Actuation of CRP activating region 3 by formylation modulates the Vibrio cholerae response to oxidative DNA damage

The cyclic AMP receptor protein or CRP is a global regulator of bacterial metabolism. CRP activates transcription of genes required for utilization of alternative carbon sources in response to the second messenger cAMP, which is synthesized in the setting of glucose scarcity. Transcription is activated through contact with RNA polymerase at three sites termed activating regions (ARs) 1-3. AR3 was previously reported to be functional only when CRP K52 was mutated to a neutral residue and to be essential for transcription only in the absence of AR1 and AR2. To probe the role of AR3 at the genome level, we used chromatin immunoprecipitation sequencing and RNA sequencing to compare WT CRP with a CRP K52Q mutant. This mutation resulted in hundreds of novel CRP chromosomal binding sites and differentially regulated transcripts including the small RNA CrbZ which represses acetate utilization. CrbZ was expressed by wild-type Vibrio cholerae only in cultures grown to stationary phase in maltose, and proteomic analysis of CRP isolated under these conditions demonstrated formylation of CRP K52. N ε -lysine formylation arises from a reaction with a high energy formylphosphate, which is a byproduct of oxidative DNA damage. Consistent with this, we find that CRP K52Q activates transcription of genes involved in the response to oxidative stress, DNA repair, and protein refolding as well as virulence and catabolism of specific carbon sources. We propose a model in which CRP K52 formylation signals oxidative DNA damage and alters the CRP regulon to protect the cell.