Nitrate repression of the Escherichia coli pfl operon is mediated by the dual sensors NarQ and NarX and the dual regulators NarL and NarP

How FocA facilitates fermentation and respiration of formate by Escherichia coli

Formic acid is an important source of reductant and energy for many microorganisms. Formate is also produced as a fermentation product, e.g., by enterobacteria like Escherichia coli. As such, formic acid shares many features in common with dihydrogen, explaining perhaps why their metabolism and physiology show considerable overlap. At physiological pH, formic acid is mainly present as the dissociated formate anion and therefore cannot diffuse freely across the cytoplasmic membrane. Specific and bidirectional translocation of formate across the cytoplasmic membrane is, however, achieved in E. coli by the homopentameric membrane protein, FocA. Formic acid translocation from the cytoplasm into the periplasm (efflux) serves to maintain a near-neutral cytosolic pH and to deliver formate to the periplasmically-oriented respiratory formate dehydrogenases, Fdh-N and Fdh-O. These enzymes oxidize formate, with the electrons being used to reduce nitrate, oxygen, or other acceptors. In the absence of exogenous electron acceptors, formate is re-imported into the cytoplasm by FocA, where it is sensed by the transcriptional regulator FhlA, resulting in induction of the formate regulon. The genes and operons of the formate regulon encode enzymes necessary to assemble the formate hydrogenlyase complex, which disproportionates formic acid into H2 and CO2. Combined, these mechanisms of dealing with formate help to maintain cellular pH homeostasis and are suggested to maintain the proton gradient during growth and in stationary phase cells. This review highlights our current understanding of how formate metabolism helps balance cellular pH, how it responds to the redox status, and how it helps conserve energy.

The formate-hydrogen axis and its impact on the physiology of enterobacterial fermentation

Formic acid (HCOOH) and dihydrogen (H2) are characteristic products of enterobacterial mixed-acid fermentation, with H2 generation increasing in conjunction with a decrease in extracellular pH. Formate and acetyl-CoA are generated by radical-based and coenzyme A-dependent cleavage of pyruvate catalysed by pyruvate formate-lyase (PflB). Formate is also the source of H2, which is generated along with carbon dioxide through the action of the membrane-associated, cytoplasmically-oriented formate hydrogenlyase (FHL-1) complex. Synthesis of the FHL-1 complex is completely dependent on the cytoplasmic accumulation of formate. Consequently, formate determines its own disproportionation into H2 and CO2 by the FHL-1 complex. Cytoplasmic formate levels are controlled by FocA, a pentameric channel that translocates formic acid/formate bidirectionally between the cytoplasm and periplasm. Each protomer of FocA has a narrow hydrophobic pore through which neutral formic acid can pass. Two conserved amino acid residues, a histidine and a threonine, at the center of the pore control directionality of translocation. The histidine residue is essential for pH-dependent influx of formic acid. Studies with the formate analogue hypophosphite and amino acid variants of FocA suggest that the mechanisms of formic acid efflux and influx differ. Indeed, current data suggest, depending on extracellular formate levels, two separate uptake mechanisms exist, both likely contributing to maintain pH homeostasis. Bidirectional formate/formic acid translocation is dependent on PflB and influx requires an active FHL-1 complex. This review describes the coupling of formate and H2 production in enterobacteria.

Bacterial approaches to sensing and responding to respiration and respiration metabolites

Bacterial respiration of diverse substrates is a primary contributor to the diversity of life. Respiration also drives alterations in the geosphere and tethers ecological nodes together. It provides organisms with a means to dissipate reductants and generate potential energy in the form of an electrochemical gradient. Mechanisms have evolved to sense flux through respiratory pathways and sense the altered concentrations of respiration substrates or byproducts. These genetic regulatory systems promote efficient utilization of respiration substrates, as well as fine tune metabolism to promote cellular fitness and negate the accumulation of toxic byproducts. Many bacteria can respire one or more chemicals, and these regulatory systems promote the prioritization of high energy metabolites. Herein we focus on regulatory paradigms and discuss systems that sense the concentrations of respiration substrates and flux through respiratory pathways. This is a broad field of study, and therefore we focus on key fundamental and recent developments and highlight specific systems that capture the diversity of sensing mechanisms.

Effect of Varying Nitrate Concentrations on Denitrifying Phosphorus Uptake by DPAOs With a Molecular Insight Into Pho Regulon Gene Expression

Bacterial Pho regulon is a key regulator component in biological phosphorus-uptake. Poly-phosphate accumulating bacteria used in enhanced biological phosphorus removal (EBPR) system encounter negative regulation of the Pho regulon, resulting in reduced phosphorus-uptake from phosphorus-replete waste effluents. This study demonstrates possible trends of overcoming the PhoU negative regulation, resulting in excessive PO4 3--P uptake at varying concentrations of NO3 --N through denitrifying phosphorus removal process. We investigated the Pho regulon gene expression pattern and kinetic studies of P-removal by denitrifying phosphate accumulating organisms (DPAOs) which are able to remove both PO4 3--P and NO3 --N in single anoxic stage with the utilization of external carbon sources, without the use of stored polyhydroxyalkanoate (PHA) and without any anaerobic-aerobic or anaerobic-anoxic switches. Our study establishes that a minimum addition of 100 ppm NO3 --N leads to the withdrawal of the negative regulation of Pho regulon and results in ∼100% P-removal with concomitant escalated poly-phosphate accumulation by our established DPAO isolates and their artificially made consortium, isolated from sludge sample of PO4 3- -rich parboiled rice mill effluent, in a settling tank within 12 h of treatment. The same results were obtained when a phosphate rich effluent (stillage from distillery) mixed with a nitrate rich effluent (from explosive industry) was treated together in a single phase anoxic batch reactor, eliminating the need for alternating anaerobic/aerobic or anaerobic/anoxic switches for removing both the pollutants simultaneously. The highest poly-phosphate accumulation was observed to be more than 17% of cell dry weight. Our studies unequivocally establish that nitrate induction of Pho regulon is parallely associated with the repression of PhoU gene transcription, which is the negative regulator of Pho regulon. Based on earlier observations where similar nitrate mediated transcriptional repression was cited, we hypothesize the possible involvement of NarL/NarP transcriptional regulator proteins in PhoU repression. At present, we propose this denitrifying phosphorus removal endeavor as an innovative methodology to overcome the negative regulation of Pho regulon for accelerated unhindered phosphorus remediation from phosphate rich wastewater in India and the developing world where the stringency of EBPR and other reactors prevent their use due to financial reasons.

Bacterial transmembrane signalling systems and their engineering for biosensing

Every living cell possesses numerous transmembrane signalling systems that receive chemical and physical stimuli from the environment and transduce this information into an intracellular signal that triggers some form of cellular response. As unicellular organisms, bacteria require these systems for survival in rapidly changing environments. The receptors themselves act as ‘sensory organs’, while subsequent signalling circuits can be regarded as forming a ‘neural network’ that is involved in decision making, adaptation and ultimately in ensuring survival. Bacteria serve as useful biosensors in industry and clinical diagnostics, in addition to producing drugs for therapeutic purposes. Therefore, there is a great demand for engineered bacterial strains that contain transmembrane signalling systems with high molecular specificity, sensitivity and dose dependency. In this review, we address the complexity of transmembrane signalling systems and discuss principles to rewire receptors and their signalling outputs.

Differential effects of isc operon mutations on the biosynthesis and activity of key anaerobic metalloenzymes in Escherichia coli

Escherichia coli has two machineries for the synthesis of FeS clusters, namely Isc (iron-sulfur cluster) and Suf (sulfur formation). The Isc machinery, encoded by the iscRSUA-hscBA-fdx-iscXoperon, plays a crucial role in the biogenesis of FeS clusters for the oxidoreductases of aerobic metabolism. Less is known, however, about the role of ISC in the maturation of key multi-subunit metalloenzymes of anaerobic metabolism. Here, we determined the contribution of each iscoperon gene product towards the functionality of the major anaerobic oxidoreductases in E. coli, including three [NiFe]-hydrogenases (Hyd), two respiratory formate dehydrogenases (FDH) and nitrate reductase (NAR). Mutants lacking the cysteine desulfurase, IscS, lacked activity of all six enzymes, as well as the activity of fumaratereductase, and this was due to deficiencies in enzyme biosynthesis, maturation or FeS cluster insertion into electron-transfer components. Notably, based on anaerobic growth characteristics and metabolite patterns, the activity of the radical-S-adenosylmethionine enzyme pyruvate formate-lyase activase was independent of IscS, suggesting that FeS biogenesis for this ancient enzyme has different requirements. Mutants lacking either the scaffold protein IscU, the ferredoxin Fdx or the chaperones HscA or HscB had similar enzyme phenotypes: five of the oxidoreductases were essentially inactive, with the exception being the Hyd-3 enzyme, which formed part of the H2-producing formate hydrogenlyase (FHL) complex. Neither the frataxin-homologue CyaY nor the IscX protein was essential for synthesis of the three Hyd enzymes. Thus, while IscS is essential for H2 production in E. coli, the other ISC components are non-essential.

Engineering Hybrid Chemotaxis Receptors in Bacteria

Most bacteria use transmembrane sensors to detect a wide range of environmental stimuli. A large class of such sensors are the chemotaxis receptors used by motile bacteria to follow environmental chemical gradients. In Escherichia coli, chemotaxis receptors are known to mediate highly sensitive responses to ligands, making them potentially useful for biosensory applications. However, with only four ligand-binding chemotaxis receptors, the natural ligand spectrum of E. coli is limited. The design of novel chemoreceptors to extend the sensing capabilities of E. coli is therefore a critical aspect of chemotaxis-based biosensor development. One path for novel sensor design is to harvest the large natural diversity of chemosensory functions found in bacteria by creating hybrids that have the signaling domain from E. coli chemotaxis receptors and sensory domains from other species. In this work, we demonstrate that the E. coli receptor Tar can be successfully combined with most typical sensory domains found in chemotaxis receptors and in evolutionary-related two-component histidine kinases. We show that such functional hybrids can be generated using several different fusion points. Our work further illustrates how hybrid receptors could be used to quantitatively characterize ligand specificity of chemotaxis receptors and histidine kinases using standardized assays in E. coli.

Fermentative Pyruvate and Acetyl-Coenzyme A Metabolism

Pyruvate and acetyl-CoA form the backbone of central metabolism. The nonoxidative cleavage of pyruvate to acetyl-CoA and formate by the glycyl radical enzyme pyruvate formate lyase is one of the signature reactions of mixed-acid fermentation in enterobacteria. Under these conditions, formic acid accounts for up to one-third of the carbon derived from glucose. The further metabolism of acetyl-CoA to acetate via acetyl-phosphate catalyzed by phosphotransacetylase and acetate kinase is an exemplar of substrate-level phosphorylation. Acetyl-CoA can also be used as an acceptor of the reducing equivalents generated during glycolysis, whereby ethanol is formed by the polymeric acetaldehyde/alcohol dehydrogenase (AdhE) enzyme. The metabolism of acetyl-CoA via either the acetate or the ethanol branches is governed by the cellular demand for ATP and the necessity to reoxidize NADH. Consequently, in the absence of an electron acceptor mutants lacking either branch of acetyl-CoA metabolism fail to cleave pyruvate, despite the presence of PFL, and instead reduce it to D-lactate by the D-lactate dehydrogenase. The conversion of PFL to the active, radical-bearing species is controlled by a radical-SAM enzyme, PFL-activase. All of these reactions are regulated in response to the prevalent cellular NADH:NAD+ ratio. In contrast to Escherichia coli and Salmonella species, some genera of enterobacteria, e.g., Klebsiella and Enterobacter, produce the more neutral product 2,3-butanediol and considerable amounts of CO2 as fermentation products. In these bacteria, two molecules of pyruvate are converted to α-acetolactate (AL) by α-acetolactate synthase (ALS). AL is then decarboxylated and subsequently reduced to the product 2,3-butandiol.

Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals

Bioprocesses conducted under conditions with restricted O₂ supply are increasingly exploited for the synthesis of reduced biochemicals using different biocatalysts. The model facultative aerobe Escherichia coli, the microbial cell factory par excellence, has elaborate sensing and signal transduction mechanisms that respond to the availability of electron acceptors and alternative carbon sources in the surrounding environment. In particular, the ArcBA and CreBC two-component signal transduction systems are largely responsible for the metabolic regulation of redox control in response to O₂ availability and carbon source utilization, respectively. Significant advances in the understanding of the biochemical, genetic, and physiological duties of these regulatory systems have been achieved in recent years. This situation allowed to rationally-design novel engineering approaches that ensure optimal carbon and energy flows within central metabolism, as well as to manipulate redox homeostasis, in order to optimize the production of industrially-relevant metabolites. In particular, metabolic flux analysis provided new clues to understand the metabolic regulation mediated by the ArcBA and CreBC systems. Genetic manipulation of these regulators proved useful for designing microbial cells factories tailored for the synthesis of reduced biochemicals with added value, such as poly(3-hydroxybutyrate), under conditions with restricted O₂ supply. This network-wide strategy is in contrast with traditional metabolic engineering approaches, that entail direct modification of the pathway(s) at stake, and opens new avenues for the targeted modulation of central catabolic pathways at the transcriptional level.

Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data

It is of practical interest to investigate the effect of nitrates on bacterial metabolic regulation of both fermentation and energy generation, as compared to aerobic and anaerobic growth without nitrates. Although gene level regulation has previously been studied for nitrate assimilation, it is important to understand this metabolic regulation in terms of global regulators. In the present study, therefore, we measured gene expression using DNA microarrays, intracellular metabolite concentrations using CE-TOFMS, and metabolic fluxes using the (13)C-labeling technique for wild-type E. coli and the ΔarcA (a global regulatory gene for anoxic response control, ArcA) mutant to compare the metabolic state under nitrate conditions to that under aerobic and anaerobic conditions without nitrates in continuous culture conditions at a dilution rate of 0.2 h(-1). In wild-type, although the measured metabolite concentrations changed very little among the three culture conditions, the TCA cycle and the pentose phosphate pathway fluxes were significantly different under each condition. These results suggested that the ATP production rate was 29% higher under nitrate conditions than that under anaerobic conditions, whereas the ATP production rate was 10% lower than that under aerobic conditions. The flux changes in the TCA cycle were caused by changes in control at the gene expression level. In ΔarcA mutant, the TCA cycle flux was significantly increased (4.4 times higher than that of the wild type) under nitrate conditions. Similarly, the intracellular ATP/ADP ratio increased approximately two-fold compared to that of the wild-type strain.

Gene expression profiling of Corynebacterium glutamicum during Anaerobic nitrate respiration: induction of the SOS response for cell survival

The gene expression profile of Corynebacterium glutamicum under anaerobic nitrate respiration revealed marked differences in the expression levels of a number of genes involved in a variety of cellular functions, including carbon metabolism and respiratory electron transport chain, compared to the profile under aerobic conditions using DNA microarrays. Many SOS genes were upregulated by the shift from aerobic to anaerobic nitrate respiration. An elongated cell morphology, similar to that induced by the DivS-mediated suppression of cell division upon cell exposure to the DNA-damaging reagent mitomycin C, was observed in cells subjected to anaerobic nitrate respiration. None of these transcriptional and morphological differences were observed in a recA mutant strain lacking a functional RecA regulator of the SOS response. The recA mutant cells additionally showed significantly reduced viability compared to wild-type cells similarly grown under anaerobic nitrate respiration. These results suggest a role for the RecA-mediated SOS response in the ability of cells to survive any DNA damage that may result from anaerobic nitrate respiration in C. glutamicum.

MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations

Valuable binding-site annotation data are stored in databases. However, several types of errors can, and do, occur in the process of manually incorporating annotation data from the scientific literature into these databases. Here, we introduce MotifAdjuster http://dig.ipk-gatersleben.de/MotifAdjuster.html, a tool that helps to detect these errors, and we demonstrate its efficacy on public data sets.

Structural analysis of ligand stimulation of the histidine kinase NarX

Histidine kinase receptors are a large family of membrane-spanning proteins found in many prokaryotes and some eukaryotes. They are a part of two-component signal transduction systems, which each comprise a sensor kinase and a response regulator and are involved with the regulation of many cellular processes. NarX is a histidine kinase receptor that responds to nitrate and nitrite to effect regulation of anaerobic respiration in various bacteria. We present high-resolution X-ray crystal structures of the periplasmic sensor domain from Escherichia coli NarX in a complex with nitrate and in the apo state. Our analysis reveals that nitrate-binding induces conformation changes that result in a piston-type displacement between the N- and C-terminal helices of the periplasmic domain. Such conformational changes might represent a conserved mechanism of signaling in histidine kinases by which ligand binding is communicated across the lipid bilayer.

Anaerobic gene expression in Staphylococcus aureus

An investigation of gene expression in Staphylococcus aureus after a switch from aerobic to anaerobic growth was initiated by using the proteomic and transcriptomic approaches. In the absence of external electron acceptors like oxygen or nitrate, an induction of glycolytic enzymes was observed. At the same time the amount of tricarboxylic acid cycle enzymes was very low. NAD is regenerated by mixed acid and butanediol fermentation, as indicated by an elevated synthesis level of fermentation enzymes like lactate dehydrogenases (Ldh1 and Ldh2), alcohol dehydrogenases (AdhE and Adh), alpha-acetolactate decarboxylase (BudA1), acetolactate synthase (BudB), and acetoin reductase (SACOL0111) as well as an accumulation of fermentation products as lactate and acetate. Moreover, the transcription of genes possibly involved in secretion of lactate (SACOL2363) and formate (SACOL0301) was found to be induced. The formation of acetyl-coenzyme A or acetyl-phosphate might be catalyzed by pyruvate formate lyase, whose synthesis was found to be strongly induced as well. Although nitrate was not present, the expression of genes related to nitrate respiration (NarH, NarI, and NarJ) and nitrate reduction (NirD) was found to be upregulated. Of particular interest, oxygen concentration might affect the virulence properties of S. aureus by regulating the expression of some virulence-associated genes such as pls, hly, splC and splD, epiG, and isaB. To date, the mechanism of anaerobic gene expression in S. aureus has not been fully characterized. In addition to srrA the mRNA levels of several other regulatory genes with yet unknown functions (e.g., SACOL0201, SACOL2360, and SACOL2658) were found to be upregulated during anaerobic growth, indicating a role in the regulation of anaerobic gene expression.

Hierarchical control of anaerobic gene expression in Escherichia coli K-12: the nitrate-responsive NarX-NarL regulatory system represses synthesis of the fumarate-responsive DcuS-DcuR regulatory system

Hierarchical control ensures that facultative bacteria preferentially use the available respiratory electron acceptor with the most positive standard redox potential. Thus, nitrate is used before other electron acceptors such as fumarate for anaerobic respiration. Nitrate regulation is mediated by the NarX-NarL two-component system, which activates the transcription of operons encoding nitrate respiration enzymes and represses the transcription of operons for other anaerobic respiratory enzymes, including enzymes involved in fumarate respiration. These are fumarate reductase (encoded by the frdABCD operon), fumarase B, which generates fumarate from malate, and the DcuB permease for fumarate, malate, and aspartate. The transcription of the corresponding structural genes is activated by the DcuS-DcuR two-component system in response to fumarate or its dicarboxylate precursors. We report results from preliminary transcription microarray experiments that revealed two previously unknown members of the NarL regulon: the aspA gene encoding aspartate-ammonia lyase, which generates fumarate; and the dcuSR operon encoding the dicarboxylate-responsive regulatory system. We measured beta-galactosidase expression from monocopy aspA-lacZ, frdA-lacZ, and dcuS-lacZ operon fusions in response to added nitrate and fumarate and with respect to the dcuR and narL genotypes. Nitrate, acting through the NarX-NarL regulatory system, repressed the transcription of all three operons. Only frdA-lacZ expression, however, was responsive to added fumarate or a dcuR(+) genotype. Phospho-NarL protein protected operator sites in the aspA and dcuS promoter regions from DNase I cleavage in vitro. The overall results are consistent with the hypothesis that nitrate represses frdA operon transcription not only directly, by repressing frdA promoter activity, but also indirectly, by repressing dcuS promoter activity.

Expression of fnr is constrained by an upstream IS5 insertion in certain Escherichia coli K-12 strains

FNR is a global transcriptional regulator that controls anaerobic gene expression in Escherichia coli. Through the use of a number of approaches it was shown that fnr gene expression is reduced approximately three- to fourfold in E. coli strain MC4100 compared with the results seen with strain MG1655. This reduction in fnr expression is due to the insertion of IS5 (is5F) in the regulatory region of the gene at position -41 relative to the transcription initiation site. Transcription of the fnr gene nevertheless occurs from its own promoter in strain MC4100, but transcript levels are reduced approximately fourfold compared with those seen with strain MG1655. Remarkably, in strains bearing is5F the presence of Hfq prevents IS5-dependent transcriptional silencing of fnr expression. Thus, an hfq mutant of MC4100 is devoid of FNR protein and has the phenotype of an fnr mutant. In strain MG1655, or a derivative of MC4100 lacking is5F, mutation of hfq had no effect on fnr transcript levels. This finding indicates that IS5 mediates the effect of Hfq on fnr expression in MC4100. Western blot analysis revealed that cellular levels of FNR were reduced threefold in strain MC4100 compared with strain MG1655 results. A selection of FNR-dependent genes fused to lacZ were analyzed for the effects of reduced FNR levels on anaerobic gene expression. Expression of some operons, e.g., focA-pfl and fdnGHJI, was unaffected by reduction in the level of FNR, while the expression of other genes such as ndh and nikA was clearly affected.

Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli

Synthesis of the [NiFe] hydrogenases 1 and 2 of Escherichia coli is induced in response to anaerobiosis and is repressed when nitrate is present in the growth medium. The hydrogenase 1 and hydrogenase 2 enzymes are encoded by the polycistronic hyaABCDEF and hybOABCDEFG operons, respectively. Primer extension analysis was used to determine the initiation site of transcription of both operons. This permitted the construction of single-copy lacZ operon fusions, which were used to examine the transcriptional regulation of the two operons. Expression of both was induced by anaerobiosis and repressed by nitrate, which is in complete accord with earlier biochemical studies. Anaerobic induction of the hyb operon was only partially dependent on the FNR protein and, surprisingly, was enhanced by an arcA mutation. This latter result indicated that ArcA suppresses anaerobic hyb expression and that a further factor, which remains to be identified, is involved in controlling anaerobic induction of operon expression. Nitrate repression of hyb expression was mediated by the NarL/NarX and NarP/NarQ two-component regulatory systems. Remarkably, a narP mutant lacked anaerobic induction of hyb expression, even in the absence of added nitrate. Anaerobic induction of hya expression was dependent on the ArcA and AppY regulators, which confirms earlier observations by other authors. Nitrate repression of the hya operon was mediated by both NarL and NarP. Taken together, these data indicate that although the hya and hyb operons share common regulators, there are important differences in the control of expression of the individual operons.

Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors

The electron-transport chains of Escherichia coli are composed of many different dehydrogenases and terminal reductases (or oxidases) which are linked by quinones (ubiquinone, menaquinone and demethylmenaquinone). Quinol:cytochrome c oxido-reductase ('bc1 complex') is not present. For various electron acceptors (O2, nitrate) and donors (formate, H2, NADH, glycerol-3-P) isoenzymes are present. The enzymes show great variability in membrane topology and energy conservation. Energy is conserved by conformational proton pumps, or by arrangement of substrate sites on opposite sides of the membrane resulting in charge separation. Depending on the enzymes and isoenzymes used, the H+/e- ratios are between 0 and 4 H+/e- for the overall chain. The expression of the terminal reductases is regulated by electron acceptors. O2 is the preferred electron acceptor and represses the terminal reductases of anaerobic respiration. In anaerobic respiration, nitrate represses other terminal reductases, such as fumarate or DMSO reductases. Energy conservation is maximal with O2 and lowest with fumarate. By this regulation pathways with high ATP or growth yields are favoured. The expression of the dehydrogenases is regulated by the electron acceptors, too. In aerobic growth, non-coupling dehydrogenases are expressed and used preferentially, whereas in fumarate or DMSO respiration coupling dehydrogenases are essential. Coupling and non-coupling isoenzymes are expressed correspondingly. Thus the rationale for expression of the dehydrogenases is not maximal energy yield, but could be maximal flux or growth rates. Nitrate regulation is effected by two-component signal transfer systems with membraneous nitrate/nitrite sensors (NarX, NarQ) and cytoplasmic response regulators (NarL, NarP) which communicate by protein phosphorylation. O2 regulates by a two-component regulatory system consisting of a membraneous sensor (ArcB) and a response regulator (ArcA). ArcA is the major regulator of aerobic metabolism and represses the genes of aerobic metabolism under anaerobic conditions. FNR is a cytoplasmic O2 responsive regulator with a sensory and a regulatory DNA-binding domain. FNR is the regulator of genes required for anaerobic respiration and related pathways. The binding sites of NarL, NarP, ArcA and FNR are characterized for various promoters. Most of the genes are regulated by more than one of the regulators, which can act in any combination and in a positive or negative mode. By this the hierarchical expression of the genes in response to the electron acceptors is achieved. FNR is located in the cytoplasm and contains a 4Fe4S cluster in the sensory domain. The regulatory concentrations of O2 are 1-5 mbar. Under these conditions O2 diffuses to the cytoplasm and is able to react directly with FNR without involvement of other specific enzymes or protein mediators. By oxidation of the FeS cluster, FNR is converted to the inactive state in a reversible process. Reductive activation could be achieved by cellular reductants in the absence of O2. In addition, O2 may cause destruction and loss of the FeS cluster. It is not known whether this process is required for regulation of FNR function.

Structure of the Escherichia coli response regulator NarL

The crystal structure analysis of the NarL protein provides a first look at interactions between receiver and effector domains of a full-length bacterial response regulator. The N-terminal receiver domain, with 131 amino acids, is folded into a 5-strand beta sheet flanked by 5 alpha helices, as seen in CheY and in the N-terminal domain of NTRC. The C-terminal DNA-binding domain, with 62 amino acids, is a compact bundle of 4 alpha helices, of which the middle 2 form a helix-turn-helix motif closely related to that of Drosophila paired protein and other H-T-H DNA-binding proteins. The 2 domains are connected by an alpha helix of 10 amino acids and a 13-residue flexible tether that is not visible and presumably disordered in the X-ray structure. In this unphosphorylated form of NarL, the C-terminal domain is turned against the receiver domain in a manner that would preclude DNA binding. Activation of NarL via phosphorylation of Asp59 must involve transfer of information to the interdomain interface and either rotation or displacement of the DNA-binding C-terminal domain. Docking of a B-DNA duplex against the isolated C-terminal domain in the manner observed in paired protein and other H-T-H proteins suggests a stereochemical basis for DNA sequence preference: T-R-C-C-Y (high affinity) or T-R-C-T-N (low affinity), which is close to the experimentally observed consensus sequence: T-A-C-Y-N. The NarL structure is a model for other members of the FixJ or LuxR family of bacterial transcriptional activators, and possibly to the more distant OmpR and NtrC families as well.