Cyclic di‐GMP sensing histidine kinase PdtaS controls mycobacterial adaptation to carbon sources

Abstract

Cell signaling relies on second messengers to transduce signals from the sensory apparatus to downstream signaling pathway components. In bacteria, one of the most important and ubiquitous second messenger is the small molecule cyclic diguanosine monophosphate (c‐di‐GMP). While the biosynthesis, degradation, and regulatory pathways controlled by c‐di‐GMP are well characterized, the mechanisms through which c‐di‐GMP controls these processes are not entirely understood. Herein we present the report of a c‐di‐GMP sensing sensor histidine kinase PdtaS (Rv3220c), which binds to c‐di‐GMP at submicromolar concentrations, subsequently perturbing signaling of the PdtaS‐PdtaR (Rv1626) two‐component system. Aided by biochemical analysis, genetics, molecular docking, FRET microscopy, and structural modelling, we have characterized the binding of c‐di‐GMP in the GAF domain of PdtaS. We show that a pdtaS knockout in Mycobacterium smegmatis is severely compromised in growth on amino acid deficient media and exhibits global transcriptional dysregulation. The perturbation of the c‐di‐GMP‐PdtaS‐PdtaR axis results in a cascade of cellular changes recorded by a multiparametric systems’ approach of transcriptomics, unbiased metabolomics, and lipid analyses.

Integrated sensing of host stresses by inhibition of a cytoplasmic two-component system controls M. tuberculosis acute lung infection

“…Genetic deletion of pdtaS / R relieves this inhibition and restores wild-type stress resistance. Although the PdtaS GAF domain was recently reported to bind cyclic di-GMP ( Hariharan et al, 2021 ), the full set of ligands that interact with the PdtaS sensing domains are not known. To determine whether PdtaS/R directly senses cytosolic metals and/or nitric oxide, we reconstituted the PdtaS/R phosphotransfer reaction using purified proteins.…”

Two‐component sensor histidine kinases of Mycobacterium tuberculosis: Beacons for niche navigation

“…The kinase activity of purified PdtaS was also shown by Buglino et al (2021) to be regulated by zinc and copper, indicating that the PdtaRS pathway may have additional functions in regulating M. tuberculosis responses to these metals. Recently, the activity of the PdtaRS pathway has been shown to be regulated by intracellular levels of cyclic di‐GMP, which increases when Mycobacterium smegmatis is cultured in a nutrient‐poor medium to activate the PdtaRS TCS (Hariharan et al, 2021), implicating this system in the adaptation of M. tuberculosis to nutrient starvation during infection in addition to the aforementioned environments. Taken together, these in vitro models have begun to shed light on the role of TCSs in host adaptation during M. tuberculosis infection.…”

“…Copper, Zinc, NO (Buglino et al, 2021), Cyclic di-GMP (Hariharan et al, 2021) Yes (Preu et al, 2012) PdtaR (Morth et al, 2005) No (Agrawal et al, 2015) NCA NCA MtrB NCA NCA MtrA (Friedland et al, 2007) PhoP, NarL, KdpE, TcrX, TcrA (Agrawal et al, 2015; Phosphotransfer not observed by Agrawal et al (2015).…”

“…The structure of the cytoplasmically-localized SK PdtaS has been solved (Preu et al, 2012), and two recent reports suggest cyclic diguanosine monophosphate (di-GMP), copper, zinc, and NO may be regulatory ligands of PdtaS activity (Buglino et al, 2021;Hariharan et al, 2021). Cyclic di-GMP binds to purified PdtaS with high affinity and enhances its autokinase activity in a dose-dependent manner.…”

“…MprB activation is inhibited when bound to DnaK, however, it is proposed that under conditions of cell envelope stress, dissociation of DnaK from MprB promotes SK activity (Bretl et al, 2014; Rao et al, 2021). The structure of the cytoplasmically‐localized SK PdtaS has been solved (Preu et al, 2012), and two recent reports suggest cyclic diguanosine monophosphate (di‐GMP), copper, zinc, and NO may be regulatory ligands of PdtaS activity (Buglino et al, 2021; Hariharan et al, 2021). Cyclic di‐GMP binds to purified PdtaS with high affinity and enhances its autokinase activity in a dose‐dependent manner.…”