Conserved +1 translational frameshifting in the Saccharomyces cerevisiae gene encoding YPL034W
Year: 2025
Type: article
Abstract: Cells have developed exquisite mechanisms to ensure accurate translation of mRNA, including preventing a change in reading frame during translation elongation.A minority of chromosomally encoded genes have evolved sequences that subvert standard decoding to program +1 translational frameshifting, either constitutively or in response to external stimuli.In the yeast Saccharomyces cerevisiae, three chromosomal genes are known to employ programmed +1 translational frameshifting for expression of full-length functional products.Here, we identify a fourth yeast gene, YFS1, encompassing the existing predicted open reading frame YPL034W, with conserved programmed +1 frameshifting.Like the previously known examples, YFS1 appears to exploit peculiarities in tRNA abundance in S. cerevisiae to promote frameshifting.translation reading frame after ribosomes have committed to the start of translation.Nevertheless, a small group of genes have evolved sequences that act in cis to subvert standard decoding, often for regulatory purposesa process known as recoding (8).Recoding encompasses phenomena like stop codon readthrough, ribosome hopping, and ribosomal frameshifting.In the latter, a fraction of translocating ribosomes slip forward (5') or backward (3') resulting in "+" or "-" frameshifting (9, 10).Most known cases of programmed frameshifting involve either +1 or -1 frameshifts that, while superficially similar, are mechanistically distinct.Well studied examples of -1 frameshifting result from simultaneous slippage of tRNAs relative to mRNA when both the A and P sites of the ribosome are occupied by tRNAs decoding a heptanucleotide sequence with the signature motif X-XXY-YYZ (11), wherein the tRNA decoding the triplet XXY can also decode XXX and the tRNA decoding YYZ can also decode YYY.By contrast, +1 frameshifting usually occurs when the ribosome P site is occupied by peptidyl-tRNA, but the A site is empty owing to slow decoding of the A site triplet (12, 13).In addition to a defined frameshift site sequence, most cases of programmed frameshifting include additional sequences, present 5' or 3' of the shift site, that dramatically alter the efficiency of frameshifting (9).Work on translation of the gag-pol fusion proteins encoded by the Ty1 and Ty3 retrotransposons of S. cerevisiae provided important insights into the mechanism of +1 frameshifting.Ty1 frameshifting occurs on the heptanucleotide sequence CUU-AGG-C when the CUU Leu codon is in the ribosome P site and AGG Arg codon is in the A site ( 14).This sequence alone, without any additional cis-elements, supports ≥40% frameshifting depending on the reporter.A larger cassette, including additional sequences naturally surrounding the shift site, yields somewhat lower +1 frameshifting of 12-20%, suggesting the potential presence of frameshift suppressing sequences (15, 16).The CUU-AGG-C sequence also directs +1 frameshifting in ABP140 (17), one of three S. cerevisiae chromosomal genes known to employ programmed +1 frameshifting.Another yeast gene requiring +1 frameshifting for expression, EST3, employs a derivative of the Ty1shift site, CUU-AGU-U (18).The third S. cerevisiae chromosomal gene, OAZ1, has the shift site GCG-UGA-C (19), which shares the same P-site codon as the Ty3 shift site, GCG-AGU-U (20).The latter, in turn, shares its A-site triplet with that of the EST3 shift site.If the shift prone Ty1 sequence CUU-AGG-C is present in-frame within a main Open Reading Frame (mORF), which otherwise does not require +1 frameshifting, it is predicted to trigger a high frequency of spurious switches in the reading frame, producing truncated polypeptides, which could be detrimental to cell physiology.Consistent with this prediction, computational analysis revealed a significant underrepresentation of the heptanucleotide CUU-AGG-C in-frame in yeast mORFs, even when codon usage and nucleotide composition are taken into account (21).Here, we show that the previously annotated yeast ORF YPL034W is part of a larger conserved ORF lacking an initiation codon that is instead accessed following initiation at an overlapping ORF initiated further upstream.A fraction of ribosomes initiating on the first ORF frameshift in the +1 direction while translating the heptanucleotide sequence CUU-AGG-C.This frameshift sequence, and the frameshifting itself, is conserved in most sequenced members of the budding yeast Saccharomycetaceae family.We propose to name the newly identified gene Yeast Frame Shift 1 (YFS1). ResultsEvidence that expression of YPL034W requires +1 frameshifting J o u r n a l P r e -p r o o f
Source: Journal of Biological Chemistry
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,430
OpenAlex ID: W4415880390