Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins

Abstract

Utilization of non-AUG alternative translation start sites is most common in bacteria and viruses, but it has been also reported in other organisms. This phenomenon increases proteome complexity by allowing expression of multiple protein isoforms from a single gene. In Saccharomyces cerevisiae, a few described cases concern proteins that are translated from upstream near-cognate start codons as N-terminally extended variants that localize to mitochondria. Using bioinformatics tools, we provide compelling evidence that in yeast the potential for producing alternative protein isoforms by non-AUG translation initiation is much more prevalent than previously anticipated and may apply to as many as a few thousand proteins. Several hundreds of candidates are predicted to gain a mitochondrial targeting signal (MTS), generating an unrecognized pool of mitochondrial proteins. We confirmed mitochondrial localization of a subset of proteins previously not identified as mitochondrial, whose standard forms do not carry an MTS. Our data highlight the potential of non-canonical translation initiation in expanding the capacity of the mitochondrial proteome and possibly also other cellular features.

Genetic dissection of the mitochondrial lipoylation pathway in yeast

“…Very weak hints of growth may be detected for some mutant strain backgrounds when minimal medium is supplemented with LA (e.g., Figure 2 ), an effect that is enhanced on YP-based media (Additional File Figure A 1 ). Although we are not inclined to score these yeast “ghost” imprints as positive for growth, we would like to point out that FAM1/FAA2 was recently identified as one of many yeast genes possibly encoding a mitochondrially localized variant of a protein, produced by translation initiation from a non-canonical start codon [ 42 , 43 ]. Mitochondrial localization of minute amounts of native Fam1/Faa2, due to altered translation initiation under certain environmental or metabolic conditions, may allow slight growth.…”

Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context

“…We previously provided evolutionary evidence that non-AUG codons are used to produce proteoforms extended at the N terminus in comparison with AUG-initiated proteoforms in vertebrates (Ivanov et al 2011). The existence of alternative proteoforms with non-AUG-initiated extensions with mitochondrial localization signals is also evident in yeast (Monteuuis et al 2019). Others provided evidence for the existence of alternatively initiated proteoforms using variants of ribosome profiling (Ingolia et al 2011;Gao et al 2015) and mass spectrometry (Koch et al 2014;Van Damme et al 2014;Gawron et al 2016).…”

Start codon context controls translation initiation in the fungal kingdom

“…Recent work on meiosis (69) and stress (70) shows that 5’-extended transcript leaders that contain repressive uAUGs (“long undecoded transcript isoforms”) are more common during alternative growth conditions for this yeast. Moreover, in S. cerevisiae , near-cognate codons appear to be more common starts for alternative N-terminal formation (71). This suggests that leaky scanning from near-cognate codons, more than from AUGs, might be an important mode of regulation in S. cerevisiae.…”