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

Abstract

Abstract Iron-sulfur (Fe-S) clusters are important cofactors conserved in all domains of life, yet their synthesis and stability are compromised in stressful conditions such as iron deprivation or oxidative stress. Two conserved machineries, Isc and Suf, assemble and transfer Fe-S clusters to client proteins. The model bacterium Escherichia coli possesses both Isc and Suf, and in this bacterium utilization of these machineries is under the control of a complex regulatory network. To better understand the dynamics behind Fe-S cluster biogenesis in E. coli, we here built a logical model describing its regulatory network. This model comprises three biological processes: 1) Fe-S cluster biogenesis, containing Isc and Suf, the carriers NfuA and ErpA, and the transcription factor IscR, the main regulator of Fe-S clusters homeostasis; 2) iron homeostasis, containing the free intracellular iron regulated by the iron sensing regulator Fur and the non-coding regulatory RNA RyhB involved in iron sparing; 3) oxidative stress, representing intracellular H2O2 accumulation, which activates OxyR, the regulator of catalases and peroxidases that decompose H2O2 and limit the rate of the Fenton reaction. Analysis of this comprehensive model reveals a modular structure that displays five different types of system behaviors depending on environmental conditions, and provides a better understanding on how oxidative stress and iron homeostasis combine and control Fe-S cluster 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 early in life, when oxygen tension was low and iron plentiful, and have been used since as 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 networks 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 organisms and is for instance involved in resistance of bacteria to certain antibiotics. We here used a modeling approach to gain a global systemic understanding of the process. We 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 cluster biogenesis.