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Conserved upstream open reading frames in higher plants.

Tran MK, Schultz CJ, Baumann U - BMC Genomics (2008)

Bottom Line: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency.In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci.We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

View Article: PubMed Central - HTML - PubMed

Affiliation: Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia. michael.tran@acpfg.com.au

ABSTRACT

Background: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

Results: We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

Conclusion: This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

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Tran_Figure3.eps. 'A frequency distribution of the length (nt) of rice uORFs conserved in four other cereals and in Arabidopsis.
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Figure 3: Tran_Figure3.eps. 'A frequency distribution of the length (nt) of rice uORFs conserved in four other cereals and in Arabidopsis.

Mentions: Since earlier reports showed that plant uORFs can vary in length from 6 to 156 nucleotides [7,9,29-31,46], we examined the length distribution of the cereal uORFs. There are two peaks in the distribution that were found between 1 to 40 nucleotides, and 81 to 120 nucleotides (Figure 3). The uORFs found in the first peak are tiny with 9 (out of 14) uORFs having a length of nine nucleotides. Some of these tiny uORFs could be artefactual as a result of point mutations that insert an in-frame start and/or stop codon in the 5'-UTR. If these artefactual uORFs were removed then the uORF length distribution would move towards a normal distribution. Seventy six percent of the uORFs in the length distribution are shorter than 100 nucleotides, and 48% are shorter than 40 nucleotides. The shortest conserved uORF found in four independent cDNAs was nine nucleotides, even though the cut-off length used by uORFSCAN to identify uORFs was six nucleotides (a start and a stop codon). One of the nine nucleotide uORFs was the 5' tiny uORF found in the S-adenosylmethionine decarboxylase cDNA [9], and three new uORFs, two found in a cDNA encoding alkaline phytoceramidase, and one in a cDNA encoding oxidoreductase, (Table 1). Two long conserved uORFs (>181 nucleotides) were found in cDNAs encoding protein kinases that included one uORF found in a cDNA encoding a CBL-interacting protein kinase and another uORF found in a cDNA encoding a ribosomal protein S6 kinase.


Conserved upstream open reading frames in higher plants.

Tran MK, Schultz CJ, Baumann U - BMC Genomics (2008)

Tran_Figure3.eps. 'A frequency distribution of the length (nt) of rice uORFs conserved in four other cereals and in Arabidopsis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2527020&req=5

Figure 3: Tran_Figure3.eps. 'A frequency distribution of the length (nt) of rice uORFs conserved in four other cereals and in Arabidopsis.
Mentions: Since earlier reports showed that plant uORFs can vary in length from 6 to 156 nucleotides [7,9,29-31,46], we examined the length distribution of the cereal uORFs. There are two peaks in the distribution that were found between 1 to 40 nucleotides, and 81 to 120 nucleotides (Figure 3). The uORFs found in the first peak are tiny with 9 (out of 14) uORFs having a length of nine nucleotides. Some of these tiny uORFs could be artefactual as a result of point mutations that insert an in-frame start and/or stop codon in the 5'-UTR. If these artefactual uORFs were removed then the uORF length distribution would move towards a normal distribution. Seventy six percent of the uORFs in the length distribution are shorter than 100 nucleotides, and 48% are shorter than 40 nucleotides. The shortest conserved uORF found in four independent cDNAs was nine nucleotides, even though the cut-off length used by uORFSCAN to identify uORFs was six nucleotides (a start and a stop codon). One of the nine nucleotide uORFs was the 5' tiny uORF found in the S-adenosylmethionine decarboxylase cDNA [9], and three new uORFs, two found in a cDNA encoding alkaline phytoceramidase, and one in a cDNA encoding oxidoreductase, (Table 1). Two long conserved uORFs (>181 nucleotides) were found in cDNAs encoding protein kinases that included one uORF found in a cDNA encoding a CBL-interacting protein kinase and another uORF found in a cDNA encoding a ribosomal protein S6 kinase.

Bottom Line: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency.In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci.We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

View Article: PubMed Central - HTML - PubMed

Affiliation: Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia. michael.tran@acpfg.com.au

ABSTRACT

Background: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.

Results: We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.

Conclusion: This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.

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