From modules to networks: A systems-level analysis of the bacitracin stress response inBacillus subtilis

Abstract

13Bacterial resistance against antibiotics often involves multiple mechanisms that are 14 interconnected to ensure robust protection. So far, the knowledge about underlying 15 regulatory features of those resistance networks is sparse, since they can hardly be 16 determined by experimentation alone. Here, we present the first computational approach to 17 elucidate the interplay between multiple resistance modules against a single antibiotic, and 18 how regulatory network structure allows the cell to respond to and compensate for 19 perturbations of resistance. Based on the response of B. subtilis towards the cell wall 20 synthesis-inhibiting antibiotic bacitracin, we developed a mathematical model that 21 comprehensively describes the protective effect of two well-studied resistance modules 22 (BceAB and BcrC) on the progression of the lipid II cycle. By integrating experimental 23 measurements of expression levels, the model accurately predicts the efficacy of bacitracin 24 against the B. subtilis wild-type as well as mutant strains lacking one or both of the 25 resistance modules. Our study reveals that bacitracin-induced changes in the properties of 26 the lipid II cycle itself control the interplay between the two resistance modules. In particular, 27variations in the concentrations of UPP, the lipid II cycle intermediate that is targeted by 28 bacitracin, connect the effect of the BceAB transporter and the homeostatic response via 29 BcrC to an overall resistance response. We propose that monitoring changes in pathway 30 properties caused by a stressor allows the cell to fine-tune deployment of multiple resistance 31 systems and may serve as a cost-beneficial strategy to control the overall response towards 32 this stressor. 34 Importance 35Antibiotic resistance poses a major threat to global health and systematic studies to 36 understand the underlying resistance mechanisms are urgently needed. Although significant 37 progress has been made in deciphering the mechanistic basis of individual resistance 38 determinants, many bacterial species rely on the induction of a whole battery of resistance 39 modules, and the complex regulatory networks controlling these modules in response to 40 antibiotic stress are often poorly understood. In this work we combine experiments and 41 theoretical modelling to decipher the resistance network of Bacillus subtilis against bacitracin, 42 which inhibits cell wall biosynthesis in Gram-positive bacteria. In response to bacitracin 43 stress we find a high level of cross-regulation between the two major resistance modules and 44 quantify their effects on bacterial resistance. To rationalize our experimental data, we expand 45 a previously established computational model for the lipid II cycle through incorporating the 46 quantitative action of the resistance modules. This leads us to a systems-level description of 47 the bacitracin stress response network that captures the complex interplay between 48 resistance modules and the essential lipid II cycle of cell wall biosynthesis...