Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP
Date
2023-09-06
Journal Title
Journal ISSN
Volume Title
Publisher
Nucleic Acids Research
Abstract
Translational fidelity is critical for microbial fitness, survival and stress responses. Much remains unknown about the genetic and environmental control of translational fidelity and its single-cell heterogeneity. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library of Escherichia coli and identified over 20 genes critical for stop-codon readthrough. Most of these identified genes were not previously known to affect translational fidelity. Intriguingly, we show that several genes controlling metabolism, including cyaA and crp, enhance stop-codon readthrough. CyaA catalyzes the synthesis of cyclic adenosine monophosphate (cAMP). Combining RNA sequencing, metabolomics and biochemical analyses, we show that deleting cyaA impairs amino acid catabolism and production of ATP, thus repressing the transcription of rRNAs and tRNAs to decrease readthrough. Single-cell analyses further show that cAMP is a major driver of heterogeneity in stop-codon readthrough and rRNA expression. Our results highlight that carbon metabolism is tightly coupled with stop-codon readthrough.
Graphical Abstract available at: https://doi.org/10.1093/nar/gkad725
Description
This article was originally published in Nucleic Acids Research. The version of record is available at: https://doi.org/10.1093/nar/gkad725. © The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Citation
Zhihui Lyu, Patricia Villanueva, Liam O’Malley, Parker Murphy, Jacques Augenstreich, Volker Briken, Abhyudai Singh, Jiqiang Ling, Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP, Nucleic Acids Research, Volume 51, Issue 18, 13 October 2023, Pages 9905–9919, https://doi.org/10.1093/nar/gkad725