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Function-selective domain architecture plasticity potentials in eukaryotic genome evolution

Function-selective domain architecture plasticity potentials in eukaryotic genome evolution
Function-selective domain architecture plasticity potentials in eukaryotic genome evolution
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.
Animals, Cell Lineage, Cell Plasticity, Databases, Genetic, Databases, Protein, Eukaryota/cytology, Evolution, Molecular, Genome, Genomics/methods, Humans, Internet, Models, Genetic, Phylogeny, Protein Structure, Tertiary, Proteome/chemistry, Search Engine, Structural Homology, Protein
0300-9084
269-277
Linkeviciute, Viktorija
892f3b05-4699-4863-90bc-c91c4356cca1
Rackham, Owen J. L.
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Gough, Julian
019ed039-9fd4-45d6-aa7a-12a8fcf7245c
Oates, Matt E.
c90996e2-2ae0-4784-9633-a1db986b1831
Fang, Hai
58424580-2d92-4db2-934f-4c393989cea9
Linkeviciute, Viktorija
892f3b05-4699-4863-90bc-c91c4356cca1
Rackham, Owen J. L.
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Gough, Julian
019ed039-9fd4-45d6-aa7a-12a8fcf7245c
Oates, Matt E.
c90996e2-2ae0-4784-9633-a1db986b1831
Fang, Hai
58424580-2d92-4db2-934f-4c393989cea9

Linkeviciute, Viktorija, Rackham, Owen J. L., Gough, Julian, Oates, Matt E. and Fang, Hai (2015) Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. Biochimie, 119, 269-277. (doi:10.1016/j.biochi.2015.05.003).

Record type: Article

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.

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More information

Accepted/In Press date: 6 May 2015
e-pub ahead of print date: 15 May 2015
Published date: December 2015
Additional Information: Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.
Keywords: Animals, Cell Lineage, Cell Plasticity, Databases, Genetic, Databases, Protein, Eukaryota/cytology, Evolution, Molecular, Genome, Genomics/methods, Humans, Internet, Models, Genetic, Phylogeny, Protein Structure, Tertiary, Proteome/chemistry, Search Engine, Structural Homology, Protein

Identifiers

Local EPrints ID: 446717
URI: http://eprints.soton.ac.uk/id/eprint/446717
ISSN: 0300-9084
PURE UUID: 083cf9dc-07a7-4da8-856e-b275cc132d7c
ORCID for Owen J. L. Rackham: ORCID iD orcid.org/0000-0002-4390-0872

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Date deposited: 19 Feb 2021 17:30
Last modified: 09 Jan 2022 04:11

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Contributors

Author: Viktorija Linkeviciute
Author: Julian Gough
Author: Matt E. Oates
Author: Hai Fang

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