Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: new insights into microbial physiology

RNA was isolated from cultures of Escherichia coli strain MG1655 and derivatives defective in fnr, narXL, or narXL with narP, during aerobic growth, or anaerobic growth in the presence or absence of nitrate or nitrite, in non-repressing media in which both strain MG1655 and an fnr deletion mutant grew at similar rates. Glycerol was used as the non-repressing carbon source and both trimethylamine-N-oxide and fumarate were added as terminal electron acceptors. Microarray data supplemented with bioinformatic data revealed that the FNR (fumarate and nitrate reductase regulator) regulon includes at least 104, and possibly as many as 115, operons, 68 of which are activated and 36 are repressed during anaerobic growth. A total of 51 operons were directly or indirectly activated by NarL in response to nitrate; a further 41 operons were repressed. Four subgroups of genes implicated in management of reactive nitrogen compounds, NO and products of NO metabolism, were identified; they included proteins of previously unknown function. Global repression by the nitrate- and nitrite-responsive two-component system, NarQ-NarP, was shown for the first time. In contrast with the frdABCD, aspA and ansB operons that are repressed only by NarL, the dcuB-fumB operon was among 37 operons that are repressed by NarP.

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Different responses to nitrate and nitrite by the model organism Escherichia coli and the human pathogen Neisseria gonorrhoeae

Biochemical Society Transactions ◽

10.1042/bst0340111 ◽

2006 ◽

Vol 34 (1) ◽

pp. 111-114 ◽

Cited By ~ 7

Author(s):

R.N. Whitehead ◽

J.A. Cole

Keyword(s):

Escherichia Coli ◽

Neisseria Gonorrhoeae ◽

Model Organism ◽

Anaerobic Growth ◽

Human Pathogen ◽

Regulate Gene Expression ◽

E Coli ◽

Regulatory Systems ◽

Two Component ◽

Nitrate And Nitrite

The ability of Escherichia coli to use both nitrate and nitrite as terminal electron acceptors during anaerobic growth is mediated by the dual-acting two-component regulatory systems NarX-NarL and NarQ-NarP. In contrast, Neisseria gonorrhoeae responds only to nitrite: it expresses only NarQ-NarP. We have shown that although N. gonorrhoeae NarQ can phosphorylate E. coli NarL and NarP, the N. gonorrhoeae NarP is unable to regulate gene expression in E. coli. Mutagenesis experiments have revealed residues in E. coli NarQ that are essential for nitrate and nitrite sensing. Chimaeric proteins revealed domains of NarQ that are important for ligand sensing.

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Reduction of Turgor Is Not the Stimulus for the Sensor Kinase KdpD of Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.01635-07 ◽

2008 ◽

Vol 190 (7) ◽

pp. 2360-2367 ◽

Cited By ~ 27

Author(s):

Knut Hamann ◽

Petra Zimmann ◽

Karlheinz Altendorf

Keyword(s):

Escherichia Coli ◽

Cytoplasmic Membrane ◽

Current View ◽

Sensor Kinase ◽

Two Component System ◽

Intracellular Atp ◽

Two Component ◽

Stimulus Perception ◽

First Time

ABSTRACT Stimulus perception by the KdpD/KdpE two-component system of Escherichia coli is still controversial with respect to the nature of the stimulus that is perceived by the sensor kinase KdpD. Limiting potassium concentrations in the medium or high osmolality leads to KdpD/KdpE signal transduction, resulting in kdpFABC expression. It has been hypothesized that changes in turgor are sensed by KdpD through alterations in the physical state of the cytoplasmic membrane. However, in this study the quantitative determination of expression levels of the kdpFABC operon revealed that the system responds very effectively to K+-limiting conditions in the medium but barely and to various degrees to salt and sugar stress. Since the current view of stimulus perception calls for mainly intracellular parameters, which might be sensed by KdpD, we set out to test the cytoplasmic concentrations of ATP, K+, Na+, glutamate, proline, glycine, trehalose, putrescine, and spermidine under K+-limiting conditions. As a first result, the determination of the cytoplasmic volume, which is a prerequisite for such measurements, revealed that a transient shrinkage of the cytoplasmic volume, which is indicative of a reduction in turgor, occurred only under osmotic upshift but not under K+-limiting conditions. Furthermore, the intracellular ATP concentration significantly increased under osmotic upshift, whereas only a slight increase occurred after a potassium downshift. Finally, the cytoplasmic K+ concentration rose severalfold only after an osmotic upshock. For the first time, these data indicate that stimulus perception by KdpD correlates neither with changes in the cytoplasmic volume nor with changes in the intracellular ATP or K+ concentration or those of the other solutes tested. In conclusion, we propose that a reduction in turgor cannot be the stimulus for KdpD.

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Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli

10.1101/2020.05.11.089920 ◽

2020 ◽

Author(s):

Henri Gerken ◽

Phu Vuong ◽

Ketaki Soparkar ◽

Rajeev Misra

Keyword(s):

Escherichia Coli ◽

Iron Homeostasis ◽

Anaerobic Growth ◽

Transport Systems ◽

Uptake System ◽

Two Component System ◽

Transport Pathway ◽

Component System ◽

Two Component ◽

Positive Effect

ABSTRACTEscherichia coli secretes high-affinity Fe3+ chelators to solubilize and transport chelated Fe3+ via specific outer membrane receptors. In microaerobic and anaerobic growth environments, where the reduced Fe2+ form is predominant, ferrous transport systems fulfill the bacterial need for iron. Expression of genes coding for iron metabolism is controlled by Fur, which when bound to Fe2+ acts as a repressor. Work carried out in this paper shows that the constitutively activated EnvZ/OmpR two-component system, which normally controls expression of the ompC and ompF porin genes, dramatically increases the intracellular pool of accessible iron, as determined by whole-cell electron paramagnetic resonance (EPR) spectroscopy, by inducing the OmpC/FeoB-mediated ferrous transport pathway. Elevated levels of intracellular iron in turn activated Fur, which inhibited the ferric but not the ferrous transport pathway. The data show that the positive effect of constitutively activated EnvZ/OmpR on feoB expression is sufficient to overcome the negative effect of activated Fur on feoB. In a tonB mutant, which lacks functional ferric transport systems, deletion of ompR severely impairs growth on rich medium not supplemented with iron, while the simultaneous deletion of ompC and ompF is not viable. These data, together with the observation of de-repression of the Fur regulon in an OmpC mutant, show that the porins play an important role in iron homeostasis. The work presented here also resolves a long-standing paradoxical observation of the effect of certain mutant envZ alleles on iron regulon.IMPORTANCEThe work presented here solved a long-standing paradox of the negative effects of certain missense alleles of envZ, which codes for kinase of the EnvZ/OmpR two component system, on the expression of ferric uptake genes. The data revealed that the constitutive envZ alleles activate the Feo- and OmpC-mediated ferrous uptake pathway to flood the cytoplasm with accessible ferrous iron. This activates the ferric uptake regulator, Fur, which inhibits ferric uptake system but cannot inhibit the feo operon due to the positive effect of activated EnvZ/OmpR. The data also revealed importance of porins in iron homeostasis.

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Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli

mBio ◽

10.1128/mbio.01192-20 ◽

2020 ◽

Vol 11 (3) ◽

Author(s):

Henri Gerken ◽

Phu Vuong ◽

Ketaki Soparkar ◽

Rajeev Misra

Keyword(s):

Escherichia Coli ◽

Iron Homeostasis ◽

Anaerobic Growth ◽

Transport Systems ◽

Uptake System ◽

Two Component System ◽

Transport Pathway ◽

Component System ◽

Two Component ◽

Positive Effect

ABSTRACT Escherichia coli secretes high-affinity Fe3+ chelators to solubilize and transport chelated Fe3+ via specific outer membrane receptors. In microaerobic and anaerobic growth environments, where the reduced Fe2+ form is predominant, ferrous transport systems fulfill the bacterial need for iron. Expression of genes coding for iron metabolism is controlled by Fur, which when bound to Fe2+ acts as a repressor. Work carried out here shows that the constitutively activated EnvZ/OmpR two-component system, which normally controls expression of the ompC and ompF porin genes, dramatically increases the intracellular pool of accessible iron, as determined by whole-cell electron paramagnetic resonance spectroscopy, by inducing the OmpC/FeoB-mediated ferrous transport pathway. Elevated levels of intracellular iron in turn activated Fur, which inhibited the ferric transport pathway but not the ferrous transport pathway. The data show that the positive effect of constitutively activated EnvZ/OmpR on feoB expression is sufficient to overcome the negative effect of activated Fur on feoB. In a tonB mutant, which lacks functional ferric transport systems, deletion of ompR severely impairs growth on rich medium not supplemented with iron, while the simultaneous deletion of ompC and ompF is not viable. These data, together with the observation of derepression of the Fur regulon in an OmpC mutant, show that the porins play an important role in iron homeostasis. The work presented here also resolves a long-standing paradoxical observation of the effect of certain mutant envZ alleles on iron regulon. IMPORTANCE The work presented here solved a long-standing paradox of the negative effects of certain missense alleles of envZ, which codes for kinase of the EnvZ/OmpR two-component system, on the expression of ferric uptake genes. The data revealed that the constitutive envZ alleles activate the Feo- and OmpC-mediated ferrous uptake pathway to flood the cytoplasm with accessible ferrous iron. This activates the ferric uptake regulator, Fur, which inhibits ferric uptake system but cannot inhibit the feo operon due to the positive effect of activated EnvZ/OmpR. The data also revealed the importance of porins in iron homeostasis.

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Degradation of cyclic diguanosine monophosphate by a hybrid two-component protein protects Azoarcus sp. strain CIB from toluene toxicity

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1615981113 ◽

2016 ◽

Vol 113 (46) ◽

pp. 13174-13179 ◽

Cited By ~ 6

Author(s):

Zaira Martín-Moldes ◽

Blas Blázquez ◽

Claudine Baraquet ◽

Caroline S. Harwood ◽

María T. Zamarro ◽

...

Keyword(s):

Aromatic Hydrocarbons ◽

Response Regulator ◽

Anaerobic Growth ◽

Two Component System ◽

Component System ◽

Bacterial Physiology ◽

Toxic Concentration ◽

Two Component ◽

Cyclic Diguanosine Monophosphate ◽

Diguanosine Monophosphate

Cyclic diguanosine monophosphate (c-di-GMP) is a second messenger that controls diverse functions in bacteria, including transitions from planktonic to biofilm lifestyles, virulence, motility, and cell cycle. Here we describe TolR, a hybrid two-component system (HTCS), from the β-proteobacterium Azoarcus sp. strain CIB that degrades c-di-GMP in response to aromatic hydrocarbons, including toluene. This response protects cells from toluene toxicity during anaerobic growth. Whereas wild-type cells tolerated a sudden exposure to a toxic concentration of toluene, a tolR mutant strain or a strain overexpressing a diguanylate cyclase gene lost viability upon toluene shock. TolR comprises an N-terminal aromatic hydrocarbon-sensing Per–Arnt–Sim (PAS) domain, followed by an autokinase domain, a response regulator domain, and a C-terminal c-di-GMP phosphodiesterase (PDE) domain. Autophosphorylation of TolR in response to toluene exposure initiated an intramolecular phosphotransfer to the response regulator domain that resulted in c-di-GMP degradation. The TolR protein was engineered as a functional sensor histidine kinase (TolRSK) and an independent response regulator (TolRRR). This classic two-component system (CTCS) operated less efficiently than TolR, suggesting that TolR was evolved as a HTCS to optimize signal transduction. Our results suggest that TolR enables Azoarcus sp. CIB to adapt to toxic aromatic hydrocarbons under anaerobic conditions by modulating cellular levels of c-di-GMP. This is an additional role for c-di-GMP in bacterial physiology.

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A Crp-Dependent Two-Component System Regulates Nitrate and Nitrite Respiration in Shewanella oneidensis

PLoS ONE ◽

10.1371/journal.pone.0051643 ◽

2012 ◽

Vol 7 (12) ◽

pp. e51643 ◽

Cited By ~ 45

Author(s):

Yangyang Dong ◽

Jixuan Wang ◽

Huihui Fu ◽

Guangqi Zhou ◽

Miaomiao Shi ◽

...

Keyword(s):

Shewanella Oneidensis ◽

Two Component System ◽

Component System ◽

Two Component ◽

Nitrite Respiration ◽

Nitrate And Nitrite

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HprSR is a Reactive Chlorine Species-Sensing, Two-Component System in Escherichia coli

Journal of Bacteriology ◽

10.1128/jb.00449-21 ◽

2021 ◽

Author(s):

Sara El Hajj ◽

Camille Henry ◽

Camille Andrieu ◽

Alexandra Vergnes ◽

Laurent Loiseau ◽

...

Keyword(s):

Escherichia Coli ◽

Hypochlorous Acid ◽

Methionine Sulfoxide ◽

Methionine Sulfoxide Reductase ◽

Repair System ◽

Bacterial Cells ◽

Two Component System ◽

Component System ◽

Two Component ◽

Redox Switch

Two-component systems (TCS) are signalling pathways that allow bacterial cells to sense, respond and adapt to fluctuating environments. Among the classical TCS of Escherichia coli , HprSR has recently been shown to be involved in the regulation of msrPQ , which encodes the periplasmic methionine sulfoxide reductase system. In this study, we demonstrate that hypochlorous acid (HOCl) induces the expression of msrPQ in an HprSR-dependant manner, whereas H 2 O 2 , NO and paraquat (a superoxide generator) do not. Therefore, HprS appears to be an HOCl-sensing histidine kinase. Using a directed mutagenesis approach, we show that Met residues located in the periplasmic loop of HprS are important for its activity: as HOCl preferentially oxidizes Met residues, we provide evidence that HprS could be activated via the reversible oxidation of its methionine residues, meaning that MsrPQ plays a role in switching HprSR off. We propose that the activation of HprS by HOCl could occur through a Met redox switch. HprSR appears to be the first characterized TCS able to detect reactive chlorine species (RCS) in E. coli . This study represents an important step towards understanding the mechanisms of RCS resistance in prokaryotes. IMPORTANCE Understanding how bacteria respond to oxidative stress at the molecular level is crucial in the fight against pathogens. HOCl is one of the most potent industrial and physiological microbiocidal oxidants. Therefore bacteria have developed counterstrategies to survive HOCl-induced stress. Over the last decade, important insights into these bacterial protection factors have been obtained. Our work establishes HprSR as a reactive chlorine species-sensing, two-component system in Escherichia coli MG1655, which regulates the expression of MsrPQ, a repair system for HOCl-oxidized proteins. Moreover we provide evidence suggesting that HOCl could activate HprS through a methionine redox switch.

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Involvement of AtoSC two-component system in Escherichia coli flagellar regulon

Amino Acids ◽

10.1007/s00726-011-1140-7 ◽

2011 ◽

Vol 43 (2) ◽

pp. 833-844 ◽

Cited By ~ 11

Author(s):

Marina C. Theodorou ◽

Evaggelos C. Theodorou ◽

Dimitrios A. Kyriakidis

Keyword(s):

Escherichia Coli ◽

Two Component System ◽

Component System ◽

Two Component ◽

Flagellar Regulon

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Polar Localization of a Tripartite Complex of the Two-Component System DcuS/DcuR and the Transporter DctA in Escherichia coli Depends on the Sensor Kinase DcuS

PLoS ONE ◽

10.1371/journal.pone.0115534 ◽

2014 ◽

Vol 9 (12) ◽

pp. e115534 ◽

Cited By ~ 7

Author(s):

Patrick D. Scheu ◽

Philipp A. Steinmetz ◽

Felix Dempwolff ◽

Peter L. Graumann ◽

Gottfried Unden

Keyword(s):

Escherichia Coli ◽

Sensor Kinase ◽

Two Component System ◽

Component System ◽

Polar Localization ◽

Two Component

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Regulation of tartrate metabolism by TtdR and relation to the DcuS–DcuR-regulated C4-dicarboxylate metabolism of Escherichia coli

Microbiology ◽

10.1099/mic.0.031401-0 ◽

2009 ◽

Vol 155 (11) ◽

pp. 3632-3640 ◽

Cited By ~ 12

Author(s):

Ok Bin Kim ◽

Julia Reimann ◽

Hanna Lukas ◽

Uwe Schumacher ◽

Jan Grimpo ◽

...

Keyword(s):

Escherichia Coli ◽

Promoter Region ◽

Anaerobic Conditions ◽

Two Component System ◽

Two Component ◽

Fumarate Respiration ◽

Mutual Regulation ◽

Genes Encoding ◽

Type Gene ◽

Tartrate Dehydratase

Escherichia coli catabolizes l-tartrate under anaerobic conditions to oxaloacetate by the use of l-tartrate/succinate antiporter TtdT and l-tartrate dehydratase TtdAB. Subsequently, l-malate is channelled into fumarate respiration and degraded to succinate by the use of fumarase FumB and fumarate reductase FrdABCD. The genes encoding the latter pathway (dcuB, fumB and frdABCD) are transcriptionally activated by the DcuS–DcuR two-component system. Expression of the l-tartrate-specific ttdABT operon encoding TtdAB and TtdT was stimulated by the LysR-type gene regulator TtdR in the presence of l- and meso-tartrate, and repressed by O2 and nitrate. Anaerobic expression required a functional fnr gene, and nitrate repression depended on NarL and NarP. Expression of ttdR, encoding TtdR, was repressed by O2, nitrate and glucose, and positively regulated by TtdR and DcuS. Purified TtdR specifically bound to the ttdR–ttdA promoter region. TtdR was also required for full expression of the DcuS–DcuR-dependent dcuB gene in the presence of tartrate. Overall, expression of the ttdABT genes is subject to l-/meso-tartrate-dependent induction, and to aerobic and nitrate repression. The control is exerted directly at ttdA and in addition indirectly by regulating TtdR levels. TtdR recognizes a subgroup (l- and meso-tartrate) of the stimuli perceived by the sensor DcuS, which responds to all C4-dicarboxylates; both systems apparently communicate by mutual regulation of the regulatory genes.

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