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Key Points Bacterial proteins can be damaged by oxidants that are present in the environment. Cys and Met residues are easily oxidized. Bacterial cells have a range of proteins that repair oxidized proteins. Thioredoxins (Trxs) and glutaredoxins (Grxs) repair oxidized cysteine residues. Methionine sulfoxide reductases (Msrs) repair oxidized methionine residues. Antioxidant defences are present in the bacterial cytoplasm and in extracytoplasmic compartments. Oxidative damage can have a devastating effect on the structure and activity of proteins, leading to cell death. This Review discusses how bacteria repair oxidized proteins and highlights the importance of these repair systems in physiology and virulence. Oxidative damage can have a devastating effect on the structure and activity of proteins, and may even lead to cell death. The sulfur-containing amino acids cysteine and methionine are particularly susceptible to reactive oxygen species (ROS) and reactive chlorine species (RCS), which can damage proteins. In this Review, we discuss our current understanding of the reducing systems that enable bacteria to repair oxidatively damaged cysteine and methionine residues in the cytoplasm and in the bacterial cell envelope. We highlight the importance of these repair systems in bacterial physiology and virulence, and we discuss several examples of proteins that become activated by oxidation and help bacteria to respond to oxidative stress.

Establishing the origin of mitochondria and plastids is key to understand 2 founding events in the origin and early evolution of eukaryotes. Recent advances in the exploration of microbial diversity and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids during the diversification of Alphaproteobacteria and Cyanobacteria , respectively. Here, we strongly support these placements by analyzing the machineries for assembly of iron–sulfur ([Fe–S]) clusters, an essential function in eukaryotic cells that is carried out in mitochondria by the ISC machinery and in plastids by the SUF machinery. We assessed the taxonomic distribution of ISC and SUF in representatives of major eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins show an early branching of mitochondria within Alphaproteobacteria , right after the emergence of Magnetococcales . Similar analyses with the SUF machinery place primary plastids as sister to Gloeomargarita within Cyanobacteria . Our results add to the growing evidence of an early emergence of primary organelles and show that the analysis of essential machineries of endosymbiotic origin provide a robust signal to resolve ancient and fundamental steps in eukaryotic evolution.

Many bacteria possess all the machineries required to grow on fatty acids (FA) as a unique source of carbon and energy. FA degradation proceeds through the β-oxidation cycle that produces acetyl-CoA and reduced NADH and FADH cofactors. In addition to all the enzymes required for β-oxidation, FA degradation also depends on sophisticated systems for its genetic regulation and for FA transport. The fact that these machineries are conserved in bacteria suggests a crucial role in environmental conditions, especially for enterobacteria. Bacteria also possess specific enzymes required for the degradation of FAs from their environment, again showing the importance of this metabolism for bacterial adaptation. In this review, we mainly describe FA degradation in the Escherichia coli model, and along the way, we highlight and discuss important aspects of this metabolism that are still unclear. We do not detail exhaustively the diversity of the machineries found in other bacteria, but we mention them if they bring additional information or enlightenment on specific aspects.

Building iron-sulfur (Fe-S) clusters and assembling Fe-S proteins are essential actions for life on Earth. The three processes that sustain life, photosynthesis, nitrogen fixation, and respiration, require Fe-S proteins. Building iron-sulfur (Fe-S) clusters and assembling Fe-S proteins are essential actions for life on Earth. The three processes that sustain life, photosynthesis, nitrogen fixation, and respiration, require Fe-S proteins. Genes coding for Fe-S proteins can be found in nearly every sequenced genome. Fe-S proteins have a wide variety of functions, and therefore, defective assembly of Fe-S proteins results in cell death or global metabolic defects. Compared to alternative essential cellular processes, there is less known about Fe-S cluster synthesis and Fe-S protein maturation. Moreover, new factors involved in Fe-S protein assembly continue to be discovered. These facts highlight the growing need to develop a deeper biological understanding of Fe-S cluster synthesis, holo-protein maturation, and Fe-S cluster repair. Here, we outline bacterial strategies used to assemble Fe-S proteins and the genetic regulation of these processes. We focus on recent and relevant findings and discuss future directions, including the proposal of using Fe-S protein assembly as an antipathogen target.

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 phenotypic 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 regulates negatively the expression of nuo and sdh, presumably by binding to their mRNAs and, as a consequence, inhibiting their translation. We further show that Isc Fe-S biogenesis machinery is essential for the maturation of Nuo. As RyhB also limits levels of the Isc machinery, we propose that RyhB may also indirectly impact the maturation of Nuo and Sdh. Notably, our study 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 consequence of its role in iron starvation stress response.

Key Points Fe–S clusters are among the most conserved cofactors in prokaryotes and eukaryotes. Fe–S proteins participate in a wide array of cellular processes, from metabolism to gene regulation and DNA replication. Fe–S clusters are highly unstable and, upon destabilization, they can lead to oxidative stress via Fenton chemistry. Dedicated systems have therefore evolved for building, protecting and inserting these clusters into apoproteins. The components required for Fe–S cluster biogenesis have been identified in the model systems Escherichia coli , Saccharomyces cerevisiae and Arabidopsis thaliana and exhibit structural and functional homologies. They constitute the so-called Fe–S cluster (Isc) and sulphur mobilization (Suf) systems. In eukaryotes, the Isc system is located in the mitochondria and the Suf system in chloroplasts. E. coli also has both systems. Both in vitro and in vivo analyses have revealed that Fe–S biogenesis comprises two steps: a 'building' step, during which iron and sulphur are collected and assembled into a cluster, and a 'delivery' step, during which the cluster is transported to the apoprotein targets. The origin of the sulphur is L -cysteine, and the way in which cysteine desulphurase mobilizes sulphur for Fe–S cluster formation is well understood. The origin of the iron remains unclear, and several sources are likely to be used. A key step in Fe–S cluster biogenesis is catalysed by a scaffold protein, which can accept both iron and sulphur, allowing them to form a cluster that is eventually transferred either to downstream components in the Fe–S cluster biogenesis process or, under certain conditions, directly to apoproteins. In vivo approaches have revealed the existence of a complex trafficking step, in which ready-made clusters can use different routes to reach their final targets. So-called A-type transporters (ATC) are required for this step. Genetic studies in E. coli allowed the existence of seemingly redundant ATCs to be rationalized: environmental conditions, gene regulation and preferential partnerships seem to control the route that a cluster takes from its site of building to its final destination. Several Fe–S cluster biogenesis factors that do not belong to either the Isc system or the Suf system have been identified; their roles and how they cooperate with the Isc and Suf systems remain to be clarified. Fe–S proteins participate in a wide array of cellular processes, from metabolism to gene regulation and DNA replication. Here, Py and Barras discuss the basic requirements for a bacterial cell to build and insert Fe–S clusters into apoproteins and summarize our current knowledge and understanding of this process in vivo . The broad range of cellular activities carried out by Fe–S proteins means that they have a central role in the life of most organisms. At the interface between biology and chemistry, studies of bacterial Fe–S protein biogenesis have taken advantage of the specific approaches of each field and have begun to reveal the molecular mechanisms involved. The multiprotein systems that are required to build Fe–S proteins have been identified, but the in vivo roles of some of the components remain to be clarified. The way in which cellular Fe–S cluster trafficking pathways are organized remains a key issue for future studies.

The therapeutic arsenal against bacterial infections is rapidly shrinking, as drug resistance spreads and pharmaceutical industry are struggling to produce new antibiotics. In this review we cover the efficacy of silver as an antibacterial agent. In particular we recall experimental evidences pointing to the multiple targets of silver, including DNA, proteins and small molecules, and we review the arguments for and against the hypothesis that silver acts by enhancing oxidative stress. We also review the recent use of silver as an adjuvant for antibiotics. Specifically, we discuss the state of our current understanding on the potentiating action of silver ions on aminoglycoside antibiotics.

The spread of antimicrobial resistance has become a serious public health concern, making once-treatable diseases deadly again and undermining the achievements of modern medicine 1 , 2 . Drug combinations can help to fight multi-drug-resistant bacterial infections, yet they are largely unexplored and rarely used in clinics. Here we profile almost 3,000 dose-resolved combinations of antibiotics, human-targeted drugs and food additives in six strains from three Gram-negative pathogens— Escherichia coli , Salmonella enterica serovar Typhimurium and Pseudomonas aeruginosa —to identify general principles for antibacterial drug combinations and understand their potential. Despite the phylogenetic relatedness of the three species, more than 70% of the drug–drug interactions that we detected are species-specific and 20% display strain specificity, revealing a large potential for narrow-spectrum therapies. Overall, antagonisms are more common than synergies and occur almost exclusively between drugs that target different cellular processes, whereas synergies are more conserved and are enriched in drugs that target the same process. We provide mechanistic insights into this dichotomy and further dissect the interactions of the food additive vanillin. Finally, we demonstrate that several synergies are effective against multi-drug-resistant clinical isolates in vitro and during infections of the larvae of the greater wax moth Galleria mellonella , with one reverting resistance to the last-resort antibiotic colistin. Screening pairwise combinations of antibiotics and other drugs against three bacterial pathogens reveals that antagonistic and synergistic drug–drug interactions are specific to microbial species and strains.

Efflux pumps are membrane protein complexes conserved in all living organisms. Beyond being involved in antibiotic extrusion in several bacteria, efflux pumps are emerging as relevant players in pathogen-host interactions. We have investigated on the possible role of the efflux pump network in Shigella flexneri , the etiological agent of bacillary dysentery. We have found that S . flexneri has retained 14 of the 20 pumps characterized in Escherichia coli and that their expression is differentially modulated during the intracellular life of Shigella . In particular, the emrKY operon, encoding an efflux pump of the Major Facilitator Superfamily, is specifically and highly induced in Shigella -infected U937 macrophage-like cells and is activated in response to a combination of high K + and acidic pH, which are sensed by the EvgS/EvgA two-component system. Notably, we show that following S . flexneri infection, macrophage cytosol undergoes a mild reduction of intracellular pH, permitting EvgA to trigger the emrKY activation. Finally, we present data suggesting that EmrKY is required for the survival of Shigella in the harsh macrophage environment, highlighting for the first time the key role of an efflux pump during the Shigella invasive process.

The identification of an enzymatic system repairing proteins containing oxidized methionine in the bacterial cell envelope, a compartment particularly susceptible to oxidative damage by host defence mechanisms. A novel repair system for oxidative damage Frédéric Barras and colleagues report the identification of an enzyme system, MsrPQ, which repairs a wide range of periplasmic proteins with oxidatively damaged methionine (methionine sulfoxide, Met-O) in the bacterial cell envelope, a compartment that is particularly susceptible to oxidative damage by host defence mechanisms. MsrP and MsrQ are widely distributed in Gram-negative bacteria and are expressed following exposure to hypochlorous acid, a powerful antimicrobial agent that is released by neutrophils. Interestingly, the MsrPQ repair system is functionally distinct from conventional methionine sulfoxide reductases as it exhibits non-stereospecificity and can reduce both R - and S -diastereoisomers of Met-O. Furthermore, the authors report a novel mechanism of action for MsrPQ in which electrons from the respiratory chain are used for reducing power, establishing a new link between metabolism and cellular integrity. The reactive species of oxygen and chlorine damage cellular components, potentially leading to cell death. In proteins, the sulfur-containing amino acid methionine is converted to methionine sulfoxide, which can cause a loss of biological activity. To rescue proteins with methionine sulfoxide residues, living cells express methionine sulfoxide reductases (Msrs) in most subcellular compartments, including the cytosol, mitochondria and chloroplasts 1 , 2 , 3 . Here we report the identification of an enzymatic system, MsrPQ, repairing proteins containing methionine sulfoxide in the bacterial cell envelope, a compartment particularly exposed to the reactive species of oxygen and chlorine generated by the host defence mechanisms. MsrP, a molybdo-enzyme, and MsrQ, a haem-binding membrane protein, are widely conserved throughout Gram-negative bacteria, including major human pathogens. MsrPQ synthesis is induced by hypochlorous acid, a powerful antimicrobial released by neutrophils. Consistently, MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation, including the primary periplasmic chaperone SurA. For this activity, MsrPQ uses electrons from the respiratory chain, which represents a novel mechanism to import reducing equivalents into the bacterial cell envelope. A remarkable feature of MsrPQ is its capacity to reduce both rectus ( R -) and sinister ( S -) diastereoisomers of methionine sulfoxide, making this oxidoreductase complex functionally different from previously identified Msrs. The discovery that a large class of bacteria contain a single, non-stereospecific enzymatic complex fully protecting methionine residues from oxidation should prompt a search for similar systems in eukaryotic subcellular oxidizing compartments, including the endoplasmic reticulum.