title: Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner.
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.
authors.affiliation: Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.
authors.forename: Isao
authors.initials: I
authors.lastname: Ebina
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Mariko
authors.initials: M
authors.lastname: Takemoto-Tsutsumi
authors.affiliation: Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan.
authors.forename: Shun
authors.initials: S
authors.lastname: Watanabe
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Koyama
authors.affiliation: Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Yayoi
authors.initials: Y
authors.lastname: Endo
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Kaori
authors.initials: K
authors.lastname: Kimata
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Igarashi
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Karin
authors.initials: K
authors.lastname: Murakami
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Rin
authors.initials: R
authors.lastname: Kudo
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Arisa
authors.initials: A
authors.lastname: Ohsumi
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Abdul Latif
authors.initials: AL
authors.lastname: Noh
authors.affiliation: Graduate School of Horticulture, Chiba University, Matsudo 271-8510, Japan.
authors.forename: Hiro
authors.initials: H
authors.lastname: Takahashi
authors.affiliation: Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Naito
authors.affiliation: Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan onouchi@abs.agr.hokudai.ac.jp.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Onouchi
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics*; D018388:Codon, Terminator; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D016366:Open Reading Frames; D010455:Peptides / Q000737:chemistry*; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D018388:Codon, Terminator; D010455:Peptides; D012333:RNA, Messenger