Nitrite activates the transcription of the Pseudomonas aeruginosa nitrite reductase and cytochrome c-551 operon under anaerobic conditions

Mechanisms of chlorate toxicity and resistance in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that often encounters hypoxic/anoxic environments within the host, which increases its tolerance to many conventional antibiotics. Toward identifying novel treatments, we explored the therapeutic potential of chlorate, a pro-drug that kills hypoxic/anoxic, antibiotic-tolerant P. aeruginosa populations. While chlorate itself is relatively nontoxic, it is enzymatically reduced to the toxic oxidizing agent, chlorite, by hypoxically induced nitrate reductase. To better assess chlorate's therapeutic potential, we investigated mechanisms of chlorate toxicity and resistance in P. aeruginosa. We used transposon mutagenesis to identify genes that alter P. aeruginosa fitness during chlorate treatment, finding that methionine sulfoxide reductases (Msr), which repair oxidized methionine residues, support survival during chlorate stress. Chlorate treatment leads to proteome-wide methionine oxidation, which is exacerbated in a ∆msrA∆msrB strain. In response to chlorate, P. aeruginosa upregulates proteins involved in a wide range of functions, including metabolism, DNA replication/repair, protein repair, transcription, and translation, and these newly synthesized proteins are particularly vulnerable to methionine oxidation. The addition of exogenous methionine partially rescues P. aeruginosa survival during chlorate treatment, suggesting that widespread methionine oxidation contributes to death. Finally, we found that mutations that decrease nitrate reductase activity are a common mechanism of chlorate resistance.

Metabolic Compensation of Fitness Costs Is a General Outcome for Antibiotic-Resistant Pseudomonas aeruginosa Mutants Overexpressing Efflux Pumps

It is generally assumed that the acquisition of antibiotic resistance is associated with a fitness cost. We have shown that overexpression of the MexEF-OprN efflux pump does not decrease the fitness of a resistant Pseudomonas aeruginosa strain compared to its wild-type counterpart. This lack of fitness cost was associated with a metabolic rewiring that includes increased expression of the anaerobic nitrate respiratory chain when cells are growing under fully aerobic conditions. It was not clear whether this metabolic compensation was exclusive to strains overexpressing MexEF-OprN or if it extended to other resistant strains that overexpress similar systems. To answer this question, we studied a set of P. aeruginosa mutants that independently overexpress the MexAB-OprM, MexCD-OprJ, or MexXY efflux pumps. We observed increased expression of the anaerobic nitrate respiratory chain in all cases, with a concomitant increase in NO₃ consumption and NO production. These efflux pumps are proton/substrate antiporters, and their overexpression may lead to intracellular H⁺ accumulation, which may in turn offset the pH homeostasis. Indeed, all studied mutants showed a decrease in intracellular pH under anaerobic conditions. The fastest way to eliminate the excess of protons is by increasing oxygen consumption, a feature also displayed by all analyzed mutants. Taken together, our results support metabolic rewiring as a general mechanism to avoid the fitness costs derived from overexpression of P. aeruginosa multidrug efflux pumps. The development of drugs that block this metabolic “reaccommodation” might help in reducing the persistence and spread of antibiotic resistance elements among bacterial populations.

It is widely accepted that the acquisition of resistance confers a fitness cost in such a way that in the absence of antibiotics, resistant populations will be outcompeted by susceptible ones. Based on this assumption, antibiotic cycling regimes have been proposed in the belief that they will reduce the persistence and spread of resistance among bacterial pathogens. Unfortunately, trials testing this possibility have frequently failed, indicating that resistant microorganisms are not always outcompeted by susceptible ones. Indeed, some mutations do not result in a fitness cost, and in case they do, the cost may be compensated for by a secondary mutation. Here we describe an alternative nonmutational mechanism for compensating for fitness costs, which consists of the metabolic rewiring of resistant mutants. Deciphering the mechanisms involved in the compensation of fitness costs of antibiotic-resistant mutants may help in the development of drugs that will reduce the persistence of resistance by increasing said costs.

Metabolic compensation of fitness costs associated with overexpression of the multidrug efflux pump MexEF-OprN in Pseudomonas aeruginosa

The acquisition of antibiotic resistance has been associated with a possible nonspecific, metabolic burden that is reflected in decreased fitness among resistant bacteria. We have recently demonstrated that overexpression of the MexEF-OprN multidrug efflux pump does not produce a metabolic burden when measured by classical competitions tests but rather leads to a number of changes in the organism's physiology. One of these changes is the untimely activation of the nitrate respiratory chain under aerobic conditions. MexEF-OprN is a proton/substrate antiporter. Overexpression of this element should result in a constant influx of protons, which may lead to cytoplasmic acidification. Acidification was not observed in aerobiosis, a situation in which the MexEF-overproducing mutant increases oxygen consumption. This enhanced oxygen uptake serves to eliminate intracellular proton accumulation, preventing the cytoplasmic acidification that was observed exclusively under anaerobic conditions, a situation in which the fitness of the MexEF-OprN-overproducing mutant decreases. Finally, we determined that the early activation of the nitrate respiratory chain under aerobic conditions plays a role in preventing a deleterious effect associated with the overexpression of MexEF-OprN. Our results show that metabolic rewiring may assist in overcoming the potential fitness cost associated with the acquisition of antibiotic resistance. Furthermore, the capability to metabolically compensate for this effect is habitat dependent, as demonstrated by our results under anaerobic conditions. The development of drugs that prevent metabolic compensation of fitness costs may help to reduce the persistence and dissemination of antibiotic resistance.

Regulation and Function of Versatile Aerobic and Anaerobic Respiratory Metabolism in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitously distributed opportunistic pathogen that inhabits soil and water as well as animal-, human-, and plant-host-associated environments. The ubiquity would be attributed to its very versatile energy metabolism. P. aeruginosa has a highly branched respiratory chain terminated by multiple terminal oxidases and denitrification enzymes. Five terminal oxidases for aerobic respiration have been identified in the P. aeruginosa cells. Three of them, the cbb₃-1 oxidase, the cbb₃-2 oxidase, and the aa₃ oxidase, are cytochrome c oxidases and the other two, the bo₃ oxidase and the cyanide-insensitive oxidase, are quinol oxidases. Each oxidase has a specific affinity for oxygen, efficiency of energy coupling, and tolerance to various stresses such as cyanide and reactive nitrogen species. These terminal oxidases are used differentially according to the environmental conditions. P. aeruginosa also has a complete set of the denitrification enzymes that reduce nitrate to molecular nitrogen via nitrite, nitric oxide (NO), and nitrous oxide. These nitrogen oxides function as alternative electron acceptors and enable P. aeruginosa to grow under anaerobic conditions. One of the denitrification enzymes, NO reductase, is also expected to function for detoxification of NO produced by the host immune defense system. The control of the expression of these aerobic and anaerobic respiratory enzymes would contribute to the adaptation of P. aeruginosa to a wide range of environmental conditions including in the infected hosts. Characteristics of these respiratory enzymes and the regulatory system that controls the expression of the respiratory genes in the P. aeruginosa cells are overviewed in this article.

The anaerobic regulatory network required for Pseudomonas aeruginosa nitrate respiration

In Pseudomonas aeruginosa, the narK(1)K(2)GHJI operon encodes two nitrate/nitrite transporters and the dissimilatory nitrate reductase. The narK(1) promoter is anaerobically induced in the presence of nitrate by the dual activity of the oxygen regulator Anr and the N-oxide regulator Dnr in cooperation with the nitrate-responsive two-component regulatory system NarXL. The DNA bending protein IHF is essential for this process. Similarly, narXL gene transcription is enhanced under anaerobic conditions by Anr and Dnr. Furthermore, Anr and NarXL induce expression of the N-oxide regulator gene dnr. Finally, NarXL in cooperation with Dnr is required for anaerobic nitrite reductase regulatory gene nirQ transcription. A cascade regulatory model for the fine-tuned genetic response of P. aeruginosa to anaerobic growth conditions in the presence of nitrate was deduced.

Denitrifying genes in bacterial and Archaeal genomes

Denitrification, the reduction of nitrate or nitrite to nitrous oxide or dinitrogen, is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Although the denitrifying ability has been found in microorganisms belonging to numerous groups of bacteria and Archaea, the genes encoding the denitrifying reductases have been studied in only few species. Recent investigations have led to the identification of new classes of denitrifying reductases, indicating a more complex genetic basis of this process than previously recognized. The increasing number of genome sequencing projects has opened a new way to study the genetics of the denitrifying process in bacteria and Archaea. In this review, we summarized the current knowledge on denitrifying genes and compared their genetic organizations by using new sequences resulting from the analysis of finished and unfinished microbial genomes with a special attention paid to the clustering of genes encoding different classes of reductases. In addition, some evolutionary relationships between the structural genes are presented.

Effect of nitrogen oxides on expression of the nir and nor genes for denitrification in Pseudomonas aeruginosa

The activity of the promoters involved in transcription of the genes (nirS, nirQ and norC) required for anaerobic reduction of nitrite and nitric oxide was investigated in NIR- and NOR-deficient mutants of Pseudomonas aeruginosa. The transcriptional activity of these three promoters was induced by nitrite in a wild-type strain and the activity was low in an nirS mutant. In norCBD and nirQOP mutants, which were expected to accumulate nitric oxide because of a lack of nitric oxide reductase activity, the norC and nirQ promoters showed significantly enhanced activity in promoting transcription relative to the parental strain, even at low nitrite concentrations. These results suggest that the nirQ and norC promoters are regulated by the concentration of endogenous nitric oxide rather than that of nitrite.

Kinetics of nirS expression (cytochrome cd1 nitrite reductase) in Pseudomonas stutzeri during the transition from aerobic respiration to denitrification: evidence for a denitrification-specific nitrate- and nitrite-responsive regulatory system

After shifting an oxygen-respiring culture of Pseudomonas stutzeri to nitrate or nitrite respiration, we directly monitored the expression of the nirS gene by mRNA analysis. nirS encodes the 62-kDa subunit of the homodimeric cytochrome cd1 nitrite reductase involved in denitrification. Information was sought about the requirements for gene activation, potential regulators of such activation, and signal transduction pathways triggered by the alternative respiratory substrates. We found that nirS, together with nirT and nirB (which encode tetra- and diheme cytochromes, respectively), is part of a 3.4-kb operon. In addition, we found a 2-kb monocistronic transcript. The half-life of each of these messages was approximately 13 min in denitrifying cells with a doubling time of around 2.5 h. When the culture was subjected to a low oxygen tension, we observed a transient expression of nirS lasting for about 30 min. The continued transcription of the nirS operon required the presence of nitrate or nitrite. This anaerobically manifested N-oxide response was maintained in nitrate sensor (NarX) and response regulator (NarL) knockout strains. Similar mRNA stability and transition kinetics were observed for the norCB operon, encoding the NO reductase complex, and the nosZ gene, encoding nitrous oxide reductase. Our results suggest that a nitrate- and nitrite-responsive regulatory circuit independent of NarXL is necessary for the activation of denitrification genes.

Activation of a consensus FNR-dependent promoter by DNR of Pseudomonas aeruginosa in response to nitrite

Expression of the enzymes for anaerobic nitrate respiration of Pseudomonas aeruginosa requires two CRP/FNR-related transcriptional regulators, ANR and DNR. Activity of the consensus CRP- or FNR-dependent promoter in the anr and dnr deficient mutants was investigated. The CRP-dependent promoter was active in the mutant strains. Both regulators could activate the promoter with a consensus FNR-binding motif. DNR-dependent activation was nitrite-dependent, whereas activation by ANR was not, suggesting that only DNR is involved in sensing nitrogen oxides.

Cell biology and molecular basis of denitrification

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

Diversity of oxygen and N-oxide regulation of nitrite reductases in denitrifying bacteria

We examined alpha, beta and gamma Proteobacteria with Cu and heme-type dissimilatory nitrite reductases for patterns of nir regulation. Six of seven strains expressed nitrite reductase under aerobic growth conditions. In only one strain, G-179, was it stringently regulated by O2. Growth with NO-3 or NO-2 enhanced nitrite reductase production in four of seven strains under anaerobic growth conditions, but in only one strain, Pseudomonas aeruginosa PA01, under aerobic conditions. In this strain the nitrite reductase production was primarily regulated by an anr gene when grown under anaerobic conditions, but when grown under aerobic conditions it was regulated by both an anr gene and nitrogen oxide. Constitutive production of nitrite reductase was a common phenomenon rather than the exception among denitrifiers from the environment, which helps explain the prevalence of denitrifying enzymes in aerobic soils.

Sequencing and characterization of the downstream region of the genes encoding nitrite reductase and cytochrome c-551 (nirSM) from Pseudomonas aeruginosa: identification of the gene necessary for biosynthesis of heme d1

The nirC and nirF genes were identified downstream from nirSM, the structural genes encoding nitrite reductase (NIR) and cytochrome c-551 from Pseudomonas aeruginosa (Pa). The nirC gene encodes a probable c-type cytochrome with a signal sequence for membrane translocation. The nirF gene codes for a protein of 392 amino acids. A nirF mutant of Pa, constructed by marker exchange mutagenesis, synthesized an inactive NIR protein whose activity was restored by adding purified heme d1. The mutant strain produced an active NIR, when it was transformed by a broad-host-range plasmid carrying nirF. These results showed that the product of nirF was essential for the biosynthesis of heme d1 in Pa.

Expression of the nir and nor genes for denitrification of Pseudomonas aeruginosa requires a novel CRP/FNR-related transcriptional regulator, DNR, in addition to ANR

A gene, designated dnr, was identified in the vicinity of the structural genes for nitrite reductase (nirS) and nitric oxide reductase (norCB), and the gene for activation of the reductases (nirQ) from Pseudomonas aeruginosa. It encodes a protein of 227 amino acids homologous with the CRP/FNR-family transcriptional regulators. Promoter activities for nirS, nirQ and norCB were considerably reduced in the dnr mutant as well as in the mutant of anr, the other fnr-like regulatory gene from P. aeruginosa. This is the first finding that two CRP/FNR-related regulators are involved in denitrification in one strain.

Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr, an analog of Fnr

The Pseudomonas aeruginosa gene anr, which encodes a structural and functional analog of the anaerobic regulator Fnr in Escherichia coli, was mapped to the SpeI fragment R, which is at about 59 min on the genomic map of P. aeruginosa PAO1. Wild-type P. aeruginosa PAO1 grew under anaerobic conditions with nitrate, nitrite, and nitrous oxide as alternative electron acceptors. An anr deletion mutant, PAO6261, was constructed. It was unable to grow with these alternative electron acceptors; however, its ability to denitrify was restored upon the introduction of the wild-type anr gene. In addition, the activities of two enzymes in the denitrification pathway, nitrite reductase and nitric oxide reductase, were not detectable under oxygen-limiting conditions in strain PAO6261 but were restored when complemented with the anr+ gene. These results indicate that the anr gene product plays a key role in anaerobically activating the entire denitrification pathway.

The structural genes for nitric oxide reductase from Pseudomonas aeruginosa

The genes for nitric oxide reductase (norCB) from Pseudomonas aeruginosa were identified and sequenced. They are located about 2 kb upstream of nirS, the structural gene for nitrite reductase. norC and norB encode cytochrome c (16 kDa) and cytochrome b (52 kDa) subunits of the enzyme, respectively. norCB is immediately followed by an open reading frame encoding a protein of 612 residues.

Pseudomonas aeruginosa nitrite reductase (or cytochrome oxidase): an overview

The biochemistry and molecular biology of nitrite reductase, a key enzyme in the dissimilatory denitrification pathway of Ps aeruginosa which reduces nitrite to NO, is reviewed in this paper. The enzyme is a non-covalent homodimer, each subunit containing one heme c and one heme d1. The reaction mechanisms of nitrite and oxygen reduction are discussed in detail, as well as the interaction of the enzyme with its macromolecular substrates, azurin and cytochrome c551. Special attention is paid to new structural information, such as the chemistry of the d1 prosthetic group and the primary sequence of the gene and the protein. Finally, results on the expression both in Ps aeruginosa and in heterologous systems are presented.

Anaerobic control of denitrification in Pseudomonas stutzeri escapes mutagenesis of an fnr-like gene

The synthesis of proteins necessary for the respiratory reduction of nitrate to dinitrogen is induced in most denitrifying bacteria by a shift to anaerobiosis. A homolog of the fur gene, which encodes a redox-active transcriptional activator in Escherichia coli, was isolated from Pseudomonas stutzeri by using the anr gene of Pseudomonas aeruginosa as the hybridization probe (R. G. Sawers, Mol. Microbiol. 5:1469-1481, 1991). The coding region was located on a 3-kb SmaI fragment. An open reading frame of 735 nucleotides, designated fnrA, had the coding potential for a protein of 244 amino acids (M(r) = 27,089) with 51.2% positional identity to the Fnr protein of E. coli and 86.1% to the Anr protein of P. aeruginosa. The fnrA gene gave a single transcript of 0.85 kb and complemented nitrate-dependent anaerobic growth of an fnr deletion mutant of E. coli. An open reading frame immediately downstream of fnrA encoded adenine phosphoribosyltransferase (EC 2.4.2.7). Mutations in fnrA were generated in vitro by insertional mutagenesis followed by gene replacement. Gene inactivation was shown by loss of the fnrA transcript and detection of an arginine deiminase (EC 3.5.3.6)-negative phenotype in the mutants. However, neither the enzymatic activities nor the levels of anaerobic expression of the respiratory enzymes nitrate reductase (EC 1.7.99.4), nitrate reductase (EC 1.9.3.2), NO reductase (EC 1.7.99.7), and N2O reductase (EC 1.7.99.6) were changed in fnrA mutants versus the P. stutzeri wild type. A promoter-probe vector for Fnr-dependent transcription was activated anaerobically in the fnrA mutants, suggesting the existence of a second Fnr homolog in the same bacterium. The Fnr-binding motifs, apparent in the promoter region of genes encoding denitrification components of P. stutzeri, are likely to be recognized by this second Fnr homolog. Preliminary evidence indicates also the presence of the catabolite activator protein, Crp, in P. stutzeri.