The RNA binding protein CsrA controls cyclic di-GMP metabolism by directly regulating the expression of GGDEF proteins

Mol Microbiol. 2008 Oct;70(1):236-57. doi: 10.1111/j.1365-2958.2008.06411.x. Epub 2008 Aug 18.


The carbon storage regulator CsrA is an RNA binding protein that controls carbon metabolism, biofilm formation and motility in various eubacteria. Nevertheless, in Escherichia coli only five target mRNAs have been shown to be directly regulated by CsrA at the post-transcriptional level. Here we identified two new direct targets for CsrA, ycdT and ydeH, both of which encode proteins with GGDEF domains. A csrA mutation caused mRNA levels of ycdT and ydeH to increase more than 10-fold. RNA mobility shift assays confirmed the direct and specific binding of CsrA to the mRNA leaders of ydeH and ycdT. Overexpression of ycdT and ydeH resulted in a more than 20-fold increase in the cellular concentration of the second messenger cyclic di-GMP (c-di-GMP), implying that both proteins possess diguanylate cyclase activity. Phenotypic characterization revealed that both proteins are involved in the regulation of motility in a c-di-GMP-dependent manner. CsrA was also found to regulate the expression of five additional GGDEF/EAL proteins and a csrA mutation led to modestly increased cellular levels of c-di-GMP. All together, these data demonstrate a global role for CsrA in the regulation of c-di-GMP metabolism by regulating the expression of GGDEF proteins at the post-transcriptional level.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cyclic GMP / analogs & derivatives*
  • Cyclic GMP / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial*
  • Genes, Bacterial
  • Genome, Bacterial
  • Genotype
  • Microscopy, Atomic Force
  • Mutagenesis, Site-Directed
  • Mutation
  • Oligonucleotide Array Sequence Analysis
  • Phenotype
  • Plasmids
  • Protein Binding
  • RNA Processing, Post-Transcriptional
  • RNA, Bacterial / metabolism
  • RNA, Messenger / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism*
  • Reverse Transcriptase Polymerase Chain Reaction


  • CsrA protein, E coli
  • Escherichia coli Proteins
  • RNA, Bacterial
  • RNA, Messenger
  • RNA-Binding Proteins
  • Repressor Proteins
  • bis(3',5')-cyclic diguanylic acid
  • Cyclic GMP