Shared functions of FeS cluster assembly and Moco biosynthesis

Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In the recent years it has become evident that the availability of FeS clusters play an important role for the biosynthesis of Moco. First, the MoaA protein binds two [4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional [4Fe4S] cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the L-cysteine desulfurase IscS, which is an enzyme involved in the transfer of sulfur to various acceptor proteins with a main role in the assembly of FeS clusters. In this review, we dissect the dependence of the production of active molybdoenzymes in detail, starting from the regulation of gene expression and further explaining sulfur delivery and FeS cluster insertion into target enzymes. Further, FeS cluster assembly is also linked to iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, we explain that the expression of the genes is dependent on an active FNR protein. FNR is a very important transcription factor that represents the master-switch for the expression of target genes in response to anaerobiosis. Moco biosynthesis is further directly dependent on the presence of ArcA and also on an active Fur protein.

Research on regional ozone prevention and control strategies in eastern China based on pollutant transport network and FNR

O3 pollution in China has worsened sharply in recent years, and O3 formation sensitivity (OFS) in many regions have gradually changed, with eastern China as the most typical region. This study constructed the transport networks of O3 and NO2 in different seasons from 2017 to 2020. The transport trends and the clustering formation patterns were summarized by analyzing the topological characteristics of the transport networks, and the patterns of OFS changes were diagnosed by analyzing the satellite remote sensing data. Based on that, the main clusters that each province or city belongs to in different pollutant transport networks were summarized and proposals for the inter-regional joint prevention and control were put forward. As the results showed, O3 transport activity was most active in spring and summer and least active in winter, while NO2 transport activity was most active in autumn and winter and least active in summer. OFS in summer mainly consisted of transitional regimes and NOx-limited regimes, while that in other seasons was mainly VOC-limited regimes. Notably, there was a significant upward trend in the proportion of transitional regimes and NOx-limited regimes in spring, autumn, and winter. For regions showing NOx-limited regime, areas with higher out-weighted degrees in the NO2 transport network should focus on controlling local NOx emissions, such as central regions in summer. For regions showing VOC-limited regime, areas with higher out-weighted degrees in the O3 transport network should focus on controlling local VOCs emissions, such as central and south-central regions in summer. For regions that belong to the same cluster and present the same OFS in each specific season, regional cooperative emission reduction strategies should be established to block important transmission paths and weaken regional pollution consistency.

Iron limitation indirectly reduces the Escherichia coli torCAD operon expression by a reduction of molybdenum cofactor availability

The expression of most molybdoenzymes in Escherichia coli has so far been revealed to be regulated by anaerobiosis and requires the presence of iron, based on the necessity of the transcription factor FNR to bind one [4Fe-4S] cluster. One exception is trimethylamine-N-oxide reductase encoded by the torCAD operon, which has been described to be expressed independently from FNR. In contrast to other alternative anaerobic respiratory systems, the expression of the torCAD operon was shown not to be completely repressed by the presence of dioxygen. To date, the basis for the O2-dependent expression of the torCAD operon has been related to the abundance of the transcriptional regulator IscR, which represses the transcription of torS and torT, and is more abundant under aerobic conditions than under anaerobic conditions. In this study, we reinvestigated the regulation of the torCAD operon and its dependence on the presence of iron and identified a novel regulation that depends on the presence of the bis-molybdopterin guanine dinucleotide (bis-MGD) molybdenum cofactor . We confirmed that the torCAD operon is directly regulated by the heme-containing protein TorC and is indirectly regulated by ArcA and by the availability of iron via active FNR and Fur, both regulatory proteins that influence the synthesis of the molybdenum cofactor. Furthermore, we identified a novel regulation mode of torCAD expression that is dependent on cellular levels of bis-MGD and is not used by other bis-MGD-containing enzymes like nitrate reductase.IMPORTANCEIn bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. FNR is a very important transcription factor that represents the master switch for the expression of target genes in response to anaerobiosis. Only Escherichia coli trimethylamine-N-oxide (TMAO) reductase escapes this regulation by FNR. We identified that the expression of TMAO reductase is regulated by the amount of bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor synthesized by the cell itself, representing a novel regulation pathway for the expression of an operon coding for a molybdoenzyme. Furthermore, TMAO reductase gene expression is indirectly regulated by the presence of iron, which is required for the production of the bis-MGD cofactor in the cell.

The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

IMPORTANCE

This work has broad relevance due to the ubiquity of dyes containing azo bonds in food and drugs. We report that azo dyes can be degraded by human gut bacteria through both enzymatic and nonenzymatic mechanisms, even from a single gut bacterial species. Furthermore, we revealed that environmental factors, oxygen, and L-Cysteine control the ability of E. coli to degrade azo dyes due to their impacts on bacterial transcription and metabolism. These results open up new opportunities to manipulate the azoreductase activity of the gut microbiome through the manipulation of host diet, suggest that azoreductase potential may be altered in patients suffering from gastrointestinal disease, and highlight the importance of studying bacterial enzymes for drug metabolism in their natural cellular and ecological context.

The Role of the si-Face Tyrosine of a Homodimeric Ferredoxin-NADP+ Oxidoreductase from Bacillus subtilis during Complex Formation and Redox Equivalent Transfer with NADP+/H and Ferredoxin

In the crystal structure of ferredoxin-NADP+ oxidoreductase from Bacillus subtilis (BsFNR), Tyr50 stacks on the si-face of the isoalloxazine ring portion of the FAD prosthetic group. This configuration is highly conserved among the homodimeric ferredoxin-NAD(P)+ oxidoreductases (FNR) from Gram-positive bacteria and photosynthetic bacteria. In this report, pre-steady state reactions of Tyr50 variants with NADP+/NADPH and ferredoxin from B. subtilis (BsFd) were examined with stopped-flow spectrophotometry to assess the effects of the mutation on the formation of FNR-substrate complexes and following redox equivalent transfer. Mixing oxidized BsFNRs with NADPH resulted in a rapid complex formation followed by a rate-limiting hydride transfer. The substitution substantially modulated the intensity of the charge transfer absorption band and decreased the observed hydride transfer rates compared to the wild type. Reduction of the Y50W mutant by NADPH proceeded in a monophasic manner, while the Y50G and Y50S mutants did in biphasic phases. The reduced Tyr50 mutants hardly promoted the reduction of NADP+. Mixing oxidized BsFNRs with reduced BsFd resulted in the reduction of the FNRs. The observed FNR reduction rates of the three variants were comparable, but in the Y50G and Y50S mutants, the amount of the reduced FNR at the rapid phase was decreased, and a slow FNR reduction phase was observed. The obtained results suggest that the replacements of Tyr50 with Gly and Ser permitted the conformational change in the reduced form, which induced an asymmetric kinetic behavior between the protomers of the homodimeric BsFNR.

Fibrinogen-to-Neutrophil Ratio as a New Predictor of Central Lymph Node Metastasis in Patients with Papillary Thyroid Cancer and Type 2 Diabetes Mellitus

Background

Many patients have a higher risk of thyroid cancer if they have both papillary thyroid carcinoma (PTC) and Type 2 diabetes mellitus (T2DM). Meanwhile, the primary reason for local PTC recurrence is cervical lymph node metastasis. Therefore, the prognosis of patients affects how cervical lymph nodes are managed during surgery. Due to surgical complications such as laryngeal nerve palsy and hypocalcemia, it is still debatable whether to prevent central lymph node dissection (CLND). Predicting central lymph node metastasis (CLNM) is crucial to direct CLND. It is unclear how important the fibrinogen-to-neutrophil ratio (FNR) is in thyroid cancer, so we looked into how it might help patients with PTC and T2DM predict CLNM.

Patients and methods

Wenzhou Medical University's First Affiliated Hospital provided us with 413 patients with PTC and T2DM, randomly divided into a training set (N = 292) and a validation set (N = 121). Univariate and multivariate logistic regression analyses were used to identify independent risk factors. After constructing a nomogram, the validity of the model was evaluated.

Results

The maximum tumor diameter, high-density lipoprotein, thyroxine, triglyceride, lymphocyte, and FNR were all identified as independent risk factors by multivariate logistic regression analysis. The C index of the training set was 0.775, and the validation set was 0.654.

Conclusion

In patients with PTC and T2DM, preoperative FNR was an independent risk factor for CLNM.

Enhancing bacterial cellulose production with hypoxia-inducible factors

Komagataeibacter xylinus is an aerobic strain that produces bacterial cellulose (BC). Oxygen levels play a critical role in regulating BC synthesis in K. xylinus, and an increase in oxygen tension generally means a decrease in BC production. Fumarate nitrate reduction protein (FNR) and aerobic respiration control protein A (ArcA) are hypoxia-inducible factors, which can signal whether oxygen is present in the environment. In this study, FNR and ArcA were used to enhance the efficiency of oxygen signaling in K. xylinus, and globally regulate the transcription of the genome to cope with hypoxic conditions, with the goal of improving growth and BC production. FNR and ArcA were individually overexpressed in K. xylinus, and the engineered strains were cultivated under different oxygen tensions to explore how their overexpression affects cellular metabolism and regulation. Although FNR overexpression did not improve BC production, ArcA overexpression increased BC production by 24.0% and 37.5% as compared to the control under oxygen tensions of 15% and 40%, respectively. Transcriptome analysis showed that FNR and ArcA overexpression changed the way K. xylinus coped with oxygen tension changes, and that both FNR and ArcA overexpression enhanced the BC synthesis pathway. The results of this study provide a new perspective on the effect of oxygen signaling on growth and BC production in K. xylinus and suggest a promising strategy for enhancing BC production through metabolic engineering. KEY POINTS: • K. xylinus BC production increased after overexpression of ArcA • The young's modulus is enhanced by the ArcA overexpression • ArcA and FNR overexpression changed how cells coped with changes in oxygen tension.

Changing the tracks: screening for electron transfer proteins to support hydrogen production

Abstract

Ferredoxins are essential electron transferring proteins in organisms. Twelve plant-type ferredoxins in the green alga Chlamydomonas reinhardtii determine the fate of electrons, generated in multiple metabolic processes. The two hydrogenases HydA1 and HydA2 of. C. reinhardtii compete for electrons from the photosynthetic ferredoxin PetF, which is the first stromal mediator of the high-energy electrons derived from the absorption of light energy at the photosystems. While being involved in many chloroplast-located metabolic pathways, PetF shows the highest affinity for ferredoxin-NADP⁺ oxidoreductase (FNR), not for the hydrogenases. Aiming to identify other potential electron donors for the hydrogenases, we screened as yet uncharacterized ferredoxins Fdx7, 8, 10 and 11 for their capability to reduce the hydrogenases. Comparing the performance of the Fdx in presence and absence of competitor FNR, we show that Fdx7 has a higher affinity for HydA1 than for FNR. Additionally, we show that synthetic FeS-cluster-binding maquettes, which can be reduced by NADPH alone, can also be used to reduce the hydrogenases. Our findings pave the way for the creation of tailored electron donors to redirect electrons to enzymes of interest.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00775-022-01956-1.

Spatio-temporal characterization of tropospheric ozone and its precursor pollutants NO2 and HCHO over South Asia

In recent decades, South Asia has experienced declining air quality, with much of the attention being focused on extremely high levels of particulate matter. Here, we analyze tropospheric ozone (O₃), formaldehyde (HCHO), and nitrogen dioxide (NO₂) to assess other measures of air quality across South Asia from 2008 to 2018. The IASI-Forli retrieved tropospheric ozone data was validated with ozonesonde, reanalysis (ERA5), satellite (TES), and model simulation products (GEOS-Chem and TOMCAT/SLIMCAT). Space-based observations of these three trace gases were used to conduct a spatio temporal analysis over South Asia using trend analysis (Theil-Sen and linear regression), change-point detection (Pettitt's test), and hotspot identification (Getis-Ord G_i*). We used the formaldehyde-nitrogen dioxide ratio (FNR) to identify NO_x limited, VOC limited, and transitional regimes in South Asia. Counter to previous studies, a statistically significant decrease of HCHO (-0.0041 DU yr^-1) and O₃ (-0.064 DU yr^-1) was detected for South Asia; however, NO₂ is increasing the 0.001 DU yr^-1 over South Asia during 2008-18. The Indo-Gangetic Plains emerged as being critically affected by the three trace gases. Certain parts of southern and south-eastern India are gradually emerging as NO₂ and HCHO hotpots. No significant O₃ hotspots were discernible, though coldspots existed along the Himalaya belt of India, Nepal, and Bhutan and mountainous tracts of Pakistan. FNR indicates the reduction of NO_x in NO_x-limited regime of the Indo-Gangetic Plains reduced the formation of tropospheric O₃ over South Asia.

Dioxygen reactivity of a biomimetic [4Fe-4S] compound exhibits [4Fe-4S] to [2Fe-2S] cluster conversion

Fumarate and nitrate reductase (FNR) is a gene regulatory protein that controls anaerobic to aerobic respiration in Escherichia coli, for which O₂ serves as a control switch to induce a protein structural change by converting [4Fe-4S] cofactors to [2Fe-2S] clusters. Although biomimetic models can aid in understanding the complex functions of their protein counterparts, the inherent sensitivity of discrete [Fe-S] molecules to aerobic conditions poses a unique challenge to mimic the O₂-sensing capability of FNR. Herein, we report unprecedented biomimetic O₂ reactivity of a discrete [4Fe-4S] complex, [Fe₄S₄(SPh^F)₄]^2- (1) where SPh^F is 4-fluorothiophenolate, in which the reaction of 1 with O_2(g) in the presence of thiolate produces its [2Fe-2S] analogue, [Fe₂S₂(SPh^F)₄]^2- (2), at room temperature. The cluster conversion of 1 to 2 can also be achieved by employing disulfide as an oxidant under the same reaction conditions. The [4Fe-4S] to [2Fe-2S] cluster conversion by O₂ was found to be significantly faster than that by disulfide, while the reaction with disulfide produced higher yields of 2.

Involvement of an FNR-like oxygen sensor in Komagataeibacter medellinensis for survival under oxygen depletion

During acetic acid fermentation, acetic acid bacteria face oxygen depletion stress caused by the vigorous oxidation of ethanol to acetic acid. However, the molecular mechanisms underlying the response to oxygen depletion stress remain largely unknown. Here, we focused on an oxygen-sensing FNR homolog, FnrG, in Komagataeibacter medellinensis. Comparative transcriptomic analysis between the wild-type and fnrG-disrupted strains revealed that FnrG upregulated eight genes (fold change > 3). Recombinant FnrG bound to a specific DNA sequence only when FnrG was reconstituted anaerobically. An operon consisting of acetate kinase and xylulose-5-phosphate/fructose-6-phosphate phosphoketolase genes was found to be an FnrG regulon involved in cell survival under oxygen-limiting conditions. Moreover, a strain that overexpressed these two genes accumulated more acetic acid than the wild-type strain harboring an empty vector. Thus, these two genes could be new targets for the molecular breeding of acetic acid bacteria with high acetic acid productivity.

FNR-Type Regulator GoxR of the Obligatorily Aerobic Acetic Acid Bacterium Gluconobacter oxydans Affects Expression of Genes Involved in Respiration and Redox Metabolism

Gene expression in the obligately aerobic acetic acid bacterium Gluconobacter oxydans responds to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed a transcriptional regulator named GoxR (GOX0974), which is the only member of the fumarate-nitrate reduction regulator (FNR) family in this species. Evidence that GoxR contains an iron-sulfur cluster was obtained, suggesting that GoxR functions as an oxygen sensor similar to FNR. The direct target genes of GoxR were determined by combining several approaches, including a transcriptome comparison of a ΔgoxR mutant with the wild-type strain and detection of in vivo GoxR binding sites by chromatin affinity purification and sequencing (ChAP-Seq). Prominent targets were the cioAB genes encoding a cytochrome bd oxidase with low O₂ affinity, which were repressed by GoxR, and the pnt operon, which was activated by GoxR. The pnt operon encodes a transhydrogenase (pntA1A2B), an NADH-dependent oxidoreductase (GOX0313), and another oxidoreductase (GOX0314). Evidence was obtained for GoxR being active despite a high dissolved oxygen concentration in the medium. We suggest a model in which the very high respiration rates of G. oxydans due to periplasmic oxidations cause an oxygen-limited cytoplasm and insufficient reoxidation of NAD(P)H in the respiratory chain, leading to inhibited cytoplasmic carbohydrate degradation. GoxR-triggered induction of the pnt operon enhances fast interconversion of NADPH and NADH by the transhydrogenase and NADH reoxidation by the GOX0313 oxidoreductase via reduction of acetaldehyde formed by pyruvate decarboxylase to ethanol. In fact, small amounts of ethanol were formed by G. oxydans under oxygen-restricted conditions in a GoxR-dependent manner.IMPORTANCE Gluconobacter oxydans serves as a cell factory for oxidative biotransformations based on membrane-bound dehydrogenases and as a model organism for elucidating the metabolism of acetic acid bacteria. Surprisingly, to our knowledge none of the more than 100 transcriptional regulators encoded in the genome of G. oxydans has been studied experimentally until now. In this work, we analyzed the function of a regulator named GoxR, which belongs to the FNR family. Members of this family serve as oxygen sensors by means of an oxygen-sensitive [4Fe-4S] cluster and typically regulate genes important for growth under anoxic conditions by anaerobic respiration or fermentation. Because G. oxydans has an obligatory aerobic respiratory mode of energy metabolism, it was tempting to elucidate the target genes regulated by GoxR. Our results show that GoxR affects the expression of genes that support the interconversion of NADPH and NADH and the NADH reoxidation by reduction of acetaldehyde to ethanol.

Transcriptional and Post-transcriptional Control of the Nitrate Respiration in Bacteria

In oxygen (O2) limiting environments, numerous aerobic bacteria have the ability to shift from aerobic to anaerobic respiration to release energy. This process requires alternative electron acceptor to replace O2 such as nitrate (NO3 -), which has the next best reduction potential after O2. Depending on the organism, nitrate respiration involves different enzymes to convert NO3 - to ammonium (NH4 +) or dinitrogen (N2). The expression of these enzymes is tightly controlled by transcription factors (TFs). More recently, bacterial small regulatory RNAs (sRNAs), which are important regulators of the rapid adaptation of microorganisms to extremely diverse environments, have also been shown to control the expression of genes encoding enzymes or TFs related to nitrate respiration. In turn, these TFs control the synthesis of multiple sRNAs. These results suggest that sRNAs play a central role in the control of these metabolic pathways. Here we review the complex interplay between the transcriptional and the post-transcriptional regulators to efficiently control the respiration on nitrate.

A Fast Neutron Radiography System Using a High Yield Portable DT Neutron Source

Resolution measurements were made using 14.1 MeV neutrons from a high-yield, portable DT neutron generator and a neutron camera based on a scintillation screen viewed by a digital camera. Resolution measurements were made using a custom-built, plastic, USAF-1951 resolution chart, of dimensions 125 × 98 × 25.4 mm³, and by calculating the modulation transfer function from the edge-spread function from edges of plastic and steel objects. A portable neutron generator with a yield of 3 × 10⁹ n/s (DT) and a spot size of 1.5 mm was used to irradiate the object with neutrons for 10 min. The neutron camera, based on a ⁶LiF/ZnS:Cu-doped polypropylene scintillation screen and digital camera was placed at a distance of 140 cm, and produced an image with a spatial resolution of 0.35 cycles per millimeter.

Screening virulence factors of porcine extraintestinal pathogenic Escherichia coli (an emerging pathotype) required for optimal growth in swine blood

Porcine extraintestinal pathogenic Escherichia coli (ExPEC) is occurring with increasing frequency in China, which causes acute septicemia and sudden death in pigs leading to significant economic losses. Bacterial survival and even proliferation within host bloodstream are a common manifestation of a number of bacterial septicemias, including porcine ExPEC diseases. However, the underlying pathogenesis for this novel pathotype of ExPEC has not been explored deeply. Here, we used a conjunction with transposon mutagenesis to identify the mechanisms of bacterial fitness involved in optimal growth of porcine ExPEC in swine serum ex vivo under static culture. Our work identified 28 genes involved in nucleotide biosynthesis, extracellular polysaccharide biosynthesis, regulators Fur and FNR, acid/zinc resistance, and Deley-Douderoff carbon metabolism that are required for the serum fitness. Subsequent functional analyses revealed that either interruption of de novo nucleotide biosynthesis or blocking of several extracellular polysaccharide biosynthesis including O2-antigen, Lipid A-core, and ECA significantly affect porcine ExPEC's growth in swine serum and proliferation in host bloodstream. Furthermore, the reasonable regulations of iron and anaerobic metabolisms in response to host stimuli by global regulators Fur and FNR also play key roles during systemic infection of porcine ExPEC. These findings provide compelling evidences that de novo nucleotide biosynthesis may enable porcine ExPEC to adapt to swine blood-specific nutrient availability, and the effective assembly of O-antigen, lipid A-core, and ECA is required to resist the bactericidal activity of swine serum. These studies contribute to better understand the underlying mechanisms employed by porcine ExPEC to survive, grow in the swine bloodstream, and cause disease. These related factors may serve as therapeutic targets for countering or preventing ExPEC serum resistance in the clinic.

Aerobic Barley Mg-protoporphyrin IX Monomethyl Ester Cyclase is Powered by Electrons from Ferredoxin

Chlorophyll is the light-harvesting molecule central to the process of photosynthesis. Chlorophyll is synthesized through 15 enzymatic steps. Most of the reactions have been characterized using recombinant proteins. One exception is the formation of the isocyclic E-ring characteristic of chlorophylls. This reaction is catalyzed by the Mg-protoporphyrin IX monomethyl ester cyclase encoded by Xantha-l in barley (Hordeum vulgare L.). The Xantha-l gene product (XanL) is a membrane-bound diiron monooxygenase, which requires additional soluble and membrane-bound components for its activity. XanL has so far been impossible to produce as an active recombinant protein for in vitro assays, which is required for deeper biochemical and structural analyses. In the present work, we performed cyclase assays with soluble and membrane-bound fractions of barley etioplasts. Addition of antibodies raised against ferredoxin or ferredoxin-NADPH oxidoreductase (FNR) inhibited assays, strongly suggesting that reducing electrons for the cyclase reaction involves ferredoxin and FNR. We further developed a completely recombinant cyclase assay. Expression of active XanL required co-expression with an additional protein, Ycf54. In vitro cyclase activity was obtained with recombinant XanL in combination with ferredoxin and FNR. Our experiment demonstrates that the cyclase is a ferredoxin-dependent enzyme. Ferredoxin is part of the photosynthetic electron-transport chain, which suggests that the cyclase reaction might be connected to photosynthesis under light conditions.

Preferential use of carbon central metabolism and anaerobic respiratory chains in porcine extraintestinal pathogenic Escherichia coli during bloodstream infection

Porcine extraintestinal pathogenic Escherichia coli (ExPEC) is occurring with increasing frequency in China, and leads to significant economic and welfare costs in the swine industry. The underlying mechanisms of porcine ExPEC in blood colonization during systematic infection is poorly understood. Here we measured the gene expression of porcine ExPEC in infected animal bloodstream in vivo and fresh swine blood in vitro. Using comparisons with P values of ≤ 0.01, we identified 354 and 313 genes as being significantly up- or down-regulated at least 2-fold change during bloodstream infection, respectively. Excepting for an array of iron acquisition systems, numerous genes involved in carbon central metabolism and anaerobic respiratory chains were upregulated here. These genes were categorized into several clusters including the TCA-cycle (frdABCD, citCEFXG), d-ribose transporter (rbsDACB), nickel transporter (nikABCDER), NiFe hydrogenase (hybOABCDEF, hycBCDEFG), Hyp-complex (hypABCDE), DMSO reductase (dmsABC and ynfEFGHI), format dehydrogenase (fdnGHI) and NADH dehydrogenase I (nuoA-N). The mutant with simultaneous inactivation of ribose and citrate imports showed significant reduced fitness in host blood, suggesting these two carbohydrates are utilized by central metabolism network as important carbon-source during bloodstream infection. Similar deficiency was also observed in the mutant double deleted NiFe hydrogenase 2 and 3 anaerobic respiratory chains. Further study found that FNR (a global regulator facilitating bacterial adaptation to anaerobic conditions) is an important regulator in response to bloodstream to activate center metabolism and anaerobic respiratory chains, thus contribute to the full-virulence of porcine ExPEC. These findings provide compelling evidence to support the notion that carbon central metabolism network and anaerobic respiratory chains play key roles for porcine ExPEC fitness within host bloodstream.

Relationships of ozone formation sensitivity with precursors emissions, meteorology and land use types, in Guangdong-Hong Kong-Macao Greater Bay Area, China

Due to the influences of precursors emissions, meteorology, geography and other factors, ozone formation sensitivity (OFS) is generally spatially and temporally heterogeneous. This study characterized detailed spatial and temporal variations of OFS in Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 2012 to 2016 based on OMI satellite data, and analyzed the relationships of OFS with precursors emissions, meteorology and land use types (LUTs). From 2012 to 2016, the OFS tended to be NO_x-limited in GBA, with the value of FNR (HCHO/NO₂) increasing from 2.04 to 2.22. According to the total annual emission statistics of precursors, NO_x emissions decreased by 33.1% and VOCs emissions increased by 35.2% from 2012 to 2016, directly resulting in OFS tending to be NO_x-limited. The Grey Relation Analysis results show that total column water (TCW), surface net solar radiation (SSR), air temperature at 2 m (T2) and surface pressure (SP) are the top four meteorological factors with the greatest influences on OFS. There are significant positive correlations between FNR and T2, SSR, TCW, and significant negative correlations between FNR and SP. In GBA, the OFS tends to be NO_x-limited regime in wet season (higher T2, SSR, TCW and lower SP) and VOCs-limited regime in dry season (lower T2, SSR, TCW and higher SP). The FNR displays obvious gradient variations on different LUTs, with the highest in "Rural areas", second in "Suburban areas" and lowest in "Urban areas".

Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor

Regulation of the expression of the gene for chlorite dismutase (cld), located on the chlorate reduction composite transposon of the chlorate reducer Ideonella dechloratans, was studied. A 200 bp upstream sequence of the cld gene, and mutated and truncated versions thereof, was used in a reporter system in Escherichia coli. It was found that a sequence within this upstream region, which is nearly identical to the canonical FNR-binding sequence of E. coli, is necessary for anaerobic induction of the reporter gene. Anaerobic induction was regained in an FNR-deficient strain of E. coli when supplemented either with the fnr gene from E. coli or with a candidate fnr gene cloned from I. dechloratans. In vivo transcription of the suggested fnr gene of I. dechloratans was demonstrated by qRT-PCR. Based on these results, the cld promoter of I. dechloratans is suggested to be a class II-activated promoter regulated by an FNR-type protein of I. dechloratans. No fnr-type genes have been found on the chlorate reduction composite transposon of I. dechloratans, making anaerobic upregulation of the cld gene after a gene transfer event dependent on the presence of an fnr-type gene in the recipient.

Qualitative and quantitative dataset of TROL protein interaction with C3 and C4 ferredoxin: NADP+ oxidoreductases

Last step of electron transport from ferredoxin to NADP+ in photosynthesis light reactions catalyses ferredoxin: NADP⁺ oxidoreductase (FNR). FNR is present as soluble protein in stroma, but also bound to the protein complexes on the membrane with thylakoid rhodanase-like protein (TROL) and translocon on the inner envelope chloroplast membrane (Tic62), which have identical C terminal FNR binding domain [1,2]. During the electron transport, FNR anchored by TROL protein transfers electrons on NADP+ and forms NADPH which is then used in Calvin cycle as reducing agent. TROL is an integral membrane protein [3] with an inactive rhodanase-like domain (RHO) facing stroma which, as proposed earlier [4], could bind a small ligand leading to releasing or binding of FNR. FNR-TROL protein complex is necessary for optimal photosynthetic electron flow [1]. It has been shown that C4 plant maize FNR isomers have different N-terminal structure which determines binding affinity to protein complexes and different ratios of bound and unbound FNR in bundle sheath and mesophyll cells, depending on preferable photosynthetic electron transport [5]. Mutant Arabidopsis plant that contain maize FNR1 protein showed influence on dynamic association of FNR and change in excitation balance between photosystems which then influenced photo induced electron transport and finally photosynthesis [5]. In order to determine the influence of maize FNR1 on photosynthesis in C3 plants and difference in interaction strength with TROL, we preformed Yeast two hybrid screening, x-alpha-gal assay and β-galactosidase assay.

Comparative proteomic analysis of Salmonella Typhimurium wild type and its isogenic fnr null mutant during anaerobiosis reveals new insight into bacterial metabolism and virulence

AIM

The aim of this study was to understand the role of anaerobic regulator FNR (Fumarate Nitrate Reduction) in Salmonella Typhimurium through proteomic approach.

METHODS AND RESULTS

We did label free quantitative proteomic analysis of Salmonella Typhimurium PM45 wild type and the fnr null mutant cultured under anaerobic conditions. The data revealed 153 significantly differentially expressed proteins (DEPs) in the mutant out of 1798 total proteins identified. Out of 153 DEPs, 94 proteins were up-regulated (repressed by FNR) and 59 proteins were down-regulated (activated by FNR) in the mutant. The network analysis indicated up-regulation of TCA cycle, electron transport chain and ethanolamine metabolism and down regulation of pyruvate metabolism and glycerol and glycerophospholipid metabolism.

CONCLUSIONS

Our study showed that FNR represses ethanolamine utilization. The different metabolic pathways such as pyruvate metabolism, glycerol metabolism and glycerophospholipid metabolism were activated by FNR. Further, FNR positively regulated the DNA binding protein Fis, one of the global regulators of virulence in Salmonella Typhimurium. Thus, our finding highlights the pivotal role of FNR in regulating bacterial metabolism and virulence during anaerobiosis for systemic infection of the host.

FNR-Dependent RmpA and RmpA2 Regulation of Capsule Polysaccharide Biosynthesis in Klebsiella pneumoniae

Fumarate nitrate reduction regulator (FNR) is a direct oxygen-responsive transcriptional regulator containing an iron-sulfur (Fe–S) cluster. During anaerobic growth, the [4Fe–4S] cluster in FNR (holo-FNR) binds specifically to DNA, whereas exposure to oxygen results in the loss of its DNA-binding activity via oxidation of the [4Fe–4S] cluster. In this study, we aimed to investigate the role of FNR in regulation of capsular polysaccharide (CPS) biosynthesis, serum resistance, and anti-phagocytosis of K. pneumoniae. We found that the CPS amount in K. pneumoniae increased in anaerobic conditions, compared to that in aerobic conditions. An fnr deletion mutant and a site-directed mutant (fnr_3CA), with the three cysteines (C20, C23, and C29) replaced with alanines to mimic an FNR lacking the [4Fe-4S] cluster, showed marked increase in CPS amount under anaerobic conditions. A promoter-reporter assay and qRT-PCR confirmed that the transcription of the cps genes was repressed by holo-FNR. In addition, we found that holo-FNR could repress the transcription of rmpA and rmpA2, encoding cps transcriptional activators. Deletion of rmpA or rmpA2 in the Δfnr strain reduced CPS biosynthesis, suggesting that RmpA and RmpA2 participated in the holo-FNR–mediated repression of cps transcription, thereby regulating the CPS amount, serum resistance, and anti-phagocytosis. Taken together, our results provided evidence that RmpA and RmpA2 participated in the holo-FNR–mediated repression of CPS biosynthesis, and resistance to the host defense in response to oxygen availability.

Regulation of metE+ mRNA expression by FnrS small RNA in Salmonella enterica serovar Typhimurium

Methionine is critical for variety of metabolic processes in biological organisms, acting as a precursor or intermediate for many final products. The last step for the synthesis of methionine is the methylation of homocysteine, which is catalyzed by MetE. Here, we use Salmonella enterica serovar Typhimurium LT2 to study the regulation of the metE⁺ gene by an anaerobically induced small non-coding RNA-FnrS, the expression of which is strictly dependent on the anaerobic regulator-FNR. The MetE-HA protein was expressed at an increased level in the fnrS^- and hfq^- deficient strains under anaerobic conditions. The Hfq protein is predicted to stabilize the binding between small RNA(s) and their target mRNA(s). A transcriptional (op) and translational (pr) metE::lacZ fusion gene were separately constructed, with the metE⁺-promoter fused to a lacZ reporter gene. In an anaerobic environment, the metE::lacZ (pr) fusion gene and reverse transcription-PCR identified that FnrS and/or FNR negatively regulate metE⁺ mRNA levels in the rich media. Analysis of FnrS revealed a sequence complementary to the 5' mRNA translational initiation region (TIR) of the metE⁺ gene. Mutation(s) predicted to disrupt base pairing between FnrS and metE⁺ TIR were constructed in fnrS, and most of those resulted in the loss of repressive activity. When compensatory mutation(s) were made in metE⁺ 5' TIR to restore base pairing with FnrS, the repressive regulation was completely restored. Therefore, in this study, we identified that in anaerobic phase, there is a repression of metE⁺ gene expression by FnrS and that base-paring, between both expressive transcripts, plays an important role for this negative regulation.

Iron-Dependent Regulation of Molybdenum Cofactor Biosynthesis Genes in Escherichia coli

Molybdenum cofactor (Moco) biosynthesis is a complex process that involves the coordinated function of several proteins. In recent years it has become obvious that the availability of iron plays an important role in the biosynthesis of Moco. First, the MoaA protein binds two [4Fe-4S] clusters per monomer. Second, the expression of the moaABCDE and moeAB operons is regulated by FNR, which senses the availability of oxygen via a functional [4Fe-4S] cluster. Finally, the conversion of cyclic pyranopterin monophosphate to molybdopterin requires the availability of the l-cysteine desulfurase IscS, which is a shared protein with a main role in the assembly of Fe-S clusters. In this report, we investigated the transcriptional regulation of the moaABCDE operon by focusing on its dependence on cellular iron availability. While the abundance of selected molybdoenzymes is largely decreased under iron-limiting conditions, our data show that the regulation of the moaABCDE operon at the level of transcription is only marginally influenced by the availability of iron. Nevertheless, intracellular levels of Moco were decreased under iron-limiting conditions, likely based on an inactive MoaA protein in addition to lower levels of the l-cysteine desulfurase IscS, which simultaneously reduces the sulfur availability for Moco production.IMPORTANCE FNR is a very important transcriptional factor that represents the master switch for the expression of target genes in response to anaerobiosis. Among the FNR-regulated operons in Escherichia coli is the moaABCDE operon, involved in Moco biosynthesis. Molybdoenzymes have essential roles in eukaryotic and prokaryotic organisms. In bacteria, molybdoenzymes are crucial for anaerobic respiration using alternative electron acceptors. This work investigates the connection of iron availability to the biosynthesis of Moco and the production of active molybdoenzymes.

Binding of ferredoxin NADP+ oxidoreductase (FNR) to plant photosystem I

The binding of FNR to PSI has been postulated long ago, however, a clear evidence is still missing. In this work, using isothermal titration calorimetry (ITC), we found that FNR binds to photosystem I with its light harvesting complex I (PSI-LHCI) from C. reinhardtii with a 1:1 stoichiometry, a Kd of ~0.8 μM and ∆H of -20.7 kcal/mol. Titrations at different temperatures were used to determine the heat capacity change, ∆CP, of the binding, through which the size of the interface area between the proteins was assessed as ~3000 Ų. In a different set of ITC experiments, introduction of various sucrose concentrations was used to estimate that ~95 water molecules are released to the solvent. These observations support the notion of a binding site shared by few of the photosystem I - light harvesting complex I (PSI-LHCI) subunits in addition to PsaE. Based on these results, a hypothetical model was built for the binding site of FNR at PSI, using known crystallographic structures of: cyanobacterial PSI in complex with ferredoxin (Fd), plant PSI-LHCI and Fd:FNR complex from cyanobacteria. FNR binding site location is proposed to be at the foot of the stromal ridge and above the inner LHCI belt. It is expected to form contacts with PsaE, PsaB, PsaF and at least one of the LHCI. In addition, a ~4.5-fold increased affinity between FNR and PSI-LHCI under crowded 1 M sucrose environment led us to conclude that in C. reinhardtii FNR also functions as a subunit of PSI-LHCI.

Reassessing the Structure and Function Relationship of the O2 Sensing Transcription Factor FNR

SIGNIFICANCE

The Escherichia coli regulatory protein fumarate nitrate reduction (FNR) mediates a global transcriptional response upon O₂ deprivation. Spanning nearly 40 years of research investigations, our understanding of how FNR senses and responds to O₂ has considerably progressed despite a lack of structural information for most of that period. This knowledge has established the paradigm for how facultative anaerobic bacteria sense changes in O₂ tension. Recent Advances: Recently, the X-ray crystal structure of Aliivibrio fischeri FNR with its [4Fe-4S] cluster cofactor was solved and has provided valuable new insight into FNR structure and function. These findings have alluded to the conformational changes that may occur to alter FNR activity in response to O₂.

CRITICAL ISSUES

Here, we review the major features of this structure in context of previously acquired data. In doing so, we discuss additional mechanistic aspects of FNR function that warrant further investigation.

FUTURE DIRECTIONS

To complement the [4Fe-4S]-FNR structure, the structures of apo-FNR and FNR bound to DNA or RNA polymerase are needed. Together, these structures would elevate our understanding of how ligation of its [4Fe-4S] cluster allows FNR to regulate transcription according to the level of environmental O₂.

Enterotoxigenic E. coli virulence gene regulation in human infections

Enterotoxigenic Escherichia coli (ETEC) is a global diarrheal pathogen that utilizes adhesins and secreted enterotoxins to cause disease in mammalian hosts. Decades of research on virulence factor regulation in ETEC has revealed a variety of environmental factors that influence gene expression, including bile, pH, bicarbonate, osmolarity, and glucose. However, other hallmarks of the intestinal tract, such as low oxygen availability, have not been examined. Further, determining how ETEC integrates these signals in the complex host environment is challenging. To address this, we characterized ETEC's response to the human host using samples from a controlled human infection model. We found ETEC senses environmental oxygen to globally influence virulence factor expression via the oxygen-sensitive transcriptional regulator fumarate and nitrate reduction (FNR) regulator. In vitro anaerobic growth replicates the in vivo virulence factor expression profile, and deletion of fnr in ETEC strain H10407 results in a significant increase in expression of all classical virulence factors, including the colonization factor antigen I (CFA/I) adhesin operon and both heat-stable and heat-labile enterotoxins. These data depict a model of ETEC infection where FNR activity can globally influence virulence gene expression, and therefore proximity to the oxygenated zone bordering intestinal epithelial cells likely influences ETEC virulence gene expression in vivo. Outside of the host, ETEC biofilms are associated with seasonal ETEC epidemics, and we find FNR is a regulator of biofilm production. Together these data suggest FNR-dependent oxygen sensing in ETEC has implications for human infection inside and outside of the host.

Biosynthesis of Orthogonal Molecules Using Ferredoxin and Ferredoxin-NADP+ Reductase Systems Enables Genetically Encoded PhyB Optogenetics

Transplanting metabolic reactions from one species into another has many uses as a research tool with applications ranging from optogenetics to crop production. Ferredoxin (Fd), the enzyme that most often supplies electrons to these reactions, is often overlooked when transplanting enzymes from one species to another because most cells already contain endogenous Fd. However, we have shown that the production of chromophores used in Phytochrome B (PhyB) optogenetics is greatly enhanced in mammalian cells by expressing bacterial and plant Fds with ferredoxin-NADP+ reductases (FNR). We delineated the rate limiting factors and found that the main metabolic precursor, heme, was not the primary limiting factor for producing either the cyanobacterial or plant chromophores, phycocyanobilin or phytochromobilin, respectively. In fact, Fd is limiting, followed by Fd+FNR and finally heme. Using these findings, we optimized the PCB production system and combined it with a tissue penetrating red/far-red sensing PhyB optogenetic gene switch in animal cells. We further characterized this system in several mammalian cell lines using red and far-red light. Importantly, we found that the light-switchable gene system remains active for several hours upon illumination, even with a short light pulse, and requires very small amounts of light for maximal activation. Boosting chromophore production by matching metabolic pathways with specific ferredoxin systems will enable the unparalleled use of the many PhyB optogenetic tools and has broader implications for optimizing synthetic metabolic pathways.

Rational redesign of the ferredoxin-NADP+-oxido-reductase/ferredoxin-interaction for photosynthesis-dependent H2-production

Utilization of electrons from the photosynthetic water splitting reaction for the generation of biofuels, commodities as well as application in biotransformations requires a partial rerouting of the photosynthetic electron transport chain. Due to its rather negative redox potential and its bifurcational function, ferredoxin at the acceptor side of Photosystem 1 is one of the focal points for such an engineering. With hydrogen production as model system, we show here the impact and potential of redox partner design involving ferredoxin (Fd), ferredoxin-oxido-reductase (FNR) and [FeFe]‑hydrogenase HydA1 on electron transport in a future cyanobacterial design cell of Synechocystis PCC 6803. X-ray-structure-based rational design and the allocation of specific interaction residues by NMR-analysis led to the construction of Fd- and FNR-mutants, which in appropriate combination enabled an about 18-fold enhanced electron flow from Fd to HydA1 (in competition with equimolar amounts of FNR) in in vitro assays. The negative impact of these mutations on the Fd-FNR electron transport which indirectly facilitates H₂ production (with a contribution of ≤42% by FNR variants and ≤23% by Fd-variants) and the direct positive impact on the Fd-HydA1 electron transport (≤23% by Fd-mutants) provide an excellent basis for the construction of a hydrogen-producing design cell and the study of photosynthetic efficiency-optimization with cyanobacteria.

FNR Regulates the Expression of Important Virulence Factors Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is the etiologic agent of colibacillosis, an important cause of morbidity and mortality in poultry. Though, many virulence factors associated with APEC pathogenicity are known, their regulation remains unclear. FNR (fumarate and nitrate reduction) is a well-known global regulator that works as an oxygen sensor and has previously been described as a virulence regulator in bacterial pathogens. The goal of this study was to examine the role of FNR in the regulation of APEC virulence factors, such as Type I fimbriae, and processes such as adherence and invasion, type VI secretion, survival during oxidative stress, and growth in iron-restricted environments. To accomplish this goal, APEC O1, a well-characterized, highly virulent, and fully sequenced strain of APEC harboring multiple virulence mechanisms, some of which are plasmid-linked, was compared to its FNR mutant for expression of various virulence traits. Deletion of FNR was found to affect APEC O1's adherence, invasion and expression of ompT, a plasmid-encoded outer membrane protein, type I fimbriae, and aatA, encoding an autotransporter. Indeed, the fnr⁻ mutant showed an 8-fold reduction in expression of type I fimbriae and a highly significant (P < 0.0001) reduction in expression of fimA, ompT (plasmid-borne), and aatA. FNR was also found to regulate expression of the type VI secretion system, affecting the expression of vgrG. Further, FNR was found to be important to APEC O1's growth in iron-deficient media and survival during oxidative stress with the mutant showing a 4-fold decrease in tolerance to oxidative stress, as compared to the wild type. Thus, our results suggest that FNR functions as an important regulator of APEC virulence.

Expression of Flavone Synthase II and Flavonoid 3'-Hydroxylase Is Associated with Color Variation in Tan-Colored Injured Leaves of Sorghum

Sorghum (Sorghum bicolor L. Moench) exhibits various color changes in injured leaves in response to cutting stress. Here, we aimed to identify key genes for the light brown and dark brown color variations in tan-colored injured leaves of sorghum. For this purpose, sorghum M36001 (light brown injured leaves), Nakei-MS3B (purple), and a progeny, #7 (dark brown), from Nakei-MS3B × M36001, were used. Accumulated pigments were detected by using high-performance liquid chromatography: M36001 accumulated only apigenin in its light brown leaves; #7 accumulated both luteolin and a small amount of apigenin in its dark brown leaves, and Nakei-MS3B accumulated 3-deoxyanthocyanidins (apigeninidin and luteolinidin) in its purple leaves. Apigenin or luteolin glucoside derivatives were also accumulated, in different proportions. Differentially expressed genes before and after cutting stress were identified by using RNA sequencing (RNA-seq). Integration of our metabolic and RNA-seq analyses suggested that expression of only flavone synthase II (FNSII) led to the synthesis of apigenin in M36001, expression of both FNSII and flavonoid 3'-hydroxylase (F3'H) led to the synthesis of apigenin and luteolin in #7, and expression of both flavanone 4-reductase and F3'H led to the synthesis of 3-deoxyanthocyanidins in Nakei-MS3B. These results suggest that expression of FNSII is related to the synthesis of flavones (apigenin and luteolin) and the expression level of F3'H is related to the balance of apigenin and luteolin. Expression of FNSII and F3'H is thus associated with dark or light brown coloration in tan-colored injured leaves of sorghum.

Data supporting the absence of FNR dynamic photosynthetic membrane recruitment in trol mutants

In photosynthesis, the flavoenzyme ferredoxin:NADP(+) oxidoreductase (FNR) catalyses the final electron transfer from ferredoxin to NADP(+), which is considered as the main pathway of high-energy electron partitioning in chloroplasts (DOI: 10.1111/j.1365-313X.2009.03999.x[1], DOI: 10.1038/srep10085[2]). Different detergents and pH treatments of photosynthetic membranes isolated from the Arabidopsis wild-type (WT) and the loss-of-function mutants of the thylakoid rhodanase-like protein TROL (trol), pre-acclimated to either dark, growth-light, or high-light conditions, were used to probe the strength of FNR-membrane associations. Detergents β-DM (decyl-β-D-maltopyranoside) or β-DDM (n-dodecyl-β-D-maltopyranoside) were used to test the stability of FNR binding to the thylakoid membranes, and to assess different membrane domains containing FNR. Further, the extraction conditions mimicked pH status of chloroplast stroma during changing light regimes. Plants without TROL are incapable of the dynamic FNR recruitment to the photosynthetic membranes.

Tract Orientation and Angular Dispersion Deviation Indicator (TOADDI): A framework for single-subject analysis in diffusion tensor imaging

The purpose of this work is to develop a framework for single-subject analysis of diffusion tensor imaging (DTI) data. This framework is termed Tract Orientation and Angular Dispersion Deviation Indicator (TOADDI) because it is capable of testing whether an individual tract as represented by the major eigenvector of the diffusion tensor and its corresponding angular dispersion are significantly different from a group of tracts on a voxel-by-voxel basis. This work develops two complementary statistical tests based on the elliptical cone of uncertainty, which is a model of uncertainty or dispersion of the major eigenvector of the diffusion tensor. The orientation deviation test examines whether the major eigenvector from a single subject is within the average elliptical cone of uncertainty formed by a collection of elliptical cones of uncertainty. The shape deviation test is based on the two-tailed Wilcoxon-Mann-Whitney two-sample test between the normalized shape measures (area and circumference) of the elliptical cones of uncertainty of the single subject against a group of controls. The False Discovery Rate (FDR) and False Non-discovery Rate (FNR) were incorporated in the orientation deviation test. The shape deviation test uses FDR only. TOADDI was found to be numerically accurate and statistically effective. Clinical data from two Traumatic Brain Injury (TBI) patients and one non-TBI subject were tested against the data obtained from a group of 45 non-TBI controls to illustrate the application of the proposed framework in single-subject analysis. The frontal portion of the superior longitudinal fasciculus seemed to be implicated in both tests (orientation and shape) as significantly different from that of the control group. The TBI patients and the single non-TBI subject were well separated under the shape deviation test at the chosen FDR level of 0.0005. TOADDI is a simple but novel geometrically based statistical framework for analyzing DTI data. TOADDI may be found useful in single-subject, graph-theoretic and group analyses of DTI data or DTI-based tractography techniques.

A discrete role for FNR in the transcriptional response to moderate changes in oxygen by Haemophilus influenzae Rd KW20

The survival by pathogenic bacteria within the specific conditions of an anatomical niche is critical for their persistence. These conditions include the combination of toxic chemicals, such as reactive oxygen (ROS) and reactive nitrogen species (RNS), with factors relevant to cell growth, such as oxygen. Haemophilus influenzae senses oxygen levels largely through the redox state of the intracellular fumarate-nitrate global regulator (FNR). H. influenzae certainly encounters oxygen levels that fluctuate, but in reality, these would rarely reach a state that results in FNR being fully reduced or oxidized. We were therefore interested in the response of H. influenzae to ROS and RNS at moderately high or low oxygen levels and the corresponding role of FNR. At these levels of oxygen, even though the growth rate of an H. influenzae fnr mutant was similar to wild type, its ROS and RNS tolerance was significantly different. Additionally, the subtle changes in oxygen did alter the whole cell transcriptional profile and this was different between the wild type and fnr mutant strains. It was the changed whole cell profile that impacted on ROS/RNS defence, but surprisingly, the FNR-regulated, anaerobic nitrite reductase (NrfA) continued to be expressed and had a role in this phenotype.

Transcriptional regulation of bacterial virulence gene expression by molecular oxygen and nitric oxide

Molecular oxygen (O₂) and nitric oxide (NO) are diatomic gases that play major roles in infection. The host innate immune system generates reactive oxygen species and NO as bacteriocidal agents and both require O₂ for their production. Furthermore, the ability to adapt to changes in O₂ availability is crucial for many bacterial pathogens, as many niches within a host are hypoxic. Pathogenic bacteria have evolved transcriptional regulatory systems that perceive these gases and respond by reprogramming gene expression. Direct sensors possess iron-containing co-factors (iron–sulfur clusters, mononuclear iron, heme) or reactive cysteine thiols that react with O₂ and/or NO. Indirect sensors perceive the physiological effects of O₂ starvation. Thus, O₂ and NO act as environmental cues that trigger the coordinated expression of virulence genes and metabolic adaptations necessary for survival within a host. Here, the mechanisms of signal perception by key O₂- and NO-responsive bacterial transcription factors and the effects on virulence gene expression are reviewed, followed by consideration of these aspects of gene regulation in two major pathogens, Staphylococcus aureus and Mycobacterium tuberculosis.

Glyceraldehyde-3-phosphate dehydrogenase is regulated by ferredoxin-NADP reductase in the diatom Asterionella formosa

Diatoms are a widespread and ecologically important group of heterokont algae that contribute c. 20% to global productivity. Previous work has shown that regulation of their key Calvin cycle enzymes differs from that of the Plantae, and that in crude extracts, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) can be inhibited by nicotinamide adenine dinucleotide phosphate reduced (NADPH) under oxidizing conditions. The freshwater diatom, Asterionella formosa, was studied using enzyme kinetics, chromatography, surface plasmon resonance, mass spectrometry and sequence analysis to determine the mechanism behind this GAPDH inhibition. GAPDH interacted with ferredoxin-nicotinamide adenine dinucleotide phosphate (NADP) reductase (FNR) from the primary phase of photosynthesis, and the small chloroplast protein, CP12. Sequences of copurified GAPDH and FNR were highly homologous with published sequences. However, the widespread ternary complex among GAPDH, phosphoribulokinase and CP12 was absent. Activity measurements under oxidizing conditions showed that NADPH can inhibit GAPDH-CP12 in the presence of FNR, explaining the earlier observed inhibition within crude extracts. Diatom plastids have a distinctive metabolism, including the lack of the oxidative pentose phosphate pathway, and so cannot produce NADPH in the dark. The observed down-regulation of GAPDH in the dark may allow NADPH to be rerouted towards other reductive processes contributing to their ecological success.

Oxygen sensing strategies in mammals and bacteria

The ability to sense and adapt to changes in pO2 is crucial for basic metabolism in most organisms, leading to elaborate pathways for sensing hypoxia (low pO2). This review focuses on the mechanisms utilized by mammals and bacteria to sense hypoxia. While responses to acute hypoxia in mammalian tissues lead to altered vascular tension, the molecular mechanism of signal transduction is not well understood. In contrast, chronic hypoxia evokes cellular responses that lead to transcriptional changes mediated by the hypoxia inducible factor (HIF), which is directly controlled by post-translational hydroxylation of HIF by the non-heme Fe(II)/αKG-dependent enzymes FIH and PHD2. Research on PHD2 and FIH is focused on developing inhibitors and understanding the links between HIF binding and the O2 reaction in these enzymes. Sulfur speciation is a putative mechanism for acute O2-sensing, with special focus on the role of H2S. This sulfur-centered model is discussed, as are some of the directions for further refinement of this model. In contrast to mammals, bacterial O2-sensing relies on protein cofactors that either bind O2 or oxidatively decompose. The sensing modality for bacterial O2-sensors is either via altered DNA binding affinity of the sensory protein, or else due to the actions of a two-component signaling cascade. Emerging data suggests that proteins containing a hemerythrin-domain, such as FBXL5, may serve to connect iron sensing to O2-sensing in both bacteria and humans. As specific molecular machinery becomes identified, these hypoxia sensing pathways present therapeutic targets for diseases including ischemia, cancer, or bacterial infection.

Genome wide survey and molecular modeling of hypothetical proteins containing 2Fe-2S and FMN binding domains suggests Rieske Dioxygenase Activity highlighting their potential roles in bioremediation

‘Conserved hypothetical’ proteins pose a challenge not just for functional genomics, but also to biology in general. As long as there are hundreds of conserved proteins with unknown function in model organisms such as Escherichia coli, Bacillus subtilis or Saccharomyces cerevisiae, any discussion towards a ‘complete’ understanding of these biological systems will remain a wishful thinking. Insilico approaches exhibit great promise towards attempts that enable appreciating the plausible roles of these hypothetical proteins. Among the majority of genomic proteins, two-thirds in unicellular organisms and more than 80% in metazoa, are multi-domain proteins, created as a result of gene duplication events. Aromatic ring-hydroxylating dioxygenases, also called Rieske dioxygenases (RDOs), are class of multi-domain proteins that catalyze the initial step in microbial aerobic degradation of many aromatic compounds. Investigations here address the computational characterization of hypothetical proteins containing Ferredoxin and Flavodoxin signatures. Consensus sequence of each class of oxidoreductase was obtained by a phylogenetic analysis, involving clustering methods based on evolutionary relationship. A synthetic sequence was developed by combining the consensus, which was used as the basis to search for their homologs via BLAST. The exercise yielded 129 multidomain hypothetical proteins containing both 2Fe-2S (Ferredoxin) and FNR (Flavodoxin) domains. In the current study, 17 proteins with N-terminus FNR domain and C-terminus 2Fe-2S domain are characterized, through homology modelling and docking exercises which suggest dioxygenase activity indicate their plausible roles in degradation of aromatic moieties.

Proteomic analysis of pakchoi leaves and roots under glycine-nitrogen conditions

The physiological and differential proteomic responses of pakchoi leaves and roots to glycine-nitrogen (Gly-N) treatments were determined. Two pakchoi (Brassica campestris ssp. chinensis L. Makino. var. communis Tsen et Lee) cultivars, 'Huawang' and 'Wuyueman', were grown under sterile hydroponic conditions with different N forms (Gly-N and nitrate-N). Gly-N-treated pakchoi exhibited decreased fresh weights, total N uptake, leaf areas, and net photosynthetic rates than those treated with nitrate-N. Differentially regulated proteins were selected after image analysis and identified using MALDI-TOF MS. A total of 23 proteins was up- or down-regulated following Gly-N treatment. These spots are involved in several processes, such as energy synthesis, N metabolism, photosynthesis, and active antioxidant defense mechanisms, that could enhance plant adaptation to Gly-N. The superior Gly tolerance of 'Huawang' was predominantly associated with a less severe down-regulation of proteins that are involved in the electron transport chain and N metabolism. Other factors could include less ribulose-1,5-bisphosphate carboxylase/oxygenase turnover or a higher up-regulation of stress defense proteins. These characteristics demonstrated that maintaining ATP synthesis, N metabolism, photosynthesis, and active defense mechanisms play a critical role in pakchoi adaptation to Gly-N.

External loops at the ferredoxin-NADP(+) reductase protein-partner binding cavity contribute to substrates allocation

Ferredoxin-NADP(+) reductase (FNR) is the structural prototype of a family of FAD-containing reductases that catalyze electron transfer between low potential proteins and NAD(P)(+)/H, and that display a two-domain arrangement with an open cavity at their interface. The inner part of this cavity accommodates the reacting atoms during catalysis. Loops at its edge are highly conserved among plastidic FNRs, suggesting that they might contribute to both flavin stabilization and competent disposition of substrates. Here we pay attention to two of these loops in Anabaena FNR. The first is a sheet-loop-sheet motif, loop102-114, that allocates the FAD adenosine. It was thought to determine the extended FAD conformation, and, indirectly, to modulate isoalloxazine electronic properties, partners binding, catalytic efficiency and even coenzyme specificity. The second, loop261-269, contains key residues for the allocation of partners and coenzyme, including two glutamates, Glu267 and Glu268, proposed as candidates to facilitate the key displacement of the C-terminal tyrosine (Tyr303) from its stacking against the isoalloxazine ring during the catalytic cycle. Our data indicate that the main function of loop102-114 is to provide the inter-domain cavity with flexibility to accommodate protein partners and to guide the coenzyme to the catalytic site, while the extended conformation of FAD must be induced by other protein determinants. Glu267 and Glu268 appear to assist the conformational changes that occur in the loop261-269 during productive coenzyme binding, but their contribution to Tyr303 displacement is minor than expected. Additionally, loop261-269 appears a determinant to ensure reversibility in photosynthetic FNRs.

How does iron deficiency disrupt the electron flow in photosystem I of lettuce leaves?

The changes observed photosystem I activity of lettuce plants exposed to iron deficiency were investigated. Photooxidation/reduction kinetics of P700 monitored as ΔA820 in the presence and absence of electron transport inhibitors and acceptors demonstrated that deprivation in iron decreased the population of active photo-oxidizable P700. In the complete absence of iron, the addition of plant inhibitors (DCMU and MV) could not recover the full PSI activity owing to the abolition of a part of P700 centers. In leaves with total iron deprivation (0μM Fe), only 15% of photo-oxidizable P700 remained. In addition, iron deficiency appeared to affect the pool size of NADP(+) as shown by the decline in the magnitude of the first phase of the photooxidation kinetics of P700 by FR-light. Concomitantly, chlorophyll content gradually declined with the iron concentration added to culture medium. In addition, pronounced changes were found in chlorophyll fluorescence spectra. Also, the global fluorescence intensity was affected. The above changes led to an increased rate of cyclic electron transport around PSI mainly supported by stromal reductants.

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization of posttranslational modifications. It is furthermore common practice to quantify the identified entities, a task supported by a panel of different methods. Finally, the results can also be enriched with functional knowledge gained on the proteins, detecting for instance differentially expressed gene ontology terms or biological pathways. In this study, we review the resources, methods and tools available for the researcher to achieve such a quantitative functional analysis. These include statistics for the post-processing of identification and quantification results, online resources and public repositories. With a focus on free but user-friendly software, preferably also open-source, we provide a list of tools designed to help the researcher manage the vast amount of data generated. We also indicate where such applications currently remain lacking. Moreover, we stress the eventual pitfalls of every step of such studies. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.

Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer

NADH-Cytochrome b5 reductase (b5R), a flavoprotein consisting of NADH and flavin adenine dinucleotide (FAD) binding domains, catalyzes electron transfer from the two-electron carrier NADH to the one-electron carrier cytochrome b5 (Cb5). The crystal structures of both the fully reduced form and the oxidized form of porcine liver b5R were determined. In the reduced b5R structure determined at 1.68Å resolution, the relative configuration of the two domains was slightly shifted in comparison with that of the oxidized form. This shift resulted in an increase in the solvent-accessible surface area of FAD and created a new hydrogen-bonding interaction between the N5 atom of the isoalloxazine ring of FAD and the hydroxyl oxygen atom of Thr66, which is considered to be a key residue in the release of a proton from the N5 atom. The isoalloxazine ring of FAD in the reduced form is flat as in the oxidized form and stacked together with the nicotinamide ring of NAD(+). Determination of the oxidized b5R structure, including the hydrogen atoms, determined at 0.78Å resolution revealed the details of a hydrogen-bonding network from the N5 atom of FAD to His49 via Thr66. Both of the reduced and oxidized b5R structures explain how backflow in this catalytic cycle is prevented and the transfer of electrons to one-electron acceptors such as Cb5 is accelerated. Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R.

Genome-scale approaches to identify genes essential for Haemophilus influenzae pathogenesis

Haemophilus influenzae is a Gram-negative bacterium that has no identified natural niche outside of the human host. It primarily colonizes the nasopharyngeal mucosa in an asymptomatic mode, but has the ability to disseminate to other anatomical sites to cause otitis media, upper, and lower respiratory tract infections, septicemia, and meningitis. To persist in diverse environments the bacterium must exploit and utilize the nutrients and other resources available in these sites for optimal growth/survival. Recent evidence suggests that regulatory factors that direct such adaptations also control virulence determinants required to resist and evade immune clearance mechanisms. In this review, we describe the recent application of whole-genome approaches that together provide insight into distinct survival mechanisms of H. influenzae in the context of different sites of pathogenesis.

Interaction of Ferredoxin-NADP(+) Reductase with its Substrates: Optimal Interaction for Efficient Electron Transfer

Electron transfer (ET) reactions in systems involving proteins require an oriented interaction between electron donor and acceptor in order to accommodate their respective redox centres in optimal orientation for efficient ET. Such type of reactions are critical for the maintenance of the physiological functions of living organisms, since they are implicated in vital actions, as is, for example, in the photosynthetic ET chain that leads to NADPH reduction. In this particular case, a small redox protein ET chain is responsible for ET from Photosystem I (PS I) to NADP(+). In this system the enzyme responsible for NADP(+) reduction is ferredoxin-NADP(+) reductase (FNR), a FAD-containing NADP(+) dependent reductase. In order to produce such reduction, this enzyme receives electrons from a [2Fe-2S] plant-type ferredoxin (Fd), which is previously reduced by PS I. Moreover, in the case of some algae and cyanobacteria, an FMN-dependent protein, flavodoxin (Fld), has been shown to replace Fd in this function. The processes of interaction and ET between FNR and all of its substrates involved in the photosynthetic ET chain, namely Fd, Fld and NADP(+)/H have been extensively investigated in recent years using a large number of techniques, including the introduction of site-specific mutations in combination with kinetic and structural studies of the produced mutants. The present manuscript summarises the information so far reported for an efficient interaction between FNR and its substrates, compares such information with that revealed by other systems for which the FNR structure is a prototype and, finally, discusses the implications of the processes of association in ET between FNR and its substrates.