traits highlighted here represent just a sample of the traits also underlie the evolution of the taxonomically characteristics that have evolved in fungi, including polarized and phenotypically hyperdiverse fungal kingdom, which multicellular growth, fruiting body development, dimorphism, could fill up a volume on its own. -
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. -
Eremothecium Coryli によるダイズ子実汚斑病(新称)
日植病報 73: 283–288(2007)4 Jpn. J. Phytopathol. 73: 283–288 (2007) Eremothecium coryli によるダイズ子実汚斑病(新称) 木村 重光 1* ABSTRACT KIMURA, S. (2007). Yeast-spot disease of soybean caused by Eremothecium coryli (Peglion) Kurtzman in Japan. Jpn. J. Phythopathol. 73: 283–288. An ascomycetous, yeast-like fungus was isolated from lesions of soybean (cv. Murasakizukin) seeds that had been sucked by pentato- mid bugs (Hemiptera: Pentatomidae) in Kyoto prefecture. Based on morphological and physiological characteristics and sequence data of the internal transcribed spacer (ITS) regions including 5.8S rDNA, these yeast-like fungi were identified as Eremothecium coryli (Peglion) Kurtzman (syn. Nematospora coryli). After healthy, immature soybean seeds (cv. Maihime and Enrei) were inoculated with the isolated fungus, symptoms of the disease were reproduced, and the fungus was reisolated from the lesions. This fungus is widely known as causing a “yeast-spot disease” pathogen of soybean seeds, but has not previously been reported in Japan. Thus, the common name yeast spot (‘Shijitsu-ohan-byo’ in Japanese) is proposed for this disease of soybean. (Received October 23, 2006; Accepted February 28, 2007) Key words: Eremothecium coryli, shijitsu-ohan-byo, yeast-spot disease, soybean, pentatomid bugs れており,その地域も,南北アメリカ,ヨーロッパ,アジア, 緒 言 アフリカ,オーストラリアと全世界的である.本菌による病 京都府特産の黒大豆(品種:新丹波黒)は,丹波,丹後地 害は,Ashby and Nowell(1926)により“Stigmatomycosis”と 域を中心に約 260 ha 栽培されている.また近年,枝豆として いう病名が与えられているが Preston and Ray(1943)および 出荷し,ブランド京野菜「紫ずきん」として販売される黒大 Lehman(1943)がダイズから N. coryli を分離したそれぞれ 豆(品種:紫ずきんおよび新丹波黒)も約 50 ha に面積を拡 の報告において“yeast-spot disease”を病名に用いており, 大してきた.子実害虫の防除は莢伸長期から殺虫剤をスケ 以降ダイズにおいては“yeast spot”が用いられている.ま ジュール散布することで行っているが,その被害は決して少 た,本菌は,Daugherty(1967)によりカメムシ類によりダ ないとはいえない.特に,カメムシ類の吸汁による子実の奇 イズへ伝搬されることが明らかにされている. 形や陥没は,商品化率を低下させ大きな損失をもたらしてい 本研究では,観察された酵母様微生物と Nematospora 属菌 る.そのような被害粒を切断すると,子実内部が汚白色に変 との関係およびカメムシ類によるダイズ被害粒症状との関 色し,周囲に壊死を伴うもの(Fig. -
A Worldwide List of Endophytic Fungi with Notes on Ecology and Diversity
Mycosphere 10(1): 798–1079 (2019) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/10/1/19 A worldwide list of endophytic fungi with notes on ecology and diversity Rashmi M, Kushveer JS and Sarma VV* Fungal Biotechnology Lab, Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Pondicherry 605014, Puducherry, India Rashmi M, Kushveer JS, Sarma VV 2019 – A worldwide list of endophytic fungi with notes on ecology and diversity. Mycosphere 10(1), 798–1079, Doi 10.5943/mycosphere/10/1/19 Abstract Endophytic fungi are symptomless internal inhabits of plant tissues. They are implicated in the production of antibiotic and other compounds of therapeutic importance. Ecologically they provide several benefits to plants, including protection from plant pathogens. There have been numerous studies on the biodiversity and ecology of endophytic fungi. Some taxa dominate and occur frequently when compared to others due to adaptations or capabilities to produce different primary and secondary metabolites. It is therefore of interest to examine different fungal species and major taxonomic groups to which these fungi belong for bioactive compound production. In the present paper a list of endophytes based on the available literature is reported. More than 800 genera have been reported worldwide. Dominant genera are Alternaria, Aspergillus, Colletotrichum, Fusarium, Penicillium, and Phoma. Most endophyte studies have been on angiosperms followed by gymnosperms. Among the different substrates, leaf endophytes have been studied and analyzed in more detail when compared to other parts. Most investigations are from Asian countries such as China, India, European countries such as Germany, Spain and the UK in addition to major contributions from Brazil and the USA.