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1.
Reprod Biol ; 23(3): 100790, 2023 Sep.
Article En | MEDLINE | ID: mdl-37478515

Orotic acid (OA) is a natural product that acts as a precursor in the pyrimidine nucleotide biosynthesis pathway. Most studies concerning administration of OA focus on its therapeutic effects; however, its effect on tumours is unclear. We aimed to determine whether treatment with OA influences the viability and apoptosis of normal (HGrC1) and tumour-derived (KGN) human ovarian granulosa cells. The effects of OA (10-250 µM) on viability and apoptosis of both cell lines were determined by using alamarBlue and assessing caspase-3/7 activity, respectively. Annexin V binding and loss of membrane integrity were evaluated in KGN cells. The cell cycle and proliferation of HGrC1 cells were assessed by performing flow cytometric and DNA content analyses, respectively. The influence of OA (10 and 100 µM) on cell cycle- and apoptosis-related gene expression was assessed by RT-qPCR in both cell lines. Mitochondrial activity was analysed by JC-1 staining in HGrC1 cells. In KGN cells, OA reduced viability and increased caspase-3/7 activity, but did not affect mRNA expression of Caspase 3, BAX, and BCL2. OA enhanced proliferation and mitochondrial activity in HGrC1 cells without activating apoptosis. This study demonstrates that the anti-cancer properties of OA in ovarian granulosa tumour cells are not related to changes in apoptosis-associated gene expression, but to increased caspase-3/7 activity. Thus, OA is a promising therapeutic agent for ovarian granulosa tumours. Further, our results suggest that differences in basal expression of cell cycle- and apoptosis-related genes between the two cell lines are responsible for their different responses to OA.


Orotic Acid , Ovarian Neoplasms , Female , Adult , Humans , Caspase 3/metabolism , Orotic Acid/metabolism , Orotic Acid/pharmacology , Granulosa Cells , Apoptosis , Ovarian Neoplasms/genetics
2.
Phys Chem Chem Phys ; 25(4): 3472-3484, 2023 Jan 27.
Article En | MEDLINE | ID: mdl-36637052

Orotate phosphoribosyltransferase (OPRT) catalyses the reversible phosphoribosyl transfer from α-D-5-phosphoribosyl-1-pyrophosphate (PRPP) to orotic acid (OA) to yield orotidine 5'-monophosphate (OMP) during the de novo synthesis of nucleotides. Numerous studies have reported the inhibition of this reaction as a strategy to check diseases like tuberculosis, malaria and cancer. Insight into the inhibition of this reaction is, therefore, of urgent interest. In this study, we implemented a QM/MM framework on OPRT derived from Saccharomyces cerevisiae to obtain insights into the competitive binding of OA and OA-mimetic inhibitors by quantifying their interactions with OPRT. 4-Hydroxy-6-methylpyridin-2(1H) one showed the best inhibiting activity among the structurally similar OA-mimetic inhibitors, as quantified from the binding energetics. Our analysis of protein-ligand interactions unveiled the association of this inhibitory ligand with a strong network of hydrogen bonds, a large contribution of hydrophobic contacts, and bridging water molecules in the binding site. The ortho-substituted CH3 group in the compound resulted in a large population of π-electrons in the aromatic ring of this inhibitor, supporting the ligand binding further.


Orotate Phosphoribosyltransferase , Orotic Acid , Orotic Acid/metabolism , Ligands , Orotate Phosphoribosyltransferase/chemistry , Orotate Phosphoribosyltransferase/metabolism , Binding Sites
3.
Mar Drugs ; 20(11)2022 Nov 10.
Article En | MEDLINE | ID: mdl-36355027

The sulfated echinoside A (EA) and holothurin A (HA) are two prominent saponins in sea cucumber with high hemolytic activity but also superior lipid-lowering activity. Deglycosylated derivatives EA2 and HA2 exhibit low hemolysis compared to EA and HA, but their efficacies on lipid metabolism regulation remains unknown. In this study, fatty acids-treated HepG2 cells and orotic acid-treated rats were used to investigate the lipid-lowering effects of sea cucumber saponin derivatives. Both the saponin and derivatives could effectively alleviate lipid accumulation in HepG2 model, especially EA and EA2. Moreover, though the lipid-lowering effect of EA2 was not equal with EA at the same dosage of 0.05% in diet, 0.15% dosage of EA2 significantly reduced hepatic steatosis rate, liver TC and TG contents by 76%, 41.5%, and 63.7%, respectively, compared to control and reversed liver histopathological features to normal degree according to H&E stained sections. Possible mechanisms mainly included enhancement of fatty acids ß-oxidation and cholesterol catabolism through bile acids synthesis and excretion, suppression of lipogenesis and cholesterol uptake. It revealed that the efficacy of EA2 on lipid metabolism regulation was dose-dependent, and 0.15% dosage of EA2 possessed better efficacy with lower toxicity compared to 0.05% dosage of EA.


Non-alcoholic Fatty Liver Disease , Saponins , Sea Cucumbers , Rats , Animals , Humans , Sea Cucumbers/metabolism , Orotic Acid/metabolism , Orotic Acid/pharmacology , Saponins/pharmacology , Saponins/metabolism , Fatty Acids/metabolism , Hep G2 Cells , Liver , Lipid Metabolism , Cholesterol/metabolism , Non-alcoholic Fatty Liver Disease/metabolism
4.
Angew Chem Int Ed Engl ; 61(11): e202112572, 2022 03 07.
Article En | MEDLINE | ID: mdl-35007387

A reaction between two prebiotically plausible building blocks, hydantoin and glyoxylate, generates both the nucleobase orotate, a precursor of biological pyrimidines, and pyruvate, a core metabolite in the citric acid cycle and amino acid biosynthesis. The reaction proceeds in water to provide significant yields of the two widely divergent chemical motifs. Additionally, the reaction of thiohydantoin and glyoxylate produces thioorotate in high yield under neutral aqueous conditions. The use of an open-chain thiohydantoin derivative also enables the potential pre-positioning of a nucleosidic bond prior to the synthesis of an orotate nucleoside. The observation that diverse building blocks of modern metabolism can be produced in a single reaction pot, from common reactants under mild conditions, supports the plausibility of orthogonal chemistries operating at the origins of chemical evolution.


Origin of Life , Orotic Acid/metabolism , Pyruvic Acid/metabolism , Orotic Acid/chemistry , Pyruvic Acid/chemistry
5.
Circ Heart Fail ; 14(1): e007275, 2021 01.
Article En | MEDLINE | ID: mdl-33464957

BACKGROUND: Heart failure (HF) is a heterogeneous disease characterized by significant metabolic disturbances; however, the breadth of metabolic dysfunction before the onset of overt disease is not well understood. The purpose of this study was to determine the association of circulating metabolites with incident HF to uncover novel metabolic pathways to disease. METHODS: We performed targeted plasma metabolomic profiling in a deeply phenotyped group of Black adults from the JHS (Jackson Heart Study; n=2199). We related metabolites associated with incident HF to established etiological mechanisms, including increased left ventricular mass index and incident coronary heart disease. Furthermore, we evaluated differential associations of metabolites with HF with preserved ejection fraction versus HF with reduced ejection fraction. RESULTS: Metabolites associated with incident HF included products of posttranscriptional modifications of RNA, as well as polyamine and nitric oxide metabolism. A subset of metabolite-HF associations was independent of well-established HF pathways such as increased left ventricular mass index and incident coronary heart disease and included homoarginine (per 1 SD increase in metabolite level, hazard ratio, 0.77; P=1.2×10-3), diacetylspermine (hazard ratio, 1.34; P=3.4×10-3), and uridine (hazard ratio, 0.79; P, 3×10-4). Furthermore, metabolites involved in pyrimidine metabolism (orotic acid) and collagen turnover (N-methylproline) among others were part of a distinct metabolic signature that differentiated individuals with HF with preserved ejection fraction versus HF with reduced ejection fraction. CONCLUSIONS: The integration of clinical phenotyping with plasma metabolomic profiling uncovered novel metabolic processes in nontraditional disease pathways underlying the heterogeneity of HF development in Black adults.


Black or African American , Coronary Disease/metabolism , Heart Failure/metabolism , Hypertrophy, Left Ventricular/metabolism , Metabolomics , Adult , Aged , Case-Control Studies , Collagen/metabolism , Coronary Disease/epidemiology , Effect Modifier, Epidemiologic , Female , Heart Disease Risk Factors , Heart Failure/epidemiology , Heart Failure/physiopathology , Homoarginine/metabolism , Humans , Hypertrophy, Left Ventricular/epidemiology , Incidence , Longitudinal Studies , Male , Middle Aged , Nitric Oxide/metabolism , Orotic Acid/metabolism , Polyamines/metabolism , Proline/analogs & derivatives , Proline/metabolism , Proportional Hazards Models , Pyrimidines/metabolism , RNA Processing, Post-Transcriptional , Risk , Spermine/analogs & derivatives , Spermine/metabolism , Stroke Volume/physiology , Uridine/metabolism , White People
6.
Cell Death Dis ; 11(5): 310, 2020 05 04.
Article En | MEDLINE | ID: mdl-32366892

Formate is a precursor for the de novo synthesis of purine and deoxythymidine nucleotides. Formate also interacts with energy metabolism by promoting the synthesis of adenine nucleotides. Here we use theoretical modelling together with metabolomics analysis to investigate the link between formate, nucleotide and energy metabolism. We uncover that endogenous or exogenous formate induces a metabolic switch from low to high adenine nucleotide levels, increasing the rate of glycolysis and repressing the AMPK activity. Formate also induces an increase in the pyrimidine precursor orotate and the urea cycle intermediate argininosuccinate, in agreement with the ATP-dependent activities of carbamoyl-phosphate and argininosuccinate synthetase. In vivo data for mouse and human cancers confirms the association between increased formate production, nucleotide and energy metabolism. Finally, the in vitro observations are recapitulated in mice following and intraperitoneal injection of formate. We conclude that formate is a potent regulator of purine, pyrimidine and energy metabolism.


Energy Metabolism/drug effects , Formates/pharmacology , Nucleotides/metabolism , Adenosine Triphosphate/pharmacology , Adenylate Kinase/metabolism , Aminoimidazole Carboxamide/analogs & derivatives , Aminoimidazole Carboxamide/pharmacology , Animals , Cell Line, Tumor , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Disease Models, Animal , Female , Humans , Mice, Inbred C57BL , Models, Biological , Models, Genetic , Orotic Acid/metabolism , Pyrimidines/metabolism , Ribonucleotides/pharmacology
8.
Nat Commun ; 10(1): 201, 2019 01 14.
Article En | MEDLINE | ID: mdl-30643150

Under hypoxia, most of glucose is converted to secretory lactate, which leads to the overuse of glutamine-carbon. However, under such a condition how glutamine nitrogen is disposed to avoid over-accumulating ammonia remains to be determined. Here we identify a metabolic flux of glutamine to secretory dihydroorotate, which is indispensable to glutamine-carbon metabolism under hypoxia. We found that glutamine nitrogen is necessary to nucleotide biosynthesis, but enriched in dihyroorotate and orotate rather than processing to its downstream uridine monophosphate under hypoxia. Dihyroorotate, not orotate, is then secreted out of cells. Furthermore, we found that the specific metabolic pathway occurs in vivo and is required for tumor growth. The identified metabolic pathway renders glutamine mainly to acetyl coenzyme A for lipogenesis, with the rest carbon and nitrogen being safely removed. Therefore, our results reveal how glutamine carbon and nitrogen are coordinatively metabolized under hypoxia, and provide a comprehensive understanding on glutamine metabolism.


Glutamine/metabolism , Metabolic Networks and Pathways , Metabolome , Neoplasms/metabolism , Orotic Acid/analogs & derivatives , Acetyl Coenzyme A/metabolism , Ammonia/metabolism , Ammonia/toxicity , Animals , Carbon/chemistry , Carbon/metabolism , Cell Hypoxia , Cell Line, Tumor , Cell Survival , Female , Glucose/metabolism , Glutamine/chemistry , HEK293 Cells , Humans , Lactic Acid/metabolism , Lipogenesis , Metabolomics , Mice , Mice, Nude , Neoplasms/blood , Neoplasms/mortality , Neoplasms/pathology , Nitrogen/chemistry , Nitrogen/metabolism , Nucleotides/biosynthesis , Orotic Acid/metabolism , Tumor Microenvironment , Xenograft Model Antitumor Assays
9.
N Biotechnol ; 49: 104-111, 2019 Mar 25.
Article En | MEDLINE | ID: mdl-30347258

Nucleoside triphosphates (NTPs) are important synthetic targets with diverse applications in therapeutics and diagnostics. Enzymatic routes to NTPs from simple building blocks are attractive, however the cost and complexity of assembling the requisite mixtures of multiple enzymes hinders application. Here, we describe the use of an engineered E. coli cell-free lysate as an efficient readily-prepared multi-enzyme biocatalyst for the production of uridine triphosphate (UTP) from free ribose and nucleobase. Endogenous lysate enzymes are able to support the nucleobase ribosylation and nucleotide phosphorylation steps, while uridine phosphorylation and the production of ribose phosphates (ribose 1-phosphate, ribose 5-phosphate and phosphoribosyl pyrophosphate) require recombinant enrichment of endogenous activities. Co-expression vectors encoding all required recombinant enzymes were employed for host cell transformation, such that a cell-free lysate with all necessary activities was obtained from a single bacterial culture. ATP required as phosphorylation cofactor was recycled by endogenous lysate enzymes using cheap, readily-prepared acetyl phosphate. Surprisingly, acetyl phosphate initiated spontaneous generation of ATP in the lysate, most likely from the breakdown of endogenous pools of adenosine-containing starting materials (e.g. adenosine cofactors, ribonucleic acids). The sub-stoichiometric amount of ATP produced and recycled in this way was enough to support all ATP-dependent steps without addition of any exogenous cofactor or auxiliary enzyme. Using this approach, equimolar solutions of orotic acid and ribose are transformed near quantitatively into 1.4 g L-1 UTP within 2.5 h, using a low-cost, readily-generated biocatalytic preparation.


Adenosine Triphosphate/pharmacology , Recombination, Genetic , Ribose/metabolism , Uracil/metabolism , Uridine Triphosphate/biosynthesis , Catalysis , Escherichia coli/metabolism , Hydrolysis , Orotic Acid/metabolism , Recombination, Genetic/genetics , Ribose/chemistry , Uracil/chemistry , Uridine Triphosphate/chemistry
10.
J Am Chem Soc ; 139(45): 16048-16051, 2017 11 15.
Article En | MEDLINE | ID: mdl-29058891

Orotidine 5'-monophosphate decarboxylase (OMPDC) catalyzes the decarboxylation of 5-fluoroorotate (FO) with kcat/Km = 1.4 × 10-7 M-1 s-1. Combining this and related kinetic parameters shows that the 31 kcal/mol stabilization of the transition state for decarboxylation of OMP provided by OMPDC represents the sum of 11.8 and 10.6 kcal/mol stabilization by the substrate phosphodianion and the ribosyl ring, respectively, and an 8.6 kcal/mol stabilization from the orotate ring. The transition state for OMPDC-catalyzed decarboxylation of FO is stabilized by 5.2, 7.2, and 9.0 kcal/mol, respectively, by 1.0 M phosphite dianion, d-glycerol 3-phosphate and d-erythritol 4-phosphate. The stabilization is due to the utilization of binding interactions of the substrate fragments to drive an enzyme conformational change, which locks the orotate ring of the whole substrate, or the substrate pieces in a caged complex. We propose that enzyme-activation is a possible, and perhaps probable, consequence of any substrate-induced enzyme conformational change.


Orotic Acid/analogs & derivatives , Orotidine-5'-Phosphate Decarboxylase/metabolism , Biocatalysis , Kinetics , Models, Molecular , Molecular Conformation , Orotic Acid/chemistry , Orotic Acid/metabolism , Orotidine-5'-Phosphate Decarboxylase/chemistry , Substrate Specificity
11.
Khirurgiia (Mosk) ; (3): 50-54, 2017.
Article Ru | MEDLINE | ID: mdl-28374713

AIM: To study neocollagenogenesis after implantation of polypropylene endoprosthesis and polypropylene combined with polylactic acid endoprosthesis on background of «potassium orotate¼ administration. MATERIAL AND METHODS: We used two different types of endoprosthesis in the experiment. The first type was made of just polypropylene, the second type was made of polypropylene combined with polylactic acid. Histological examination was performed using polarizing microscopy. Collagen types I and III ratio in connective tissue around the prosthesis was analyzed according to the color that was individual for each type. RESULTS: The results were significantly better in case of collagenogenesis stimulation with Potassium orotate within 30 days and later for one type of endoprosthesis. Also we revealed that collagenogenesis and paraprosthesis capsule formation were more active in case of combined endoprosthesis. We revealed stimulating action of «Potassium Orotate¼ for collegenogenesis process, this fact was proved by increased collagen I/III ratio. CONCLUSION: Optimization of collagenogenesis was based on persistent 1,37-fold increase of collagen I/III ratio in case of combined endoprosthesis after 90 days. It was manifested by accelerated formation of connective tissue capsule and facilitated early isolation of the implant from surrounding tissues.


Collagen/metabolism , Connective Tissue , Implants, Experimental , Orotic Acid , Polyesters/pharmacology , Polypropylenes/pharmacology , Prosthesis Implantation/instrumentation , Regeneration/drug effects , Animal Experimentation , Animals , Biocompatible Materials/metabolism , Biocompatible Materials/pharmacology , Biological Availability , Connective Tissue/drug effects , Connective Tissue/metabolism , Connective Tissue/pathology , Mice , Orotic Acid/metabolism , Orotic Acid/pharmacology , Potassium Compounds/metabolism , Potassium Compounds/pharmacology , Prosthesis Implantation/methods , Regeneration/physiology
12.
Biosci Biotechnol Biochem ; 81(6): 1227-1234, 2017 Jun.
Article En | MEDLINE | ID: mdl-28290772

We screened for factors involved in the cellulose-responsive induction of cellulose biomass-degrading enzyme genes from approximately 12,000 Aspergillus aculeatus T-DNA insertion mutants harboring a transcriptional fusion between the FIII-avicelase gene (cbhI) promoter and the orotidine 5'-monophosphate decarboxylase gene. Analysis of 5-fluoroorodic acid (5-FOA) sensitivity, cellulose utilization, and cbhI expression of the mutants revealed that a mutant harboring T-DNA at the dipeptidyl peptidase IV (dppIV) locus had acquired 5-FOA resistance and was deficient in cellulose utilization and cbhI expression. The deletion of dppIV resulted in a significant reduction in the cellulose-responsive expression of both cbhI as well as genes controlled by XlnR-independent and XlnR-dependent signaling pathways at an early phase in A. aculeatus. In contrast, the dppIV deletion did not affect the xylose-responsive expression of genes under the control of XlnR. These results demonstrate that DppIV participates in cellulose-responsive induction in A. aculeatus.


Aspergillus/genetics , Cellulases/genetics , Cellulose/metabolism , Dipeptidyl Peptidase 4/genetics , Fungal Proteins/genetics , Gene Expression Regulation, Fungal , Orotidine-5'-Phosphate Decarboxylase/genetics , Aspergillus/drug effects , Aspergillus/enzymology , Cellulases/metabolism , Cellulose/pharmacology , DNA, Bacterial/genetics , DNA, Bacterial/metabolism , Dipeptidyl Peptidase 4/agonists , Dipeptidyl Peptidase 4/metabolism , Fungal Proteins/metabolism , Gene Deletion , Mutagenesis, Insertional , Orotic Acid/analogs & derivatives , Orotic Acid/metabolism , Orotic Acid/pharmacology , Orotidine-5'-Phosphate Decarboxylase/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Signal Transduction , Xylose/metabolism , Xylose/pharmacology
13.
J Inherit Metab Dis ; 40(3): 423-431, 2017 05.
Article En | MEDLINE | ID: mdl-28205048

BACKGROUND: Elevated urinary excretion of orotic acid is associated with treatable disorders of the urea cycle and pyrimidine metabolism. Establishing the correct and timely diagnosis in a patient with orotic aciduria is key to effective treatment. Uridine monophosphate synthase is involved in de novo pyrimidine synthesis. Uridine monophosphate synthase deficiency (or hereditary orotic aciduria), due to biallelic mutations in UMPS, is a rare condition presenting with megaloblastic anemia in the first months of life. If not treated with the pyrimidine precursor uridine, neutropenia, failure to thrive, growth retardation, developmental delay, and intellectual disability may ensue. METHODS AND RESULTS: We identified mild and isolated orotic aciduria in 11 unrelated individuals with diverse clinical signs and symptoms, the most common denominator being intellectual disability/developmental delay. Of note, none had blood count abnormalities, relevant hyperammonemia or altered plasma amino acid profile. All individuals were found to have heterozygous alterations in UMPS. Four of these variants were predicted to be null alleles with complete loss of function. The remaining variants were missense changes and predicted to be damaging to the normal encoded protein. Interestingly, family screening revealed heterozygous UMPS variants in combination with mild orotic aciduria in 19 clinically asymptomatic family members. CONCLUSIONS: We therefore conclude that heterozygous UMPS-mutations can lead to mild and isolated orotic aciduria without clinical consequence. Partial UMPS-deficiency should be included in the differential diagnosis of mild orotic aciduria. The discovery of heterozygotes manifesting clinical symptoms such as hypotonia and developmental delay are likely due to ascertainment bias.


Multienzyme Complexes/genetics , Multienzyme Complexes/metabolism , Orotate Phosphoribosyltransferase/deficiency , Orotidine-5'-Phosphate Decarboxylase/deficiency , Purine-Pyrimidine Metabolism, Inborn Errors/metabolism , Anemia, Megaloblastic/genetics , Anemia, Megaloblastic/metabolism , Child , Child, Preschool , Female , Heterozygote , Humans , Infant , Intellectual Disability/genetics , Intellectual Disability/metabolism , Male , Mutation/genetics , Orotate Phosphoribosyltransferase/genetics , Orotate Phosphoribosyltransferase/metabolism , Orotic Acid/metabolism , Orotidine-5'-Phosphate Decarboxylase/genetics , Orotidine-5'-Phosphate Decarboxylase/metabolism , Purine-Pyrimidine Metabolism, Inborn Errors/genetics , Pyrimidines/metabolism , Urea Cycle Disorders, Inborn/genetics , Urea Cycle Disorders, Inborn/metabolism , Uridine/metabolism
14.
Nucleosides Nucleotides Nucleic Acids ; 35(10-12): 566-577, 2016 Dec.
Article En | MEDLINE | ID: mdl-27906623

Orotate (OA) is well-known as a precursor in biosynthesis of pyrimidines; in mammals it is released from the mitochondrial dihydroorotate dehydrogenase (DHODH) for conversion to UMP by the cytoplasmic UMP synthase enzyme. OA is also a normal part of the diet, being found in milk and dairy products, and it is converted to uridine for use in the pyrimidine salvage pathway predominantly in liver, kidney and erythrocytes. Early research into nutrition identified orotate as "vitamin B13," and its use as a complex with organic cations or metal ions was promulgated in body-building, and in assisting therapies of metabolic syndromes. It has recently been established that the amelioration of gout by dairy products arises from the competition of orotate and urate at the hURAT1 transporter. The orotic aciduria that arises in children with defective UMP synthase can be rescued by oral uridine therapy, since UMP is the end-product and also a feedback inhibitor of the de novo pathway. In contrast, Miller (dysmorphology) syndrome is connected with defects in DHODH, and hence in the supply of OA, and cannot be helped by uridine. Other models of dysmorphisms are connected with enzymes early in the pyrimidine de novo pathway. We conclude that the OA molecule is itself required for the regulation of genes that are important in the development of cells, tissues and organisms.


Orotic Acid/metabolism , Animals , Anticholesteremic Agents/pharmacology , Anticholesteremic Agents/therapeutic use , Diet , Humans , Orotic Acid/pharmacology , Orotic Acid/therapeutic use
15.
Biochimie ; 131: 45-53, 2016 Dec.
Article En | MEDLINE | ID: mdl-27650727

De novo pyrimidine biosynthesis pathway is well developed and functional in protozoan parasite Leishmania donovani. The dihydroorotase (LdDHOase) is third enzyme of the pathway. The enzyme was cloned, expressed in E. coli BL21 (DE3), purified to homogeneity and biochemically characterized. The estimated kcat for the forward reaction and reverse reactions were 2.1 ± 0.1 s-1 and 1.1 ± 0.15 s-1, respectively. Homology modeling and docking studies were done to find out potential inhibitors for LdDHOase. Biotin sulfone and Kaempferol were found to be potential inhibitors of LdDHOase based on docking studies. These inhibitors were verified using recombinant LdDHOase and their anti-leishmanial effect was evaluated. Moreover, alterations in expressions of de novo as well as salvage pathways enzymes, after treatment of L. donovani with dihydroorotase inhibitor(s) were evaluated and discussed as survival mechanism of the pathogen. Further, effect of inhibition of cytidine deaminase, a key enzyme of salvage pathway of pyrimidine biosynthesis, was also evaluated on parasitic survival and alteration in gene expression of enzymes of both pathways. Further, effect of both pathways inhibition was also evaluated. The data suggests that the inhibition of single pathway can be overcome by increased expression of enzyme(s) of alternate pathway and both pathways seem to be equally important in the pathogen. When both pathways are simultaneously inhibited, parasite shows significant DNA damage and parasitic death.


Dihydroorotase/metabolism , Leishmania donovani/metabolism , Protozoan Proteins/metabolism , Pyrimidines/metabolism , Biotin/analogs & derivatives , Biotin/chemistry , Biotin/pharmacology , Cytidine Deaminase/antagonists & inhibitors , Cytidine Deaminase/genetics , Cytidine Deaminase/metabolism , Dihydroorotase/antagonists & inhibitors , Dihydroorotase/genetics , Electrophoresis, Polyacrylamide Gel , Escherichia coli/genetics , Gene Expression Regulation, Enzymologic , Kaempferols/chemistry , Kaempferols/pharmacology , Kinetics , Leishmania donovani/drug effects , Leishmania donovani/genetics , Molecular Docking Simulation , Molecular Structure , Orotic Acid/analogs & derivatives , Orotic Acid/chemistry , Orotic Acid/metabolism , Protein Domains , Protozoan Proteins/antagonists & inhibitors , Protozoan Proteins/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Substrate Specificity , Sulfones/chemistry , Sulfones/pharmacology
16.
Fungal Biol ; 120(9): 1146-55, 2016 09.
Article En | MEDLINE | ID: mdl-27567720

Of all of the natural polymers, lignin, an aromatic heteropolymer in plant secondary cell walls, is the most resistant to biological degradation. White-rot fungi are the only known organisms that can depolymerize or modify wood lignin. Investigating the mechanisms underlying lignin biodegradation by white-rot fungi would contribute to the ecofriendly utilization of woody biomass as renewable resources in the future. Efficient gene disruption, which is generally very challenging in the white-rot fungi, was established in Pleurotus ostreatus (the oyster mushroom). Some of the genes encoding manganese peroxidases, enzymes that are considered to be involved in lignin biodegradation, were disrupted separately, and the phenotype of each single-gene disruptant was analysed. However, it remains difficult to generate multi-gene disruptants in this fungus. Here we developed a new genetic transformation marker in P. ostreatus and demonstrated two marker recycling methods that use counter-selection to generate a multigene disruptant. This study will enable future genetic studies of white-rot fungi, and it will increase our understanding of the complicated mechanisms, which involve various enzymes, including lignin-degrading enzymes, underlying lignin biodegradation by these fungi.


Antifungal Agents/metabolism , Flucytosine/metabolism , Orotic Acid/analogs & derivatives , Pleurotus/genetics , Pleurotus/metabolism , Selection, Genetic , Fungal Proteins/genetics , Gene Knockout Techniques/methods , Genetic Markers , Genetics, Microbial/methods , Orotic Acid/metabolism , Peroxidases/genetics
17.
J Biosci Bioeng ; 122(6): 645-651, 2016 Dec.
Article En | MEDLINE | ID: mdl-27401770

Shewanella livingstonensis Ac10, a psychrotrophic bacterium isolated from Antarctic seawater, grows well at low temperatures close to 0°C. The bacterium is useful as a host in a low-temperature protein expression system. It is also useful as a model microorganism to investigate the mechanisms of microbial cold-adaptation. Versatile genetic manipulation techniques would be useful to investigate the biology of this bacterium and to develop its applications. In this study, we developed a method for targeted gene deletion and insertion by using the gene coding for orotidine-5'-phosphate decarboxylase (pyrF), which is involved in pyrimidine synthesis. We found that S. livingstonensis Ac10 is sensitive to 5-fluoroorotic acid (5-FOA), which is converted to a highly toxic compound by the product of pyrF. A uracil-auxotrophic strain resistant to 5-FOA was constructed by deleting pyrF, thus allowing the use of a plasmid-borne copy of pyrF for selection of recombinants. We constructed the pyrF complementation suicide plasmid pKKP, which contains pyrF, the R6K replication origin, the mob site of RP4, an antibiotic marker gene, and a multiple cloning site. To demonstrate pyrF-based gene replacement, we deleted the internal region of orf5, the gene coding for an eicosapentaenoic acid (EPA) synthesis enzyme. We also successfully inserted a His6-tag-coding sequence into orf8, the gene coding for another EPA synthesis enzyme. This system allows the markerless deletion and insertion of desired sequences at specific sites in the genome, which remarkably facilitates genetic manipulation of this bacterium.


Gene Deletion , Gene Targeting/methods , Genes, Bacterial , Mutagenesis, Insertional/methods , Mutagenesis, Site-Directed/methods , Orotidine-5'-Phosphate Decarboxylase/genetics , Shewanella/genetics , Adaptation, Biological/genetics , Base Sequence , Cold Temperature , Organisms, Genetically Modified , Orotic Acid/analogs & derivatives , Orotic Acid/metabolism , Orotidine-5'-Phosphate Decarboxylase/metabolism , Shewanella/enzymology , Shewanella/metabolism
18.
Gene ; 583(2): 102-111, 2016 Jun 01.
Article En | MEDLINE | ID: mdl-26861612

Biosynthesis pathways of pyrimidine and purine are shown to play an important role in regular cellular activities. The biosynthesis can occur either through de novo or salvage pathways based on the requirement of the cell. The pyrimidine biosynthesis pathway has been linked to several disorders and various autoimmune diseases. Orotate phosphoribosyl transferase (OPRTase) is an important enzyme which catalyzes the conversion of orotate to orotate monophosphate in the fifth step of pyrimidine biosynthesis. Phylogenetic analysis of 228 OPRTase sequences shows the distribution of proteins across different living forms of life. High structural similarities between Thermusthermophilus and other organisms kindled us to concentrate on OPRTase as an anti-pathogenic target. In this study, a homology model of OPRTase was constructed using 2P1Z as a template. About 100 ns molecular dynamics simulation was performed to investigate the conformational stability and dynamic patterns of the protein. The amino acid residues (Met1, Asp2, Glu43, Ala44, Glu47, Lys51, Ala157 and Leu158) lining in the binding site were predicted using SiteMap. Further, structure based virtual screening was performed on the predicted binding site using ChemBridge, Asinex, Binding, NCI, TosLab and Zinc databases. Compounds retrieved from the screening collections were manually clustered. The resultant protein-ligand complexes were subjected to molecular dynamics simulations, which further validates the binding modes of the hits. The study may provide better insight for designing potent anti-pathogenic agent.


Bacterial Proteins/chemistry , Enzyme Inhibitors/chemistry , Molecular Dynamics Simulation , Orotate Phosphoribosyltransferase/chemistry , Orotic Acid/chemistry , Thermus thermophilus/enzymology , Amino Acid Sequence , Bacterial Proteins/antagonists & inhibitors , Bacterial Proteins/metabolism , Binding Sites , Kinetics , Ligands , Molecular Docking Simulation , Molecular Sequence Data , Orotate Phosphoribosyltransferase/antagonists & inhibitors , Orotate Phosphoribosyltransferase/metabolism , Orotic Acid/metabolism , Phylogeny , Protein Binding , Protein Structure, Secondary , Protein Structure, Tertiary , Sequence Alignment , Structural Homology, Protein , Substrate Specificity , Thermus thermophilus/chemistry
19.
Sci Rep ; 6: 19141, 2016 Jan 11.
Article En | MEDLINE | ID: mdl-26751736

The rising antibiotic resistance of bacteria imposes a severe threat on human health. Inhibition of bacterial virulence is an alternative approach to develop new antimicrobials. Molecules targeting antibiotic resistant enzymes have been used in combination with cognate antibiotics. It might be ideal that a molecule can simultaneously suppress virulence factors and antibiotic resistance. Here we combined genetic and computer-aided inhibitor screening to search for such molecules against the bacterial pathogen Pseudomonas aeruginosa. To identify target proteins that control both virulence and antibiotic resistance, we screened for mutants with defective cytotoxicity and biofilm formation from 93 transposon insertion mutants previously reported with increased antibiotic susceptibility. A pyrD mutant displayed defects in cytotoxicity, biofilm formation, quorum sensing and virulence in an acute mouse pneumonia model. Next, we employed a computer-aided screening to identify potential inhibitors of the PyrD protein, a dihydroorotate dehydrogenase (DHODase) involved in pyrimidine biosynthesis. One of the predicted inhibitors was able to suppress the enzymatic activity of PyrD as well as bacterial cytotoxicity, biofilm formation and antibiotic resistance. A single administration of the compound reduced the bacterial colonization in the acute mouse pneumonia model. Therefore, we have developed a strategy to identify novel treatment targets and antimicrobial molecules.


Anti-Bacterial Agents/pharmacology , Drug Discovery , Drug Resistance, Bacterial , Pseudomonas aeruginosa/drug effects , Pseudomonas aeruginosa/pathogenicity , Animals , Anti-Bacterial Agents/chemistry , Biofilms/drug effects , Disease Models, Animal , Gene Expression Regulation, Bacterial , Genes, Bacterial , Mice , Microbial Sensitivity Tests , Mutation , Orotic Acid/metabolism , Phenotype , Pseudomonas Infections/microbiology , Pseudomonas Infections/mortality , Pseudomonas aeruginosa/enzymology , Pseudomonas aeruginosa/genetics , Pyocyanine/biosynthesis , Type III Secretion Systems/genetics , Uracil/metabolism , Virulence/genetics , Virulence Factors
20.
J Biosci Bioeng ; 121(6): 625-630, 2016 Jun.
Article En | MEDLINE | ID: mdl-26707627

We demonstrated that a Klura3Δ, mutant of the yeast Kluyveromyces lactis is able to produce and secrete into the growth medium considerable amounts of orotic acid. Using yeast extract-peptone-glucose (YPD) based media we optimized production conditions in flask and bioreactor cultures. With cells grown in YPD 5% glucose medium, the best production in flask was obtained with a 1:12.5 ratio for flask: culture volume, 180 rpm, 28°C and 200 mM MOPS for pH stabilization at neutral values (initial culture pH at 8.0). The best production in a 2 L bioreactor was achieved at 500 rpm with 1 vvm aeration, 28°C and pH 7.0. Under these optimum conditions, similar rates of orotic acid production were obtained and maximum concentration achieved after 96 h was 6.7 g/L in flask and bioreactor cultures. These results revealed an excellent reproducibility between both systems and provided evidence for the biotechnological potential of Klura3Δ strain to produce orotic acid since the amounts obtained are comparable to the production in flask using a similar mutant of the industrially valuable Corynebacterium glutamicum.


Bioreactors/microbiology , Kluyveromyces/genetics , Kluyveromyces/metabolism , Metabolic Engineering , Mutation , Orotic Acid/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Biotechnology , Corynebacterium glutamicum/genetics , Corynebacterium glutamicum/metabolism , Culture Media/chemistry , Culture Media/metabolism , Culture Media/pharmacology , Hydrogen-Ion Concentration , Kluyveromyces/drug effects , Reproducibility of Results , Temperature , Time Factors
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