ArticleBMC evolutionary biology2008
Just how versatile are domains?
Article in BMC evolutionary biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Vector semantics of multidomain protein architectures.Bioinformatics advances · 2026Article
- Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model.Journal of molecular evolution · 2025Article
- Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths.Journal of molecular evolution · 2022Article
- Evolution of networks of protein domain organization.Scientific reports · 2021Article
- Grammar of protein domain architectures.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Predictions of novel Schistosoma mansoni - human protein interactions consistent with experimental data.Scientific reports · 2018Article
- Unique function words characterize genomic proteins.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- The complex evolutionary history of aminoacyl-tRNA synthetases.Nucleic acids research · 2017Article
- Evolution of Protein Domain Repeats in Metazoa.Molecular biology and evolution · 2016Article
- A multi-objective optimization approach accurately resolves protein domain architectures.Bioinformatics (Oxford, England) · 2016Article
- The language of the protein universe.Current opinion in genetics & development · 2015Review
- Function-selective domain architecture plasticity potentials in eukaryotic genome evolution.Biochimie · 2015Article
- Defining the RNA-binding glycine-rich (RBG) gene superfamily: new insights into nomenclature, phylogeny, and evolutionary trends obtained by genome-wide comparative analysis of Arabidopsis, Chinese cabbage, rice and maize genomes.Molecular genetics and genomics : MGG · 2015Article
- Genome-wide analysis of the expansin gene superfamily reveals Brassica rapa-specific evolutionary dynamics upon whole genome triplication.Molecular genetics and genomics : MGG · 2015Article
- Lignocellulose depolymerization occurs via an environmentally adapted metabolic cascades in the wood-rotting basidiomycete Phanerochaete chrysosporium.MicrobiologyOpen · 2015Article
- Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View.PloS one · 2015Article
- Massive expansion of the calpain gene family in unicellular eukaryotes.BMC evolutionary biology · 2012Article
- Evolution of the PWWP-domain encoding genes in the plant and animal lineages.BMC evolutionary biology · 2012Article
- The interface of protein structure, protein biophysics, and molecular evolution.Protein science : a publication of the Protein Society · 2012Review
- Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures.Journal of molecular biology · 2012Article
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3 authors.
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Abstract
backgroundCreating new protein domain arrangements is a frequent mechanism of evolutionary innovation. While some domains always form the same combinations, others form many different arrangements. This ability, which is often referred to as versatility or promiscuity of domains, its a random evolutionary model in which a domain's promiscuity is based on its relative frequency of domains.
resultsWe show that there is a clear relationship across genomes between the promiscuity of a given domain and its frequency. However, the strength of this relationship differs for different domains. We thus redefine domain promiscuity by defining a new index, DV I ("domain versatility index"), which eliminates the effect of domain frequency. We explore links between a domain's versatility, when unlinked from abundance, and its biological properties.
conclusionOur results indicate that domains occurring as single domain proteins and domains appearing frequently at protein termini have a higher DV I. This is consistent with previous observations that the evolution of domain re-arrangements is primarily driven by fusion of pre-existing arrangements and single domains as well as loss of domains at protein termini. Furthermore, we studied the link between domain age, defined as the first appearance of a domain in the species tree, and the DV I. Contrary to previous studies based on domain promiscuity, it seems as if the DV I is age independent. Finally, we find that contrary to previously reported findings, versatility is lower in Eukaryotes. In summary, our measure of domain versatility indicates that a random attachment process is sufficient to explain the observed distribution of domain arrangements and that several views on domain promiscuity need to be revised.
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