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Evolutionary analyses of KCNQ1 and HERG voltage-gated potassium channel sequences reveal location-specific susceptibility and augmented chemical severities of arrhythmogenic mutations.

Jackson HA, Accili EA - BMC Evol. Biol. (2008)

Bottom Line: Using evolutionary analyses, AAMs in HERG and KCNQ1 were preferentially found at evolutionarily conserved sites and unevenly distributed among functionally conserved domains.Unlike nsSNPs, AAMs preferentially locate to evolutionarily conserved, and functionally important, sites and regions within HERG and KCNQ1, and are chemically more severe than changes which occur in evolution.Expected chemical severity may contribute to the overrepresentation of certain residues in AAMs, as well as to evolutionary change.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada. hajacks@interchange.ubc.ca

ABSTRACT

Background: Mutations in HERG and KCNQ1 potassium channels have been associated with Long QT syndrome and atrial fibrillation, and more recently with sudden infant death syndrome and sudden unexplained death. In other proteins, disease-associated amino acid mutations have been analyzed according to the chemical severity of the changes and the locations of the altered amino acids according to their conservation over metazoan evolution. Here, we present the first such analysis of arrhythmia-associated mutations (AAMs) in the HERG and KCNQ1 potassium channels.

Results: Using evolutionary analyses, AAMs in HERG and KCNQ1 were preferentially found at evolutionarily conserved sites and unevenly distributed among functionally conserved domains. Non-synonymous single nucleotide polymorphisms (nsSNPs) are under-represented at evolutionarily conserved sites in HERG, but distribute randomly in KCNQ1. AAMs are chemically more severe, according to Grantham's Scale, than changes observed in evolution and their severity correlates with the expected chemical severity of the involved codon. Expected chemical severity of a given amino acid also correlates with its relative contribution to arrhythmias. At evolutionarily variable sites, the chemical severity of the changes is also correlated with the expected chemical severity of the involved codon.

Conclusion: Unlike nsSNPs, AAMs preferentially locate to evolutionarily conserved, and functionally important, sites and regions within HERG and KCNQ1, and are chemically more severe than changes which occur in evolution. Expected chemical severity may contribute to the overrepresentation of certain residues in AAMs, as well as to evolutionary change.

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Cladograms of vertebrate HERG and KCNQ1 protein sequences. a) HERG: GenBank accession numbers/Ensembl identifiers for protein sequences used: human (NP_000229.1), dog (NP_001003145.1), zebrafish (NP_998002), monkey (ENSMMUP00000026900), rabbit (Q8WNY2), mouse (NP_038597.1), rat (NP_446401.1), opossum (ENSMODP00000004651), fugu (NEWSINFRUP00000161615), tetraodon (GSTENP00027811001). b) KCNQ1: GenBank accession numbers/Ensembl identifiers for KCNQ1 protein sequences used: human (NP_000209.2), mouse (NP_032460.2), rat (NP_114462.1), chicken (ENSGALP00000010441), fugu (NEWSINFRUP00000143259), zebrafish (ENSDARP00000077951). See methods for details.
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Figure 2: Cladograms of vertebrate HERG and KCNQ1 protein sequences. a) HERG: GenBank accession numbers/Ensembl identifiers for protein sequences used: human (NP_000229.1), dog (NP_001003145.1), zebrafish (NP_998002), monkey (ENSMMUP00000026900), rabbit (Q8WNY2), mouse (NP_038597.1), rat (NP_446401.1), opossum (ENSMODP00000004651), fugu (NEWSINFRUP00000161615), tetraodon (GSTENP00027811001). b) KCNQ1: GenBank accession numbers/Ensembl identifiers for KCNQ1 protein sequences used: human (NP_000209.2), mouse (NP_032460.2), rat (NP_114462.1), chicken (ENSGALP00000010441), fugu (NEWSINFRUP00000143259), zebrafish (ENSDARP00000077951). See methods for details.

Mentions: To determine whether AAMs and nsSNPs occur preferentially at evolutionarily diverse sites in HERG and KCNQ1, we utilized a quantitative approach developed previously [23]. The evolutionary relationships and the number of interspecific changes at each site were determined (Figure 2) and in both channels, the largest number of interspecific changes observed at any site was five. Therefore variability data was binned into six categories, ranging from completely conserved sites (0) to highly variable (5).


Evolutionary analyses of KCNQ1 and HERG voltage-gated potassium channel sequences reveal location-specific susceptibility and augmented chemical severities of arrhythmogenic mutations.

Jackson HA, Accili EA - BMC Evol. Biol. (2008)

Cladograms of vertebrate HERG and KCNQ1 protein sequences. a) HERG: GenBank accession numbers/Ensembl identifiers for protein sequences used: human (NP_000229.1), dog (NP_001003145.1), zebrafish (NP_998002), monkey (ENSMMUP00000026900), rabbit (Q8WNY2), mouse (NP_038597.1), rat (NP_446401.1), opossum (ENSMODP00000004651), fugu (NEWSINFRUP00000161615), tetraodon (GSTENP00027811001). b) KCNQ1: GenBank accession numbers/Ensembl identifiers for KCNQ1 protein sequences used: human (NP_000209.2), mouse (NP_032460.2), rat (NP_114462.1), chicken (ENSGALP00000010441), fugu (NEWSINFRUP00000143259), zebrafish (ENSDARP00000077951). See methods for details.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483723&req=5

Figure 2: Cladograms of vertebrate HERG and KCNQ1 protein sequences. a) HERG: GenBank accession numbers/Ensembl identifiers for protein sequences used: human (NP_000229.1), dog (NP_001003145.1), zebrafish (NP_998002), monkey (ENSMMUP00000026900), rabbit (Q8WNY2), mouse (NP_038597.1), rat (NP_446401.1), opossum (ENSMODP00000004651), fugu (NEWSINFRUP00000161615), tetraodon (GSTENP00027811001). b) KCNQ1: GenBank accession numbers/Ensembl identifiers for KCNQ1 protein sequences used: human (NP_000209.2), mouse (NP_032460.2), rat (NP_114462.1), chicken (ENSGALP00000010441), fugu (NEWSINFRUP00000143259), zebrafish (ENSDARP00000077951). See methods for details.
Mentions: To determine whether AAMs and nsSNPs occur preferentially at evolutionarily diverse sites in HERG and KCNQ1, we utilized a quantitative approach developed previously [23]. The evolutionary relationships and the number of interspecific changes at each site were determined (Figure 2) and in both channels, the largest number of interspecific changes observed at any site was five. Therefore variability data was binned into six categories, ranging from completely conserved sites (0) to highly variable (5).

Bottom Line: Using evolutionary analyses, AAMs in HERG and KCNQ1 were preferentially found at evolutionarily conserved sites and unevenly distributed among functionally conserved domains.Unlike nsSNPs, AAMs preferentially locate to evolutionarily conserved, and functionally important, sites and regions within HERG and KCNQ1, and are chemically more severe than changes which occur in evolution.Expected chemical severity may contribute to the overrepresentation of certain residues in AAMs, as well as to evolutionary change.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Cellular and Physiological Sciences, Faculty of Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada. hajacks@interchange.ubc.ca

ABSTRACT

Background: Mutations in HERG and KCNQ1 potassium channels have been associated with Long QT syndrome and atrial fibrillation, and more recently with sudden infant death syndrome and sudden unexplained death. In other proteins, disease-associated amino acid mutations have been analyzed according to the chemical severity of the changes and the locations of the altered amino acids according to their conservation over metazoan evolution. Here, we present the first such analysis of arrhythmia-associated mutations (AAMs) in the HERG and KCNQ1 potassium channels.

Results: Using evolutionary analyses, AAMs in HERG and KCNQ1 were preferentially found at evolutionarily conserved sites and unevenly distributed among functionally conserved domains. Non-synonymous single nucleotide polymorphisms (nsSNPs) are under-represented at evolutionarily conserved sites in HERG, but distribute randomly in KCNQ1. AAMs are chemically more severe, according to Grantham's Scale, than changes observed in evolution and their severity correlates with the expected chemical severity of the involved codon. Expected chemical severity of a given amino acid also correlates with its relative contribution to arrhythmias. At evolutionarily variable sites, the chemical severity of the changes is also correlated with the expected chemical severity of the involved codon.

Conclusion: Unlike nsSNPs, AAMs preferentially locate to evolutionarily conserved, and functionally important, sites and regions within HERG and KCNQ1, and are chemically more severe than changes which occur in evolution. Expected chemical severity may contribute to the overrepresentation of certain residues in AAMs, as well as to evolutionary change.

Show MeSH
Related in: MedlinePlus