Nitric oxide formation by Escherichia coli. Dependence on nitrite reductase, the NO-sensing regulator Fnr, and flavohemoglobin Hmp

Operando Spectroscopic Elucidation of the Bubble Sunshade Effect in Inorganic-Biological Hybrids for Photosynthetic Hydrogen Production

Hydrogen production by photosynthetic hybrid systems (PBSs) offers a promising avenue for renewable energy. However, the light-harvesting efficiency of PBSs remains constrained due to unclear intracellular kinetic factors. Here, we present an operando elucidation of the sluggish light-harvesting behavior for existing PBSs and strategies to circumvent them. By quantifying the spectral shift in the structural color scattering of individual PBSs during the photosynthetic process, we observe the accumulation of product hydrogen bubbles on their outer membrane. These bubbles act as a sunshade and inhibit light absorption. This phenomenon elucidates the intrinsic constraints on the light-harvesting efficiency of PBSs. The introduction of a tension eliminator into the PBSs effectively improves the bubble sunshade effect and results in a 4.5-fold increase in the light-harvesting efficiency. This work provides valuable insights into the dynamics of transmembrane transport gas products and holds the potential to inspire innovative designs for improving the light-harvesting efficiency of PBSs.

Nitrate-dependent anaerobic methane oxidation coupled to Fe(III) reduction as a source of ammonium and nitrous oxide

'Candidatus Methanoperedens nitroreducens' is an archaeal methanotroph with global importance that links carbon and nitrogen cycles and great potential for sustainable operation of wastewater treatment. It has been reported to mediate the anaerobic oxidation of methane through a reverse methanogenesis pathway while reducing nitrate to nitrite. Here, we demonstrate that 'Ca. M. nitroreducens' reduces ferric iron forming ammonium (23.1 %) and nitrous oxide (N2O, 46.5 %) from nitrate. These results are supported with the upregulation of genes coding for proteins responsible for dissimilatory nitrate reduction to ammonium (nrfA), N2O formation (norV, cyt P460), and multiple multiheme c-type cytochromes for ferric iron reduction. Concomitantly, an increase in the N2O-reducing SJA-28 lineage and a decrease in the nitrite-reducing 'Candidatus Methylomirabilis oxyfera' are consistent with the changes in 'Ca. M. nitroreducens' end products. These findings demonstrate the highly flexible physiology of 'Ca. M. nitroreducens' in anaerobic ecosystems with diverse electron acceptor conditions, and further reveals its roles in linking methane oxidation to global biogeochemical cycles. 'Ca. M. nitroreducens' could significantly affect the bioavailability of nitrogen sources as well as the emission of greenhouse gas in natural ecosystems and wastewater treatment plants.

Dietary fibre confers therapeutic effects in a preclinical model of Huntington's disease

Huntington's disease (HD) is a neurodegenerative disorder involving psychiatric, cognitive and motor deficits, as well as peripheral symptoms, including gastrointestinal dysfunction. The R6/1 HD mouse model expresses a mutant human huntingtin transgene and has been shown to provide an accurate disease model. Recent evidence of gut microbiome disruption was shown in preclinical and clinical HD. Therefore, we aimed to assess the potential role of gut microbial modulation in the treatment of HD. The R6/1 HD mice and wild-type littermate controls were randomised to receive diets containing different amounts of fibre: high-fibre (10 % fibre), control (5 % fibre), or zero-fibre (0 % fibre), from 6 to 20 weeks of age. We characterized the onset and progression of motor, cognitive and affective deficits, as well as gastrointestinal function and gut morphological changes. Faeces were collected for gut microbiome profiling using 16S rRNA sequencing, at 14 and 20 weeks of age. When compared to the control diet, high-fibre diet improved the performance of HD mice in behavioral tests of cognitive and affective function, as well as the gastrointestinal function of both HD and wild-type mice. While the diets changed the beta diversity of wild-type mice, no statistical significance was observed at 14 or 20 weeks of age within the HD mice. Analysis of Composition of Microbiomes with Bias Correction (ANCOM-BC) models were performed to evaluate microbiota composition, which identified differences, including a decreased relative abundance of the phyla Actinobacteriota, Campylobacterota and Proteobacteria and an increased relative abundance of the families Bacteroidaceae, Oscillospiraceae and Ruminococcaceae in HD mice when compared to wild-type mice after receiving high-fibre diet. PICRUSt2 revealed that high-fibre diet also decreased potentially pathogenic functional pathways in HD. In conclusion, high-fibre intake was effective in enhancing gastrointestinal function, cognition and affective behaviors in HD mice. These findings indicate that dietary fibre interventions may have therapeutic potential in Huntington's disease to delay clinical onset, and have implications for related disorders exhibiting dysfunction of the gut-brain axis.

Engineering and Characterization of 3-Aminotyrosine-Derived Red Fluorescent Variants of Circularly Permutated Green Fluorescent Protein

Introducing 3-aminotyrosine (aY), a noncanonical amino acid (ncAA), into green fluorescent protein (GFP)-like chromophores shows promise for achieving red-shifted fluorescence. However, inconsistent results, including undesired green fluorescent species, hinder the effectiveness of this approach. In this study, we optimized expression conditions for an aY-derived cpGFP (aY-cpGFP). Key factors like rich culture media and oxygen restriction pre- and post-induction enabled high-yield, high-purity production of the red-shifted protein. We also engineered two variants of aY-cpGFP with enhanced brightness by mutating a few amino acid residues surrounding the chromophore. We further investigated the sensitivity of the aY-derived protein to metal ions, reactive oxygen species (ROS), and reactive nitrogen species (RNS). Incorporating aY into cpGFP had minimal impact on metal ion reactivity but increased the response to RNS. Expanding on these findings, we examined aY-cpGFP expression in mammalian cells and found that reductants in the culture media significantly increased the red-emitting product. Our study indicates that optimizing expression conditions to promote a reduced cellular state proved effective in producing the desired red-emitting product in both E. coli and mammalian cells, while targeted mutagenesis-based protein engineering can further enhance brightness and increase method robustness.

Influence of C/N ratio and ammonia on nitrogen removal and N2O emissions from one-stage partial denitrification coupled with anammox

The development of low carbon treatment processes is an important issue worldwide. Partial denitrification coupled with anammox (PD/A) is a novel strategy to remove nitrogen and reduce N2O emissions. The influence of C/N ratio and NH4+ concentration on nitrogen removal and N2O emissions was investigated in batch reactors filled with PD/A coupled sludge. A C/N ratio of 2.1 was effective for nitrogen removal and N2O reduction; higher ammonia concentration might make anammox more active and indirectly reduce N2O emissions. Long-term operation further confirmed that a C/N ratio of 2.1 resulted in a minimum effluent N2O concentration (mean value of 0.94 μmol L-1); as the influent NH4+ concentration decreased to 50 mg L-1 (NH4+-N/NO3--N: 1), the nitrogen removal rate increased to 82.41%. Microbial analysis showed that anammox bacteria (Candidatus Jettenia and Ca. Brocadia) were enriched in the PD/A system and Ca. Brocadia gradually dominated the anammox community, with the relative abundance increasing from 1.69% to 18.44% between days 97 and 141. Finally, functional gene analysis indicated that the abundance of nirS/K and hao involved in partial denitrification and anammox, respectively, increased during long-term operation of the reactor; this change benefitted nitrogen metabolism in anammox, which could indirectly reduce N2O emissions.

Mycothiol maintains the homeostasis and signalling of nitric oxide in Streptomyces coelicolor A3(2) M145

BACKGROUND

Previous studies have revealed a nitric oxide (NO) metabolic cycle in which NO, nitrate (NO3-), and nitrite (NO2-) circulate. The NO produced in this cycle serves as a signalling molecule that regulates actinorhodin (ACT) production via the DevS/DevR NO-dependent two-component system (TCS) in Streptomyces coelicolor A3(2) M145. However, the mechanisms involved in the regulation of NO signalling in S. coelicolor have not yet been elucidated. Mycothiol (MSH), a thiol molecule produced by Actinomyces, is involved in the defence mechanisms against oxidative stress. Therefore, this study focused on the correlation between intracellular NO and MSH levels.

RESULTS

To investigate the interaction of MSH with endogenously produced NO, we generated an S. coelicolor A3(2) strain deficient in MSH biosynthesis. This mutant strain exhibited a decrease in low-molecular-weight S-nitrosothiols and intracellular NO levels during culture compared to those of the wild-type strain. Moreover, the mutant strain exhibited reduced activity of the DevS/DevR TCS, a regulator of NO homeostasis and ACT production, from the early stage of culture, along with a decrease in ACT production compared to those of the wild-type strain.

CONCLUSIONS

This study suggests that MSH maintains intracellular NO homeostasis by forming S-nitrosomycothiol, which induces NO signalling. Finally, we propose a metabolic model in which MSH from endogenously produced NO facilitates the maintenance of both NO homeostasis and signalling in S. coelicolor A3(2) M145.

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.

Reductases Produce Nitric Oxide in an Alternative Pathway to Form the Diazeniumdiolate Group of l-Alanosine

l-Alanosine is a diazeniumdiolate (N-nitrosohydroxylamine) antibiotic that inhibits MTAP-deficient tumor cells by blocking de novo adenine biosynthesis. Previous work revealed the early steps in the biosynthesis of l-alanosine. In the present study, we used genome mining to discover two new l-alanosine-producing strains that lack the aspartate-nitrosuccinate pathway genes found in the original l-alanosine producer. Instead, nitrate is reduced with a unique set of nitrate-nitrite reductases. These enzymes are typically used as part of the nitrogen cycle for denitrification or assimilation, and our report here shows how enzymes from the nitrogen cycle can be repurposed for the biosynthesis of specialized metabolites. The widespread distribution of nitric-oxide-producing reductases also indicates a potential for the discovery of new nitric-oxide-derived natural products.

Nitric oxide is a host cue for Salmonella Typhimurium systemic infection in mice

Nitric oxide (NO) is produced as an innate immune response against microbial infections. Salmonella Typhimurium (S. Typhimurium), the major causative pathogen of human gastroenteritis, induces more severe systemic disease in mice. However, host factors contributing to the difference in species-related virulence are unknown. Here, we report that host NO production promotes S. Typhimurium replication in mouse macrophages at the early infection stage by activating Salmonella pathogenicity island-2 (SPI-2). The NO signaling-induced SPI-2 activation is mediated by Fnr and PhoP/Q two-component system. NO significantly induced fnr transcription, while Fnr directly activated phoP/Q transcription. Mouse infection assays revealed a NO-dependent increase in bacterial burden in systemic organs during the initial days of infection, indicating an early contribution of host NO to virulence. This study reveals a host signaling-mediated virulence activation pathway in S. Typhimurium that contributes significantly to its systemic infection in mice, providing further insights into Salmonella pathogenesis and host-pathogen interaction.

Mycobacterium smegmatis strains genetically resistant to moxifloxacin emerge de novo from the moxifloxacin-surviving population containing high levels of superoxide, H2O2, hydroxyl radical, and Fe (II)

Background

The antibiotic-exposed bacteria often contain the reactive oxygen species (ROS), hydroxyl radical, which inflicts genome-wide mutations, causing the de novo formation of antibiotic-resistant strains. Hydroxyl radical is generated by Fenton reaction of Fe (II) with the ROS, H₂O₂, which, in turn, is formed by the dismutation of the ROS, superoxide. Therefore, for the emergence of bacterial strains genetically resistant to antibiotics, increased levels of superoxide, H₂O₂, hydroxyl radical, and Fe (II) should be present in the antibiotic-exposed bacteria. Here, we verified this premise by finding out whether the in vitro cultures of M. smegmatis, exposed to MBC of moxifloxacin for a prolonged duration, contain significantly high levels of superoxide, H₂O₂, hydroxyl radical, and Fe (II).

Methods

Biological triplicate cultures of M. smegmatis, were exposed to MBC of moxifloxacin for 84 h. The colony-forming units (CFUs) of the cultures were determined on moxifloxacin-free and moxifloxacin-containing plates for the entire 84 h at a regular interval of 6 h. The cultures were analyzed at specific time points of killing phase (KP), antibiotic-surviving phase (ASP), and regrowth phase (RGP) for the presence of superoxide, H₂O₂, hydroxyl radical, and Fe (II) using the ROS- and Fe (II)-detecting fluorescence probes. The experimental cultures were grown in the presence of ROS and Fe (II) quenchers also and determined the levels of fluorescence corresponding to the ROS- and Fe (II)-specific probes. This was performed to establish the specificity of detection of ROS and Fe (II). Biological triplicate cultures, unexposed to moxifloxacin but cultured for 84 h, were used as the control for the measurement of ROS and Fe (II) levels. The CFUs of the cultures were determined on moxifloxacin-free and moxifloxacin-containing plates for the entire 84 h at regular intervals of 6 h. Flow cytometry analyses were performed for the detection and quantitation of the levels of fluorescence of the ROS-and Fe (II)-specific probes. The experimental cultures were grown in the presence of thiourea and bipyridyl as the ROS and Fe (II) quenchers, respectively, for the determination of the levels of fluorescence corresponding to the ROS- and Fe (II)-specific probes. Paired t-test was used to calculate statistical significance (n = 3).

Results

The moxifloxacin-exposed cultures, but not the cultures unexposed to moxifloxacin, showed a triphasic response with a KP, ASP, and RGP. The cells in the late KP and ASP contained significantly elevated levels of superoxide, H₂O₂, hydroxyl radical, and Fe (II). Thus, high levels of the ROS and Fe (II) were found in the small population (in the ASP) of M. smegmatis cells that survived the moxifloxacin-mediated killing. From this moxifloxacin-surviving population (in the ASP), moxifloxacin-resistant genetic resisters emerged de novo at high frequency, regrew, divided, and populated the cultures. The levels of these ROS, Fe (II), and the high moxifloxacin resister generation frequency were quenched in the cultures grown in the presence of the respective ROS and Fe (II) quenchers. The cultures unexposed to moxifloxacin did not show any of these responses, indicating that the whole response was specific to antibiotic exposure.

Conclusions

Significantly high levels of superoxide, H₂O₂, hydroxyl radical, and Fe (II) were generated in the M. smegmatis cultures exposed to moxifloxacin for a prolonged duration. It promoted the de novo emergence of genetic resisters to moxifloxacin at high frequency.

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.

Nitric Oxide Signaling for Actinorhodin Production in Streptomyces coelicolor A3(2) via the DevS/R Two-Component System

Nitric oxide (NO) is an important signaling molecule in eukaryotic and prokaryotic cells. A previous study revealed an NO synthase-independent NO production metabolic cycle in which the three nitrogen oxides, nitrate (NO₃^-), nitrite (NO₂^-), and NO, were generated in the actinobacterium Streptomyces coelicolor A3(2). NO was suggested to act as a signaling molecule, functioning as a hormone that regulates secondary metabolism. Here, we demonstrate the NO-mediated regulation of the production of the blue-pigmented antibiotic actinorhodin (ACT), via the heme-based DevS/R two-component system (TCS). Intracellular NO controls the stabilization or inactivation of DevS, depending on the NO concentration. An electrophoretic mobility shift assay and chromatin immunoprecipitation-quantitative PCR analysis revealed the direct binding between DevR and the promoter region of actII-ORF4, resulting in gene expression. Our results indicate that NO regulates the DevS/R TCS, thereby strictly controlling the secondary metabolism of S. coelicolor A3(2). IMPORTANCE Diverse organisms, such as mammals, plants, and bacteria, utilize NO via well-known signal transduction mechanisms. Many useful secondary metabolite-producing bacteria of the Streptomyces genus had been also suggested for the metabolism regulated by endogenously produced NO; however, the regulatory mechanisms remain to be elucidated. In this study, we demonstrated the molecular mechanism by which endogenously produced NO regulates antibiotic production via the DevS/R TCS in S. coelicolor A3(2). NO serves as both a stabilizer and a repressor in the regulation of antibiotic production. This report shows the mechanism by which Streptomyces utilizes endogenously produced NO to modulate its normal life cycle. Moreover, this study implies that studying NO signaling in actinobacteria can help in the development of both clinical strategies against pathogenic actinomycetes and the actinobacterial industries.

Refinement of the Griess method for measuring nitrite in biological samples

Nitric oxide (NO) is a reactive gas that participates in many physiological as well as pathogenic processes in higher eukaryotic organisms. Inflammatory responses elicit higher levels of this molecule. Nevertheless, there are many technical challenges to accurately measure the amount of NO produced. Previously, a method using whole-cell extracts from Escherichia coli was able to generate the conversion of nitrate into nitrite to measure the amount of nitrate or indirectly the NO present in a sample using the Griess reaction. Here we present an improvement to this method, by using E. coli whole-cell extracts lacking one of the two nitrite reductases, rendered a more precise measurement when coupled with the Griess reaction than our previous report. Alternatively, osmotic stress showed to downregulate the expression of both nitrate reductases, which can be an alternative for indirect nitrate and NO reduction. The results presented here show an easy method for nitrate and NO reduction to nitrite and avoid the reconversion to nitrate, also as an alternative for other analytical methods that are based on cadmium, purified nitrate reductase enzyme, or salicylic methods to reduce NO. This method can be widely used for measuring NO production in living organisms, soil, and other relevant microbiological samples.

Mechanism of deoxynivalenol mediated gastrointestinal toxicity: Insights from mitochondrial dysfunction

Deoxynivalenol (DON) is a mycotoxin predominantly produced by Fusarium genus, and widely contaminates cereals and associated products all over the world. The intestinal toxicity of DON is well established. However, intestinal homeostasis involves mitochondria, which has rarely been considered in the context of DON exposure. We summarize the recent knowledge on mitochondria as a key player in maintaining intestinal homeostasis based on their functions in cellular energy metabolism, redox homeostasis, apoptosis, intestinal immune responses, and orchestrated bidirectional cross-talk with gut microbe. In addition, we discuss the pivotal roles of mitochondrial dysfunction in the intestinal toxicity of DON and highlight promising mitochondrial-targeted therapeutics for DON-induced intestinal injury. Recent studies support that the intestinal toxicity of DON is attributed to mitochondrial dysfunction as a critical factor. Mitochondrial dysfunction characterized by failure in respiratory capacities and ROS overproduction has been demonstrated in intestinal cells exposed to DON. Perturbation of mitochondrial respiration leading to ROS accumulation is implicated in the early initiation of apoptosis. DON-induced intestinal inflammatory response is tightly linked to the mitochondrial ROS, whereas immunosuppression is intimately associated with mitophagy inhibition. DON perturbs the orchestrated bidirectional cross-talk between gut microbe and host mitochondria, which may be involved in DON-induced intestinal toxicity.

Lifestyle-specific S-nitrosylation of protein cysteine thiols regulates Escherichia coli biofilm formation and resistance to oxidative stress

Communities of bacteria called biofilms are characterized by reduced diffusion, steep oxygen, and redox gradients and specific properties compared to individualized planktonic bacteria. In this study, we investigated whether signaling via nitrosylation of protein cysteine thiols (S-nitrosylation), regulating a wide range of functions in eukaryotes, could also specifically occur in biofilms and contribute to bacterial adaptation to this widespread lifestyle. We used a redox proteomic approach to compare cysteine S-nitrosylation in aerobic and anaerobic biofilm and planktonic Escherichia coli cultures and we identified proteins with biofilm-specific S-nitrosylation status. Using bacterial genetics and various phenotypic screens, we showed that impairing S-nitrosylation in proteins involved in redox homeostasis and amino acid synthesis such as OxyR, KatG, and GltD altered important biofilm properties, including motility, biofilm maturation, or resistance to oxidative stress. Our study therefore revealed that S-nitrosylation constitutes a physiological basis underlying functions critical for E. coli adaptation to the biofilm environment.

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.

Nitrite reduction in fermented meat products and its impact on aroma

Fermented meat products are important not only for their sensory characteristics, nutrient content and cultural heritage, but also for their stability and convenience. The aroma of fermented meat products is unique and its formation mechanisms are not completely understood; however, the presence of nitrite and nitrate is essential for the development of cured aroma. The use of nitrite and nitrate as curing agents in meat products is based on its preservation activity. Even though their presence has been associated with several risks due to the formation of nitrosamines, their use is guarantee due to their antimicrobial action against Clostridium botulinum. Recent trends and recommendations by international associations are directed to use nitrite but at the minimum concentration necessary to provide the antimicrobial activity against Clostridium botulinum. This chapter discuss the actual limits of nitrite and nitrite content and their role as curing agents in meat products with special impact on dry fermented products. Regulatory considerations, antimicrobial mechanisms and actual trends regarding nitrite reduction and its effect on sensory and aroma properties are also considered.

Involvement of NO3 - in Ecophysiological Regulation of Dissimilatory Nitrate/Nitrite Reduction to Ammonium (DNRA) Is Implied by Physiological Characterization of Soil DNRA Bacteria Isolated via a Colorimetric Screening Method

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) has recently regained attention as a nitrogen retention pathway that may potentially be harnessed to alleviate nitrogen loss resulting from denitrification. Until recently, the ecophysiology of DNRA bacteria inhabiting agricultural soils has remained largely unexplored, due to the difficulty in targeted enrichment and isolation of DNRA microorganisms. In this study, >100 DNRA bacteria were isolated from NO₃ ^--reducing anoxic enrichment cultures established with rice paddy soils using a newly developed colorimetric screening method. Six of these isolates, each assigned to a different genus, were characterized to improve the understanding of DNRA physiology. All the isolates carried nrfA and/or nirB, and the Bacillus sp. strain possessed a clade II nosZ gene conferring the capacity for N₂O reduction. A common prominent physiological feature observed in the isolates was NO₂ ^- accumulation before NH₄ ⁺ production, which was further examined with Citrobacter sp. strain DNRA3 (possessing nrfA and nirB) and Enterobacter sp. strain DNRA5 (possessing only nirB). Both isolates showed inhibition of NO₂ ^--to-NH₄ ⁺ reduction at submillimolar NO₃ ^- concentrations and downregulation of nrfA or nirB transcription when NO₃ ^- was being reduced to NO₂ ^- In batch and chemostat experiments, both isolates produced NH₄ ⁺ from NO₃ ^- reduction when incubated with excess organic electron donors, while incubation with excess NO₃ ^- resulted in NO₂ ^- buildup but no substantial NH₄ ⁺ production, presumably due to inhibitory NO₃ ^- concentrations. This previously overlooked link between NO₃ ^- repression of NO₂ ^--to-NH₄ ⁺ reduction and the C-to-N ratio regulation of DNRA activity may be a key mechanism underpinning denitrification-versus-DNRA competition in soil.IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is an anaerobic microbial pathway that competes with denitrification for common substrates NO₃ ^- and NO₂ ^- Unlike denitrification, which leads to nitrogen loss and N₂O emission, DNRA reduces NO₃ ^- and NO₂ ^- to NH₄ ⁺, a reactive nitrogen compound with a higher tendency to be retained in the soil matrix. Therefore, stimulation of DNRA has often been proposed as a strategy to improve fertilizer efficiency and reduce greenhouse gas emissions. Such attempts have been hampered by lack of insights into soil DNRA bacterial ecophysiology. Here, we have developed a new screening method for isolating DNRA-catalyzing organisms from agricultural soils without apparent DNRA activity. Physiological characteristics of six DNRA isolates were closely examined, disclosing a previously overlooked link between NO₃ ^- repression of NO₂ ^--to-NH₄ ⁺ reduction and the C-to-N ratio regulation of DNRA activity, which may be a key to understanding why DNRA activity is rarely observed at substantial levels in nitrogen-rich agricultural soils.

The Nitrite Transporter Facilitates Biofilm Formation via Suppression of Nitrite Reductase and Is a New Antibiofilm Target in Pseudomonas aeruginosa

Bacterial biofilms play roles in infections and avoidance of host defense mechanisms of medically important pathogens and increase the antibiotic resistance of the bacteria. Nitric oxide (NO) is reported to be involved in both biofilm formation and dispersal, which are conflicting processes. The mechanism by which NO regulates biofilm dispersal is relatively understood, but there are no reports about how NO is involved in biofilm formation. Here, by investigating the mechanism by which complestatin inhibits biofilm formation, we describe a novel mechanism for governing biofilm formation in Escherichia coli and Pseudomonas aeruginosa. Nitrite transporter is required for biofilm formation via regulation of NO levels and subsequent c-di-GMP production. Additionally, the nitrite transporter contributes more to P. aeruginosa virulence than quorum sensing. Thus, this study identifies nitrite transporters as new antibiofilm targets for future practical and therapeutic agent development.

Biofilm-forming bacteria, including the Gram-negative Pseudomonas aeruginosa, cause multiple types of chronic infections and are responsible for serious health burdens in humans, animals, and plants. Nitric oxide (NO) has been shown to induce biofilm dispersal via triggering a reduction in cyclic-di-GMP levels in a variety of bacteria. However, how NO, at homeostatic levels, also facilitates biofilm formation is unknown. Here, we found that complestatin, a structural analog of vancomycin isolated from Streptomyces, inhibits P. aeruginosa biofilm formation by upregulating NO production via nitrite reductase (NIR) induction and c-di-GMP degradation via phosphodiesterase (PDE) stimulation. The complestatin protein target was identified as a nitrite transporter from a genome-wide screen using the Keio Escherichia coli knockout library and confirmed using nitrite transporter knockout and overexpression strains. We demonstrated that the nitrite transporter stimulated biofilm formation by controlled NO production via appropriate NIR suppression and subsequent diguanylate cyclase (DGC) activation, not PDE activity, and c-di-GMP production in E. coli and P. aeruginosa. Thus, this study provides a mechanism for NO-mediated biofilm formation, which was previously not understood.

Comparative Proteomic Analysis of Adhesion/Invasion Related Proteins in Cronobacter sakazakii Based on Data-Independent Acquisition Coupled With LC-MS/MS

Cronobacter sakazakii is foodborne pathogen that causes serious illnesses such as necrotizing enterocolitis, meningitis and septicemia in infants. However, the virulence determinants and mechanisms of pathogenicity of these species remain unclear. In this study, multilocus sequence typing (MLST) was performed on 34 C. sakazakii strains and two strains with the same sequence type (ST) but distinct adhesion/invasion capabilities were selected for identification of differentially expressed proteins using data-independent acquisition (DIA) proteomic analysis. A total of 2,203 proteins were identified and quantified. Among these proteins, 210 exhibited differential expression patterns with abundance ratios ≥3 or ≤0.33 and P values ≤0.05. Among these 210 proteins, 67 were expressed higher, and 143 were expressed lower in C. sakazakii SAKA80220 (strongly adhesive/invasive strain) compared with C. sakazakii SAKA80221 (weakly adhesive/invasive strain). Based on a detailed analysis of the differentially expressed proteins, the highly expressed genes involved in flagellar assembly, lipopolysaccharide synthesis, LuxS/AI-2, energy metabolic pathways and iron-sulfur cluster may be associated with the adhesion/invasion capability of C. sakazakii. To verify the accuracy of the proteomic results, real-time qPCR was used to analyze the expression patterns of some genes at the transcriptional level, and consistent results were observed. This study, for the first time, used DIA proteomic to investigate potential adhesion/invasion related factors as a useful reference for further studies on the pathogenic mechanism of C. sakazakii.

Anaerobic Transcription by OxyR: A Novel Paradigm for Nitrosative Stress

Significance: S-nitrosylation, the post-translational modification by nitric oxide (NO) to form S-nitrosothiols (SNOs), regulates diverse aspects of cellular function, and aberrant S-nitrosylation (nitrosative stress) is implicated in disease, from neurodegeneration to cancer. Essential roles for S-nitrosylation have been demonstrated in microbes, plants, and animals; notably, bacteria have often served as model systems for elucidation of general principles. Recent Advances: Recent conceptual advances include the idea of a molecular code through which proteins sense and differentiate S-nitrosothiol (SNO) from alternative oxidative modifications, providing the basis for specificity in SNO signaling. In Escherichia coli, S-nitrosylation relies on an enzymatic cascade that regulates, and is regulated by, the transcription factor OxyR under anaerobic conditions. S-nitrosylated OxyR activates an anaerobic regulon of >100 genes that encode for enzymes that both mediate S-nitrosylation and protect against nitrosative stress. Critical Issues: Mitochondria originated from endosymbiotic bacteria and generate NO under hypoxic conditions, analogous to conditions in E. coli. Nitrosative stress in mitochondria has been implicated in Alzheimer's and Parkinson's disease, among others. Many proteins that are S-nitrosylated in mitochondria are also S-nitrosylated in E. coli. Insights into enzymatic regulation of S-nitrosylation in E. coli may inform the identification of disease-relevant regulatory machinery in mammalian systems. Future Directions: Using E. coli as a model system, in-depth analysis of the anaerobic response controlled by OxyR may lead to the identification of enzymatic mechanisms regulating S-nitrosylation in particular, and hypoxic signaling more generally, providing novel insights into analogous mechanisms in mammalian cells and within dysfunctional mitochondria that characterize neurodegenerative diseases.

Quantitative Modeling Extends the Antibacterial Activity of Nitric Oxide

Numerous materials have been developed to try and harness the antimicrobial properties of nitric oxide (NO). However, the short half-life and reactivity of NO have made precise, tunable delivery difficult. As such, conventional methodologies have generally relied on donors that spontaneously release NO at different rates, and delivery profiles have largely been constrained to decaying dynamics. In recent years, the possibility of finely controlling NO release, for instance with light, has become achievable and this raises the question of how delivery dynamics influence therapeutic potential. Here we investigated this relationship using Escherichia coli as a model organism and an approach that incorporated both experimentation and mathematical modeling. We found that the best performing delivery mode was dependent on the NO payload, and developed a mathematical model to quantitatively dissect those observations. Those analyses suggested that the duration of respiratory inhibition was a major determinant of NO-induced growth inhibition. Inspired by this, we constructed a delivery schedule that leveraged that insight to extend the antimicrobial activity of NO far beyond what was achievable by traditional delivery dynamics. Collectively, these data and analyses suggest that the delivery dynamics of NO have a considerable impact on its ability to achieve and maintain bacteriostasis.

The nature of the electron acceptor (MnIV/NO3) triggers the differential expression of genes associated with stress and ammonium limitation responses in Shewanella algae C6G3

Shewanella algae C6G3 can dissimilatively reduce nitrate into ammonium and manganese oxide (MnIV) into MnII. It has the unusual ability to anaerobically produce nitrite from ammonium in the presence of MnIV. To gain insight into their metabolic capabilities, global mRNA expression patterns were investigated by RNA-seq and qRT-PCR in cells growing with lactate and ammonium as carbon and nitrogen sources, and with either MnIV or nitrate as electron acceptors. Genes exhibiting higher expression levels in the presence of MnIV belonged to functional categories of carbohydrate, coenzyme, lipid metabolisms and inorganic ion transport. The comparative transcriptomic pattern between MnIV and NO3 revealed that the strain presented an ammonium limitation status with MnIV, despite the presence of a non-limiting concentration of ammonium under both culture conditions. In addition, in the presence of MnIV, ntrB/nrtC regulators, ammonium channel, nitrogen regulatory protein P-II, glutamine synthetase and asparagine synthetase glutamine-dependent genes were over-represented. Under the nitrate condition, the expression of genes involved in the synthesis of several amino acids was increased. Finally, the expression level of genes associated with the general stress response was also amplified in both conditions and among them, katE, a putative catalase/peroxidase present on several Shewanella genomes, was highly expressed with a median value relatively higher in the MnIV condition.

Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms

The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.

Dioxygen controls the nitrosylation reactions of a protein-bound [4Fe4S] cluster

Iron–sulfur clusters are exceptionally tuneable protein cofactors, and as one of their many roles they are involved in biological responses to nitrosative stress.

Influence of nitrate and nitrite concentration on N2 O production via dissimilatory nitrate/nitrite reduction to ammonium in Bacillus paralicheniformis LMG 6934

Until now, the exact mechanisms for N2 O production in dissimilatory nitrate/nitrite reduction to ammonium (DNRA) remain underexplored. Previously, we investigated this mechanism in Bacillus licheniformis and Bacillus paralicheniformis, ubiquitous gram-positive bacteria with many industrial applications, and observed significant strain dependency and media dependency in N2 O production which was thought to correlate with high residual NO2- . Here, we further studied the influence of several physicochemical factors on NO3- (or NO2- ) partitioning and N2 O production in DNRA to shed light on the possible mechanisms of N2 O production. The effects of NO3- concentrations under variable or fixed C/N-NO3- ratios, NO2- concentrations under variable or fixed C/N-NO2- ratios, and NH4+ concentrations under fixed C/N-NO3- ratios were tested during anaerobic incubation of soil bacterium B. paralicheniformis LMG 6934 (previously known as B. licheniformis), a strain with a high nitrite reduction capacity. Monitoring of growth, NO3- , NO2- , NH4+ concentration, and N2 O production in physiological tests revealed that NO3- as well as NO2- concentration showed a linear correlation with N2 O production. Increased NO3- concentration under fixed C/N-NO3- ratios, NO2- concentration, and NH4+ concentration had a significant positive effect on NO3- (or NO2- ) partitioning ([N-NH4+ ]/[N-N2 O]) toward N2 O, which may be a consequence of the (transient) accumulation and subsequent detoxification of NO2- . These findings extend the information on several physiological parameters affecting DNRA and provide a basis for further study on N2 O production during this process.

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.

Anaerobic Bacterial Response to Nitrosative Stress

This chapter provides an overview of current knowledge of how anaerobic bacteria protect themselves against nitrosative stress. Nitric oxide (NO) is the primary source of this stress. Aerobically its removal is an oxidative process, whereas reduction is required anaerobically. Mechanisms required to protect aerobic and anaerobic bacteria are therefore different. Several themes recur in the review. First, how gene expression is regulated often provides clues to the physiological function of the gene products. Second, the physiological significance of reports based upon experiments under extreme conditions that bacteria do not encounter in their natural environment requires reassessment. Third, responses to the primary source of stress need to be distinguished from secondary consequences of chemical damage due to failure of repair mechanisms to cope with extreme conditions. NO is generated by many mechanisms, some of which remain undefined. An example is the recent demonstration that the hybrid cluster protein combines with YtfE (or RIC protein, for repair of iron centres damaged by nitrosative stress) in a new pathway to repair key iron-sulphur proteins damaged by nitrosative stress. The functions of many genes expressed in response to nitrosative stress remain either controversial or are completely unknown. The concentration of NO that accumulates in the bacterial cytoplasm is essentially unknown, so dogmatic statements cannot be made that damage to transcription factors (Fur, FNR, SoxRS, MelR, OxyR) occurs naturally as part of a physiologically relevant signalling mechanism. Such doubts can be resolved by simple experiments to meet six proposed criteria.

Affected energy metabolism under manganese stress governs cellular toxicity

Excessive manganese exposure is toxic, but a comprehensive biochemical picture of this assault is poorly understood. Whether oxidative stress or reduced energy metabolism under manganese exposure causes toxicity is still a debate. To address this, we chose ΔmntPEscherichia coli, a highly manganese-sensitive strain, in this study. Combining microarray, proteomics, and biochemical analyses, we show that the chronic manganese exposure rewires diverse regulatory and metabolic pathways. Manganese stress affects protein and other macromolecular stability, and envelope biogenesis. Most importantly, manganese exposure disrupts both iron-sulfur cluster and heme-enzyme biogenesis by depleting cellular iron level. Therefore, the compromised function of the iron-dependent enzymes in the tricarboxylic acid cycle, and electron transport chain impede ATP synthesis, leading to severe energy deficiency. Manganese stress also evokes reactive oxygen species, inducing oxidative stress. However, suppressing oxidative stress does not improve oxidative phosphorylation and cell growth. On the contrary, iron supplementation resumed cell growth stimulating oxidative phosphorylation. Therefore, we hypothesize that affected energy metabolism is the primal cause of manganese toxicity.

Determination of NO and CSF Levels Produced by Bacillus subtilis

The cell-to-cell communication and division of labour that occurs inside a beneficial biofilm produce significant differences in gene expression compared with the gene expression pattern of cells grew under planktonic conditions. In this sense, the levels of NO (nitric oxide) and CSF (Competence Sporulation Stimulating Factor) produced in Bacillus subtilis cultures have been measured only under planktonic growth conditions. We sought to determine whether NO and/or CSF production is affected in B. subtilis cells that develop as a biofilm. To measure the production levels of the two prolongevity molecules, we grew B. subtilis cells under planktonic and biofilm supporting condition.

Bacillus subtilis biofilm extends Caenorhabditis elegans longevity through downregulation of the insulin-like signalling pathway

Beneficial bacteria have been shown to affect host longevity, but the molecular mechanisms mediating such effects remain largely unclear. Here we show that formation of Bacillus subtilis biofilms increases Caenorhabditis elegans lifespan. Biofilm-proficient B. subtilis colonizes the C. elegans gut and extends worm lifespan more than biofilm-deficient isogenic strains. Two molecules produced by B. subtilis — the quorum-sensing pentapeptide CSF and nitric oxide (NO) — are sufficient to extend C. elegans longevity. When B. subtilis is cultured under biofilm-supporting conditions, the synthesis of NO and CSF is increased in comparison with their production under planktonic growth conditions. We further show that the prolongevity effect of B. subtilis biofilms depends on the DAF-2/DAF-16/HSF-1 signalling axis and the downregulation of the insulin-like signalling (ILS) pathway.

Probiotic bacteria can improve host health, but the mechanisms underlying such beneficial effects are often unclear. Here, the authors show that biofilm formation of the probiotic bacterium B. subtilis extends the lifespan of its host, the nematode C. elegans, by reducing insulin-like signalling.

Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment

Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.

New Methyloceanibacter diversity from North Sea sediments includes methanotroph containing solely the soluble methane monooxygenase

Marine methylotrophs play a key role in the global carbon cycle by metabolizing reduced one-carbon compounds that are found in high concentrations in marine environments. Genome, physiology and diversity studies have been greatly facilitated by the numerous model organisms brought into culture. However, the availability of marine representatives remains poor. Here, we report the isolation of four novel species from North Sea sediment enrichments closely related to the Alphaproteobacterium Methyloceanibacter caenitepidi. Each of the newly isolated Methyloceanibacter species exhibited a clear genome sequence divergence which was reflected in physiological differences. Notably one strain R-67174 was capable of oxidizing methane as sole source of carbon and energy using solely a soluble methane monooxygenase and represents the first marine Alphaproteobacterial methanotroph brought into culture. Differences in maximum cell density of >1.5 orders of magnitude were observed. Furthermore, three strains were capable of producing nitrous oxide from nitrate. Together, these findings highlight the metabolic and physiologic variability within closely related Methyloceanibacter species and provide a new understanding of the physiological basis of marine methylotrophy.

Proteomic Analyses Reveal the Mechanism of Dunaliella salina Ds-26-16 Gene Enhancing Salt Tolerance in Escherichia coli

We previously screened the novel gene Ds-26-16 from a 4 M salt-stressed Dunaliella salina cDNA library and discovered that this gene conferred salt tolerance to broad-spectrum organisms, including E. coli (Escherichia coli), Haematococcus pluvialis and tobacco. To determine the mechanism of this gene conferring salt tolerance, we studied the proteome of E. coli overexpressing the full-length cDNA of Ds-26-16 using the iTRAQ (isobaric tags for relative and absolute quantification) approach. A total of 1,610 proteins were identified, which comprised 39.4% of the whole proteome. Of the 559 differential proteins, 259 were up-regulated and 300 were down-regulated. GO (gene ontology) and KEGG (Kyoto encyclopedia of genes and genomes) enrichment analyses identified 202 major proteins, including those involved in amino acid and organic acid metabolism, energy metabolism, carbon metabolism, ROS (reactive oxygen species) scavenging, membrane proteins and ABC (ATP binding cassette) transporters, and peptidoglycan synthesis, as well as 5 up-regulated transcription factors. Our iTRAQ data suggest that Ds-26-16 up-regulates the transcription factors in E. coli to enhance salt resistance through osmotic balance, energy metabolism, and oxidative stress protection. Changes in the proteome were also observed in E. coli overexpressing the ORF (open reading frame) of Ds-26-16. Furthermore, pH, nitric oxide and glycerol content analyses indicated that Ds-26-16 overexpression increases nitric oxide content but has no effect on glycerol content, thus confirming that enhanced nitric oxide synthesis via lower intercellular pH was one of the mechanisms by which Ds-26-16 confers salt tolerance to E. coli.

Transcriptomic Analysis Reveals Adaptive Responses of an Enterobacteriaceae Strain LSJC7 to Arsenic Exposure

Arsenic (As) resistance determinant ars operon is present in many bacteria and has been demonstrated to enhance As(V) resistance of bacteria. However, whole molecular mechanism adaptations of bacteria in response to As(V) stress remain largely unknown. In this study, transcriptional profiles of Enterobacteriaceae strain LSJC7 responding to As(V) stress were analyzed using RNA-seq and qRT-PCR. As expected, genes involved in As(V) uptake were down-regulated, those involved in As(V) reduction and As(III) efflux were up-regulated, which avoided cellular As accumulation. Reactive oxygen species and nitric oxide (NO) were induced, which caused cellular damages including DNA, protein, and Fe–S cluster damage in LSJC7. The expression of specific genes encoding transcriptional regulators, such as nsrR and soxRS were also induced. NsrR and SoxRS modulated many critical metabolic activities in As(V) stressed LSJC7 cells, including reactive species scavenging and repairing damaged DNA, proteins, and Fe–S clusters. Therefore, besides As uptake, reduction, and efflux; oxidative stress defense and damage repair were the main cellular adaptive responses of LSJC7 to As(V) stress.

Homologous regulators, CnfR1 and CnfR2, activate expression of two distinct nitrogenase gene clusters in the filamentous cyanobacterium Anabaena variabilis ATCC 29413

The cyanobacterium Anabaena variabilis has two Mo-nitrogenases that function under different environmental conditions in different cell types. The heterocyst-specific nitrogenase encoded by the large nif1 gene cluster and the similar nif2 gene cluster that functions under anaerobic conditions in vegetative cells are under the control of the promoter for the first gene of each cluster, nifB1 or nifB2 respectively. Associated with each of these clusters is a putative regulatory gene called cnfR (patB) whose product has a C-terminal HTH domain and an N-terminal ferredoxin-like domain. CnfR1 activates nifB1 expression in heterocysts, while CnfR2 activates nifB2 expression. A cnfR1 mutant was unable to make nitrogenase under aerobic conditions in heterocysts while the cnfR2 mutant was unable to make nitrogenase under anaerobic conditions. Mutations in cnfR1 and cnfR2 reduced transcripts for the nif1 and nif2 genes respectively. The closely related cyanobacterium, Anabaena sp. PCC 7120 has the nif1 system but lacks nif2. Expression of nifB2:lacZ from A. variabilis in anaerobic vegetative cells of Anabaena sp. PCC 7120 depended on the presence of cnfR2. This suggests that CnfR2 is necessary and sufficient for activation of the nifB2 promoter and that the CnfR1/CnfR2 family of proteins are the primary activators of nitrogenase gene expression in cyanobacteria.

Response to Gaseous NO2 Air Pollutant of P. fluorescens Airborne Strain MFAF76a and Clinical Strain MFN1032

Human exposure to nitrogen dioxide (NO₂), an air pollutant of increasing interest in biology, results in several toxic effects to human health and also to the air microbiota. The aim of this study was to investigate the bacterial response to gaseous NO₂. Two Pseudomonas fluorescens strains, namely the airborne strain MFAF76a and the clinical strain MFN1032 were exposed to 0.1, 5, or 45 ppm concentrations of NO₂, and their effects on bacteria were evaluated in terms of motility, biofilm formation, antibiotic resistance, as well as expression of several chosen target genes. While 0.1 and 5 ppm of NO₂did not lead to any detectable modification in the studied phenotypes of the two bacteria, several alterations were observed when the bacteria were exposed to 45 ppm of gaseous NO₂. We thus chose to focus on this high concentration. NO₂-exposed P. fluorescens strains showed reduced swimming motility, and decreased swarming in case of the strain MFN1032. Biofilm formed by NO₂-treated airborne strain MFAF76a showed increased maximum thickness compared to non-treated cells, while NO₂ had no apparent effect on the clinical MFN1032 biofilm structure. It is well known that biofilm and motility are inversely regulated by intracellular c-di-GMP level. The c-di-GMP level was however not affected in response to NO₂ treatment. Finally, NO₂-exposed P. fluorescens strains were found to be more resistant to ciprofloxacin and chloramphenicol. Accordingly, the resistance nodulation cell division (RND) MexEF-OprN efflux pump encoding genes were highly upregulated in the two P. fluorescens strains. Noticeably, similar phenotypes had been previously observed following a NO treatment. Interestingly, an hmp-homolog gene in P. fluorescens strains MFAF76a and MFN1032 encodes a NO dioxygenase that is involved in NO detoxification into nitrites. Its expression was upregulated in response to NO₂, suggesting a possible common pathway between NO and NO₂ detoxification. Taken together, our study provides evidences for the bacterial response to NO₂ toxicity.

Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers

Background

Copper dependent nitrite reductase, NirK, catalyses the key step in denitrification, i.e. nitrite reduction to nitric oxide. Distinct structural NirK classes and phylogenetic clades of NirK-type denitrifiers have previously been observed based on a limited set of NirK sequences, however, their environmental distribution or ecological strategies are currently unknown. In addition, environmental nirK-type denitrifiers are currently underestimated in PCR-dependent surveys due to primer coverage limitations that can be attributed to their broad taxonomic diversity and enormous nirK sequence divergence. Therefore, we revisited reported analyses on partial NirK sequences using a taxonomically diverse, full-length NirK sequence dataset.

Results

Division of NirK sequences into two phylogenetically distinct clades was confirmed, with Clade I mainly comprising Alphaproteobacteria (plus some Gamma- and Betaproteobacteria) and Clade II harbouring more diverse taxonomic groups like Archaea, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Nitrospirae, Firmicutes, Actinobacteria, Planctomycetes and Proteobacteria (mainly Beta and Gamma). Failure of currently available primer sets to target diverse NirK-type denitrifiers in environmental surveys could be attributed to mismatches over the whole length of the primer binding regions including the 3′ site, with Clade II sequences containing higher sequence divergence than Clade I sequences. Simultaneous presence of both the denitrification and DNRA pathway could be observed in 67 % of all NirK-type denitrifiers.

Conclusion

The previously reported division of NirK into two distinct phylogenetic clades was confirmed using a taxonomically diverse set of full-length NirK sequences. Enormous sequence divergence of nirK gene sequences, probably due to variable nirK evolutionary trajectories, will remain an issue for covering diverse NirK-type denitrifiers in amplicon-based environmental surveys. The potential of a single organism to partition nitrate to either denitrification or dissimilatory nitrate reduction to ammonium appeared to be more widespread than originally anticipated as more than half of all NirK-type denitrifiers were shown to contain both pathways in their genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2465-0) contains supplementary material, which is available to authorized users.

Nitrogen oxide cycle regulates nitric oxide levels and bacterial cell signaling

Nitric oxide (NO) signaling controls various metabolic pathways in bacteria and higher eukaryotes. Cellular enzymes synthesize and detoxify NO; however, a mechanism that controls its cellular homeostasis has not been identified. Here, we found a nitrogen oxide cycle involving nitrate reductase (Nar) and the NO dioxygenase flavohemoglobin (Fhb), that facilitate inter-conversion of nitrate, nitrite, and NO in the actinobacterium Streptomyces coelicolor. This cycle regulates cellular NO levels, bacterial antibiotic production, and morphological differentiation. NO down-regulates Nar and up-regulates Fhb gene expression via the NO-dependent transcriptional factors DevSR and NsrR, respectively, which are involved in the auto-regulation mechanism of intracellular NO levels. Nitrite generated by the NO cycles induces gene expression in neighboring cells, indicating an additional role of the cycle as a producer of a transmittable inter-cellular communication molecule.

Differentiated, Promoter-specific Response of [4Fe-4S] NsrR DNA Binding to Reaction with Nitric Oxide

NsrR is an iron-sulfur cluster protein that regulates the nitric oxide (NO) stress response of many bacteria. NsrR from Streptomyces coelicolor regulates its own expression and that of only two other genes, hmpA1 and hmpA2, which encode HmpA enzymes predicted to detoxify NO. NsrR binds promoter DNA with high affinity only when coordinating a [4Fe-4S] cluster. Here we show that reaction of [4Fe-4S] NsrR with NO affects DNA binding differently depending on the gene promoter. Binding to the hmpA2 promoter was abolished at ∼2 NO per cluster, although for the hmpA1 and nsrR promoters, ∼4 and ∼8 NO molecules, respectively, were required to abolish DNA binding. Spectroscopic and kinetic studies of the NO reaction revealed a rapid, multi-phase, non-concerted process involving up to 8–10 NO molecules per cluster, leading to the formation of several iron-nitrosyl species. A distinct intermediate was observed at ∼2 NO per cluster, along with two further intermediates at ∼4 and ∼6 NO. The NsrR nitrosylation reaction was not significantly affected by DNA binding. These results show that NsrR regulates different promoters in response to different concentrations of NO. Spectroscopic evidence indicates that this is achieved by different NO-FeS complexes.

Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis

Background

Firmicutes have the capacity to remove excess nitrate from the environment via either denitrification, dissimilatory nitrate reduction to ammonium or both. The recent renewed interest in their nitrogen metabolism has revealed many interesting features, the most striking being their wide variety of dissimilatory nitrate reduction pathways. In the present study, nitrous oxide production from Bacillus licheniformis, a ubiquitous Gram-positive, spore-forming species with many industrial applications, is investigated.

Results

B. licheniformis has long been considered a denitrifier but physiological experiments on three different strains demonstrated that nitrous oxide is not produced from nitrate in stoichiometric amounts, rather ammonium is the most important end-product, produced during fermentation. Significant strain dependency in end-product ratios, attributed to nitrite and ammonium, and medium dependency in nitrous oxide production were also observed. Genome analyses confirmed the lack of a nitrite reductase to nitric oxide, the key enzyme of denitrification. Based on the gene inventory and building on knowledge from other non-denitrifying nitrous oxide emitters, hypothetical pathways for nitrous oxide production, involving NarG, NirB, qNor and Hmp, are proposed. In addition, all publically available genomes of B. licheniformis demonstrated similar gene inventories, with specific duplications of the nar operon, narK and hmp genes as well as NarG phylogeny supporting the evolutionary separation of previously described distinct BALI1 and BALI2 lineages.

Conclusions

Using physiological and genomic data we have demonstrated that the common soil bacterium B. licheniformis does not denitrify but is capable of fermentative dissimilatory nitrate/nitrite reduction to ammonium (DNRA) with concomitant production of N₂O. Considering its ubiquitous nature and non-fastidious growth in the lab, B. licheniformis is a suitable candidate for further exploration of the actual mechanism of N₂O production in DNRA bacteria and its relevance in situ.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2382-2) contains supplementary material, which is available to authorized users.