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TM6SF2 and MAC30, new enzyme homologs in sterol metabolism and common metabolic disease.

Sanchez-Pulido L, Ponting CP - Front Genet (2014)

Bottom Line: We identified a new domain, the EXPERA domain, which is conserved among TM6SF, MAC30/TMEM97 and EBP (D8, D7 sterol isomerase) protein families.EBP mutations are the cause of chondrodysplasia punctata 2 X-linked dominant (CDPX2), also known as Conradi-Hünermann-Happle syndrome, a defective cholesterol biosynthesis disorder.Our analysis of evolutionary conservation among EXPERA domain-containing families and the previously suggested catalytic mechanism for the EBP enzyme, indicate that TM6SF and MAC30/TMEM97 families are both highly likely to possess, as for the EBP family, catalytic activity as sterol isomerases.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford Oxford, UK.

ABSTRACT
Carriers of the Glu167Lys coding variant in the TM6SF2 gene have recently been identified as being more susceptible to non-alcoholic fatty liver disease (NAFLD), yet exhibit lower levels of circulating lipids and hence are protected against cardiovascular disease. Despite the physiological importance of these observations, the molecular function of TM6SF2 remains unknown, and no sequence similarity with functionally characterized proteins has been identified. In order to trace its evolutionary history and to identify functional domains, we embarked on a computational protein sequence analysis of TM6SF2. We identified a new domain, the EXPERA domain, which is conserved among TM6SF, MAC30/TMEM97 and EBP (D8, D7 sterol isomerase) protein families. EBP mutations are the cause of chondrodysplasia punctata 2 X-linked dominant (CDPX2), also known as Conradi-Hünermann-Happle syndrome, a defective cholesterol biosynthesis disorder. Our analysis of evolutionary conservation among EXPERA domain-containing families and the previously suggested catalytic mechanism for the EBP enzyme, indicate that TM6SF and MAC30/TMEM97 families are both highly likely to possess, as for the EBP family, catalytic activity as sterol isomerases. This unexpected prediction of enzymatic functions for TM6SF and MAC30/TMEM97 is important because it now permits detailed experiments to investigate the function of these key proteins in various human pathologies, from cardiovascular disease to cancer.

No MeSH data available.


Related in: MedlinePlus

Representative multiple sequence alignment of the EXPERA domain. Putative EBP catalytic residues (identified by alanine-scanning) described by Moebius et al. are label in black (Moebius et al., 1999). A mutation identified in TM6SF2 is label in red (Holmen et al., 2014; Kozlitina et al., 2014; Sookoian et al., 2014). Human sequence names are highlighted and the only member of the EXPERA superfamily in Saccharomyces cerevisiae, part of the MAC30/TMEM97 family, is indicated by a yellow box. Numbers shown in green represent inserted amino acids that have been removed from the alignment. Different groups of the EXPERA sequences identified by sequence similarity are shown by colored lines to the left of the alignment: light red, TM6SF family first repeat; dark red, TM6SF family second repeat; yellow, MAC30/TMEM97 family; purple, EBP family. DUF2781 (in blue), previously defined in Pfam (includes TM6SF second repeat and MAC30 family). The TMHMM helix transmembrane (Krogh et al., 2001) consensus prediction are shown below the alignment for each family, in red, yellow, and violet cylinders for TM6SF (repeats 1 and 2), MAC30/TMEM97, and EBP families, respectively (see Figures S1–S3). The limits of the protein sequences included in the alignment are indicated by flanking residue positions. Alignments were produced with T-Coffee, HMMer, and HHpred (Eddy, 1996; Notredame et al., 2000; Söding et al., 2005; Finn et al., 2011) using default parameters and slightly refined manually. The alignment was presented with the program Belvu (Sonnhammer and Hollich, 2005) using a coloring scheme indicating the average BLOSUM62 scores (which are correlated with amino acid conservation) of each alignment column: red (>0.7), violet (between 0.7 and 0.4) and light yellow (between 0.4 and 0.2). Sequences are named according to their UniProt identifications (Wu et al., 2006). Species abbreviations: ARATH, Arabidopsis thaliana (Mouse-ear cress); ASPFC, Neosartorya fumigata (Fungus); AURDE, Auricularia delicata (White-rot fungus); CAEEL, Caenorhabditis elegans; CANGA, Candida glabrata (Yeast); CHLRE, A8JGX8_CHLRE, Chlamydomonas reinhardtii (Green alga); CIOIN, Ciona intestinalis; CRAGI, Crassostrea gigas (Pacific oyster); DEBHA, Debaryomyces hansenii (Yeast); DICDI, Dictyostelium discoideum (Slime mold); EMIHU, Emiliania huxleyi (Chromalveolata); HUMAN, Homo sapiens; LOTGI, Lottia gigantea (Giant owl limpet); MALGO, Malassezia globosa (Fungus); MONBE, Monosiga brevicollis (Choanoflagellate); NAEGR, Naegleria gruberi (Amoeba); NEMVE, Nematostella vectensis (Starlet sea anemone); NEUCR, Neurospora crassa (Fungus); OSTTA, Ostreococcus tauri (Green alga); PHACS, Phanerochaete carnosa (Fungus); PICPG, Komagataella pastoris (Yeast); PIRID, Piriformospora indica (Fungus); SALR5, Salpingoeca rosetta (Choanoflagellate); SCHPO, Schizosaccharomyces pombe (Fission yeast); SELML, Selaginella moellendorffii (Spikemoss); STRPU, Strongylocentrotus purpuratus (Purple sea urchin); THAPS, Thalassiosira pseudonana (Marine diatom); TRIAD, Trichoplax adhaerens; VOLCA, Volvox carteri (Green alga); YARLI, Yarrowia lipolytica (Yeast); YEAST, Saccharomyces cerevisiae (Baker's yeast).
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Figure 3: Representative multiple sequence alignment of the EXPERA domain. Putative EBP catalytic residues (identified by alanine-scanning) described by Moebius et al. are label in black (Moebius et al., 1999). A mutation identified in TM6SF2 is label in red (Holmen et al., 2014; Kozlitina et al., 2014; Sookoian et al., 2014). Human sequence names are highlighted and the only member of the EXPERA superfamily in Saccharomyces cerevisiae, part of the MAC30/TMEM97 family, is indicated by a yellow box. Numbers shown in green represent inserted amino acids that have been removed from the alignment. Different groups of the EXPERA sequences identified by sequence similarity are shown by colored lines to the left of the alignment: light red, TM6SF family first repeat; dark red, TM6SF family second repeat; yellow, MAC30/TMEM97 family; purple, EBP family. DUF2781 (in blue), previously defined in Pfam (includes TM6SF second repeat and MAC30 family). The TMHMM helix transmembrane (Krogh et al., 2001) consensus prediction are shown below the alignment for each family, in red, yellow, and violet cylinders for TM6SF (repeats 1 and 2), MAC30/TMEM97, and EBP families, respectively (see Figures S1–S3). The limits of the protein sequences included in the alignment are indicated by flanking residue positions. Alignments were produced with T-Coffee, HMMer, and HHpred (Eddy, 1996; Notredame et al., 2000; Söding et al., 2005; Finn et al., 2011) using default parameters and slightly refined manually. The alignment was presented with the program Belvu (Sonnhammer and Hollich, 2005) using a coloring scheme indicating the average BLOSUM62 scores (which are correlated with amino acid conservation) of each alignment column: red (>0.7), violet (between 0.7 and 0.4) and light yellow (between 0.4 and 0.2). Sequences are named according to their UniProt identifications (Wu et al., 2006). Species abbreviations: ARATH, Arabidopsis thaliana (Mouse-ear cress); ASPFC, Neosartorya fumigata (Fungus); AURDE, Auricularia delicata (White-rot fungus); CAEEL, Caenorhabditis elegans; CANGA, Candida glabrata (Yeast); CHLRE, A8JGX8_CHLRE, Chlamydomonas reinhardtii (Green alga); CIOIN, Ciona intestinalis; CRAGI, Crassostrea gigas (Pacific oyster); DEBHA, Debaryomyces hansenii (Yeast); DICDI, Dictyostelium discoideum (Slime mold); EMIHU, Emiliania huxleyi (Chromalveolata); HUMAN, Homo sapiens; LOTGI, Lottia gigantea (Giant owl limpet); MALGO, Malassezia globosa (Fungus); MONBE, Monosiga brevicollis (Choanoflagellate); NAEGR, Naegleria gruberi (Amoeba); NEMVE, Nematostella vectensis (Starlet sea anemone); NEUCR, Neurospora crassa (Fungus); OSTTA, Ostreococcus tauri (Green alga); PHACS, Phanerochaete carnosa (Fungus); PICPG, Komagataella pastoris (Yeast); PIRID, Piriformospora indica (Fungus); SALR5, Salpingoeca rosetta (Choanoflagellate); SCHPO, Schizosaccharomyces pombe (Fission yeast); SELML, Selaginella moellendorffii (Spikemoss); STRPU, Strongylocentrotus purpuratus (Purple sea urchin); THAPS, Thalassiosira pseudonana (Marine diatom); TRIAD, Trichoplax adhaerens; VOLCA, Volvox carteri (Green alga); YARLI, Yarrowia lipolytica (Yeast); YEAST, Saccharomyces cerevisiae (Baker's yeast).

Mentions: By iteratively improving the phyletic coverage in each protein family using HMMer database searches (Eddy, 1996), we obtained statistical significance from profile-profile comparisons that link these three sequence families (specifically, the two TM6SF repeats and the single MAC30/TMEM97 repeat) to the Emopamil binding protein (EBP) family (Figures 3, 4). The significance of these sequence similarities, their common transmembrane helix configuration, and their shared predicted C-terminal ER retention signal (Figures 1, 2) (Jackson et al., 1990) imply that these domains are homologous, having derived from a common evolutionary ancestor. We name this four transmembrane region the EXPERA (EXPanded EBP superfamily) domain.


TM6SF2 and MAC30, new enzyme homologs in sterol metabolism and common metabolic disease.

Sanchez-Pulido L, Ponting CP - Front Genet (2014)

Representative multiple sequence alignment of the EXPERA domain. Putative EBP catalytic residues (identified by alanine-scanning) described by Moebius et al. are label in black (Moebius et al., 1999). A mutation identified in TM6SF2 is label in red (Holmen et al., 2014; Kozlitina et al., 2014; Sookoian et al., 2014). Human sequence names are highlighted and the only member of the EXPERA superfamily in Saccharomyces cerevisiae, part of the MAC30/TMEM97 family, is indicated by a yellow box. Numbers shown in green represent inserted amino acids that have been removed from the alignment. Different groups of the EXPERA sequences identified by sequence similarity are shown by colored lines to the left of the alignment: light red, TM6SF family first repeat; dark red, TM6SF family second repeat; yellow, MAC30/TMEM97 family; purple, EBP family. DUF2781 (in blue), previously defined in Pfam (includes TM6SF second repeat and MAC30 family). The TMHMM helix transmembrane (Krogh et al., 2001) consensus prediction are shown below the alignment for each family, in red, yellow, and violet cylinders for TM6SF (repeats 1 and 2), MAC30/TMEM97, and EBP families, respectively (see Figures S1–S3). The limits of the protein sequences included in the alignment are indicated by flanking residue positions. Alignments were produced with T-Coffee, HMMer, and HHpred (Eddy, 1996; Notredame et al., 2000; Söding et al., 2005; Finn et al., 2011) using default parameters and slightly refined manually. The alignment was presented with the program Belvu (Sonnhammer and Hollich, 2005) using a coloring scheme indicating the average BLOSUM62 scores (which are correlated with amino acid conservation) of each alignment column: red (>0.7), violet (between 0.7 and 0.4) and light yellow (between 0.4 and 0.2). Sequences are named according to their UniProt identifications (Wu et al., 2006). Species abbreviations: ARATH, Arabidopsis thaliana (Mouse-ear cress); ASPFC, Neosartorya fumigata (Fungus); AURDE, Auricularia delicata (White-rot fungus); CAEEL, Caenorhabditis elegans; CANGA, Candida glabrata (Yeast); CHLRE, A8JGX8_CHLRE, Chlamydomonas reinhardtii (Green alga); CIOIN, Ciona intestinalis; CRAGI, Crassostrea gigas (Pacific oyster); DEBHA, Debaryomyces hansenii (Yeast); DICDI, Dictyostelium discoideum (Slime mold); EMIHU, Emiliania huxleyi (Chromalveolata); HUMAN, Homo sapiens; LOTGI, Lottia gigantea (Giant owl limpet); MALGO, Malassezia globosa (Fungus); MONBE, Monosiga brevicollis (Choanoflagellate); NAEGR, Naegleria gruberi (Amoeba); NEMVE, Nematostella vectensis (Starlet sea anemone); NEUCR, Neurospora crassa (Fungus); OSTTA, Ostreococcus tauri (Green alga); PHACS, Phanerochaete carnosa (Fungus); PICPG, Komagataella pastoris (Yeast); PIRID, Piriformospora indica (Fungus); SALR5, Salpingoeca rosetta (Choanoflagellate); SCHPO, Schizosaccharomyces pombe (Fission yeast); SELML, Selaginella moellendorffii (Spikemoss); STRPU, Strongylocentrotus purpuratus (Purple sea urchin); THAPS, Thalassiosira pseudonana (Marine diatom); TRIAD, Trichoplax adhaerens; VOLCA, Volvox carteri (Green alga); YARLI, Yarrowia lipolytica (Yeast); YEAST, Saccharomyces cerevisiae (Baker's yeast).
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Figure 3: Representative multiple sequence alignment of the EXPERA domain. Putative EBP catalytic residues (identified by alanine-scanning) described by Moebius et al. are label in black (Moebius et al., 1999). A mutation identified in TM6SF2 is label in red (Holmen et al., 2014; Kozlitina et al., 2014; Sookoian et al., 2014). Human sequence names are highlighted and the only member of the EXPERA superfamily in Saccharomyces cerevisiae, part of the MAC30/TMEM97 family, is indicated by a yellow box. Numbers shown in green represent inserted amino acids that have been removed from the alignment. Different groups of the EXPERA sequences identified by sequence similarity are shown by colored lines to the left of the alignment: light red, TM6SF family first repeat; dark red, TM6SF family second repeat; yellow, MAC30/TMEM97 family; purple, EBP family. DUF2781 (in blue), previously defined in Pfam (includes TM6SF second repeat and MAC30 family). The TMHMM helix transmembrane (Krogh et al., 2001) consensus prediction are shown below the alignment for each family, in red, yellow, and violet cylinders for TM6SF (repeats 1 and 2), MAC30/TMEM97, and EBP families, respectively (see Figures S1–S3). The limits of the protein sequences included in the alignment are indicated by flanking residue positions. Alignments were produced with T-Coffee, HMMer, and HHpred (Eddy, 1996; Notredame et al., 2000; Söding et al., 2005; Finn et al., 2011) using default parameters and slightly refined manually. The alignment was presented with the program Belvu (Sonnhammer and Hollich, 2005) using a coloring scheme indicating the average BLOSUM62 scores (which are correlated with amino acid conservation) of each alignment column: red (>0.7), violet (between 0.7 and 0.4) and light yellow (between 0.4 and 0.2). Sequences are named according to their UniProt identifications (Wu et al., 2006). Species abbreviations: ARATH, Arabidopsis thaliana (Mouse-ear cress); ASPFC, Neosartorya fumigata (Fungus); AURDE, Auricularia delicata (White-rot fungus); CAEEL, Caenorhabditis elegans; CANGA, Candida glabrata (Yeast); CHLRE, A8JGX8_CHLRE, Chlamydomonas reinhardtii (Green alga); CIOIN, Ciona intestinalis; CRAGI, Crassostrea gigas (Pacific oyster); DEBHA, Debaryomyces hansenii (Yeast); DICDI, Dictyostelium discoideum (Slime mold); EMIHU, Emiliania huxleyi (Chromalveolata); HUMAN, Homo sapiens; LOTGI, Lottia gigantea (Giant owl limpet); MALGO, Malassezia globosa (Fungus); MONBE, Monosiga brevicollis (Choanoflagellate); NAEGR, Naegleria gruberi (Amoeba); NEMVE, Nematostella vectensis (Starlet sea anemone); NEUCR, Neurospora crassa (Fungus); OSTTA, Ostreococcus tauri (Green alga); PHACS, Phanerochaete carnosa (Fungus); PICPG, Komagataella pastoris (Yeast); PIRID, Piriformospora indica (Fungus); SALR5, Salpingoeca rosetta (Choanoflagellate); SCHPO, Schizosaccharomyces pombe (Fission yeast); SELML, Selaginella moellendorffii (Spikemoss); STRPU, Strongylocentrotus purpuratus (Purple sea urchin); THAPS, Thalassiosira pseudonana (Marine diatom); TRIAD, Trichoplax adhaerens; VOLCA, Volvox carteri (Green alga); YARLI, Yarrowia lipolytica (Yeast); YEAST, Saccharomyces cerevisiae (Baker's yeast).
Mentions: By iteratively improving the phyletic coverage in each protein family using HMMer database searches (Eddy, 1996), we obtained statistical significance from profile-profile comparisons that link these three sequence families (specifically, the two TM6SF repeats and the single MAC30/TMEM97 repeat) to the Emopamil binding protein (EBP) family (Figures 3, 4). The significance of these sequence similarities, their common transmembrane helix configuration, and their shared predicted C-terminal ER retention signal (Figures 1, 2) (Jackson et al., 1990) imply that these domains are homologous, having derived from a common evolutionary ancestor. We name this four transmembrane region the EXPERA (EXPanded EBP superfamily) domain.

Bottom Line: We identified a new domain, the EXPERA domain, which is conserved among TM6SF, MAC30/TMEM97 and EBP (D8, D7 sterol isomerase) protein families.EBP mutations are the cause of chondrodysplasia punctata 2 X-linked dominant (CDPX2), also known as Conradi-Hünermann-Happle syndrome, a defective cholesterol biosynthesis disorder.Our analysis of evolutionary conservation among EXPERA domain-containing families and the previously suggested catalytic mechanism for the EBP enzyme, indicate that TM6SF and MAC30/TMEM97 families are both highly likely to possess, as for the EBP family, catalytic activity as sterol isomerases.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford Oxford, UK.

ABSTRACT
Carriers of the Glu167Lys coding variant in the TM6SF2 gene have recently been identified as being more susceptible to non-alcoholic fatty liver disease (NAFLD), yet exhibit lower levels of circulating lipids and hence are protected against cardiovascular disease. Despite the physiological importance of these observations, the molecular function of TM6SF2 remains unknown, and no sequence similarity with functionally characterized proteins has been identified. In order to trace its evolutionary history and to identify functional domains, we embarked on a computational protein sequence analysis of TM6SF2. We identified a new domain, the EXPERA domain, which is conserved among TM6SF, MAC30/TMEM97 and EBP (D8, D7 sterol isomerase) protein families. EBP mutations are the cause of chondrodysplasia punctata 2 X-linked dominant (CDPX2), also known as Conradi-Hünermann-Happle syndrome, a defective cholesterol biosynthesis disorder. Our analysis of evolutionary conservation among EXPERA domain-containing families and the previously suggested catalytic mechanism for the EBP enzyme, indicate that TM6SF and MAC30/TMEM97 families are both highly likely to possess, as for the EBP family, catalytic activity as sterol isomerases. This unexpected prediction of enzymatic functions for TM6SF and MAC30/TMEM97 is important because it now permits detailed experiments to investigate the function of these key proteins in various human pathologies, from cardiovascular disease to cancer.

No MeSH data available.


Related in: MedlinePlus