Cell signalling relies on second messengers to transduce signals from the sensory 16 apparatus to downstream components of the signalling pathway. In bacteria, one of the most 17 important and ubiquitous second messengers is the small molecule cyclic diguanosine 18 monophosphate (c-di-GMP). While the biosynthesis, degradation and regulatory pathways 19 controlled by c-di-GMP are well characterized, the mechanisms through which c-di-GMP 20 controls these processes is not completely understood. Here we present the first report of a c-21 di-GMP regulated sensor histidine kinase previously named PdtaS (Rv3220c), which binds to 22 c-di-GMP at sub-micromolar concentrations, subsequently perturbing signalling of the PdtaS-23 PdtaR (Rv1626) two component system. Aided by biochemical analysis, molecular docking 24 and structural modelling, we have characterized the binding site of c-di-GMP in the GAF 25 domain of PdtaS. We show that a pdtaS knockout in M. smegmatis is severely compromised in 26 growth on amino acid deficient media and exhibits global transcriptional dysregulation. 27Perturbation of the c-di-GMP-PdtaS-PdtaR axis results in a cascade of cellular changes 28 recorded by a multi-parametric systems approach of transcriptomics, unbiased metabolomics 29 and lipid analyses. 30One-sentence summary: The universal bacterial second messenger cyclic di-GMP controls 31 the mycobacterial nutrient stress response 32Among the less understood TCSs of Mtb is the highly conserved PdtaS-PdtaR TCS. Studies 48 have shown PdtaR to be essential for survival on medium containing cholesterol as the sole 49 carbon source (6) and intracellular growth during macrophage infection (7). Its cognate SK 50PdtaS has been implicated in controlling ribosomal protein composition and sensitivity to 51 ribosome targeting antibiotics, membrane transport inhibitors and respiratory chain antagonists 52in Mycobacterium smegmatis (8). However, neither the ligands that triggers the activation of 53 this TCS nor the adaptive responses that result from PdtaS-PdtaR signalling are known. 54In this study, we use a knockout of pdtaS in Mycobacterium smegmatis to identify the role of 55 this conserved TCS in mycobacterial physiology. Using comparative metabolomics and in 56 silico docking, we have identified c-di-GMP as a ligand for PdtaS. Furthermore, we show that 57PdtaS phosphorylation and integrity of the c-di-GMP binding site are essential for growth, lipid 58 homeostasis and transcriptional adaptation during nutrient deprivation. Finally, using protein-59 protein interaction network modelling of the transcriptomic data, we uncover a novel 60 interactome that connects diverse metabolic pathways in mycobacteria. 61
Results 62
PdtaS deficiency results in poor growth during nutrient deprivation 63In order to study the role of PdtaS and PdtaS-PdtaR signalling in the physiology of 64 mycobacteria, we deleted pdtaS (MSMEG_1918) in M. smegmatis using specialized 65 transduction as described previously (9) and verified the deletion using PCR and Southern blot 66...