A cryptic transcription factor regulates Caulobacter crescentus adhesion [ChIP-seq]

Alphaproteobacteria commonly produce a polar adhesin that is anchored to the exterior of the cell envelope. In Caulobacter crescentus, this adhesin enables permanent attachment to solid surfaces and is known as the holdfast. An ensemble of two-component signal transduction (TCS) proteins control C. crescentus holdfast biogenesis by indirectly regulating expression of HfiA, a potent holdfast inhibitor. We designed a genetic screen to identify regulators of hfiA that function downstream of the TCS adhesion regulatory system. This screen identified a hypothetical protein that we have named RtrC. Though the primary structure of RtrC does not match any defined sequence family, we demonstrate that RtrC directly binds and regulates dozens of sites on the C. crescentus chromosome via a pseudo-palindromic motif. Among these binding sites is the hfiA promoter where RtrC functions to repress transcription and thereby activate holdfast biogenesis. RtrC forms an OR-gated type I coherent feedforward loop with the DNA-binding response regulator SpdR and the adhesion regulator RtrB. This type of network motif is known to buffer gene expression against transient loss of regulating signals. We further demonstrate that, in addition to promoting adhesion, RtrC expression influences cell motility in soft agar. We conclude that the formerly hypothetical gene, rtrC, encodes a transcription factor that functions downstream of the C. crescentus TCS adhesion control system to regulate holdfast biogenesis and motility. Chromatin Immunoprecipitation sequencing (ChIP-seq) for 3xFLAG-tagged rtrC