The G Protein–Coupled Receptor Subset of the Chicken Genome

Abstract

G protein–coupled receptors (GPCRs) are one of the largest families of proteins, and here we scan the recently sequenced chicken genome for GPCRs. We use a homology-based approach, utilizing comparisons with all human GPCRs, to detect and verify chicken GPCRs from translated genomic alignments and Genscan predictions. We present 557 manually curated sequences for GPCRs from the chicken genome, of which 455 were previously not annotated. More than 60% of the chicken Genscan gene predictions with a human ortholog needed curation, which drastically changed the average percentage identity between the human–chicken orthologous pairs (from 56.3% to 72.9%). Of the non-olfactory chicken GPCRs, 79% had a one-to-one orthologous relationship to a human GPCR. The Frizzled, Secretin, and subgroups of the Rhodopsin families have high proportions of orthologous pairs, although the percentage of amino acid identity varies. Other groups show large differences, such as the Adhesion family and GPCRs that bind exogenous ligands. The chicken has only three bitter Taste 2 receptors, and it also lacks an ortholog to human TAS1R2 (one of three GPCRs in the human genome in the Taste 1 receptor family [TAS1R]), implying that the chicken's ability and mode of detecting both bitter and sweet taste may differ from the human's. The chicken genome contains at least 229 olfactory receptors, and the majority of these (218) originate from a chicken-specific expansion. To our knowledge, this dataset of chicken GPCRs is the largest curated dataset from a single gene family from a non-mammalian vertebrate. Both the updated human GPCR dataset, as well the chicken GPCR dataset, are available for download.

The solute carrier (SLC) complement of the human genome: Phylogenetic classification reveals four major families

“…The searches were originally made on RefSeq version 29, and Ensembl version 35, and later redone on versions 30 and 36, respectively. In the resulting SLC dataset, all duplicate hits, incomplete sequences and splice variants were removed as we have previously described [18]. This resulted in a dataset of 384 sequences.…”

“…The default alignment parameters were applied. Phylogenetic trees were calculated as previously described [18]. Briefly, the alignment was bootstrapped 1000 and Maximum Parsimony and Neighbor Joining Trees were calculated on these alignments.…”

Data mining of protein families using common peptides

“…2. Histogram of the number of peptides hits for each chicken GPCR from (Lagerström et al, 2006). Only the area of high values from x=26 to x=254 contains intact and pseudogenes of chicken ORs.…”

Present Perspectives on the Automated Classification of the G-Protein Coupled Receptors (GPCRs) at the Protein Sequence Level

“…GRAFS divides the GPCR superfamily into the Glutamates, Rhodopsins, Adhesions, Frizzled/Taste 2 and Secretin families, from which the acronym GRAFS is derived. The authors of GRAFS were able successfully to differentiate pseudogenes from functional genes, and were also able to classify all human GPCR and leading to the identification of several new GPCRs [42][43][44][45][46][47][48][49].…”

“…Takeda and colleagues extracted approximately 950 open reading frames from the human genome that had 200-1500 amino acid residues similar to those of GPCRs [72]. The GPCR repertoires of several other species have also been published, including mouse [41], rat [46], chicken [45], pufferfish [73], amongst several others.…”