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Genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.

Liu LY, Charng YC - Evol. Bioinform. Online (2012)

Bottom Line: Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron.The number of interior protein isoforms would be twice that of C-terminal isoforms, on average.TE exonization provides a promising way for functional expansion of the plant proteome.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan, Republic of China.

ABSTRACT
Insertion of transposable elements (TEs) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization which can enrich the complexity of transcriptomes and proteomes. Previously, we performed the first experimental assessment of TE exonization by inserting a Ds element into each intron of the rice epsps gene. Exonization of Ds in plants was biased toward providing splice donor sites from the beginning of the inserted Ds sequence. Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron. The current study involved genome-wide computational analysis of Ds exonization events in the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice). Up to 71% of the exonized transcripts were putative targets for the nonsense-mediated decay (NMD) pathway. The insertion patterns of Ds and the polymorphic splice donor sites increased the transcripts and subsequent protein isoforms. Protein isoforms contain protein sequence due to unspliced intron-TE region and/or a shift of the reading frame. The number of interior protein isoforms would be twice that of C-terminal isoforms, on average. TE exonization provides a promising way for functional expansion of the plant proteome.

No MeSH data available.


Related in: MedlinePlus

Number of additional amino acids in the interior protein isoforms in rice (A) and Arabidopsis (B) genomes.Notes: ‘Min’ and ‘max’ are the minimum and maximum number of additional amino acids, respectively; p15, p30, and p50 are the cumulative proportions of interior variants with additional number of amino acids ≤15, ≤30, and ≤50, respectively.
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f5-ebo-8-2012-575: Number of additional amino acids in the interior protein isoforms in rice (A) and Arabidopsis (B) genomes.Notes: ‘Min’ and ‘max’ are the minimum and maximum number of additional amino acids, respectively; p15, p30, and p50 are the cumulative proportions of interior variants with additional number of amino acids ≤15, ≤30, and ≤50, respectively.

Mentions: Although many exonization events can produce different protein isoforms, the extent of this production needs further analysis. We analyzed the translated products yielded by type V transcripts and non-NMD transcripts of type IV. The translated protein isoforms were characterized as C-terminal or interior variants. For C-terminal isoforms, peptides from the new reading frame replace the C terminus of the reference protein. All type V transcripts yielded this kind of isoforms. For interior isoforms, the exonized transcripts have the same termination codon as the reference transcript. In these transcripts, the upcoming transcripts of the exonized junction have the same reading frame as the reference gene, and therefore, the translation products of the TE and intron transcripts act as a “peptide insertion” in the reference gene products. Figure 3 shows the ratio of interior to C-terminal isoforms of type IV non-NMD proteins in rice and Arabidopsis. Interestingly, the number of 4F interior variants are about 6-fold that of C-terminal variants. To analyze the similarity to the reference proteins, C-terminal variants were further graded by the proportion of amino acids that were identical to the reference protein. The proportions are classified as <25% (very low), 25% to 50% (low), 50% to 75% (medium) and >75% (high). Figure 4 shows that in most chromosomes, the proportion of H and M variants was more than 40% and 20%, respectively, in Ds inserted at forward or reverse direction. For the interior variants, Figure 5 shows the length of inserted peptides for all interior isoforms from each chromosome. The number of amino acids of this type of insertion can vary from 5 to 725. The extremely long insertion of peptide resulted from Ds reverse-inserted in intron 2, position 2147, of rice gene Os05s0162500, which originally created a translation product of 126 amino acids. Interestingly, more than 30% of interior isoforms differ from the reference proteins by ≤15 amino acids and among these, 70,359 isoforms (about 2%) differ from the reference proteins by an additional 5 amino acids. Therefore, many interior isoforms contain short insertions. Specifically, a 5 amino acid insertion may occur in different introns of a single gene and result in fine modification of different domains of the reference protein. As an example, Ds reverse-inserted in each intron of position 1 of the rice gene Os11g0446500 can create 22 interior protein isoforms that have 5 additional amino acids along the corresponding introns of this gene, which is characterized as a P-type ATPase. Blast analysis revealed that all isoforms retain the conserved domains, E1-E2 ATPase, HAD_ like and ATPase-Plipid (data not shown). Comparison of each isoform to the reference protein revealed that all interior variants showed a slight modification in the secondary structure, either a helix or sheet strand (Supplementary Fig. 1: http://homepage.ntu.edu.tw/~lyliu/Exon2011/).


Genome-wide survey of ds exonization to enrich transcriptomes and proteomes in plants.

Liu LY, Charng YC - Evol. Bioinform. Online (2012)

Number of additional amino acids in the interior protein isoforms in rice (A) and Arabidopsis (B) genomes.Notes: ‘Min’ and ‘max’ are the minimum and maximum number of additional amino acids, respectively; p15, p30, and p50 are the cumulative proportions of interior variants with additional number of amino acids ≤15, ≤30, and ≤50, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3475393&req=5

f5-ebo-8-2012-575: Number of additional amino acids in the interior protein isoforms in rice (A) and Arabidopsis (B) genomes.Notes: ‘Min’ and ‘max’ are the minimum and maximum number of additional amino acids, respectively; p15, p30, and p50 are the cumulative proportions of interior variants with additional number of amino acids ≤15, ≤30, and ≤50, respectively.
Mentions: Although many exonization events can produce different protein isoforms, the extent of this production needs further analysis. We analyzed the translated products yielded by type V transcripts and non-NMD transcripts of type IV. The translated protein isoforms were characterized as C-terminal or interior variants. For C-terminal isoforms, peptides from the new reading frame replace the C terminus of the reference protein. All type V transcripts yielded this kind of isoforms. For interior isoforms, the exonized transcripts have the same termination codon as the reference transcript. In these transcripts, the upcoming transcripts of the exonized junction have the same reading frame as the reference gene, and therefore, the translation products of the TE and intron transcripts act as a “peptide insertion” in the reference gene products. Figure 3 shows the ratio of interior to C-terminal isoforms of type IV non-NMD proteins in rice and Arabidopsis. Interestingly, the number of 4F interior variants are about 6-fold that of C-terminal variants. To analyze the similarity to the reference proteins, C-terminal variants were further graded by the proportion of amino acids that were identical to the reference protein. The proportions are classified as <25% (very low), 25% to 50% (low), 50% to 75% (medium) and >75% (high). Figure 4 shows that in most chromosomes, the proportion of H and M variants was more than 40% and 20%, respectively, in Ds inserted at forward or reverse direction. For the interior variants, Figure 5 shows the length of inserted peptides for all interior isoforms from each chromosome. The number of amino acids of this type of insertion can vary from 5 to 725. The extremely long insertion of peptide resulted from Ds reverse-inserted in intron 2, position 2147, of rice gene Os05s0162500, which originally created a translation product of 126 amino acids. Interestingly, more than 30% of interior isoforms differ from the reference proteins by ≤15 amino acids and among these, 70,359 isoforms (about 2%) differ from the reference proteins by an additional 5 amino acids. Therefore, many interior isoforms contain short insertions. Specifically, a 5 amino acid insertion may occur in different introns of a single gene and result in fine modification of different domains of the reference protein. As an example, Ds reverse-inserted in each intron of position 1 of the rice gene Os11g0446500 can create 22 interior protein isoforms that have 5 additional amino acids along the corresponding introns of this gene, which is characterized as a P-type ATPase. Blast analysis revealed that all isoforms retain the conserved domains, E1-E2 ATPase, HAD_ like and ATPase-Plipid (data not shown). Comparison of each isoform to the reference protein revealed that all interior variants showed a slight modification in the secondary structure, either a helix or sheet strand (Supplementary Fig. 1: http://homepage.ntu.edu.tw/~lyliu/Exon2011/).

Bottom Line: Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron.The number of interior protein isoforms would be twice that of C-terminal isoforms, on average.TE exonization provides a promising way for functional expansion of the plant proteome.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, National Taiwan University, Taipei, Taiwan, Republic of China.

ABSTRACT
Insertion of transposable elements (TEs) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization which can enrich the complexity of transcriptomes and proteomes. Previously, we performed the first experimental assessment of TE exonization by inserting a Ds element into each intron of the rice epsps gene. Exonization of Ds in plants was biased toward providing splice donor sites from the beginning of the inserted Ds sequence. Additionally, Ds inserted in the reverse direction resulted in a continuous splice donor consensus region by offering 4 donor sites in the same intron. The current study involved genome-wide computational analysis of Ds exonization events in the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice). Up to 71% of the exonized transcripts were putative targets for the nonsense-mediated decay (NMD) pathway. The insertion patterns of Ds and the polymorphic splice donor sites increased the transcripts and subsequent protein isoforms. Protein isoforms contain protein sequence due to unspliced intron-TE region and/or a shift of the reading frame. The number of interior protein isoforms would be twice that of C-terminal isoforms, on average. TE exonization provides a promising way for functional expansion of the plant proteome.

No MeSH data available.


Related in: MedlinePlus