Update on the olfactory receptor (OR) gene superfamily

Abstract

The olfactory receptor gene (OR) superfamily is the largest in the human genome. The superfamily contains 390 putatively functional genes and 465 pseudogenes arranged into 18 gene families and 300 subfamilies. Even members within the same subfamily are often located on different chromosomes. OR genes are located on all autosomes except chromosome 20, plus the X chromosome but not the Y chromosome. The gene:pseudogene ratio is lowest in human, higher in chimpanzee and highest in rat and mouse--most likely reflecting the greater need of olfaction for survival in the rodent than in the human. The OR genes undergo allelic exclusion, each sensory neurone expressing usually only one odourant receptor allele; the mechanism by which this phenomenon is regulated is not yet understood. The nomenclature system (based on evolutionary divergence of genes into families and subfamilies of the OR gene superfamily) has been designed similarly to that originally used for the CYP gene superfamily.

Figure 1

A phylogenetic analysis of one representative from each family of the human OR gene repertoire. In this tree, one can see the following: (1) a general guideline for how the different families relate to one another (although this is very general, and the branching is not always this well defined); (2) the numbers near each branch denote the OR family number; (3) each pie chart size is scaled to represent the number of the OR genes inside that family (black = functional genes, grey = pseudogenes, yellow = segregating pseudogenes [SPGs]). SPGs are genes that segregate in populations between intact genes and pseudogenes -- due to a disruptive SNP [34]. This disruptive mutation can introduce a stop codon, or alter a highly conserved amino acid that is important for proper function of the protein. In Tables 1-5, the SPGs are counted as 'functional genes' or 'pseudogenes', according to the Human Genome Project public version. Additional information can be found at the HORDE database (http://bioportal.weizmann.ac.il/HORDE/).

Figure 2

A phylogenetic analysis of platypus, opossum and human OR genes for the new family 14 only. Opossum = black for intact genes, grey for pseudogenes. Platypus = red for intact genes, pink for pseudogenes. Human = blue. ORI4 is an expansion of three ancestral OR gene subfamilies (A, B and C); the expansion, in both platypus and opossum, took place after speciation, whereas only one branch shows an orthologous relationship between platypus and human (marked with *). The tree was generated with MEGA4, using the nearest-neighbour-joining algorithm, and distances with the Poisson correction model. Bootstrap units are also indicated [34]. This tree is grounded with the OR5IEI gene. Only genes with no more than two frame disruptions were considered in the analysis.