Modular analysis of a logical regulatory network reveals how Fe-S cluster biogenesis is controlled in the face of stress

Abstract

AbstractIron-sulfur (Fe-S) clusters are important cofactors conserved in all domains of life, yet their synthesis and stability is compromised in stressful conditions such as iron deprivation and oxidative stress. Two conserved machineries, Isc and Suf, assemble and transfer Fe-S clusters to client proteins. The model bacterium Escherichia coli, where Fe-S biogenesis has been extensively studied, possesses both Isc and Suf machineries and their utilisation is under the control of a complex regulatory network. To better understand the underlying regulatory mechanisms and the dynamics behind Fe-S biogenesis in function of environmental conditions, we built a logical model describing Fe-S biogenesis in E. coli. This logical model is centered on three modules : 1) the Fe-S biogenesis module containing the Fe-S cluster assembly machineries Isc and Suf and the transcription factor IscR, the main regulator of Fe-S homeostasis; 2) the iron homeostasis module containing the free intracellular iron regulated by the iron sensing regulator Fur and the non-coding regulatory RNA RyhB involved in iron sparing; 3) the oxidative stress module representing intracellular H2O2 accumulation, which activates OxyR, the regulator of catalases and peroxidases that decompose H2O2 and limit Fenton reaction. Inputs of the model represent extracellular iron and oxygen environmental conditions, whereas ErpA, NfuA (Fe-S carrier proteins), and Suf are output nodes of the model. Analysis of this comprehensive model reveals 5 different types of system behaviours depending on environmental conditions, and provides a better understanding on how oxidative stress and iron homeostasis combine and control Fe-S biogenesis. Using the model, we were able to predict that an iscR mutant would present growth defects in iron starvation, due to partial inability to build Fe-S clusters, and we validated this prediction experimentally.Author summaryIron sulfur (Fe-S) clusters appeared at the origins of life, when oxygen tension was low and iron plentiful, and have been used since as important cofactors for a wide variety of proteins involved in a plethora of reactions. However, synthesis and stability of Fe-S clusters is compromised in conditions where iron is low or in presence of reactive oxygen species. Living organisms have developed complex regulatory network to allow biogenesis of Fe-S clusters in function of environmental conditions. Thus, understanding this regulation is of primary importance as changes in Fe-S cluster biogenesis impact the physiology of the cell and is for instance involved in resistance of bacteria to certain antibiotics. To do this, we used a modeling approach to gain a global systemic understanding of the process. We thus developed a mathematical logical model which extensively describes the regulatory network that controls biogenesis of Fe-S clusters in the model bacterium Escherichia coli. Analysis of the model reveals how Fe-S biogenesis is organized in function of environmental conditions and reveals how oxidative stress and iron homeostasis combine and control Fe-S biogenesis.