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Genome Biol Evol. 2015 Nov 27;8(1):109-25. doi: 10.1093/gbe/evv237.

The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling.

Author information

1
School of Life Sciences, University of Dundee, Dundee, United Kingdom.
2
Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany.
3
The Genome Institute, Washington University School of Medicine, St Louis.
4
Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan.
5
Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom.
6
UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR-7622, Paris, France.
7
Biochemistry Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.
8
Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham Department of Physics, Duke University, Durham.
9
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.
10
Department of Ecology & Evolutionary Biology, Princeton University, Princeton.
11
Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria.
12
Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany.
13
IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany.
14
Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France.
15
The University of Texas at Dallas, Biological Sciences, Richardson.
16
Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany.
17
Carleton University, Ottawa, Ontario, Canada.
18
Institute for Anatomy III / Cell Biology, BioMedCenter, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany.
19
Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany.
20
Department of Biological Sciences, Graduate School of Science and JST ERATO Higashiyama Live-holonics Project, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan.
21
Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg.
22
Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, Cleveland.
23
Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
24
Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany wolfgang.marwan@ovgu.de.

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.

KEYWORDS:

Amoebozoa; phytochrome; signaling; two-component system; tyrosine kinase receptor

PMID:
26615215
PMCID:
PMC4758236
DOI:
10.1093/gbe/evv237
[Indexed for MEDLINE]
Free PMC Article

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