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The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs.

Loot C, Santiago N, Sanz A, Casacuberta JM - Nucleic Acids Res. (2006)

Bottom Line: We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon, a pogo-related element, to specifically bind Emigrant elements.Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs.The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases.

View Article: PubMed Central - PubMed

Affiliation: Departament de Genètica Molecular, Laboratori de Genètica Molecular Vegetal, CSIC-IRTA, Jordi Girona 18, 08034 Barcelona, Spain.

ABSTRACT
MITEs (miniature inverted-repeated transposable elements) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements. Although an active MITE, the mPing element, has recently been characterized in rice, the transposition mechanism of MITEs remains unknown. It has been proposed that transposases of related transposons could mobilize MITEs in trans. Moreover, it has also been proposed that the presence of conserved terminal inverted-repeated (TIR) sequences could be the only requirement of MITEs for mobilization, allowing divergent or unrelated elements to be mobilized by a particular transposase. We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon, a pogo-related element, to specifically bind Emigrant elements. This suggests that Lemi1 could mobilize Emigrant elements and makes the Lemi1/Emigrant couple an ideal system to study the transposition mechanism of MITEs. Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs. The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases.

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Emigrant insertion and excision polymorphisms. (A) PCR amplification with oligonucleotides flanking the Emi158 insertion from water (0) or DNA from the following Arabidopsis ecotypes: 1, Columbia; 2, Landsberg; 3, RLD; 4, Wassilewskija; 5, Canterbury-1; 6, Coimbra-4; 7, Dijon-G; 8, Estland; 9, Geneva-0; 10, Kashmir-1; 11, Moscow; 12, Niederzenz-1; 13, Tsu-0; 14, Nossen. (B) PCR using DNA from 10 different Coimbra-4 individuals. (C) Comparison of the sequences loci corresponding to two polymorphic Emigrant insertions. The name of the polymorphic elements, as well as the name of the ecotypes compared, is shown on the left. The sequence of the theoretical empty site is shown below the sequences for comparison.
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fig1: Emigrant insertion and excision polymorphisms. (A) PCR amplification with oligonucleotides flanking the Emi158 insertion from water (0) or DNA from the following Arabidopsis ecotypes: 1, Columbia; 2, Landsberg; 3, RLD; 4, Wassilewskija; 5, Canterbury-1; 6, Coimbra-4; 7, Dijon-G; 8, Estland; 9, Geneva-0; 10, Kashmir-1; 11, Moscow; 12, Niederzenz-1; 13, Tsu-0; 14, Nossen. (B) PCR using DNA from 10 different Coimbra-4 individuals. (C) Comparison of the sequences loci corresponding to two polymorphic Emigrant insertions. The name of the polymorphic elements, as well as the name of the ecotypes compared, is shown on the left. The sequence of the theoretical empty site is shown below the sequences for comparison.

Mentions: A genome-wide analysis of Arabidopsis (Columbia ecotype) showed that this genome contains different subfamilies of the Emigrant family of MITEs generated by the burst owing to amplification that occurred at different times during the evolution of this genome (11). The EmiA subfamily groups young Emigrant elements while the Emi0 subfamily probably contains the oldest ones (11). In order to look for evidence of recent mobility, we amplified 10 regions containing five EmiA and five Emi0 insertions in the Columbia ecotype from DNA obtained from 14 Arabidopsis ecotypes by using PCR. Two out of five EmiA insertions (Emi126 and Emi158) were found to be polymorphic whereas none of the Emi0 showed insertion polymorphism. The amplification of the Emi158 region gave two bands in the Coimbra-4 ecotype (Figure 1A, lane 6), suggesting that individuals of this ecotype are polymorphic for the Emi158 insertion. The PCR analysis of 10 different individuals indeed revealed that some Coimbra-4 individuals contain the insertion, some do not contain the insertion and some are heterozygous for the insertion (Figure 1B).


The proteins encoded by the pogo-like Lemi1 element bind the TIRs and subterminal repeated motifs of the Arabidopsis Emigrant MITE: consequences for the transposition mechanism of MITEs.

Loot C, Santiago N, Sanz A, Casacuberta JM - Nucleic Acids Res. (2006)

Emigrant insertion and excision polymorphisms. (A) PCR amplification with oligonucleotides flanking the Emi158 insertion from water (0) or DNA from the following Arabidopsis ecotypes: 1, Columbia; 2, Landsberg; 3, RLD; 4, Wassilewskija; 5, Canterbury-1; 6, Coimbra-4; 7, Dijon-G; 8, Estland; 9, Geneva-0; 10, Kashmir-1; 11, Moscow; 12, Niederzenz-1; 13, Tsu-0; 14, Nossen. (B) PCR using DNA from 10 different Coimbra-4 individuals. (C) Comparison of the sequences loci corresponding to two polymorphic Emigrant insertions. The name of the polymorphic elements, as well as the name of the ecotypes compared, is shown on the left. The sequence of the theoretical empty site is shown below the sequences for comparison.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1636448&req=5

fig1: Emigrant insertion and excision polymorphisms. (A) PCR amplification with oligonucleotides flanking the Emi158 insertion from water (0) or DNA from the following Arabidopsis ecotypes: 1, Columbia; 2, Landsberg; 3, RLD; 4, Wassilewskija; 5, Canterbury-1; 6, Coimbra-4; 7, Dijon-G; 8, Estland; 9, Geneva-0; 10, Kashmir-1; 11, Moscow; 12, Niederzenz-1; 13, Tsu-0; 14, Nossen. (B) PCR using DNA from 10 different Coimbra-4 individuals. (C) Comparison of the sequences loci corresponding to two polymorphic Emigrant insertions. The name of the polymorphic elements, as well as the name of the ecotypes compared, is shown on the left. The sequence of the theoretical empty site is shown below the sequences for comparison.
Mentions: A genome-wide analysis of Arabidopsis (Columbia ecotype) showed that this genome contains different subfamilies of the Emigrant family of MITEs generated by the burst owing to amplification that occurred at different times during the evolution of this genome (11). The EmiA subfamily groups young Emigrant elements while the Emi0 subfamily probably contains the oldest ones (11). In order to look for evidence of recent mobility, we amplified 10 regions containing five EmiA and five Emi0 insertions in the Columbia ecotype from DNA obtained from 14 Arabidopsis ecotypes by using PCR. Two out of five EmiA insertions (Emi126 and Emi158) were found to be polymorphic whereas none of the Emi0 showed insertion polymorphism. The amplification of the Emi158 region gave two bands in the Coimbra-4 ecotype (Figure 1A, lane 6), suggesting that individuals of this ecotype are polymorphic for the Emi158 insertion. The PCR analysis of 10 different individuals indeed revealed that some Coimbra-4 individuals contain the insertion, some do not contain the insertion and some are heterozygous for the insertion (Figure 1B).

Bottom Line: We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon, a pogo-related element, to specifically bind Emigrant elements.Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs.The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases.

View Article: PubMed Central - PubMed

Affiliation: Departament de Genètica Molecular, Laboratori de Genètica Molecular Vegetal, CSIC-IRTA, Jordi Girona 18, 08034 Barcelona, Spain.

ABSTRACT
MITEs (miniature inverted-repeated transposable elements) are a particular class of defective DNA transposons usually present within genomes as high copy number populations of highly homogeneous elements. Although an active MITE, the mPing element, has recently been characterized in rice, the transposition mechanism of MITEs remains unknown. It has been proposed that transposases of related transposons could mobilize MITEs in trans. Moreover, it has also been proposed that the presence of conserved terminal inverted-repeated (TIR) sequences could be the only requirement of MITEs for mobilization, allowing divergent or unrelated elements to be mobilized by a particular transposase. We present here evidence for a recent mobility of the Arabidopsis Emigrant MITE and we report on the capacity of the proteins encoded by the related Lemi1 transposon, a pogo-related element, to specifically bind Emigrant elements. This suggests that Lemi1 could mobilize Emigrant elements and makes the Lemi1/Emigrant couple an ideal system to study the transposition mechanism of MITEs. Our results show that Lemi1 proteins bind Emigrant TIRs but also bind cooperatively to subterminal repeated motifs. The requirement of internal sequences for the formation of proper DNA/protein structure could affect the capacity of divergent MITEs to be mobilized by distantly related transposases.

Show MeSH
Related in: MedlinePlus