DOCSLIB.ORG

A User's Guide for Cell Biologists and Parasitologists

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A User's Guide for Cell Biologists and Parasitologists 1638 Eukaryotic systematics: a user’s guide for cell biologists and parasitologists GISELLE WALKER1*, RICHARD G. DORRELL2†, ALEXANDER SCHLACHT3† and JOEL B. DACKS3* 1 Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK 2 Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge, UK, CB2 1QW 3 Department of Cell Biology, School of Molecular and Systems Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2H7 (Received 12 November 2010; revised 22 November 2010; accepted 23 November 2010; first published online 15 February 2011) SUMMARY Single-celled parasites like Entamoeba, Trypanosoma, Phytophthora and Plasmodium wreak untold havoc on human habitat and health. Understanding the position of the various protistan pathogens in the larger context of eukaryotic diversity informs our study of how these parasites operate on a cellular level, as well as how they have evolved. Here, we review the literature that has brought our understanding of eukaryotic relationships from an idea of parasites as primitive cells to a crystallized view of diversity that encompasses 6 major divisions, or supergroups, of eukaryotes. We provide an updated taxonomic scheme (for 2011), based on extensive genomic, ultrastructural and phylogenetic evidence, with three differing levels of taxonomic detail for ease of referencing and accessibility (see supplementary material at Cambridge Journals On-line). Two of the most pressing issues in cellular evolution, the root of the eukaryotic tree and the evolution of photosynthesis in complex algae, are also discussed along with ideas about what the new generation of genome sequencing technologies may contribute to the field of eukaryotic systematics. We hope that, armed with this user’s guide, cell biologists and parasitologists will be encouraged about taking an increasingly evolutionary point of view in the battle against parasites representing real dangers to our livelihoods and lives. Keywords: Algae, primitive, phylogeny, parasite. INTRODUCTION development, as many diseases caused by protistan pathogens have their biggest impacts in Africa, To look around, the diversity of life would appear to South America and South-East Asia (see the World be populated by animals, plants and fungi. Health Organization webpage for the most recent and Appearances can be deceiving. Bacteria aside, the motivating statistics, http://www.who.int/vaccine_ vast diversity of cells on the planet today is composed research/diseases/en/). of unicellular eukaryotic microbes, or protists. These While the traditional approach to parasitology predominantly single-celled creatures can be at the involves focused experimental work in the individual same time beautiful, bizarre and deadly. Plasmodium organisms, a complementary way forward is to take a falciparum, the causative agent of cerebral malaria broader sweep, knitting together genetic, medical and which kills close to a million people a year (Snow et al. cell biological information across a framework of 2005), may be the most notorious protistan pathogen. eukaryotic relationships. This allows for comparisons It is hardly the only one. From our top (the brain- between distantly related parasites, yielding insight eating amoeba Naegleria fowleri) to our tail (gut into convergently evolved pathogenic mechanisms parasites Giardia and Entamoeba), a myriad array of (e.g. the regulations of antigenic variation in microbial eukaryotes – may inhabit, parasitise, and Plasmodium and Trypanosoma (Duraisingh et al. ravage the human body. Understanding the biology 2005; Horn and Barry, 2005)) or similarities that of these organisms and how they kill is a critical can be exploited in a single treatment (e.g. the use of task impacting not only human health but global metronidazole against anaerobic microbes). It also allows for comparisons between the parasites and * To whom correspondence should be addressed: Department of Cell Biology, School of Molecular and their free-living relatives. This can uncover the Systems Medicine, Faculty of Medicine and Dentistry, evolutionary path taken to parasitism and highlight University of Alberta, Edmonton, Alberta, Canada, T6 G lab-safe model organisms for study (e.g. the free- 2H7. Tel: +1-780-248-1493. Fax: +1-780-492-0450. living soil amoeba Naegleria gruberi instead of its E-mail: [email protected]. Department of Anatomy and deadly cousin Naegleria fowleri (Fritz-Laylin et al. Structural Biology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand. E-mails: [email protected]; 2010)). Finally, comparisons amongst parasitic [email protected]. sister-taxa allow for knowledge translation between † Contributed equally. experimental models and less studied related Parasitology (2011), 138, 1638–1663. © Cambridge University Press 2011 doi:10.1017/S0031182010001708 Downloaded from https:/www.cambridge.org/core. Open University Library, on 20 Jan 2017 at 08:23:37, subject to the Cambridge Core terms of use, available at https:/www.cambridge.org/core/terms. https://doi.org/10.1017/S0031182010001708 Eukaryotic systematics 1639 organisms. A result in Plasmodium might be appli- of gene sequences of mitochondrial origin (HSP60, cable to Eimeria:afinding in Trypanosoma brucei may HSP70, IscU) and later, the localizing of these gene be of relevance in Leishmania aetheopica. products (by immuno-microscopy) to double mem- This comparative approach means delving into brane-bound organelles found in these taxa (Clark fields initially appearing tangential to parasitology. and Roger, 1995; Bui et al. 1996; Roger et al. 1996, Our current understanding of eukaryotic systematics 1998; Tovar et al. 2003). Secondly, it has been shown is based both on molecular and microscopic evidence. that systematic phylogenetic error, such as ‘long Consequently molecular phylogenetics and genomics branch attraction’, has had a major effect on the are playing an increasingly important role. positioning of these organisms in the tree (Philippe Evolutionary cell biology and ancient eukaryotic and Germot, 2000; Dacks et al. 2002). The less evolution are two of the high-profile fields dependent conserved gene sequences were clustered together on eukaryotic systemics. They, in turn, are crucial for regardless of whether the divergence was due to rapid the interpretation of parasitological and cell biologi- evolution (as in many parasitic taxa) or a protracted cal data in this comparative framework. period of time in which to accumulate independent In this review, we will discuss the latest literature mutations (as in the prokaryotic sequences used as on higher-level protist systematics and provide an outgroups for the eukaryotic analyses). This artifact updated scheme of the major divisions of eukaryotic caused otherwise highly divergent protists to be diversity. Each of these divisions will be described, mistaken for basal eukaryotes. When accounted for, highlighting some of the parasitic organisms and the by algorithms and models that take different modes of current and upcoming genome projects. Finally, we sequence evolution into account (Holder and Lewis, will explore two of the most pressing controversies in 2003), the ‘primitive’ parasites and other proposed eukaryotic systematics and discuss the anticipated basal eukaryotes were either clearly linked with role that next generation sequencing might play in the relatives elsewhere in the tree (as in the case of evolutionary study of parasites and eukaryotes in Microsporidia and fungi (Keeling and Fast, 2002)) or general. were unresolved. The period following the demise of the Archezoa hypothesis was one of taxonomic agnosticism and SHIFTING VIEWS ON EUKARYOTIC SYSTEMATICS: caution with respect to interpretation of molecular FROM ‘ PRIMITIVE’ PROTOZOA TO DIVERSE sequence data and the evolution of eukaryotes. Such SUPERGROUPS data were still of immense value but a growing The tree of eukaryotes perhaps most familiar to many number of researchers abandoned the search for a parasitologists is that of a collection of crown single gene that would resolve relationships, great eukaryotes (animals, plants, fungi and many algae) and small, in favour of a strategy whereby different with a ladder-like sequential divergence of prominent genes were used to test hypotheses about particular parasites such as Giardia, Trichomonas, Encephalito- taxonomic relationships (e.g. EF2 demonstrating the zoon and Trypanosoma from the base. This view of monophyly of red and green algae (Moreira et al. eukaryotic relationships, and the place of parasites in 2000) or actin phylogenies uniting the cercozoans and it, was based on analyses of SSU rDNA genes and foraminiferans (Keeling, 2001)). These resolved single protein coding genes performed during the relationships would then contribute to a consensus early to mid-1990s (Sogin, 1991; Sogin and Silber- view of the eukaryotic tree as a whole. It was also a man, 1998). Such a phylogeny very much supported time for a renewed appreciation of ultrastructural the Archezoa hypothesis (Cavalier-Smith, 1983, data and the realization of the need for this to be 1987), a prevailing paradigm at the time (and still interpreted in the light of molecular results (Taylor, one sometimes held today) that these “amitochondri- 1999). ate” protists represent basal eukaryotic lineages that These ideas crystallized in a seminal paper by diverged before the acquisition of the mitochondrial
Load more

Recommended publications
  • Culturing and Targeted Pacbio RS Amplicon Sequencing Reveals a Higher Order Taxonomic Diversity and Global Distribution
    bioRxiv preprint doi: https://doi.org/10.1101/199125; this version posted October 8, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Enigmatic Diphyllatea eukaryotes: Culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution Orr Russell J.S.1,2*, Zhao Sen3,4, Klaveness Dag5, Yabuki Akinori6, Ikeda Keiji7, Makoto M. Watanabe7, Shalchian-Tabrizi Kamran1,2* 1 Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway 2 Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway 3 Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway 4 Medical Faculty, Center for Cancer Biomedicine, University of Oslo University Hospital, Oslo, Norway 5 Section for Aquatic Biology and Toxicology (AQUA), Department of Biosciences, University of Oslo, Oslo, Norway 6 Japan Agency for Marine-Earth Sciences and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan 7 Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan * Corresponding authors: Russell J. S. Orr & Kamran Shalchian-Tabrizi Email: [email protected] Mobile: +4748187013 Email: [email protected] Mobile: +4741045328 Address: Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway Keywords: Diphyllatea, PacBio, rRNA, phylogeny, diversity, Collodictyon, amplicon, Sulcozoa 1 bioRxiv preprint doi: https://doi.org/10.1101/199125; this version posted October 8, 2017.
    [Show full text]
  • Multigene Eukaryote Phylogeny Reveals the Likely Protozoan Ancestors of Opis- Thokonts (Animals, Fungi, Choanozoans) and Amoebozoa
    Accepted Manuscript Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opis- thokonts (animals, fungi, choanozoans) and Amoebozoa Thomas Cavalier-Smith, Ema E. Chao, Elizabeth A. Snell, Cédric Berney, Anna Maria Fiore-Donno, Rhodri Lewis PII: S1055-7903(14)00279-6 DOI: http://dx.doi.org/10.1016/j.ympev.2014.08.012 Reference: YMPEV 4996 To appear in: Molecular Phylogenetics and Evolution Received Date: 24 January 2014 Revised Date: 2 August 2014 Accepted Date: 11 August 2014 Please cite this article as: Cavalier-Smith, T., Chao, E.E., Snell, E.A., Berney, C., Fiore-Donno, A.M., Lewis, R., Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa, Molecular Phylogenetics and Evolution (2014), doi: http://dx.doi.org/10.1016/ j.ympev.2014.08.012 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 1 1 Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts 2 (animals, fungi, choanozoans) and Amoebozoa 3 4 Thomas Cavalier-Smith1, Ema E. Chao1, Elizabeth A. Snell1, Cédric Berney1,2, Anna Maria 5 Fiore-Donno1,3, and Rhodri Lewis1 6 7 1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
    [Show full text]
  • A Wide Diversity of Previously Undetected Freeliving
    Environmental Microbiology (2010) 12(10), 2700–2710 doi:10.1111/j.1462-2920.2010.02239.x A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitatsemi_2239 2700..2710 Martin Kolisko,1 Jeffrey D. Silberman,2 Kipferlia n. gen. The remaining isolates include rep- Ivan Cepicka,3 Naoji Yubuki,4† Kiyotaka Takishita,5 resentatives of three other lineages that likely repre- Akinori Yabuki,4 Brian S. Leander,6 Isao Inouye,4 sent additional undescribed genera (at least). Small- Yuji Inagaki,7 Andrew J. Roger8 and subunit ribosomal RNA gene phylogenies show that Alastair G. B. Simpson1* CLOs form a cloud of six major clades basal to the Departments of 1Biology and 8Biochemistry and diplomonad-retortamonad grouping (i.e. each of the Molecular Biology, Dalhousie University, Halifax, Nova six CLO clades is potentially as phylogenetically Scotia, Canada. distinct as diplomonads and retortamonads). CLOs 2Department of Biological Sciences, University of will be valuable for tracing the evolution of Arkansas, Fayetteville, AR, USA. diplomonad cellular features, for example, their 3Department of Zoology, Faculty of Science, Charles extremely reduced mitochondrial organelles. It is University in Prague, Prague, Czech Republic. striking that the majority of CLO diversity was unde- 4Institute of Biological Sciences, Graduate School of Life tected by previous light microscopy surveys and and Environmental Sciences and 7Center for environmental PCR studies, even though they inhabit Computational Sciences and Institute of Biological a commonly sampled environment. There is no Sciences, University of Tsukuba, Tsukuba, Ibaraki, reason to assume this is a unique situation – it is Japan. likely that undersampling at the level of major lin- 5Japan Agency for Marine-Earth Science and eages is still widespread for protists.
    [Show full text]
  • A Revised Classification of Naked Lobose Amoebae (Amoebozoa
    Protist, Vol. 162, 545–570, October 2011 http://www.elsevier.de/protis Published online date 28 July 2011 PROTIST NEWS A Revised Classification of Naked Lobose Amoebae (Amoebozoa: Lobosa) Introduction together constitute the amoebozoan subphy- lum Lobosa, which never have cilia or flagella, Molecular evidence and an associated reevaluation whereas Variosea (as here revised) together with of morphology have recently considerably revised Mycetozoa and Archamoebea are now grouped our views on relationships among the higher-level as the subphylum Conosa, whose constituent groups of amoebae. First of all, establishing the lineages either have cilia or flagella or have lost phylum Amoebozoa grouped all lobose amoe- them secondarily (Cavalier-Smith 1998, 2009). boid protists, whether naked or testate, aerobic Figure 1 is a schematic tree showing amoebozoan or anaerobic, with the Mycetozoa and Archamoe- relationships deduced from both morphology and bea (Cavalier-Smith 1998), and separated them DNA sequences. from both the heterolobosean amoebae (Page and The first attempt to construct a congruent molec- Blanton 1985), now belonging in the phylum Per- ular and morphological system of Amoebozoa by colozoa - Cavalier-Smith and Nikolaev (2008), and Cavalier-Smith et al. (2004) was limited by the the filose amoebae that belong in other phyla lack of molecular data for many amoeboid taxa, (notably Cercozoa: Bass et al. 2009a; Howe et al. which were therefore classified solely on morpho- 2011). logical evidence. Smirnov et al. (2005) suggested The phylum Amoebozoa consists of naked and another system for naked lobose amoebae only; testate lobose amoebae (e.g. Amoeba, Vannella, this left taxa with no molecular data incertae sedis, Hartmannella, Acanthamoeba, Arcella, Difflugia), which limited its utility.
    [Show full text]
  • Emerging Genomic and Proteomic Evidence on Relationships Among the Animal, Plant and Fungal Kingdoms
    Review Emerging Genomic and Proteomic Evidence on Relationships Among the Animal, Plant and Fungal Kingdoms John W. Stiller Department of Biology, East Carolina University, Greenville, NC 27858, USA. Sequence-based molecular phylogenies have provided new models of early eu- karyotic evolution. This includes the widely accepted hypothesis that animals are related most closely to fungi, and that the two should be grouped together as the Opisthokonta. Although most published phylogenies have supported an opisthokont relationship, a number of genes contain a tree-building signal that clusters animal and green plant sequences, to the exclusion of fungi. The alter- native tree-building signal is especially intriguing in light of emerging data from genomic and proteomic studies that indicate striking and potentially synapomor- phic similarities between plants and animals. This paper reviews these new lines of evidence, which have yet to be incorporated into models of broad scale eukaryotic evolution. Key words: genomics, proteomics, evolution, animals, plants, fungi Introduction The results of sequence-based, molecular phylogenetic two di®erent and conflicting phylogenetic signals; analyses have reshaped current thinking about an- most available sequences supported an animals + cient evolutionary relationships, and have begun to es- fungi relationship, but a smaller subset of genes in- tablish a new framework for systematizing broad-scale dicated a closer relationship between animals and eukaryotic diversity. Among the most widely accepted plants. Curiously, there was little or no support of the new evolutionary hypotheses is a proposed for the third possible relationship (plants + fungi). sister relationship between animals (+ choanoflagel- This suggested that a persistent phylogenetic artifact, lates) and fungi (see ref.
    [Show full text]
  • Evidence for Glycolytic Reactions in the Mitochondrion?
    Broad Distribution of TPI-GAPDH Fusion Proteins among Eukaryotes: Evidence for Glycolytic Reactions in the Mitochondrion? Takuro Nakayama1, Ken-ichiro Ishida2, John M. Archibald1* 1 Department of Biochemistry & Molecular Biology, Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Dalhousie University, Halifax, Nova Scotia, Canada, 2 Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan Abstract Glycolysis is a central metabolic pathway in eukaryotic and prokaryotic cells. In eukaryotes, the textbook view is that glycolysis occurs in the cytosol. However, fusion proteins comprised of two glycolytic enzymes, triosephosphate isomerase (TPI) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were found in members of the stramenopiles (diatoms and oomycetes) and shown to possess amino-terminal mitochondrial targeting signals. Here we show that mitochondrial TPI- GAPDH fusion protein genes are widely spread across the known diversity of stramenopiles, including non-photosynthetic species (Bicosoeca sp. and Blastocystis hominis). We also show that TPI-GAPDH fusion genes exist in three cercozoan taxa (Paulinella chromatophora, Thaumatomastix sp. and Mataza hastifera) and an apusozoan protist, Thecamonas trahens. Interestingly, subcellular localization predictions for other glycolytic enzymes in stramenopiles and a cercozoan show that a significant fraction of the glycolytic enzymes in these species have mitochondrial-targeted isoforms. These results suggest that part
    [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]
  • Molecular Identification and Evolution of Protozoa Belonging to the Parabasalia Group and the Genus Blastocystis
    UNIVERSITAR DEGLI STUDI DI SASSARI SCUOLA DI DOTTORATO IN SCIENZE BIOMOLECOLARI E BIOTECNOLOGICHE (Intenational PhD School in Biomolecular and Biotechnological Sciences) Indirizzo: Microbiologia molecolare e clinica Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Direttore della scuola: Prof. Masala Bruno Relatore: Prof. Pier Luigi Fiori Correlatore: Dott. Eric Viscogliosi Tesi di Dottorato : Dionigia Meloni XXIV CICLO Nome e cognome: Dionigia Meloni Titolo della tesi : Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Tesi di dottorato in scienze Biomolecolari e biotecnologiche. Indirizzo: Microbiologia molecolare e clinica Universit degli studi di Sassari UNIVERSITAR DEGLI STUDI DI SASSARI SCUOLA DI DOTTORATO IN SCIENZE BIOMOLECOLARI E BIOTECNOLOGICHE (Intenational PhD School in Biomolecular and Biotechnological Sciences) Indirizzo: Microbiologia molecolare e clinica Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Direttore della scuola: Prof. Masala Bruno Relatore: Prof. Pier Luigi Fiori Correlatore: Dott. Eric Viscogliosi Tesi di Dottorato : Dionigia Meloni XXIV CICLO Nome e cognome: Dionigia Meloni Titolo della tesi : Molecular identification and evolution of protozoa belonging to the Parabasalia group and the genus Blastocystis Tesi di dottorato in scienze Biomolecolari e biotecnologiche. Indirizzo: Microbiologia molecolare e clinica Universit degli studi di Sassari Abstract My thesis was conducted on the study of two groups of protozoa: the Parabasalia and Blastocystis . The first part of my work was focused on the identification, pathogenicity, and phylogeny of parabasalids. We showed that Pentatrichomonas hominis is a possible zoonotic species with a significant potential of transmission by the waterborne route and could be the aetiological agent of gastrointestinal troubles in children.
    [Show full text]
  • The Revised Classification of Eukaryotes
    See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/231610049 The Revised Classification of Eukaryotes Article in Journal of Eukaryotic Microbiology · September 2012 DOI: 10.1111/j.1550-7408.2012.00644.x · Source: PubMed CITATIONS READS 961 2,825 25 authors, including: Sina M Adl Alastair Simpson University of Saskatchewan Dalhousie University 118 PUBLICATIONS 8,522 CITATIONS 264 PUBLICATIONS 10,739 CITATIONS SEE PROFILE SEE PROFILE Christopher E Lane David Bass University of Rhode Island Natural History Museum, London 82 PUBLICATIONS 6,233 CITATIONS 464 PUBLICATIONS 7,765 CITATIONS SEE PROFILE SEE PROFILE Some of the authors of this publication are also working on these related projects: Biodiversity and ecology of soil taste amoeba View project Predator control of diversity View project All content following this page was uploaded by Smirnov Alexey on 25 October 2017. The user has requested enhancement of the downloaded file. The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists J. Eukaryot. Microbiol., 59(5), 2012 pp. 429–493 © 2012 The Author(s) Journal of Eukaryotic Microbiology © 2012 International Society of Protistologists DOI: 10.1111/j.1550-7408.2012.00644.x The Revised Classification of Eukaryotes SINA M. ADL,a,b ALASTAIR G. B. SIMPSON,b CHRISTOPHER E. LANE,c JULIUS LUKESˇ,d DAVID BASS,e SAMUEL S. BOWSER,f MATTHEW W. BROWN,g FABIEN BURKI,h MICAH DUNTHORN,i VLADIMIR HAMPL,j AARON HEISS,b MONA HOPPENRATH,k ENRIQUE LARA,l LINE LE GALL,m DENIS H. LYNN,n,1 HILARY MCMANUS,o EDWARD A. D.
    [Show full text]
  • Group of Microorganisms at the Animal-Fungal Boundary
    16 Aug 2002 13:56 AR AR168-MI56-14.tex AR168-MI56-14.SGM LaTeX2e(2002/01/18) P1: GJC 10.1146/annurev.micro.56.012302.160950 Annu. Rev. Microbiol. 2002. 56:315–44 doi: 10.1146/annurev.micro.56.012302.160950 First published online as a Review in Advance on May 7, 2002 THE CLASS MESOMYCETOZOEA: A Heterogeneous Group of Microorganisms at the Animal-Fungal Boundary Leonel Mendoza,1 John W. Taylor,2 and Libero Ajello3 1Medical Technology Program, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing Michigan, 48824-1030; e-mail: [email protected] 2Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102; e-mail: [email protected] 3Centers for Disease Control and Prevention, Mycotic Diseases Branch, Atlanta Georgia 30333; e-mail: [email protected] Key Words Protista, Protozoa, Neomonada, DRIP, Ichthyosporea ■ Abstract When the enigmatic fish pathogen, the rosette agent, was first found to be closely related to the choanoflagellates, no one anticipated finding a new group of organisms. Subsequently, a new group of microorganisms at the boundary between an- imals and fungi was reported. Several microbes with similar phylogenetic backgrounds were soon added to the group. Interestingly, these microbes had been considered to be fungi or protists. This novel phylogenetic group has been referred to as the DRIP clade (an acronym of the original members: Dermocystidium, rosette agent, Ichthyophonus, and Psorospermium), as the class Ichthyosporea, and more recently as the class Mesomycetozoea. Two orders have been described in the mesomycetozoeans: the Der- mocystida and the Ichthyophonida. So far, all members in the order Dermocystida have been pathogens either of fish (Dermocystidium spp.
    [Show full text]
  • Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts.
    [Show full text]
  • A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments Haydn Rubelmann III University of South Florida, [email protected]
    University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 11-12-2014 A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments Haydn Rubelmann III University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Marine Biology Commons, and the Microbiology Commons Scholar Commons Citation Rubelmann, Haydn III, "A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments" (2014). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/5432 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. A Functional Approach to Resolving the Biogeocomplexity of Two Extreme Environments by Haydn Rubelmann III A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Cell Biology, Microbiology and Molecular Biology College of Arts and Sciences University of South Florida Major Professor: James R. Garey, Ph.D. Randy Larsen, Ph.D. Kathleen Scott, Ph.D. David Merkler, Ph.D. Date of Approval: November 12, 2014 Keywords: environmental microbiology, extremophiles, shallow-water hydrothermal vents, anoxic marine pits Copyright © 2014, Haydn Rubelmann III DEDICATION I would like to dedicate this dissertation to three of my personal champions: my grandfather, Haydn Rubelmann Sr. (1929 - 2004), who encouraged me to pursue an academic career; my stepfather, Dale Jones (1954 - 2008), who was the best father anyone could ever hope for, and my husband, Eduardo Godoy, who suffered through not only 8 years of my doctoral tenure, but a grueling civil liberty injustice that almost wedged the Caribbean Sea between us.
    [Show full text]