Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half- lives

• 成果类型: Article
• 署名作者: Jenniches, Laura; Michaux, Charlotte; Popella, Linda; Reichardt, Sarah; Vogel, Joerg; Westermann, Alexander J.; Barquist, Lars
• 署名单位: Helmholtz Association; Helmholtz-Center for Infection Research; University of Wurzburg; University of Wurzburg; University of Toronto; University Toronto Mississauga
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8646
• DOI: 10.1073/pnas.2308814121
• 发表日期: 2024-04-02
• 关键词: escherichia-coli; cspa-family; proq; hfq; degradation; rifampicin; DISCOVERY; proteins; patterns; GROWTH

摘要

RNA decay is a crucial mechanism for regulating gene expression in response to environmental stresses. In bacteria, RNA- binding proteins (RBPs) are known to be involved in posttranscriptional regulation, but their global impact on RNA half - lives has not been extensively studied. To shed light on the role of the major RBPs ProQ and CspC/E in maintaining RNA stability, we performed RNA sequencing of Salmonella enterica over a time course following treatment with the transcription initiation inhibitor rifampicin (RIF-seq) in the presence and absence of these RBPs. We developed a hierarchical Bayesian model that corrects for confounding factors in rifampicin RNA stability assays and enables us to identify differentially decaying transcripts transcriptome-wide. Our analysis revealed that the median RNA half - life in Salmonella in early stationary phase is less than 1 min, a third of previous estimates. We found that over half of the 500 most long - lived transcripts are bound by at least one major RBP, suggesting a general role for RBPs in shaping the transcriptome. Integrating differential stability estimates with cross- linking and immunoprecipitation followed by RNA sequencing (CLIP-seq) revealed that approximately 30% of transcripts with ProQ binding sites and more than 40% with CspC/E binding sites in coding or 3 ' untranslated regions decay differentially in the absence of the respective RBP. Analysis of differentially destabilized transcripts identified a role for ProQ in the oxidative stress response. Our findings provide insights into posttranscriptional regulation by ProQ and CspC/E, and the importance of RBPs in regulating gene expression.