Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

Abstract

Background: Transposons, i.e. transposable elements (TEs), are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue of whether transposons mediate genomic changes in environment-adaptation genes, we scanned two alleles per each of the six xenobiotic-metabolizing Helicoverpa zea cytochrome P450 loci, including CYP6B8, CYP6B27, CYP321A1, CYP321A2, CYP9A12v3 and CYP9A14, for the presence of transposon insertions by genome walking and sequence analysis. We also scanned thirteen Drosophila melanogaster P450s genes for TE insertions by in silico mapping and literature search.

Results: Twelve novel transposons, including LINEs (long interspersed nuclear elements), SINEs (short interspersed nuclear elements), MITEs (miniature inverted-repeat transposable elements), one full-length transib-like transposon, and one full-length Tcl-like DNA transpson, are identified from the alleles of the six H. zea P450 genes. The twelve transposons are inserted into the 5'flanking region, 3'flanking region, exon, or intron of the six environment-adaptation P450 genes. In D. melanogaster, seven out of the eight Drosophila P450s (CYP4E2, CYP6A2, CYP6A8, CYP6A9, CYP6G1, CYP6W1, CYP12A4, CYP12D1) implicated in insecticide resistance are associated with a variety of transposons. By contrast, all the five Drosophila P450s (CYP302A1, CYP306A1, CYP307A1, CYP314A1 and CYP315A1) involved in ecdysone biosynthesis and developmental regulation are free of TE insertions.

Conclusion: These results indicate that TEs are selectively retained within or in close proximity to xenobiotic-metabolizing P450 genes.

Figure 1

Schematic representation of the six P450 genes and the inserted twelve transposons. The P450 genes are shown to scale with exons depicted as filled pink boxes, introns as pink lines, and 5'/3'-flanking sequences as blue lines. The transposons are represented as colored inverted triangles with their names, orientations (horizontal arrows above triangles) and insertion positions (vertical arrows below triangles). Triangles with an identical color are different copies of one transposon. The red vertical arrow below the CYP321A2 indicates its heme-binding site in protein.

Figure 2

Schematic structures of the 12 transposons. The structure of the 12 transposons are drawn to scale (except for Hztransib1) with horizontal arrows representing putative TSDs (sequence shown underneath). Arrowheads represent TIR (length shown above), filled black boxes represent putative ORF and black lines represent non-coding sequences. Microsatellite sequences within some transposons are shown in parentheses, followed by the corresponding repeat number.

Figure 3

Nucleotide alignments of CYP6B8 and CYP6B28 introns (a) and of two HzMITE2 copies (b). Sequence alignments were generated using the Genedoc software. HzMITE1 and HzMITE3 are indicated by inverted triangles. TSDs flanking each element are underlined and in bold. TIRs for HzMITE2-1and HzMITE2-2 are shown in italic. While HzMITE2-1 is inserted in the 8th intron of CYP9A14, HzMITE2-2 is inserted in the 1st intron of the H. zea delta-9 like acyl-CoA desaturase (HzPGDs3) in an opposite orientation. Accession numbers of CYP6B8 and HzPGDs3 are [GenBank: AF285186] and [GenBank: AF297109], respectively.

Figure 4

Nucleotide alignments of three Hz IS1 copies (a) and of two HzRTE-1 copies (b). Sequence alignments were generated using the Genedoc software. TSDs flanking each TE are underlined and in bold.