Birth of three stowaway-like MITE families via microhomology-mediated miniaturization of a Tc1/Mariner element in the yellow fever mosquito

Abstract

Eukaryotic genomes contain numerous DNA transposons that move by a cut-and-paste mechanism. The majority of these elements are self-insufficient and dependent on their autonomous relatives to transpose. Miniature inverted repeat transposable elements (MITEs) are often the most numerous nonautonomous DNA elements in a higher eukaryotic genome. Little is known about the origin of these MITE families as few of them are accompanied by their direct ancestral elements in a genome. Analyses of MITEs in the yellow fever mosquito identified its youngest MITE family, designated as Gnome, that contains at least 116 identical copies. Genome-wide search for direct ancestral autonomous elements of Gnome revealed an elusive single copy Tc1/Mariner-like element, named as Ozma, that encodes a transposase with a DD37E triad motif. Strikingly, Ozma also gave rise to two additional MITE families, designated as Elf and Goblin. These three MITE families were derived at different times during evolution and bear internal sequences originated from different regions of Ozma. Upon close inspection of the sequence junctions, the internal deletions during the formation of these three MITE families always occurred between two microhomologous sites (6-8 bp). These results suggest that multiple MITE families may originate from a single ancestral autonomous element, and formation of MITEs can be mediated by sequence microhomology. Ozma and its related MITEs are exceptional candidates for the long sought-after endogenous active transposon tool in genetic control of mosquitoes.

Keywords: MITEs; microhomology; origin; transposable elements.

Fig. 1.—

Sequence alignment of representative Gnome MITE sequences. The copy numbers of identical elements are shown to the right of each sequence. Gray arrowheads, TSDs; TIR-L, left TIR; TIR-R, right TIR; blue box, signature base for the left TIR; red box, signature base for the right TIR.

Fig. 2.—

The autonomous element Ozma for Gnome. Sequences on top, the flanking sequence for Ozma element and related empty site. “-” in sequences, gaps in the alignment. Blue and red triangles, left and right TIRs; brown bars, repeats inserted in Ozma; red bar, 270 a.a. ORF; gray stripes, corresponding regions between Gnome and Ozma; percentage, sequence identity; range numbers in red, coordinates for the 270 a.a. ORF; gray number ranges, coordinates of homologous regions with Gnome on Ozma. Element length is to scale.

Fig. 3.—

Autonomous elements related to Ozma. (A) Alignment of the left TIRs of Ozma, Ozana, Ozga, and Ozgana with that of Mos1. (B) Phylogenetic tree of the full-length ORF of the elements. Bootstrap value, 1,000 iterations; see supplementary fig. 1, Supplementary Material online, for alignment. Numbers on branches, percentages of boostrap iterations.

Fig. 4.—

Elf and Goblin MITE families derived from Ozma. (A) Elf element derived from Ozma. (B) Goblin element derived from Ozma. Bubble, close up view of homologous regions between Ozma and Goblin right ends. (C) A deletion derivative of Gnome. Blue and red triangles, left and right TIRs; gray stripes, homologous regions; percentage, sequence similarity; brown bars, repeats inserted in Ozma; red bar, 270 a.a. ORF; number ranges, coordinates of homologous regions with Gnome on Ozma. Hour glass shape, inversed orientation of the region of Ozma on Goblin. Black arrow heads in bubble, inverted sequences of the Ozma subterminal regions on Goblin.

Fig. 5.—

Distribution of sequence divergence for Gnome, Elf, and Goblin families. The numbers of elements in a certain range of divergence from the consensus sequences are plotted against the divergence range. Bin size, 0.005. Dashed lines, broken y axis for better view of the three families. x axis, divergence value; y axis, number of elements in a certain range of divergence value.

Fig. 6.—

Microhomology between break point sequences. Green sequences, left break points; red sequences, right break points; black base letters, aberrant nucleotides introduced; vertical black lines in sequences, junctions; number of bases, length between the two break points; underlined letters, microhomologous sequences.

Fig. 7.—

Hypothetical model for the formation of Goblin. The microhomologous sites at the break points are located in the 3′ subterminal region of Ozma element. Yellow and green short bars, complementary microhomologous sites. Ozma is drawn as a loop structure for convenient illustration of template switching. (A) Double-stranded break formed after the excision of Ozma on one of the two sister chromatids. (B) Gap repair initiated and template switching occurred after the replication of the left TIR. When the 3′-end of the top strand of the left TIR is synthesized, it invades the DNA sequences on the right TIR for replication. (C) Gap repair aborted and the newly synthesized strands are released from the template and the lagging strands synthesized. Microhomologous sites on the newly synthesized DNA are in direct repeat orientation of that on the sequences close to the right TIR. (D) Resection occurs to expose the microhomologous sites that anneal to each other, forming single-stranded flaps with the unannealed strands. (E) Flap trimming, synthesis, and ligation, the newly synthesized double-stranded DNA joins the sequences on the right end between the left distal and the right proximal microhomologous sites. Maroon lines, the sequences flanking the excised Ozma; black lines, unexcised Ozma with flanking sequences; blue lines, newly synthesized DNA from the left; red lines, newly synthesized DNA from the right.