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.
Type
Journal articleSubject
Amoebozoaphytochrome
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
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https://hdl.handle.net/10161/11511Published Version (Please cite this version)
10.1093/gbe/evv237Publication 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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Show full item recordScholars@Duke
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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