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bioRxiv · 10.1101/2023.02.03.526509

Comprehensive and Comparative Transcriptional Profiling of the Cell Wall Stress Response in Bacillus subtilis

Zhang, Q.·Cornilleau, C.·Muller, R. R.·Meier, D.·Flores, P.·Guerin, C.·Wolf, D.·Fromion, V.·Carballido-Lopez, R.·Mascher, T.
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Abstract

The bacterial cell wall (CW) is an essential protective barrier and the frontline of cellular interactions with the environment and also a target for numerous antimicrobial agents. Accordingly, its integrity and homeostasis are closely monitored and rapid adaptive responses by transcriptional reprogramming induce appropriate counter-measures against perturbations. Here, we report a comprehensive and comparative transcriptional profiling of the primary cell envelope stress responses (CESR), based on combining RNAseq and high-resolution tiling array studies of the Gram-positive model bacterium Bacillus subtilis exposed to a range of antimicrobial compounds that interfere with cytoplasmic, membrane-coupled or extracellular steps of peptidoglycan (PG) biosynthesis. It revealed the complexity of the CESR of B. subtilis and unraveled the contribution of extracytoplasmic function sigma factors (ECFs) and two-component signal transduction systems (TCSs) to protect the cell envelope. While membrane-anchored steps are tightly controlled, early cytoplasmic and late extracellular steps of PG biosynthesis are hardly monitored at all. The ECF {sigma} factors {sigma}W and particularly {sigma}M provide a general CESR, while {sigma}V is almost exclusively induced by lysozyme, against which it provides specific resistance. Remarkably, {sigma}X was slightly repressed by most antibiotics, pointing towards a role in envelope homeostasis rather than CESR. It shares this role with the WalRK TCS, which balances CW growth with controlled autolysis. In contrast, all remaining TCSs are envelope stress-inducible systems. LiaRS is induced by a wide range of PG synthesis inhibitors, while the three paralogous systems BceAB, PsdRS and ApeRS are more compound-specific detoxification modules. Induction of the CssRS TCS by all antibiotics interfering with membrane-anchored steps of PG biosynthesis points towards a physiological link between CESR and secretion stress. Based on the expression signatures, a suite of CESR-specific B. subtilis whole cell biosensors were developed and carefully evaluated. This is the first comprehensive transcriptomic study focusing exclusively on the primary effects of envelope perturbances that shall provide a reference point for future studies on Gram-positive CESR.

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Zhang, Q., Cornilleau, C., Muller, R. R., Meier, D., Flores, P., Guerin, C., Wolf, D., Fromion, V., Carballido-Lopez, R., Mascher, T.. 2023-02-04. Comprehensive and Comparative Transcriptional Profiling of the Cell Wall Stress Response in Bacillus subtilis. https://doi.org/10.1101/2023.02.03.526509

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