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

Date

2015-11-27

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Oxford University Press on behalf of the Society for Molecular Biology and Evolution

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Abstract

Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to the 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 ca. 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, i.e. 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.

Description

Includes supplementary material.

Keywords

Phytochrome, Protein-tyrosine kinase, Cell Cycle Checkpoints, Gene Transfer, Horizontal, Protein Kinases, Dictyostelium discoideum

item.page.sponsorship

National Institutes of Health (NIH) grant HG003079; Wellcome Trust (100293/Z/12/Z); BBSRC BB/K000799/1; German Federal Ministry of Education and Research (BMBF) via the FORSYS program FKZ 0313922; Austrian Science Fund (FWF), P22406; National Institutes of Health (NIH) grant GM54663 and National Science Foundation (NSF) grant MCB-1243687.

Rights

CC BY 4.0 (Attribution), ©2015 The Authors

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