A framework for exploring funtional variability in olfactory receptor genes

Abstract

Background. Olfactory receptors (ORs) are the largest gene family in mammalian genomes. Since nearly all OR genes are orphan receptors, inference of functional similarity or differences between odorant receptors typically relies on sequence comparisons. Based on the alignment of entire coding region sequence, OR genes are classified into families and subfamilies, a classification that is believed to be a proxy for OR gene functional variability. However, the assumption that overall protein sequence diversity is a good proxy for functional properties is untested. Methodology. Here, we propose ap alternative sequence-based approach to infer the similarities and differences in OR binding capacity. Our approach to based on similarities and differences in the predicted binding pockets of OR genes, rather than on the entire OR coding region. Conclusions. Interestingly, our approach yields markedly different results compared to the analysis based on the entire OR coding-regoins. While neither approach can be tested at this time, the discrepancy between the two calls into question the assumption that the current classification reliably reflects OR gene functional variability. © 2007 Man et al.