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.

Highlights

  • Creating new protein domain arrangements is a frequent mechanism of evolutionary innovation

  • Measures of domain promiscuity and the domain versatility index Existing measures of domain promiscuity First we asked whether different measures for asserting domain promiscuity produce similar results

  • We compared the following methods: number of different direct neighbours of a given domain (NN), number of domains with which a given domain occurs in the same arrangement (NCO) and number of triplets (NTRP) (Tab. 1, see Methods for details)

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Summary

Introduction

Creating 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. Domains are protein structural units that are evolutionarily conserved on sequence level [1,2,3] (see review by Bornberg-Bauer et al [4] and references therein). Domains can be viewed as the building blocks of proteins: most known proteins are composed of a limited number of domains and some other structural units such as coiled-coils. Some domains form (page number not for citation purposes)

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