DOCSLIB.ORG

Biology 1015 General Biology Lab Taxonomy Handout

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Biology 1015 General Biology Lab Taxonomy Handout Biology 1015 General Biology Lab Taxonomy Handout Section 1: Introduction Taxonomy is the branch of science concerned with classification of organisms. This involves defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. Something that you will learn quickly is there is a lot of uncertainty and debate when it comes to taxonomy. It is important to remember that the system of classification is binomial. This means that the species name is made up of two names: one is the genus name and the other the specific epithet. These names are preferably italicized, or underlined. The scientific name for the human species is Homo sapiens. Homo is the genus name and sapiens is the trivial name meaning wise. For green beans or pinto beans, the scientific name is Phaseolus vulgaris where Phaseolus is the genus for beans and vulgaris means common. Sugar maple is Acer saccharum (saccharum means sugar or sweet), and bread or brewer's yeast is Saccharomyces cerevisiae (the fungus myces that uses sugar saccharum for making beer cerevisio). In taxonomy, we frequently use dichotomous keys. A dichotomous key is a tool for identifying organisms based on a series of choices between alternative characters. Taxonomy has been called "the world's oldest profession", and has likely been taking place as long as mankind has been able to communicate (Adam and Eve?). Over the years, taxonomy has changed. For example, Carl Linnaeus the most renowned taxonomist ever, established three kingdoms, namely Regnum Animale, Regnum Vegetabile and Regnum Lapideum (the Animal, Vegetable and Mineral Kingdoms, respectively). Notice that his system does not include bacteria or other microscopic organisms as microscopes have not yet been invented. Since this time several different classification systems have developed, each with different proposal on the number of kingdoms. For lab we will use a 7-kingdom system with two empires (superkingdoms). The superkingdom Prokaryota will have two kingdoms: Eubacteria and Archaebacteria. The superkingdom Eukaryota with have five kingdoms: Protozoa, Plantae, Chromista, Fungi and Animalia. Prokaryota: DNA is dissolved in cytoplasm to form a nucleoid with no endomembrane system, no cytoskeleton and no mitosis. Eubacteria: Unicellular, peptidoglycan cell wall and ester linkages in their membrane phospholipids. Archaebacteria: Unicellular, adapted to harsh environments, ether linkages in membrane phospholipids, central dogma similar to eukaryotes (i.e. introns). Eukaryota: Linear DNA chromosomes contained in the nuclear envelope, cytoskeleton, ancestrally cilia or flagella, will be able to carry out mitosis, descended from sexual ancestors. Protozoa: Largely unicellular, colonial, filamentous or pseudo-parenchymatous. Plantae: Multicellular, photosynthetic, mostly terrestrial, chloroplast envelope contains two membranes Chromista: Multicellular, photosynthetic, mostly aquatic, chloroplast envelope contains four membranes Fungi: Multicellular, heterotrophic (do not photosynthesize), chitin cell walls, made up of filaments called hyphae, non-motile, absorb food through extracellular enzymes Animalia: Muliticellular, heterotrophic (do not photosynthesize), no cell wall, made up of tissues, motile at least part of their life cycle, ingest food Section 2: Prokaryotoa Overview Prokaryota will have the two kingdoms: Eubacteria and Archaebacteria. Prokaryotes have DNA that is dissolved in the cytoplasm to form a nucleoid with no endomembrane system, no cytoskeleton and no mitosis will be found in either. Eubacteria: These organisms are commonly called bacteria. Eubacteria have ester linkages in their membrane phospholipids, muramic acid and D-amino acids in the peptidoglycan cell wall, One of the most important ways of classifying the eubacteria is based on a staining procedure called the Gram stain. Gram-positive bacteria have a thick out peptidoglycan cell wall that retains crystal violet when stained, whereas the Gram-negative bacteria have a thing peptidoglycan cells wall between and inner and outer membrane and does not hold the satin. Another main characteristic to identify bacteria is the shape. Baccilii (rod) and cooci (sphere) are the most common. Archaebacteria: Archaebacteria live in harsh environments, have ether linkages their membrane phospholipids, and DNA transcription, mRNA translation (protein synthesis) and tDNA introns that resemble eukaryote systems. Section 3: Eubacteria Key Eubacteria Kingdom -- ester linkages in phospholipid bilayer; muramic acid in peptidoglycan cell walls, no protein-spliced tRNA introns; may inhabit a wide range of environments utilizing a vast array of metabolic strategies Negibacteria subkingdom -- (mostly stain Gram-negative) double cell envelope, outer membrane lipid bilayer with porins and separated from cytoplasmic or plasma membrane by cell wall of peptidoglycan Eobacteria infrakingdom --(eos is Greek for dawn) primitive traits Eobacteria division or phylum Class Chlorobacteria -- (khloros is Greek for yellow-green) filamentous green bacteria with bacteriochlorophyll a and usually chlorosomes Example: Chloroflexus - carbon is fixed in photoheterotrophic by unique hydroxypropionate pathway. Class Hadobacteria (hades is Greek for hell) -- heterotrophic thermophiles such Example: Thermus aquaticus from which Taq polymerase is extracted for PCR Example: Deinococcus highly radiation resistant with a thick peptidoglycan cell wall (despite being Gram -) Glycobacteria (glukus is Greek for sweet) infrakingdom Cyanobacteria division or phylum -- (kuanos is Greek for blue-green) oxygenic photosynthesis Gloeobacteria subphylum -- no thylakoids Example: Gloeobacter Phycobacteria subphylum -- thylakoids present; Examples: Fix nitrogen in heterocysts. sometimes in symbiosis with ferns or cycads or fungi; Anabaena, Nostoc and Rivularia, Examples: Major contributors to freshwater food chains. Oscillatoria, Lyngbya, Tolypothrix, Scytonema, Hapalosiphon, Gloeocapsa, Merismopedia, and Stigonema. Example: A protein-rich food source for birds, humans in Lake Chad, Mexico City, spirillum Spirulina Example: Adapted to hot springs; Spirulina, Arthrospira, Oscillatoria, Lyngbya and Synechococcus. Example: Prochlorophyte; sea squirt or ascidian symbiont producing oxygen for the animal Prochloron Example: Free-living pico-phytoplankton (about 100,000 per liter of tropical sea water) Prochlorothrix Spirochaetae division or phylum -- spiral or helical cells with periplasmic flagella; flexible outer membrane; Class Spirochaetes -- aerobic to facultatively anaerobic or obligately anaerobic; motile; many pathogens – Example: Borrelia burgdorferi is tick-borne cause of Lyme disease, Example: Treponema pallidum is cause of the venereal (sexually transmitted) disease syphilis and the tropical skin disease yaws Sphingobacteria division or phylum -- cytoplasmic membrane with sphingolipids; outer membrane with lipopolysaccharide; secondary loss of exoflagella Class Flavobacteria -- aerobic heterotrophs Example: Flavobacterium Class Chlorobea -- anaerobic phototrophs; anoxygenic photosynthesis, green bacteriochlorophyll and yellow to orange carotenoid pigments, diverse environments, some in hot springs Example: Green Sulfur bacteria that lack rubisco and use the reverse or Krebs cycle to fix carbon dioxide into organic molecules; Chlorobium, Pelodictyon Planctobacteria division or phylum -- some lack peptidoglycan; flagella with flagellin protein Class Planctomycea -- protein walls but no peptidoglycan; free-living (saprobes); often (exo)flagellate, aquatic heterotrophs with budding division Examples: Pirellula and Planctomyces have holdfasts and form rosettes, Gemmata Class Verrucomicrobiae -- prosthecate, free-living bacteria with peptidoglycan, or intracellular parasites lacking Example: Verrucomicrobium Class Chlamydiae -- peptidoglycan in cell walls replaced by protein; obligate intracellular parasites of eukaryotes; secondary loss of flagella. Example: Chlamydia is cause of psittacosis in birds and sometimes humans. It is also responsible for a difficult to detect sexually transmitted disease (NGU) Class Spirochaetes -- aerobic to facultatively anaerobic or obligately anaerobic; motile; many pathogens Example: Borrelia burgdorferi is tick-borne cause of Lyme disease, Example: Treponema pallidum is cause of the venereal (sexually transmitted) disease syphilis and the tropical skin disease yaws. Sphingobacteria division or phylum -- cytoplasmic membrane with sphingolipids; outer membrane with lipopolysaccharide; secondary loss of exoflagella Class Flavobacteria -- aerobic heterotrophs Example: Flavobacterium Class Chlorobea -- anaerobic phototrophs (either auto or hetero) Example: Chlorobium, Pelodictyon Planctobacteria division or phylum -- some lack peptidoglycan; flagella with flagellin protein in flagellar shaft present, or secondarily absent Class Planctomycea -- protein walls but no peptidoglycan; free-living (saprobes); often (exo)flagellate, aquatic heterotrophs with budding division Example: Pirellula, Planctomyces, Gemmata Class Verrucomicrobiae -- prosthecate, free-living bacteria Example: Verrucomicrobium with peptidoglycan Class Chlamydiae -- peptidoglycan in cell walls replaced by protein; obligate intracellular parasites of eukaryotes Example: Chlamydia is cause of psittacosis in birds and sometimes humans. It is also responsible for a difficult to detect sexually transmitted disease Proteobacteria division or phylum -- peptidoglycan and lipopolysaccharide
Load more

Recommended publications
  • Novel Contributions to the Peritrich Family Vaginicolidae
    applyparastyle “fig//caption/p[1]” parastyle “FigCapt” Zoological Journal of the Linnean Society, 2019, 187, 1–30. With 13 figures. Novel contributions to the peritrich family Vaginicolidae (Protista: Ciliophora), with morphological and Downloaded from https://academic.oup.com/zoolinnean/article-abstract/187/1/1/5434147/ by Ocean University of China user on 08 October 2019 phylogenetic analyses of poorly known species of Pyxicola, Cothurnia and Vaginicola BORONG LU1, LIFANG LI2, XIAOZHONG HU1,5,*, DAODE JI3,*, KHALED A. S. AL-RASHEID4 and WEIBO SONG1,5 1Institute of Evolution and Marine Biodiversity, & Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, China 2Marine College, Shandong University, Weihai 264209, China 3School of Ocean, Yantai University, Yantai 264005, China 4Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia 5Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China Received 29 September 2018; revised 26 December 2018; accepted for publication 13 February 2019 The classification of loricate peritrich ciliates is difficult because of an accumulation of several taxonomic problems. In the present work, three poorly described vaginicolids, Pyxicola pusilla, Cothurnia ceramicola and Vaginicola tincta, were isolated from the surface of two freshwater/marine algae in China. In our study, the ciliature of Pyxicola and Vaginicola is revealed for the first time, demonstrating the taxonomic value of infundibular polykineties. The small subunit rDNA, ITS1-5.8S rDNA-ITS2 region and large subunit rDNA of the above species were sequenced for the first time. Phylogenetic analyses based on these genes indicated that Pyxicola and Cothurnia are closely related.
    [Show full text]
  • Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide
    antioxidants Review Anoxygenic Photosynthesis in Photolithotrophic Sulfur Bacteria and Their Role in Detoxication of Hydrogen Sulfide Ivan Kushkevych 1,* , Veronika Bosáková 1,2 , Monika Vítˇezová 1 and Simon K.-M. R. Rittmann 3,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (V.B.); [email protected] (M.V.) 2 Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic 3 Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Vienna, Austria * Correspondence: [email protected] (I.K.); [email protected] (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.) Abstract: Hydrogen sulfide is a toxic compound that can affect various groups of water microorgan- isms. Photolithotrophic sulfur bacteria including Chromatiaceae and Chlorobiaceae are able to convert inorganic substrate (hydrogen sulfide and carbon dioxide) into organic matter deriving energy from photosynthesis. This process takes place in the absence of molecular oxygen and is referred to as anoxygenic photosynthesis, in which exogenous electron donors are needed. These donors may be reduced sulfur compounds such as hydrogen sulfide. This paper deals with the description of this metabolic process, representatives of the above-mentioned families, and discusses the possibility using anoxygenic phototrophic microorganisms for the detoxification of toxic hydrogen sulfide. Moreover, their general characteristics, morphology, metabolism, and taxonomy are described as Citation: Kushkevych, I.; Bosáková, well as the conditions for isolation and cultivation of these microorganisms will be presented. V.; Vítˇezová,M.; Rittmann, S.K.-M.R.
    [Show full text]
  • Identification of a Novel Fused Gene Family Implicates Convergent
    Chen et al. BMC Genomics (2018) 19:306 https://doi.org/10.1186/s12864-018-4685-y RESEARCH ARTICLE Open Access Identification of a novel fused gene family implicates convergent evolution in eukaryotic calcium signaling Fei Chen1,2,3, Liangsheng Zhang1, Zhenguo Lin4 and Zong-Ming Max Cheng2,3* Abstract Background: Both calcium signals and protein phosphorylation responses are universal signals in eukaryotic cell signaling. Currently three pathways have been characterized in different eukaryotes converting the Ca2+ signals to the protein phosphorylation responses. All these pathways have based mostly on studies in plants and animals. Results: Based on the exploration of genomes and transcriptomes from all the six eukaryotic supergroups, we report here in Metakinetoplastina protists a novel gene family. This family, with a proposed name SCAMK,comprisesSnRK3 fused calmodulin-like III kinase genes and was likely evolved through the insertion of a calmodulin-like3 gene into an SnRK3 gene by unequal crossover of homologous chromosomes in meiosis cell. Its origin dated back to the time intersection at least 450 million-year-ago when Excavata parasites, Vertebrata hosts, and Insecta vectors evolved. We also analyzed SCAMK’s unique expression pattern and structure, and proposed it as one of the leading calcium signal conversion pathways in Excavata parasite. These characters made SCAMK gene as a potential drug target for treating human African trypanosomiasis. Conclusions: This report identified a novel gene fusion and dated its precise fusion time
    [Show full text]
  • Predatory Prokaryotes: Predation Andprimary Consumption Evolved in Bacteria
    Proc. Nati. Acad. Sci. USA Vol. 83, pp. 2138-2142, April 1986 Evolution and Microbiology Predatory prokaryotes: Predation and primary consumption evolved in bacteria (microbial ecology/microbial evolution/Chromalium/Daptobacter/Vampirococcus) RICARDO GUERRERO*, CARLOS PEDR6S-ALI6*, ISABEL ESTEVE*, JORDI MAS*, DAVID CHASEt, AND LYNN MARGULISt *Department of Microbiology and Institute for Fundamental Biology, Autonomous University of Barcelona, Bellaterra (Barcelona), Spain; tCell Biology Laboratory (151iB), Sepulveda Veterans Administration Hospital, Sepulveda, CA 91343; and tDepartment of Biology, Boston University, Boston, MA 02215 Contributed by Lynn Margulis, November 12, 1985 ABSTRACT Two kinds of predatory bacteria have been We report here bacterial scavenging and predation by two observed and characterized by light and electron microscopy in new bacteria, one epibiotic (Vampirococcus) and the other samples from freshwater sulfurous lakes in northeastern Spain. cytoplasmic (Daptobacter). Vampirococcus attacks different The first bacterium, named Vampirococcus, is Gram-negative species of the genus Chromatium, a purple sulfur bacterium and ovoidal (0.6 jam wide). An anaerobic epibiont, it adheres (9). It does not penetrate its prey cells and remains attached to the surface of phototrophic bacteria (Chromatium spp.) by to the Chromatium cell wall. Vampirococcus reproduces specific attachment structures and, as it grows and divides by while "sucking" the innards of its prey in a fashion reminis- fission, destroys its prey. An important
    [Show full text]
  • US 2019 / 0029266 A1 SAWANT ( 43 ) Pub
    US 20190029266A1 ( 19) United States (12 ) Patent Application Publication ( 10) Pub . No. : US 2019 / 0029266 A1 SAWANT ( 43 ) Pub . Date : Jan . 31 , 2019 ( 54 ) NOVEL CROP FORTIFICATION , (52 ) U .S . CI. NUTRITION AND CROP PROTECTION CPC .. .. .. A01N 63/ 04 ( 2013 .01 ) ; AOIN 25 / 12 COMPOSITION ( 2013 .01 ) ; A01N 63/ 00 ( 2013 .01 ) ; C05G 3 / 02 (2013 .01 ) ; C050 9 / 00 (2013 .01 ) ; C05C 9 / 00 (71 ) Applicant: Arun Vitthal SAWANT, Mumbai ( IN ) ( 2013. 01 ) ; C05F 11/ 00 ( 2013 .01 ) ( 72 ) Inventor: Arun Vitthal SAWANT, Mumbai ( IN ) (57 ) ABSTRACT (21 ) Appl. No. : 16 /047 ,834 The invention relates to an algal granular composition . More (22 ) Filed : Jul. 27 , 2018 particularly , the invention relates to an algal granular com position comprising at least one alga, and at least one (30 ) Foreign Application Priority Data agrochemically acceptable excipients selected from one or more of surfactants , binders or disintegrant having weight Jul. 27, 2017 (IN ) .. .. .. .. 201721026745 ratio of algae to at least one of surfactant, binder or disin tegrant in the range of 99 : 1 to 1 : 99 . The algae comprise Publication Classification 0 . 1 % to 90 % by weight of the total composition . The (51 ) Int . Cl. composition has a particle size in the range of 0 . 1 microns AOIN 63 / 04 ( 2006 .01 ) to 60 microns . Furthermore , the invention relates to a AOIN 25 / 12 ( 2006 . 01 ) process of preparing the algal granular composition com A01N 63 / 00 ( 2006 . 01 ) prising at least one alga and at least one agrochemically C05F 11/ 00 ( 2006 . 01 ) acceptable excipient. The invention further relates to a C05D 9 / 00 ( 2006 .01 ) method of treating the plants , seeds, crops , plantpropagation C05C 9 /00 ( 2006 .01 ) material, locus , parts thereof or the soil with the algal C05G 3 / 02 ( 2006 .01 ) granular composition .
    [Show full text]
  • Functional Equivalence and Evolutionary Convergence In
    Functional equivalence and evolutionary convergence PNAS PLUS in complex communities of microbial sponge symbionts Lu Fana,b, David Reynoldsa,b, Michael Liua,b, Manuel Starkc,d, Staffan Kjelleberga,b,e, Nicole S. Websterf, and Torsten Thomasa,b,1 aSchool of Biotechnology and Biomolecular Sciences and bCentre for Marine Bio-Innovation, University of New South Wales, Sydney, New South Wales 2052, Australia; cInstitute of Molecular Life Sciences and dSwiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland; eSingapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Republic of Singapore; and fAustralian Institute of Marine Science, Townsville, Queensland 4810, Australia Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved May 21, 2012 (received for review February 24, 2012) Microorganisms often form symbiotic relationships with eukar- ties (11, 12). Symbionts also can be transmitted vertically through yotes, and the complexity of these relationships can range from reproductive cells and larvae, as has been demonstrated in those with one single dominant symbiont to associations with sponges (13, 14), insects (15), ascidians (16), bivalves (17), and hundreds of symbiont species. Microbial symbionts occupying various other animals (18). Vertical transmission generally leads equivalent niches in different eukaryotic hosts may share func- to microbial communities with limited variation in taxonomy and tional aspects, and convergent genome evolution has been function among host individuals. reported for simple symbiont systems in insects. However, for Niches with similar selections may exist in phylogenetically complex symbiont communities, it is largely unknown how prev- divergent hosts that lead comparable lifestyles or have similar alent functional equivalence is and whether equivalent functions physiological properties.
    [Show full text]
  • Announcements Protists - Outline Reading: Chap
    Announcements Protists - Outline Reading: Chap. 29 • Relevant reading BEFORE lab this week: Ch. 31 I. Introduction • Bring lab atlas AND textbook to lab. A. Diversity of life styles IV. Evolutionary history • Extra credit opportunity: B. Functional classifications A. Kingdom Protista? – Salmon Summit: Wed. 11/3/10, 8-4:45 pm II. Ecological importance B. How are they related St. Luke’s Community Health Education Center to each other? A. Algae C. How did they arise? Bellingham, WA (checking on registration) B. Protozoans D. How are they related III. Life cycles to plants? A. The three basic types B. Examples Diatom I.A. Diversity of life styles Size 1. Size 10 μm 2. Morphology 3. Motility Kelp 4. Energy sources 6 orders of magnitude! 60 m Filamentous (Golden algae) Morphology Gradient in complexity Unicellular (Euglena) Colonial (Pandorina) Multicellular (kelp) 1 Crawling (pseudopodia) Cell walls – protection & support Planktonic Amoeba Diatoms Cilia Flagella Motility Fastened Amoeba Paramecium Euglena Kelp No cell wall Energy source - photoautotrophs Variation in photosynthetic pigments Energy source - heterotrophs Ingestive feeders Absorptive feeders: decomp., parasites I.B. Functional classifications Particle feeder (Stentor) Protozoans - “animal like” Parasite Algae - “plant-like”, i.e., photosynthetic (Trypanosoma) - Eukaryotic photosynthetic organisms that are not plants Decomposer Mix - simple to bizarre (slime mold Don’t necessarily relate to taxonomic Physarum) (ingestive) relationships and evolutionary history Predator (Amoeba) 2 Cellular slime mold – unicellular or multicellular? Mixotroph example - Euglena Cells (n) aggregate when food is scarce Amoebae (n) Spores germinate Amoebae (n) germinate (n) from zygote from spores SEXUAL ASEXUAL REPRODUCTION REPRODUCTION Fruiting body Stalk Giant cell Migrating individual (2n) (slug) (n) Two cells (n) in aggregation fuse, then consume other cells Fig.
    [Show full text]
  • 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]
  • Extensive Molecular Tinkering in the Evolution of the Membrane Attachment Mode of the Rheb Gtpase
    www.nature.com/scientificreports OPEN Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb Received: 14 December 2017 Accepted: 15 March 2018 GTPase Published: xx xx xxxx Kristína Záhonová1, Romana Petrželková1, Matus Valach 2, Euki Yazaki3, Denis V. Tikhonenkov4, Anzhelika Butenko1, Jan Janouškovec5, Štěpánka Hrdá6, Vladimír Klimeš1, Gertraud Burger 2, Yuji Inagaki7, Patrick J. Keeling8, Vladimír Hampl6, Pavel Flegontov1, Vyacheslav Yurchenko1 & Marek Eliáš1 Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifcations include: (1) accretion to the N-terminus of two diferent phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the frst proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed fagellate SRT308; (2) acquisition of lipidic modifcations of the N-terminal region, namely myristoylation and/ or S-palmitoylation in seven diferent protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa.
    [Show full text]
  • Orthologs of the Small RPB8 Subunit of the Eukaryotic RNA Polymerases
    Biology Direct BioMed Central Discovery notes Open Access Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and "Korarchaeota" Eugene V Koonin*1, Kira S Makarova1 and James G Elkins2 Address: 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and 2Microbial Ecology and Physiology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA Email: Eugene V Koonin* - [email protected]; Kira S Makarova - [email protected]; James G Elkins - [email protected] * Corresponding author Published: 14 December 2007 Received: 13 December 2007 Accepted: 14 December 2007 Biology Direct 2007, 2:38 doi:10.1186/1745-6150-2-38 This article is available from: http://www.biology-direct.com/content/2/1/38 © 2007 Koonin 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. Abstract : Although most of the key components of the transcription apparatus, and in particular, RNA polymerase (RNAP) subunits, are conserved between archaea and eukaryotes, no archaeal homologs of the small RPB8 subunit of eukaryotic RNAP have been detected. We report that orthologs of RPB8 are encoded in all sequenced genomes of hyperthermophilic Crenarchaeota and a recently sequenced "korarchaeal" genome, but not in Euryarchaeota or the mesophilic crenarchaeon Cenarchaeum symbiosum. These findings suggest that all 12 core subunits of eukaryotic RNAPs were already present in the last common ancestor of the extant archaea.
    [Show full text]
  • Structural Features of the Vesicle of Frankia Sp. Cpi1 in Culture
    Structural features of the vesicle of Frankia sp. CpIl in culture JOHNG. TORREYAND DALECALLAHAM Cabot Foundation, Harvard University, Petersham, MA, U.S.A.01366 and Department of Botany, University of Massachusetts, Amherst, MA, U.S.A.01003 Accepted March 16, 1982 TORREY,J. G., and D. CALLAHAM.1982. Structural features of the vesicle of Frankia sp. CpII inculture. Can. J. Microbiol. 28: 749-757. The filamentous bacterium Frankia sp. CpIl of the Actinomycetales, responsible for symbiotic nitrogen fixation in the nodules of certain woody dicots, also fixes dinitrogen when grown independently of the host in a nitrogen-free synthetic nutrient medium under aerobic conditions. In structural studies of Frankla grown in culture it has been shown that the bacterial filaments form vesicles, enlarged terminal endings in which the enzyme nitrogenase is formed. Microscopic examination of cultures shows that the vesicles possess a specialized envelope consisting of a number of thin layers or laminae which In polarized light show birefringence and in freeze-etch electron microscopy are resolved as multiple (12-15) laminae approximately 35-40 A (1 A = 0.1 nm) in thickness. Comparisons are made between the structure of the veslcle envelope in cultured Frankia and the ; strikingly similar innermost laminated layer in the dinitrogen-fixing heterocysts of the cyanobacterium Anabaena. Comparable protective functions in limiting oxygen to the dinitrogen-fixing sites are suggested for these similar structures in two quite unrelated microorganisms. 1 TORREY,J. G., et D. CALLAHAM.1982. Structural features of the vesicle of Frankia sp. CpIl in culture. Can. J. Microbiol. 28: 749-757. I La bactkrie filamenteuse Frankia sp.
    [Show full text]
  • Phylogeny and Assemblage Composition of Frankia in Alnus Tenuifolia Nodules Across a Primary Successional Sere in Interior Alaska
    Molecular Ecology (2013) 22, 3864–3877 doi: 10.1111/mec.12339 Phylogeny and assemblage composition of Frankia in Alnus tenuifolia nodules across a primary successional sere in interior Alaska M. D. ANDERSON,*† D. L. TAYLOR† and R. W. RUESS† *Department of Biology, Macalester College, 1600 Grand Ave, Saint Paul, MN 55105, USA, †Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775, USA Abstract In nitrogen (N) fixing symbioses, host-symbiont specificity, genetic variation in bacte- rial symbionts and environmental variation represent fundamental constraints on the ecology, evolution and practical uses of these interactions, but detailed information is lacking for many naturally occurring N-fixers. This study examined phylogenetic host specificity of Frankia in field-collected nodules of two Alnus species (A. tenuifolia and A. viridis) in interior Alaska and, for A. tenuifolia, distribution, diversity, spatial auto- correlation and correlation with specific soil factors of Frankia genotypes in nodules collected from replicated habitats representing endpoints of a primary sere. Frankia genotypes most commonly associated with each host belonged to different clades within the Alnus-infective Frankia clade, and for A. tenuifolia, were divergent from previously described Frankia. A. tenuifolia nodules from early and late succession hab- itats harboured distinct Frankia assemblages. In early succession, a single genotype inhabited 71% of nodules with no discernable autocorrelation at any scale, while late succession Frankia were more diverse, differed widely among plants within a site and were significantly autocorrelated within and among plants. Early succession Frankia genotype occurrence was strongly correlated with carbon/nitrogen ratio in the mineral soil fraction, while in late succession, the most common genotypes were correlated with different soil variables.
    [Show full text]