Alternative translation start sites are conserved in eukaryotic genomes

Abstract

Alternative start AUG codons within a single transcript can contribute to diversity of the proteome; however, their functional significance remains controversial. Here, we provide comparative genomics evidence that alternative start codons are under negative selection in vertebrates, insects and yeast. In genes where the annotated start codon (sAUG) resides within the suboptimal nucleotide context, the downstream in-frame AUG codons (dAUG) among the first ∼30 codon sites are significantly more conserved between species than in genes where the sAUG resides within the optimal context. Proteomics data show that this difference is not an annotation artifact and that dAUGs are in fact under selection as alternative start sites. The key optimal, and sometimes suboptimal, context-determining nucleotides of both the sAUG and dAUGs are conserved. Selection for secondary start sites is stronger in genes with the weak primary start site. Genes with multiple conserved start sites are enriched for transcription factors, and tend to have longer 5′UTRs and higher degree of alternative splicing. Together, these results imply that the use of alternative start sites by means of leaky mRNA scanning is a functional mechanism under selection for increased efficiency of translation and/or for translation of different N-terminal protein variants.

N-terminal Proteomics and Ribosome Profiling Provide a Comprehensive View of the Alternative Translation Initiation Landscape in Mice and Men

“…In general, the phastCons score (between 0 and 1) gives a probability that each nucleotide belongs to a conserved element (see Material and Methods for detailed explanation). Overall, the human and mouse conservation plot indicated that the dTIS are highly conserved, with a mean conservation score of 0.97 (Ϯ 0.002, 95% confidence interval) and 0.97 (Ϯ 0.005) for respectively the Exon1 and ExonϾ1 groups compared with the dbTIS with a mean conservation score of 0.96 (Ϯ 0.01) and are thus indicative for the fact that the dTIS translation start sites are very well conserved within eukaryotic genomes in analogy to what was previously reported by Bazykin et al (87) using in silico predictive analyses and using in vivo GTI-seq experiments (33).…”

Keratinocyte-associated protein 2 is a bona fide subunit of the mammalian oligosaccharyltransferase

“…Although we cannot formally exclude the possibility that this major KCP2 species results from the proteolytic processing of a longer form, our results indicate that the Met27 codon of human KCP2 mRNA is the principal site of translation initiation, and we conclude that this is most probably the case for the majority of vertebrates (supplementary material Fig. S2) (see also Bazykin and Kochetov, 2011;Kochetov, 2005).…”

The amino terminus extension in the long dipeptidyl peptidase 9 isoform contains a nuclear localization signal targeting the active peptidase to the nucleus

“…One possibility is that the two forms are produced from one single transcript, with two alternative translation initiation sites, in a process termed leaky scanning. the use of alternative start codons to generate various protein variants is a conserved feature in eukaryotes [43]. examples for leaky scanning were reported for several proteins including human-insulin-degrading enzyme (IDe) [44] and human neuropeptide Y [45].…”