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Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members.

Hughes I, Binkley J, Hurle B, Green ED, NISC Comparative Sequencing ProgramSidow A, Ornitz DM - BMC Evol. Biol. (2008)

Bottom Line: Multi-species comparison of the predicted primary sequences and predicted secondary structures of 62 vertebrate otopetrin, and arthropod and nematode DUF270 proteins, has established that the genes encoding these proteins constitute a single family that we renamed the Otopetrin Domain Protein (ODP) gene family.Signature features of ODP proteins are three "Otopetrin Domains" that are highly conserved between vertebrates, arthropods and nematodes, and a highly constrained predicted loop structure.The high degree of sequence and structural similarity of the ODP proteins may suggest a conserved role in the intracellular trafficking of calcium and the formation of biominerals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Developmental Biology, Washington University School of Medicine, St, Louis, MO 63110, USA. Inna_Hughes@urmc.rochester.edu

ABSTRACT

Background: Otopetrin 1 (Otop1) encodes a multi-transmembrane domain protein with no homology to known transporters, channels, exchangers, or receptors. Otop1 is necessary for the formation of otoconia and otoliths, calcium carbonate biominerals within the inner ear of mammals and teleost fish that are required for the detection of linear acceleration and gravity. Vertebrate Otop1 and its paralogues Otop2 and Otop3 define a new gene family with homology to the invertebrate Domain of Unknown Function 270 genes (DUF270; pfam03189).

Results: Multi-species comparison of the predicted primary sequences and predicted secondary structures of 62 vertebrate otopetrin, and arthropod and nematode DUF270 proteins, has established that the genes encoding these proteins constitute a single family that we renamed the Otopetrin Domain Protein (ODP) gene family. Signature features of ODP proteins are three "Otopetrin Domains" that are highly conserved between vertebrates, arthropods and nematodes, and a highly constrained predicted loop structure.

Conclusion: Our studies suggest a refined topologic model for ODP insertion into the lipid bilayer of 12 transmembrane domains, and highlight conserved amino-acid residues that will aid in the biochemical examination of ODP family function. The high degree of sequence and structural similarity of the ODP proteins may suggest a conserved role in the intracellular trafficking of calcium and the formation of biominerals.

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Predicted secondary structure and topologic model for Otop1 insertion into the lipid bilayer. A) Hydrophobicity (red) and evolutionary constraint (blue) are plotted against the amino-acid position of mouse Otop1. A total of 12 evolutionarily constrained regions are found in the ODP family that are highly hydrophobic and have a helical structure consistent with TM domains (dark green), as predicted by TMAP (orange) and PsiPred (purple). Green, pink, and blue brackets define the highly conserved subdomains: Otopetrin Domain-I, -II, and -III (OD-I, OD-II, and OD-III, respectively). B) Linear model of mouse Otop1a inserted in a lipid bilayer, in which each amino acid is represented as a circle and the chemical properties of amino-acids are denoted by color: charged residues (red), polar residues (blue), and non-polar residue (green). Cysteine (yellow) and proline (dark green) are noted. The two consensus N-glycosylation sites (N) are indicated in loop 5. The predicted intracellular and extracellular loops and TM domains are numbered L1 to L11 and TM1 to TM12, respectively. The locations of the tlt, mlh, and bks mutations are noted by arrows. The three OD subdomains are shaded with the color code used in A.
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Figure 2: Predicted secondary structure and topologic model for Otop1 insertion into the lipid bilayer. A) Hydrophobicity (red) and evolutionary constraint (blue) are plotted against the amino-acid position of mouse Otop1. A total of 12 evolutionarily constrained regions are found in the ODP family that are highly hydrophobic and have a helical structure consistent with TM domains (dark green), as predicted by TMAP (orange) and PsiPred (purple). Green, pink, and blue brackets define the highly conserved subdomains: Otopetrin Domain-I, -II, and -III (OD-I, OD-II, and OD-III, respectively). B) Linear model of mouse Otop1a inserted in a lipid bilayer, in which each amino acid is represented as a circle and the chemical properties of amino-acids are denoted by color: charged residues (red), polar residues (blue), and non-polar residue (green). Cysteine (yellow) and proline (dark green) are noted. The two consensus N-glycosylation sites (N) are indicated in loop 5. The predicted intracellular and extracellular loops and TM domains are numbered L1 to L11 and TM1 to TM12, respectively. The locations of the tlt, mlh, and bks mutations are noted by arrows. The three OD subdomains are shaded with the color code used in A.

Mentions: Conserved primary sequence is indicative of an underlying conserved tertiary structure, and the evolutionary information contained in an alignment of related sequences can be leveraged to improve predictions of shared structures [16]. We took advantage of the deep multi-sequence alignment and phylogenetic tree of the ODP family to reexamine the predicted topology of the ODPs (Figure 2A). A hydropathy profile was generated that employs phylogenetic averaging [17] on hydropathy scale values for amino acids [18] to improve the detection of conserved hydrophobic regions, which might correspond to TM domains. The hydropathy profile revealed 12 strong hydrophobic regions, ten of which overlap with the originally predicted TM domains [7]. Likewise, the MEMSAT3 [19] and TMAP [20] algorithms, which take into account leveraged evolutionary information, also predicted 12 TM helices for ODP family members that overlap well with the constrained regions and hydrophobic regions in our profile (Figure 2A).


Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members.

Hughes I, Binkley J, Hurle B, Green ED, NISC Comparative Sequencing ProgramSidow A, Ornitz DM - BMC Evol. Biol. (2008)

Predicted secondary structure and topologic model for Otop1 insertion into the lipid bilayer. A) Hydrophobicity (red) and evolutionary constraint (blue) are plotted against the amino-acid position of mouse Otop1. A total of 12 evolutionarily constrained regions are found in the ODP family that are highly hydrophobic and have a helical structure consistent with TM domains (dark green), as predicted by TMAP (orange) and PsiPred (purple). Green, pink, and blue brackets define the highly conserved subdomains: Otopetrin Domain-I, -II, and -III (OD-I, OD-II, and OD-III, respectively). B) Linear model of mouse Otop1a inserted in a lipid bilayer, in which each amino acid is represented as a circle and the chemical properties of amino-acids are denoted by color: charged residues (red), polar residues (blue), and non-polar residue (green). Cysteine (yellow) and proline (dark green) are noted. The two consensus N-glycosylation sites (N) are indicated in loop 5. The predicted intracellular and extracellular loops and TM domains are numbered L1 to L11 and TM1 to TM12, respectively. The locations of the tlt, mlh, and bks mutations are noted by arrows. The three OD subdomains are shaded with the color code used in A.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 2: Predicted secondary structure and topologic model for Otop1 insertion into the lipid bilayer. A) Hydrophobicity (red) and evolutionary constraint (blue) are plotted against the amino-acid position of mouse Otop1. A total of 12 evolutionarily constrained regions are found in the ODP family that are highly hydrophobic and have a helical structure consistent with TM domains (dark green), as predicted by TMAP (orange) and PsiPred (purple). Green, pink, and blue brackets define the highly conserved subdomains: Otopetrin Domain-I, -II, and -III (OD-I, OD-II, and OD-III, respectively). B) Linear model of mouse Otop1a inserted in a lipid bilayer, in which each amino acid is represented as a circle and the chemical properties of amino-acids are denoted by color: charged residues (red), polar residues (blue), and non-polar residue (green). Cysteine (yellow) and proline (dark green) are noted. The two consensus N-glycosylation sites (N) are indicated in loop 5. The predicted intracellular and extracellular loops and TM domains are numbered L1 to L11 and TM1 to TM12, respectively. The locations of the tlt, mlh, and bks mutations are noted by arrows. The three OD subdomains are shaded with the color code used in A.
Mentions: Conserved primary sequence is indicative of an underlying conserved tertiary structure, and the evolutionary information contained in an alignment of related sequences can be leveraged to improve predictions of shared structures [16]. We took advantage of the deep multi-sequence alignment and phylogenetic tree of the ODP family to reexamine the predicted topology of the ODPs (Figure 2A). A hydropathy profile was generated that employs phylogenetic averaging [17] on hydropathy scale values for amino acids [18] to improve the detection of conserved hydrophobic regions, which might correspond to TM domains. The hydropathy profile revealed 12 strong hydrophobic regions, ten of which overlap with the originally predicted TM domains [7]. Likewise, the MEMSAT3 [19] and TMAP [20] algorithms, which take into account leveraged evolutionary information, also predicted 12 TM helices for ODP family members that overlap well with the constrained regions and hydrophobic regions in our profile (Figure 2A).

Bottom Line: Multi-species comparison of the predicted primary sequences and predicted secondary structures of 62 vertebrate otopetrin, and arthropod and nematode DUF270 proteins, has established that the genes encoding these proteins constitute a single family that we renamed the Otopetrin Domain Protein (ODP) gene family.Signature features of ODP proteins are three "Otopetrin Domains" that are highly conserved between vertebrates, arthropods and nematodes, and a highly constrained predicted loop structure.The high degree of sequence and structural similarity of the ODP proteins may suggest a conserved role in the intracellular trafficking of calcium and the formation of biominerals.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Developmental Biology, Washington University School of Medicine, St, Louis, MO 63110, USA. Inna_Hughes@urmc.rochester.edu

ABSTRACT

Background: Otopetrin 1 (Otop1) encodes a multi-transmembrane domain protein with no homology to known transporters, channels, exchangers, or receptors. Otop1 is necessary for the formation of otoconia and otoliths, calcium carbonate biominerals within the inner ear of mammals and teleost fish that are required for the detection of linear acceleration and gravity. Vertebrate Otop1 and its paralogues Otop2 and Otop3 define a new gene family with homology to the invertebrate Domain of Unknown Function 270 genes (DUF270; pfam03189).

Results: Multi-species comparison of the predicted primary sequences and predicted secondary structures of 62 vertebrate otopetrin, and arthropod and nematode DUF270 proteins, has established that the genes encoding these proteins constitute a single family that we renamed the Otopetrin Domain Protein (ODP) gene family. Signature features of ODP proteins are three "Otopetrin Domains" that are highly conserved between vertebrates, arthropods and nematodes, and a highly constrained predicted loop structure.

Conclusion: Our studies suggest a refined topologic model for ODP insertion into the lipid bilayer of 12 transmembrane domains, and highlight conserved amino-acid residues that will aid in the biochemical examination of ODP family function. The high degree of sequence and structural similarity of the ODP proteins may suggest a conserved role in the intracellular trafficking of calcium and the formation of biominerals.

Show MeSH