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Evolutionary history and functional implications of protein domains and their combinations in eukaryotes.

Itoh M, Nacher JC, Kuma K, Goto S, Kanehisa M - Genome Biol. (2007)

Bottom Line: In other groups, the connectivities of older domains were greater on average.Our results indicate that there is a correlation between the differences in domain combinations among different phylogenetic groups and different global behaviors.We therefore suggest that the strategy for achieving complex multicellular systems in animals differs from that of other eukaryotes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

ABSTRACT

Background: In higher multicellular eukaryotes, complex protein domain combinations contribute to various cellular functions such as regulation of intercellular or intracellular signaling and interactions. To elucidate the characteristics and evolutionary mechanisms that underlie such domain combinations, it is essential to examine the different types of domains and their combinations among different groups of eukaryotes.

Results: We observed a large number of group-specific domain combinations in animals, especially in vertebrates. Examples include animal-specific combinations in tyrosine phosphorylation systems and vertebrate-specific combinations in complement and coagulation cascades. These systems apparently underwent extensive evolution in the ancestors of these groups. In extant animals, especially in vertebrates, animal-specific domains have greater connectivity than do other domains on average, and contribute to the varying number of combinations in each animal subgroup. In other groups, the connectivities of older domains were greater on average. To observe the global behavior of domain combinations during evolution, we traced the changes in domain combinations among animals and fungi in a network analysis. Our results indicate that there is a correlation between the differences in domain combinations among different phylogenetic groups and different global behaviors.

Conclusion: Rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no such trends were observed in other clades of eukaryotes. We therefore suggest that the strategy for achieving complex multicellular systems in animals differs from that of other eukaryotes.

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Domain combination. (a) Domain architectures in a protein set can be represented as a network. A domain corresponds to a node, and edges refer to the co-occurrence or combination of a domain in the protein set under consideration. In a domain co-occurrence network, two domains are connected by an edge if they co-occurred in the same protein sequence. Here, we considered a domain combination network in which two domains must be located consecutively. Domain B is located between domains A and C, and so nodes A and C are not connected. (b) Combinations (A + B) and (B + A) are distinguished in this work.
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Figure 2: Domain combination. (a) Domain architectures in a protein set can be represented as a network. A domain corresponds to a node, and edges refer to the co-occurrence or combination of a domain in the protein set under consideration. In a domain co-occurrence network, two domains are connected by an edge if they co-occurred in the same protein sequence. Here, we considered a domain combination network in which two domains must be located consecutively. Domain B is located between domains A and C, and so nodes A and C are not connected. (b) Combinations (A + B) and (B + A) are distinguished in this work.

Mentions: Domain combinations can be defined in several ways, such as by co-occurrence in a protein sequence. Here, in order to distinguish domain architectures possibly generated by individual evolutionary events, we defined a combination as two consecutively located domains (Figure 2a). We also distinguished between combinations when the order of two domains on a protein was inverted (Figure 2b). In total, 6,977 unique combinations were found in the 47 eukaryote protein sets (Figure 1). The number of domain combinations found in multicellular animals was large (>800), as well as in the multicellular fungi (Neurospora crassa and Magnaporthe grisea), land plants (Arabidopsis thaliana and Oryza sativa), and Dictyostelium discoideum (about 700 to 1,500). It should be noted that species with a large number of proteins do not always have a large number of domain combinations; for instance, Entamoeba histolytica and Trypanosoma cruzi have large numbers of proteins and few combinations.


Evolutionary history and functional implications of protein domains and their combinations in eukaryotes.

Itoh M, Nacher JC, Kuma K, Goto S, Kanehisa M - Genome Biol. (2007)

Domain combination. (a) Domain architectures in a protein set can be represented as a network. A domain corresponds to a node, and edges refer to the co-occurrence or combination of a domain in the protein set under consideration. In a domain co-occurrence network, two domains are connected by an edge if they co-occurred in the same protein sequence. Here, we considered a domain combination network in which two domains must be located consecutively. Domain B is located between domains A and C, and so nodes A and C are not connected. (b) Combinations (A + B) and (B + A) are distinguished in this work.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394772&req=5

Figure 2: Domain combination. (a) Domain architectures in a protein set can be represented as a network. A domain corresponds to a node, and edges refer to the co-occurrence or combination of a domain in the protein set under consideration. In a domain co-occurrence network, two domains are connected by an edge if they co-occurred in the same protein sequence. Here, we considered a domain combination network in which two domains must be located consecutively. Domain B is located between domains A and C, and so nodes A and C are not connected. (b) Combinations (A + B) and (B + A) are distinguished in this work.
Mentions: Domain combinations can be defined in several ways, such as by co-occurrence in a protein sequence. Here, in order to distinguish domain architectures possibly generated by individual evolutionary events, we defined a combination as two consecutively located domains (Figure 2a). We also distinguished between combinations when the order of two domains on a protein was inverted (Figure 2b). In total, 6,977 unique combinations were found in the 47 eukaryote protein sets (Figure 1). The number of domain combinations found in multicellular animals was large (>800), as well as in the multicellular fungi (Neurospora crassa and Magnaporthe grisea), land plants (Arabidopsis thaliana and Oryza sativa), and Dictyostelium discoideum (about 700 to 1,500). It should be noted that species with a large number of proteins do not always have a large number of domain combinations; for instance, Entamoeba histolytica and Trypanosoma cruzi have large numbers of proteins and few combinations.

Bottom Line: In other groups, the connectivities of older domains were greater on average.Our results indicate that there is a correlation between the differences in domain combinations among different phylogenetic groups and different global behaviors.We therefore suggest that the strategy for achieving complex multicellular systems in animals differs from that of other eukaryotes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.

ABSTRACT

Background: In higher multicellular eukaryotes, complex protein domain combinations contribute to various cellular functions such as regulation of intercellular or intracellular signaling and interactions. To elucidate the characteristics and evolutionary mechanisms that underlie such domain combinations, it is essential to examine the different types of domains and their combinations among different groups of eukaryotes.

Results: We observed a large number of group-specific domain combinations in animals, especially in vertebrates. Examples include animal-specific combinations in tyrosine phosphorylation systems and vertebrate-specific combinations in complement and coagulation cascades. These systems apparently underwent extensive evolution in the ancestors of these groups. In extant animals, especially in vertebrates, animal-specific domains have greater connectivity than do other domains on average, and contribute to the varying number of combinations in each animal subgroup. In other groups, the connectivities of older domains were greater on average. To observe the global behavior of domain combinations during evolution, we traced the changes in domain combinations among animals and fungi in a network analysis. Our results indicate that there is a correlation between the differences in domain combinations among different phylogenetic groups and different global behaviors.

Conclusion: Rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no such trends were observed in other clades of eukaryotes. We therefore suggest that the strategy for achieving complex multicellular systems in animals differs from that of other eukaryotes.

Show MeSH