Hidden coding potential of eukaryotic genomes: nonAUG started ORFs

Abstract

It is widely considered that the vast majority of eukaryotic mRNAs contain only one open reading frame (ORF) and encode single protein. However, eukaryotic ribosomes can initiate translation at alternative start codons due to leaky scanning or reinitiation mechanisms that provides an opportunity to synthesize several protein products. Recent investigations also demonstrated that alternative translation from nonAUG start codons and AUG codons in a weak nucleotide context could make an important contribution to eukaryotic proteomes. However, accurate prediction of alternative start codons demands detailed investigation of mRNA features influencing their recognition by eukaryotic ribosomes. In this work, we present the results of computational analysis of characteristics of yeast and mammalian mRNAs potentially involved in the recognition of nonAUG start codons. It was found that sequence features of nonAUG started Saccharomyces cerevisiae upstream ORFs (uORFs) were adjusted for efficient translation and these uORFs could frequently encode functional polypeptides. In particular, our initial studies revealed that predicted tertiary structures downstream of nonAUG start sites in mammalian mRNAs were energetically more stable than those predicted for AUG start sites with strong Kozak context. We hypothesize that presence of such stable tertiary structure downstream of nonAUG start sites could be an important factor for the ribosome to recognize noncanonical start codons.

The mTOR Signaling Pathway Activity and Vitamin D Availability Control the Expression of Most Autism Predisposition Genes

“…Furthermore, a clear connection between ASD and mTOR-mediated translational control also attracts attention to other related mechanisms (e.g., alternative ORFs, eIF2a-mediated control, nonAUG started uORFs, IRES, etc.) that may interfere in some particular cases [46][47][48].…”

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

“…Although AUG remains the main translation initiation site, recent ribosome profiling studies clearly indicate the use of non-AUG start sites [34]. Yet, we did not take into account non-AUG initiation sites as an accurate prediction method for such functional translation start sites is not yet available [58]. Although there is strong evidence that short peptides are also translated [19], we introduced a cut-off of 40 amino acids to discard from our databases polypeptides shorter than 40 residues, which are less readily detected by conventional mass spectrometry approaches, and to keep the database to a reasonable size.…”

The Stringency of Start Codon Selection in the Filamentous Fungus Neurospora crassa

“…Seven of the nine near-cognate codons in a preferred context demonstrably initiated translation in N. crassa in vivo, showing that in this organism non-AUG codons initiate translation. Near-cognate codons can initiate translation of uORFs (71) and synthesis of alternative N-terminally extended protein isoforms (2). Some proteins are synthesized exclusively from near-cognate codons, including mammalian eIF4G2 (22), P. anserina IDI-4 (23), and S. cerevisiae glycyl-tRNA synthetase (24).…”