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Functional Evolution of BRCT Domains from Binding DNA to Protein.

Sheng ZZ, Zhao YQ, Huang JF - Evol. Bioinform. Online (2011)

Bottom Line: The third phase is after the divergence between animals and plants.Both sGroup I and sGroup II BRCT domains originating in this phase lost the phosphate-binding pocket and many evolved protein-binding sites.Many dGroup I members were evolved in this stage but few dGroup II members were observed.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

ABSTRACT
The BRCT domain (BRCA1 C-terminal domain) is an important signaling and protein targeting motif in the DNA damage response system. The BRCT domain, which mainly occurs as a singleton (single BRCT) or tandem pair (double BRCT), contains a phosphate-binding pocket that can bind the phosphate from either the DNA end or a phosphopeptide. In this work, we performed a database search, phylogeny reconstruction, and phosphate-binding pocket comparison to analyze the functional evolution of the BRCT domain. We identified new BRCT-containing proteins in bacteria and eukaryotes, and found that the number of BRCT-containing proteins per genome is correlated with genome complexity. Phylogeny analyses revealed that there are two groups of single BRCT domains (sGroup I and sGroup II) and double BRCT domains (dGroup I and dGroup II). These four BRCT groups differ in their phosphate-binding pockets. In eukaryotes, the evolution of the BRCT domain can be divided into three phases. In the first phase, the sGroup I BRCT domain with the phosphate-binding pocket that can bind the phosphate of nicked DNA invaded eukaryotic genome. In the second phase, the phosphate-binding pocket changed from a DNA-binding type to a protein-binding type in sGroup II. The tandem duplication of sGroup II BRCT domain gave birth to double BRCT domain, from which two structurally and functionally distinct groups were evolved. The third phase is after the divergence between animals and plants. Both sGroup I and sGroup II BRCT domains originating in this phase lost the phosphate-binding pocket and many evolved protein-binding sites. Many dGroup I members were evolved in this stage but few dGroup II members were observed. The results further suggested that the BRCT domain expansion and functional change in eukaryote may be driven by the evolution of the DNA damage response system.

No MeSH data available.


Related in: MedlinePlus

Domain architectures of bacteria and eukaryote BRCT-containing proteins. New observed BRCT domains are colored with blue rectangles, while known ones are colored with green rectangles. The red color region in the middle of BRCT domain represents insertion. Domain architectures were predicted by HMMER. Protein names are linked with species name underlined. The species or clades distribution of these new observed BRCT-containing proteins are: DNA polymerase III ɛ subunit in species of Actinobacteria, Firmicutes, Proteobacteria, and Planctomycetes; PARP3 in clade Magnoliophyta; N-acetylase in Viridiplantae; CHS5 in Fungi; TOPBP1 in eukaryotes; ECT2 in metazoan; MUTATOR2 in Drosophila; ANKRD32 in vertebrates; BAF155 in eukaryotes. Other new observed BRCT-containing proteins are only identified in one species.
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f1-ebo-7-2011-087: Domain architectures of bacteria and eukaryote BRCT-containing proteins. New observed BRCT domains are colored with blue rectangles, while known ones are colored with green rectangles. The red color region in the middle of BRCT domain represents insertion. Domain architectures were predicted by HMMER. Protein names are linked with species name underlined. The species or clades distribution of these new observed BRCT-containing proteins are: DNA polymerase III ɛ subunit in species of Actinobacteria, Firmicutes, Proteobacteria, and Planctomycetes; PARP3 in clade Magnoliophyta; N-acetylase in Viridiplantae; CHS5 in Fungi; TOPBP1 in eukaryotes; ECT2 in metazoan; MUTATOR2 in Drosophila; ANKRD32 in vertebrates; BAF155 in eukaryotes. Other new observed BRCT-containing proteins are only identified in one species.

Mentions: Database search results showed that BRCT-containing proteins are mainly observed in bacteria and eukaryotes. In bacteria, eight further species-specific single BRCT-containing proteins were identified (Fig. 1 and Table S1), the BRCT domains of which show high sequence identity with that of bacteria NAD+-dependent DNA ligase (average identity approximately 40%). In eukaryotes, new BRCT-containing proteins were also identified, including BRG1-associated factor BAF155, BAF170, ANK-containing protein ANKRD32, and GCN5-related N-acetyltransferase (Fig. 1 and Fig. S1). Because most archaea lineages do not contain BRCT-containing protein, except for the homolog of bacteria NAD+-dependent DNA ligase in some species of euryarchaeotes, these results are consistent with the hypothesis that the eukaryotic BRCT domain may be from bacteria through horizontal gene transfer.13


Functional Evolution of BRCT Domains from Binding DNA to Protein.

Sheng ZZ, Zhao YQ, Huang JF - Evol. Bioinform. Online (2011)

Domain architectures of bacteria and eukaryote BRCT-containing proteins. New observed BRCT domains are colored with blue rectangles, while known ones are colored with green rectangles. The red color region in the middle of BRCT domain represents insertion. Domain architectures were predicted by HMMER. Protein names are linked with species name underlined. The species or clades distribution of these new observed BRCT-containing proteins are: DNA polymerase III ɛ subunit in species of Actinobacteria, Firmicutes, Proteobacteria, and Planctomycetes; PARP3 in clade Magnoliophyta; N-acetylase in Viridiplantae; CHS5 in Fungi; TOPBP1 in eukaryotes; ECT2 in metazoan; MUTATOR2 in Drosophila; ANKRD32 in vertebrates; BAF155 in eukaryotes. Other new observed BRCT-containing proteins are only identified in one species.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3140412&req=5

f1-ebo-7-2011-087: Domain architectures of bacteria and eukaryote BRCT-containing proteins. New observed BRCT domains are colored with blue rectangles, while known ones are colored with green rectangles. The red color region in the middle of BRCT domain represents insertion. Domain architectures were predicted by HMMER. Protein names are linked with species name underlined. The species or clades distribution of these new observed BRCT-containing proteins are: DNA polymerase III ɛ subunit in species of Actinobacteria, Firmicutes, Proteobacteria, and Planctomycetes; PARP3 in clade Magnoliophyta; N-acetylase in Viridiplantae; CHS5 in Fungi; TOPBP1 in eukaryotes; ECT2 in metazoan; MUTATOR2 in Drosophila; ANKRD32 in vertebrates; BAF155 in eukaryotes. Other new observed BRCT-containing proteins are only identified in one species.
Mentions: Database search results showed that BRCT-containing proteins are mainly observed in bacteria and eukaryotes. In bacteria, eight further species-specific single BRCT-containing proteins were identified (Fig. 1 and Table S1), the BRCT domains of which show high sequence identity with that of bacteria NAD+-dependent DNA ligase (average identity approximately 40%). In eukaryotes, new BRCT-containing proteins were also identified, including BRG1-associated factor BAF155, BAF170, ANK-containing protein ANKRD32, and GCN5-related N-acetyltransferase (Fig. 1 and Fig. S1). Because most archaea lineages do not contain BRCT-containing protein, except for the homolog of bacteria NAD+-dependent DNA ligase in some species of euryarchaeotes, these results are consistent with the hypothesis that the eukaryotic BRCT domain may be from bacteria through horizontal gene transfer.13

Bottom Line: The third phase is after the divergence between animals and plants.Both sGroup I and sGroup II BRCT domains originating in this phase lost the phosphate-binding pocket and many evolved protein-binding sites.Many dGroup I members were evolved in this stage but few dGroup II members were observed.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.

ABSTRACT
The BRCT domain (BRCA1 C-terminal domain) is an important signaling and protein targeting motif in the DNA damage response system. The BRCT domain, which mainly occurs as a singleton (single BRCT) or tandem pair (double BRCT), contains a phosphate-binding pocket that can bind the phosphate from either the DNA end or a phosphopeptide. In this work, we performed a database search, phylogeny reconstruction, and phosphate-binding pocket comparison to analyze the functional evolution of the BRCT domain. We identified new BRCT-containing proteins in bacteria and eukaryotes, and found that the number of BRCT-containing proteins per genome is correlated with genome complexity. Phylogeny analyses revealed that there are two groups of single BRCT domains (sGroup I and sGroup II) and double BRCT domains (dGroup I and dGroup II). These four BRCT groups differ in their phosphate-binding pockets. In eukaryotes, the evolution of the BRCT domain can be divided into three phases. In the first phase, the sGroup I BRCT domain with the phosphate-binding pocket that can bind the phosphate of nicked DNA invaded eukaryotic genome. In the second phase, the phosphate-binding pocket changed from a DNA-binding type to a protein-binding type in sGroup II. The tandem duplication of sGroup II BRCT domain gave birth to double BRCT domain, from which two structurally and functionally distinct groups were evolved. The third phase is after the divergence between animals and plants. Both sGroup I and sGroup II BRCT domains originating in this phase lost the phosphate-binding pocket and many evolved protein-binding sites. Many dGroup I members were evolved in this stage but few dGroup II members were observed. The results further suggested that the BRCT domain expansion and functional change in eukaryote may be driven by the evolution of the DNA damage response system.

No MeSH data available.


Related in: MedlinePlus