title: Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.
abstract: To help evaluate how protein function impacts on genome evolution, we introduce a new concept of 'architecture plasticity potential' - the capacity to form distinct domain architectures - both for an individual domain, or more generally for a set of domains grouped by shared function. We devise a scoring metric to measure the plasticity potential for these domain sets, and evaluate how function has changed over time for different species. Applying this metric to a phylogenetic tree of eukaryotic genomes, we find that the involvement of each function is not random but highly selective. For certain lineages there is strong bias for evolution to involve domains related to certain functions. In general eukaryotic genomes, particularly animals, expand complex functional activities such as signalling and regulation, but at the cost of reducing metabolic processes. We also observe differential evolution of transcriptional regulation and a unique evolutionary role of channel regulators; crucially this is only observable in terms of the architecture plasticity potential. Our findings provide a new layer of information to understand the significance of function in eukaryotic genome evolution. A web search tool, available at http://supfam.org/Pevo, offers a wide spectrum of options for exploring functional importance in eukaryotic genome evolution.
authors.affiliation: Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK; School of Biological Sciences, University of Edinburgh, Darwin Building, The King's Buildings, Edinburgh EH9 3BF, UK.
authors.forename: Viktorija
authors.initials: V
authors.lastname: Linkeviciute
authors.affiliation: Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK; Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
authors.forename: Owen J L
authors.initials: OJ
authors.lastname: Rackham
authors.affiliation: Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.
authors.forename: Julian
authors.initials: J
authors.lastname: Gough
authors.affiliation: Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK.
authors.forename: Matt E
authors.initials: ME
authors.lastname: Oates
authors.affiliation: Computational Genomics Group, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Electronic address: hfang@cs.bris.ac.uk.
authors.forename: Hai
authors.initials: H
authors.lastname: Fang
mesh_terms: D000818:Animals; D019070:Cell Lineage; D000066670:Cell Plasticity; D030541:Databases, Genetic; D030562:Databases, Protein; D056890:Eukaryota / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D008957:Models, Genetic; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D057386:Search Engine; D040681:Structural Homology, Protein
chemical_list: D020543:Proteome
keywords: Domain architectures; Eukaryotic genomes; Evolution; Function