Revisiting the classification of adhesion GPCRs

Abstract

G protein-coupled receptors (GPCRs) are encoded by over 800 genes in the human genome. Motivated by different scientific rationales, the two classification systems that are mainly in use, the ABC and GRAFS systems, organize GPCRs according to their pharmacological features and phylogenetic relations, respectively. Within those systems, adhesion GPCRs (aGPCRs) constitute a group of over 30 mammalian homologs, most of which are still orphans with undefined activating signals and signal transduction properties. Previous efforts have further subdivided mammalian aGPCRs into nine subfamilies to indicate phylogenetic relationships. However, this subclassification scheme has shortcomings and inconsistencies that require attention. Here, we have reassessed the phylogenetic relationships of aGPCRs from vertebrate and invertebrate species. Our findings confirm that secretin receptor-like GPCRs most probably emerged from ancestral aGPCRs. We show that reassignment of several aGPCRs to families essentially requires input from functional data. Our analyses establish the need for introducing novel aGPCR subfamilies due to aGPCR sequences from invertebrate species that are not readily assignable to any existing subfamily. We conclude that the current classification systems ought to be updated to consider an unambiguous taxonomy of a hierarchically organized classification and pharmacological properties, and to accommodate phylogenetic affiliations between aGPCR genes within mammals and across the animal kingdom.

Keywords: GPCR; adhesion GPCR; classification; phylogeny.

Figure 1

Current nomenclature of aGPCRs based on phylogenetic analyses. The evolutionary relationships of (A) only human aGPCRs and (B) human, mouse, chicken, and zebrafish aGPCRs are shown. Muscarinic acetylcholine receptors (AChR) served as the outgroup. The evolutionary history was inferred using the neighbor‐joining method.67 The optimal trees with the sum of branch lengths of 14.06117543 (A) and 27.58139556 (B) are shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches.68 The trees are drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method69 and are represented in the units of the number of amino acid substitutions per site. The analyses involved 37 (A) and 150 (B) amino acid sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There was a total of 216 (A) and 196 (B) positions in the final dataset. Evolutionary analyses were conducted in MEGA7.22

Figure 2

Molecular phylogenetic analysis of selected rhodopsin‐like GPCRs, secretin receptor–like GPCRs, and aGPCRs by the maximum likelihood method. The evolutionary history was inferred by using the maximum likelihood method based on the JTT matrix–based model.70 The tree with the highest log likelihood (–52401.93) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying neighbor‐joining and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 425 amino acid sequences, where orthologous sequences of human, mouse, chicken, and zebrafish were included when available. All positions containing gaps and missing data were eliminated. There was a total of 129 positions in the final dataset. Evolutionary analyses were conducted in MEGA7.22 The orthologs and paralogs of individual receptors and receptor subgroups, respectively, were condensed and depicted as triangles. The red and blue scale bars represent the branch lengths of the purine cluster within the delta group and secretin class members, respectively.

Figure 3

Molecular phylogenetic analysis of selected rhodopsin‐like GPCRs, secretin receptor–like GPCRs, and aGPCRs by the maximum likelihood method. The evolutionary history was inferred by using the maximum likelihood method based on the JTT matrix–based model.70 The tree with the highest log likelihood (–52401.93) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying neighbor‐joining and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 425 amino acid sequences, where orthologous sequences of human, mouse, chicken, and zebrafish were included when available. All positions containing gaps and missing data were eliminated. There was a total of 129 positions in the final dataset. Evolutionary analyses were conducted in MEGA7.22 The inset depicts the full phylogenetic tree, which was enlarged for rhodopsin‐like GPCRs (A) and the aGPCR/secretin receptor‐like class (B). The orthologs and paralogs of individual receptors and receptor subgroups, respectively, were condensed and depicted as triangles. The red and blue scale bars represent the branch lengths of the opioid receptor family (OPR) and the histamine type 1 and type 2 family (HRH1/2), respectively.

Figure 4

Phylogenetic relationship of Drosophila melanogaster aGPCR‐like sequences with vertebrate aGPCRs. The evolutionary relationships of D. melanogaster, human, mouse, chicken, and zebrafish aGPCRs are shown. Muscarinic acetylcholine receptors served as the outgroup. (A) The evolutionary history was inferred using the neighbor‐joining method.67 The optimal tree with the sum of branch lengths of 42.71172243 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches.68 The trees are drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method69 and are in the units of the number of amino acid substitutions per site. (B) The evolutionary history was inferred the maximum likelihood method based on the JTT matrix–based model.70 The tree with the highest log likelihood (–29511.43) is shown. Initial tree(s) for the heuristic search were obtained automatically by applying neighbor‐joining and BioNJ algorithms to a matrix of pairwise distances estimated using a JTT model, and then selecting the topology with superior log likelihood value. The analyses involved 225 amino acid sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There was a total of 193 (A) and 141 (B) positions in the final dataset. Evolutionary analyses were conducted in MEGA7.22 dm, D. melanogaster.

Figure 5

Phylogenetic analysis of selected invertebrate and vertebrate aGPCRs. The evolutionary relationships of selected invertebrate aGPCRs and human, mouse, chicken, and zebrafish aGPCRs are shown. Muscarinic acetylcholine receptors (AChR) served as the outgroup. The evolutionary history was inferred using the neighbor‐joining method.67 The optimal tree with the sum of branch length = 138.25837393 is shown. The evolutionary distances were computed using the Poisson correction method69 and are in the units of the number of amino acid substitutions per site. The analyses involved 525 amino acid sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There was a total of 183 positions in the final dataset. Evolutionary analyses were conducted in MEGA7.22 Current subfamilies of aGPCRs are condensed and shown in bold red characters. aGPCR clusters found in invertebrates are shown in blue and the number of receptors included in the cluster is given in parenthesis. Species included in the analysis (aGPCRs from D. melanogaster, including the newly identified genes, are boxed): vertebrate: Homo sapiens (hs), Mus musculus (mm), Gallus gallus (gg), Danio rerio (dr); Cephalochordata: Branchiostoma belcheri (bb); Tunicata: Ciona intestinalis (ci); Hemichordata: Saccoglossus_kowalevskii (sk); Brachiopoda: Lingula anatina (la); Echinodermata: Acanthaster planci (ap); Mollusca Octopus bimaculoides (ob); Neoptera: Drosophila melanogaster (dm); Nematoda: Caenorhabditis elegans (ce); Parazoa: Amphimedon queenslandica (aq).