title: Evolution of protein phosphorylation across 18 fungal species.
abstract: Living organisms have evolved protein phosphorylation, a rapid and versatile mechanism that drives signaling and regulates protein function. We report the phosphoproteomes of 18 fungal species and a phylogenetic-based approach to study phosphosite evolution. We observe rapid divergence, with only a small fraction of phosphosites conserved over hundreds of millions of years. Relative to recently acquired phosphosites, ancient sites are enriched at protein interfaces and are more likely to be functionally important, as we show for sites on H2A1 and eIF4E. We also observe a change in phosphorylation motif frequencies and kinase activities that coincides with the whole-genome duplication event. Our results provide an evolutionary history for phosphosites and suggest that rapid evolution of phosphorylation can contribute strongly to phenotypic diversity.
authors.affiliation: European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
authors.forename: Romain A
authors.initials: RA
authors.lastname: Studer
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Ricard A
authors.initials: RA
authors.lastname: Rodriguez-Mias
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Kelsey M
authors.initials: KM
authors.lastname: Haas
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Joanne I
authors.initials: JI
authors.lastname: Hsu
authors.affiliation: Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain. EMBL, Genome Biology Unit, 69117 Heidelberg, Germany.
authors.forename: Cristina
authors.initials: C
authors.lastname: Viéitez
authors.affiliation: Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.
authors.forename: Carme
authors.initials: C
authors.lastname: Solé
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Danielle L
authors.initials: DL
authors.lastname: Swaney
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Lindsay B
authors.initials: LB
authors.lastname: Stanford
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Liachko
authors.affiliation: Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.
authors.forename: René
authors.initials: R
authors.lastname: Böttcher
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
authors.forename: Maitreya J
authors.initials: MJ
authors.lastname: Dunham
authors.affiliation: Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.
authors.forename: Eulàlia
authors.initials: E
authors.lastname: de Nadal
authors.affiliation: Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.
authors.forename: Francesc
authors.initials: F
authors.lastname: Posas
authors.affiliation: European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK. EMBL, Genome Biology Unit, 69117 Heidelberg, Germany. pbeltrao@ebi.ac.uk jvillen@u.washington.edu.
authors.forename: Pedro
authors.initials: P
authors.lastname: Beltrao
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. pbeltrao@ebi.ac.uk jvillen@u.washington.edu.
authors.forename: Judit
authors.initials: J
authors.lastname: Villén
mesh_terms: D000595:Amino Acid Sequence; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D005658:Fungi / Q000235:genetics / Q000378:metabolism*; D016681:Genome, Fungal; D023281:Genomics; D010641:Phenotype; D010750:Phosphoproteins / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D010766:Phosphorylation / Q000235:genetics; D010802:Phylogeny; D011499:Protein Processing, Post-Translational; D017346:Protein Serine-Threonine Kinases / Q000145:classification / Q000235:genetics / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction
chemical_list: D005656:Fungal Proteins; D010750:Phosphoproteins; D020543:Proteome; C071570:SNF1-related protein kinases; D017346:Protein Serine-Threonine Kinases