Regulation of plant translation by upstream open reading frames

Abstract

We review the evidence that upstream open reading frames (uORFs) function as RNA sequence elements for post-transcriptional control of gene expression, specifically translation. uORFs are highly abundant in the genomes of angiosperms. Their negative effect on translation is often attenuated by ribosomal translation reinitiation, a process whose molecular biochemistry is still being investigated. Certain uORFs render translation responsive to small molecules, thus offering a path for metabolic control of gene expression in evolution and synthetic biology. In some cases, uORFs form modular logic gates in signal transduction. uORFs thus provide eukaryotes with a functionality analogous to, or comparable to, riboswitches and attenuators in prokaryotes. uORFs exist in many genes regulating development and point toward translational control of development. While many uORFs appear to be poorly conserved, and the number of genes with conserved-peptide uORFs is modest, many mRNAs have a conserved pattern of uORFs. Evolutionarily, the gain and loss of uORFs may be a widespread mechanism that diversifies gene expression patterns. Last but not least, this review includes a dedicated uORF database for Arabidopsis.

Keywords: AGI#; Arabidopsis gene identifier; Arabidopsis thaliana; CPuORF; CaMV; Development; NMD; Protein synthesis; RPL; RPS; Sensor; Translation initiation factor; UTR; Upstream open reading frame; cauliflower mosaic virus; conserved peptide uORF; eIF; eukaryotic translation initiation factor; mORF; major open reading frame; nonsense mediated decay; ribosomal protein of the large subunit; ribosomal protein of the small subunit; uORF; untranslated region; upstream open reading frame.