Research Article Reconstructing the Backbone of the Saccharomycotina
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Evolution and Application of Inteins in Candida Species: a Review
fmicb-07-01585 October 6, 2016 Time: 13:7 # 1 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Frontiers - Publisher Connector REVIEW published: 10 October 2016 doi: 10.3389/fmicb.2016.01585 Evolution and Application of Inteins in Candida species: A Review José A. L. Fernandes1†, Tâmara H. R. Prandini2†, Maria da Conceição A. Castro1, Thales D. Arantes1,3, Juliana Giacobino2, Eduardo Bagagli2 and Raquel C. Theodoro1* 1 Institute of Tropical Medicine of Rio Grande do Norte, Universidade Federal do Rio Grande do Norte, Natal, Brazil, 2 Department of Microbiology and Immunology, Institute of Biosciences, Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Brazil, 3 Post-graduation Program in Biochemistry, Universidade Federal do Rio Grande do Norte, Natal, Brazil Inteins are invasive intervening sequences that perform an autocatalytic splicing from their host proteins. Among eukaryotes, these elements are present in many fungal species, including those considered opportunistic or primary pathogens, such as Candida spp. Here we reviewed and updated the list of Candida species containing inteins in the genes VMA, THRRS and GLT1 and pointed out the importance of these elements as molecular markers for molecular epidemiological researches and species- specific diagnosis, since the presence, as well as the size of these inteins, is polymorphic Edited by: among the different species. Although absent in Candida albicans, these elements are Joshua D. Nosanchuk, present in different sizes, in some environmental Candida spp. and also in most of the Albert Einstein College of Medicine, USA non-albicans Candida spp. considered emergent opportunistic pathogens. -
Variable Absorption of Mutational Trends by Prion-Forming Domains During Saccharomycetes Evolution
Variable absorption of mutational trends by prion-forming domains during Saccharomycetes evolution Paul M. Harrison Department of Biology, McGill University, Monteal, Quebec, Canada ABSTRACT Prions are self-propagating alternative states of protein domains. They are linked to both diseases and functional protein roles in eukaryotes. Prion-forming domains in Saccharomyces cerevisiae are typically domains with high intrinsic protein disorder (i.e., that remain unfolded in the cell during at least some part of their functioning), that are converted to self-replicating amyloid forms. S. cerevisiae is a member of the fungal class Saccharomycetes, during the evolution of which a large population of prion-like domains has appeared. It is still unclear what principles might govern the molecular evolution of prion-forming domains, and intrinsically disordered domains generally. Here, it is discovered that in a set of such prion-forming domains some evolve in the fungal class Saccharomycetes in such a way as to absorb general mutation biases across millions of years, whereas others do not, indicating a spectrum of selection pressures on composition and sequence. Thus, if the bias-absorbing prion formers are conserving a prion-forming capability, then this capability is not interfered with by the absorption of bias changes over the duration of evolutionary epochs. Evidence is discovered for selective constraint against the occurrence of lysine residues (which likely disrupt prion formation) in S. cerevisiae prion-forming domains as they evolve across Saccharomycetes. These results provide a case study of the absorption of mutational trends by compositionally biased domains, and suggest methodology for assessing selection pressures on the composition of intrinsically disordered regions. -
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. -
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. -
Timeline of the Evolutionary History of Life
Timeline of the evolutionary history of life This timeline of the evolutionary history of life represents the current scientific theory Life timeline Ice Ages outlining the major events during the 0 — Primates Quater nary Flowers ←Earliest apes development of life on planet Earth. In P Birds h Mammals – Plants Dinosaurs biology, evolution is any change across Karo o a n ← Andean Tetrapoda successive generations in the heritable -50 0 — e Arthropods Molluscs r ←Cambrian explosion characteristics of biological populations. o ← Cryoge nian Ediacara biota – z ← Evolutionary processes give rise to diversity o Earliest animals ←Earliest plants at every level of biological organization, i Multicellular -1000 — c from kingdoms to species, and individual life ←Sexual reproduction organisms and molecules, such as DNA and – P proteins. The similarities between all present r -1500 — o day organisms indicate the presence of a t – e common ancestor from which all known r Eukaryotes o species, living and extinct, have diverged -2000 — z o through the process of evolution. More than i Huron ian – c 99 percent of all species, amounting to over ←Oxygen crisis [1] five billion species, that ever lived on -2500 — ←Atmospheric oxygen Earth are estimated to be extinct.[2][3] Estimates on the number of Earth's current – Photosynthesis Pong ola species range from 10 million to 14 -3000 — A million,[4] of which about 1.2 million have r c been documented and over 86 percent have – h [5] e not yet been described. However, a May a -3500 — n ←Earliest oxygen 2016 -
Arxula Adeninivorans
Biernacki et al. Microb Cell Fact (2017) 16:144 DOI 10.1186/s12934-017-0751-4 Microbial Cell Factories RESEARCH Open Access Enhancement of poly(3‑hydroxybutyrate‑co‑ 3‑hydroxyvalerate) accumulation in Arxula adeninivorans by stabilization of production Mateusz Biernacki1, Marek Marzec1,6, Thomas Roick2, Reinhard Pätz3, Kim Baronian4, Rüdiger Bode5 and Gotthard Kunze1* Abstract Background: In recent years the production of biobased biodegradable plastics has been of interest of research- ers partly due to the accumulation of non-biodegradable plastics in the environment and to the opportunity for new applications. Commonly investigated are the polyhydroxyalkanoates (PHAs) poly(hydroxybutyrate) and poly(hydroxybutyrate-co-hydroxyvalerate) (PHB-V). The latter has the advantage of being tougher and less brittle. The production of these polymers in bacteria is well established but production in yeast may have some advantages, e.g. the ability to use a broad spectrum of industrial by-products as a carbon sources. Results: In this study we increased the synthesis of PHB-V in the non-conventional yeast Arxula adeninivorans by stabilization of polymer accumulation via genetic modifcation and optimization of culture conditions. An A. adenini- vorans strain with overexpressed PHA pathway genes for β-ketothiolase, acetoacetyl-CoA reductase, PHAs synthase and the phasin gene was able to accumulate an unexpectedly high level of polymer. It was found that an opti- 1 mized strain cultivated in a shaking incubator is able to produce up to 52.1% of the DCW of PHB-V (10.8 g L− ) with 12.3%mol of PHV fraction. Although further optimization of cultivation conditions in a fed-batch bioreactor led to lower polymer content (15.3% of the DCW of PHB-V), the PHV fraction and total polymer level increased to 23.1%mol 1 and 11.6 g L− respectively. -
Supplementary Materials
Supplementary Materials C4Y5P9|C4Y5P9_CLAL4 ------------------MS-EDLTKKTE------ELSLDSEKTVLSSKEEFTAKHPLNS 35 Q9P975|IF4E_CANAL ------------------MS-EELAQKTE------ELSLDS-KTVFDSKEEFNAKHPLNS 34 Q6BXX3|Q6BXX3_DEBHA --MKVF------TNKIAKMS-EELSKQTE------ELSLENKDTVLSNKEEFTAKHPLNN 45 C5DJV3|C5DJV3_LACTC ------------------MSVEEVTQKTG-D-----LNIDEKSTVLSSEKEFQLKHPLNT 36 P07260|IF4E_YEAST ------------------MSVEEVSKKFE-ENVSVDDTTATPKTVLSDSAHFDVKHPLNT 41 I2JS39|I2JS39_DEKBR MQMNLVGRTFPASERTRQSREEKPVE----AEVAKPEEEKKDVTVLENKEEFTVKHPLNS 56 A0A099P1Q5|A0A099P1Q5_PICKU ------------------MSTEELNN----ATKDLSLDEKKDVTALENPAEFNVKHPLNS 38 P78954|IF4E1_SCHPO ------------------MQTEQPPKESQTENTVSEPQEKALRTVFDDKINFNLKHPLAR 42 *. : *.:.. .* **** C4Y5P9|C4Y5P9_CLAL4 KWTLWYTKPQTNKSETWSDLLKPVITFSSVEEFWGIYNSIPVANQLPMKSDYHLFKEGIK 95 Q9P975|IF4E_CANAL RWTLWYTKPQTNKSENWHDLLKPVITFSSVEEFWGIYNSIPPANQLPLKSDYHLFKEGIR 94 Q6BXX3|Q6BXX3_DEBHA KWTLWYTKPQVNKSENWHDLLKPVITFSSVEEFWGIYNSIPQANQLPMKSDYHLFKEGIK 105 C5DJV3|C5DJV3_LACTC KWTLWYTKPPVDKSESWSDLLRPVTSFETVEEFWAIHNAIPKPRYLPLKSDYHLFRNDIR 96 P07260|IF4E_YEAST KWTLWYTKPAVDKSESWSDLLRPVTSFQTVEEFWAIIQNIPEPHELPLKSDYHVFRNDVR 101 I2JS39|I2JS39_DEKBR KWTLWYTKPAVDKNESWADLLKPIVSFDTVEEFWGIYHAVPKAVDLPLKSDYHLFRNDIK 116 A0A099P1Q5|A0A099P1Q5_PICKU TWTLWYTKPAVDNTESWADLLKPVVTFNTVEEFWGIFHAIPKVNELPLKSDYHLFRGDIK 98 P78954|IF4E1_SCHPO PWTLWFLMPPTPG-LEWNELQKNIITFNSVEEFWGIHNNINPASSLPIKSDYSFFREGVR 101 ****: * . * :* : : :*.:*****.* : : **:**** .*: .:: C4Y5P9|C4Y5P9_CLAL4 PEWEDEQNAKGGRWQYSFNNKRDVAQVINDLWLRGLLAVIGETIEDD---ENEVNGIVLN 152 Q9P975|IF4E_CANAL PEWEDEANSKGGKWQFSFNKKSEVNPIINDLWLRGLLAVIGETIEDE---ENEVNGIVLN -
10-ELS-OXF Kurtzman1610423 CH002 7..20
Part II Importance of Yeasts Kurtzman 978-0-444-52149-1 00002 Kurtzman 978-0-444-52149-1 00002 Chapter 2 c0002 Yeasts Pathogenic to Humans Chester R. Cooper, Jr. regularly encounter the organisms described below. In fact, many s0010 1. INTRODUCTION TO THE MEDICALLY medical mycologists spend entire careers without direct clinical expo- IMPORTANT YEASTS sure to many of these fungi. Rather, the purpose of this review is to enlighten the non-medical mycologist as to the diversity of yeast and p0010 Prior to global emergence of the human immunodeficiency virus mold species regularly associated with human and animal disease (HIV), which is the causative agent of acquired immunodeficiency that also, at least in part, present a unicellular mode of growth in vivo. syndrome (AIDS), approximately 200 fungal pathogens were recog- The following descriptions present a concise overview of the key p0025 nized from among the more than 100,000 then-known fungal spe- biological and clinical features of these fungi. Where appropriate, refer- cies (Kwon-Chung and Bennett 1992, Rippon 1988). About 50 of ences to recent reviews of particular disease agents and their patholo- these species were regularly associated with fungal disease (myco- gies are provided. For a global perspective of fungal diseases, including sis). Since then, there has been a concurrent dramatic increase in in-depth clinical discussions of specific pathologies, diagnoses, and both the number of known fungal species and the incidence of treatments, the reader is referred to several outstanding and recently mycoses that they cause. Moreover, the spectrum of pathogenic fungi published texts (Anaissie et al. -
Studies of the Laboulbeniomycetes: Diversity, Evolution, and Patterns of Speciation
Studies of the Laboulbeniomycetes: Diversity, Evolution, and Patterns of Speciation The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:40049989 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA ! STUDIES OF THE LABOULBENIOMYCETES: DIVERSITY, EVOLUTION, AND PATTERNS OF SPECIATION A dissertation presented by DANNY HAELEWATERS to THE DEPARTMENT OF ORGANISMIC AND EVOLUTIONARY BIOLOGY in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Biology HARVARD UNIVERSITY Cambridge, Massachusetts April 2018 ! ! © 2018 – Danny Haelewaters All rights reserved. ! ! Dissertation Advisor: Professor Donald H. Pfister Danny Haelewaters STUDIES OF THE LABOULBENIOMYCETES: DIVERSITY, EVOLUTION, AND PATTERNS OF SPECIATION ABSTRACT CHAPTER 1: Laboulbeniales is one of the most morphologically and ecologically distinct orders of Ascomycota. These microscopic fungi are characterized by an ectoparasitic lifestyle on arthropods, determinate growth, lack of asexual state, high species richness and intractability to culture. DNA extraction and PCR amplification have proven difficult for multiple reasons. DNA isolation techniques and commercially available kits are tested enabling efficient and rapid genetic analysis of Laboulbeniales fungi. Success rates for the different techniques on different taxa are presented and discussed in the light of difficulties with micromanipulation, preservation techniques and negative results. CHAPTER 2: The class Laboulbeniomycetes comprises biotrophic parasites associated with arthropods and fungi. -
A Critique of Phanerozoic Climatic Models Involving Changes in The
Earth-Science Reviews 56Ž. 2001 1–159 www.elsevier.comrlocaterearscirev A critique of Phanerozoic climatic models involving changes in the CO2 content of the atmosphere A.J. Boucot a,), Jane Gray b,1 a Department of Zoology, Oregon State UniÕersity, CorÕallis, OR 97331, USA b Department of Biology, UniÕersity of Oregon, Eugene, OR 97403, USA Received 28 April 1998; accepted 19 April 2001 Abstract Critical consideration of varied Phanerozoic climatic models, and comparison of them against Phanerozoic global climatic gradients revealed by a compilation of Cambrian through Miocene climatically sensitive sedimentsŽ evaporites, coals, tillites, lateritic soils, bauxites, calcretes, etc.. suggests that the previously postulated climatic models do not satisfactorily account for the geological information. Nor do many climatic conclusions based on botanical data stand up very well when examined critically. Although this account does not deal directly with global biogeographic information, another powerful source of climatic information, we have tried to incorporate such data into our thinking wherever possible, particularly in the earlier Paleozoic. In view of the excellent correlation between CO2 present in Antarctic ice cores, going back some hundreds of thousands of years, and global climatic gradient, one wonders whether or not the commonly postulated Phanerozoic connection between atmospheric CO2 and global climatic gradient is more coincidence than cause and effect. Many models have been proposed that attempt to determine atmospheric composition and global temperature through geological time, particularly for the Phanerozoic or significant portions of it. Many models assume a positive correlation between atmospheric CO2 and surface temperature, thus viewing changes in atmospheric CO2 as playing the critical role in r regulating climate temperature, but none agree on the levels of atmospheric CO2 through time. -
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.