Biology subjects

Mandin, P.

Publications and source records attributed to Mandin, P..

3 recordsLinked to original sources

bioRxiv2023

Small RNA regulation of an essential process induces bacterial resistance to aminoglycosides during oxidative stress

Fe-S clusters are essential cofactors involved in many reactions across all domains of life. In Escherichia coli and other enterobacteria, Fe-S cluster synthesis involves two machineries: Isc and Suf. While Isc functions as a housekeeping system, Suf is activated under stress conditions such as iron starvation or oxidative stress. Interestingly, cells functioning under Suf show reduced entry of aminoglycosides, leading to resistance to these antibiotics. The transcriptional regulator IscR, itself an Fe-S cluster containing protein, controls the transition between Isc and Suf machineries. Noteworthy, IscR has a critical impact on the virulence of various bacterial pathogens by regulating both Fe-S biogenesis and other pathways directly linked to host adaptation. Here, we discovered that two small regulatory RNAs (sRNAs), FnrS and OxyS, control iscR expression by base-pairing to the 5 UTR of the iscR mRNA. Remarkably, these sRNAs act in opposite ways and in opposite conditions: FnrS, expressed in anaerobiosis, represses the expression of iscR while OxyS, expressed during oxidative stress, activates it. Using an E. coli strain experiencing protracted oxidative stress, we further demonstrate that iscR expression is rapidly and significantly enhanced in the presence of OxyS. Strikingly, we further show that OxyS induces resistance to aminoglycosides during oxidative stress through this unexpected regulation of Fe-S clusters biogenesis, revealing a new role for this sRNA. Significance StatementThis study sheds light on the regulatory mechanisms controlling the synthesis of essential Fe-S clusters in bacteria, revealing unexpected roles for two small RNAs (FnrS and OxyS) in modulating the expression of the transcriptional regulator IscR. The findings suggest that this regulatory network could lead bacterial resistance to aminoglycoside antibiotics during oxidative stress, a condition associated with chronic infections. Ultimately, this work highlights the importance of understanding the intricate regulatory networks controlling bacterial metabolism and adaptation to stress, which could have significant implications for public health.

microbiology↗

bioRxiv2022

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

Iron-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.

systems biology↗

bioRxiv2018

A small RNA controls bacterial resistance to gentamicin during iron starvation

Phenotypic resistance describes a bacterial population that becomes transiently resistant to an antibiotic without requiring a genetic change. We here investigated the role of the small regulatory RNA (sRNA) RyhB, a key contributor to iron homeostasis, in the phenotypic resistance of Escherichia coli to various classes of antibiotics. We found that RyhB induces resistance to gentamicin, an aminoglycoside that targets the ribosome, when iron is scarce. RyhB induced resistance is due to the inhibition of respiratory complexes Nuo and Sdh activities. These complexes, which contain numerous Fe-S clusters, are crucial for generating a proton motive force (pmf) that allows gentamicin uptake. RyhB directly represses the expression of nuo and sdh operons by binding to their mRNAs, thereby inhibiting their translation. Indirectly, RyhB also inhibits the maturation of Nuo and Sdh by repressing synthesis of the Isc Fe-S biogenesis machinery. Notably, our study identifies nuo as a new direct RyhB target and shows that respiratory complexes activity levels are predictive of the bacterial sensitivity to gentamicin. Altogether, these results unveil a new role for RyhB in the adaptation to antibiotic stress, an unprecedented consequences of its role in iron starvation stress response.\n\nAUTHORS SUMMARYUnderstanding the mechanisms at work behind bacterial antibiotic resistance has become a major health issue in the face of the antibiotics crisis. Here, we show that RyhB, a bacterial small regulatory RNA, induces resistance of Escherichia coli to the antibiotic gentamicin when iron is scarce, an environmental situation prevalent during host-pathogen interactions. This resistance is due to RyhB repression of the synthesis and post-translational maturation of the respiratory complexes Nuo and Sdh. These complexes are crucial in producing the proton motive force that allows uptake of the antibiotics in the cell. Altogether, these data point out to a major role for RyhB in escaping antibacterial action.

molecular biology↗