What is meant by translational repression by an upstream open reading frame?
Summary

The statement refers to the small but significant translation of short open reading frames (ORFs) of huntingtin mRNA, 5′ to the main open reading frame that encodes the large (3144 amino acid) functional product of the mRNA (and gene). It has been reported that the translation of these short ORFs decreases (i.e. inhibits) the translation from the main ORF. It is implied that this is a mechanism for regulating the expression of the gene, and, as it occurs on the mRNA in the cytoplasm, it is an example of ‘translational regulation’ — specifically inhibition. The precise mechanism of this regulation — although not unique to this mRNA — is apparently unknown.

Translation of ORFs in eukaryotic mRNA

Most eukaryotic mRNAs are functionally monocistronic — i.e. they encode only a single protein — unlike bacterial mRNAs. Initiation of protein synthesis involves selection of an initiation codon (usually AUG) by a complex of initiator-tRNA and the small ribosome subunit, but, in contrast to prokaryotes, the mechanism in eukaryotes involves scanning along the mRNA from the 5′ end. In the majority of cases the initiation codon of the protein product is the first AUG, but the significant number of exceptions suggest an effect of sequence context or mRNA secondary structure.

In recent years evidence has accumulated that in cases where the first AUG is not that of the main protein product, a small amount of translation from such 5′ upstream ORFs does often occur.



Diagrammatical representation of mRNA with upstream ORF (blue with initiation codon represented as an open triangle) and main ORF (black with initiation codon as closed triangle.)

Regulatory role of upstream ORFs

Johnstone et al. (2016) have reviewed a large body of evidence that indicates that upstream ORFs are translational repressors in eukaryotes. This has generally been established by measuring the extent of translation of the main ORF after manipulation or removal of the upstream ORFs. Much less is known about the actually mechanism of such regulation, which may vary from case to case, and certainly the paper on huntingtin only offered speculative possibilities. These include:


Binding of small peptide products of the upstream ORFs to the AUG of the main ORF
Pausing of ribosomal initiation complex at upstream ORFs impeding the progress of other to the AUG of the main ORF
Change of mRNA secondary structure by the binding of the ribosomal initiation complex at upstream ORFs increasing the difficulty of the initiation step in which the 5′ end is ’melted‘.


It also appears that the extent of the translation of upstream ORFs — and hence the extent of the repression — can itself be regulated by mechanisms such as the phosphorylation of initiation factor eIF2.