Unique Endomembrane Systems and Virulence in Pathogenic Protozoa
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Basal Body Structure and Composition in the Apicomplexans Toxoplasma and Plasmodium Maria E
Francia et al. Cilia (2016) 5:3 DOI 10.1186/s13630-016-0025-5 Cilia REVIEW Open Access Basal body structure and composition in the apicomplexans Toxoplasma and Plasmodium Maria E. Francia1* , Jean‑Francois Dubremetz2 and Naomi S. Morrissette3 Abstract The phylum Apicomplexa encompasses numerous important human and animal disease-causing parasites, includ‑ ing the Plasmodium species, and Toxoplasma gondii, causative agents of malaria and toxoplasmosis, respectively. Apicomplexans proliferate by asexual replication and can also undergo sexual recombination. Most life cycle stages of the parasite lack flagella; these structures only appear on male gametes. Although male gametes (microgametes) assemble a typical 9 2 axoneme, the structure of the templating basal body is poorly defined. Moreover, the rela‑ tionship between asexual+ stage centrioles and microgamete basal bodies remains unclear. While asexual stages of Plasmodium lack defined centriole structures, the asexual stages of Toxoplasma and closely related coccidian api‑ complexans contain centrioles that consist of nine singlet microtubules and a central tubule. There are relatively few ultra-structural images of Toxoplasma microgametes, which only develop in cat intestinal epithelium. Only a subset of these include sections through the basal body: to date, none have unambiguously captured organization of the basal body structure. Moreover, it is unclear whether this basal body is derived from pre-existing asexual stage centrioles or is synthesized de novo. Basal bodies in Plasmodium microgametes are thought to be synthesized de novo, and their assembly remains ill-defined. Apicomplexan genomes harbor genes encoding δ- and ε-tubulin homologs, potentially enabling these parasites to assemble a typical triplet basal body structure. -
Molecular Data and the Evolutionary History of Dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Un
Molecular data and the evolutionary history of dinoflagellates by Juan Fernando Saldarriaga Echavarria Diplom, Ruprecht-Karls-Universitat Heidelberg, 1993 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE STUDIES Department of Botany We accept this thesis as conforming to the required standard THE UNIVERSITY OF BRITISH COLUMBIA November 2003 © Juan Fernando Saldarriaga Echavarria, 2003 ABSTRACT New sequences of ribosomal and protein genes were combined with available morphological and paleontological data to produce a phylogenetic framework for dinoflagellates. The evolutionary history of some of the major morphological features of the group was then investigated in the light of that framework. Phylogenetic trees of dinoflagellates based on the small subunit ribosomal RNA gene (SSU) are generally poorly resolved but include many well- supported clades, and while combined analyses of SSU and LSU (large subunit ribosomal RNA) improve the support for several nodes, they are still generally unsatisfactory. Protein-gene based trees lack the degree of species representation necessary for meaningful in-group phylogenetic analyses, but do provide important insights to the phylogenetic position of dinoflagellates as a whole and on the identity of their close relatives. Molecular data agree with paleontology in suggesting an early evolutionary radiation of the group, but whereas paleontological data include only taxa with fossilizable cysts, the new data examined here establish that this radiation event included all dinokaryotic lineages, including athecate forms. Plastids were lost and replaced many times in dinoflagellates, a situation entirely unique for this group. Histones could well have been lost earlier in the lineage than previously assumed. -
Expanding the Chlamydiae Tree
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040 Expanding the Chlamydiae tree Insights into genome diversity and evolution JENNAH E. DHARAMSHI ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-513-1203-3 UPPSALA urn:nbn:se:uu:diva-439996 2021 Dissertation presented at Uppsala University to be publicly examined in A1:111a, Biomedical Centre (BMC), Husargatan 3, Uppsala, Tuesday, 8 June 2021 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: Prof. Dr. Alexander Probst (Faculty of Chemistry, University of Duisburg-Essen). Abstract Dharamshi, J. E. 2021. Expanding the Chlamydiae tree. Insights into genome diversity and evolution. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 2040. 87 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-513-1203-3. Chlamydiae is a phylum of obligate intracellular bacteria. They have a conserved lifecycle and infect eukaryotic hosts, ranging from animals to amoeba. Chlamydiae includes pathogens, and is well-studied from a medical perspective. However, the vast majority of chlamydiae diversity exists in environmental samples as part of the uncultivated microbial majority. Exploration of microbial diversity in anoxic deep marine sediments revealed diverse chlamydiae with high relative abundances. Using genome-resolved metagenomics various marine sediment chlamydiae genomes were obtained, which significantly expanded genomic sampling of Chlamydiae diversity. These genomes formed several new clades in phylogenomic analyses, and included Chlamydiaceae relatives. Despite endosymbiosis-associated genomic features, hosts were not identified, suggesting chlamydiae with alternate lifestyles. Genomic investigation of Anoxychlamydiales, newly described here, uncovered genes for hydrogen metabolism and anaerobiosis, suggesting they engage in syntrophic interactions. -
The Planktonic Protist Interactome: Where Do We Stand After a Century of Research?
bioRxiv preprint doi: https://doi.org/10.1101/587352; this version posted May 2, 2019. 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. Bjorbækmo et al., 23.03.2019 – preprint copy - BioRxiv The planktonic protist interactome: where do we stand after a century of research? Marit F. Markussen Bjorbækmo1*, Andreas Evenstad1* and Line Lieblein Røsæg1*, Anders K. Krabberød1**, and Ramiro Logares2,1** 1 University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N- 0316 Oslo, Norway 2 Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain * The three authors contributed equally ** Corresponding authors: Ramiro Logares: Institute of Marine Sciences (ICM-CSIC), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Catalonia, Spain. Phone: 34-93-2309500; Fax: 34-93-2309555. [email protected] Anders K. Krabberød: University of Oslo, Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), Blindernv. 31, N-0316 Oslo, Norway. Phone +47 22845986, Fax: +47 22854726. [email protected] Abstract Microbial interactions are crucial for Earth ecosystem function, yet our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2,500 ecological interactions from ~500 publications, spanning the last 150 years. -
Sex Is a Ubiquitous, Ancient, and Inherent Attribute of Eukaryotic Life
PAPER Sex is a ubiquitous, ancient, and inherent attribute of COLLOQUIUM eukaryotic life Dave Speijera,1, Julius Lukešb,c, and Marek Eliášd,1 aDepartment of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands; bInstitute of Parasitology, Biology Centre, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 370 05 Ceské Budejovice, Czech Republic; cCanadian Institute for Advanced Research, Toronto, ON, Canada M5G 1Z8; and dDepartment of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic Edited by John C. Avise, University of California, Irvine, CA, and approved April 8, 2015 (received for review February 14, 2015) Sexual reproduction and clonality in eukaryotes are mostly Sex in Eukaryotic Microorganisms: More Voyeurs Needed seen as exclusive, the latter being rather exceptional. This view Whereas absence of sex is considered as something scandalous for might be biased by focusing almost exclusively on metazoans. a zoologist, scientists studying protists, which represent the ma- We analyze and discuss reproduction in the context of extant jority of extant eukaryotic diversity (2), are much more ready to eukaryotic diversity, paying special attention to protists. We accept that a particular eukaryotic group has not shown any evi- present results of phylogenetically extended searches for ho- dence of sexual processes. Although sex is very well documented mologs of two proteins functioning in cell and nuclear fusion, in many protist groups, and members of some taxa, such as ciliates respectively (HAP2 and GEX1), providing indirect evidence for (Alveolata), diatoms (Stramenopiles), or green algae (Chlor- these processes in several eukaryotic lineages where sex has oplastida), even serve as models to study various aspects of sex- – not been observed yet. -
Unique Characteristics of the Kinetoplast DNA Replication
CHAPTER 2 Unique Characteristics of the Kinetoplast DNA Replication Machinery Provide Potential Drug Targets in Trypanosomatids Dotan Sela, Neta Milman, Irit Kapeller, Aviad Zick, Rachel Bezalel, Nurit Yaffe and Joseph Shlomai* Reevaluating the Kinetoplast as a Potential Target for Anti-Trypanosomal Drugs inetoplast DNA (kDNA) is a remarkable DNA structure found in the single mitohondrion of flagellated protozoa of the order Kinetoplastida. In various parasitic Kspecies of the family Trypanosomatidae, it consists of 5,000-10,000 duplex DNA minicircles (0.5-10 kb) and 25-50 maxicircles (20-40 kb), which are linked topologically into a two dimensional DNA network. Maxicircles encode for typical mitochondrial proteins and ribosomal RNA, whereas minicircles encode for guide RNA (gRNA) molecules that function in the editing of maxicircles’ mRNA transcripts. The replication of kDNA includes the dupli- cation of free detached minicircles and catenated maxicircles, and the generation of two prog- eny kDNA networks. It is catalyzed by an enzymatic machinery, consisting of kDNA replica- tion proteins that are located at defined sites flanking the kDNA disk in the mitochondrial matrix (for recent reviews on kDNA see refs. 1-8). The unusual structural features of kDNA and its mode of replication, make this system an attractive target for anti-trypanosomal and anti-leishmanial drugs. However, in evaluating the potential promise held in the development of drugs against mitochondrial targets in trypanosomatids, one has to consider the observations that dyskinetoplastic (Dk) bloodstream forms of trypanosomes survive and retain their infectivity, despite the substantial loss of their mitochondrial genome (recently reviewed in ref. 9). Survival of Dk strains has led to the notion that kDNA and mitochondrial functions are dispensable for certain stages of the life cycle of trypanosomatids. -
Whole-Proteome Tree of Life Suggests a Deep Burst of Organism Diversity
Whole-proteome tree of life suggests a deep burst of organism diversity JaeJin Choia,b,c and Sung-Hou Kima,b,c,1 aDepartment of Chemistry, University of California, Berkeley, CA 94720; bCenter for Computational Biology, University of California, Berkeley, CA 94720; and cMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Contributed by Sung-Hou Kim, December 11, 2019 (sent for review September 12, 2019; reviewed by Se-Ran Jun and Charles G. Kurland) An organism tree of life (organism ToL) is a conceptual and addition, an important issue of rooting gene ToLs has not been well metaphorical tree to capture a simplified narrative of the evolution- resolved and still is being debated (ref. 13 and references within). ary course and kinship among the extant organisms. Such a tree These and other issues of gene ToLs highlight the need for cannot be experimentally validated but may be reconstructed based alternative surrogates for the organism ToL built based on as on characteristics associated with the organisms. Since the whole- completely different assumptions as possible from those of gene genome sequence of an organism is, at present, the most compre- ToLs. A “genome ToL” (see below) constructed based on in- hensive descriptor of the organism, a whole-genome sequence-based formation theory (14) may provide an independent and alter- ToL can be an empirically derivable surrogate for the organism ToL. native view of the organism ToL. However, experimentally determining the whole-genome sequences of many diverse organisms was practically impossible until recently. Genome ToL We have constructed three types of ToLs for diversely sampled Following the commonly used definition of gene ToL (see organisms using the sequences of whole genome, of whole tran- above), the term genome ToL is used in this study for the ToLs scriptome, and of whole proteome. -
7Fa228ee469dc6254b4b09b017
GBE Multigenomic Delineation of Plasmodium Species of the Laverania Subgenus Infecting Wild-Living Chimpanzees and Gorillas Weimin Liu1, Sesh A. Sundararaman1,2, Dorothy E. Loy1,2, Gerald H. Learn1,YingyingLi1, Lindsey J. Plenderleith3, Jean-Bosco N. Ndjango4, Sheri Speede5,RebecaAtencia6,DebbyCox6,7, George M. Shaw1,2, Ahidjo Ayouba8, Martine Peeters8,JulianC.Rayner9, Beatrice H. Hahn1,2,and Paul M. Sharp3,* 1Department of Medicine, Perelman School of Medicine, University of Pennsylvania 2Department of Microbiology, Perelman School of Medicine, University of Pennsylvania 3Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, United Kingdom 4Faculty of Sciences, University of Kisangani, Democratic Republic of the Congo 5Sanaga-Yong Chimpanzee Rescue Center, IDA-Africa, Portland, Oregon 6Tchimpounga Chimpanzee Rehabilitation Center, Pointe-Noire, Republic of the Congo 7Africa Programmes, Jane Goodall Institute, Vienna, Virginia 8UMI 233, Institut de Recherche pour le De´veloppement (IRD), INSERM U1175, and University of Montpellier, France 9Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK *Corresponding author: E-mail: [email protected]. Accepted: May 24, 2016 Data deposition: This project has been deposited at NCBI GenBank under the accession numbers listed in supplementary table S5, Supplementary Material online. Abstract Plasmodium falciparum, the major cause of malaria morbidity and mortality worldwide, is only distantly related -
4/9/15 1 Alveolates
4/9/15 Bayli Russ ALVEOLATES April 9, 2015 WHAT IS IT? ¡ Alveolates- Major superphylum of protists ¡ Group of single-celled eukaryotes that get their nutrition by predation, photoautotrophy, and intracellular parasitism ¡ Spherical basophilic organisms (6-9 µm diameter) ¡ Most notable shared characteristic is presence of cortical alveoli, flattened vesicles packed into linear layer supporting the membrane, typically forming a flexible pellicle (Leander, 2008) WHAT IS IT? ¡ 3 main subgroups: § Ciliatesà predators that inhabit intestinal tracts and flesh § Dinoflagellatesà mostly free living predators or photoautotrophs, release toxins § Apicomplexansà obligate parasite; invade host cells ¡ Several other lineages such as: § Colpodella § Chromera § Colponema § Ellobiopsids § Oxyrrhis § Rastrimonas § Parvilucifera § Perkinsus (Leander, 2008) 1 4/9/15 HOW DOES IT KILL AMPHIBIANS? ¡ Cause infection and disease in amphibian populations § Infection = parasite occurs in host; occupying intestinal lumen § Disease = advanced infection; presence of spores in tissues; occupying intestinal mucosa, liver, skin, rectum, mesentery, adipose tissue, pancreas, spleen, kidney, and somatic musculature ¡ Effects on organs § Filters into host’s internal organs in mass amounts § Causes organ enlargement and severe tissue alteration § Obliterates kidney and liver structure § System shut-down = DEATH ¡ How its introduced to environment § Birds § Insects ¡ How it spreads/transmission: § Ingestion of spores § Feces of infected individuals § Tissues from dead/dying -
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. -
Predatory Flagellates – the New Recently Discovered Deep Branches of the Eukaryotic Tree and Their Evolutionary and Ecological Significance
Protistology 14 (1), 15–22 (2020) Protistology Predatory flagellates – the new recently discovered deep branches of the eukaryotic tree and their evolutionary and ecological significance Denis V. Tikhonenkov Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, 152742, Russia | Submitted March 20, 2020 | Accepted April 6, 2020 | Summary Predatory protists are poorly studied, although they are often representing important deep-branching evolutionary lineages and new eukaryotic supergroups. This short review/opinion paper is inspired by the recent discoveries of various predatory flagellates, which form sister groups of the giant eukaryotic clusters on phylogenetic trees, and illustrate an ancestral state of one or another supergroup of eukaryotes. Here we discuss their evolutionary and ecological relevance and show that the study of such protists may be essential in addressing previously puzzling evolutionary problems, such as the origin of multicellular animals, the plastid spread trajectory, origins of photosynthesis and parasitism, evolution of mitochondrial genomes. Key words: evolution of eukaryotes, heterotrophic flagellates, mitochondrial genome, origin of animals, photosynthesis, predatory protists, tree of life Predatory flagellates and diversity of eu- of the hidden diversity of protists (Moon-van der karyotes Staay et al., 2000; López-García et al., 2001; Edg- comb et al., 2002; Massana et al., 2004; Richards The well-studied multicellular animals, plants and Bass, 2005; Tarbe et al., 2011; de Vargas et al., and fungi immediately come to mind when we hear 2015). In particular, several prevailing and very abun- the term “eukaryotes”. However, these groups of dant ribogroups such as MALV, MAST, MAOP, organisms represent a minority in the real diversity MAFO (marine alveolates, stramenopiles, opistho- of evolutionary lineages of eukaryotes. -
Plasmodium Falciparum Is Not As Lonely As Previously Considered
AUTOPHAGIC PUNCTUM ARTICLE ADDENDUM Virulence 2:1, 71-76; January/February 2011; © 2011 Landes Bioscience Plasmodium falciparum is not as lonely as previously considered Franck Prugnolle,1,* Francisco Ayala,2 Benjamin Ollomo,3 Céline Arnathau,1 Patrick Durand1 and François Renaud1,* 1Laboratoire MIVEGEC; UM1-CNRS 5290-IRD 224, IRD Montpellier, France; 2Department of Ecology and Evolutionary Biology; University of California; Irvine, CA USA; 3Centre International de Recherches Médicales de Franceville; Franceville, Gabon ntil very recently, only one species The identification of Plasmodium spe- U(P. reichenowi) was known to be a cies circulating in great apes in Africa phylogenetic sister lineage of P. falciparum, was primarily done during the first half the main malignant agent of human of the twentieth century, on the basis of malaria. In 2009 and 2010, new studies morphological features.1 This approach have revealed the existence of several new has several limitations.4 First, phenotypic phylogenetic species related to this deadly plasticity can lead to incorrect identifica- parasite and infecting chimpanzees and tions. Second, morphological keys are gorillas in Africa. These discoveries invite often effective only for a particular life us to explore a whole set of new questions, stage which cannot always be observed which we briefly do in this article. or is difficult to be. Finally, and perhaps most important, this approach overlooks The Plasmodium species infecting morphologically cryptic taxa. These limi- humans and non-human primates cluster tations, together with the difficulty to into two distinct phylogenetic lineages collect and manipulate great apes, were (Fig. 1). One of these lineages (in yellow certainly, at least in part, responsible for in Fig.