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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. -
Succession and Persistence of Microbial Communities and Antimicrobial Resistance Genes Associated with International Space Stati
Singh et al. Microbiome (2018) 6:204 https://doi.org/10.1186/s40168-018-0585-2 RESEARCH Open Access Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces Nitin Kumar Singh1, Jason M. Wood1, Fathi Karouia2,3 and Kasthuri Venkateswaran1* Abstract Background: The International Space Station (ISS) is an ideal test bed for studying the effects of microbial persistence and succession on a closed system during long space flight. Culture-based analyses, targeted gene-based amplicon sequencing (bacteriome, mycobiome, and resistome), and shotgun metagenomics approaches have previously been performed on ISS environmental sample sets using whole genome amplification (WGA). However, this is the first study reporting on the metagenomes sampled from ISS environmental surfaces without the use of WGA. Metagenome sequences generated from eight defined ISS environmental locations in three consecutive flights were analyzed to assess the succession and persistence of microbial communities, their antimicrobial resistance (AMR) profiles, and virulence properties. Metagenomic sequences were produced from the samples treated with propidium monoazide (PMA) to measure intact microorganisms. Results: The intact microbial communities detected in Flight 1 and Flight 2 samples were significantly more similar to each other than to Flight 3 samples. Among 318 microbial species detected, 46 species constituting 18 genera were common in all flight samples. Risk group or biosafety level 2 microorganisms that persisted among all three flights were Acinetobacter baumannii, Haemophilus influenzae, Klebsiella pneumoniae, Salmonella enterica, Shigella sonnei, Staphylococcus aureus, Yersinia frederiksenii,andAspergillus lentulus.EventhoughRhodotorula and Pantoea dominated the ISS microbiome, Pantoea exhibited succession and persistence. K. pneumoniae persisted in one location (US Node 1) of all three flights and might have spread to six out of the eight locations sampled on Flight 3. -
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. -
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. -
Rhodotorula Kratochvilovae CCY 20-2-26—The Source of Multifunctional Metabolites
microorganisms Article Rhodotorula kratochvilovae CCY 20-2-26—The Source of Multifunctional Metabolites Dana Byrtusová 1,2 , Martin Szotkowski 2, Klára Kurowska 2, Volha Shapaval 1 and Ivana Márová 2,* 1 Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway; [email protected] (D.B.); [email protected] (V.S.) 2 Faculty of Chemistry, Brno University of Technology, Purkyˇnova464/118, 612 00 Brno, Czech Republic; [email protected] (M.S.); [email protected] (K.K.) * Correspondence: [email protected]; Tel.: +420-739-997-176 Abstract: Multifunctional biomass is able to provide more than one valuable product, and thus, it is attractive in the field of microbial biotechnology due to its economic feasibility. Carotenogenic yeasts are effective microbial factories for the biosynthesis of a broad spectrum of biomolecules that can be used in the food and feed industry and the pharmaceutical industry, as well as a source of biofuels. In the study, we examined the effect of different nitrogen sources, carbon sources and CN ratios on the co-production of intracellular lipids, carotenoids, β–glucans and extracellular glycolipids. Yeast strain R. kratochvilovae CCY 20-2-26 was identified as the best co-producer of lipids (66.7 ± 1.5% of DCW), exoglycolipids (2.42 ± 0.08 g/L), β-glucan (11.33 ± 1.34% of DCW) and carotenoids (1.35 ± 0.11 mg/g), with a biomass content of 15.2 ± 0.8 g/L, by using the synthetic medium with potassium nitrate and mannose as a carbon source. -
ISSN 0513-5222 Official Publication of the International Commission on Yeasts of the International Union of Microbiological Soci
ISSN 0513-5222 Official Publication of the International Commission on Yeasts of the International Union of Microbiological Societies (IUMS) DECEMBER 2012 Volume LXI, Number II Marc-André Lachance, Editor University of Western Ontario, London, Ontario, Canada N6A 5B7 <[email protected] > http://www.uwo.ca/biology/YeastNewsletter/Index.html Associate Editors Peter Biely Patrizia Romano Kyria Boundy-Mills Institute of Chemistry Dipartimento di Biologia, Herman J. Phaff Culture Slovak Academy of Sciences Difesa e Biotecnologie Collection Dúbravská cesta 9, 842 3 Agro-Forestali Department of Food Science 8 Bratislava, Slovakia Università della Basilicata, and Technology Via Nazario Sauro, 85, 85100 University of California Davis Potenza, Italy Davis California 95616-5224 WI Golubev, Puschino, Russia . 30 CP Kurtzman, Peoria, Illinois, USA . 42 M Kopecká, Brno, Czech Republic . 30 A Caridi, Reggio Calabria, Italie . 45 GI Naumov and E.S. Naumova, E Breirerová, Bratislava, Slovakia . 47 Moscow, Russia ..................... 31 P Buzzini, Perugia, Italy. 49 J du Preez, Bloemfontein, South Africa . 32 M Sipiczki, Debrecen, Hungary . 49 D Kregiel, Lodz, Poland ................. 34 JP Tamang, Tadong, Gangtok, India . 52 B Gibson, VTT, Finland ................. 35 MA Lachance, London, Ontario, Canada . 52 G Miloshev, Sofia, Bulgaria . 36 Forthcoming Meeting .................... 54 D Begerow and A Yurkov, Bochum, Germany 38 Fifty Years Ago ........................ 54 A Yurkov, Braunshweig, Gremany . 41 Editorial Complete Archive of Yeast Newsletter Back Issues Available Thanks to Kyria Boundy-Mills, readers can now have access to all back issues of the Yeast Newsletter as PDF scans. The archive is available at the following link: http://www.uwo.ca/biology/YeastNewsletter/BackIssues.html Addition of these large files made it necessary to move the YNL web site to a new server. -
A Cellulase and Lipase Producing Oleaginous Yeast ⇑ Sachin Vyas, Meenu Chhabra
Bioresource Technology 223 (2017) 250–258 Contents lists available at ScienceDirect Bioresource Technology journal homepage: www.elsevier.com/locate/biortech Isolation, identification and characterization of Cystobasidium oligophagum JRC1: A cellulase and lipase producing oleaginous yeast ⇑ Sachin Vyas, Meenu Chhabra Environmental Biotechnology Laboratory, Department of Biology, Indian Institute of Technology Jodhpur (IIT J), Jodhpur, Rajasthan 342011, India highlights graphical abstract Oleaginous yeast capable of cellulase and lipase production was isolated. It can grow on wide range of substrates including carboxylmethylcellulose (CMC). It can accumulate 36.46% (w/w) lipid on the medium with CMC as sole carbon source. Intracellular and extracellular lipase activity: 2.16 and 2.88 IU/mg respectively. The FAME composition suitable for use as biodiesel (glucose medium). article info abstract Article history: Oleaginous yeast closely related to Cystobasidium oligophagum was isolated from soil rich in cellulosic Received 15 August 2016 waste. The yeast was isolated based on its ability to accumulate intracellular lipid, grow on car- Received in revised form 12 October 2016 boxymethylcellulose (CMC) and produce lipase. It could accumulate up to 39.44% lipid in a glucose med- Accepted 13 October 2016 ium (12.45 ± 0.97 g/l biomass production). It was able to grow and accumulate lipids (36.46%) in the Available online 15 October 2016 medium containing CMC as the sole carbon source. The specific enzyme activities obtained for endoglu- canase, exoglucanase, and b-glucosidase were 2.27, 1.26, and 0.98 IU/mg respectively. The specific Keywords: enzyme activities obtained for intracellular and extracellular lipase were 2.16 and 2.88 IU/mg respec- Cystobasidium oligophagum tively. -
Yeast Biodiversity Evolution Over Decades in Dealu Mare-Valea Calugareasca Vineyard
Romanian Biotechnological Letters Vol. 16, No.1, 2011, Supplement Copyright © 2011 University of Buchare Printed in Romania. All rights reserved ORIGINAL PAPER Yeast biodiversity evolution over decades in Dealu Mare-Valea Calugareasca vineyard Received for publication, November 6, 2010 Accepted, February 11, 2011 MATEI RADOI FLORENTINA 1, BRINDUSE ELENA2, NICOALE GETUTA1, TUDORACHE AURELIA2, TEODORESCU RAZVAN 3 1 University of Agronomical Sciences and Veterinary Medicine of Bucharest, Faculty of Biotechnology 59, Marasti Ave., Bucharest, 010464 Romania, e-mail: [email protected] 2ICDVV Valea Calugareasca, Prahova, Romania 3University of Agronomical Sciences and Veterinary Medicine of Bucharest, FIFIM Abstract Belonging to a wider national project of yeast biodiversity conservation from consecrated Romanian vineyards, this study has been performed in a red wine recognized area, Valea Calugareasca from Dealu Mare County. The main goal has been to isolate yeasts from the vineyard, from the grape and during different phases of alcoholic fermentation and to perform their identification. The yeast isolation has been done from vine plantation of Cabernet Sauvignon, Merlot, Feteasca Neagra and Pinot Noir grape wines. We have used classical methodology for isolation and purification on YEPD, finally obtaining 262 isolates. The identification has followed two approaches: one by classical morphological and cultural analysis, using Barnett J.L. (2000) guide and the second one, employed rapid physiological tests of API 20 C Biomerieux galleries. A comparison between the two identification methods has been performed. A secondary goal of our study, but very important in the context to microbiota evolution, has been to compare our results (2007-2009) to former results obtained by Dr. -
Molecular Characterization of Rhodotorula Spp. Isolated from Poultry Meat
International Journal of ChemTech Research CODEN (USA): IJCRGG, ISSN: 0974-4290, ISSN(Online):2455-9555 Vol.9, No.05 pp 200-206, 2016 Molecular Characterization of Rhodotorula Spp. Isolated From Poultry Meat Randa. M. Alarousi1*, Sohad M. Dorgham1, El-Kewaiey I. A.2, Amal A. Al-Said3 1Department of Microbiology, National Research Center, Dokki, Giza, Egypt. *Department of Medical Laboratories, College of Applied Medical Sciences, Majmaah University, KSA 2Food Hygiene Unit,Damanhour Provincial Lab., Animal Health Research Institute, Egypt . 3Microbiology Unit, Damanhour Provincial Lab., Animal Health Research Institute, Egypt . Abstract: A total of 50 Rhodotorula spp strains were isolated from 200 fresh Chicken and quail products, represented by chicken breast and thigh (Chicken: n=50 breast, n=50 thigh and quail: n=50 breast, n=50 thigh) with an incidence 25%. PCR was applied on 5 positive samples out of 15 samples derived from chicken breasts; 5 positive samples out of 12 samples from chicken thigh meat; 5 positive samples out of 13 from quail breasts and 5 samples out of 10 positive of quail thigh meat samples, CrtR gene was detected at 560bp. High incidence of Rhodotorula spp, it may be due to un hygienic measures during rearing and slaughtering of poultry, which represent potential public health risk. Key words: Rhodotorula, PCR, CrtR gene, quail. Introduction Microbial nourishment security and sustenance borne diseases are critical general wellbeing concern worldwide.There have been various sustenance borne illuness coming about because of ingestion of contaminated nourishments, for example, chicken meats. Poultry meat is one of the exceedingly expended creature started nourishment thing. -
Evaluation of the Chitin-Binding Dye Congo Red As a Selection Agent for the Isolation, Classification, and Enumeration of Ascomycete Yeasts
Archives of Microbiology (2018) 200:671–675 https://doi.org/10.1007/s00203-018-1498-y SHORT COMMUNICATION Evaluation of the chitin-binding dye Congo red as a selection agent for the isolation, classification, and enumeration of ascomycete yeasts Tomas Linder1 Received: 3 February 2018 / Revised: 19 February 2018 / Accepted: 21 February 2018 / Published online: 23 February 2018 © The Author(s) 2018. This article is an open access publication Abstract Thirty-nine strains of ascomycete yeasts representing 35 species and 33 genera were tested for their ability to grow on solid agar medium containing increasing concentrations of the chitin-binding dye Congo red. Six strains were classified as hyper- sensitive (weak or no growth at 10 mg/l Congo red), five were moderately sensitive (weak or no growth at 50 mg/l), three were moderately tolerant (weak or no growth at 100 mg/l), while the remaining 25 strains were classified as resistant (robust growth at ≥ 100 mg/l) with 20 of these strains classified as hyper-resistant (robust growth at 200 mg/l). Congo red growth phenotypes were consistent within some families but not others. The frequency of Congo red resistance among ascomycete yeasts was deemed too high for the practical use of Congo red as a selection agent for targeted isolation, but can be useful for identification and enumeration of yeasts. Keywords Antifungal · Cell wall · Phenotype · Yeast Introduction groups of yeasts. For example, chemically defined growth medium containing methanol as the sole carbon source is The development of genome sequencing over the past four commonly used to isolate species of methylotrophic yeasts decades has revolutionized yeast taxonomy and now enables (van Dijken and Harder 1974).