Evolutionary conservation suggests a regulatory function of AUG triplets in 5'-UTRs of eukaryotic genes

Abstract

By comparing sequences of human, mouse and rat orthologous genes, we show that in 5′-untranslated regions (5′-UTRs) of mammalian cDNAs but not in 3′-UTRs or coding sequences, AUG is conserved to a significantly greater extent than any of the other 63 nt triplets. This effect is likely to reflect, primarily, bona fide evolutionary conservation, rather than cDNA annotation artifacts, because the excess of conserved upstream AUGs (uAUGs) is seen in 5′-UTRs containing stop codons in-frame with the start AUG and many of the conserved AUGs are found in different frames, consistent with the location in authentic non-coding sequences. Altogether, conserved uAUGs are present in at least 20–30% of mammalian genes. Qualitatively similar results were obtained by comparison of orthologous genes from different species of the yeast genus Saccharomyces. Together with the observation that mammalian and yeast 5′-UTRs are significantly depleted in overall AUG content, these findings suggest that AUG triplets in 5′-UTRs are subject to the pressure of purifying selection in two opposite directions: the uAUGs that have no specific function tend to be deleterious and get eliminated during evolution, whereas those uAUGs that do serve a function are conserved. Most probably, the principal role of the conserved uAUGs is attenuation of translation at the initiation stage, which is often additionally regulated by alternative splicing in the mammalian 5′-UTRs. Consistent with this hypothesis, we found that open reading frames starting from conserved uAUGs are significantly shorter than those starting from non-conserved uAUGs, possibly, owing to selection for optimization of the level of attenuation.

A systematic study of gene expression variation at single-nucleotide resolution reveals widespread regulatory roles for uAUGs

“…We found evidence for strong purifying selection against uAUGs in yeast 59 UTRs, an observation that is consistent with previous studies (Churbanov et al 2005;Iacono et al 2005). In agreement with Churbanov et al, we also found that, for the 20% of genes in yeast that do contain uAUGs in their 59 UTRs, these trinucleotides tend to be conserved, suggesting that while in general uAUGs are deleterious, for a subset of yeast genes, they play an important regulatory role that confers a selective advantage to the organism.…”

Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data

“…Previous work reported that AUG triplets are depleted from mammalian transcript leaders, yet they are also highly conserved (Churbanov et al 2005). Although similar results were reported in yeast, only about 250 genes had annotated transcript leaders at the time.…”

Alternative translation start sites and hidden coding potential of eukaryotic mRNAs

“…(41,(67)(68)(69) Functional roles of many uORFs and uORFencoded peptides were predicted with the aid of various computational approaches. (78)(79)(80)(81)(82) It was found that some orthologous eukaryotic genes are characterized by conservative uAUG triplets, which suggests their importance in expression control. (78) Similarly, ca.…”

“…(78)(79)(80)(81)(82) It was found that some orthologous eukaryotic genes are characterized by conservative uAUG triplets, which suggests their importance in expression control. (78) Similarly, ca. 200 uORF-encoded peptides were characterized by a high level of evolutionary conservation between human and mouse genes, which allows the assumption of their functional significance.…”