Dictyostelid Cellular Slime Molds from Caves
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
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. -
Comparative Genomics of the Social Amoebae Dictyostelium Discoideum
Sucgang et al. Genome Biology 2011, 12:R20 http://genomebiology.com/2011/12/2/R20 RESEARCH Open Access Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Richard Sucgang1†, Alan Kuo2†, Xiangjun Tian3†, William Salerno1†, Anup Parikh4, Christa L Feasley5, Eileen Dalin2, Hank Tu2, Eryong Huang4, Kerrie Barry2, Erika Lindquist2, Harris Shapiro2, David Bruce2, Jeremy Schmutz2, Asaf Salamov2, Petra Fey6, Pascale Gaudet6, Christophe Anjard7, M Madan Babu8, Siddhartha Basu6, Yulia Bushmanova6, Hanke van der Wel5, Mariko Katoh-Kurasawa4, Christopher Dinh1, Pedro M Coutinho9, Tamao Saito10, Marek Elias11, Pauline Schaap12, Robert R Kay8, Bernard Henrissat9, Ludwig Eichinger13, Francisco Rivero14, Nicholas H Putnam3, Christopher M West5, William F Loomis7, Rex L Chisholm6, Gad Shaulsky3,4, Joan E Strassmann3, David C Queller3, Adam Kuspa1,3,4* and Igor V Grigoriev2 Abstract Background: The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. Results: We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. -
Protistology Mitochondrial Genomes of Amoebozoa
Protistology 13 (4), 179–191 (2019) Protistology Mitochondrial genomes of Amoebozoa Natalya Bondarenko1, Alexey Smirnov1, Elena Nassonova1,2, Anna Glotova1,2 and Anna Maria Fiore-Donno3 1 Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia 2 Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 194064 Saint Petersburg, Russia 3 University of Cologne, Institute of Zoology, Terrestrial Ecology, 50674 Cologne, Germany | Submitted November 28, 2019 | Accepted December 10, 2019 | Summary In this mini-review, we summarize the current knowledge on mitochondrial genomes of Amoebozoa. Amoebozoa is a major, early-diverging lineage of eukaryotes, containing at least 2,400 species. At present, 32 mitochondrial genomes belonging to 18 amoebozoan species are publicly available. A dearth of information is particularly obvious for two major amoebozoan clades, Variosea and Tubulinea, with just one mitochondrial genome sequenced for each. The main focus of this review is to summarize features such as mitochondrial gene content, mitochondrial genome size variation, and presence or absence of RNA editing, showing if they are unique or shared among amoebozoan lineages. In addition, we underline the potential of mitochondrial genomes for multigene phylogenetic reconstruction in Amoebozoa, where the relationships among lineages are not fully resolved yet. With the increasing application of next-generation sequencing techniques and reliable protocols, we advocate mitochondrial -
The Social Amoeba Polysphondylium Pallidum Loses Encystation And
Protist, Vol. 165, 569–579, September 2014 http://www.elsevier.de/protis Published online date 14 July 2014 ORIGINAL PAPER The Social Amoeba Polysphondylium pallidum Loses Encystation and Sporulation, but Can Still Erect Fruiting Bodies in the Absence of Cellulose 1 Qingyou Du, and Pauline Schaap College of Life Sciences, University of Dundee, MSI/WTB/JBC complex, Dow Street, Dundee, DD15EH, UK Submitted May 20, 2014; Accepted July 8, 2014 Monitoring Editor: Michael Melkonian Amoebas and other freely moving protists differentiate into walled cysts when exposed to stress. As cysts, amoeba pathogens are resistant to biocides, preventing treatment and eradication. Lack of gene modification procedures has left the mechanisms of encystation largely unexplored. Genetically tractable Dictyostelium discoideum amoebas require cellulose synthase for formation of multicellular fructifications with cellulose-rich stalk and spore cells. Amoebas of its distant relative Polysphondylium pallidum (Ppal), can additionally encyst individually in response to stress. Ppal has two cellulose syn- thase genes, DcsA and DcsB, which we deleted individually and in combination. Dcsa- mutants formed fruiting bodies with normal stalks, but their spore and cyst walls lacked cellulose, which obliterated stress-resistance of spores and rendered cysts entirely non-viable. A dcsa-/dcsb- mutant made no walled spores, stalk cells or cysts, although simple fruiting structures were formed with a droplet of amoeboid cells resting on an sheathed column of decaying cells. DcsB is expressed in prestalk and stalk cells, while DcsA is additionally expressed in spores and cysts. We conclude that cellulose is essential for encystation and that cellulose synthase may be a suitable target for drugs to prevent encystation and render amoeba pathogens susceptible to conventional antibiotics. -
Activated Camp Receptors Switch Encystation Into Sporulation
Activated cAMP receptors switch encystation into sporulation Yoshinori Kawabea, Takahiro Moriob, John L. Jamesa, Alan R. Prescottb, Yoshimasa Tanakab, and Pauline Schaapa,1 aCollege of Life Sciences, University of Dundee, Dundee, Angus, DD15EH, United Kingdom; and bGraduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, 305-8572, Japan Edited by Peter N. Devreotes, Johns Hopkins University School of Medicine, Baltimore, MD, and approved March 12, 2009 (received for review February 13, 2009) Metazoan embryogenesis is controlled by a limited number of in the most derived group 4 (4). During D. discoideum devel- signaling modules that are used repetitively at successive devel- opment, the deeply conserved intracellular messenger cAMP opmental stages. The development of social amoebas shows sim- has multiple roles as a secreted signal, detected by 4 homologous ilar reiterated use of cAMP-mediated signaling. In the model cAMP receptors (cAR1–4) (5). cAMP pulses coordinate the Dictyostelium discoideum, secreted cAMP acting on 4 cAMP recep- aggregation of starving cells and organize the construction of tors (cARs1-4) coordinates cell movement during aggregation and fruiting bodies with a highly regulated pattern of spores and stalk fruiting body formation, and induces the expression of aggrega- cells. Secreted cAMP also up-regulates expression of aggrega- tion and sporulation genes at consecutive developmental stages. tion genes, induces expression of spore genes, and inhibits stalk To identify hierarchy in the multiple roles of cAMP, we investigated gene expression (6). cAR heterogeneity and function across the social amoeba phylog- Single cAR genes were previously detected in 3 more basal eny. The gene duplications that yielded cARs 2-4 occurred late in dictyostelid taxa, but were only expressed after aggregation. -
Genetic Heterogeneity in Wild Isolates of Cellular Slime Mold Social Groups
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Publications of the IAS Fellows Microb Ecol (2010) 60:137–148 DOI 10.1007/s00248-010-9635-4 ORIGINAL ARTICLE Genetic Heterogeneity in Wild Isolates of Cellular Slime Mold Social Groups Santosh Sathe & Sonia Kaushik & Albert Lalremruata & Ramesh K. Aggarwal & James C. Cavender & Vidyanand Nanjundiah Received: 27 September 2009 /Accepted: 26 December 2009 /Published online: 24 February 2010 # Springer Science+Business Media, LLC 2010 Abstract This study addresses the issues of spatial distri- Introduction bution, dispersal, and genetic heterogeneity in social groups of the cellular slime molds (CSMs). The CSMs are soil The existence and implication of spatial structuring in amoebae with an unusual life cycle that consists of microbial populations is a theme of long-standing interest in alternating solitary and social phases. Because the social ecology [36]. At one extreme, there is the hypothesis that— phase involves division of labor with what appears to be an as with large animals—populations tend to be more or less extreme form of “altruism”, the CSMs raise interesting viscous, and spatial structure is determined by patterns of evolutionary questions regarding the origin and maintenance dispersal. At the other extreme, there is the view that of sociality. Knowledge of the genetic structure of social dispersal is rampant (“everything is everywhere”) and what groups in the wild is necessary for answering these persists is determined by adaptations to local conditions. In questions. We confirm that CSMs are widespread in the case of social organisms, an important aspect of spatial undisturbed forest soil from South India. -
What Substrate Cultures Can Reveal: Myxomycetes and Myxomycete-Like Organisms from the Sultanate of Oman
Mycosphere 6 (3): 356–384(2015) ISSN 2077 7019 www.mycosphere.org Article Mycosphere Copyright © 2015 Online Edition Doi 10.5943/mycosphere/6/3/11 What substrate cultures can reveal: Myxomycetes and myxomycete-like organisms from the Sultanate of Oman Schnittler M1, Novozhilov YK2, Shadwick JDL3, Spiegel FW3, García-Carvajal E4, König P1 1Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, Soldmannstr. 15, D-17487 Greifswald, Germany 2V.L. Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov St. 2, 197376 St. Petersburg, Russia 3University of Arkansas, Department of Biological Sciences, SCEN 601, 1 University of Arkansas, Fayetteville, AR 72701, USA 4Royal Botanic Garden (CSIC), Plaza de Murillo, 2, Madrid, E-28014, Spain Schnittler M, Novozhilov YK, Shadwick JDL, Spiegel FW, García-Carvajal E, König P 2015 – What substrate cultures can reveal: Myxomycetes and myxomycete-like organisms from the Sultanate of Oman. Mycosphere 6(3), 356–384, doi 10.5943/mycosphere/6/3/11 Abstract A total of 299 substrate samples collected throughout the Sultanate of Oman were analyzed for myxomycetes and myxomycete-like organisms (MMLO) with a combined approach, preparing one moist chamber culture and one agar culture for each sample. We recovered 8 forms of Myxobacteria, 2 sorocarpic amoebae (Acrasids), 19 known and 6 unknown taxa of protostelioid amoebae (Protostelids), and 50 species of Myxomycetes. Moist chambers and agar cultures completed each other. No method alone can detect the whole diversity of myxomycetes as the most species-rich group of MMLO. A significant overlap between the two methods was observed only for Myxobacteria and some myxomycetes with small sporocarps. -
Raper (Personal Communication) with More Extensive Ex- Perience Has Confirmed This Observation
68 BOTANY: A. L. COHEN PROC. N. A. S. THE EFFECT OF AMMONIA ON MORPHOGENESIS IN THE A CRASIEAE* By ARTHUR L. COHEN OGLETHORPE UNIVERSITY, GEORGIA Communicated by F. W. Went, November 10, 1952 The peculiar separation of mass increase and morphogenesis in the Acrasieae has led to renewed interest by several workers, among them RaPer,1 2 Bonner,3 Gregg,4 and Sussman,5 all of whom have taken advan- tage of this fact. The remarkable life history is well given by Raper6 and by Bonnr.7 The present paper is the initial report of a program of studies on the influence of physicochemical factors in the morphogenesis of these organisms. The Acrasieae described by Olive8 in the most extensive monograph df the group show a well-graded series of increasing complexity as pointed out by Raper6 from the almost chance aggregation of cysts in Sappinia through sessile and stalked fruits in Guttulina and Guttulinopsis in which stalk and spore cells are indistinctly differentiated to the complex differentiation of stalk and spore mass in Dictyostelium and a regularly branching arrange- ment in Polysphondylium. It would therefore be worth while to get a range of these forms in culture for the study of the factors involved in in- creasing morphogenetic complexity. For ten years I have cultured soil samples as opportunity permitted in an attempt to obtain a series of forms. During the last two years a systematic selective culture of 79 soil samples from diverse habitats in Georgia, Florida, Massachusetts, and Michigan has yielded about as many strains of Dictyostelium and Polysphondylium species, but no member of the "lower Acrasieae." Raper (personal communication) with more extensive ex- perience has confirmed this observation. -
Virus World As an Evolutionary Network of Viruses and Capsidless Selfish Elements
Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Koonin, E. V., & Dolja, V. V. (2014). Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements. Microbiology and Molecular Biology Reviews, 78(2), 278-303. doi:10.1128/MMBR.00049-13 10.1128/MMBR.00049-13 American Society for Microbiology Version of Record http://cdss.library.oregonstate.edu/sa-termsofuse Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements Eugene V. Koonin,a Valerian V. Doljab National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USAa; Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USAb Downloaded from SUMMARY ..................................................................................................................................................278 INTRODUCTION ............................................................................................................................................278 PREVALENCE OF REPLICATION SYSTEM COMPONENTS COMPARED TO CAPSID PROTEINS AMONG VIRUS HALLMARK GENES.......................279 CLASSIFICATION OF VIRUSES BY REPLICATION-EXPRESSION STRATEGY: TYPICAL VIRUSES AND CAPSIDLESS FORMS ................................279 EVOLUTIONARY RELATIONSHIPS BETWEEN VIRUSES AND CAPSIDLESS VIRUS-LIKE GENETIC ELEMENTS ..............................................280 Capsidless Derivatives of Positive-Strand RNA Viruses....................................................................................................280 -
2019 International Dictyostelium Conference Ann Arbor, MI 48109, USA
2019 International Dictyostelium Conference Ann Arbor, MI 48109, USA Organizers Cynthia Damer, Central Michigan University Richard Gomer, Texas A&M Carole Parent, University of Michigan Matt Scaglione, Duke University 1 SPONSORS 2 Walking maps from lodging to the Michigan League From Graduate Ann Arbor: 3 From North Quad Residential Hall: 4 From the Residence Inn: 5 Map of the 2nd floor of the Michigan League MICHIGAN LEAGUE Registraton: Concourse Meetng Locaton: Hussey DICTY CONFERENCE 2019 Meals & Posters: Ballroom Michigan League Contact Information: MI League Address: 911 North University Ann Arbor, MI 48109 Information Desk Phone Number: 734-647-5343 6 2019 International Dictyostelium Meeting, Ann Arbor, MI Sunday, August 4th 2:00 – 6:00 Registration – Michigan League Concourse 6:00 – 7:00 Keynote Lecture- Hussey Room Cell migration from a heterotrimeric G protein biologist’s perspective: it all starts here! Alan Smrcka, Ph.D. Benedict R. Lucchesi Collegiate Professor of Cardiovascular Pharmacology Department of Pharmacology, University of Michigan Medical School 7:00 – 10:00 Reception/Mixer- Ballroom 7 Monday, August 5th 7:30 – 9:00 Breakfast- Ballroom Session 1: Cell Biology 1 (9:00 – 10:40)- Hussey Room Chair: Rob Huber, Trent University 9:00 – 9:25 1. Cell-Autonomous and non-autonomous functions for growth and density-dependent development of Dictyostelium regulated by ectodomain shedding Fu-Sheng Chang, Pundrik Jaiswal, Netra Pal Meena, Joseph Brzostowski, and Alan R. Kimmel 9:25 – 9:50 2. Profiling of cytokinin levels during the Dictyostelium life cycle and their effects on cell proliferation and spore germination Megan M. Aoki, Craig Brunetti, Robert J.