The ChvG–ChvI and NtrY–NtrX two-component systems coordinately regulate growth ofCaulobacter crescentus

Abstract

Two-component signaling systems (TCSs) regulate cellular homeostasis in response to changes in the environment. Typical TCSs comprise a sensor histidine kinase and a response regulator; the kinase senses environmental conditions and relays this information via phosphoryl transfer to its cognate response regulator, which controls gene expression. Bacteria often express many TCS gene pairs that control distinct physiological processes, but the regulatory connections between TCSs remain underexplored. We have identified regulatory links between the ChvG–ChvI (ChvGI) and NtrY–NtrX (NtrYX) TCSs, which control important and often overlapping processes in α-proteobacteria, including maintenance of the cell envelope. Deletion of chvG and chvI in Caulobacter crescentus limited growth in defined medium and a selection for genetic suppressors of this growth phenotype uncovered interactions among chvGI, ntrYX, and ntrZ. We found that NtrZ, a previously uncharacterized periplasmic protein, functions upstream of the NtrY sensor kinase. We observed significant overlap in the ChvI and NtrX transcriptional regulons, which provides support for the genetic connection between ntrYX and chvGI. Our analyses indicated that the growth defect of strains lacking ChvGI is determined by the phosphorylation state of NtrX and, to some extent, by the level of the TonB-dependent receptor ChvT. To explain the genetic interaction between these TCSs, we propose a model in which NtrZ functions in the periplasm to regulate the NtrY kinase, promoting phosphorylation of NtrX and modulating the regulatory overlap between NtrX and ChvI. Importance: Two-component signaling systems (TCSs) enable bacteria to regulate gene expression in response to physiochemical changes in their environment. The ChvGI and NtrYX TCSs regulate diverse pathways associated with pathogenesis, growth, and cell-envelope function in many α-proteobacteria. We used Caulobacter crescentus as a model to investigate regulatory connections between ChvGI and NtrYX. Our work defined the ChvI transcriptional regulon in C. crescentus and uncovered significant overlap with the NtrX regulon. We revealed a genetic interaction between ChvGI and NtrYX, whereby modulation of NtrYX signaling affects the survival of cells lacking ChvGI. Finally, we identified NtrZ as a novel NtrY regulator. Our work establishes C. crescentus as an excellent model to investigate multi-level regulatory connections between ChvGI and NtrYX in α-proteobacteria.

Proteomic survey of the DNA damage response inCaulobacter crescentus

“…The copyright holder for this preprint this version posted March 25, 2023. ; https://doi.org/10.1101/2023.03.24.534141 doi: bioRxiv preprint characterization as membrane proteins may alter MMC import and NtrX might have confounding effects because of its role in cell cycle regulation (21,22).…”

“…Our Tn-seq results identified six of these genes as more likely to contain transposon insertions upon MMC damage: CCNA_03681: ABC transporter ATP-binding protein, CCNA_00299: PurD, CCNA_00099: FzlC, CCNA_01034: TonB-dependent outer membrane receptor, and CCNA_01817: NtrX. We decided to focus on PurD and FzlC for further characterization as membrane proteins may alter MMC import and NtrX might have confounding effects because of its role in cell cycle regulation (21,22).…”