Alternative processing of the human FMO6 gene renders transcripts incapable of encoding a functional flavin-containing monooxygenase

The flavin-containing monooxygenases (FMOs) are a family of five microsomal enzymes important for the oxidative metabolism of environmental toxicants, natural products, and therapeutics. With the exception of FMO5, the FMO are encoded within a single gene cluster on human chromosome 1q23-25. As part of the human genome effort, an FMO-like gene, FMO6, was identified between FMO3 and FMO2 (GenBank accession no. ALO21026). Sequence analysis of this putative FMO family member revealed nothing that would a priori argue against a functional gene and encoded protein. When FMO6 expression was examined by reverse transcriptase coupled polymerase chain reaction DNA amplification, transcripts were identified in 8 of 11 human liver samples, but 0 of 4 kidney biopsy samples. However, in all cases, the observed transcripts were shorter than predicted. Sequence analysis revealed skipping of exon 4, exons 3 and 4, and/ or the use of alternative splice donor or acceptor sites in introns 3, 4, 6, and 8, resulting in nine unique transcripts. Based on an analysis of possible open reading frames, none of these transcripts would encode a functional FMO enzyme. Taking advantage of the high sequence identity between FMO3 and FMO6, it is posited that the loss of binding sites for the serine-arginine-rich splicing factor protein family within exons 3 and 4 contributes to the exon skipping events, although the most commonly observed alternative splice event results from a 21-bp insertion immediately 3' to the predicted FMO6 intron 8 splice acceptor site, diminishing the efficiency of this site.