Ver, the statistical support for this grouping is extremely low (the bootstrap value is 17). Furthermore, this clade is not observed in phylogenetic trees reconstructed using different methods (Figure S1). These results strongly suggest that this grouping is not reliable. This notion is consistent with the absence of this grouping in the RPE65/BCMO phylogenetic tree from the recent paper by Albalat [18]. As the vertebrate BCMO1 and BCMO2 families have numerous paralogs in fish genomes (Figure S1), species tree inferences and functional predictions are very complicated for these families. The phylogeny of the vertebrate RPE65 family follows the species tree with some deviations for fish-specific duplications (Figure S1), which suggests that all members of the family are true MedChemExpress Licochalcone-A orthologs that perform the same function. This idea is further supported by experimental evidence for many vertebrate species, including the lamprey RPE65 (Figure 2a and Figure 2b). The RPE65 family is separated from the rest of the tree by an extremely long branch (the branch A, Figure 1). This branch suggests that an ancestor of RPE65 experienced relatively fast evolution compared to other parts of the tree. The length of this branch is almost two times longer than the branch leading to the lamprey RPE65 sequence (the branch B, Figure 1). The branch A corresponds to approximately 50 million years, whereas the branch B corresponds to 500 million years [19,20,21,22]. Thus the ancestor of RPE65 experienced ,10 time faster evolutionary rate compared to the slow evolutionary rates of the RPE65 family (Figure 1). Such obvious acceleration of evolutionary rates is expected for proteins that are in the process of gaining a new Acetovanillone custom synthesis function [23,24,25]. Based on this hypothesis, deuterostome carotenoid oxygenase proteins outside the RPE65 family do not have isomerohydrolase function and are likely to retain the original oxygenase activity since we did not find any other internal branches that experienced such dramatic acceleration of evolution (Figure 1). Thus, although the Ciona intestinalis BCMOa was initially annotated as RPE65 and was predicted by sequence alignment to be an isomerohydrolase [14], this is not supported by the branch length/time estimates presented in this study, or by our experimental evidence (see below). Analysis of functionally important residues using DIVERGE2 (see Materials and Methods) suggested 7 residues that were substantially functionally diverged from the BCMO2 clade (divergence value .3 at positions L49, Q64, A92, K332, A415, L437, N451). We chose the BCMO2 clade 1407003 for analysis because pairwise alignment of mouse BCMO2, BCMO1 and RPE65 proteins revealed more identities for the RPE65/BCMO2 and BCMO1/BCMO2 pairs than for the BCMO1/RPE65 pair (Table S1), and so we believe the RPE65 and BCMO1 clades diverged from the BCMO2 clade. Out of these 7 residues, four are the closest neighbors of residues that are critically important for the function of RPE65 [7,26]. This result is not unexpected because it has been suggested by different authors that there is an evolutionary coupling between neighboring sites [27,28,29,30,31]. We estimated the significance of this observation using a list of 36 critical residues of RPE65 reported in the literature, taken from studies of pathogenic RPE65 single amino acid changes, and single amino acid changes significantly impairing RPE65 isomerohydrolase activity (more than 50 ) in cell-based assay [7,26]. The probability th.Ver, the statistical support for this grouping is extremely low (the bootstrap value is 17). Furthermore, this clade is not observed in phylogenetic trees reconstructed using different methods (Figure S1). These results strongly suggest that this grouping is not reliable. This notion is consistent with the absence of this grouping in the RPE65/BCMO phylogenetic tree from the recent paper by Albalat [18]. As the vertebrate BCMO1 and BCMO2 families have numerous paralogs in fish genomes (Figure S1), species tree inferences and functional predictions are very complicated for these families. The phylogeny of the vertebrate RPE65 family follows the species tree with some deviations for fish-specific duplications (Figure S1), which suggests that all members of the family are true orthologs that perform the same function. This idea is further supported by experimental evidence for many vertebrate species, including the lamprey RPE65 (Figure 2a and Figure 2b). The RPE65 family is separated from the rest of the tree by an extremely long branch (the branch A, Figure 1). This branch suggests that an ancestor of RPE65 experienced relatively fast evolution compared to other parts of the tree. The length of this branch is almost two times longer than the branch leading to the lamprey RPE65 sequence (the branch B, Figure 1). The branch A corresponds to approximately 50 million years, whereas the branch B corresponds to 500 million years [19,20,21,22]. Thus the ancestor of RPE65 experienced ,10 time faster evolutionary rate compared to the slow evolutionary rates of the RPE65 family (Figure 1). Such obvious acceleration of evolutionary rates is expected for proteins that are in the process of gaining a new function [23,24,25]. Based on this hypothesis, deuterostome carotenoid oxygenase proteins outside the RPE65 family do not have isomerohydrolase function and are likely to retain the original oxygenase activity since we did not find any other internal branches that experienced such dramatic acceleration of evolution (Figure 1). Thus, although the Ciona intestinalis BCMOa was initially annotated as RPE65 and was predicted by sequence alignment to be an isomerohydrolase [14], this is not supported by the branch length/time estimates presented in this study, or by our experimental evidence (see below). Analysis of functionally important residues using DIVERGE2 (see Materials and Methods) suggested 7 residues that were substantially functionally diverged from the BCMO2 clade (divergence value .3 at positions L49, Q64, A92, K332, A415, L437, N451). We chose the BCMO2 clade 1407003 for analysis because pairwise alignment of mouse BCMO2, BCMO1 and RPE65 proteins revealed more identities for the RPE65/BCMO2 and BCMO1/BCMO2 pairs than for the BCMO1/RPE65 pair (Table S1), and so we believe the RPE65 and BCMO1 clades diverged from the BCMO2 clade. Out of these 7 residues, four are the closest neighbors of residues that are critically important for the function of RPE65 [7,26]. This result is not unexpected because it has been suggested by different authors that there is an evolutionary coupling between neighboring sites [27,28,29,30,31]. We estimated the significance of this observation using a list of 36 critical residues of RPE65 reported in the literature, taken from studies of pathogenic RPE65 single amino acid changes, and single amino acid changes significantly impairing RPE65 isomerohydrolase activity (more than 50 ) in cell-based assay [7,26]. The probability th.
