title: Distinct evolutionary rate in the eye field transcription factors found by estimation of ancestral protein structure.
abstract: Eye-field transcription factors (EFTFs) are a set of genes that compose a regulatory network for eye development in animals, which are highly conserved among various animal phyla. To investigate the processes of conservation and diversification of the transcription factors for eye development, we examined the structural changes in the EFTF proteins by estimating the ancestral sequences with the available genome information. Among the different types of EFTFs, we selected otx2, tbx3, rx1, pax6, six3/6, lhx2 and nr2e1 because they are highly conserved in bilaterian animals. We searched the genome sequences of representative animal phyla for EFTF protein sequences. With deduced ancestral sequences and three-dimensional structures of EFTFs, we traced the evolutionary changes in amino acid residues and found that the DNA-binding domains were always more conserved than other regions, and that the other regions showed distinct evolutionary rates. The EFTF rx1, which resides at the pivotal part of the EFTF network, had a faster evolutionary rate than the others. These results indicated that the evolutionary rates of each protein in the EFTF network, which were expected to be consistent with each other to maintain the interactions in the network, were not constant among or within the factors, but rather, varied to a significant extent.
authors.affiliation: Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan.
authors.forename: Ai
authors.initials: A
authors.lastname: Kamijyo
authors.affiliation: Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; Center for Informational Biology, Ochanomizu University 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan; National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Kei
authors.initials: K
authors.lastname: Yura
authors.affiliation: Department of Computer Bio-Science, Nagahama Institute of BioScience and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan. Electronic address: aogu@wheilx.info.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Ogura
mesh_terms: D000818:Animals; D019295:Computational Biology; D019143:Evolution, Molecular; D005123:Eye / Q000378:metabolism; D005136:Eye Proteins / Q000378:metabolism*; D005786:Gene Expression Regulation; D016678:Genome; D018398:Homeodomain Proteins / Q000378:metabolism; D006801:Humans; D016013:Likelihood Functions; D051761:Paired Box Transcription Factors / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000235:genetics
chemical_list: D005136:Eye Proteins; D018398:Homeodomain Proteins; D051761:Paired Box Transcription Factors; D012097:Repressor Proteins
keywords: Ancestral structure estimation; Evolution of eye development; Transcription factor