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BMC Genomics
2009 Jun 09;10:263. doi: 10.1186/1471-2164-10-263.
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The repertoire of G-protein-coupled receptors in Xenopus tropicalis.
Ji Y
,
Zhang Z
,
Hu Y
.
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The G-protein-coupled receptor (GPCR) superfamily represents the largest protein family in the human genome. These proteins have a variety of physiological functions that give them well recognized roles in clinical medicine. In Xenopus tropicalis, a widely used animal model for physiology research, the repertoire of GPCRs may help link the GPCR evolutionary history in vertebrates from teleost fish to mammals. We have identified 1452 GPCRs in the X. tropicalis genome. Phylogenetic analyses classified these receptors into the following seven families: Glutamate, Rhodopsin, Adhesion, Frizzled, Secretin, Taste 2 and Vomeronasal 1. Nearly 70% of X. tropicalis GPCRs are represented by the following three types of receptors thought to receive chemosensory information from the outside world: olfactory, vomeronasal 1 and vomeronasal 2 receptors. X. tropicalis shares a more similar repertoire of GPCRs with mammals than it does with fish. An examination of the three major groups of receptors related to olfactory/pheromone detection shows that in X. tropicalis, these groups have undergone lineage specific expansion. A comparison of GPCRs in X. tropicalis, teleost fish and mammals reveals the GPCR evolutionary history in vertebrates.
Figure 1. Sequence analysis strategy for the identification of X. tropicalis GPCRs. Two parallel methods were used for searching the crude sequence database. One was retrieval of proteins with six to eight TM domains from the X. tropicalis proteome database, and the other was extraction of the BLASTP top 20 hits by comparing the GPCR sequences from GPCRDB against the X. tropicalis proteome database. The crude database, which eliminated polymorphism, splice variants, pseudogenes and duplicates by CD-HIT 90% sequence identity, was searched for GPCR conserved domains using CDD v2.14 (E-value = 10-4) and Plam 22.0 (E-value = 0.01). The sequences with conserved seven TM domain were searched using BLASTP against the NCBI non-redundant database. Phylogenetic analyses were carried out to separate the GPCR sequences into rhodopsin like receptors and non-rhodopsin like receptors.
Figure 2. Phylogenetic tree of the non-rhodopsin receptors. The tree was calculated using the neighbour-joining method with 1000 bootstrap replicas. The 339 CaSR like receptors in Glutamate receptors were represented by 25 members in this group using CD-HIT 40% sequence identity. The position of the Rhodopsin family was established by including twelve random receptors from the Rhodopsin family.
Figure 3. Distribution of the number of different GPCR families in 7 different species. The species displayed, from left to right, were Homo sapiens [7], Mus musculus [7], Gallus gallus [11], Xenopus tropicalis, Tetraodon nigroviridis [6], Branchiostoma floridae [12] and Ciona intestinalis [13].
Figure 4. Phylogenetic tree of Adhesion, Frizzled, Secretin and Glutamate families. The trees were calculated using the neighbour-joining method with 1000 bootstrap replicas. The one-to-one orthologous pairs are represented in red. (A) The Adhesion receptor family. I-VIII represent the different groups of the Adhesion family. (B) The Frizzled receptor family. (C) The Secretin receptor family. (D) The Glutamate receptor family.
Figure 5. Phylogenetic tree of vomeronasal 2 receptors. (A) The tree was calculated using the neighbour-joining method with 1000 bootstrap replicas and contained CaSRs and V2Rs from X. tropicalis (green branch), pufferfish (blue branch), human (red branch) and mice (purple branch). The GPRC6A genes were used as an outgroup. (B) Magnification of the marked clade (yellow solid circle) in A. Only one CaSR and one family C V2R were found in X. tropicalis according to the phylogenetic tree.
Figure 6. Phylogenetic tree of X. tropicalis, fish (Takifugu rubripes) and human MCHRs. The tree was calculated using the neighbour-joining method with 1000 bootstrap replicas and contained four X. tropicalis MCHRs (green branch), two fish MCHRs (blue branch) and two human MCHRs (red branch). Each X. tropicalis MCHR formed a monophyletic clade with that of humans or fish MCHR.
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