Decoding sORF translation – from small proteins to gene regulation

Abstract

Translation is best known as the fundamental mechanism by which the ribosome converts a sequence of nucleotides into a string of amino acids. Extensive research over many years has elucidated the key principles of translation, and the majority of translated regions were thought to be known. The recent discovery of wide-spread translation outside of annotated protein-coding open reading frames (ORFs) came therefore as a surprise, raising the intriguing possibility that these newly discovered translated regions might have unrecognized protein-coding or gene-regulatory functions. Here, we highlight recent findings that provide evidence that some of these newly discovered translated short ORFs (sORFs) encode functional, previously missed small proteins, while others have regulatory roles. Based on known examples we will also speculate about putative additional roles and the potentially much wider impact that these translated regions might have on cellular homeostasis and gene regulation.

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

“…However, as it has been found for sORFs or ncRNAs, intraRNAs encoded isoforms might present fine tuning regulatory roles that are yet to be discovered. It is also possible that the isoform itself does not play a role as protein but, similarly to what is known for uORF products [20,75], its translation process could regulate a downstream gene translation via ribosome interference if the intraRNA is part of a polycistronic transcriptional unit. In this scenario, it would be conceptually appropriate to rethink an intraORF as an uORF of the following gene.…”

“…Moreover, recent findings that prokaryotes in general have high fractions of translated leaderless mRNAs [18,19] and sORFs (small open reading frames) [20,21] make the realization of intraRNAs coding potential worth investigating. Pervasive translation of intraRNAs would include prokaryotes into the meaningfulness of protein isoforms debate [22,23].…”

Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship

“…Indeed, several examples show that mutations creating or suppressing an uORF led to a decrease or increase in the downstream canonical protein expression (Cabrera-Quio et al 2016). One of the best studied examples of protein expression regulation by uORF translation is that of the GCN4 protein (Natarajan et al 2001).…”

“…Upon starvation, translation re-initiation at the multiple uORFs is down-regulated and the GCN4 protein expression level thus rises (Hinnebusch 2005;Gunišová et al 2016). Multiple examples of uORF-mediated regulation of protein levels have been published; however, numerous studies also highlight the biological role of uORF-encoded peptides Cabrera-Quio et al 2016;Plaza et al 2017). In 2004, a proteomics study detected 54 novel microproteins mapped back to uORFs (Oyama et al 2004) and 40% of identified smORF-encoded peptides (SEPs) were from uORFs in Slavoff et al (2013).…”

“…Notwithstanding, we could also question the arbitrary cut-off taken by groups studying alternative ORFs. For instance, the smORF community only reports ORFs shorter than 100 codons, but they would then miss all longer alternative ORFs (Cabrera-Quio et al 2016;Hellens et al 2016). The OpenProt team does not limit itself to alternative ORFs shorter than 100 codons, but it still uses an arbitrary minimal cut-off of 30 codons (openprot.org).…”