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Spliceosomal introns in the 5' untranslated region of plant BTL RING-H2 ubiquitin ligases are evolutionary conserved and required for gene expression.

Aguilar-Hernández V, Guzmán P - BMC Plant Biol. (2013)

Bottom Line: Promoter-GUS fusion lines were used to confirm the IME effect of these 5'UTR introns on gene expression.IMEter scores of BTLs were compared with the 5'UTR introns of two gene families MHX and polyubiquitin genes.Our results indicated that gene expression dependent on a 5'UTR intron is an efficient regulatory mechanism in BTL E3 ligases that has been preserved throughout plant evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Apartado Postal 629, Irapuato, Gto 36821, Mexico. pguzman@ira.cinvestav.mx.

ABSTRACT

Background: Introns located close to the 5' end of a gene or in the 5' untranslated region often exert positive effects on gene expression. This effect, known as intron-mediated enhancement (IME), has been observed in diverse eukaryotic organisms, including plants. The sequences involved in IME seem to be spread across the intron and function in an additive manner. The IMEter algorithm was developed to predict plant introns that may enhance gene expression. We have identified several plant members of the BTL class of E3s, which may have orthologs across eukaryotes, that contain a 5'UTR intron. The RING finger E3 ligases are key enzymes of the ubiquitination system that mediate the transfer of ubiquitin to substrates.

Results: In this study, we retrieved BTL sequences from several angiosperm species and found that 5'UTR introns showing a strong IMEter score were predicted, suggesting that they may be conserved by lineage. Promoter-GUS fusion lines were used to confirm the IME effect of these 5'UTR introns on gene expression. IMEter scores of BTLs were compared with the 5'UTR introns of two gene families MHX and polyubiquitin genes.

Conclusions: Analysis performed in two Arabidopsis BTL E3 ligases genes indicated that the 5'UTR introns were essential for gene expression in all the tissues tested. Comparison of the average 5'UTR intron size on three gene families in ten angiosperm species suggests that a prevalent size for a 5'UTR intron is in the range of 600 nucleotides, and that the overall IMEter score within a gene family is preserved across several angiosperms. Our results indicated that gene expression dependent on a 5'UTR intron is an efficient regulatory mechanism in BTL E3 ligases that has been preserved throughout plant evolution.

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IMEter of 5′UTR introns in AthBTL from groups A and B. Distribution of IMEter scores of the seven A. thaliana BTL genes. In the horizontal axis, the genomic exon-intron structure is shown. The lines represent introns and boxes denote exons. The coding sequence is in a shadowed box and the 5′UTR and 3′UTR are shown in open boxes. The 5′UTR is represented by continuous line. The vertical axis shows the IMEter v2.0 score density in 80 nucleotide windows.
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Figure 3: IMEter of 5′UTR introns in AthBTL from groups A and B. Distribution of IMEter scores of the seven A. thaliana BTL genes. In the horizontal axis, the genomic exon-intron structure is shown. The lines represent introns and boxes denote exons. The coding sequence is in a shadowed box and the 5′UTR and 3′UTR are shown in open boxes. The 5′UTR is represented by continuous line. The vertical axis shows the IMEter v2.0 score density in 80 nucleotide windows.

Mentions: To provide additional information regarding the presence of sequences that enhance expression in the 5′UTR intron, the IMEter scores were determined within the gene length of the seven A. thaliana BTLs. Except for AthBTL5, which displayed a low IMEter score of the 5′UTR intron, AthBTL1, AthBTL2, AthBTL3, AthBTL4, AthBTL6 and AthBTL7 showed strong scores, supporting the speculation that the 5′ region of these genes contain sequences involved in the enhancement of gene expression (Figure 3).


Spliceosomal introns in the 5' untranslated region of plant BTL RING-H2 ubiquitin ligases are evolutionary conserved and required for gene expression.

Aguilar-Hernández V, Guzmán P - BMC Plant Biol. (2013)

IMEter of 5′UTR introns in AthBTL from groups A and B. Distribution of IMEter scores of the seven A. thaliana BTL genes. In the horizontal axis, the genomic exon-intron structure is shown. The lines represent introns and boxes denote exons. The coding sequence is in a shadowed box and the 5′UTR and 3′UTR are shown in open boxes. The 5′UTR is represented by continuous line. The vertical axis shows the IMEter v2.0 score density in 80 nucleotide windows.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4225707&req=5

Figure 3: IMEter of 5′UTR introns in AthBTL from groups A and B. Distribution of IMEter scores of the seven A. thaliana BTL genes. In the horizontal axis, the genomic exon-intron structure is shown. The lines represent introns and boxes denote exons. The coding sequence is in a shadowed box and the 5′UTR and 3′UTR are shown in open boxes. The 5′UTR is represented by continuous line. The vertical axis shows the IMEter v2.0 score density in 80 nucleotide windows.
Mentions: To provide additional information regarding the presence of sequences that enhance expression in the 5′UTR intron, the IMEter scores were determined within the gene length of the seven A. thaliana BTLs. Except for AthBTL5, which displayed a low IMEter score of the 5′UTR intron, AthBTL1, AthBTL2, AthBTL3, AthBTL4, AthBTL6 and AthBTL7 showed strong scores, supporting the speculation that the 5′ region of these genes contain sequences involved in the enhancement of gene expression (Figure 3).

Bottom Line: Promoter-GUS fusion lines were used to confirm the IME effect of these 5'UTR introns on gene expression.IMEter scores of BTLs were compared with the 5'UTR introns of two gene families MHX and polyubiquitin genes.Our results indicated that gene expression dependent on a 5'UTR intron is an efficient regulatory mechanism in BTL E3 ligases that has been preserved throughout plant evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Apartado Postal 629, Irapuato, Gto 36821, Mexico. pguzman@ira.cinvestav.mx.

ABSTRACT

Background: Introns located close to the 5' end of a gene or in the 5' untranslated region often exert positive effects on gene expression. This effect, known as intron-mediated enhancement (IME), has been observed in diverse eukaryotic organisms, including plants. The sequences involved in IME seem to be spread across the intron and function in an additive manner. The IMEter algorithm was developed to predict plant introns that may enhance gene expression. We have identified several plant members of the BTL class of E3s, which may have orthologs across eukaryotes, that contain a 5'UTR intron. The RING finger E3 ligases are key enzymes of the ubiquitination system that mediate the transfer of ubiquitin to substrates.

Results: In this study, we retrieved BTL sequences from several angiosperm species and found that 5'UTR introns showing a strong IMEter score were predicted, suggesting that they may be conserved by lineage. Promoter-GUS fusion lines were used to confirm the IME effect of these 5'UTR introns on gene expression. IMEter scores of BTLs were compared with the 5'UTR introns of two gene families MHX and polyubiquitin genes.

Conclusions: Analysis performed in two Arabidopsis BTL E3 ligases genes indicated that the 5'UTR introns were essential for gene expression in all the tissues tested. Comparison of the average 5'UTR intron size on three gene families in ten angiosperm species suggests that a prevalent size for a 5'UTR intron is in the range of 600 nucleotides, and that the overall IMEter score within a gene family is preserved across several angiosperms. Our results indicated that gene expression dependent on a 5'UTR intron is an efficient regulatory mechanism in BTL E3 ligases that has been preserved throughout plant evolution.

Show MeSH