title: Topology assessment, G protein-coupled receptor (GPCR) prediction, and in vivo interaction assays to identify plant candidate GPCRs.
abstract: Genomic sequencing has provided a vast resource for identifying interesting genes, but often an exact "gene-of-interest" is unknown and is only described as putatively present in a genome by an observed phenotype, or by the known presence of a conserved signaling cascade, such as that facilitated by the heterotrimeric G-protein. The low sequence similarity of G protein-coupled receptors (GPCRs) and the absence of a known ligand with an associated high-throughput screening system in plants hampers their identification by simple BLAST queries or brute force experimental assays. Combinatorial bioinformatic analysis is useful in that it can reduce a large pool of possible candidates to a number manageable by medium or even low-throughput methods. Here we describe a method for the bioinformatic identification of candidate GPCRs from whole proteomes and their subsequent in vivo analysis for G-protein coupling using a membrane based yeast two-hybrid variant (Gookin et al., Genome Biol 9:R120, 2008). Rather than present the bioinformatic process in a format requiring scripts or computer programming knowledge, we describe procedures here in a simple, biologist-friendly outline that only utilizes the basic syntax of regular expressions.
authors.affiliation: Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA, USA.
authors.forename: Timothy E
authors.initials: TE
authors.lastname: Gookin
authors.forename: Jannick D
authors.initials: JD
authors.lastname: Bendtsen
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant; D023281:Genomics; D008024:Ligands; D010944:Plants / Q000235:genetics; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D008024:Ligands; D043562:Receptors, G-Protein-Coupled