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Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.

Hatayama M, Aruga J - BMC Evol. Biol. (2010)

Bottom Line: We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates) and Amoebozoa (amoeba, Dictyostelium discoideum).Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs).These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan.

ABSTRACT

Background: The C2H2 zinc finger (ZF) domain is widely conserved among eukaryotic proteins. In Zic/Gli/Zap1 C2H2 ZF proteins, the two N-terminal ZFs form a single structural unit by sharing a hydrophobic core. This structural unit defines a new motif comprised of two tryptophan side chains at the center of the hydrophobic core. Because each tryptophan residue is located between the two cysteine residues of the C2H2 motif, we have named this structure the tandem CWCH2 (tCWCH2) motif.

Results: Here, we characterized 587 tCWCH2-containing genes using data derived from public databases. We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates) and Amoebozoa (amoeba, Dictyostelium discoideum). By comparison, the C2H2 ZF motif is distributed widely among the eukaryotes. The structure and organization of the tCWCH2 motif, its phylogenetic distribution, and molecular phylogenetic analysis suggest that prototypical tCWCH2 genes existed in the Opisthokonta ancestor. Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs).

Conclusion: These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.

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Sequence conservation among the classes of tCWCH2 sequence motifs. Amino acid sequences were aligned and consensus sequences were generated (see Methods). Mizf ZF1-2, Mizf ZF3-4, and Zap1/ZafA ZF1-2 and ZF3-4 are indicated separately. The PDOC00028 C2H2 consensus is shown at the bottom as a general C2H2 consensus sequence (indicated by the tandem repeat of the consensus sequence). The short insertion sequences listed below were initially located at the sites indicated by the colored arrowheads in the alignments described above, but were separated to allow more comprehensive analyses. These sequences represent the longer linker sequences and the insertion of extra sequences described in the Results section. To achieve this analysis we omitted the four sequences AAWT01013938 (Schmidtea mediterranea Aebp2), CAG05504 (Tetraodon nigroviridis Gli), XP_001602003 (Nasonia vitripennis Gli), and XP_785526 (Strongylocentrotus purpuratus Gli) because these sequences contain exceptionally divergent sequences that disrupt the alignments.
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Figure 5: Sequence conservation among the classes of tCWCH2 sequence motifs. Amino acid sequences were aligned and consensus sequences were generated (see Methods). Mizf ZF1-2, Mizf ZF3-4, and Zap1/ZafA ZF1-2 and ZF3-4 are indicated separately. The PDOC00028 C2H2 consensus is shown at the bottom as a general C2H2 consensus sequence (indicated by the tandem repeat of the consensus sequence). The short insertion sequences listed below were initially located at the sites indicated by the colored arrowheads in the alignments described above, but were separated to allow more comprehensive analyses. These sequences represent the longer linker sequences and the insertion of extra sequences described in the Results section. To achieve this analysis we omitted the four sequences AAWT01013938 (Schmidtea mediterranea Aebp2), CAG05504 (Tetraodon nigroviridis Gli), XP_001602003 (Nasonia vitripennis Gli), and XP_785526 (Strongylocentrotus purpuratus Gli) because these sequences contain exceptionally divergent sequences that disrupt the alignments.

Mentions: We generated tCWCH2 consensus sequences for each gene class as well as for all classes to identify any additional sequence features. The Prosite database PDOC00028 alignment was used for the reference consensus sequence of general C2H2. The extent of conservation is indicated by the size of letters, and the consensus sequences are aligned graphically (Figure 5). Classical C2H2 ZFs are known to have a consensus sequence of "(F/Y)xCx2CxFx7Lx2Hx4H" [1]. The tCWCH2 motifs also contain conserved phenylalanine and leucine residues between the cysteine and histidine residues. Phenylalanine and leucine are hydrophobic residues that generally mediate a hydrophobic interaction within a single ZF (data not shown). These data indicate that the general structure of a single ZF is well conserved in the tCWCH2 motif (Figure 6A) and that there are some tCWCH2-specific structures apart from the conserved tryptophan residues.


Characterization of the tandem CWCH2 sequence motif: a hallmark of inter-zinc finger interactions.

Hatayama M, Aruga J - BMC Evol. Biol. (2010)

Sequence conservation among the classes of tCWCH2 sequence motifs. Amino acid sequences were aligned and consensus sequences were generated (see Methods). Mizf ZF1-2, Mizf ZF3-4, and Zap1/ZafA ZF1-2 and ZF3-4 are indicated separately. The PDOC00028 C2H2 consensus is shown at the bottom as a general C2H2 consensus sequence (indicated by the tandem repeat of the consensus sequence). The short insertion sequences listed below were initially located at the sites indicated by the colored arrowheads in the alignments described above, but were separated to allow more comprehensive analyses. These sequences represent the longer linker sequences and the insertion of extra sequences described in the Results section. To achieve this analysis we omitted the four sequences AAWT01013938 (Schmidtea mediterranea Aebp2), CAG05504 (Tetraodon nigroviridis Gli), XP_001602003 (Nasonia vitripennis Gli), and XP_785526 (Strongylocentrotus purpuratus Gli) because these sequences contain exceptionally divergent sequences that disrupt the alignments.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2837044&req=5

Figure 5: Sequence conservation among the classes of tCWCH2 sequence motifs. Amino acid sequences were aligned and consensus sequences were generated (see Methods). Mizf ZF1-2, Mizf ZF3-4, and Zap1/ZafA ZF1-2 and ZF3-4 are indicated separately. The PDOC00028 C2H2 consensus is shown at the bottom as a general C2H2 consensus sequence (indicated by the tandem repeat of the consensus sequence). The short insertion sequences listed below were initially located at the sites indicated by the colored arrowheads in the alignments described above, but were separated to allow more comprehensive analyses. These sequences represent the longer linker sequences and the insertion of extra sequences described in the Results section. To achieve this analysis we omitted the four sequences AAWT01013938 (Schmidtea mediterranea Aebp2), CAG05504 (Tetraodon nigroviridis Gli), XP_001602003 (Nasonia vitripennis Gli), and XP_785526 (Strongylocentrotus purpuratus Gli) because these sequences contain exceptionally divergent sequences that disrupt the alignments.
Mentions: We generated tCWCH2 consensus sequences for each gene class as well as for all classes to identify any additional sequence features. The Prosite database PDOC00028 alignment was used for the reference consensus sequence of general C2H2. The extent of conservation is indicated by the size of letters, and the consensus sequences are aligned graphically (Figure 5). Classical C2H2 ZFs are known to have a consensus sequence of "(F/Y)xCx2CxFx7Lx2Hx4H" [1]. The tCWCH2 motifs also contain conserved phenylalanine and leucine residues between the cysteine and histidine residues. Phenylalanine and leucine are hydrophobic residues that generally mediate a hydrophobic interaction within a single ZF (data not shown). These data indicate that the general structure of a single ZF is well conserved in the tCWCH2 motif (Figure 6A) and that there are some tCWCH2-specific structures apart from the conserved tryptophan residues.

Bottom Line: We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates) and Amoebozoa (amoeba, Dictyostelium discoideum).Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs).These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan.

ABSTRACT

Background: The C2H2 zinc finger (ZF) domain is widely conserved among eukaryotic proteins. In Zic/Gli/Zap1 C2H2 ZF proteins, the two N-terminal ZFs form a single structural unit by sharing a hydrophobic core. This structural unit defines a new motif comprised of two tryptophan side chains at the center of the hydrophobic core. Because each tryptophan residue is located between the two cysteine residues of the C2H2 motif, we have named this structure the tandem CWCH2 (tCWCH2) motif.

Results: Here, we characterized 587 tCWCH2-containing genes using data derived from public databases. We categorized genes into 11 classes including Zic/Gli/Glis, Arid2/Rsc9, PacC, Mizf, Aebp2, Zap1/ZafA, Fungl, Zfp106, Twincl, Clr1, and Fungl-4ZF, based on sequence similarity, domain organization, and functional similarities. tCWCH2 motifs are mostly found in organisms belonging to the Opisthokonta (metazoa, fungi, and choanoflagellates) and Amoebozoa (amoeba, Dictyostelium discoideum). By comparison, the C2H2 ZF motif is distributed widely among the eukaryotes. The structure and organization of the tCWCH2 motif, its phylogenetic distribution, and molecular phylogenetic analysis suggest that prototypical tCWCH2 genes existed in the Opisthokonta ancestor. Within-group or between-group comparisons of the tCWCH2 amino acid sequence identified three additional sequence features (site-specific amino acid frequencies, longer linker sequence between two C2H2 ZFs, and frequent extra-sequences within C2H2 ZF motifs).

Conclusion: These features suggest that the tCWCH2 motif is a specialized motif involved in inter-zinc finger interactions.

Show MeSH