A common problem in molecular comparative geno- mics is the identification of genes that are under positive, adaptive selection [1]. Such genes are likely to be crucial for speciation, species differentiation, and fun...A common problem in molecular comparative geno- mics is the identification of genes that are under positive, adaptive selection [1]. Such genes are likely to be crucial for speciation, species differentiation, and func- tional specialization. However, discerning the difference between positive selection and relaxation of func- tional constraint can be difficult using current methods. Both processes generally increase the rate of ami- no acid change relative to synonymous changes within coding regions, and unless the amino acid rate is over- whelmingly high across an entire gene, the signature of positive selection can be obscured [2]. Some methodologies do not explicitly determine the difference be- tween a relaxation of functional constraint and positive selection, leaving researchers to determine via other means whether the trajectory of a gene has been specialization or creation of a new function, or removal from the genome via a process of degeneration.展开更多
Phosphatidylinositol transfer proteins (PITP) are a family of monomeric proteins that bind and transfer phosphatidylinositol and phosphatidylcholine between membrane compartments. They are required for production of i...Phosphatidylinositol transfer proteins (PITP) are a family of monomeric proteins that bind and transfer phosphatidylinositol and phosphatidylcholine between membrane compartments. They are required for production of inositol and diacylglycerol second messengers, and are found in most metazoan organisms. While PITPs are known to carry out crucial cell-signaling roles in many organisms, the structure, function and evolution of the majority of family members remains unexplored;primarily because the ubiquity and diversity of the family thwarts traditional methods of global alignment. To surmount this obstacle, we instead took a novel approach, using MEME and a parsimony-based analysis to create a cladogram of conserved sequence motifs in 56 PITP family proteins from 26 species. In keeping with previous functional annotations, three clades were supported within our evolutionary analysis;two classes of soluble proteins and a class of membrane-associat- ed proteins. By, focusing on conserved regions, the analysis allowed for in depth queries regarding possible functional roles of PITP proteins in both intra- and extra- cellular signaling.展开更多
文摘A common problem in molecular comparative geno- mics is the identification of genes that are under positive, adaptive selection [1]. Such genes are likely to be crucial for speciation, species differentiation, and func- tional specialization. However, discerning the difference between positive selection and relaxation of func- tional constraint can be difficult using current methods. Both processes generally increase the rate of ami- no acid change relative to synonymous changes within coding regions, and unless the amino acid rate is over- whelmingly high across an entire gene, the signature of positive selection can be obscured [2]. Some methodologies do not explicitly determine the difference be- tween a relaxation of functional constraint and positive selection, leaving researchers to determine via other means whether the trajectory of a gene has been specialization or creation of a new function, or removal from the genome via a process of degeneration.
文摘Phosphatidylinositol transfer proteins (PITP) are a family of monomeric proteins that bind and transfer phosphatidylinositol and phosphatidylcholine between membrane compartments. They are required for production of inositol and diacylglycerol second messengers, and are found in most metazoan organisms. While PITPs are known to carry out crucial cell-signaling roles in many organisms, the structure, function and evolution of the majority of family members remains unexplored;primarily because the ubiquity and diversity of the family thwarts traditional methods of global alignment. To surmount this obstacle, we instead took a novel approach, using MEME and a parsimony-based analysis to create a cladogram of conserved sequence motifs in 56 PITP family proteins from 26 species. In keeping with previous functional annotations, three clades were supported within our evolutionary analysis;two classes of soluble proteins and a class of membrane-associat- ed proteins. By, focusing on conserved regions, the analysis allowed for in depth queries regarding possible functional roles of PITP proteins in both intra- and extra- cellular signaling.
