Identification of human genes related to olfactory-specific CYP2G1

CYP2G2, pseudogenized in human, is expressed in nasal mucosa of cynomolgus monkey and encodes a functional drug-metabolizing enzyme

CYP2G2P is pseudogenized in humans because of two nonsense mutations (c.76C>T in exon 1 and c.382C>T in exon 3) in the putative coding region of the gene sequence, whereas mouse, rat, and rabbit CYP2Gs are expressed and functional in nasal mucosa. In this study, we assessed the intactness of CYP2G in a cynomolgus monkey, a macaque species important for drug metabolism studies because of its evolutionary closeness to human. On the basis of a gene sequence (highly identical to human CYP2G2P) found in the macaque genome, CYP2G2 cDNA was successfully isolated from cynomolgus monkey nasal mucosa. CYP2G2 cDNA, containing an open reading frame of 494 amino acids, was shown to share high sequence identity (nearly 95%) with the putative coding region of human CYP2G2P. Cynomolgus monkey CYP2G2 shared the highest sequence identity (59-61%) with CYP2A23, CYP2A24, and CYP2A26 among cynomolgus monkey cytochromes P450. Cynomolgus monkey CYP2G2 mRNA was predominantly expressed in the nasal mucosa, where CYP2G2 protein expression was also detected. Metabolic assays indicated that cynomolgus monkey CYP2G2 metabolized coumarin, similar to cynomolgus monkey CYP2A23, CYP2A24, and CYP2A26. Moreover, among 39 cynomolgus monkeys and 11 rhesus monkeys examined in this study, only 2 cynomolgus monkeys and 1 rhesus monkey were heterozygous for c.76C>T. No animals carried c.382C>T. These results suggest that cynomolgus monkey CYP2G2 is a functional drug-metabolizing enzyme in nasal mucosa.

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates

Novel human pseudogenes are identified that had previous functionality and their age is estimated. The rate of loss-of-function occurred uniformly.

Background

Unitary pseudogenes are a class of unprocessed pseudogenes without functioning counterparts in the genome. They constitute only a small fraction of annotated pseudogenes in the human genome. However, as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution.

Results

We have developed a pipeline to detect human unitary pseudogenes through analyzing the global inventory of orthologs between the human genome and its mammalian relatives. We focus on gene losses along the human lineage after the divergence from rodents about 75 million years ago. In total, we identify 76 unitary pseudogenes, including previously annotated ones, and many novel ones. By comparing each of these to its functioning ortholog in other mammals, we can approximately date the creation of each unitary pseudogene (that is, the gene 'death date') and show that for our group of 76, the functional genes appear to be disabled at a fairly uniform rate throughout primate evolution - not all at once, correlated, for instance, with the 'Alu burst'. Furthermore, we identify 11 unitary pseudogenes that are polymorphic - that is, they have both nonfunctional and functional alleles currently segregating in the human population. Comparing them with their orthologs in other primates, we find that two of them are in fact pseudogenes in non-human primates, suggesting that they represent cases of a gene being resurrected in the human lineage.

Conclusions

This analysis of unitary pseudogenes provides insights into the evolutionary constraints faced by different organisms and the timescales of functional gene loss in humans.

Organization, structure and evolution of the CYP2 gene cluster on human chromosome 19

The cytochrome P450 superfamily of mixed-function oxygenases has been extensively studied due to its many critical metabolic roles, and also because it is a fascinating example of gene family evolution. The cluster of genes on human chromosome 19 from the CYP2A, 2B, and 2F subfamilies has been previously described as having a complex organization and many pseudogenes. We describe the discovery of genes from three more CYP2 subfamilies inside the cluster, and assemble a complete map of the region. We comprehensively review the organization, structure, and expression of genes from all six subfamilies. A general hypothesis for the evolution of this complex gene cluster is also presented.

Characterization of human CYP2G genes: widespread loss-of-function mutations and genetic polymorphism

CYP2G1 is an abundant, olfactory mucosa-specific cytochrome P450 enzyme active in the metabolism of sex steroids and xenobiotic substrates in mammalian animals. Two different human CYP2G genes, CYP2GP1 and CYP2GP2, were characterized in the present study. Polymorphisms in these genes were also studied. CYP2GP1 contained a single nucleotide deletion in exon 2 (deltaC) and a 2.4-kb deletion between exons 3 and 7 (deltaE4-6), whereas CYP2GP2 contained a nonsense mutation in exon 1 and another in exon 3. The coding region sequences in exons 1-3 and 7-9 of the two genes were 96.7% identical. Both genes were localized to human chromosome 19, and Southern blot analysis of human genomic DNA did not detect any additional copies of the CYP2G gene. The occurrence of these loss-of-function mutations was analysed by polymerase chain reaction-based genotyping in more than 200 individuals. The deltaE4-6 deletion in CYP2GP1 was detected in 94% of subjects (either homozygous or heterozygous), and an allele which does not contain this deletion was detected in 11.6% of individuals. The nonsense mutation in CYP2GP2 exon 3 was detected in 86% of individuals (either homozygous or heterozygous); however, a potentially functional CYP2GP2 allele based on the absence of the nonsense mutation in exon 3 was also detected in 31% of individuals. These results indicate that a functional CYP2G allele is rare in humans. Analysis of the allelic distribution in different ethnic groups suggested that a functional CYP2G allele, if present, is more likely to be found in Black and Hispanic subjects.

cDNA cloning, heterologous expression, and characterization of mouse CYP2G1, an olfactory-specific steroid hydroxylase

CYP2G1 is expressed specifically in the olfactory mucosa in rabbits and rats. In the present study, a full-length cDNA for mouse CYP2G1 was obtained using a PCR approach with RNA preparations from the olfactory mucosa of C57BL/6 mice. Sequence comparisons indicated that mouse CYP2G1 is highly homologous in deduced amino acid sequence to rabbit (82.4% identity) and rat CYP2G1 (94.9% identity). RNA blot and immunoblot analyses indicated that mouse CYP2G1 is expressed only in the olfactory mucosa. The coding region of the mouse CYP2G1 cDNA was cloned into a baculoviral expression vector for heterologous production of the enzyme in cultured insect cells. Heterologously expressed mouse CYP2G1 was active in a reconstituted system toward testosterone and progesterone, producing all the major metabolites detected in olfactory microsomal reactions, including 15 alpha-, 15 beta-, and 2 beta-hydroxytestosterone from testosterone and two unidentified metabolites from progesterone. Kinetic analysis indicated that mouse CYP2G1 has relatively high affinities toward the steroid substrates, with K(m) values in the micromolar range for both testosterone and progesterone. At a substrate concentration of 10 microM, microsomes of olfactory mucosa had much higher turnover numbers toward testosterone and progesterone than hepatic microsomes, consistent with the olfactory-specific expression of a high-affinity sex steroid hydroxylase. These findings will facilitate further molecular genetics studies on the biological function of CYP2G1 in a mouse model.