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

Nat Commun. 2017 Nov 17;8(1):1596. doi: 10.1038/s41467-017-01613-1.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics*
  • Escherichia coli Proteins / metabolism
  • Gene Expression Profiling*
  • Gene Expression Regulation, Bacterial*
  • Gene Regulatory Networks
  • High-Throughput Nucleotide Sequencing / methods
  • Metabolic Networks and Pathways / genetics
  • Models, Genetic
  • Protein Binding
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism
  • RNA-Binding Proteins / genetics*
  • RNA-Binding Proteins / metabolism
  • Repressor Proteins / genetics*
  • Repressor Proteins / metabolism
  • Ribosomes / genetics
  • Ribosomes / metabolism


  • CsrA protein, E coli
  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA-Binding Proteins
  • Repressor Proteins