DOCSLIB.ORG

Séquençage Du Génome Du Parasite Intestinal Blastocystis Sp. (ST7) : Vers Une Meilleure Compréhension Des Capacités Métabo

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Séquençage Du Génome Du Parasite Intestinal Blastocystis Sp. (ST7) : Vers Une Meilleure Compréhension Des Capacités Métabo S´equen¸cagedu g´enomedu parasite intestinal Blastocystis sp. (ST7) : vers une meilleure compr´ehension des capacit´esm´etaboliques d'organites apparent´esaux mitochondries chez ce microorganisme ana´erobie Micha¨elRoussel To cite this version: Micha¨elRoussel. S´equen¸cagedu g´enomedu parasite intestinal Blastocystis sp. (ST7) : vers une meilleure compr´ehensiondes capacit´esm´etaboliques d'organites apparent´esaux mitochondries chez ce microorganisme ana´erobie. Sciences agricoles. Universit´eBlaise Pascal - Clermont- Ferrand II, 2011. Fran¸cais. <NNT : 2011CLF22164>. <tel-00678598> HAL Id: tel-00678598 https://tel.archives-ouvertes.fr/tel-00678598 Submitted on 13 Mar 2012 HAL is a multi-disciplinary open access L'archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destin´eeau d´ep^otet `ala diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publi´esou non, lished or not. The documents may come from ´emanant des ´etablissements d'enseignement et de teaching and research institutions in France or recherche fran¸caisou ´etrangers,des laboratoires abroad, or from public or private research centers. publics ou priv´es. N°D.U. : 2164 Université Blaise Pascal ECOLE DOCTORALE DES SCIENCES DE LA VIE, SANTE, AGRONOMIE, ENVIRONNEMENT N° d’ordre : 557 Thèse pour obtenir le grade de DOCTEUR D’UNIVERSITE Spécialité : Microbiologie Présentée et soutenue publiquement par ROUSSEL Michaël le 27 septembre 2011 Séquençage du génome du parasite intestinal Blastocystis sp. (ST7) : vers une meilleure compréhension des capacités métaboliques d’organites apparentés aux mitochondries chez ce microorganisme anaérobie Directeur de la thèse : M. DELBAC Frédéric, Professeur, Université Blaise Pascal Membres du jury : M. BRINGAUD Frédéric, DR CNRS, RMSB, Université Bordeaux Segalen (Bordeaux) M. HIRT Robert, Senior Lecturer, ICAMB, Université de Newcastle (Newcastle) Mme. DARFEUILLE-MICHAUD Arlette, Professeur, Université d’Auvergne (Clermont-Ferrand) M. VIVARES Christian, Professeur émérite, Université Blaise Pascal (Clermont-Ferrand) M. VISCOGLIOSI Eric, CR CNRS, Institut Pasteur Lille, Université Lille Nord, (Lille) LMGE, UMR-CNRS 6023 Equipe Interactions hôtes-parasites Université Blaise Pascal 24 Avenue des Landais, 63177 Aubière cedex A mes parents, Pour m’avoir encouragé et soutenu pendant toutes ces années, Je vous dédie cette thèse car c’est grâce à vous que je la soutiens aujourd’hui. Soyez certains de toute ma reconnaissance, admiration et affection A tous ceux qui me sont chers Remerciements Je remercie sincèrement, Messieurs les Docteurs Frédéric Bringaud et Robert Hirt d’avoir aimablement accepté d’être les rapporteurs de cette thèse. Je suis fier de vous compter parmi mes juges et vous assure ma reconnaissance et mon respect. Madame le Professeur Arlette Darfeuille-Michaud, d’avoir aimablement accepté de participer à ce jury, et de m’avoir permis de terminer ma thèse en m’acceptant sur un poste d’ATER. Monsieur Christian Vivares, pour m’avoir accompagné et soutenu en Master 2 et durant le concours de l’attribution des bourses de thèse, pour ses conseils avisés. Merci ! Monsieur Eric Viscogliosi, pour sa collaboration et son engagement dans nos travaux communs sur Blastocystis. Nous ne sommes pas au bout de nos surprises Eric ! Monsieur le professeur Frédéric Delbac, pour m’avoir suivi tout au long de cette thèse, pour sa disponibilité, sa confiance, son écoute, son soutien et ses conseils. Cela a été un plaisir de travailler dans ton équipe et sous ta direction Fred. Trouve ici toute ma gratitude et mon respect sincère. Je tiens à remercier, Tous ceux de l’équipe « Interactions hôtes-parasites » et du LMGE, pour leur accueil, leurs conseils, et leur gentillesse. Je tiens également à remercier tous ceux qui ont participé à ce travail. ROUSSEL Michaël Séquençage du génome du parasite intestinal Blastocystis sp. (ST7) : vers une meilleure compréhension des capacités métaboliques d’organites apparentés aux mitochondries chez ce microorganisme anaérobie Résumé Blastocystis sp., est un straménopile parasite anaérobie fréquemment rencontré dans le tractus gastro-intestinal de l’homme et de divers animaux. Ce microorganisme, parfois responsable de désordres digestifs aigus, pourrait conduire à des troubles fonctionnels intestinaux tels que le syndrome de l’intestin irritable (IBS). Le génome de Blastocystis sp., qui a fait l'objet d'un projet de séquençage en collaboration avec le Génoscope d’Evry, nous a permis de caractériser le plus petit génome de straménopile séquencé à ce jour (18,8 Mpb), avec une capacité codante de 6020 gènes. L’acquisition de nombreux gènes par transferts horizontaux est une caractéristique majeure de ce génome, qui montre d’abondants réarrangements génomiques. Bien qu’évoluant en anaérobiose, Blastocystis sp. possède des organites morphologiquement proches des mitochondries, appelés mitochondrion-like organelles (MLOs). Nous avons montré que ces organites comportaient un génome circulaire de type mitochondrial de 29,27 kpb, mais dépourvu des gènes codant pour les cytochromes. Des analyses in silico nous ont permis de caractériser le protéome des MLOs (365 protéines), conduisant à l’établissement d’un modèle prédictif des voies métaboliques associées à ces organites, avec notamment une chaine respiratoire limitée aux complexes I et II. Nous avons ainsi montré que les MLOs présentent des caractères communs aux mitochondries anaérobies et aux hydrogénosomes (présence d’une PFOR et d’une hydrogénase à fer), suggérant que Blastocystis sp. comporte des mitochondries anaérobies modifiées, qui résulteraient d’une adaptation du parasite à son environnement. Par ailleurs, la prédiction du sécrétome de Blastocystis sp. révèle la présence de facteurs de virulence potentiels, pouvant être impliqués dans l’altération de l’épithélium intestinal et le contournement du système immunitaire de l’hôte. Mots-clefs : génome, analyse in silico, mitochondrie anaérobie, hydrogénosome, sécrétome Abstract Blastocystis sp. is a highly prevalent anaerobic eukaryotic stramenopile parasite found in the intestinal tract of humans and various animals. This microorganism, sometimes associated with acute intestinal disorders, could be responsible for functional intestinal disorders such as the irritable bowel syndrom (IBS). As part of a collaborative sequencing project with the Genoscope (CEA Evry, France), we were able to caracterize the smallest stramenopile genome sequenced to date (18.8 Mbp) with a 6020 genes coding capacity. The gain of many genes through horizontal gene transfer is a major characteristic of this genome, which shows extensive genomic rearrangements. Despite the anaerobic nature of Blastocytists sp., this eukaryote harbours nevertheless mitochondrion-like organelles (MLOs). We have shown that these organelles have a 29.27 kbp mitochondrial-type circular genome that lacks cytochrome coding genes. In silico analysis allowed us to predict the MLOs proteome (365 proteins), with the subsequent predictive model of the metabolic pathways associated with these organelles, including an electron transport chain (ETC) restricted to complex I and II. We have shown that MLOs shared common characteristics with anaerobic mitochondrion and hydrogenosomes (presence of a PFOR and an iron-hydrogenase), which could mean that Blastocystis sp. harbours modifiedSOMMAIRE anaerobic mitochondrion that resulted from the parasite adaptation to its anaerobic environment. In addition, Blastocytis sp. secretome prediction reveals the presence of potential virulence factors, which could be involved in the degradation of the intestinal epithelium as well as the host immune system bypass. Key-words : genome, in silico analysis, anaerobic mitochondria, hydrogenosome, secretome SOMMAIRE LISTE DES ABREVIATIONS ..................................................................................... 1 INTRODUCTION .................................................................................................... 2 CHAPITRE I - REVUE BIBLIOGRAPHIQUE I. BLASTOCYSTIS SP., UN PARASITE INTESTINAL POLYMORPHE A LA DIVERSITE GENETIQUE COMPLEXE .................................................................................... 5 A. TAXONOMIE ET DIVERSITE GENETIQUE DE BLASTOCYSTIS SP. ........................................ 5 A.1 UNE IDENTIFICATION LABORIEUSE ............................................................................ 5 A.2 UN STRAMENOPILE PEU COMMUN ........................................................................... 6 A.3 DIVERSITE GENETIQUE ET CLASSIFICATION .................................................................. 8 A.3.1 Une diversité génétique complexe ................................................................... 9 A.3.2 Spéciation et classification .............................................................................. 11 B. LA BIOLOGIE DE BLASTOCYSTIS SP. ......................................................................... 14 B.1 UN ORGANISME POLYMORPHE .............................................................................. 14 B.1.1 La forme vacuolaire ......................................................................................... 15 B.1.2 La forme granulaire ......................................................................................... 17 B.1.3 La forme amiboïde .......................................................................................... 17 B.1.4 La forme kystique ...........................................................................................
Load more

Recommended publications
  • Protist Phylogeny and the High-Level Classification of Protozoa
    Europ. J. Protistol. 39, 338–348 (2003) © Urban & Fischer Verlag http://www.urbanfischer.de/journals/ejp Protist phylogeny and the high-level classification of Protozoa Thomas Cavalier-Smith Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK; E-mail: [email protected] Received 1 September 2003; 29 September 2003. Accepted: 29 September 2003 Protist large-scale phylogeny is briefly reviewed and a revised higher classification of the kingdom Pro- tozoa into 11 phyla presented. Complementary gene fusions reveal a fundamental bifurcation among eu- karyotes between two major clades: the ancestrally uniciliate (often unicentriolar) unikonts and the an- cestrally biciliate bikonts, which undergo ciliary transformation by converting a younger anterior cilium into a dissimilar older posterior cilium. Unikonts comprise the ancestrally unikont protozoan phylum Amoebozoa and the opisthokonts (kingdom Animalia, phylum Choanozoa, their sisters or ancestors; and kingdom Fungi). They share a derived triple-gene fusion, absent from bikonts. Bikonts contrastingly share a derived gene fusion between dihydrofolate reductase and thymidylate synthase and include plants and all other protists, comprising the protozoan infrakingdoms Rhizaria [phyla Cercozoa and Re- taria (Radiozoa, Foraminifera)] and Excavata (phyla Loukozoa, Metamonada, Euglenozoa, Percolozoa), plus the kingdom Plantae [Viridaeplantae, Rhodophyta (sisters); Glaucophyta], the chromalveolate clade, and the protozoan phylum Apusozoa (Thecomonadea, Diphylleida). Chromalveolates comprise kingdom Chromista (Cryptista, Heterokonta, Haptophyta) and the protozoan infrakingdom Alveolata [phyla Cilio- phora and Miozoa (= Protalveolata, Dinozoa, Apicomplexa)], which diverged from a common ancestor that enslaved a red alga and evolved novel plastid protein-targeting machinery via the host rough ER and the enslaved algal plasma membrane (periplastid membrane).
    [Show full text]
  • Author's Manuscript (764.7Kb)
    1 BROADLY SAMPLED TREE OF EUKARYOTIC LIFE Broadly Sampled Multigene Analyses Yield a Well-resolved Eukaryotic Tree of Life Laura Wegener Parfrey1†, Jessica Grant2†, Yonas I. Tekle2,6, Erica Lasek-Nesselquist3,4, Hilary G. Morrison3, Mitchell L. Sogin3, David J. Patterson5, Laura A. Katz1,2,* 1Program in Organismic and Evolutionary Biology, University of Massachusetts, 611 North Pleasant Street, Amherst, Massachusetts 01003, USA 2Department of Biological Sciences, Smith College, 44 College Lane, Northampton, Massachusetts 01063, USA 3Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 4Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Providence, Rhode Island 02912, USA 5Biodiversity Informatics Group, Marine Biological Laboratory, 7 MBL Street, Woods Hole, Massachusetts 02543, USA 6Current address: Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520, USA †These authors contributed equally *Corresponding author: L.A.K - [email protected] Phone: 413-585-3825, Fax: 413-585-3786 Keywords: Microbial eukaryotes, supergroups, taxon sampling, Rhizaria, systematic error, Excavata 2 An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses.
    [Show full text]
  • Faculty Publications and Presentations 2010-11
    UNIVERSITY OF ARKANSAS FAYETTEVILLE, ARKANSAS PUBLICATIONS & PRESENTATIONS JULY 1, 2010 – JUNE 30, 2011 Table of Contents Bumpers College of Agricultural, Food and Life Sciences………………………………….. Page 3 School of Architecture…………………………………... Page 125 Fulbright College of Arts and Sciences…………………. Page 133 Walton College of Business……………………………... Page 253 College of Education and Health Professions…………… Page 270 College of Engineering…………………………………... Page 301 School of Law……………………………………………. Page 365 University Libraries……………………………………… Page 375 BUMPERS COLLEGE OF AGRICULTURE, FOOD AND LIFE SCIENCES Agricultural Economic and Agribusiness Alviola IV, P. A., and O. Capps, Jr. 2010 “Household Demand Analysis of Organic and Conventional Fluid Milk in the United States Based on the 2004 Nielsen Homescan Panel.” Agribusiness: an International Journal 26(3):369-388. Chang, Hung-Hao and Rodolfo M. Nayga Jr. 2010. “Childhood Obesity and Unhappiness: The Influence of Soft Drinks and Fast Food Consumption.” J Happiness Stud 11:261–275. DOI 10.1007/s10902-009-9139-4 Das, Biswa R., and Daniel V. Rainey. 2010. "Agritourism in the Arkansas Delta Byways: Assessing the Economic Impacts." International Journal of Tourism Research 12(3): 265-280. Dixon, Bruce L., Bruce L. Ahrendsen, Aiko O. Landerito, Sandra J. Hamm, and Diana M. Danforth. 2010. “Determinants of FSA Direct Loan Borrowers’ Financial Improvement and Loan Servicing Actions.” Journal of Agribusiness 28,2 (Fall):131-149. Drichoutis, Andreas C., Rodolfo M. Nayga Jr., Panagiotis Lazaridis. 2010. “Do Reference Values Matter? Some Notes and Extensions on ‘‘Income and Happiness Across Europe.” Journal of Economic Psychology 31:479–486. Flanders, Archie and Eric J. Wailes. 2010. “ECONOMICS AND MARKETING: Comparison of ACRE and DCP Programs with Simulation Analysis of Arkansas Delta Cotton and Rotation Crops.” The Journal of Cotton Science 14:26–33.
    [Show full text]
  • Diversity, Phylogeny and Phylogeography of Free-Living Amoebae
    School of Doctoral Studies in Biological Sciences University of South Bohemia in České Budějovice Faculty of Science Diversity, phylogeny and phylogeography of free-living amoebae Ph.D. Thesis RNDr. Tomáš Tyml Supervisor: Mgr. Martin Kostka, Ph.D. Department of Parasitology, Faculty of Science, University of South Bohemia in České Budějovice Specialist adviser: Prof. MVDr. Iva Dyková, Dr.Sc. Department of Botany and Zoology, Faculty of Science, Masaryk University České Budějovice 2016 This thesis should be cited as: Tyml, T. 2016. Diversity, phylogeny and phylogeography of free living amoebae. Ph.D. Thesis Series, No. 13. University of South Bohemia, Faculty of Science, School of Doctoral Studies in Biological Sciences, České Budějovice, Czech Republic, 135 pp. Annotation This thesis consists of seven published papers on free-living amoebae (FLA), members of Amoebozoa, Excavata: Heterolobosea, and Cercozoa, and covers three main topics: (i) FLA as potential fish pathogens, (ii) diversity and phylogeography of FLA, and (iii) FLA as hosts of prokaryotic organisms. Diverse methodological approaches were used including culture-dependent techniques for isolation and identification of free-living amoebae, molecular phylogenetics, fluorescent in situ hybridization, and transmission electron microscopy. Declaration [in Czech] Prohlašuji, že svoji disertační práci jsem vypracoval samostatně pouze s použitím pramenů a literatury uvedených v seznamu citované literatury. Prohlašuji, že v souladu s § 47b zákona č. 111/1998 Sb. v platném znění souhlasím se zveřejněním své disertační práce, a to v úpravě vzniklé vypuštěním vyznačených částí archivovaných Přírodovědeckou fakultou elektronickou cestou ve veřejně přístupné části databáze STAG provozované Jihočeskou univerzitou v Českých Budějovicích na jejích internetových stránkách, a to se zachováním mého autorského práva k odevzdanému textu této kvalifikační práce.
    [Show full text]
  • Research Papers-Biology / Medicine/Download/7585
    Eukaryotes: an update Eukaryotic Taxonomy I added 8 taxons: Colponema, Fonticula, Telonema, Katablepharidae, Haplosporidia, Paramyxia, Ellobiopsida, and Hemimastigota, and split Celestina and Heterolobosa, making 51 taxons. I also added 17 characteristics and excluded 6 (because of errors), making 331. The added ones were: 320. posteriorly-directed flagella with fold 321. tripartite mastigonemes 322. myzocytosis 323. nuclear dualism 324. haplosporosomes 325. cell-within-cell division 326. pellicular plates with 2-fold rotationl symmetry 327. metaboly 328. trailing flagellum circumferential 329. ameboid streaming 330. siliceous skeleton 0 - 1+ 2 opaline 331. rpl36 plastid gene 332. flagellar apparatus with 2 concentric microtubular arrays 333. telonemasome-K body 334. ejectisome-R body 335. dodecagonal axonemal microtubular pattern 336. celestite (strontium sulfate) The TNT format for the data set (starts with 0) was kept. PAUP (Swofford, 2018), Wagner, and ACCTRAN were used. There were no topological constraints, and there was no weighting. There were 12 optimal trees, 14.67 mln. rearrangements, 1247 steps, and 278 parsimony-informative characteristics. The score of the best tree or trees was 1122, the CI was .35, and the RI was .45. The new PAUP version is better as it recognizes the largest clade, so Eukaryota shows up, but the percentage of optimal trees it appears in and the resampling values for it are not given; presumably the MPT percentage is 100 and the resampling values are high. In the majority consensus Histonia again appears in all optimal trees, but the probabilty values also continue to be under 50. Cercobiota, Excavata, Nuclearidae-Fonticula, and Pelomyxida- Myxobiota appeared in all optimal trees, but not Cellulosa, Filosa, Chromista, Euchromista, nor Taxopoda-Eulobosa.
    [Show full text]
  • CURRICULUM VITAE Dr. Mitchell Loyd Sogin Distinguished Scientist
    CURRICULUM VITAE Dr. Mitchell Loyd Sogin (508) 289-7246 Distinguished Scientist [email protected] Josephine Bay Paul Center for Comparative http://www.mbl.edu/jbpc/staff/sogin/ Molecular Biology and Evolution The Marine Biological Laboratory Woods Hole, MA 02543 Education: 1963-1967 University of Illinois, Urbana, Illinois B.S. in Chemistry and Microbiology 1967-1969 University of Illinois, Urbana, Illinois under Z. John Ordal, M.S. in Industrial Microbiology Research Activities: Bacterial endospore germination 1969-1972 University of Illinois, Urbana, Illinois under Carl R. Woese, Ph.D. in Microbiology and Molecular Biology NIH Predoctoral fellowship Sigma Xi Research Award Research Activities: Ribosomal RNA processing, Molecular evolution 1972-1976 National Jewish Center, Denver, Colorado with Norman R. Pace, NIH Postdoctoral Fellowship Research Activities: in vitro rRNA processing Professional Appointments: 1976-1989 National Jewish Center, Denver, Colorado, Senior Staff Scientist in the Department of Molecular and Cellular Biology. 1980-1986 Assistant Professor, University of Colorado Health Sciences Center, Department of Biochemistry and Biophysics 1986-1999 Associate Fellow of the Canadian Institute for Advanced Research 1987-1989 Associate Professor, University of Colorado Health Sciences Center, Department of Microbiology 1989-present Senior Scientist, Marine Biological Laboratory at Woods Hole 1997-1998 Visiting Miller Research Professor, University of California at Berkeley 1997-2013 Founding Director, Josephine Bay Paul Center
    [Show full text]
  • The Evolutionary History of Histone H3 Suggests a Deep Eukaryotic Root of Chromatin Modifying Mechanisms Jan Postberg1*, Sakeh Forcob1, Wei-Jen Chang2, Hans J Lipps1
    Postberg et al. BMC Evolutionary Biology 2010, 10:259 http://www.biomedcentral.com/1471-2148/10/259 RESEARCH ARTICLE Open Access The evolutionary history of histone H3 suggests a deep eukaryotic root of chromatin modifying mechanisms Jan Postberg1*, Sakeh Forcob1, Wei-Jen Chang2, Hans J Lipps1 Abstract Background: The phenotype of an organism is an outcome of both its genotype, encoding the primary sequence of proteins, and the developmental orchestration of gene expression. The substrate of gene expression in eukaryotes is the chromatin, whose fundamental units are nucleosomes composed of DNA wrapped around each two of the core histone types H2A, H2B, H3 and H4. Key regulatory steps involved in the determination of chromatin conformations are posttranslational modifications (PTM) at histone tails as well as the assembly of histone variants into nucleosomal arrays. Although the mechanistic background is fragmentary understood, it appears that the chromatin signature of metazoan cell types is inheritable over generations. Even less understood is the conservation of epigenetic mechanisms among eukaryotes and their origins. Results: In the light of recent progress in understanding the tree of eukaryotic life we discovered the origin of histone H3 by phylogenetic analyses of variants from all supergroups, which allowed the reconstruction of ancestral states. We found that H3 variants evolved frequently but independently within related species of almost all eukaryotic supergroups. Interestingly, we found all core histone types encoded in the genome of a basal dinoflagellate and H3 variants in two other species, although is was reported that dinoflagellate chromatin is not organized into nucleosomes. Most probably one or more animal/nuclearid H3.3-like variants gave rise to H3 variants of all opisthokonts (animals, choanozoa, fungi, nuclearids, Amoebozoa).
    [Show full text]
  • Protozoologica
    Acta Protozool. (2011) 50: 43–50 ActA http://www.eko.uj.edu.pl/ap Protozoologica A New Thermophilic Heterolobosean Amoeba, Fumarolamoeba ceborucoi, gen. nov., sp. nov., Isolated Near a Fumarole at a Volcano in Mexico Johan F. De JoNckHeere1,2, Jun MurAse3 and Fred r. opperDoes4 1 research unit for Tropical Diseases, de Duve Institute, B-1200 Brussels, Belgium; 3 scientific Institute of public Health, B-1050 Brussels, Belgium; 3Graduate school of Bioagricultural sciences, Nagoya university, Nagoya, Japan; 4 université catholique de Louvain, B-1200 Brussels, Belgium summary. An amoeba was isolated from a soil sample collected at the edge of a fumarole of the volcano Ceboruco in the state of Nayarit, Mexico. The trophozoites of this new isolate have eruptive pseudopodes and do not transform into flagellates. The strain forms cysts that have a double wall. This thermophilic amoeba grows at temperatures up to 50°C. Molecular phylogenetic analysis of the small subunit ribosomal DNA (SSU rDNA) places the amoeba into the Heterolobosea. The closest relatives are Paravahlkampfia spp. Like some other heterolobosean species, this new isolate has a group I intron in the SSU rDNA. Because of its position in the molecular phylogenetic tree, and because there is no species found in the literature with similar morphological and physiological characteristics, this isolate is described as a new genus and a new species, Fumarolamoeba ceborucoi gen. nov., sp. nov. key words: Group I intron, Heterolobosea, new genus, new species, SSU rDNA, thermophilic. INTroDucTIoN one Vahlkampfia sp. did transform into flagellates it was transferred to a newly established genus, Paratetrami- tus (Darbyshire et al.
    [Show full text]
  • Marine Biological Laboratory) Data Are All from EST Analyses
    TABLE S1. Data characterized for this study. rDNA 3 - - Culture 3 - etK sp70cyt rc5 f1a f2 ps22a ps23a Lineage Taxon accession # Lab sec61 SSU 14 40S Actin Atub Btub E E G H Hsp90 M R R T SUM Cercomonadida Heteromita globosa 50780 Katz 1 1 Cercomonadida Bodomorpha minima 50339 Katz 1 1 Euglyphida Capsellina sp. 50039 Katz 1 1 1 1 4 Gymnophrea Gymnophrys sp. 50923 Katz 1 1 2 Cercomonadida Massisteria marina 50266 Katz 1 1 1 1 4 Foraminifera Ammonia sp. T7 Katz 1 1 2 Foraminifera Ovammina opaca Katz 1 1 1 1 4 Gromia Gromia sp. Antarctica Katz 1 1 Proleptomonas Proleptomonas faecicola 50735 Katz 1 1 1 1 4 Theratromyxa Theratromyxa weberi 50200 Katz 1 1 Ministeria Ministeria vibrans 50519 Katz 1 1 Fornicata Trepomonas agilis 50286 Katz 1 1 Soginia “Soginia anisocystis” 50646 Katz 1 1 1 1 1 5 Stephanopogon Stephanopogon apogon 50096 Katz 1 1 Carolina Tubulinea Arcella hemisphaerica 13-1310 Katz 1 1 2 Cercomonadida Heteromita sp. PRA-74 MBL 1 1 1 1 1 1 1 7 Rhizaria Corallomyxa tenera 50975 MBL 1 1 1 3 Euglenozoa Diplonema papillatum 50162 MBL 1 1 1 1 1 1 1 1 8 Euglenozoa Bodo saltans CCAP1907 MBL 1 1 1 1 1 5 Alveolates Chilodonella uncinata 50194 MBL 1 1 1 1 4 Amoebozoa Arachnula sp. 50593 MBL 1 1 2 Katz lab work based on genomic PCRs and MBL (Marine Biological Laboratory) data are all from EST analyses. Culture accession number is ATTC unless noted. GenBank accession numbers for new sequences (including paralogs) are GQ377645-GQ377715 and HM244866-HM244878.
    [Show full text]
  • The Hydrogenosomes of Psalteriomonas Lanterna
    BMC Evolutionary Biology BioMed Central Research article Open Access The hydrogenosomes of Psalteriomonas lanterna Rob M de Graaf†1, Isabel Duarte†2, Theo A van Alen1, Jan WP Kuiper1,4, Klaas Schotanus1,5, Jörg Rosenberg3, Martijn A Huynen2,6 and Johannes HP Hackstein*1 Address: 1Department of Evolutionary Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands, 2Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525GA Nijmegen, The Netherlands, 3Sommerhaus 45, D-50129 Bergheim, Germany, 4CIHR Group in Matrix Dynamics, University of Toronto, 150 College Street, Toronto, Ontario, Canada M5S 3E2, 5Department of Ecology and Evolutionary Biology, 106A Guyot Hall, Princeton University, Princeton NJ 08554-2016, USA and 6Netherlands Bioinformatic Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands Email: Rob M de Graaf - [email protected]; Isabel Duarte - [email protected]; Theo A van Alen - [email protected]; Jan WP Kuiper - [email protected]; Klaas Schotanus - [email protected]; Jörg Rosenberg - [email protected]; Martijn A Huynen - [email protected]; Johannes HP Hackstein* - [email protected] * Corresponding author †Equal contributors Published: 9 December 2009 Received: 20 July 2009 Accepted: 9 December 2009 BMC Evolutionary Biology 2009, 9:287 doi:10.1186/1471-2148-9-287 This article is available from: http://www.biomedcentral.com/1471-2148/9/287 © 2009 de Graaf et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    [Show full text]
  • The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists
    J. Eukaryot. Microbiol., 52(5), 2005 pp. 399–451 r 2005 by the International Society of Protistologists DOI: 10.1111/j.1550-7408.2005.00053.x The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists SINA M. ADL,a ALASTAIR G. B. SIMPSON,a MARK A. FARMER,b ROBERT A. ANDERSEN,c O. ROGER ANDERSON,d JOHN R. BARTA,e SAMUEL S. BOWSER,f GUY BRUGEROLLE,g ROBERT A. FENSOME,h SUZANNE FREDERICQ,i TIMOTHY Y. JAMES,j SERGEI KARPOV,k PAUL KUGRENS,1 JOHN KRUG,m CHRISTOPHER E. LANE,n LOUISE A. LEWIS,o JEAN LODGE,p DENIS H. LYNN,q DAVID G. MANN,r RICHARD M. MCCOURT,s LEONEL MENDOZA,t ØJVIND MOESTRUP,u SHARON E. MOZLEY-STANDRIDGE,v THOMAS A. NERAD,w CAROL A. SHEARER,x ALEXEY V. SMIRNOV,y FREDERICK W. SPIEGELz and MAX F. J. R. TAYLORaa aDepartment of Biology, Dalhousie University, Halifax, NS B3H 4J1, Canada, and bCenter for Ultrastructural Research, Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, USA, and cBigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575, USA, and dLamont-Dogherty Earth Observatory, Palisades, New York 10964, USA, and eDepartment of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada, and fWadsworth Center, New York State Department of Health, Albany, New York 12201, USA, and gBiologie des Protistes, Universite´ Blaise Pascal de Clermont-Ferrand, F63177 Aubiere cedex, France, and hNatural Resources Canada, Geological Survey of Canada (Atlantic), Bedford Institute of Oceanography, PO Box 1006 Dartmouth, NS B2Y 4A2, Canada, and iDepartment of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana 70504, USA, and jDepartment of Biology, Duke University, Durham, North Carolina 27708-0338, USA, and kBiological Faculty, Herzen State Pedagogical University of Russia, St.
    [Show full text]
  • Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella Incarcerata Article Open Access
    Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata Michelle M. Leger,1 Laura Eme,1 Laura A. Hug,‡,1 and Andrew J. Roger*,1 1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada ‡Present address: Department of Biology, University of Waterloo, Waterloo, ON, Canada *Corresponding author: E-mail: [email protected]. Associate editor: Inaki~ Ruiz-Trillo Abstract Mitochondrion-related organelles (MROs) have arisen independently in a wide range of anaerobic protist lineages. Only a few of these organelles and their functions have been investigated in detail, and most of what is known about MROs comes from studies of parasitic organisms such as the parabasalid Trichomonas vaginalis. Here, we describe the MRO of a free-living anaerobic jakobid excavate, Stygiella incarcerata. We report an RNAseq-based reconstruction of S. incarcerata’s MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas. This elegant example of convergent evolution is suggestive of an anaerobic biochemical ‘module’ of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a variety of mitochondrial processes not Downloaded from found in Trichomonas, including intermembrane space components of the mitochondrial protein import apparatus, and enzymes involved in amino acid metabolism and cardiolipin biosynthesis. In this respect, the MROs of S. incarcerata more closely resemble those of the much more distantly related free-living organisms Pygsuia biforma and Cantina marsupialis, likely reflecting these organisms’ shared lifestyle as free-living anaerobes.
    [Show full text]