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

Anastasia H. Potts, Christopher A. Vakulskas, Archana Pannuri, Helen Yakhnin, Paul Babitzke and Tony Romeo ()
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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
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

Nature Communications, 2017, vol. 8, issue 1, 1-15

Abstract: 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.

Date: 2017
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DOI: 10.1038/s41467-017-01613-1

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