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Nucleic Acids Res. 2015 Feb 18;43(3):1562-76. doi: 10.1093/nar/gkv018. Epub 2015 Jan 23.

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner.

Author information

1
Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.
2
Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
3
Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
4
Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan.
5
Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
6
Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan onouchi@abs.agr.hokudai.ac.jp.

Abstract

Upstream open reading frames (uORFs) are often found in the 5'-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression.

PMID:
25618853
PMCID:
PMC4330380
DOI:
10.1093/nar/gkv018
[Indexed for MEDLINE]
Free PMC Article

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