The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana

Abstract

The nucleotide sequence around the translational initiation site is an important cis-acting element for post-transcriptional regulation. However, it has not been fully understood how the sequence context at the 5′-untranslated region (5′-UTR) affects the translational efficiency of individual mRNAs. In this study, we provide evidence that the 5′-UTRs of Arabidopsis genes showing a great difference in the nucleotide sequence vary greatly in translational efficiency with more than a 200-fold difference. Of the four types of nucleotides, the A residue was the most favourable nucleotide from positions −1 to −21 of the 5′-UTRs in Arabidopsis genes. In particular, the A residue in the 5′-UTR from positions −1 to −5 was required for a high-level translational efficiency. In contrast, the T residue in the 5′-UTR from positions −1 to −5 was the least favourable nucleotide in translational efficiency. Furthermore, the effect of the sequence context in the −1 to −21 region of the 5′-UTR was conserved in different plant species. Based on these observations, we propose that the sequence context immediately upstream of the AUG initiation codon plays a crucial role in determining the translational efficiency of plant genes.

The role of RNA structure at 5′ untranslated region in microRNA-mediated gene regulation

“…This is compatible with previous findings that the 5 ′ UTR sequence near the start codon is significantly more unstructured than randomized sequences and other genomic regions (de Smit and van Duin 1990; Ringnér and Krogh 2005;Kudla et al 2009;Gu et al 2010;Goodman et al 2013;Kim et al 2014). Several recent experimental studies have confirmed the importance of reduced mRNA stability in the region near the start codon in the regulation of translation initiation and final gene expression (Dvir et al 2013;Kim et al 2014). Hence, we suggest that the 5 ′ UTR mRNA structure plays multiple roles in regulating post-transcriptional processes and that local mRNA secondary structure near the 5 ′ cap site, but not the structure of the full-length 5 ′ UTR, plays an important role in miRNA-mediated gene regulation.…”

“…The positive Z ΔG in the windows near the 3 ′ end of the 5 ′ UTR indicates that decreased mRNA stability is favored near the start codon. This is compatible with previous findings that the 5 ′ UTR sequence near the start codon is significantly more unstructured than randomized sequences and other genomic regions (de Smit and van Duin 1990; Ringnér and Krogh 2005;Kudla et al 2009;Gu et al 2010;Goodman et al 2013;Kim et al 2014). Several recent experimental studies have confirmed the importance of reduced mRNA stability in the region near the start codon in the regulation of translation initiation and final gene expression (Dvir et al 2013;Kim et al 2014).…”

“…In contrast, in yeast, the secondary structure of the 5 ′ UTR close to the start codon is selectively loose (Ringnér and Krogh 2005). Mutagenesis studies in both yeast (Dvir et al 2013) and Arabidopsis thaliana (Kim et al 2014) demonstrated that the local RNA secondary structure immediately upstream of the start codon plays a crucial role in determining translational efficiency and thus affects protein production.…”

Mechanism of Cytoplasmic mRNA Translation

“…In Arabidopsis plants exposed to dehydration stress, transcripts that were better associated with polysomes during the stress were enriched in A nucleotides just upstream of the start codon . A recent study of Arabidopsis 5'UTRs further showed that the positions of A residues in the -1 to -5 region from the AUG were highly correlated with translational efficiency and uracil (U) residues in the same region were negatively correlated (Kim et al, 2014b). These results suggest that the region 5' to the AUG in Arabidopsis strongly influences translational efficiency in plants (Kim et al, 2014b).…”

“…A recent study of Arabidopsis 5'UTRs further showed that the positions of A residues in the -1 to -5 region from the AUG were highly correlated with translational efficiency and uracil (U) residues in the same region were negatively correlated (Kim et al, 2014b). These results suggest that the region 5' to the AUG in Arabidopsis strongly influences translational efficiency in plants (Kim et al, 2014b). mRNAs with a 5'UTR that was shorter than average (125 nt) and had low potential for secondary structure formation had higher levels of ribosome occupancy.…”