Characterization of pigment epithelium‐derived factor receptor (PEDF‐R) using bioinformatics tools

Abstract

PEDF is an extracellular multifunctional protein with demonstrable neurotrophic, antiangiogenic and antitumorigenic properties, and affinity for collagens and cell-surface receptors. Using bioinformatic tools we examined the sequence of a novel gene from human retinal pigment epithelium (PEDF-R) to reveal a role as PEDF receptor. ENSEMBLE searches showed that the PEDF-R maps to locus 11p15.5 on human chromosome 11. BLASTn searches revealed putative PEDF-R homologues in other species. PEDF-R sequence fragments were found from various human organs, and RT-PCR confirmed expression. The PEDF-R sequence revealed 2.1kb transcripts coding for a 504-residue polypeptide with four N-glycosylation sites. Hydrophobicity plots anticipated 4 transmembrane domains with 3 intracellular and 2 extracellular loops. Northerns confirmed size of transcripts. Westerns revealed a PEDF-R protein (81-kDa) in eukaryotic membranes and cytosol. Immunohistochemistry with specific anti-peptides confirmed transmembrane topology. BLASTp searches identified relatedness with members of the PNLP2 family, which exhibit lipase activities. A center PEDF-R region with homology to collagen I interacted with PEDF. Bioinformatics revealed PEDF-R as a lipase-linked membrane protein with affinity for PEDF, suggesting a molecular pathway by which ligand/receptor interaction on the cell-surface could generate a cellular signal.