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

Yang G, Fattash I, Lee CN, Liu K, Cavinder B - Genome Biol Evol (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Toronto Mississauga, Ontario, Canada.

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.

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Related in: MedlinePlus

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.
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evt146-F3: 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.

Mentions: MITEs can be cross-mobilized by transposases encoded by elements different from, but closely related to, their direct ancestral element(s). To identify such related autonomous elements, the Ozma transposase sequence was used with the TpTE function of MAK. Among the elements in the output, three elements (here designated as Ozana, Ozga, and Ozgana) showing the most similar TIRs to that of Ozma were analyzed further. Ozana has 332 copies in the genome and encodes an intact transposase of 336 a.a. Ozga and Ozgana have only 17 and 16 copies, respectively. When the TIRs of these elements were aligned, TIRs of Ozana are the closest to those of Ozma. The TIRs of the other two elements share 6 nt at the 5′-end but differ significantly toward the 3′-end of the TIRs (fig. 3A). When the transposases of the elements were aligned with the mariner element Mos1 (Medhora et al. 1991) and phylogenetic trees were constructed, it is apparent that the transposase of Ozana is the most closely related to Ozma transposase (fig. 3B and supplementary fig. S1, Supplementary Material online).Fig. 3.—


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

Yang G, Fattash I, Lee CN, Liu K, Cavinder B - Genome Biol Evol (2013)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3814204&req=5

evt146-F3: 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.
Mentions: MITEs can be cross-mobilized by transposases encoded by elements different from, but closely related to, their direct ancestral element(s). To identify such related autonomous elements, the Ozma transposase sequence was used with the TpTE function of MAK. Among the elements in the output, three elements (here designated as Ozana, Ozga, and Ozgana) showing the most similar TIRs to that of Ozma were analyzed further. Ozana has 332 copies in the genome and encodes an intact transposase of 336 a.a. Ozga and Ozgana have only 17 and 16 copies, respectively. When the TIRs of these elements were aligned, TIRs of Ozana are the closest to those of Ozma. The TIRs of the other two elements share 6 nt at the 5′-end but differ significantly toward the 3′-end of the TIRs (fig. 3A). When the transposases of the elements were aligned with the mariner element Mos1 (Medhora et al. 1991) and phylogenetic trees were constructed, it is apparent that the transposase of Ozana is the most closely related to Ozma transposase (fig. 3B and supplementary fig. S1, Supplementary Material online).Fig. 3.—

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Toronto Mississauga, Ontario, Canada.

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.

Show MeSH
Related in: MedlinePlus