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Biological Research Feb 2022Aerobic metabolism generates reactive oxygen species that may cause critical harm to the cell. The aim of this study is the characterization of the stress responses in...
BACKGROUND
Aerobic metabolism generates reactive oxygen species that may cause critical harm to the cell. The aim of this study is the characterization of the stress responses in the model aromatic-degrading bacterium Paraburkholderia xenovorans LB400 to the oxidizing agents paraquat and HO.
METHODS
Antioxidant genes were identified by bioinformatic methods in the genome of P. xenovorans LB400, and the phylogeny of its OxyR and SoxR transcriptional regulators were studied. Functionality of the transcriptional regulators from strain LB400 was assessed by complementation with LB400 SoxR of null mutant P. aeruginosa ΔsoxR, and the construction of P. xenovorans pIZoxyR that overexpresses OxyR. The effects of oxidizing agents on P. xenovorans were studied measuring bacterial susceptibility, survival and ROS formation after exposure to paraquat and HO. The effects of these oxidants on gene expression (qRT-PCR) and the proteome (LC-MS/MS) were quantified.
RESULTS
P. xenovorans LB400 possesses a wide repertoire of genes for the antioxidant defense including the oxyR, ahpC, ahpF, kat, trxB, dpsA and gorA genes, whose orthologous genes are regulated by the transcriptional regulator OxyR in E. coli. The LB400 genome also harbors the soxR, fumC, acnA, sodB, fpr and fldX genes, whose orthologous genes are regulated by the transcriptional regulator SoxR in E. coli. The functionality of the LB400 soxR gene was confirmed by complementation of null mutant P. aeruginosa ΔsoxR. Growth, susceptibility, and ROS formation assays revealed that LB400 cells were more susceptible to paraquat than HO. Transcriptional analyses indicated the upregulation of the oxyR, ahpC1, katE and ohrB genes in LB400 cells after exposure to HO, whereas the oxyR, fumC, ahpC1, sodB1 and ohrB genes were induced in presence of paraquat. Proteome analysis revealed that paraquat induced the oxidative stress response proteins AhpCF and DpsA, the universal stress protein UspA and the RNA chaperone CspA. Both oxidizing agents induced the Ohr protein, which is involved in organic peroxide resistance. Notably, the overexpression of the LB400 oxyR gene in P. xenovorans significantly decreased the ROS formation and the susceptibility to paraquat, suggesting a broad OxyR-regulated antioxidant response.
CONCLUSIONS
This study showed that P. xenovorans LB400 possess a broad range oxidative stress response, which explain the high resistance of this strain to the oxidizing compounds paraquat and HO.
Topics: Bacterial Proteins; Burkholderiaceae; Chromatography, Liquid; Escherichia coli; Escherichia coli Proteins; Gene Expression Regulation, Bacterial; Hydrogen Peroxide; Oxidation-Reduction; Oxidative Stress; Repressor Proteins; Tandem Mass Spectrometry
PubMed: 35184754
DOI: 10.1186/s40659-022-00373-7 -
Biomolecules Jan 2021A novel temperature stable alkaline protease yielding bacteria was isolated from the soils of Dachigam National Park, which is known to be inhabited by a wide variety of...
A novel temperature stable alkaline protease yielding bacteria was isolated from the soils of Dachigam National Park, which is known to be inhabited by a wide variety of endemic plant and animal species of Western Himalaya. This high-potential protease producing isolate was characterized and identified as strain HM48 by morphological, Gram's staining and biochemical techniques followed by molecular characterization using 16S rRNA approach. The extracellular protease of HM48 was purified by precipitating with ammonium sulfate (80%), followed by dialysis and Gel filtration chromatography increasing its purity by 5.8-fold. The SDS-PAGE analysis of the purified enzyme confirmed a molecular weight of about ≈25 kDa. The enzyme displayed exceptional activity in a broad temperature range (10-90 °C) at pH 8.0, retaining its maximum at 70 °C, being the highest reported for this proteolytic sp., with K and V of 11.71 mg/mL and 357.14 µmol/mL/min, respectively. The enzyme exhibited remarkable activity and stability against various metal ions, surfactants, oxidizing agent (HO), organic solvents and displayed outstanding compatibility with widely used detergents. This protease showed effective wash performance by exemplifying complete blood and egg-yolk stains removal at 70 °C and efficiently disintegrated chicken feathers making it of vital importance for laundry purpose and waste management. For functional analysis, protease gene amplification of strain HM48 yielded a nucleotide sequence of about 700 bp, which, when checked against the available sequences in NCBI, displayed similarity with subtilisin-like serine protease of . The structure of this protease and its highest-priority substrate β-casein was generated through protein modeling. These protein models were validated through futuristic algorithms following which protein-protein (protease from HM48 and β-casein) docking was performed. The interaction profile of these proteins in the docked state with each other was also generated, shedding light on their finer details. Such attributes make this thermally stable protease novel and suitable for high-temperature industrial and environmental applications.
Topics: Animals; Bacillus amyloliquefaciens; Caseins; Chickens; Edetic Acid; Enzyme Stability; Feathers; Geography; Hot Temperature; Hydrogen-Ion Concentration; India; Ions; Kinetics; Metals; Microbial Sensitivity Tests; Molecular Docking Simulation; Molecular Weight; Oxidants; Peptide Hydrolases; Proteolysis; RNA, Ribosomal, 16S; Reproducibility of Results; Soil Microbiology; Solvents; Substrate Specificity; Surface-Active Agents
PubMed: 33477596
DOI: 10.3390/biom11010117 -
Scientific Reports Feb 2020Felids have a high incidence of chronic kidney disease (CKD), for which the most common renal lesion is chronic interstitial nephritis (CIN). CIN can be induced by...
Felids have a high incidence of chronic kidney disease (CKD), for which the most common renal lesion is chronic interstitial nephritis (CIN). CIN can be induced by tissue oxidative stress, which is determined by the cellular balance of pro- and anti-oxidant metabolites. Fish-flavoured foods are more often fed to cats than dogs, and such foods tend to have higher arsenic content. Arsenic is a pro-oxidant metallic element. We propose that renal accumulation of pro-oxidant elements such as arsenic and depletion of anti-oxidant elements such as zinc, underpin the high incidence of CIN in domestic cats. Total arsenic and other redox-reactive metal elements were measured in kidneys (after acid-digestion) and urine (both by inductively-coupled plasma-mass spectrometry) of domestic cats (kidneys, n = 56; urine, n = 21), domestic dogs (kidneys, n = 54; urine, n = 28) and non-domesticated Scottish Wildcats (kidneys, n = 17). Renal lesions were graded by severity of CIN. In our randomly sampled population, CIN was more prevalent in domestic cat versus domestic dog (51%, n = 32 of 62 cats; 15%, 11 of 70 dogs were positive for CIN, respectively). CIN was absent from all Scottish wildcats. Tissue and urinary (corrected for creatinine) arsenic content was higher in domestic cats, relative to domestic dogs and wildcats. Urine arsenic was higher in domestic cats and dogs with CIN. Arsenobetaine, an organic and relatively harmless species of arsenic, was the primary form of arsenic found in pet foods. In summary, the kidneys of domestic cats appear to have greater levels of pro-oxidant trace elements, as compared to dogs and wildcats. Since there was no difference in renal arsenic levels in cats with or without CIN, renal arsenic accumulation does not appear a primary driver of excess CIN in cats. Given clear differences in renal handling of pro vs. anti-oxidant minerals between cats and dogs, further in vivo balance studies are warranted. These may then inform species-specific guidelines for trace element incorporation into commercial diets.
Topics: Animal Feed; Animals; Antioxidants; Arsenic; Arsenicals; Cat Diseases; Cats; Dogs; Female; Fibrosis; Fishes; Food Contamination; Kidney; Male; Mass Spectrometry; Nephritis, Interstitial; Oxidants; Oxidation-Reduction; Reactive Oxygen Species; Renal Insufficiency, Chronic; Trace Elements
PubMed: 32081923
DOI: 10.1038/s41598-020-59876-6 -
Scientific Reports Nov 2015Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy...
Graphene oxide (GO) is an emerging material for energy and environmental applications, but it has been primarily produced using chemical processes involving high energy consumption and hazardous chemicals. In this study, we reported a new bioelectrochemical method to produce GO from graphite under ambient conditions without chemical amendments, value-added organic compounds and high rate H2 were also produced. Compared with abiotic electrochemical electrolysis control, the microbial assisted graphite oxidation produced high rate of graphite oxide and graphene oxide (BEGO) sheets, CO2, and current at lower applied voltage. The resultant electrons are transferred to a biocathode, where H2 and organic compounds are produced by microbial reduction of protons and CO2, respectively, a process known as microbial electrosynthesis (MES). Pseudomonas is the dominant population on the anode, while abundant anaerobic solvent-producing bacteria Clostridium carboxidivorans is likely responsible for electrosynthesis on the cathode. Oxygen production through water electrolysis was not detected on the anode due to the presence of facultative and aerobic bacteria as O2 sinkers. This new method provides a sustainable route for producing graphene materials and renewable H2 at low cost, and it may stimulate a new area of research in MES.
Topics: Carbon Dioxide; Clostridium; Electrochemical Techniques; Electrodes; Graphite; Hydrogen; Oxidation-Reduction; Oxides; Oxygen; Pseudomonas; Water
PubMed: 26573014
DOI: 10.1038/srep16242 -
Scientific Reports Dec 2019Manganese (Mn) oxide minerals influence the availability of organic carbon, nutrients and metals in the environment. Oxidation of Mn(II) to Mn(III/IV) oxides is largely...
Manganese (Mn) oxide minerals influence the availability of organic carbon, nutrients and metals in the environment. Oxidation of Mn(II) to Mn(III/IV) oxides is largely promoted by the direct and indirect activity of microorganisms. Studies of biogenic Mn(II) oxidation have focused on bacteria and fungi, with phototrophic organisms (phototrophs) being generally overlooked. Here, we isolated phototrophs from Mn removal beds in Pennsylvania, USA, including fourteen Chlorophyta (green algae), three Bacillariophyta (diatoms) and one cyanobacterium, all of which consistently formed Mn(III/IV) oxides. Isolates produced cell-specific oxides (coating some cells but not others), diffuse biofilm oxides, and internal diatom-specific Mn-rich nodules. Phototrophic Mn(II) oxidation had been previously attributed to abiotic oxidation mediated by photosynthesis-driven pH increases, but we found a decoupling of Mn oxide formation and pH alteration in several cases. Furthermore, cell-free filtrates of some isolates produced Mn oxides at specific time points, but this activity was not induced by Mn(II). Manganese oxide formation in cell-free filtrates occurred via reaction with the oxygen radical superoxide produced by soluble extracellular proteins. Given the known widespread ability of phototrophs to produce superoxide, the contribution of phototrophs to Mn(II) oxidation in the environment may be greater and more nuanced than previously thought.
Topics: Chlorophyta; Cyanobacteria; Diatoms; Hydrogen-Ion Concentration; Manganese Compounds; Metabolic Networks and Pathways; Oxidation-Reduction; Oxides; Phototrophic Processes; Superoxides
PubMed: 31796791
DOI: 10.1038/s41598-019-54403-8 -
FEMS Microbiology Ecology Jul 2015In this study, the effects, fate and transport of ENPs in wastewater treatment plants (WWTP) were investigated using three parallel pilot WWTPs operated under identical...
In this study, the effects, fate and transport of ENPs in wastewater treatment plants (WWTP) were investigated using three parallel pilot WWTPs operated under identical conditions. The WWTPs were spiked with (i) an ENP mixture consisting of silver oxide, titanium dioxide and zinc oxide, and (ii) bulk metal salts. The third plant served as control (unspiked). ENP effects were evaluated for (i) bulk contaminant removal, (ii) activated sludge (AS) process performance, (iii) microbial community structure and dynamics and (iv) microbial inhibition. ENPs showed a strong affinity for biosolids and induced a specific oxygen uptake rate two times higher than the control. The heterotrophic biomass retained its ability to nitrify and degrade organic matter. However, non-recovery of ammonia- and nitrite-oxidizing bacteria such as Nitrosomonas, Nitrobacter or Nitrospira in the ENP spiked reactors suggests selective inhibitory effects. The results further suggest that ENPs and metal salts have antimicrobial properties which can reduce synthesis of extracellular polymeric substances and therefore floc formation. Scanning electron microscopy evidenced selective damage to some microbes, whereas lipid fingerprinting and 454 pyrosequencing indicated a temporal shift in the microbial community structure and diversity. Acidovorax, Rhodoferax, Comamonas and Methanosarcina were identified as nano-tolerant species. Competitive growth advantage of the nano-tolerant species influenced the removal processes and unlike other xenobiotic compounds, ENPs can hasten the natural selection of microbial species in AS.
Topics: Ammonia; Biomass; Comamonas; Heterotrophic Processes; Methanosarcina; Nanoparticles; Nitrification; Nitrites; Nitrobacter; Nitrosomonas; Oxides; Oxygen; Sewage; Silver Compounds; Titanium; Water Purification; Zinc Oxide
PubMed: 26187478
DOI: 10.1093/femsec/fiv082 -
Scientific Reports Mar 2022The idea of applying ultrasound (US) as a green activation method in chemical transformations, especially in catalytic alcohol oxidations, technically and ecologically...
The idea of applying ultrasound (US) as a green activation method in chemical transformations, especially in catalytic alcohol oxidations, technically and ecologically appeals to chemists. In the present work, as an attempt to fulfill the idea of designing an eco-friendly system to oxidize alcoholic substrates into corresponding aldehydes, we developed multifunctional tungstate-decorated CQD base catalyst, A-CQDs/W, and examined its sonooxidation performance in presence of HO as a green oxidant in aqua media. By comparing the catalyst performance in oxidize benzyl alcohol as a testing model to benzaldehyde (BeOH) prior and after US irradiation-trace vs 93%- the key role of ultrasonic irradiation in achieving high yield is completely appreciated. Exceptional thermal and compression condition that is created as a result of acoustic waves is in charge of unparalleled yield results in this type of activation method. The immense degree of reagent interaction in this method, ensures the maximum yield in notably low time, which in turn leads to decrease in the number of unreacted reagents and by-products. Meanwhile, the need for using toxic organic solvents and hazardous oxidants, auxiliaries and phase transfer catalyst (PTC) is completely obviated.
Topics: Alcohols; Aldehydes; Catalysis; Hydrogen Peroxide; Oxidants; Tungsten Compounds
PubMed: 35233016
DOI: 10.1038/s41598-022-06874-5 -
Molecules (Basel, Switzerland) Jun 2020A simple, efficient, and selective oxidation under flow conditions of sulfides into their corresponding sulfoxides and sulfones is reported herein, using as a catalyst...
A simple, efficient, and selective oxidation under flow conditions of sulfides into their corresponding sulfoxides and sulfones is reported herein, using as a catalyst perselenic acid generated in situ by the oxidation of selenium (IV) oxide in a diluted aqueous solution of hydrogen peroxide as the final oxidant. The scope of the proposed methodology was investigated using aryl alkyl sulfides, aryl vinyl sulfides, and dialkyl sulfides as substrates, evidencing, in general, a good applicability. The scaled-up synthesis of (methylsulfonyl)benzene was also demonstrated, leading to its gram-scale preparation.
Topics: Catalysis; Hydrogen Peroxide; Molecular Structure; Oxidation-Reduction; Selenium Oxides; Sulfides; Sulfones; Sulfoxides
PubMed: 32545303
DOI: 10.3390/molecules25112711 -
The ISME Journal Apr 2018High and low rates of ammonium supply are believed to favour ammonia-oxidising bacteria (AOB) and archaea (AOA), respectively. Although their contrasting affinities for...
High and low rates of ammonium supply are believed to favour ammonia-oxidising bacteria (AOB) and archaea (AOA), respectively. Although their contrasting affinities for ammonium are suggested to account for these differences, the influence of ammonia concentration on AOA and AOB has not been tested under environmental conditions. In addition, while both AOB and AOA contribute to nitrous oxide (NO) emissions from soil, NO yields (NO-N produced per NO-N generated from ammonia oxidation) of AOA are lower, suggesting lower emissions when AOA dominate ammonia oxidation. This study tested the hypothesis that ammonium supplied continuously at low rates is preferentially oxidised by AOA, with lower NO yield than expected for AOB-dominated processes. Soil microcosms were supplied with water, urea or a slow release, urea-based fertiliser and 1-octyne (inhibiting only AOB) was applied to distinguish AOA and AOB activity and associated NO production. Low ammonium supply, from mineralisation of organic matter, or of the fertiliser, led to growth, ammonia oxidation and NO production by AOA only, with low NO yield. High ammonium supply, from free urea within the fertiliser or after urea addition, led to growth of both groups, but AOB-dominated ammonia oxidation was associated with twofold greater NO yield than that dominated by AOA. This study therefore demonstrates growth of both AOA and AOB at high ammonium concentration, confirms AOA dominance during low ammonium supply and suggests that slow release or organic fertilisers potentially mitigate NO emissions through differences in niche specialisation and NO production mechanisms in AOA and AOB.
Topics: Ammonia; Archaea; Fertilizers; Nitrification; Nitrous Oxide; Oxidation-Reduction; Soil; Soil Microbiology; Urea
PubMed: 29386627
DOI: 10.1038/s41396-017-0025-5 -
Chemosphere Mar 2024Oxides of silicon (Si), manganese (Mn), and zinc (Zn) have been used as soil amendments to reduce As mobility and uptake in paddy soil systems. However, these amendments...
Temporal development of arsenic speciation and extractability in acidified and non-acidified paddy soil amended with silicon-rich fly ash and manganese- or zinc-oxides under flooded and drainage conditions.
Oxides of silicon (Si), manganese (Mn), and zinc (Zn) have been used as soil amendments to reduce As mobility and uptake in paddy soil systems. However, these amendments are hypothesized to be affected differently depending on the soil pH and their effect on As speciation in rice paddy systems is not fully understood. Herein, we used a microcosm experiment to investigate the effects of natural Si-rich fly ash and synthetic Mn and Zn oxides on the temporal development of porewater chemistry, including aqueous As speciation (As(III), As(V), MMA, DMA, and DMMTA) and solid-phase As solubility, in a naturally calcareous soil with or without soil acidification (with sulfuric acid) during 28 days of flooding and subsequent 14 days of drainage. We found that soil acidification to pH 4.5 considerably increased the solubility of Si, Fe, Mn, and Zn compared to the non-acidified soil. Additions of Mn and Zn oxides decreased the concentrations of dissolved arsenite and arsenate in the non-acidified soil whereas additions of Zn oxide and combined Si-Zn oxides increased them in the acidified soil. The Si-rich fly ash did not increase dissolved Si and As in the acidified and non-acidified soils. Dimethylated monothioarsenate (DMMTA) was mainly observed in the acidified soil during the later stage of soil flooding. The initial 28 days of soil flooding decreased the levels of soluble and exchangeable As and increased As associated with Mn oxides, whereas the subsequent 14 days of soil drainage reversed the trend. This study highlighted that soil acidification considerably controlled the solubilization of Ca and Fe, thus influencing the soil pH-Eh buffering capacity, the solubility of Si, Mn, and Zn oxides, and the mobility of different As species in carbonate-rich and acidic soils under redox fluctuations.
Topics: Arsenic; Manganese; Soil; Silicon; Coal Ash; Zinc Oxide; Oxides; Organic Chemicals; Zinc; Soil Pollutants; Oryza
PubMed: 38190943
DOI: 10.1016/j.chemosphere.2024.141140