title: The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.
abstract: Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.
authors.affiliation: School of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Pauline
authors.initials: P
authors.lastname: Schaap
authors.affiliation: Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany.
authors.forename: Israel
authors.initials: I
authors.lastname: Barrantes
authors.affiliation: The Genome Institute, Washington University School of Medicine, St Louis.
authors.forename: Pat
authors.initials: P
authors.lastname: Minx
authors.affiliation: Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan.
authors.forename: Narie
authors.initials: N
authors.lastname: Sasaki
authors.affiliation: Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
authors.forename: Roger W
authors.initials: RW
authors.lastname: Anderson
authors.affiliation: UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR-7622, Paris, France.
authors.forename: Marianne
authors.initials: M
authors.lastname: Bénard
authors.affiliation: Biochemistry Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
authors.forename: Kyle K
authors.initials: KK
authors.lastname: Biggar
authors.affiliation: Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham Department of Physics, Duke University, Durham.
authors.forename: Nicolas E
authors.initials: NE
authors.lastname: Buchler
authors.affiliation: Department of Physics and Center for RNA Biology, The Ohio State University, Columbus Department of Chemistry & Biochemistry, The Ohio State University, Columbus Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus.
authors.forename: Ralf
authors.initials: R
authors.lastname: Bundschuh
authors.affiliation: Department of Ecology & Evolutionary Biology, Princeton University, Princeton.
authors.forename: Xiao
authors.initials: X
authors.lastname: Chen
authors.affiliation: The Genome Institute, Washington University School of Medicine, St Louis.
authors.forename: Catrina
authors.initials: C
authors.lastname: Fronick
authors.affiliation: The Genome Institute, Washington University School of Medicine, St Louis.
authors.forename: Lucinda
authors.initials: L
authors.lastname: Fulton
authors.affiliation: Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Georg
authors.initials: G
authors.lastname: Golderer
authors.affiliation: Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
authors.forename: Niels
authors.initials: N
authors.lastname: Jahn
authors.affiliation: IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany.
authors.forename: Volker
authors.initials: V
authors.lastname: Knoop
authors.affiliation: Department of Ecology & Evolutionary Biology, Princeton University, Princeton.
authors.forename: Laura F
authors.initials: LF
authors.lastname: Landweber
authors.affiliation: Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France.
authors.forename: Chrystelle
authors.initials: C
authors.lastname: Maric
authors.affiliation: The University of Texas at Dallas, Biological Sciences, Richardson.
authors.forename: Dennis
authors.initials: D
authors.lastname: Miller
authors.affiliation: Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany.
authors.forename: Angelika A
authors.initials: AA
authors.lastname: Noegel
authors.affiliation: Carleton University, Ottawa, Ontario, Canada.
authors.forename: Rob
authors.initials: R
authors.lastname: Peace
authors.affiliation: Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France.
authors.forename: Gérard
authors.initials: G
authors.lastname: Pierron
authors.affiliation: Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan.
authors.forename: Taeko
authors.initials: T
authors.lastname: Sasaki
authors.affiliation: IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany.
authors.forename: Mareike
authors.initials: M
authors.lastname: Schallenberg-Rüdinger
authors.affiliation: Institute for Anatomy III / Cell Biology, BioMedCenter, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Schleicher
authors.affiliation: School of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Reema
authors.initials: R
authors.lastname: Singh
authors.affiliation: Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Spaller
authors.affiliation: Carleton University, Ottawa, Ontario, Canada.
authors.forename: Kenneth B
authors.initials: KB
authors.lastname: Storey
authors.affiliation: Department of Biological Sciences, Graduate School of Science and JST ERATO Higashiyama Live-holonics Project, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan.
authors.forename: Takamasa
authors.initials: T
authors.lastname: Suzuki
authors.affiliation: The Genome Institute, Washington University School of Medicine, St Louis.
authors.forename: Chad
authors.initials: C
authors.lastname: Tomlinson
authors.affiliation: Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg.
authors.forename: John J
authors.initials: JJ
authors.lastname: Tyson
authors.affiliation: The Genome Institute, Washington University School of Medicine, St Louis.
authors.forename: Wesley C
authors.initials: WC
authors.lastname: Warren
authors.affiliation: Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Ernst R
authors.initials: ER
authors.lastname: Werner
authors.affiliation: Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Werner-Felmayer
authors.affiliation: The Genome Institute, Washington University School of Medicine, St Louis.
authors.forename: Richard K
authors.initials: RK
authors.lastname: Wilson
authors.affiliation: Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Winckler
authors.affiliation: Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, Cleveland.
authors.forename: Jonatha M
authors.initials: JM
authors.lastname: Gott
authors.affiliation: Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
authors.forename: Gernot
authors.initials: G
authors.lastname: Glöckner
authors.affiliation: Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany wolfgang.marwan@ovgu.de.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Marwan
mesh_terms: D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D056426:Genetic Loci; D018503:Genome, Protozoan; D016839:Physarum polycephalum / Q000235:genetics*; D015800:Protozoan Proteins / Q000235:genetics* / Q000378:metabolism; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D018797:Cell Cycle Proteins; D015800:Protozoan Proteins; D020794:Receptor Protein-Tyrosine Kinases
keywords: Amoebozoa; phytochrome; signaling; two-component system; tyrosine kinase receptor