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Evolution of protein domain architectures

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Item Type:Article
Title:Evolution of protein domain architectures
Creators Name:Forslund, S.K. and Kaduk, M. and Sonnhammer, E.L.L.
Abstract:This chapter reviews current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this will directly impact which domain architectures can be formed in different species. Studies relating domain family size to occurrence have shown that they generally follow power law distributions, both within genomes and larger evolutionary groups. These findings were subsequently extended to multi-domain architectures. Genome evolution models that have been suggested to explain the shape of these distributions are reviewed, as well as evidence for selective pressure to expand certain domain families more than others. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain arrangements. Following this, we review inferences of ancestral domain architecture and the conclusions concerning domain architecture evolution mechanisms that can be drawn from these. Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly). We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution.
Keywords:Protein Domain, Protein Domain Architecture, Superfamily, Monophyly, Polyphyly, Convergent Evolution, Domain Evolution, Kingdoms of Life, Domain Co-Occurrence Network, Node Degree Distribution, Power Law, Parsimony
Source:Methods in Molecular Biology
Series Name:Methods in Molecular Biology
Title of Book:Evolutionary Genomics
Publisher:Springer / Humana Press
Page Range:469-504
Official Publication:https://doi.org/10.1007/978-1-4939-9074-0_15
PubMed:View item in PubMed

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