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Functional divergence after gene duplication and sequence–structure relationship: a case study of G‐protein alpha subunits
Author(s) -
Zheng Ying,
Xu Dongping,
Gu Xun
Publication year - 2006
Publication title -
journal of experimental zoology part b: molecular and developmental evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.823
H-Index - 63
eISSN - 1552-5015
pISSN - 1552-5007
DOI - 10.1002/jez.b.21140
Subject(s) - functional divergence , gene duplication , gene , biology , genetics , amino acid , peptide sequence , gene family , protein sequencing , g alpha subunit , sequence (biology) , computational biology , protein subunit , genome
In this article, we use animal G‐protein alpha subunit family as an example to illustrate a comprehensive analytical pipeline for detecting different types of functional divergence of protein families, which is phylogeny‐dependent, combined with ancestral sequence inference and available protein structure information. In particular, we focus on (i) Type‐I functional divergence, or site‐specific rate shift, as typically exemplified by amino acid residue highly conserved in a subset of homologous genes but highly variable in a different subset of homologous genes, and (ii) Type‐II functional divergence, or the shift of cluster‐specific amino acid property, as exemplified by a radical shift of amino acid property between duplicate genes, which is otherwise evolutionally conserved. We utilized the software DIVERGE2 to carry out these analyses. In the case of G‐protein alpha subunit gene family, we have predicted amino acid residues that are related to either Type‐I or Type‐II functional divergence. The inferred ancestral sequences for these sites are helpful to explore the trends of functional divergence. Finally, these predicted residues are mapped to the protein structures to test whether these residues may have 3D structure or solvent accessibility preference. J. Exp. Zool. (Mol. Dev. Evol.) 306B, 2006 . © 2006 Wiley‐Liss, Inc.