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Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics

Author

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  • Anastasia H. Potts

    (University of Florida, Institute of Food and Agricultural Sciences)

  • Christopher A. Vakulskas

    (University of Florida, Institute of Food and Agricultural Sciences
    Molecular Genetics Department)

  • Archana Pannuri

    (University of Florida, Institute of Food and Agricultural Sciences)

  • Helen Yakhnin

    (Center for RNA Molecular Biology, Pennsylvania State University, University Park)

  • Paul Babitzke

    (Center for RNA Molecular Biology, Pennsylvania State University, University Park)

  • Tony Romeo

    (University of Florida, Institute of Food and Agricultural Sciences)

Abstract

CsrA is a post-transcriptional regulatory protein that is widely distributed among bacteria. This protein influences bacterial lifestyle decisions by binding to the 5′ untranslated and/or early coding regions of mRNA targets, causing changes in translation initiation, RNA stability, and/or transcription elongation. Here, we assess the contribution of CsrA to gene expression in Escherichia coli on a global scale. UV crosslinking immunoprecipitation and sequencing (CLIP-seq) identify RNAs that interact directly with CsrA in vivo, while ribosome profiling and RNA-seq uncover the impact of CsrA on translation, RNA abundance, and RNA stability. This combination of approaches reveals unprecedented detail about the regulatory role of CsrA, including novel binding targets and physiological roles, such as in envelope function and iron homeostasis. Our findings highlight the integration of CsrA throughout the E. coli regulatory network, where it orchestrates vast effects on gene expression.

Suggested Citation

  • Anastasia H. Potts & Christopher A. Vakulskas & Archana Pannuri & Helen Yakhnin & Paul Babitzke & Tony Romeo, 2017. "Global role of the bacterial post-transcriptional regulator CsrA revealed by integrated transcriptomics," Nature Communications, Nature, vol. 8(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01613-1
    DOI: 10.1038/s41467-017-01613-1
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    Cited by:

    1. Trevor R. Simmons & Gina Partipilo & Ryan Buchser & Anna C. Stankes & Rashmi Srivastava & Darian Chiu & Benjamin K. Keitz & Lydia M. Contreras, 2024. "Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Hualiang Pi & Andy Weiss & Clare L. Laut & Caroline M. Grunenwald & Hannah K. Lin & Xinjie I. Yi & Devin L. Stauff & Eric P. Skaar, 2022. "An RNA-binding protein acts as a major post-transcriptional modulator in Bacillus anthracis," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

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