Dictyostelium Discoideum
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Quantitative Evolutionary Analysis of the Life Cycle of Social Amoebae Darja Dubravcic
Quantitative evolutionary analysis of the life cycle of social amoebae Darja Dubravcic To cite this version: Darja Dubravcic. Quantitative evolutionary analysis of the life cycle of social amoebae. Agricultural sciences. Université René Descartes - Paris V, 2013. English. NNT : 2013PA05T033. tel-00914467 HAL Id: tel-00914467 https://tel.archives-ouvertes.fr/tel-00914467 Submitted on 5 Dec 2013 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Université Paris Descartes Ecole doctorale « Interdisciplinaire Européen Frontières de vivant » Laboratory « Ecology & Evolution » UMR7625 Laboratory of Interdisciplinary Physics UMR5588 Quantitative evolutionary analysis of the life cycle of social amoebae By Darja Dubravcic PhD Thesis in: Evolutionary Biology Directed by Minus van Baalen and Clément Nizak Presented on the 15th November 2013 PhD committee: Dr. M. van Baalen, PhD director Dr. C. Nizak, PhD Co-director Prof. V. Nanjundiah, Reviewer Prof. P. Rainey, Reviewer Prof. A. Gardner Prof. J-P. Rieu Prof. J-M Di Meglio Dr. S. de Monte, Invited 2 Abstract Social amoebae are eukaryotic organisms that inhabit soil of almost every climate zone. They are remarkable for their switch from unicellularity to multicellularity as an adaptation to starvation. -
Protozoologica Special Issue: Protists in Soil Processes
Acta Protozool. (2012) 51: 201–208 http://www.eko.uj.edu.pl/ap ActA doi:10.4467/16890027AP.12.016.0762 Protozoologica Special issue: Protists in Soil Processes Review paper Ecology of Soil Eumycetozoans Steven L. STEPHENSON1 and Alan FEEST2 1Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA; 2Institute of Advanced Studies, University of Bristol and Ecosulis ltd., Newton St Loe, Bath, United Kingdom Abstract. Eumycetozoans, commonly referred to as slime moulds, are common to abundant organisms in soils. Three groups of slime moulds (myxogastrids, dictyostelids and protostelids) are recognized, and the first two of these are among the most important bacterivores in the soil microhabitat. The purpose of this paper is first to provide a brief description of all three groups and then to review what is known about their distribution and ecology in soils. Key words: Amoebae, bacterivores, dictyostelids, myxogastrids, protostelids. INTRODUCTION that they are amoebozoans and not fungi (Bapteste et al. 2002, Yoon et al. 2008, Baudalf 2008). Three groups of slime moulds (myxogastrids, dic- One of the idiosyncratic branches of the eukary- tyostelids and protostelids) are recognized (Olive 1970, otic tree of life consists of an assemblage of amoe- 1975). Members of the three groups exhibit consider- boid protists referred to as the supergroup Amoebozoa able diversity in the type of aerial spore-bearing struc- (Fiore-Donno et al. 2010). The most diverse members tures produced, which can range from exceedingly of the Amoebozoa are the eumycetozoans, common- small examples (most protostelids) with only a single ly referred to as slime moulds. Since their discovery, spore to the very largest examples (certain myxogas- slime moulds have been variously classified as plants, trids) that contain many millions of spores. -
Fold-Change Detection and Scale Invariance of Cell–Cell Signaling In
Fold-change detection and scale invariance of cell–cell PNAS PLUS signaling in social amoeba Keita Kaminoa,1, Yohei Kondoa, Akihiko Nakajimab, Mai Honda-Kitaharaa, Kunihiko Kanekoa,b, and Satoshi Sawaia,b,c,1 aDepartment of Basic Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan; bResearch Center for Complex Systems Biology, University of Tokyo, Tokyo 153-8902, Japan; and cPrecursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan Edited by Peter N. Devreotes, The Johns Hopkins University School of Medicine, Baltimore, MD, and approved April 9, 2017 (received for review February 9, 2017) Cell–cell signaling is subject to variability in the extracellular volume, process called “cAMP relay” (13). After prolonged exposure to cell number, and dilution that potentially increase uncertainty in the cAMP, the rise in extracellular cAMP level ceases due to inacti- absolute concentrations of the extracellular signaling molecules. To vation of adenylyl cyclase (14). As extracellular cAMP level is direct cell aggregation, the social amoebae Dictyostelium discoideum lowered by degradation, the cells exit from the state of reduced collectively give rise to oscillations and waves of cyclic adenosine responsivity over the course of several minutes (15, 16), and hence 3′,5′-monophosphate (cAMP) under a wide range of cell density. To the extracellular cAMP level once again starts to elevate. This date, the systems-level mechanism underlying the robustness is un- tendency for the extracellular cAMP level to rise when it is lowered, clear. By using quantitative live-cell imaging, here we show that the and to be lowered when it is raised, essentially renders extracellular magnitude of the cAMP relay response of individual cells is deter- cAMP level unstable and oscillatory. -
Dictyostelium: a Model for Studying the Extracellular Vesicle Messengers Involved in Human Health and Disease
cells Review Dictyostelium: A Model for Studying the Extracellular Vesicle Messengers Involved in Human Health and Disease Irène Tatischeff Honorary CNRS (Centre de la Recherche Scientifique, Paris, France) and UPMC (Université Pierre et Marie Curie, Paris, France) Research Director, Founder of RevInterCell, a Scientific Consulting Service, 91400 Orsay, France; [email protected]; Tel.: +33-683-147-187 Received: 30 January 2019; Accepted: 1 March 2019; Published: 8 March 2019 Abstract: Cell-derived extracellular vesicles (EVs) are newly uncovered messengers for intercellular communication. They are released by almost all cell types in the three kingdoms, Archeabacteria, Bacteria and Eukaryotes. They are known to mediate important biological functions and to be increasingly involved in cell physiology and in many human diseases, especially in oncology. The aim of this review is to recapitulate the current knowledge about EVs and to summarize our pioneering work about Dictyostelium discoideum EVs. However, many challenges remain unsolved in the EV research field, before any EV application for theranostics (diagnosis, prognosis, and therapy) of human cancers, can be efficiently implemented in the clinics. Dictyostelium might be an outstanding eukaryotic cell model for deciphering the utmost challenging problem of EV heterogeneity, and for unraveling the still mostly unknown mechanisms of their specific functions as mediators of intercellular communication. Keywords: extracellular vesicles; microvesicles; exosomes; oncosomes; apoptotic bodies; intercellular communication; human disease; cancer; Dictyostelium discoideum 1. Introduction After a brief presentation of the extracellular vesicles (EVs) and of the eukaryotic microorganism Dictyostelium, an overview will be given about the properties of EVs and their involvement in human health and disease. -
Ptolemeba N. Gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea, Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba
The Journal of Published by the International Society of Eukaryotic Microbiology Protistologists Journal of Eukaryotic Microbiology ISSN 1066-5234 ORIGINAL ARTICLE Ptolemeba n. gen., a Novel Genus of Hartmannellid Amoebae (Tubulinea, Amoebozoa); with an Emphasis on the Taxonomy of Saccamoeba Pamela M. Watsona, Stephanie C. Sorrella & Matthew W. Browna,b a Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, 39762 b Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, 39762 Keywords ABSTRACT 18S rRNA; amoeba; amoeboid; Cashia; cristae; freshwater amoebae; Hartmannella; Hartmannellid amoebae are an unnatural assemblage of amoeboid organisms mitochondrial morphology; SSU rDNA; SSU that are morphologically difficult to discern from one another. In molecular phy- rRNA; terrestrial amoebae; tubulinid. logenetic trees of the nuclear-encoded small subunit rDNA, they occupy at least five lineages within Tubulinea, a well-supported clade in Amoebozoa. The Correspondence polyphyletic nature of the hartmannellids has led to many taxonomic problems, M.W. Brown, Department of Biological in particular paraphyletic genera. Recent taxonomic revisions have alleviated Sciences, Mississippi State University, some of the problems. However, the genus Saccamoeba is paraphyletic and is Mississippi State, MS 39762, USA still in need of revision as it currently occupies two distinct lineages. Here, we Telephone number: +1 662-325-2406; report a new clade on the tree of Tubulinea, which we infer represents a novel FAX number: +1 662-325-7939; genus that we name Ptolemeba n. gen. This genus subsumes a clade of hart- e-mail: [email protected] mannellid amoebae that were previously considered in the genus Saccamoeba, but whose mitochondrial morphology is distinct from Saccamoeba. -
Dictyostelid Cellular Slime Molds from Caves
John C. Landolt, Steven L. Stephenson, and Michael E. Slay – Dictyostelid cellular slime molds from caves. Journal of Cave and Karst Studies, v. 68, no. 1, p. 22–26. DICTYOSTELID CELLULAR SLIME MOLDS FROM CAVES JOHN C. LANDOLT Department of Biology, Shepherd University, Shepherdstown, WV 2544 USA [email protected] STEVEN L. STEPHENSON Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701 USA [email protected] MICHAEL E. SLAY The Nature Conservancy, 601 North University Avenue, Little Rock, AR 72205 USA [email protected] Dictyostelid cellular slime molds associated with caves in Alabama, Arkansas, Indiana, Missouri, New York, Oklahoma, South Carolina, Tennessee, West Virginia, Puerto Rico, and San Salvador in the Bahamas were investigated during the period of 1990–2005. Samples of soil material collected from more than 100 caves were examined using standard methods for isolating dictyostelids. At least 17 species were recovered, along with a number of isolates that could not be identified completely. Four cos- mopolitan species (Dictyostelium sphaerocephalum, D. mucoroides, D. giganteum and Polysphondylium violaceum) and one species (D. rosarium) with a more restricted distribution were each recorded from more than 25 different caves, but three other species were present in more than 20 caves. The data gen- erated in the present study were supplemented with all known published and unpublished records of dic- tyostelids from caves in an effort to summarize what is known about their occurrence in this habitat. INTRODUCTION also occur on dung and were once thought to be primarily coprophilous (Raper, 1984). However, perhaps the most Dictyostelid cellular slime molds (dictyostelids) are single- unusual microhabitat for dictyostelids is the soil material celled, eukaryotic, phagotrophic bacterivores usually present found in caves. -
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. -
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. -
Multiple Roots of Fruiting Body Formation in Amoebozoa
GBE Multiple Roots of Fruiting Body Formation in Amoebozoa Falk Hillmann1,*, Gillian Forbes2, Silvia Novohradska1, Iuliia Ferling1,KonstantinRiege3,MarcoGroth4, Martin Westermann5,ManjaMarz3, Thomas Spaller6, Thomas Winckler6, Pauline Schaap2,and Gernot Glo¨ ckner7,* 1Junior Research Group Evolution of Microbial Interaction, Leibniz Institute for Natural Product Research and Infection Biology – Hans Kno¨ ll Institute (HKI), Jena, Germany 2Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, United Kingdom 3Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Germany 4CF DNA-Sequencing, Leibniz Institute on Aging Research, Jena, Germany 5Electron Microscopy Center, Jena University Hospital, Germany 6Pharmaceutical Biology, Institute of Pharmacy, Friedrich Schiller University Jena, Germany 7Institute of Biochemistry I, Medical Faculty, University of Cologne, Germany *Corresponding authors: E-mails: [email protected]; [email protected]. Accepted: January 11, 2018 Data deposition: The genome sequence and gene predictions of Protostelium aurantium and Protostelium mycophagum were deposited in GenBank under the Accession Numbers MDYQ00000000 and MZNV00000000, respectively. The mitochondrial genome of P. mycophagum was deposited under the Accession number KY75056 and that of P. aurantium under the Accession number KY75057. The RNAseq reads can be found in Bioproject Accession PRJNA338377. All sequence and annotation data are also available directly from the authors. The P. aurantium strain is deposited in the Jena Microbial Resource Collection (JMRC) under accession number SF0012540. Abstract Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyos- teliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree, differ by producing only one or few single stalked spores. -
CH28 PROTISTS.Pptx
9/29/14 Biosc 41 Announcements 9/29 Review: History of Life v Quick review followed by lecture quiz (history & v How long ago is Earth thought to have formed? phylogeny) v What is thought to have been the first genetic material? v Lecture: Protists v Are we tetrapods? v Lab: Protozoa (animal-like protists) v Most atmospheric oxygen comes from photosynthesis v Lab exam 1 is Wed! (does not cover today’s lab) § Since many of the first organisms were photosynthetic (i.e. cyanobacteria), a LOT of excess oxygen accumulated (O2 revolution) § Some organisms adapted to use it (aerobic respiration) Review: History of Life Review: Phylogeny v Which organelles are thought to have originated as v Homology is similarity due to shared ancestry endosymbionts? v Analogy is similarity due to convergent evolution v During what event did fossils resembling modern taxa suddenly appear en masse? v A valid clade is monophyletic, meaning it consists of the ancestor taxon and all its descendants v How many mass extinctions seem to have occurred during v A paraphyletic grouping consists of an ancestral species and Earth’s history? Describe one? some, but not all, of the descendants v When is adaptive radiation likely to occur? v A polyphyletic grouping includes distantly related species but does not include their most recent common ancestor v Maximum parsimony assumes the tree requiring the fewest evolutionary events is most likely Quiz 3 (History and Phylogeny) BIOSC 041 1. How long ago is Earth thought to have formed? 2. Why might many organisms have evolved to use aerobic respiration? PROTISTS! Reference: Chapter 28 3. -
Testate Lobose Amoebae)
Palaeontologia Electronica palaeo-electronica.org Mediolus, a new genus of Arcellacea (Testate Lobose Amoebae) R. Timothy Patterson ABSTRACT Mediolus, a new arcellacean genus of the Difflugidae (informally known as the- camoebia, testate rhizopods, or testate lobose amoebae) differs from other genera of the family in having distinctive tooth-like inward oriented apertural crenulations and tests generally characterized by a variable number of hollow basal spines. R. Timothy Patterson. Ottawa-Carleton Geoscience Centre and Department of Earth Sciences, Carleton University, Ottawa, Ontario, K1S 5B6, Canada. [email protected] Keywords: Arcellacea; thecamoebian; testate lobose amoebae; Quaternary, new genus INTRODUCTION of the simple unilocular test (e.g., Bonnet, 1975; Medioli et al., 1987, 1990; Beyens and Meisterfeld, Arcellacea (also informally known as the- 2001), although some researchers have placed camoebians, testate amoebae, testate rhizopods, more emphasis on test composition (e.g., Ander- or testate lobose amoebae; Patterson et al., 2012) son, 1988). The proliferation of species descrip- are a diverse group of unicellular testate rhizopods tions within the Difflugia, often based on subtle test that occur in a wide array of aquatic and terrestrial differences, has resulted in considerable taxo- environments (Patterson and Kumar, 2002) from nomic confusion (Patterson and Kumar, 2002). the tropics to poles (Dalby et al., 2000). Although Researchers have often described new species most common in Quaternary sediments fossil based on regional interest, often with little consid- arcellaceans have been found preserved in sedi- eration of the previous literature or the systematic ments deposited under freshwater and brackish value of distinguishing characters (see discussions conditions spanning the Phanerozoic and into the in Medioli and Scott, 1983; Medioli et al., 1987; Neoproterozoic (Porter and Knoll, 2000; Van Ogden and Hedley, 1980; Tolonen, 1986; Bobrov Hengstum, 2007). -
Social Amoeba Farmers Carry Defensive Symbionts to Protect and Privatize Their Crops
ARTICLE Received 8 Apr 2013 | Accepted 31 Jul 2013 | Published 13 Sep 2013 DOI: 10.1038/ncomms3385 Social amoeba farmers carry defensive symbionts to protect and privatize their crops Debra A. Brock1, Silven Read2, Alona Bozhchenko2, David C. Queller1 & Joan E. Strassmann1 Agricultural crops are investments that can be exploited by others. Farmer clones of the social amoeba Dictyostelium discoideum carry bacteria to seed out new food populations but they also carry other non-food bacteria such as Burkholderia spp. Here we demonstrate that these farmer-carried Burkholderia inhibit the growth of non-farmer D. discoideum clones that could exploit the farmers’ crops. Using supernatants, we show that inhibition is due to molecules secreted by Burkholderia. When farmer and non-farmer amoebae are mixed together at various frequencies and allowed to complete the social stage, the ability of non-farmers to produce spores falls off rapidly with an increase in the percentage of farmers and their defensive symbionts. Conversely, farmer spore production is unaffected by the frequency of non-farmers. Our results suggest that successful farming is a complex evolutionary adaptation because it requires additional strategies, such as recruiting third parties, to effectively defend and privatize crops. 1 Department of Biology, Washington University at St. Louis, St. Louis, Missouri 63130, USA. 2 Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA. Correspondence and requests for materials should be addressed to D.A.B. (email: [email protected]). NATURE COMMUNICATIONS | 4:2385 | DOI: 10.1038/ncomms3385 | www.nature.com/naturecommunications 1 & 2013 Macmillan Publishers Limited. All rights reserved.