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1.
Nat Genet ; 56(3): 442-457, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38361033

ABSTRACT

Clear cell renal cell carcinoma (ccRCC) is a complex disease with remarkable immune and metabolic heterogeneity. Here we perform genomic, transcriptomic, proteomic, metabolomic and spatial transcriptomic and metabolomic analyses on 100 patients with ccRCC from the Tongji Hospital RCC (TJ-RCC) cohort. Our analysis identifies four ccRCC subtypes including De-clear cell differentiated (DCCD)-ccRCC, a subtype with distinctive metabolic features. DCCD cancer cells are characterized by fewer lipid droplets, reduced metabolic activity, enhanced nutrient uptake capability and a high proliferation rate, leading to poor prognosis. Using single-cell and spatial trajectory analysis, we demonstrate that DCCD is a common mode of ccRCC progression. Even among stage I patients, DCCD is associated with worse outcomes and higher recurrence rate, suggesting that it cannot be cured by nephrectomy alone. Our study also suggests a treatment strategy based on subtype-specific immune cell infiltration that could guide the clinical management of ccRCC.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Humans , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/pathology , Kidney Neoplasms/genetics , Kidney Neoplasms/pathology , Multiomics , Proteomics , Metabolic Reprogramming , Dicyclohexylcarbodiimide , Disease Progression , Prognosis
2.
Arch Biochem Biophys ; 752: 109877, 2024 02.
Article in English | MEDLINE | ID: mdl-38159898

ABSTRACT

Pentameric FocA permeates either formate or formic acid bidirectionally across the cytoplasmic membrane of anaerobically growing Escherichia coli. Each protomer of FocA has its own hydrophobic pore, but it is unclear whether formate or neutral formic acid is translocated in vivo. Here, we measured total and dicyclohexylcarbodiimide (DCCD)-inhibited proton flux out of resting, fermentatively grown, stationary-phase E. coli cells in dependence on FocA. Using a wild-type strain synthesizing native FocA, it was shown that using glucose as a source of formate, DCCD-independent proton efflux was ∼2.5 mmol min-1, while a mutant lacking FocA showed only DCCD-inhibited, FOF1-ATPase-dependent proton-efflux. A strain synthesizing a chromosomally-encoded FocAH209N variant that functions exclusively to translocate formic acid out of the cell, showed a further 20 % increase in FocA-dependent proton efflux relative to the parental strain. Cells synthesizing a FocAT91A variant, which is unable to translocate formic acid out of the cell, showed only DCCD-inhibited proton efflux. When exogenous formate was added, formic acid uptake was shown to be both FocA- and proton motive force-dependent. By measuring rates of H2 production, potassium ion flux and ATPase activity, these data support a role for coupling between formate, proton and K+ ion translocation in maintaining pH and ion gradient homeostasis during fermentation. FocA thus plays a key role in maintaining this homeostatic balance in fermenting cells by bidirectionally translocating formic acid.


Subject(s)
Escherichia coli Proteins , Escherichia coli , Escherichia coli/genetics , Escherichia coli/metabolism , Membrane Transport Proteins/genetics , Escherichia coli Proteins/metabolism , Protons , Dicyclohexylcarbodiimide/pharmacology , Formates , Adenosine Triphosphatases , Hydrogen-Ion Concentration
3.
J Chromatogr A ; 1682: 463526, 2022 Oct 25.
Article in English | MEDLINE | ID: mdl-36166884

ABSTRACT

In this research report, the post polymerization functionalization (PPF) of a carboxyethyl acrylate (CEA)-co-ethylene glycol dimethacrylate (EDMA) [poly-CEA-co-EDMA)] precursor monolith with 2-aminoanthracene was carried out in the presence of an organic solvent soluble carbodiimide, namely N,N´-dicyclohexylcarbodiimide (DCC), yielding the so-called anthracenyl-poly-CEA-co-EDMA monolith. This novel monolith proved to be an excellent monolithic stationary for reversed-phase capillary electrochromatography (RP-CEC) with hydrophobic and π-π interactions of a wide range of nonpolar solutes including those bearing aryl functional groups in their structures such as polycyclic aromatic hydrocarbons (PAHs), toluene derivatives and aniline derivatives as well as solutes carrying in their structures electron withdrawing substituents such as dinitrophenyl-amino acids (DNP-AAs) and di-DNP-AAs. The retention behaviors of the just mentioned solutes obtained on the anthracenyl-poly-CEA-co-EDMA monolithic column were compared to those obtained on octadecyl-poly-CEA-co-EDMA monolithic column prepared from the same carboxy-precursor monolith. The results demonstrated the superiority of anthracenyl column over the octadecyl column for the separation and enhanced selectivity for aromatic solutes since it provides not only hydrophobic interactions but also π-π interactions with aromatic nonpolar solutes.


Subject(s)
Capillary Electrochromatography , Polycyclic Aromatic Hydrocarbons , Acrylates/chemistry , Amino Acids , Aniline Compounds , Capillary Electrochromatography/methods , Dicyclohexylcarbodiimide , Hydrophobic and Hydrophilic Interactions , Ligands , Methacrylates/chemistry , Polycyclic Aromatic Hydrocarbons/chemistry , Polyethylene Glycols , Solvents , Toluene
5.
Biomed Res Int ; 2021: 3598000, 2021.
Article in English | MEDLINE | ID: mdl-34761004

ABSTRACT

Amides derived from ferulic acid have a wide spectrum of pharmacological activities, including antitumor and antifungal activity. In the present study, a series of ten amides were obtained by coupling reactions using the reagents (benzotriazol-1-yloxy) tripyrrolidinophosphonium hexafluorophosphate (PyBOP) and N,N'-dicyclohexylcarbodiimide (DCC). All the compounds were identified on the basis of their IR, 1H- and 13C-NMR, HRMS data, and with yields ranging from 43.17% to 91.37%. The compounds were subjected to cytotoxic tests by the alamar blue technique and antifungal screening by the broth microdilution method to determine the minimum inhibitory concentration (MIC). The amides 10 and 11 displayed the best result in both biological evaluations, and compound 10 was the most potent and selective in HL-60 cancer cells, with no cytotoxicity on healthy cells. This amide had antifungal activity in all strains and had the lowest MIC against Candida albicans and Candida tropicalis. The possible mechanism of antifungal action occurs via the fungal cell wall. Molecular modeling suggested that compounds 10 and 11 interact with the enzymes GWT1 and GSC1, which are essential for the development of C. albicans. The findings of the present study demonstrated that compounds 10 and 11 may be used as a platform in drug development in the future.


Subject(s)
Coumaric Acids/pharmacology , Dicyclohexylcarbodiimide/chemistry , Organophosphorus Compounds/chemistry , Triazoles/chemistry , Amides/chemistry , Amides/pharmacology , Antifungal Agents/pharmacology , Candida/drug effects , Coumaric Acids/chemistry , Dicyclohexylcarbodiimide/pharmacology , Inhibitory Concentration 50 , Microbial Sensitivity Tests , Molecular Docking Simulation , Oils, Volatile/chemistry , Organophosphorus Compounds/pharmacology , Triazoles/pharmacology
6.
IUBMB Life ; 73(6): 883-892, 2021 06.
Article in English | MEDLINE | ID: mdl-33773019

ABSTRACT

Escherichia coli is able to utilize the mixture of carbon sources and produce molecular hydrogen (H2 ) via formate hydrogen lyase (FHL) complexes. In current work role of transcriptional activator of formate regulon FhlA in generation of fermentation end products and proton motive force, N'N'-dicyclohexylcarbodiimide (DCCD)-sensitive ATPase activity at 20 and 72 hr growth during utilization of mixture of glucose, glycerol, and formate were investigated. It was shown that in fhlA mutant specific growth rate was ~1.5 fold lower compared to wt, while addition of DCCD abolished the growth in fhlA but not in wt. Formate was not utilized in fhlA mutant but wt cells simultaneously utilized formate with glucose. Glycerol utilization started earlier (from 2 hr) in fhlA than in wt. The DCCD-sensitive ATPase activity in wt cells membrane vesicles increased ~2 fold at 72 hr and was decreased 70% in fhlA. Addition of formate in the assays increased proton ATPase activity in wt and mutant strain. FhlA absence mainly affected the ΔpH but not ΔΨ component of Δp in the cells grown at 72 hr but not in 24 hr. The Δp in wt cells decreased from 24 to 72 hr of growth ~40 mV while in fhlA mutant it was stable. Taken together, it is suggested that FhlA regulates the concentration of fermentation end products and via influencing FO F1 -ATPase activity contributes to the proton motive force generation.


Subject(s)
Escherichia coli Proteins/genetics , Escherichia coli/genetics , Proton-Motive Force/genetics , Proton-Translocating ATPases/genetics , Trans-Activators/physiology , Acetates/metabolism , Carbon/metabolism , Dicyclohexylcarbodiimide/pharmacology , Escherichia coli/drug effects , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli Proteins/physiology , Fermentation , Formates/metabolism , Formates/pharmacology , Glucose/metabolism , Glycerol/metabolism , Hydrogen/metabolism , Hydrogen-Ion Concentration , Oxidation-Reduction , Trans-Activators/genetics
7.
Lett Appl Microbiol ; 72(6): 669-676, 2021 Jun.
Article in English | MEDLINE | ID: mdl-32955753

ABSTRACT

Acanthopanax (A.) henryi (Oliv.) Harms contain many bioactive compounds commonly used in traditional Chinese medicine. The objective of the present study was to investigate the antibacterial activity of the single constituent, Eleutheroside K (ETSK) isolated from the leaves of A. henryi (Oliv.) Harms, against methicillin-resistant Staphylococcus (S.) aureus (MRSA). Broth microdilution assay was used to measure the minimal inhibitory concentration (MIC) and the MIC values of ETSK against eight clinical S. aureus strains were all 50 µg ml-1 . At sub-inhibitory concentrations, a synergistic effect between oxacillin (OXA) and ETSK was confirmed using checkerboard dilution assay and time-kill curve analysis. The bacteriostatic effect became more pronounced when ETSK was used in combination with detergent (Triton X-100) or ATPase inhibitor (N, N'-dicyclohexylcarbodiimide). According to western blot analysis, the down-regulated expression of Penicillin-binding protein 2a (PBP2a) further validated that the bacterial activity was inhibited when treated with ETSK in a dose-dependent manner. Results based on our study verified that ETSK significantly suppressed MRSA infections and emphasized the potential application of ETSK as a novel anti-MRSA natural drug.


Subject(s)
Anti-Bacterial Agents/pharmacology , Eleutherococcus/metabolism , Methicillin-Resistant Staphylococcus aureus/drug effects , Oxacillin/pharmacology , Plant Extracts/pharmacology , Dicyclohexylcarbodiimide/pharmacology , Down-Regulation/drug effects , Drug Synergism , Drug Therapy, Combination , Eleutherococcus/chemistry , Methicillin Resistance/drug effects , Microbial Sensitivity Tests , Octoxynol/pharmacology , Penicillin-Binding Proteins/biosynthesis , Plant Leaves/chemistry
8.
Biochemistry (Mosc) ; 85(8): 930-937, 2020 Aug.
Article in English | MEDLINE | ID: mdl-33045953

ABSTRACT

The effects of N,N'-dicyclohexylcarbodiimide (DCCD), non-specific inhibitor of various transport systems functioning in biological membranes, on Na+-transporting P-type ATPase of the green halotolerant microalga Dunaliella maritima were studied in the experiments with vesicular plasma membranes isolated from the alga cells. The effects of DCCD on electrogenic/ion transport function of the enzyme and its ATP hydrolase activity were investigated. Electrogenic/ion transport function of the enzyme was recorded as a Na+-dependent generation of electric potential on the vesicle membranes with the help of the potential-sensitive probe oxonol VI. It was found that unlike many other ion-transporting ATPases, the Na+-ATPase of D. maritima is insensitive to DCCD. This agent did not inhibit either ATP hydrolysis catalyzed by this enzyme or its transport activity. At the same time DCCD affected the ability of the vesicle membranes to maintain electric potential generated by the D. maritima Na+-ATPase. The observed effects can be explained based on the assumption that DCCD interacts with the Na+/H+ antiporter in the plasma membrane of D. maritima.


Subject(s)
Adenosine Triphosphatases/metabolism , Cation Transport Proteins/metabolism , Cell Membrane/metabolism , Chlorophyceae/enzymology , Dicyclohexylcarbodiimide/pharmacology , Membrane Potentials/drug effects , Microalgae/enzymology , Signal Transduction/drug effects , Adenosine Triphosphate/metabolism , Biological Transport, Active/drug effects , Hydrogen-Ion Concentration , Hydrolysis/drug effects , Ion Transport/drug effects , P-type ATPases/metabolism , Protons
9.
Commun Biol ; 3(1): 431, 2020 08 07.
Article in English | MEDLINE | ID: mdl-32770029

ABSTRACT

rnf genes are widespread in bacteria and biochemical and genetic data are in line with the hypothesis that they encode a membrane-bound enzyme that oxidizes reduced ferredoxin and reduces NAD and vice versa, coupled to ion transport across the cytoplasmic membrane. The Rnf complex is of critical importance in many bacteria for energy conservation but also for reverse electron transport to drive ferredoxin reduction. However, the enzyme has never been purified and thus, ion transport could not be demonstrated yet. Here, we have purified the Rnf complex from the anaerobic, fermenting thermophilic bacterium Thermotoga maritima and show that is a primary Na+ pump. These studies provide the proof that the Rnf complex is indeed an ion (Na+) translocating, respiratory enzyme. Together with a Na+-F1FO ATP synthase it builds a simple, two-limb respiratory chain in T. maritima. The physiological role of electron transport phosphorylation in a fermenting bacterium is discussed.


Subject(s)
Bacterial Proteins/metabolism , Fermentation , Sodium/metabolism , Thermotoga maritima/enzymology , Adenosine Triphosphate/metabolism , Bacterial Proteins/isolation & purification , Dicyclohexylcarbodiimide/pharmacology , Fermentation/drug effects , Ferredoxins/metabolism , Glucose/metabolism , Hydrolysis , Ion Transport/drug effects , Ionophores/pharmacology , Liposomes , Models, Biological , Oxidoreductases/metabolism , Protein Subunits/isolation & purification , Proton-Translocating ATPases/isolation & purification , Proton-Translocating ATPases/metabolism , Thermotoga maritima/drug effects
10.
IUBMB Life ; 72(5): 915-921, 2020 05.
Article in English | MEDLINE | ID: mdl-31856407

ABSTRACT

Escherichia coli is able to ferment not only single but also mixtures of carbon sources. The formate metabolism and effect of formate on various enzymes have been extensively studied during sole glucose but not mixed carbon sources utilization. It was revealed that in membrane vesicles (MV) of wild type cells grown at pH 7.5 during fermentation of the mixture of glucose (2 g/L), glycerol (10 g/L), and formate (0.68 g/L), in the assays, the addition of formate (10 mM) increased the N,N'-dicyclohexylcarbodiimide (DCCD)-inhibited ATPase activity on ~30% but no effect of potassium ions (100 mM) had been detected. In selC (coding formate dehydrogenases) and fdhF (coding formate dehydrogenase H) single mutants, formate increased DCCD-inhibited ATPase activity on ~40 and ~70%, respectively. At pH 5.5, in wild type cells MV, formate decreased the DCCD-inhibited ATPase activity ~60% but unexpectedly in the presence of potassium ions, it was stimulated ~5.8 fold. The accessible SH or thiol groups number in fdhF mutant was less by 28% compared with wild type. In formate assays, the available SH groups number was less ~10% in wild type but not in fdhF mutant. Taken together, the data suggest that proton ATPase activity depends on externally added formate in the presence of potassium ions at low pH. This effect might be regulated by the changes in the number of redox-active thiol groups via formate dehydrogenase H, which might be directly related to proton ATPase FO subunit.


Subject(s)
Escherichia coli Proteins/genetics , Escherichia coli/drug effects , Formate Dehydrogenases/genetics , Formates/pharmacology , Hydrogenase/genetics , Multienzyme Complexes/genetics , Potassium/pharmacology , Proton-Translocating ATPases/genetics , Carbon/metabolism , Cell Membrane/drug effects , Cell Membrane/metabolism , Dicyclohexylcarbodiimide/pharmacology , Enzyme Inhibitors/pharmacology , Escherichia coli/enzymology , Escherichia coli/genetics , Escherichia coli Proteins/antagonists & inhibitors , Escherichia coli Proteins/metabolism , Fermentation , Formate Dehydrogenases/metabolism , Formates/metabolism , Gene Expression Regulation, Bacterial , Glucose/metabolism , Glucose/pharmacology , Glycerol/metabolism , Glycerol/pharmacology , Hydrogen-Ion Concentration , Hydrogenase/metabolism , Isoenzymes/genetics , Isoenzymes/metabolism , Multienzyme Complexes/metabolism , Mutation , Potassium/metabolism , Proton-Translocating ATPases/antagonists & inhibitors , Proton-Translocating ATPases/metabolism
11.
Sci Rep ; 9(1): 4279, 2019 03 12.
Article in English | MEDLINE | ID: mdl-30862913

ABSTRACT

During fermentation Escherichia coli excrete succinate mainly via Dcu family carriers. Current work reveals the total and N,N'-dicyclohexylcarbodiimide (DCCD) inhibited ATPase activity at pH 7.5 and 5.5 in E. coli wild type and dcu mutants upon glycerol fermentation. The overall ATPase activity was highest at pH 7.5 in dcuABCD mutant. In wild type cells 50% of the activity came from the FOF1-ATPase but in dcuD mutant it reached ~80%. K+ (100 mM) stimulate total but not DCCD inhibited ATPase activity 40% and 20% in wild type and dcuD mutant, respectively. 90% of overall ATPase activity was inhibited by DCCD at pH 5.5 only in dcuABC mutant. At pH 7.5 the H+ fluxes in E. coli wild type, dcuD and dcuABCD mutants was similar but in dcuABC triple mutant the H+ flux decreased 1.4 fold reaching 1.15 mM/min when glycerol was supplemented. In succinate assays the H+ flux was higher in the strains where DcuD is absent. No significant differences were determined in wild type and mutants specific growth rate except dcuD strain. Taken together it is suggested that during glycerol fermentation DcuD has impact on H+ fluxes, FOF1-ATPase activity and depends on potassium ions.


Subject(s)
Adenosine Triphosphatases/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Glycerol/metabolism , Adenosine Triphosphatases/genetics , Dicarboxylic Acid Transporters/genetics , Dicarboxylic Acid Transporters/metabolism , Dicyclohexylcarbodiimide/pharmacology , Escherichia coli/drug effects , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Fermentation/drug effects , Fermentation/genetics , Fermentation/physiology , Hydrogen-Ion Concentration
12.
Mater Sci Eng C Mater Biol Appl ; 97: 356-366, 2019 Apr.
Article in English | MEDLINE | ID: mdl-30678921

ABSTRACT

Synthesis of noble metal nanoparticles (NPs) on modified graphene oxide with biocompatible polymers has attracted significant due to their unique properties and various applications. In this research, covalent-modified graphene oxide (MGO) with diacid terminated poly (ethylene glycol) (PEG) was used as a substrate and stabilizing of Au (ш). The reduction of MGO-Au (ш) complex with hydrazine monohydrate under reflux condition obtained biocompatible reduced MGO (rMGO)-Au NPs. Diacid terminated PEG obtained from the reaction of PEG with succinic anhydride in the presence of N,N- dicyclohexylcarbodiimide (DCC) and 4-methylamino pyridine (DMAP) was attached to GO sheets to prevent from the aggregation of rMGO sheets and Au NPs. The resulting aqueous suspension was characterized through UV-vis, FT-IR, Raman, XRD, DLS-zeta potential, SEM, EDX and TEM. Furthermore, nanocomposite showed good catalytic behavior in Betti reaction- synthesis of 1-(α-aminoalkyl)-2-naphthols. The favorable properties of colloidal nanocomposite were attributed to the stable and well distribution Au NPs on rMGO.


Subject(s)
Biocompatible Materials/chemistry , Graphite/chemistry , Nanocomposites/chemistry , Aminopyridines/chemistry , Catalysis , Colloids/chemistry , Dicyclohexylcarbodiimide/chemistry , Metal Nanoparticles/chemistry , Microscopy, Electron, Scanning , Naphthols/chemical synthesis , Naphthols/chemistry , Oxides/chemistry , Polyethylene Glycols/chemistry , Spectrophotometry, Ultraviolet , Spectroscopy, Fourier Transform Infrared , Spectrum Analysis, Raman , Succinic Anhydrides/chemistry , X-Ray Diffraction
13.
Lett Appl Microbiol ; 68(1): 31-37, 2019 Jan.
Article in English | MEDLINE | ID: mdl-30269343

ABSTRACT

Lactobacillus acidophilus is one of the widespread probiotic bacteria that can overcome acid and bile barrier of stomach and intestine, respectively, and then have beneficial effects on the host improving its intestinal microbial balance. The cell membrane FO F1 -ATPase is an important factor in the response and tolerance to low pH through the action of controlling the H+ concentration between the cell cytoplasm and external medium. In this study, the effects of extremely high-frequency EMI at the frequencies of 51·8 GHz and 53 GHz and cetfazidime ( µmol l-1 ) on survival of L. acidophilus VKM B-1660 in the gastrointestinal model in vitro and on ATPase activity of their membrane vesicles were investigated. Irradiated L. acidophilus survived in media with acid pH; the irradiation stimulated N,N'-dicyclohexylcarbodiimide-sensitive FO F1 -ATPase activity under acidic conditions, but enhanced the inhibitory effects of ceftazidime. Probably irradiated L. acidophilus is overcoming the acid barrier even in the presence of ceftazidime due to the FO F1 -ATPase. The obtained results can allow the use of L. acidophilus in food industry, veterinary and medicine. SIGNIFICANCE AND IMPACT OF THE STUDY: The probiotic property of lactobacilli is defined with survival in different conditions of human digestive tract even in the presence of antibiotics and subjected to electromagnetic irradiation (EMI) at the extremely high frequency. Despite the fact that EMI and antibiotic ceftazidime affected Lactobacillus acidophilus; the viable number of bacterial cells was decreased in in vitro gastrointestinal model, but they could to grow in fresh growth medium. The changes in the FO F1 -ATPase activity were obtained at acidic pH. Thus, these bacteria can overcome acid barrier due to the FO F1 -ATPase: the irradiation stimulates the FO F1 -ATPase activity in the acidic conditions, but enhances the effects of ceftazidime. The results are important for identifying the mechanisms of lactobacilli survival for physical and chemical factors and valuable for use.


Subject(s)
Anti-Bacterial Agents/pharmacology , Ceftazidime/pharmacology , Electromagnetic Radiation , Lactobacillus acidophilus/growth & development , Proton-Translocating ATPases/metabolism , Bile/metabolism , Cell Membrane/drug effects , Dicyclohexylcarbodiimide , Gastrointestinal Tract/microbiology , Humans , Hydrogen-Ion Concentration , Lactobacillus acidophilus/drug effects , Lactobacillus acidophilus/radiation effects , Probiotics
14.
IUBMB Life ; 70(10): 1040-1047, 2018 10.
Article in English | MEDLINE | ID: mdl-30161297

ABSTRACT

During fermentation Escherichia coli produces di-hydrogen (H2 ) via reversible membrane-bound [Ni-Fe]-hydrogenases (Hyd). This study describes the total and N,N'-dicyclohexylcarbodiimide (DCCD) inhibited ATPase activity and H2 production at various pHs in E. coli wild type and mutants encoding Hyd enzymes and formate dehydrogenases (FDH) on fermentation of glucose, glycerol, and formate. The highest total ATPase activity was detected at pH 7.5 in hyaB hybC selC (lacking large subunits of Hyd-1 and Hyd-2 and FDH, respectively) triple mutant. This ATPase activity was mainly due to the proton-translocating ATPase but in FDH mutant the DCCD inhibition was less compared to wild type. Potassium ions stimulated total ATPase activity at pH 5.5 ~50% and ~35% in wild type and hypF (lacking all Hyd enzymes) mutant, respectively. Moreover, K+ also stimulated DCCD inhibited ATPase activity ~1.7-fold-2-fold in strains where FDH was absent only at pH 5.5. DCCD inhibited H2 production only at pH 5.5 in all assays. Taken together it is suggested that at low pH, FDH, and Hyd enzymes are linked with the FO F1 -ATPase for regulating and maintaining the cytoplasmatic pH and thus proton motive force generation. FDH and Hyd enzymes have impact on the FO F1 -ATPase activity depending on external pH and potassium ions. © 2018 IUBMB Life, 70(10):1040-1047, 2018.


Subject(s)
Escherichia coli/enzymology , Formate Dehydrogenases/genetics , Proton-Translocating ATPases/genetics , Carbon/metabolism , Dicyclohexylcarbodiimide/pharmacology , Fermentation/drug effects , Formate Dehydrogenases/metabolism , Formates/metabolism , Glucose/metabolism , Hydrogen/metabolism , Hydrogen-Ion Concentration , Hydrogenase/genetics , Iron-Sulfur Proteins/genetics
15.
J Gen Appl Microbiol ; 64(4): 174-179, 2018 Sep 27.
Article in English | MEDLINE | ID: mdl-29669961

ABSTRACT

Although Streptococcus anginosus constitutes a proportion of the normal flora of the gastrointestinal and genital tracts, and the oral cavity, it has been reported that S. anginosus infection could be closely associated with abscesses at various body sites, infective endocarditis, and upper gastrointestinal cancers. The colonization in an acidic environment due to the aciduricity of S. anginosus could be the etiology of the systemic infection of the bacteria. To elucidate the aciduricity and acid tolerance mechanisms of the microbe, we examined the viability and growth of S. anginosus under acidic conditions. The viabilities of S. anginosus NCTC 10713 and Streptococcus mutans ATCC 25175 at pH 4.0 showed as being markedly higher than those of Streptococcus sanguinis ATCC 10556, Streptococcus gordonii ATCC 10558, and Streptococcus mitis ATCC 49456; however, the viability was partially inhibited by dicyclohexylcarbodiimide, an H+-ATPase inhibitor, suggesting that H+-ATPase could play a role in the viability of S. anginosus under acidic conditions. In addition, S. anginosus NCTC 10713 could grow at pH 5.0 and showed a marked arginine deiminase (ADI) activity, unlike its ΔarcA mutant, deficient in the gene encoding ADI, and other streptococcal species, which indicated that ADI could also be associated with aciduricity. These results suggest that S. anginosus has significant aciduric properties, which can be attributed to these enzyme activities.


Subject(s)
Acids/metabolism , Hydrolases/metabolism , Proton-Translocating ATPases/metabolism , Streptococcus anginosus/drug effects , Streptococcus anginosus/physiology , Acids/pharmacology , Arginine/metabolism , Culture Media , Dicyclohexylcarbodiimide/pharmacology , Gene Deletion , Hydrogen-Ion Concentration , Hydrolases/genetics , Microbial Viability/drug effects , Proton-Translocating ATPases/antagonists & inhibitors , Proton-Translocating ATPases/genetics , Streptococcus anginosus/enzymology , Streptococcus anginosus/genetics
16.
Biochim Biophys Acta Biomembr ; 1860(2): 586-599, 2018 Feb.
Article in English | MEDLINE | ID: mdl-29179995

ABSTRACT

Cardiolipin (CL) is an anionic phospholipid at the inner mitochondrial membrane (IMM) that facilitates the formation of transient non-bilayer (non-lamellar) structures to maintain mitochondrial integrity. CL modulates mitochondrial functions including ATP synthesis. However, the biophysical mechanisms by which CL generates non-lamellar structures and the extent to which these structures contribute to ATP synthesis remain unknown. We hypothesized that CL and ATP synthase facilitate the formation of non-bilayer structures at the IMM to stimulate ATP synthesis. By using 1H NMR and 31P NMR techniques, we observed that increasing the temperature (8°C to 37°C), lowering the pH (3.0), or incubating intact mitochondria with CTII - an IMM-targeted toxin that increases the formation of immobilized non-bilayer structures - elevated the formation of non-bilayer structures to stimulate ATP synthesis. The F0 sector of the ATP synthase complex can facilitate the formation of non-bilayer structures as incubating model membranes enriched with IMM-specific phospholipids with exogenous DCCD-binding protein of the F0 sector (DCCD-BPF) elevated the formation of immobilized non-bilayer structures to a similar manner as CTII. Native PAGE assays revealed that CL, but not other anionic phospholipids, specifically binds to DCCD-BPF to promote the formation of stable lipid-protein complexes. Mechanistically, molecular docking studies identified two lipid binding sites for CL in DCCD-BPF. We propose a new model of ATP synthase regulation in which CL mediates the formation of non-bilayer structures that serve to cluster protons and ATP synthase complexes as a mechanism to enhance proton translocation to the F0 sector, and thereby increase ATP synthesis.


Subject(s)
Cardiolipins/metabolism , Lipid Bilayers/metabolism , Mitochondrial Membranes/metabolism , Mitochondrial Proton-Translocating ATPases/metabolism , Adenosine Triphosphate/metabolism , Animals , Cattle , Dicyclohexylcarbodiimide/metabolism , Magnetic Resonance Spectroscopy , Mitochondria, Heart/metabolism , Models, Biological , Molecular Docking Simulation , Protein Binding , Protons , Unilamellar Liposomes/metabolism
17.
Cell Biochem Biophys ; 76(1-2): 209-217, 2018 Jun.
Article in English | MEDLINE | ID: mdl-29039057

ABSTRACT

Microorganisms are part of the natural environments and reflect the effects of different physical factors of surrounding environment, such as gamma (γ) radiation. This work was devoted to the study of the influence of low doses of γ radiation with the intensity of 2.56 µW (m2 s)-1 (absorbed doses were 3.8 mGy for the radiation of 15 min and 7.2 mGy-for 30 min) on Escherichia coli M-17 and Pseudomonas aeruginosa GRP3 wild type cells. The changes of bacterial, growth, survival, morphology, and membrane activity had been studied after γ irradiation. Verified microbiological (specific growth rate, lag phase duration, colony-forming units (CFU) number, and light microscopy digital image analysis), biochemical (ATPase activity of bacterial membrane vesicles), and biophysical (H+ fluxes throughout cytoplasmic membrane of bacteria) methods were used for assessment of radiation implications on bacteria. It was shown that growth specific rate, lag phase duration and CFU number of these bacteria were lowered after irradiation, and average cell surface area was decreased too. Moreover ion fluxes of bacteria were changed: for P. aeruginosa they were decreased and for E. coli-increased. The N,N'-dicyclohexylcarbodiimide (DCCD) sensitive fluxes were also changed which were indicative for the membrane-associated F0F1-ATPase enzyme. ATPase activity of irradiated membrane vesicles was decreased for P. aeruginosa and stimulated for E. coli. Furthermore, DCCD sensitive ATPase activity was also changed. The results obtained suggest that these bacteria especially, P. aeruginosa are sensitive to γ radiation and might be used for developing new monitoring methods for estimating environmental changes after γ irradiation.


Subject(s)
Escherichia coli/radiation effects , Gamma Rays , Pseudomonas aeruginosa/radiation effects , Bacterial Proteins/metabolism , Cell Membrane/metabolism , Cytoplasmic Vesicles/drug effects , Cytoplasmic Vesicles/metabolism , Dicyclohexylcarbodiimide/pharmacology , Escherichia coli/growth & development , Escherichia coli/metabolism , Microscopy , Proton-Translocating ATPases/metabolism , Pseudomonas aeruginosa/growth & development , Pseudomonas aeruginosa/metabolism
18.
J Biol Chem ; 292(52): 21320-21329, 2017 12 29.
Article in English | MEDLINE | ID: mdl-29089385

ABSTRACT

Twin-arginine translocation (Tat) systems transport folded proteins across cellular membranes with the concerted action of mostly three membrane proteins: TatA, TatB, and TatC. Hetero-oligomers of TatB and TatC form circular substrate-receptor complexes with a central binding cavity for twin-arginine-containing signal peptides. After binding of the substrate, energy from an electro-chemical proton gradient is transduced into the recruitment of TatA oligomers and into the actual translocation event. We previously reported that Tat-dependent protein translocation into membrane vesicles of Escherichia coli is blocked by the compound N,N'-dicyclohexylcarbodiimide (DCCD, DCC). We have now identified a highly conserved glutamate residue in the transmembrane region of E. coli TatC, which when modified by DCCD interferes with the deep insertion of a Tat signal peptide into the TatBC receptor complex. Our findings are consistent with a hydrophobic binding cavity formed by TatB and TatC inside the lipid bilayer. Moreover, we found that DCCD mediates discrete intramolecular cross-links of E. coli TatC involving both its N- and C-tails. These results confirm the close proximity of two distant sequence sections of TatC proposed to concertedly function as the primary docking site for twin-arginine signal peptides.


Subject(s)
Escherichia coli Proteins/metabolism , Membrane Transport Proteins/metabolism , Arginine/metabolism , Cell Membrane/metabolism , Crystallography, X-Ray/methods , Dicyclohexylcarbodiimide/pharmacology , Escherichia coli/metabolism , Escherichia coli Proteins/genetics , Hydrophobic and Hydrophilic Interactions , Membrane Transport Proteins/genetics , Protein Binding , Protein Conformation , Protein Domains , Protein Folding , Protein Sorting Signals/physiology , Substrate Specificity
19.
Proc Natl Acad Sci U S A ; 114(47): E10083-E10091, 2017 11 21.
Article in English | MEDLINE | ID: mdl-29114048

ABSTRACT

EmrE is a small multidrug resistance transporter found in Escherichia coli that confers resistance to toxic polyaromatic cations due to its proton-coupled antiport of these substrates. Here we show that EmrE breaks the rules generally deemed essential for coupled antiport. NMR spectra reveal that EmrE can simultaneously bind and cotransport proton and drug. The functional consequence of this finding is an exceptionally promiscuous transporter: not only can EmrE export diverse drug substrates, it can couple antiport of a drug to either one or two protons, performing both electrogenic and electroneutral transport of a single substrate. We present a free-exchange model for EmrE antiport that is consistent with these results and recapitulates ∆pH-driven concentrative drug uptake. Kinetic modeling suggests that free exchange by EmrE sacrifices coupling efficiency but boosts initial transport speed and drug release rate, which may facilitate efficient multidrug efflux.


Subject(s)
Antiporters/chemistry , Drug Resistance, Multiple, Bacterial/genetics , Escherichia coli Proteins/chemistry , Escherichia coli/metabolism , Onium Compounds/metabolism , Organophosphorus Compounds/metabolism , Protons , Xenobiotics/metabolism , Antiporters/genetics , Antiporters/metabolism , Binding Sites , Biological Transport , Dicyclohexylcarbodiimide/toxicity , Escherichia coli/drug effects , Escherichia coli/genetics , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Gene Expression , Hydrogen-Ion Concentration , Kinetics , Molecular Dynamics Simulation , Onium Compounds/chemistry , Onium Compounds/pharmacology , Organophosphorus Compounds/chemistry , Organophosphorus Compounds/pharmacology , Phosphatidylcholines/chemistry , Phosphatidylcholines/metabolism , Phosphatidylglycerols/chemistry , Phosphatidylglycerols/metabolism , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , Proteolipids/chemistry , Proteolipids/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity , Thermodynamics , Xenobiotics/chemistry , Xenobiotics/pharmacology
20.
Biochimie ; 140: 73-81, 2017 Sep.
Article in English | MEDLINE | ID: mdl-28652018

ABSTRACT

The mitochondrial F-ATPase can be activated either by the classical cofactor Mg2+ or, with lower efficiency, by Ca2+. The latter may play a role when calcium concentration rises in mitochondria, a condition associated with cascade events leading to cell death. Common and distinctive features of these differently activated mitochondrial ATPases were pointed out in swine heart mitochondria. When Ca2+ replaces the natural cofactor Mg2+, the enzyme responsiveness to the transmembrane electrochemical gradient and to the classical F-ATPase inhibitors DCCD and oligomycin as well as the oligomycin sensitivity loss by thiol oxidation, are maintained. Consistently, the two mitochondrial ATPases apparently share the F1FO complex basic structure and mechanism. Peculiar cation-dependent properties, which may affect the F1 catalytic mechanism and/or the FO proton binding site features, may be linked to a different physiological role of the mitochondrial Ca-activated F-ATPase with respect to the Mg-activated F-ATPase.


Subject(s)
Calcium/pharmacokinetics , Magnesium/pharmacology , Mitochondria, Heart/enzymology , Proton-Translocating ATPases/metabolism , Animals , Calcium/metabolism , Dicyclohexylcarbodiimide/pharmacology , Magnesium/metabolism , Membrane Potential, Mitochondrial/drug effects , Oligomycins/pharmacology , Proton-Translocating ATPases/antagonists & inhibitors , Swine
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