Observation of the Yeasts
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Expanding the Knowledge on the Skillful Yeast Cyberlindnera Jadinii
Journal of Fungi Review Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii Maria Sousa-Silva 1,2 , Daniel Vieira 1,2, Pedro Soares 1,2, Margarida Casal 1,2 and Isabel Soares-Silva 1,2,* 1 Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; [email protected] (M.S.-S.); [email protected] (D.V.); [email protected] (P.S.); [email protected] (M.C.) 2 Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal * Correspondence: [email protected]; Tel.: +351-253601519 Abstract: Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. -
A Curated Ortholog Database for Yeasts and Fungi Spanning 600 Million Years of Evolution
bioRxiv preprint doi: https://doi.org/10.1101/237974; this version posted October 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution Kevin Correia1, Shi M. Yu1, and Radhakrishnan Mahadevan1,2,* 1Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada, ON 2Institute of Biomaterials and Biomedical Engineering, University of Toronto, Ontario, Canada Corresponding author: Radhakrishnan Mahadevan∗ Email address: [email protected] ABSTRACT Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution. OrthoMCL and OrthoDB were used to cluster protein sequence into ortholog and homolog groups, respectively; MAFFT and PhyML were used to reconstruct the phylogeny of all homolog groups. Ortholog assignments for enzymes and small metabolite transporters were compared to their phylogenetic reconstruction, and curated to resolve any discrepancies. Information on homolog and ortholog groups can be viewed in the AYbRAH web portal (https://kcorreia.github. io/aybrah/) to review ortholog groups, predictions for mitochondrial localization and transmembrane domains, literature references, and phylogenetic reconstructions. -
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. -
Taxonomy of Yeasts
^ÍV/-^ TECHmcAL BULLETIN NO. 1029 May 1951 .— 5 Taxonomy of Yeasts By LYNFERD J. WICKERHAM Zymologist Northern Regional Research Laboratory Bureau of Agricultural and Industrial Chemistry Agricultural Research Administration -- ! f^ R A R Y Jüri¿ 51951 U.Î. ainnrmm sf A«RIOüLTURí UNITED STATES DEPARTMENT OF AcKictrLTURE, WASHINGTON, D. C. PREFACE In early attempts at yeast classification, the characteristics em- ployed for separating the larger groups of yeasts were the ability to grow as filaments, the ability to produce asci which consist of two cells fused together, the shape of the ascospores, the ability to pro- duce a gaseous fermentation of one or more sugars, and the ability to produce pellicles on liquid media. Evidence obtained in the present study indicates that the use of the foregoing characteristics led to the unintentional cleavage of natural, or phylogenetic groups into sections. Moreover, sections of different phylogenetic lines which had in common only one or two of the characteristics just mentioned were often assembled into the same genus. These characteristics, applied by Hansen, Barker, and Klocker dur- ing the early 1900's, continue in use as the basis for separating genera and subgenera in the presently accepted system of yeast classification. As a result, all of the larger genera of both the ascosporogenous and nonascosporogenous yeasts contain dissimilar types. The mixing has been thorough—in many cases the true relationships which exist among species of the different genera have been concealed. Correction of this situation by the arrangement of species m what appear to be phylogenetic lines of related species is believed to be a major advance. -
PDF) S2 Table
RESEARCH ARTICLE Dramatically diverse Schizosaccharomyces pombe wtf meiotic drivers all display high gamete-killing efficiency 1 1 1 MarõÂa AngeÂlica Bravo Nu ñezID , Ibrahim M. SabbariniID , Michael T. Eickbush , 1 1 1 1,2 Yue LiangID , Jeffrey J. LangeID , Aubrey M. KentID , Sarah E. ZandersID * 1 Stowers Institute for Medical Research, Kansas City, Missouri, United States of America, 2 Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Meiotic drivers are selfish alleles that can force their transmission into more than 50% of the viable gametes made by heterozygotes. Meiotic drivers are known to cause infertility in a OPEN ACCESS diverse range of eukaryotes and are predicted to affect the evolution of genome structure Citation: Bravo NuÂñez MA, Sabbarini IM, Eickbush and meiosis. The wtf gene family of Schizosaccharomyces pombe includes both meiotic MT, Liang Y, Lange JJ, Kent AM, et al. (2020) drivers and drive suppressors and thus offers a tractable model organism to study drive sys- Dramatically diverse Schizosaccharomyces pombe tems. Currently, only a handful of wtf genes have been functionally characterized and those wtf meiotic drivers all display high gamete-killing genes only partially reflect the diversity of the wtf gene family. In this work, we functionally efficiency. PLoS Genet 16(2): e1008350. https:// doi.org/10.1371/journal.pgen.1008350 test 22 additional wtf genes for meiotic drive phenotypes. We identify eight new drivers that share between 30±90% amino acid identity with previously characterized drivers. Despite Editor: Kelly A. -
Study of Cellular Processes in Higher Eukaryotes Using the Yeast Schizosaccharomyces Pombe As a Model
Chapter 6 Study of Cellular Processes in Higher Eukaryotes Using the Yeast Schizosaccharomyces pombe as a Model Nora Hilda Rosas-Murrieta, Guadalupe Rojas-Sánchez, Sandra R. Reyes-Carmona, Rebeca D. Martínez-Contreras, Nancy Martínez-Montiel, Lourdes Millán-Pérez-Peña and Irma P. Herrera-Camacho Additional information is available at the end of the chapter http://dx.doi.org/10.5772/60720 Abstract Schizosaccharomyces pombe (Sz. pombe), or fission yeast, is an ascomycete unicellular fungus that has been used as a model system for studying diverse biological processes of higher eukaryotic cells, such as the cell cycle and the maintenance of cell shape, apoptosis, and ageing. Sz. pombe is a rod-shaped cell that grows by apical extension; it divides along the long axis by medial fission and septation. The fission yeast has a doubling time of 2–4 hours, it is easy and inexpensive to grow in simple culture conditions, and can be maintained in the haploid or the diploid state. Sz. pombe can be genetically manipulated using methods such as mutagenesis or gene disruption by homologous recombination. Fission yeast was defined as a micro-mammal because it shares many molecular, genetic, and biochemical features with cells of higher eukaryotes in mRNA splicing, post-translational modifications as N-glycosylation protein, cell-cycle regulation, nutrient-sensing pathways as the target of rapamycin (TOR) network, cAMP-PKA pathway, and autophagy. This chapter uses Sz. pombe as a useful model for studying important cellular processes that support life such as autophagy, apoptosis, and the ageing process. Therefore, the molecular analysis of these processes in fission yeast has the potential to generate new knowledge that could be applied to higher eukaryotes. -
The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México
Journal of Fungi Article The Abundance and Diversity of Fungi in a Hypersaline Microbial Mat from Guerrero Negro, Baja California, México Paula Maza-Márquez 1,*, Michael D. Lee 1,2 and Brad M. Bebout 1 1 Exobiology Branch, NASA Ames Research Center, Moffett Field, CA 94035, USA; [email protected] (M.D.L.); [email protected] (B.M.B.) 2 Blue Marble Space Institute of Science, Seattle, WA 98104, USA * Correspondence: [email protected] Abstract: The abundance and diversity of fungi were evaluated in a hypersaline microbial mat from Guerrero Negro, México, using a combination of quantitative polymerase chain reaction (qPCR) amplification of domain-specific primers, and metagenomic sequencing. Seven different layers were analyzed in the mat (Layers 1–7) at single millimeter resolution (from the surface to 7 mm in depth). The number of copies of the 18S rRNA gene of fungi ranged between 106 and 107 copies per g mat, being two logarithmic units lower than of the 16S rRNA gene of bacteria. The abundance of 18S rRNA genes of fungi varied significantly among the layers with layers 2–5 mm from surface contained the highest numbers of copies. Fifty-six fungal taxa were identified by metagenomic sequencing, classified into three different phyla: Ascomycota, Basidiomycota and Microsporidia. The prevalent genera of fungi were Thermothelomyces, Pyricularia, Fusarium, Colletotrichum, Aspergillus, Botrytis, Candida and Neurospora. Genera of fungi identified in the mat were closely related to genera known to have saprotrophic and parasitic lifestyles, as well as genera related to human and plant pathogens and fungi able to perform denitrification. -
Yarrowia Lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement
Journal of Fungi Review Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement Catherine Madzak † Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, F-78850 Thiverval-Grignon, France; [email protected] † INRAE Is France’s New National Research Institute for Agriculture, Food and Environment, Created on 1 January 2020 by the Merger of INRA, the National Institute for Agricultural Research, and IRSTEA, the National Research Institute of Science and Technology for the Environment and Agriculture. Abstract: Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill Citation: Madzak, C. Yarrowia this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by lipolytica Strains and Their illustrating the search for new genetic backgrounds and by providing data about the main publicly Biotechnological Applications: How available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances Natural Biodiversity and Metabolic in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Engineering Could Contribute to Cell Yarrowia lipolytica and of other yeasts from the Yarrowia clade. -
The 100 Years of the Fungus Collection Mucl 1894-1994
THE 100 YEARS OF THE FUNGUS COLLECTION MUCL 1894-1994 Fungal Taxonomy and Tropical Mycology: Quo vadis ? Taxonomy and Nomenclature of the Fungi Grégoire L. Hennebert Catholic University of Louvain, Belgium Notice of the editor This document is now published as an archive It is available on www.Mycotaxon.com It is also produced on CD and in few paperback copies G. L. Hennebert ed. Published by Mycotaxon, Ltd. Ithaca, New York, USA December 2010 ISBN 978-0-930845-18-6 (www pdf version) ISBN 978-0-930845-17-9 (paperback version) DOI 10.5248/2010MUCL.pdf 1894-1994 MUCL Centenary CONTENTS Lists of participants 8 Forword John Webser 13 PLENARY SESSION The 100 Year Fungus Culture Collection MUCL, June 29th, 1994 G.L. Hennebert, UCL Mycothèque de l'Université Catholique de Louvain (MUCL) 17 D. Hawksworth, IMI, U.K. Fungal genetic resource collections and biodiversity. 27 D. van der Mei, CBS, MINE, Netherlands The fungus culture collections in Europe. 34 J. De Brabandere, BCCM, Belgium The Belgian Coordinated Collections of Microorganisms. 40 Fungal Taxonomy and tropical Mycology G.L. Hennebert, UCL Introduction. Fungal taxonomy and tropical mycology: Quo vadis ? 41 C.P. Kurtzman, NRRL, USA Molecular taxonomy in the yeast fungi: present and future. 42 M. Blackwell, Louisiana State University, USA Phylogeny of filamentous fungi deduced from analysis of molecular characters: present and future. 52 J. Rammeloo, National Botanical Garden, Belgium Importance of morphological and anatomical characters in fungal taxonomy. 57 M.F. Roquebert, Natural History Museum, France Possible progress of modern morphological analysis in fungal taxonomy. 63 A.J. -
10.1101/2020.07.29.227421; This Version Posted July 30, 2020
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.29.227421; this version posted July 30, 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. 1 Title: Genomic insights into the host specific adaptation of the Pneumocystis genus and 2 emergence of the human pathogen Pneumocystis jirovecii 3 4 Short title: Pneumocystis fungi adaptation to mammals 5 6 Authors: Ousmane H. Cissé1*†, Liang Ma1*†, John P. Dekker2,3, Pavel P. Khil2,3, Jung-Ho 7 Youn3, Jason M. Brenchley4, Robert Blair5, Bapi Pahar5, Magali Chabé6, Koen K.A. Van 8 Rompay7, Rebekah Keesler7, Antti Sukura8, Vanessa Hirsch9, Geetha Kutty1, Yueqin Liu 9 1, Peng Li10, Jie Chen10, Jun Song11, Christiane Weissenbacher-Lang12, Jie Xu11, Nathan 10 S. Upham13, Jason E. Stajich14, Christina A. Cuomo15, Melanie T. Cushion16 and Joseph 11 A. Kovacs1* 12 13 Affiliations: 1 Critical Care Medicine Department, NIH Clinical Center, National 14 Institutes of Health, Bethesda, Maryland, USA. 2 Bacterial Pathogenesis and 15 Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases, 16 National Institutes of Health, Bethesda, Maryland, USA. 3 Department of Laboratory 17 Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA. 18 4 Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, 19 National Institutes of Health, Bethesda, Maryland, USA. 5 Tulane National Primate 20 Research Center, Tulane University, New Orleans, Louisiana, USA. 6 Univ. Lille, CNRS, 21 Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection 22 et d'Immunité de Lille, Lille, France. -
An Ancient Yeast for Young Geneticists: a Primer on the Schizosaccharomyces Pombe Model System
GENETICS | PRIMER An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System Charles S. Hoffman,*,1 Valerie Wood,† and Peter A. Fantes‡,2 *Biology Department, Boston College, Chestnut Hill, Massachusetts 02467, yCambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, United Kingdom, and School of Biological Sciences, College of Science and Engineering, University of Edinburgh EH9 3JR Edinburgh, United Kingdom ORCID IDs: 0000-0001-8700-1863 (C.S.H.); 0000-0001-6330-7526 (V.W.) ABSTRACT The fission yeast Schizosaccharomyces pombe is an important model organism for the study of eukaryotic molecular and cellular biology. Studies of S. pombe, together with studies of its distant cousin, Saccharomyces cerevisiae, have led to the discovery of genes involved in fundamental mechanisms of transcription, translation, DNA replication, cell cycle control, and signal transduction, to name but a few processes. However, since the divergence of the two species approximately 350 million years ago, S. pombe appears to have evolved less rapidly than S. cerevisiae so that it retains more characteristics of the common ancient yeast ancestor, causing it to share more features with metazoan cells. This Primer introduces S. pombe by describing the yeast itself, providing a brief description of the origins of fission yeast research, and illustrating some genetic and bioinformatics tools used to study protein function in fission yeast. In addition, a section on some key differences between S. pombe and S. cerevisiae is included for readers with some familiarity with budding yeast research but who may have an interest in developing research projects using S. -
Schizosaccharomyces Pombe: a Promising Biotechnology for Modulating Wine Composition
fermentation Review Schizosaccharomyces pombe: A Promising Biotechnology for Modulating Wine Composition Iris Loira * ID , Antonio Morata ID , Felipe Palomero, Carmen González and José Antonio Suárez-Lepe Departamento de Química y Tecnología de Alimentos, Universidad Politécnica de Madrid, Av. Puerta de Hierro, nº 2, 28040 Madrid, Spain; [email protected] (A.M.), [email protected] (F.P.); [email protected] (C.G.); [email protected] (J.A.S.-L.) * Correspondence: [email protected] Received: 26 July 2018; Accepted: 21 August 2018; Published: 23 August 2018 Abstract: There are numerous yeast species related to wine making, particularly non-Saccharomyces, that deserve special attention due to the great potential they have when it comes to making certain changes in the composition of the wine. Among them, Schizosaccharomyces pombe stands out for its particular metabolism that gives it certain abilities such as regulating the acidity of wine through maloalcoholic fermentation. In addition, this species is characterized by favouring the formation of stable pigments in wine and releasing large quantities of polysaccharides during ageing on lees. Moreover, its urease activity and its competition for malic acid with lactic acid bacteria make it a safety tool by limiting the formation of ethyl carbamate and biogenic amines in wine. However, it also has certain disadvantages such as its low fermentation speed or the development of undesirable flavours and aromas. In this chapter, the main oenological uses of Schizosaccharomyces pombe that have been proposed in recent years will be reviewed and discussed. Keywords: Schizosaccharomyces pombe; oenological uses; maloalcoholic fermentation; stable pigments; wine safety 1.