Escherichia coli Response to Uranyl Exposure at Low pH and Associated Protein Regulations

Khemiri, Arbia; Carrière, Marie; Brémond, Nicolas; Mlouka, Mohamed Amine Ben; Coquet, Laurent; Llorens, Isabelle; Chapon, Virginie; Jouenne, Thierry; Cosette, Pascal; Berthomieu, Catherine

doi:10.1371/journal.pone.0089863

Cited by 20 publications

(12 citation statements)

References 58 publications

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“…The US Environmental Protection Agency's maximum contaminant limit for U in drinking water is 30 lg L 21 ($0.13 lM), however, groundwater concentrations in the US frequently exceed this limit (Focazio et al, 2006;Hoover et al, 2016). Studies of the U response in anaerobic and aerobic bacteria have revealed a plethora of different stress responses that range from DNA damage, oxidative stress, protein misfolding, to cell envelope stress (Bencheikh-Latmani et al, 2005;Junier et al, 2011;Khemiri et al, 2014, Li et al, 2014. However, the lack of regulatory systems that exhibit a specific response towards U has hindered in-depth mechanistic studies.…”

Section: Introductionmentioning

confidence: 99%

Identification of a U/Zn/Cu responsive global regulatory two‐component system in Caulobacter crescentus

Park

Overton

Liou

et al. 2017

Molecular Microbiology

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Despite the well-known toxicity of uranium (U) to bacteria, little is known about how cells sense and respond to U. The recent finding of a U-specific stress response in Caulobacter crescentus has provided a foundation for studying the mechanisms of U- perception in bacteria. To gain insight into this process, we used a forward genetic screen to identify the regulatory components governing expression of the urcA promoter (P ) that is strongly induced by U. This approach unearthed a previously uncharacterized two-component system, named UzcRS, which is responsible for U-dependent activation of P . UzcRS is also highly responsive to zinc and copper, revealing a broader specificity than previously thought. Using ChIP-seq, we found that UzcR binds extensively throughout the genome in a metal-dependent manner and recognizes a noncanonical DNA-binding site. Coupling the genome-wide occupancy data with RNA-seq analysis revealed that UzcR is a global regulator of transcription, predominately activating genes encoding proteins that are localized to the cell envelope; these include metallopeptidases, multidrug-resistant efflux (MDR) pumps, TonB-dependent receptors and many proteins of unknown function. Collectively, our data suggest that UzcRS couples the perception of U, Zn and Cu with a novel extracytoplasmic stress response.

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Section: Introductionmentioning

confidence: 99%

Identification of a U/Zn/Cu responsive global regulatory two‐component system in Caulobacter crescentus

Park

Overton

Liou

et al. 2017

Molecular Microbiology

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“…However, mechanisms used by cells for combating internal U toxicity are poorly understood (14). Previous studies revealed upregulation of metal efflux pumps, NADH quinone oxidoreductases, or other reactive oxygen species (ROS) scavenging enzymes upon exposure to U in the sulfate-reducing bacterium Desulfotomaculum reducens (15), Escherichia coli grown at low pH (16), and the plant Arabidopsis thaliana (17). General and membrane stress responses were particularly pronounced when Shewanella oneidensis was exposed to U (18), and nucleic acid and protein damage have been shown to represent the primary modes of U toxicity in Desulfovibrio alaskensis G20 (19).…”

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confidence: 99%

Transposon Mutagenesis Paired with Deep Sequencing of Caulobacter crescentus under Uranium Stress Reveals Genes Essential for Detoxification and Stress Tolerance

et al. 2015

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The ubiquitous aquatic bacterium Caulobacter crescentus is highly resistant to uranium (U) and facilitates U biomineralization and thus holds promise as an agent of U bioremediation. To gain an understanding of how C. crescentus tolerates U, we employed transposon (Tn) mutagenesis paired with deep sequencing (Tn-seq) in a global screen for genomic elements required for U resistance. Of the 3,879 annotated genes in the C. crescentus genome, 37 were found to be specifically associated with fitness under U stress, 15 of which were subsequently tested through mutational analysis. Systematic deletion analysis revealed that mutants lacking outer membrane transporters (rsaF a and rsaF b ), a stress-responsive transcription factor (cztR), or a ppGpp synthetase/hydrolase (spoT) exhibited a significantly lower survival rate under U stress. RsaF a and RsaF b , which are homologues of TolC in Escherichia coli, have previously been shown to mediate S-layer export. Transcriptional analysis revealed upregulation of rsaF a and rsaF b by 4-and 10-fold, respectively, in the presence of U. We additionally show that rsaF a mutants accumulated higher levels of U than the wild type, with no significant increase in oxidative stress levels. Our results suggest a function for RsaF a and RsaF b in U efflux and/or maintenance of membrane integrity during U stress. In addition, we present data implicating CztR and SpoT in resistance to U stress. Together, our findings reveal novel gene targets that are key to understanding the molecular mechanisms of U resistance in C. crescentus. IMPORTANCECaulobacter crescentus is an aerobic bacterium that is highly resistant to uranium (U) and has great potential to be used in U bioremediation, but its mechanisms of U resistance are poorly understood. We conducted a Tn-seq screen to identify genes specifically required for U resistance in C. crescentus. The genes that we identified have previously remained elusive using other omics approaches and thus provide significant insight into the mechanisms of U resistance by C. crescentus. In particular, we show that outer membrane transporters RsaF a and RsaF b , previously known as part of the S-layer export machinery, may confer U resistance by U efflux and/or by maintaining membrane integrity during U stress. U ranium (U) contamination is widespread and poses significant concerns for environmental ecology and human health (1). Chemical and physical techniques for waste treatment or removal of U are challenging and expensive. A promising, microbially mediated method for U remediation, in situ U immobilization, is more cost-effective and environmentally friendly than conventional approaches (2). If we seek to task microbes with the cleanup of contaminated sites, an understanding of how microbes defend against U toxicity is crucial. Understanding these mechanisms is necessary for the optimization of strains intended for use as U biosensors (3) or for the purpose of bioremediation (2, 4, 5).A great deal is known about various strategies used by microbes...

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“…Previous studies suggest that an increase in pH within a range of 5 to 6 decreases U(VI) bioavailability by lowering the uranyl concentration in aquatic environments (45,46). Consistently, U(VI) complexation by organic or inorganic phosphate was shown to reduce U(VI) toxicity in C. crescentus (14), while lower-pH conditions that favor the presence of the uncomplexed uranyl ion appear to be more toxic to bacteria (47). Further analytical techniques will be required to substantiate a speciation dependency of U(VI) toxicity in our system.…”

Section: Discussionmentioning

confidence: 63%

Modulation of Medium pH by Caulobacter crescentus Facilitates Recovery from Uranium-Induced Growth Arrest

Park

Jiao

2014

Appl Environ Microbiol

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The oxidized form of uranium [U(VI)] predominates in oxic environments and poses a major threat to ecosystems. Due to its ability to mineralize U(VI), the oligotroph Caulobacter crescentus is an attractive candidate for U(VI) bioremediation. However, the physiological basis for U(VI) tolerance is unclear. Here we demonstrated that U(VI) caused a temporary growth arrest in C. crescentus and three other bacterial species, although the duration of growth arrest was significantly shorter for C. crescentus. During the majority of the growth arrest period, cell morphology was unaltered and DNA replication initiation was inhibited. However, during the transition from growth arrest to exponential phase, cells with shorter stalks were observed, suggesting a decoupling between stalk development and the cell cycle. Upon recovery from growth arrest, C. crescentus proliferated with a growth rate comparable to that of a control without U(VI), although a fraction of these cells appeared filamentous with multiple replication start sites. Normal cell morphology was restored by the end of exponential phase. Cells did not accumulate U(VI) resistance mutations during the prolonged growth arrest, but rather, a reduction in U(VI) toxicity occurred concomitantly with an increase in medium pH. Together, these data suggest that C. crescentus recovers from U(VI)-induced growth arrest by reducing U(VI) toxicity through pH modulation. Our finding represents a unique U(VI) detoxification strategy and provides insight into how microbes cope with U(VI) under nongrowing conditions, a metabolic state that is prevalent in natural environments.

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Escherichia coli Response to Uranyl Exposure at Low pH and Associated Protein Regulations

Cited by 20 publications

References 58 publications

Identification of a U/Zn/Cu responsive global regulatory two‐component system in Caulobacter crescentus

Identification of a U/Zn/Cu responsive global regulatory two‐component system in Caulobacter crescentus

Transposon Mutagenesis Paired with Deep Sequencing of Caulobacter crescentus under Uranium Stress Reveals Genes Essential for Detoxification and Stress Tolerance

Modulation of Medium pH by Caulobacter crescentus Facilitates Recovery from Uranium-Induced Growth Arrest

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