Defining relationships between the known members of the cytochrome P450 3A subfamily, including five putative chimpanzee members.
An analysis of the cytochrome P450 3A subfamily (CYP3A) was undertaken in order to define relationships across species among subfamily members. Some members were excluded due to incomplete sequences, while others were held in abeyance because of their almost complete homology. This is the first publication of five chimpanzee CYP3A genes-CYP3A4, CYP3A5, CYP3A7, CYP3A43, and CYP3A67. This project utilized two approaches for characterizing possible relationships-phylogenetic analysis and genomic structure. For the phylogenetic analysis, both nucleotide and amino acid sequences were aligned in silico using the CLUSTAL algorithm, and then visually inspected for accuracy. Three different computer software packages were utilized: MEGA 2.1, TREECON 1.3b, and PHYLIP 3.5. Multiple methods were used: neighbor-joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML). The resulting topologies were compared against each other to define the consensus topology. In addition, the chimpanzee, human, mouse, and rat genome databases were searched for intron/exon information pertaining to the included genes. Both methods suggest the same conclusion, defining orthologs is plausible between similar species (i.e., mouse and rat), but is less useful between species of different orders (i.e., primate and rodent) or classes (i.e., mammal and avian).
Williams
Eric T
ET
Department of Biochemistry and Molecular Biology, Medical School, University of Texas at Houston, Houston, TX 77030, USA.
Rodin
Andrei S
AS
Strobel
Henry W
HW
D000818:Animals; D001189:Aryl Hydrocarbon Hydroxylases / Q000145:classification* / Q000235:genetics; D019295:Computational Biology; D051544:Cytochrome P-450 CYP3A; D016678:Genome; D006801:Humans; D051379:Mice; D010089:Oxidoreductases, N-Demethylating / Q000145:classification* / Q000235:genetics; D002679:Pan troglodytes / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D051381:Rats; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein
D001189:Aryl Hydrocarbon Hydroxylases; D051544:Cytochrome P-450 CYP3A; D010089:Oxidoreductases, N-Demethylating