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

dc.contributor.authorSchaap, Paulineen_US
dc.contributor.authorBarrantes, Israelen_US
dc.contributor.authorMinx, Paten_US
dc.contributor.authorSasaki, Narieen_US
dc.contributor.authorAnderson, Roger W.en_US
dc.contributor.authorB©nard, Marianneen_US
dc.contributor.authorBiggar, Kyle K.en_US
dc.contributor.authorMiller, Dennis L.en_US
dc.contributor.utdAuthorMiller, Dennis L.en_US
dc.date.accessioned2017-02-27T22:01:03Z
dc.date.available2017-02-27T22:01:03Z
dc.date.created2015-11-27en_US
dc.date.issued2015-11-27en_US
dc.descriptionIncludes supplementary material.en_US
dc.description.abstractPhysarum 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.en_US
dc.description.sponsorshipNational 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.en_US
dc.identifier.bibliographicCitationSchaap, Pauline, Israel Barrantes, Pat Minx, Narie Sasaki, et al. 2015. "The Physarum polycephalum genome reveals extensive use of prokaryotic two-component and metazoan-type tyrosine kinase signaling." Genome Biology and Evolution 8(1), doi:10.1093/gbe/evv237.en_US
dc.identifier.issn1759-6653en_US
dc.identifier.issue1en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/5300
dc.identifier.volume8en_US
dc.publisherOxford University Press on behalf of the Society for Molecular Biology and Evolutionen_US
dc.relation.urihttp://dx.doi.org/10.1093/gbe/ew/237
dc.rightsCC BY 4.0 (Attribution)en_US
dc.rights©2015 The Authorsen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.sourceGenome Biology and Evolution
dc.subjectPhytochromeen_US
dc.subjectProtein-tyrosine kinaseen_US
dc.subjectCell Cycle Checkpointsen_US
dc.subjectGene Transfer, Horizontalen_US
dc.subjectProtein Kinasesen_US
dc.subjectDictyostelium discoideumen_US
dc.titleThe Physarum Polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signalingen_US
dc.type.genreArticleen_US

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