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

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Date
2015-11-27
Authors
Schaap, Pauline
Barrantes, Israel
Minx, Pat
Sasaki, Narie
Anderson, Roger W
Bénard, Marianne
Biggar, Kyle K
Buchler, Nicolas E
Bundschuh, Ralf
Chen, Xiao
Fronick, Catrina
Fulton, Lucinda
Golderer, Georg
Jahn, Niels
Knoop, Volker
Landweber, Laura F
Maric, Chrystelle
Miller, Dennis
Noegel, Angelika A
Peace, Rob
Pierron, Gérard
Sasaki, Taeko
Schallenberg-Rüdinger, Mareike
Schleicher, Michael
Singh, Reema
Spaller, Thomas
Storey, Kenneth B
Suzuki, Takamasa
Tomlinson, Chad
Tyson, John J
Warren, Wesley C
Werner, Ernst R
Werner-Felmayer, Gabriele
Wilson, Richard K
Winckler, Thomas
Gott, Jonatha M
Glöckner, Gernot
Marwan, Wolfgang
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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.
Type
Journal article
Subject
Amoebozoa
phytochrome
signaling
two-component system
tyrosine kinase receptor
Cell Cycle Proteins
Evolution, Molecular
Genetic Loci
Genome, Protozoan
Physarum polycephalum
Protozoan Proteins
Receptor Protein-Tyrosine Kinases
Signal Transduction
Transcriptome
Permalink
https://hdl.handle.net/10161/11511
Published Version (Please cite this version)
10.1093/gbe/evv237
Publication Info
Schaap, Pauline; Barrantes, Israel; Minx, Pat; Sasaki, Narie; Anderson, Roger W; Bénard, Marianne; ... Marwan, Wolfgang (2015). The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. Genome Biol Evol, 8(1). pp. 109-125. 10.1093/gbe/evv237. Retrieved from https://hdl.handle.net/10161/11511.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Scholars@Duke

Buchler

Nicolas Buchler

Assistant Professor of Biology
Our lab is interested in the systems biology and evolution of epigenetic switches (bistability) and clocks (oscillators) in gene regulatory networks, two functions that are essential for patterning, cell proliferation, and differentiation in biological systems. We also study biochemical oscillators such as the cell cycle, metabolic rhythms, and circadian clocks, which co-exist in the same cells and interact with one another through shared resources.
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