Biology subjects

Poehls, J.

Publications and source records attributed to Poehls, J..

5 recordsLinked to original sources

bioRxiv2026

Regulatory landscape of widespread stop codon readthrough in Drosophila

In stop codon readthrough (SCR), ribosomes continue to translate past the stop. While programmed SCR is rare in mammals, it appears remarkably widespread in insects, yet its regulation and biological significance remain poorly understood. Here, we systematically characterize SCR in Drosophila melanogaster by integrating ribosome profiling, comparative genomics, proteomics, and functional screening. We identify [~]1,400 SCR genes, reveal sequence features associated with programmed SCR, and distinguish constitutive and tissue-restricted modes. We identify conserved cis-elements sufficient to stimulate constitutive SCR and demonstrate that many remain functional in mammalian cells. Unexpectedly, the major distinction between insect and mammalian cells was not termination efficiency, but insect responsiveness to SCR-promoting regulatory elements. SCR was further associated with increased overall protein output, suggesting a function beyond proteome diversification. Our results establish SCR as a pervasive regulatory mechanism in Drosophila and provide a new framework for its study through the Drosophila Stop Codon Readthrough Atlas.

genomics↗

bioRxiv2026

Amino acid and codon usage explain amino acid misincorporation rates across the tree of life

Protein translation is an error-prone process resulting in a random population of altered protein sequences in every cell. Here, we analyzed thousands of publicly available mass spectrometry datasets to detect amino acid misincorporations and quantify error rates in 14 model organisms. We find that overall error rates and the patterns of codon to amino acid error rates correlate across species. We estimate that on average 1-2% of protein molecules in a cell harbor a misincorporation, whereas this proportion can reach 10% for long proteins. Highly expressed and very long proteins have lower error rates, indicating evolutionary selection on codon usage to reduce the cost of translation errors. While both codon-anticodon mispairing and tRNA mischarging contribute to misincorporations, we estimate that [~]70% of misincorporation events are due to mispairing. The more frequent an amino acid in the proteome, the more likely it is misincorporated (r = 0.53), likely because frequent amino acids are abundant in the cell, increasing the rate of mischarging, and have abundant tRNAs, leading to increased mispairing. Overall, we find that amino acid and codon usage explain error rates. The conserved patterns of amino acid misincorporations from bacteria to humans suggest universal mechanisms driving translational fidelity.

bioinformatics↗

bioRxiv2025

Ribosomal frameshifting is a carefully tuned modifier of proteins

Ribosomal frameshifting, occurring during protein translation, is one of the most consequential recoding events, as it leads to large changes to the protein sequence. However, beyond a few well-characterized cases, its prevalence and consequences across organisms remain poorly understood. To address this, we modeled and experimentally tested frameshifting and systematically characterized its evolutionary impact. We developed SLIPPERRS, a mechanistic model that identifies "slippery" frameshift sites achieving [~]70% accuracy. Building on SLIPPERS predictions and on our mass spectrometry and fluorescence-based assay, we characterized 165 short mRNA sequences. We identified dozens of novel sites with frameshift probabilities that often exceed those of known programmed frameshift cases, and found evidence for both translocation and decoding mechanisms. In Gammaproteobacteria, an average of [~]100 genes per species harbor frameshifting sites, which alter proteins by truncating, extending, and fusing canonical proteins. We detect selection for shorter and less disordered frameshifted proteins to mitigate their deleterious impact. We found negative correlation between GC-content and the occurrence of frameshifting sites. In GC-rich bacteria, where frameshift products are expected to be particularly long and disordered, there is selection for cryptic stop codons. While frameshifting is prevalent and expands protein diversity, it is carefully tuned to avoid its harmful consequences.

biochemistry↗

bioRxiv2023

ENVIRONMENT MODULATES PROTEIN HETEROGENEITY THROUGH TRANSCRIPTIONAL AND TRANSLATIONAL STOP CODON MISCODING

Stop codon miscoding events give rise to longer proteins, which may alter the proteins function and thereby generate short-lasting phenotypic variability from a single gene. In order to systematically assess the frequency and origin of stop codon miscoding events, we designed a library of reporters. We introduced premature stop codons into mScarlet that enabled high-throughput quantification of protein synthesis termination errors in E.coli using fluorescent microscopy. We found that under stress conditions, stop codon miscoding may occur with a rate as high as 80%, depending on the nucleotide context, suggesting that evolution frequently samples stop codon miscoding events. The analysis of selected reporters by mass spectrometry and RNA-seq showed that not only translation but also transcription errors contribute to stop codon miscoding. The RNA polymerase is more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide detection of stop codon miscoding by mass spectrometry revealed that temperature regulates the expression of cryptic sequences generated by stop codon miscoding in E.coli. Overall, our findings suggest that the environment influences the accuracy of protein production, which increases protein heterogeneity when the organisms need to adapt to new conditions.

systems biology↗

bioRxiv2022

Evolutionary impact of codon specific translation errors at the proteome scale

Errors in protein synthesis can lead to non-genetic phenotypic mutations, which contribute to generating a wide range of protein diversity. There are currently no methods to measure proteome-wide amino acid misincorporations in a high-throughput fashion, limiting their detection to specific sites and few codon-anticodon pairs. Therefore, it has been technically challenging to estimate the evolutionary impact of translation errors. Here, we developed a computational pipeline, integrated with a novel mechanistic model of translation errors, which can detect translation errors across organisms and conditions. We revealed hundreds of thousands of amino acid misincorporations and a rugged error landscape in datasets of E. coli and S. cerevisiae. We provide proteome-wide evidence of how codon choice can locally reduce translation errors. Our analysis indicates that the translation machinery prevents strongly deleterious misincorporations while allowing for advantageous ones, and the presence of missing tRNAs would increase codon-anticodon cross-reactivity and misincorporation error rates.

evolutionary biology↗