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Just how versatile are domains?

Weiner J, Moore AD, Bornberg-Bauer E - BMC Evol. Biol. (2008)

Bottom Line: We thus redefine domain promiscuity by defining a new index, DV I ("domain versatility index"), which eliminates the effect of domain frequency.Our results indicate that domains occurring as single domain proteins and domains appearing frequently at protein termini have a higher DV I.Finally, we find that contrary to previously reported findings, versatility is lower in Eukaryotes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Evolution and Biodiversity, Evolutionary Bioinformatics Group, Westphalian Wilhelms-University, Münster, Germany. january@uni-muenster.de

ABSTRACT

Background: 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.

Results: We 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.

Conclusion: Our 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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The relationship between the DVI, domain position and domain age. Left: Domain age and the DV I. OLD – domains that are common to all three main branches of life (Bacteria, Archea, Eukaryota); MID – domains that are present in all taxons of one of these branches (e.g. domains that can be found only in Bacteria, but not in Archea or Eukaryota); NEW – domains that are present only in one subgroup of one of these branches (e.g. domains that occur only in vertebrates). Right: DV I and position of the domain within the protein. NTERM – N-terminal domains; NTERM1 – next-to N-terminal domains in proteins with four domains or more; CTERM – C-terminal domains; CTERM1 – next-to N-terminal domains in proteins with four domains or more; MID – all remaining (non-terminal) domains; SINGLE – domains in single-domain proteins. On the y axis, domain versatility index (DV I). Bold line denotes the median; boxes denote the firstand second quartiles; whiskers show the minimum and maximum values not including outliers.
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Figure 4: The relationship between the DVI, domain position and domain age. Left: Domain age and the DV I. OLD – domains that are common to all three main branches of life (Bacteria, Archea, Eukaryota); MID – domains that are present in all taxons of one of these branches (e.g. domains that can be found only in Bacteria, but not in Archea or Eukaryota); NEW – domains that are present only in one subgroup of one of these branches (e.g. domains that occur only in vertebrates). Right: DV I and position of the domain within the protein. NTERM – N-terminal domains; NTERM1 – next-to N-terminal domains in proteins with four domains or more; CTERM – C-terminal domains; CTERM1 – next-to N-terminal domains in proteins with four domains or more; MID – all remaining (non-terminal) domains; SINGLE – domains in single-domain proteins. On the y axis, domain versatility index (DV I). Bold line denotes the median; boxes denote the firstand second quartiles; whiskers show the minimum and maximum values not including outliers.

Mentions: We wanted, however, to know, whether older domains are intrinsically more versatile than younger domains. Specifically, we ask whether domains that originated at the root of the tree of life have a significantly different DV I from domains that originated later. We did not find any significant differences (p = 0.16 in a one-way ANOVA). Since the domains that are specific to a clade are generally younger than domains spread throughout the tree of life, this finding shows that the average DV I does not depend on the age of a domain (Fig. 4). This means that domains arising at any time during the evolution have the same chance of becoming versatile.


Just how versatile are domains?

Weiner J, Moore AD, Bornberg-Bauer E - BMC Evol. Biol. (2008)

The relationship between the DVI, domain position and domain age. Left: Domain age and the DV I. OLD – domains that are common to all three main branches of life (Bacteria, Archea, Eukaryota); MID – domains that are present in all taxons of one of these branches (e.g. domains that can be found only in Bacteria, but not in Archea or Eukaryota); NEW – domains that are present only in one subgroup of one of these branches (e.g. domains that occur only in vertebrates). Right: DV I and position of the domain within the protein. NTERM – N-terminal domains; NTERM1 – next-to N-terminal domains in proteins with four domains or more; CTERM – C-terminal domains; CTERM1 – next-to N-terminal domains in proteins with four domains or more; MID – all remaining (non-terminal) domains; SINGLE – domains in single-domain proteins. On the y axis, domain versatility index (DV I). Bold line denotes the median; boxes denote the firstand second quartiles; whiskers show the minimum and maximum values not including outliers.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2588589&req=5

Figure 4: The relationship between the DVI, domain position and domain age. Left: Domain age and the DV I. OLD – domains that are common to all three main branches of life (Bacteria, Archea, Eukaryota); MID – domains that are present in all taxons of one of these branches (e.g. domains that can be found only in Bacteria, but not in Archea or Eukaryota); NEW – domains that are present only in one subgroup of one of these branches (e.g. domains that occur only in vertebrates). Right: DV I and position of the domain within the protein. NTERM – N-terminal domains; NTERM1 – next-to N-terminal domains in proteins with four domains or more; CTERM – C-terminal domains; CTERM1 – next-to N-terminal domains in proteins with four domains or more; MID – all remaining (non-terminal) domains; SINGLE – domains in single-domain proteins. On the y axis, domain versatility index (DV I). Bold line denotes the median; boxes denote the firstand second quartiles; whiskers show the minimum and maximum values not including outliers.
Mentions: We wanted, however, to know, whether older domains are intrinsically more versatile than younger domains. Specifically, we ask whether domains that originated at the root of the tree of life have a significantly different DV I from domains that originated later. We did not find any significant differences (p = 0.16 in a one-way ANOVA). Since the domains that are specific to a clade are generally younger than domains spread throughout the tree of life, this finding shows that the average DV I does not depend on the age of a domain (Fig. 4). This means that domains arising at any time during the evolution have the same chance of becoming versatile.

Bottom Line: We thus redefine domain promiscuity by defining a new index, DV I ("domain versatility index"), which eliminates the effect of domain frequency.Our results indicate that domains occurring as single domain proteins and domains appearing frequently at protein termini have a higher DV I.Finally, we find that contrary to previously reported findings, versatility is lower in Eukaryotes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Evolution and Biodiversity, Evolutionary Bioinformatics Group, Westphalian Wilhelms-University, Münster, Germany. january@uni-muenster.de

ABSTRACT

Background: 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.

Results: We 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.

Conclusion: Our 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.

Show MeSH
Related in: MedlinePlus