The roles of the hybrid cluster protein, Hcp and its reductase, Hcr, in high affinity nitric oxide reduction that protects anaerobic cultures ofEscherichia coliagainst nitrosative stress

Functional Nonheme Diiron(II) Complexes Catalyze the Direct Reduction of Nitrite to Nitric Oxide in Relevance to the Diiron Protein YtfE

The present work reports the functional modeling chemistry of YtfE, which features a nonheme diiron active site and mediates the direct reduction of NO2- to NO. The model complex, [Fe2(HPTP)Cl2]1+ (1), reduces NO2- to NO in a 100% yield within 12 h and generates [Fe4(HPTP)2(μ-O)3(μ-OH)]3+ (2). Similar to YtfE, the reaction involves stepwise oxidation of two Fe(II) centers and product (NO) inhibition, of which the latter produces [Fe2(HPTP)(NO)2Cl2]1+ (3). Complex 3 could also be synthesized by the reaction of [Fe2(HPTP)(NO)2(ClO4)]2+ (4) and chloride. Complex 1 catalyzes the reduction of NO2- to NO in the presence of PhS-, albeit with a low TON of 5, due to the formation of an insoluble product, [Fe2(HPTP)(μ-SPh)Cl2] (5). Another model complex [Fe2(HPTP)(OPr)]1+ (6), reduced NO2- to NO in an 80% yield after 24 h, generated [Fe2(HPTP)(OPr)(NO)2]1+ (7), and offered a TON of 19. The third model complex, [Fe2(HPTP)(ClO4)2]1+ (8), could reduce NO2- to NO in a 100% yield but only after 48 h. A comparison of these results establishes that easy oxidation of the Fe(II) centers, easy accessibility of the Fe(II) centers for the coordination of NO2-, and easy release of NO from the in situ generated dinitrosyl diiron complex increase the efficiency of the functional model complexes of YtfE.

Escherichia coli growing under antimicrobial gallium nitrate stress reveals new processes of tolerance and toxicity

Metals have been used throughout history to manage disease. With the rising incidence of antibiotic-resistant bacterial strains, metal-based antimicrobials (MBAs) have re-emerged as an alternative to combat infections. Gallium nitrate has shown promising efficacy against several pathogens. Although its main toxicity mechanisms have focused on oxidative stress and its "trojan horse" iron mimetic strategy, there are still many knowledge gaps in the full-systems response elicited to counteract its toxic effects, especially in non-acute toxicity models that evaluate longer exposure times. In this study, we explore the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 h in the presence of a sublethal inhibitory concentration of gallium nitrate. 581 genes were significantly up-regulated, and 791 down-regulated. Some of the affected biological systems identified in our analysis include iron homeostasis, sulfate metabolism, oxidative and nitrosative stress response, cysteine biosynthesis, anaerobic respiration, toxin-antitoxin interactions, and DNA repair. Altogether, this work provides a valuable snapshot of how E. coli acclimates to this MBA and expands the current knowledge of mechanisms of sensitivity and tolerance. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of toxic metals.

Regulatory Mechanisms and Synergistic Enhancement of the Diiron YtfE Protein in Nitric Oxide Reduction

The diiron-containing YtfE protein in Escherichia coli is pivotal in counteracting nitrosative stress, a critical barrier to bacterial viability. This study delves into the biochemical complexity governing YtfE's conversion of nitric oxide (NO) to nitrous oxide, a key process for alleviating nitrosative stress. Through site-directed mutagenesis, we explored YtfE's molecular structure, with a particular focus on two internal transport tunnels important for its activity. Our findings illuminate Tunnel 1 as the primary conduit for substrate transport, regulated by conformational shifts within the N-terminal domain that enable substrate access to the diiron core in the C-terminal domain. Tunnel 2 emerges as a secondary, supportive route, activated when Tunnel 1 is compromised. This result challenges a previous model of distinct tunnels for substrate entry and product exit, suggesting both tunnels are capable of transporting substrates and products. Our engineering efforts enhanced the role of Tunnel 2, enabling a synergistic operation with Tunnel 1 and tripling YtfE's enzymatic activity compared to its wild-type form. This research not only deepens our understanding of YtfE's regulatory mechanism for NO reduction but also introduces a strategy to amplify its enzymatic efficiency. The outcomes offer new ravenues for modulating bacterial stress responses.

Comparative genomics analysis of the reason for 12C6+ heavy-ion irradiation in improving Fe3O4 nanoparticle yield of Acidithiobacillus ferrooxidans

The Fe3O4 nanoparticle synthesized by Acidithiobacillus ferrooxidans have a broad practical value, while the low yield limits their commercial application. Herein, we employed a 12C6+ heavy-ion beam to induce mutagenesis of A. ferrooxidans BYM and successfully screened a mutant BYMT-200 with a 1.36 mg/L Fe3O4 nanoparticle yield, which could stably inherit over many generations based on assessing cell magnetism and Fe3O4 nanoparticle synthesis. Comparative genome analysis detected 14 mutation sites, causing six synonymous mutations, one missense mutation, and one nonsense mutation. We further annotated the genes involved in the mutation, such as hcp, hsdM, yghU, K7B00_11365, and K7B00_11355, which are responsible for the substantial changes in the Fe3O4 nanoparticle yield of A. ferrooxidans. Additionally, we performed a pan-genome analysis to understand how these genes regulate Fe3O4 nanoparticle synthesis. The core genome of 2376 orthologous clusters was identified and visualized by progressive Mauve alignment and OrthoVenn. A total of 109 regulatory genes related to iron metabolism were identified, mainly involved in electron transport, iron acquisition, iron storage, and oxidative stress. The mutant genes are closely related to iron-sulfur clusters and oxidative stress. Accordingly, we proposed a hypothetical mechanism for increasing Fe3O4 nanoparticle production in A. ferrooxidans BYMT-200 to withstand high oxidative stress caused by heavy ion radiation. Our study offers significant theoretical guidance for further acquiring the high-yield Fe3O4 nanoparticle-producing bacteria and studying the mechanism of its synthesis.

Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures

Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp-Hcr) that catalyzes the conversion of NO2- to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp-Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰-49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3- and NO2- into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking.

Microplastics enhanced the allelopathy of pyrogallol on toxic Microcystis with additional risks: Microcystins release and greenhouse gases emissions

Cyanobacteria blooms (CBs) caused by eutrophication pose a global concern, especially Microcystis aeruginosa (M. aeruginosa), which could release harmful microcystins (MCs). The impact of microplastics (MPs) on allelopathy in freshwater environments is not well understood. This study examined the joint effect of adding polystyrene (PS-MPs) as representative MPs and two concentrations (2 and 8 mg/L) of pyrogallol (PYR) on the allelopathy of M. aeruginosa. The results showed that the addition of PS-MPs intensified the inhibitory effect of 8 mg/L PYR on the growth and photosynthesis of M. aeruginosa. After a 7-day incubation period, the cell density decreased to 69.7 %, and the chl-a content decreased to 48 % compared to the condition without PS-MPs (p < 0.05). Although the growth and photosynthesis of toxic Microcystis decreased with the addition of PS-MPs, the addition of PS-MPs significantly resulted in a 3.49-fold increase in intracellular MCs and a 1.10-fold increase in extracellular MCs (p < 0.05). Additionally, the emission rates of greenhouse gases (GHGs) (carbon dioxide, nitrous oxide and methane) increased by 2.66, 2.23 and 2.17-fold, respectively (p < 0.05). In addition, transcriptomic analysis showed that the addition of PS-MPs led to the dysregulation of gene expression related to DNA synthesis, membrane function, enzyme activity, stimulus detection, MCs release and GHGs emissions in M. aeruginosa. PYR and PS-MPs triggered ROS-induced membrane damage and disrupted photosynthesis in algae, leading to increased MCs and GHG emissions. PS-MPs accumulation exacerbated this issue by impeding light absorption and membrane function, further heightening the release of MCs and GHGs emissions. Therefore, PS-MPs exhibited a synergistic effect with PYR in inhibiting the growth and photosynthesis of M. aeruginosa, resulting in additional risks such as MCs release and GHGs emissions. These results provide valuable insights for the ecological risk assessment and control of algae bloom in freshwater ecosystems.

Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent

Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits regardless of their ubiquitous distribution in diverse habitats, which is especially true for Heimdallarchaeia from deep-sea environments. In this study, we obtained 13 metagenome-assembled genomes (MAGs) of Heimdallarchaeia from the deep-sea cold seep and hydrothermal vent. These MAGs belonged to orders o_Heimdallarchaeales and o_JABLTI01, and most of them (9 MAGs) come from the family f_Heimdallarchaeaceae according to genome taxonomy database (GTDB). These are enriched for common eukaryote-specific signatures. Our results show that these Heimdallarchaeia have the metabolic potential to reduce sulfate (assimilatory) and nitrate (dissimilatory) to sulfide and ammonia, respectively, suggesting a previously unappreciated role in biogeochemical cycling. Furthermore, we find that they could perform both TCA and rTCA pathways coupled with pyruvate metabolism for energy conservation, fix CO2 and generate organic compounds through an atypical Wood-Ljungdahl pathway. In addition, many genes closely associated with bacteriochlorophyll and carotenoid biosynthesis, and oxygen-dependent metabolic pathways are identified in these Heimdallarchaeia MAGs, suggesting a potential light-utilization by pigments and microoxic lifestyle. Taken together, our results indicate that Heimdallarchaeia possess a mixotrophic lifestyle, which may give them more flexibility to adapt to the harsh deep-sea conditions.

Diversity and ecology of NrfA-dependent ammonifying microorganisms

Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.

A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans

The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.

Flagella are required to coordinately activate competition and host colonization factors in response to a mechanical signal

Bacteria employ antagonistic strategies to eliminate competitors of an ecological niche. Contact-dependent mechanisms, such as the type VI secretion system (T6SS), are prevalent in host-associated bacteria, yet we know relatively little about how T6SS+ strains make contact with competitors in highly viscous environments, such as host mucus. To better understand how cells respond to and contact one another in such environments, we performed a genome-wide transposon mutant screen of the T6SS-wielding beneficial bacterial symbiont, Vibrio fischeri, and identified two sets of genes that are conditionally required for killing. LPS/capsule and flagellar-associated genes do not affect T6SS directly and are therefore not required for interbacterial killing when cell contact is forced yet are necessary for killing in high-viscosity liquid (hydrogel) where cell-cell contact must be biologically mediated. Quantitative transcriptomics revealed that V. fischeri significantly increases expression of both T6SS genes and cell surface modification factors upon transition from low- to high-viscosity media. Consistent with coincubation and fluorescence microscopy data, flagella are not required for T6SS expression in hydrogel. However, flagella play a key role in responding to the physical environment by promoting expression of the surface modification genes identified in our screen, as well as additional functional pathways important for host colonization including uptake of host-relevant iron and carbon sources, and nitric oxide detoxification enzymes. Our findings suggest that flagella may act as a mechanosensor for V. fischeri to coordinately activate competitive strategies and host colonization factors, underscoring the significance of the physical environment in directing complex bacterial behaviors.

Enhanced treatment of sludge drying condensate by A/O-MBR process: Microbial activity and community structure

With the rapid increase of sludge production from sewage treatment plants, the treatment of sludge drying condensate rich in a large amount of pollutants urgently needs to be addressed. Due to the unique characteristics of sludge drying condensate (high ammonia nitrogen and COD concentration), there are almost no reports on biological treatment methods specifically targeting sludge drying condensate. In this study, A/O-MBR process was proposed for sludge drying condensate treatment and the effects of ammonia nitrogen loads, alkalinity and aeration intensity were explored. Experimental results show that under the ammonia nitrogen load of 0.35 kg NH4+-N/(m3·d) and the aeration intensity of 0.5 m3/(m2·min), the removal rate of COD and NH4+-N could reach 94% and 99.86% with the addition of alkalinity (m(NaHCO3): m(NH4+-N) = 7:1), respectively. The distribution of living and dead microbial cells in the activated sludge of three reactors also proved that the supplement of alkalinity in the influent can ensure the feasible living conditions for microorganisms. In addition to traditional nitrifying bacteria, through the supplementation of alkalinity and the reduction of aeration intensity, the system had also domesticated high abundance heterogeneous nitrification aerobic denitrification (HN-AD) and aerobic denitrification bacteria (both more than 10% of the total bacterial count). The denitrification process of sludge drying condensate was simplified and the denitrification efficiency was greatly improved. The findings of this study could provide important theoretical guidance for the biological treatment process of sludge drying condensate.

Nitrite Formation at a Diiron Dinitrosyl Complex

Pathogenic bacteria employ iron-containing enzymes to detoxify nitric oxide (NO•) produced by mammals as part of their immune response. Two classes of diiron proteins, flavodiiron nitric oxide reductases (FNORs) and the hemerythrin-like proteins from mycobacteria (HLPs), are upregulated in bacteria in response to an increased local NO• concentration. While FNORs reduce NO• to nitrous oxide (N2O), the HLPs have been found to either reduce nitrite to NO• (YtfE), or oxidize NO• to nitrite (Mka-HLP). Various structural and functional models of the diiron site in FNORs have been developed over the years. However, the NO• oxidation reactivity of Mka-HLP has yet to be replicated with a synthetic complex. Compared to the FNORs, the coordination environment of the diiron site in Mka-HLP contains one less carboxylate ligand and, therefore, is expected to be more electron-poor. Herein, we synthesized a new diiron complex that models the electron-poor coordination environment of the Mka-HLP diiron site. The diferrous precursor FeIIFeII reacts with NO• to form a diiron dinitrosyl species ({FeNO}72), which is in equilibrium with a mononitrosyl diiron species (FeII{FeNO}7) in solution. Both complexes can be isolated and fully characterized. However, only oxidation of {FeNO}72 produced nitrite in high yield (71%). Our study provides the first model that reproduces the NO• oxidase reactivity of Mka-HLP and suggests intermediacy of an {FeNO}6/{FeNO}7 species.

Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia

Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited chemostats with acetate as electron (e) donor, demonstrating their presence in these systems. Here, we isolated and characterized the new species Trichlorobacter ammonificans strain G1 using a combination of low redox potential and copper-depleted conditions. This allowed purification of this DNRA organism from competing denitrifiers. T. ammonificans is an extremely specialized ammonifier, actively growing only with acetate as e-donor and carbon source and nitrate as e-acceptor, but H2 can be used as an additional e-donor. The genome of G1 does not encode the classical ammonifying modules NrfAH/NrfABCD. Instead, we identified a locus encoding a periplasmic nitrate reductase immediately followed by an octaheme cytochrome c that is conserved in many Geobacteraceae species. We purified this octaheme cytochrome c protein (TaNiR), which is a highly active dissimilatory ammonifying nitrite reductase loosely associated with the cytoplasmic membrane. It presumably interacts with two ferredoxin subunits (NapGH) that donate electrons from the menaquinol pool to the periplasmic nitrate reductase (NapAB) and TaNiR. Thus, the Nap-TaNiR complex represents a novel type of highly functional DNRA module. Our results indicate that DNRA catalyzed by octaheme nitrite reductases is a metabolic feature of many Geobacteraceae, representing important community members in various anaerobic systems, such as rice paddy soil and wastewater treatment facilities.

Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases

Hybrid cluster proteins (HCPs) are Fe-S-O cluster-containing metalloenzymes in three distinct classes (class I and II: monomer, III: homodimer), all of which structurally related to homodimeric Ni, Fe-carbon monoxide dehydrogenases (CODHs). Here we show X-ray crystal structure of class III HCP from Methanothermobacter marburgensis (Mm HCP), demonstrating its homodimeric architecture structurally resembles those of CODHs. Also, despite the different architectures of class III and I/II HCPs, [4Fe-4S] and hybrid clusters are found in equivalent positions in all HCPs. Structural comparison of Mm HCP and CODHs unveils some distinct features such as the environments of their homodimeric interfaces and the active site metalloclusters. Furthermore, structural analysis of Mm HCP C67Y and characterization of several Mm HCP variants with a Cys67 mutation reveal the significance of Cys67 in protein structure, metallocluster binding and hydroxylamine reductase activity. Structure-based bioinformatics analysis of HCPs and CODHs provides insights into the structural evolution of the HCP/CODH superfamily.

Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis

BACKGROUND

Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial.

METHODS

In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions.

RESULTS

First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release.

CONCLUSION

These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.

Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon

Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.

Transcriptomic and metabolomic investigation of molecular inactivation mechanisms in Escherichia coli triggered by graphene quantum dots

Graphene quantum dots (GQDs), a novel broad-spectrum antibacterial agent, are considered potential candidates in the field of biomedical and food safety due to their outstanding antimicrobial properties and excellent biocompatibility. To uncover the molecular regulatory mechanisms underlying the phenotypes, the overall regulation of genes and metabolites in Escherichia coli (E. coli) after GQDs stimulation was investigated by RNA-sequencing and LC-MS. Gene transcription and metabolite expression related to a series of crucial biomolecular processes were influenced by the GQDs stimulation, including biofilm formation, bacterial secretion system, sulfur metabolism and nitrogen metabolism, etc. This study could provide profound insights into the GQDs stress response in E. coli, which would be useful for the development and application of GQDs in food safety.

The hydrogenosomes of Trichomonas vaginalis

This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19^th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.

The Di-Iron Protein YtfE Is a Nitric Oxide-Generating Nitrite Reductase Involved in the Management of Nitrosative Stress

Previously characterized nitrite reductases fall into three classes: siroheme-containing enzymes (NirBD), cytochrome c hemoproteins (NrfA and NirS), and copper-containing enzymes (NirK). We show here that the di-iron protein YtfE represents a physiologically relevant new class of nitrite reductases. Several functions have been previously proposed for YtfE, including donating iron for the repair of iron-sulfur clusters that have been damaged by nitrosative stress, releasing nitric oxide (NO) from nitrosylated iron, and reducing NO to nitrous oxide (N2O). Here, in vivo reporter assays confirmed that Escherichia coli YtfE increased cytoplasmic NO production from nitrite. Spectroscopic and mass spectrometric investigations revealed that the di-iron site of YtfE exists in a mixture of forms, including nitrosylated and nitrite-bound, when isolated from nitrite-supplemented, but not nitrate-supplemented, cultures. Addition of nitrite to di-ferrous YtfE resulted in nitrosylated YtfE and the release of NO. Kinetics of nitrite reduction were dependent on the nature of the reductant; the lowest Km, measured for the di-ferrous form, was ∼90 μM, well within the intracellular nitrite concentration range. The vicinal di-cysteine motif, located in the N-terminal domain of YtfE, was shown to function in the delivery of electrons to the di-iron center. Notably, YtfE exhibited very low NO reductase activity and was only able to act as an iron donor for reconstitution of apo-ferredoxin under conditions that damaged its di-iron center. Thus, YtfE is a high-affinity, low-capacity nitrite reductase that we propose functions to relieve nitrosative stress by acting in combination with the co-regulated NO-consuming enzymes Hmp and Hcp.

A Morphing [4Fe-3S-nO]-Cluster within a Carbon Monoxide Dehydrogenase Scaffold

Ni,Fe-containing carbon monoxide dehydrogenases (CODHs) catalyze the reversible reduction of CO2 to CO. Several anaerobic microorganisms encode multiple CODHs in their genome, of which some, despite being annotated as CODHs, lack a cysteine of the canonical binding motif for the active site Ni,Fe-cluster. Here, we report on the structure and reactivity of such a deviant enzyme, termed CooS-VCh . Its structure reveals the typical CODH scaffold, but contains an iron-sulfur-oxo hybrid-cluster. Although closely related to true CODHs, CooS-VCh catalyzes neither CO oxidation, nor CO2 reduction. The active site of CooS-VCh undergoes a redox-dependent restructuring between a reduced [4Fe-3S]-cluster and an oxidized [4Fe-2S-S*-2O-2(H2 O)]-cluster. Hydroxylamine, a slow-turnover substrate of CooS-VCh , oxidizes the hybrid-cluster in two structurally distinct steps. Overall, minor changes in CODHs are sufficient to accommodate a Fe/S/O-cluster in place of the Ni,Fe-heterocubane-cluster of CODHs.

Defenses of multidrug resistant pathogens against reactive nitrogen species produced in infected hosts

Bacterial pathogens have sophisticated systems that allow them to survive in hosts in which innate immunity is the frontline of defense. One of the substances produced by infected hosts is nitric oxide (NO) that together with its derived species leads to the so-called nitrosative stress, which has antimicrobial properties. In this review, we summarize the current knowledge on targets and protective systems that bacteria have to survive host-generated nitrosative stress. We focus on bacterial pathogens that pose serious health concerns due to the growing increase in resistance to currently available antimicrobials. We describe the role of nitrosative stress as a weapon for pathogen eradication, the detoxification enzymes, protein/DNA repair systems and metabolic strategies that contribute to limiting NO damage and ultimately allow survival of the pathogen in the host. Additionally, this systematization highlights the lack of available data for some of the most important human pathogens, a gap that urgently needs to be addressed.

The hemerythrin-like diiron protein from Mycobacterium kansasii is a nitric oxide peroxidase

The hemerythrin-like protein from Mycobacterium kansasii (Mka HLP) is a member of a distinct class of oxo-bridged diiron proteins that are found only in mycobacterial species that cause respiratory disorders in humans. Because it had been shown to exhibit weak catalase activity and a change in absorbance on exposure to nitric oxide (NO), the reactivity of Mka HLP toward NO was examined under a variety of conditions. Under anaerobic conditions, we found that NO was converted to nitrite (NO₂⁻) via an intermediate, which absorbed light at 520 nm. Under aerobic conditions NO was converted to nitrate (NO₃⁻). In each of these two cases, the maximum amount of nitrite or nitrate formed was at best stoichiometric with the concentration of Mka HLP. When incubated with NO and H₂O₂, we observed NO peroxidase activity yielding nitrite and water as reaction products. Steady-state kinetic analysis of NO consumption during this reaction yielded a K_m for NO of 0.44 μM and a k_cat/K_m of 2.3 × 10⁵ M⁻¹s⁻¹. This high affinity for NO is consistent with a physiological role for Mka HLP in deterring nitrosative stress. This is the first example of a peroxidase that uses an oxo-bridged diiron center and a rare example of a peroxidase utilizing NO as an electron donor and cosubstrate. This activity provides a mechanism by which the infectious Mycobacterium may combat against the cocktail of NO and superoxide (O₂^•−) generated by macrophages to defend against bacteria, as well as to produce NO₂⁻ to adapt to hypoxic conditions.

Nitric Oxide Induced stx2 Expression Is Inhibited by the Nitric Oxide Reductase, NorV, in a Clade 8 Escherichia coli O157:H7 Outbreak Strain

Escherichia coli O157:H7 pathogenesis is due to Shiga toxin (Stx) production, though variation in virulence has been observed. Clade 8 strains, for instance, were shown to overproduce Stx and were more common among hemolytic uremic syndrome cases. One candidate gene, norV, which encodes a nitric oxide (NO) reductase found in a clade 8 O157:H7 outbreak strain (TW14359), was thought to impact virulence. Hence, we screened for norV in 303 O157 isolates representing multiple clades, examined stx2 expression following NO exposure in TW14359 for comparison to an isogenic mutant (ΔnorV), and evaluated survival in THP-1 derived macrophages. norV was intact in strains representing clades 6-9, whereas a 204 bp deletion was found in clades 2 and 3. During anaerobic growth, NO induced stx2 expression in TW14359. A similar increase in stx2 expression was observed for the ΔnorV mutant in anaerobiosis, though it was not impaired in its ability to survive within macrophages relative to TW14359. Altogether, these data suggest that NO enhances virulence by inducing Stx2 production in TW14359, and that toxin production is inhibited by NorV encoded by a gene found in most clade 8 strains. The mechanism linked to these responses, however, remains unclear and likely varies across genotypes.

Advanced spectroscopic analysis and 15N-isotopic labelling study of nitrate and nitrite reduction to ammonia and nitrous oxide by E. coli

Nitrate and nitrite reduction to ammonia and nitrous oxide by anaerobic E. coli batch cultures is investigated by advanced spectroscopic analytical techniques with ¹⁵N-isotopic labelling. Non-invasive, in situ analysis of the headspace is achieved using White cell FTIR and cavity-enhanced Raman (CERS) spectroscopies alongside liquid-phase Raman spectroscopy. For gas-phase analysis, White cell FTIR measures CO₂, ethanol and N₂O while CERS allows H₂, N₂ and O₂ monitoring. The 6 m pathlength White cell affords trace gas detection of N₂O with a noise equivalent detection limit of 60 nbar or 60 ppbv in 1 atm. Quantitative analysis is discussed for all four ¹⁴N/¹⁵N-isotopomers of N₂O. Monobasic and dibasic phosphates, acetate, formate, glucose and NO₃^- concentrations are obtained by liquid-phase Raman spectroscopy, with a noise equivalent detection limit of 0.6 mM for NO₃^- at 300 s integration time. Concentrations of the phosphate anions are used to calculate the pH in situ using a modified Henderson-Hasselbalch equation. NO₂^- concentrations are determined by sampling for colorimetric analysis and NH₄⁺ by basifying samples to release ¹⁴N/¹⁵N-isotopomers of NH₃ for measurement in a second FTIR White cell. The reductions of ¹⁵NO₃^-, ¹⁵NO₂^-, and mixed ¹⁵NO₃^- and ¹⁴NO₂^- by anaerobic E. coli batch cultures are discussed. In a major pathway, NO₃^- is reduced to NH₄⁺via NO₂^-, with the bulk of NO₂^- reduction occurring after NO₃^- depletion. Using isotopically labelled ¹⁵NO₃^-, ¹⁵NH₄⁺ production is distinguished from background ¹⁴NH₄⁺ in the growth medium. In a minor pathway, NO₂^- is reduced to N₂O via the toxic radical NO. With excellent detection sensitivities, N₂O serves as a monitor for trace NO₂^- reduction, even when cells are predominantly reducing NO₃^-. The analysis of N₂O isotopomers reveals that for cultures supplemented with mixed ¹⁵NO₃^- and ¹⁴NO₂^- enzymatic activity to reduce ¹⁴NO₂^- occurs immediately, even before ¹⁵NO₃^- reduction begins. Optical density and pH measurements are discussed in the context of acetate, formate and CO₂ production. H₂ production is repressed by NO₃^-; but in experiments with NO₂^- supplementation only, CERS detects H₂ produced by formate disproportionation after NO₂^- depletion.

A bacterial bioreporter for the detection of 1,3,5-trinitro-1,3,5-triazinane (RDX)

We report the design, construction, and testing of Escherichia coli-based bioluminescent bioreporters for the detection of 1,3,5-trinitro-1,3,5-triazinane (RDX), one of the most prevalent military-grade explosives in use today. These sensor strains are based on a fusion between the promoter of either the hmp (nitric oxide dioxygenase) or the hcp (a high-affinity nitric oxide reductase) E. coli gene, to the microbial bioluminescence luxCDABEG gene cassette. Signal intensity was enhanced in ∆hmp and ∆hcp mutants, and detection sensitivity was improved when the two gene promoters were cloned in tandem. The Photobacterium leiognathi luxCDABEG reporter genes were superior to those of Aliivibrio fischeri in terms of signal intensity, but in most cases inferior in terms of detection sensitivity, due to a higher background signal. Both sensor strains were also induced by additional nitro-organic explosives, as well as by nitrate salts. Sensitive detection of RDX in a solid matrix (either LB agar or sand) was also demonstrated, with the bioreporters encapsulated in 1.5-mm calcium alginate beads. Lowest RDX concentration detected in sand was 1.67 mg/kg sand. The bioreporter strains described herein may serve as a basis for a standoff detection technology of RDX-based explosive devices, including buried landmines.

Physiological Roles of Nitrite and Nitric Oxide in Bacteria: Similar Consequences from Distinct Cell Targets, Protection, and Sensing Systems

Nitrite and nitric oxide (NO) are two active nitrogen oxides that display similar biochemical properties, especially when interacting with redox-sensitive proteins (i.e., hemoproteins), an observation serving as the foundation of the notion that the antibacterial effect of nitrite is largely attributed to NO formation. However, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. Although both nitrite and NO are formed and decomposed by enzymes participating in the transformation of these nitrogen species, NO can also be generated via amino acid metabolism by bacterial NO synthetase and scavenged by flavohemoglobin. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to heme-copper oxidases. Consequently, the homeostasis of redox-sensitive proteins may be responsible for the substantial difference in NO-targets identified to date among different bacteria. In addition, most protective systems against NO damage have no significant role in alleviating inhibitory effects of nitrite. Furthermore, when functioning as signal molecules, nitrite and NO are perceived by completely different sensing systems, through which they are linked to different biological processes.

Crystal structure of Escherichia coli class II hybrid cluster protein, HCP, reveals a [4Fe-4S] cluster at the N-terminal protrusion

Hybrid cluster protein (HCP) is a unique Fe-S-O-type metallocluster-containing enzyme present in many anaerobic organisms and is categorized into three distinct classes (I, II, and III). The class II HCP uniquely utilizes hybrid cluster protein reductase (HCR), unlike the other classes of HCPs. To gain structural insights into the electron transfer system between the class II HCP and HCR, we elucidated the X-ray crystal structure of Escherichia coli HCP (Ec HCP), representing the first report of a class II HCP structure. Surprisingly, Ec HCP was found to harbor a [4Fe-4S] cluster rather than a [2Fe-2S] cluster at the N-terminal Cys-rich region, similar to class I HCPs. It was also found that the Cys-rich motif forms a unique protrusion and that the surrounding charge distributions on the surface of class II Ec HCP are distinct from those of class I HCPs. The functional significance of the Cys-rich region was investigated using an Ec HCP variant (chimeric HCP) containing a class I HCP Cys-rich motif from Desulfovibrio desulfuricans. The biochemical analyses showed that the chimeric HCP lacks the hybrid cluster and the electron-accepting function from HCR despite the formation of the chimeric HCP-HCR complex. Furthermore, HCP-HCR molecular docking analysis suggested that the protrusion area serves as an HCR-binding region. Therefore, the protrusion of the unique Cys-rich motif and the surrounding area of class II HCP are likely important for maturation of Ec HCP and orienting HCR onto the surface of HCP to facilitate electron transfer in the HCP-HCR complex.

Dr. NO and Mr. Toxic - the versatile role of nitric oxide

Nitric oxide (NO) is present in various organisms from humans, to plants, fungus and bacteria. NO is a fundamental signaling molecule implicated in major cellular functions. The role of NO ranges from an essential molecule to a potent mediator of cellular damages. The ability of NO to react with a broad range of biomolecules allows on one hand its regulation and a gradient concentration and on the other hand to exert physiological as well as pathological functions. In humans, NO is implicated in cardiovascular homeostasis, neurotransmission and immunity. However, NO can also contribute to cardiovascular diseases (CVDs) or septic shock. For certain denitrifying bacteria, NO is part of their metabolism as a required intermediate of the nitrogen cycle. However, for other bacteria, NO is toxic and harmful. To survive, those bacteria have developed processes to resist this toxic effect and persist inside their host. NO also contributes to maintain the host/microbiota homeostasis. But little is known about the impact of NO produced during prolonged inflammation on microbiota integrity, and some pathogenic bacteria take advantage of the NO response to colonize the gut over the microbiota. Taken together, depending on the environmental context (prolonged production, gradient concentration, presence of partners for interaction, presence of oxygen, etc.), NO will exert its beneficial or detrimental function. In this review, we highlight the dual role of NO for humans, pathogenic bacteria and microbiota, and the mechanisms used by each organism to produce, use or resist NO.

Anaerobic bacterial response to nitric oxide stress: Widespread misconceptions and physiologically relevant responses

How anaerobic bacteria protect themselves against nitric oxide-induced stress is controversial, not least because far higher levels of stress were used in the experiments on which most of the literature is based than bacteria experience in their natural environments. This results in chemical damage to enzymes that inactivates their physiological function. This review illustrates how transcription control mechanisms reveal physiological roles of the encoded gene products. Evidence that the hybrid cluster protein, Hcp, is a major high affinity NO reductase in anaerobic bacteria is reviewed: if so, its trans-nitrosation activity is a nonspecific secondary consequence of chemical inactivation. Whether the flavorubredoxin, NorV, is equally effective at such low [NO] is unknown. YtfE is proposed to be an enzyme rather than a source of iron for the repair of iron-sulfur proteins damaged by nitrosative stress. Any reaction catalyzed by YtfE needs to be revealed. The concentration of NO that accumulates in the cytoplasm of anaerobic bacteria is unknown, but indirect evidence indicates that it is in the pM to low nM range. Also unknown are the functions of the NO-inducible cytoplasmic proteins YgbA, YeaR, or YoaG. Experiments to resolve some of these questions are proposed.

Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling

Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.

Role of the Nitric Oxide Reductase NorVW in the Survival and Virulence of Enterohaemorrhagic Escherichia coli during Infection

Enterohaemorrhagic Escherichia coli (EHEC) are bacterial pathogens responsible for life-threatening diseases in humans, such as hemolytic and uremic syndrome. It has been previously demonstrated that the interplay between EHEC and nitric oxide (NO), a mediator of the host immune innate response, is critical for infection outcome, since NO affects both Shiga toxin (Stx) production and adhesion to enterocytes. In this study, we investigated the role of the NO reductase NorVW in the virulence and fitness of two EHEC strains in a murine model of infection. We determined that the deletion of norVW in the strain O91:H21 B2F1 has no impact on its virulence, whereas it reduces the ability of the strain O157:H7 620 to persist in the mouse gut and to produce Stx. We also revealed that the fitness defect of strain 620 ΔnorVW is strongly attenuated when mice are treated with an NO synthase inhibitor. Altogether, these results demonstrate that the NO reductase NorVW participates in EHEC resistance against NO produced by the host and promotes virulence through the modulation of Stx synthesis. The contribution of NorVW in the EHEC infectious process is, however, strain-dependent and suggests that the EHEC response to nitrosative stress is complex and multifactorial.

Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle

Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH₄⁺) and nitrate (NO₃⁻) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N₂O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N₂O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.

A Complex Interplay between Nitric Oxide, Quorum Sensing, and the Unique Secondary Metabolite Tundrenone Constitutes the Hypoxia Response in Methylobacter

Here, we describe a novel and complex hypoxia response system in a methanotrophic bacterium that involves modules of central carbon metabolism, denitrification, quorum sensing, and a secondary metabolite, tundrenone. This intricate stress response system, so far unique to Methylobacter species, may be responsible for the persistence and activity of these species across gradients of dioxygen tensions and for the cosmopolitan distribution of these organisms in freshwater and soil environments in the Northern Hemisphere, including the fast-melting permafrosts.

Methylobacter species, members of the Methylococcales, have recently emerged as some of the globally widespread, cosmopolitan species that play a key role in the environmental consumption of methane across gradients of dioxygen tensions. In this work, we approached the question of how Methylobacter copes with hypoxia, via laboratory manipulation. Through comparative transcriptomics of cultures grown under high dioxygen partial pressure versus cultures exposed to hypoxia, we identified a gene cluster encoding a hybrid cluster protein along with sensing and regulatory functions. Through mutant analysis, we demonstrated that this gene cluster is involved in the hypoxia stress response. Through additional transcriptomic analyses, we uncovered a complex interconnection between the NO-mediated stress response, quorum sensing, the secondary metabolite tundrenone, and methanol dehydrogenase functions. This novel and complex hypoxia stress response system is so far unique to Methylobacter species, and it may play a role in the environmental fitness of these organisms and in their cosmopolitan environmental distribution.

IMPORTANCE Here, we describe a novel and complex hypoxia response system in a methanotrophic bacterium that involves modules of central carbon metabolism, denitrification, quorum sensing, and a secondary metabolite, tundrenone. This intricate stress response system, so far unique to Methylobacter species, may be responsible for the persistence and activity of these species across gradients of dioxygen tensions and for the cosmopolitan distribution of these organisms in freshwater and soil environments in the Northern Hemisphere, including the fast-melting permafrosts.

Flavohaemoglobin: the pre-eminent nitric oxide-detoxifying machine of microorganisms

Flavohaemoglobins were first described in yeast as early as the 1970s but their functions were unclear. The surge in interest in nitric oxide biology and both serendipitous and hypothesis-driven discoveries in bacterial systems have transformed our understanding of this unusual two-domain globin into a comprehensive, yet undoubtedly incomplete, appreciation of its pre-eminent role in nitric oxide detoxification. Here, I focus on research on the flavohaemoglobins of microorganisms, especially of bacteria, and update several earlier and more comprehensive reviews, emphasising advances over the past 5 to 10 years and some controversies that have arisen. Inevitably, in light of space restrictions, details of nitric oxide metabolism and globins in higher organisms are brief.

Clustering as a Means To Control Nitrate Respiration Efficiency and Toxicity in Escherichia coli

Most bacteria rely on the redox activity of respiratory complexes embedded in the cytoplasmic membrane to gain energy in the form of ATP and of an electrochemical gradient established across the membrane. Nevertheless, production of harmful and toxic nitric oxide by actively growing bacteria as either an intermediate or side-product of nitrate respiration challenges how homeostasis control is exerted. Here, we show that components of the nitrate electron transport chain are clustered, likely influencing the kinetics of the process. Nitric oxide production from this respiratory chain is controlled and handled through a multiprotein complex, including detoxifying systems. These findings point to an essential role of compartmentalization of respiratory components in bacterial cell growth.

Respiration is a fundamental process that has to optimally respond to metabolic demand and environmental changes. We previously showed that nitrate respiration, crucial for gut colonization by enterobacteria, is controlled by polar clustering of the nitrate reductase increasing the electron flux through the complex. Here, we show that the formate dehydrogenase electron-donating complex, FdnGHI, also clusters at the cell poles under nitrate-respiring conditions. Its proximity to the nitrate reductase complex was confirmed by its identification in the interactome of the latter, which appears to be specific to the nitrate-respiring condition. Interestingly, we have identified a multiprotein complex dedicated to handle nitric oxide resulting from the enhanced activity of the electron transport chain terminated by nitrate reductase. We demonstrated that the cytoplasmic NADH-dependent nitrite reductase NirBD and the hybrid cluster protein Hcp are key contributors to regulation of the nitric oxide level during nitrate respiration. Thus, gathering of actors involved in respiration and NO homeostasis seems to be critical to balancing maximization of electron flux and the resulting toxicity.

Acidic pH promotes lipopolysaccharide modification and alters colonization in a bacteria-animal mutualism

Environmental pH can be an important cue for symbiotic bacteria as they colonize their eukaryotic hosts. Using the model mutualism between the marine bacterium Vibrio fischeri and the Hawaiian bobtail squid, we characterized the bacterial transcriptional response to acidic pH experienced during the shift from planktonic to host-associated lifestyles. We found several genes involved in outer membrane structure were differentially expressed based on pH, indicating alterations in membrane physiology as V. fischeri initiates its symbiotic program. Exposure to host-like pH increased the resistance of V. fischeri to the cationic antimicrobial peptide polymixin B, which resembles antibacterial molecules that are produced by the squid to select V. fischeri from the ocean microbiota. Using a forward genetic screen, we identified a homolog of eptA, a predicted phosphoethanolamine transferase, as critical for antimicrobial defense. We used MALDI-MS to verify eptA as an ethanolamine transferase for the lipid-A portion of V. fischeri lipopolysaccharide. We then used a DNA pulldown approach to discover that eptA transcription is activated by the global regulator H-NS. Finally, we revealed that eptA promotes successful squid colonization by V. fischeri, supporting its potential role in initiation of this highly specific symbiosis.

Cooperative Roles of Nitric Oxide-Metabolizing Enzymes To Counteract Nitrosative Stress in Enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) has at least three enzymes, NorV, Hmp, and Hcp, that act independently to lower the toxicity of nitric oxide (NO), a potent antimicrobial molecule. This study aimed to reveal the cooperative roles of these defensive enzymes in EHEC against nitrosative stress. Under anaerobic conditions, combined deletion of all three enzymes significantly increased the NO sensitivity of EHEC determined by the growth at late stationary phase; however, the expression of norV restored the NO resistance of EHEC. On the other hand, the growth of Δhmp mutant EHEC was inhibited after early stationary phase, indicating that NorV and Hmp play a cooperative role in anaerobic growth. Under microaerobic conditions, the growth of Δhmp mutant EHEC was inhibited by NO, indicating that Hmp is the enzyme that protects cells from NO stress under microaerobic conditions. When EHEC cells were exposed to a lower concentration of NO, the NO level in bacterial cells of Δhcp mutant EHEC was higher than those of the other EHEC mutants, suggesting that Hcp is effective at regulating NO levels only at a low concentration. These findings of a low level of NO in bacterial cells with hcp indicate that the NO consumption activity of Hcp was suppressed by Hmp at a low range of NO concentrations. Taken together, these results show that the cooperative effects of NO-metabolizing enzymes are regulated by the range of NO concentrations to which the EHEC cells are exposed.

Hybrid cluster proteins in a photosynthetic microalga

Hybrid cluster proteins (HCPs) are metalloproteins characterized by the presence of an iron-sulfur-oxygen cluster. These proteins occur in all three domains of life. In eukaryotes, HCPs have so far been found only in a few anaerobic parasites and photosynthetic microalgae. With respect to all species harboring an HCP, the green microalga Chlamydomonas reinhardtii stands out by the presence of four HCP genes. The study of the gene and protein structures as well as the phylogenetic analyses strongly support a model in which the HCP family in the alga has emerged from a single gene of alpha proteobacterial origin and then expanded by several rounds of duplications. The spectra and redox properties of HCP1 and HCP3, produced heterologously in Escherichia coli, were analyzed by electron paramagnetic resonance spectroscopy on redox-titrated samples. Both proteins contain a [4Fe-4S]-cluster as well as a [4Fe-2O-2S]-hybrid cluster with paramagnetic properties related to those of HCPs from Desulfovibrio species. Immunoblotting experiments combined with mass spectrometry-based proteomics showed that both nitrate and darkness contribute to the strong upregulation of the HCP levels in C. reinhardtii growing under oxic conditions. The link to the nitrate metabolism is discussed in the light of recent data on the potential role of HCP in S-nitrosylation in bacteria.

How superoxide reductases and flavodiiron proteins combat oxidative stress in anaerobes

Microbial anaerobes are exposed in the natural environment and in their hosts, even if transiently, to fluctuating concentrations of oxygen and its derived reactive species, which pose a considerable threat to their anoxygenic lifestyle. To counteract these stressful conditions, they contain a multifaceted array of detoxifying systems that, in conjugation with cellular repairing mechanisms and in close crosstalk with metal homeostasis, allow them to survive in the presence of O₂ and reactive oxygen species. Some of these systems are shared with aerobes, but two families of enzymes emerged more recently that, although not restricted to anaerobes, are predominant in anaerobic microbes. These are the iron-containing superoxide reductases, and the flavodiiron proteins, endowed with O₂ and/or NO reductase activities, which are the subject of this Review. A detailed account of their physicochemical, physiological and molecular mechanisms will be presented, highlighting their unique properties in allowing survival of anaerobes in oxidative stress conditions, and comparing their properties with the most well-known detoxifying systems.

Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium

Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even higher value due to their catalytic abilities for industrial applications. Desulfovibrio alaskensis is able to capture ionic forms of both of these metals, reduce them and synthesize elemental nanoparticles. Despite this ability, very little is known about the biological pathways involved in the formation of these nanoparticles. Proteomic analysis of D. alaskensis in response to platinum and palladium has highlighted those proteins involved in both the reductive pathways and the wider stress-response system. A core set of 13 proteins was found in both treatments and consisted of proteins involved in metal transport and reduction. There were also seven proteins that were specific to either platinum or palladium. Overexpression of one of these platinum-specific genes, a NiFe hydrogenase small subunit (Dde_2137), resulted in the formation of larger nanoparticles. This study improves our understanding of the pathways involved in the metal resistance mechanism of Desulfovibrio and is informative regarding how we can tailor the bacterium for nanoparticle production, enhancing its application as a bioremediation tool and as a way to capture contaminant metals from the environment.

A comparative proteomic analysis of Desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid

Sulfate reducing bacteria (SRB) can contribute to facilitating serious concrete corrosion through the production of hydrogen sulfide in sewers. Recently, free nitrous acid (FNA) was discovered as a promising antimicrobial agent to inhibit SRB activities thereby limiting hydrogen sulfide production in sewers. However, knowledge of the bacterial response to increasing levels of the antimicrobial agent is unknown. Here we report the proteomic response of Desulfovibrio vulgaris Hildenborough and reveal that the antimicrobial effect of FNA is multi-targeted and dependent on the FNA levels. This was achieved using a sequential window acquisition of all theoretical mass spectrometry analysis to determine protein abundance variations in D. vulgaris during exposure to different FNA concentrations. When exposed to 1.0 μg N/L FNA, nitrite reduction (nitrite reductase) related proteins and nitrosative stress related proteins, including the hybrid cluster protein, showed distinct increased abundances. When exposed to 4.0 and 8.0 μg N/L FNA, increased abundance was detected for proteins putatively involved in nitrite reduction. Abundance of proteins involved in the sulfate reduction pathway (from adenylylphophosulfate to sulfite) and lactate oxidation pathway (from pyruvate to acetate) were initially inhibited in response to FNA at 8 h incubation, and then recovered at 12 h incubation. Lowered ribosomal protein abundance in D. vulgaris was detected, however, total cellular protein levels were mostly constant in the presence or absence of FNA. In addition, this study indicates that proteins coded by genes DVU2543, DVU0772, and DVU3212 potentially participate in resisting oxidative stress with FNA exposure. These findings share new insights for understanding the dynamic responses of D. vulgaris to FNA and could be useful to guide and improve the practical applications of FNA-based technologies for control of sewer corrosion.

The Porphyromonas gingivalis Hybrid Cluster Protein Hcp Is Required for Growth with Nitrite and Survival with Host Cells

Although the periodontal pathogen Porphyromonas gingivalis must withstand high levels of nitrosative stress while in the oral cavity, the mechanisms of nitrosative stress defense are not well understood in this organism. Previously we showed that the transcriptional regulator HcpR plays a significant role in defense, and here we further defined its regulon. Our study shows that hcp (PG0893), a putative nitric oxide (NO) reductase, is the only gene significantly upregulated in response to nitrite (NO₂) and that this regulation is dependent on HcpR. An isogenic mutant deficient in hcp is not able to grow with 200 μM nitrite, demonstrating that the sensitivity of the HcpR mutant is mediated through Hcp. We further define the molecular mechanisms of HcpR interaction with the hcp promoter through mutational analysis of the inverted repeat present within the promoter. Although other putative nitrosative stress protection mechanisms present on the nrfAH operon are also found in the P. gingivalis genome, we show that their gene products play no role in growth of the bacterium with nitrite. As growth of the hcp-deficient strain was also significantly diminished in the presence of a nitric oxide-producing compound, S-nitrosoglutathione (GSNO), Hcp appears to be the primary means by which P. gingivalis responds to NO₂ ^--based stress. Finally, we show that Hcp is required for survival with host cells but that loss of Hcp has no effect on association and entry of P. gingivalis into human oral keratinocytes.

Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases

Anaerobic Ni-containing carbon-monoxide dehydrogenases (Ni-CODHs) catalyze the reversible conversion between carbon monoxide and carbon dioxide as multi-enzyme complexes responsible for carbon fixation and energy conservation in anaerobic microbes. However, few biochemically characterized model enzymes exist, with most Ni-CODHs remaining functionally unknown. Here, we performed phylogenetic and structure-based Ni-CODH classification using an expanded dataset comprised of 1942 non-redundant Ni-CODHs from 1375 Ni-CODH-encoding genomes across 36 phyla. Ni-CODHs were divided into seven clades, including a novel clade. Further classification into 24 structural groups based on sequence analysis combined with structural prediction revealed diverse structural motifs for metal cluster formation and catalysis, including novel structural motifs potentially capable of forming metal clusters or binding metal ions, indicating Ni-CODH diversity and plasticity. Phylogenetic analysis illustrated that the metal clusters responsible for intermolecular electron transfer were drastically altered during evolution. Additionally, we identified novel putative Ni-CODH-associated proteins from genomic contexts other than the Wood–Ljungdahl pathway and energy converting hydrogenase system proteins. Network analysis among the structural groups of Ni-CODHs, their associated proteins and taxonomies revealed previously unrecognized gene clusters for Ni-CODHs, including uncharacterized structural groups with putative metal transporters, oxidoreductases, or transcription factors. These results suggested diversification of Ni-CODH structures adapting to their associated proteins across microbial genomes.

Host-Derived Nitric Oxide and Its Antibacterial Effects in the Urinary Tract

Urinary tract infection (UTI) is one of the most common bacterial infections in humans, and the majority are caused by uropathogenic Escherichia coli (UPEC). The rising antibiotic resistance among UPEC and the frequent failure of antibiotics to effectively treat recurrent UTI and catheter-associated UTI motivate research on alternative ways of managing UTI. Abundant evidence indicates that the toxic radical nitric oxide (NO), formed by activation of the inducible nitric oxide synthase, plays an important role in host defence to bacterial infections, including UTI. The major source of NO production during UTI is from inflammatory cells, especially neutrophils, and from the uroepithelial cells that are known to orchestrate the innate immune response during UTI. NO and reactive nitrogen species have a wide range of antibacterial targets, including DNA, heme proteins, iron-sulfur clusters, and protein thiol groups. However, UPEC have acquired a variety of defence mechanisms for protection against NO, such as the NO-detoxifying enzyme flavohemoglobin and the NO-tolerant cytochrome bd-I respiratory oxidase. The cytotoxicity of NO-derived intermediates is nonspecific and may be detrimental to host cells, and a balanced NO production is crucial to maintain the tissue integrity of the urinary tract. In this review, we will give an overview of how NO production from host cells in the urinary tract is activated and regulated, the effect of NO on UPEC growth and colonization, and the ability of UPEC to protect themselves against NO. We also discuss the attempts that have been made to develop NO-based therapeutics for UTI treatment.

Distinct Nitrite and Nitric Oxide Physiologies in Escherichia coli and Shewanella oneidensis

Nitrite has been used as a bacteriostatic agent for centuries in food preservation. It is widely accepted that this biologically inert molecule functions indirectly, serving as a stable reservoir of bioactive nitric oxide (NO) and other reactive nitrogen species to impact physiology. As a result, to date, we know surprisingly little about in vivo targets of nitrite. Here, we carry out comparative analyses of nitrite and NO physiology in Escherichia coli and in Shewanella oneidensis, a Gram-negative environmental bacterium renowned for respiratory versatility. These two bacteria differ from each other in many aspects of nitrite and NO physiology, including NO generation, NO degradation, and unexpectedly, their contrary susceptibility to nitrite and NO. In cell extracts of both bacteria, most of the NO targets are also susceptible to nitrite, and vice versa. However, with respect to growth inhibition caused by NO, the targets are impacted distinctly; NO targets are responsible for the inhibition of growth of E. coli but not of S. oneidensis More surprisingly, all proteins identified to be implicated in NO tolerance in other bacteria appear to play a dispensable role in protecting S. oneidensis against NO. These data suggest that S. oneidensis is equipped with a robust but yet unknown NO protecting system. In the case of nitrite, it is clear that the target of physiological significance in both bacteria is cytochrome heme-copper oxidase.IMPORTANCE Nitrite is toxic to living organisms at high levels, but such antibacterial effects of nitrite are attributable to the formation of nitric oxide (NO), a highly reactive radical gas molecule. Here, we report that Shewanella oneidensis is highly resistant to NO but sensitive to nitrite compared to Escherichia coli by approximately 4-fold. In both bacteria, nitrite inhibits bacterial growth by targeting cytochrome heme-copper oxidase. In contrast, the targets of NO are diverse. Although these targets are similar in E. coli and S. oneidensis, they are responsible for growth inhibition caused by NO in the former but not in the latter. Overall, the presented data, along with the previous data, solidify a proposal that the in vivo targets of NO and nitrite in bacteria are largely different.

Redox Pathways as Drug Targets in Microaerophilic Parasites

The microaerophilic parasites Entamoeba histolytica, Trichomonas vaginalis, and Giardia lamblia jointly cause hundreds of millions of infections in humans every year. Other microaerophilic parasites such as Tritrichomonas foetus and Spironucleus spp. pose a relevant health problem in veterinary medicine. Unfortunately, vaccines against these pathogens are unavailable, but their microaerophilic lifestyle opens opportunities for specifically developed chemotherapeutics. In particular, their high sensitivity towards oxygen can be exploited by targeting redox enzymes. This review focusses on the redox pathways of microaerophilic parasites and on drugs, either already in use or currently in the state of development, which target these pathways.