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Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress.
Schumacher, Kilian; Gelhausen, Rick; Kion-Crosby, Willow; Barquist, Lars; Backofen, Rolf; Jung, Kirsten.
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  • Schumacher K; Faculty of Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
  • Gelhausen R; Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
  • Kion-Crosby W; Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
  • Barquist L; University of Würzburg, Faculty of Medicine, Würzburg, Germany.
  • Backofen R; Helmholtz Institute for RNA-based Infection Research (HIRI)/Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
  • Jung K; University of Würzburg, Faculty of Medicine, Würzburg, Germany.
mSystems ; 8(6): e0103723, 2023 Dec 21.
Article en En | MEDLINE | ID: mdl-37909716
IMPORTANCE: Bacteria react very differently to survive in acidic environments, such as the human gastrointestinal tract. Escherichia coli is one of the extremely acid-resistant bacteria and has a variety of acid-defense mechanisms. Here, we provide the first genome-wide overview of the adaptations of E. coli K-12 to mild and severe acid stress at both the transcriptional and translational levels. Using ribosome profiling and RNA sequencing, we uncover novel adaptations to different degrees of acidity, including previously hidden stress-induced small proteins and novel key transcription factors for acid defense, and report mRNAs with pH-dependent differential translation efficiency. In addition, we distinguish between acid-specific adaptations and general stress response mechanisms using denoising autoencoders. This workflow represents a powerful approach that takes advantage of next-generation sequencing techniques and machine learning to systematically analyze bacterial stress responses.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteínas de Escherichia coli / Escherichia coli Límite: Humans Idioma: En Revista: MSystems Año: 2023 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Estados Unidos
Texto completo
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Proteínas de Escherichia coli / Escherichia coli Límite: Humans Idioma: En Revista: MSystems Año: 2023 Tipo del documento: Article País de afiliación: Alemania Pais de publicación: Estados Unidos