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Yadav M, Kumar T, Kanakan A, Maurya R, Pandey R, Chauhan NS. Isolation and Characterization of Human Intestinal Bacteria Cytobacillus oceanisediminis NB2 for Probiotic Potential. Front Microbiol 2022; 13:932795. [PMID: 35910631 PMCID: PMC9326467 DOI: 10.3389/fmicb.2022.932795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/27/2022] Open
Abstract
Systemic characterization of the human gut microbiota highlighted its vast therapeutic potential. Despite having enormous potential, the non-availability of their culture representatives created a bottleneck to understand the concept of microbiome-based therapeutics. The present study is aimed to isolate and evaluate the probiotic potential of a human gut isolate. Physiochemical, morphological, and phylogenetic characterization of a human gut isolate identifies it as a rod-shaped gram-negative microbe taxonomically affiliated with the Cytobacillus genus, having an optimal growth at 37°C in a partially alkaline environment (pH 8.0). This human gut isolate showed continuous growth in the presence of salts (up to 7% NaCl and 10% KCl), antibiotics, metals and metalloids [silver nitrate (up to 2 mM); lead acetate (up to 2 mM); sodium arsenate (up to 10 mM); potassium dichromate (up to 2 mM)], gastric and intestinal conditions, diverse temperature (25–50°C), and pH (5–9) conditions making it fit to survive in the highly variable gut environment. Genomic characterization identified the presence of gene clusters for diverse bio-catalytic activity, stress response, and antimicrobial activity, as well as it indicated the absence of pathogenic gene islands. A combination of functional features like anti-amylase, anti-lipase, glutenase, prolyl endopeptidase, lactase, bile salt hydrolase, cholesterol oxidase, and anti-pathogenic activity is indicative of its probiotic potential in various disorders. This was further substantiated by the CaCo-2 cell line assay confirming its cellular adherence and biosafety. Conclusively, human gut isolate possessed significant probiotic potential that can be used to promote animal and human health.
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Affiliation(s)
- Monika Yadav
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Tarun Kumar
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Akshay Kanakan
- Integrative GENomics of Host-PathogEn (INGEN-HOPE) Laboratory, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Ranjeet Maurya
- Integrative GENomics of Host-PathogEn (INGEN-HOPE) Laboratory, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Integrative GENomics of Host-PathogEn (INGEN-HOPE) Laboratory, Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
- *Correspondence: Nar Singh Chauhan
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A conserved phosphatase destroys toxic glycolytic side products in mammals and yeast. Nat Chem Biol 2016; 12:601-7. [PMID: 27294321 DOI: 10.1038/nchembio.2104] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 03/28/2016] [Indexed: 11/08/2022]
Abstract
Metabolic enzymes are very specific. However, most of them show weak side activities toward compounds that are structurally related to their physiological substrates, thereby producing side products that may be toxic. In some cases, 'metabolite repair enzymes' eliminating side products have been identified. We show that mammalian glyceraldehyde 3-phosphate dehydrogenase and pyruvate kinase, two core glycolytic enzymes, produce 4-phosphoerythronate and 2-phospho-L-lactate, respectively. 4-Phosphoerythronate strongly inhibits an enzyme of the pentose phosphate pathway, whereas 2-phospho-L-lactate inhibits the enzyme producing the glycolytic activator fructose 2,6-bisphosphate. We discovered that a single, widely conserved enzyme, known as phosphoglycolate phosphatase (PGP) in mammals, dephosphorylates both 4-phosphoerythronate and 2-phospho-L-lactate, thereby preventing a block in the pentose phosphate pathway and glycolysis. Its yeast ortholog, Pho13, similarly dephosphorylates 4-phosphoerythronate and 2-phosphoglycolate, a side product of pyruvate kinase. Our work illustrates how metabolite repair enzymes can make up for the limited specificity of metabolic enzymes and permit high flux in central metabolic pathways.
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Hürlimann HC, Laloo B, Simon-Kayser B, Saint-Marc C, Coulpier F, Lemoine S, Daignan-Fornier B, Pinson B. Physiological and toxic effects of purine intermediate 5-amino-4-imidazolecarboxamide ribonucleotide (AICAR) in yeast. J Biol Chem 2011; 286:30994-31002. [PMID: 21757731 DOI: 10.1074/jbc.m111.262659] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
5-Amino-4-imidazolecarboxamide ribonucleotide 5'-phosphate (AICAR) is a monophosphate metabolic intermediate of the de novo purine synthesis pathway that has highly promising metabolic and antiproliferative properties. Yeast mutants unable to metabolize AICAR are auxotroph for histidine. A screening for suppressors of this phenotype identified recessive and dominant mutants that result in lowering the intracellular AICAR concentration. The recessive mutants affect the adenosine kinase, which is shown here to catalyze the phosphorylation of AICAR riboside in yeast. The dominant mutants strongly enhance the capacity of the alkaline phosphatase Pho13 to dephosphorylate 5-amino-4-imidazole N-succinocarboxamide ribonucleotide 5'-phosphate(SAICAR) into its non-toxic riboside form. By combining these mutants with transcriptomics and metabolomics analyses, we establish that in yeast responses to AICAR and SAICAR are clearly linked to the concentration of the monophosphate forms, whereas the derived nucleoside moieties have no effect even at high intracellular concentration. Finally, we show that AICAR/SAICAR concentrations vary under physiological conditions known to modulate transcription of the purine and phosphate pathway genes.
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Affiliation(s)
- Hans C Hürlimann
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Benoît Laloo
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Barbara Simon-Kayser
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Christelle Saint-Marc
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
| | - Fanny Coulpier
- Institut de Biologie de l'ENS, IBENS, École normale supérieure (ENS), Paris F-75005, France; INSERM, U1024, Paris F-75005, France; UMR 8197, CNRS, Paris F-75005, France
| | - Sophie Lemoine
- Institut de Biologie de l'ENS, IBENS, École normale supérieure (ENS), Paris F-75005, France; INSERM, U1024, Paris F-75005, France; UMR 8197, CNRS, Paris F-75005, France
| | - Bertrand Daignan-Fornier
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France.
| | - Benoît Pinson
- Institut de Biochimie et Génétique Cellulaires (IBGC) Unité Mixte de Recherche (UMR) 5095, Université Ségalen, Bordeaux F-33077, France; IBGC UMR 5095, CNRS, Bordeaux F-33077, France
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Szöor B, Ruberto I, Burchmore R, Matthews KR. A novel phosphatase cascade regulates differentiation in Trypanosoma brucei via a glycosomal signaling pathway. Genes Dev 2010; 24:1306-16. [PMID: 20551176 DOI: 10.1101/gad.570310] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In the mammalian bloodstream, the sleeping sickness parasite Trypanosoma brucei is held poised for transmission by the activity of a tyrosine phosphatase, TbPTP1. This prevents differentiation of the transmissible "stumpy forms" until entry into the tsetse fly, whereupon TbPTP1 is inactivated and major changes in parasite physiology are initiated to allow colonization of the arthropod vector. Using a substrate-trapping approach, we identified the downstream step in this developmental signaling pathway as a DxDxT phosphatase, TbPIP39, which is activated upon tyrosine phosphorylation, and hence is negatively regulated by TbPTP1. In vitro, TbPIP39 promotes the activity of TbPTP1, thereby reinforcing its own repression, this being alleviated by the trypanosome differentiation triggers citrate and cis-aconitate, generating a potentially bistable regulatory switch. Supporting a role in signal transduction, TbPIP39 becomes rapidly tyrosine-phosphorylated during differentiation, and RNAi-mediated transcript ablation in stumpy forms inhibits parasite development. Interestingly, TbPIP39 localizes in glycosomes, peroxisome-like organelles that compartmentalize the trypanosome glycolytic reactions among other enzymatic activities. Our results invoke a phosphatase signaling cascade in which the developmental signal is trafficked to a unique metabolic organelle in the parasite: the glycosome. This is the first characterized environmental signaling pathway targeted directly to a peroxisome-like organelle in any eukaryotic cell.
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Affiliation(s)
- Balázs Szöor
- Centre for Immunity, Infection, and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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Reddy VS, Singh AK, Rajasekharan R. The Saccharomyces cerevisiae PHM8 gene encodes a soluble magnesium-dependent lysophosphatidic acid phosphatase. J Biol Chem 2008; 283:8846-54. [PMID: 18234677 DOI: 10.1074/jbc.m706752200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phosphate is the essential macronutrient required for the growth of all organisms. In Saccharomyces cerevisiae, phosphatases are up-regulated, and the level of lysophosphatidic acid (LPA) is drastically decreased under phosphate-starved conditions. The reduction in the LPA level is attributed to PHM8, a gene of unknown function. phm8Delta yeast showed a decreased LPA-hydrolyzing activity under phosphate-limiting conditions. Overexpression of PHM8 in yeast resulted in an increase in the LPA phosphatase activity in vivo. In vitro assays of the purified recombinant Phm8p revealed magnesium-dependent LPA phosphatase activity, with maximal activity at pH 6.5. The purified Phm8p did not hydrolyze any lipid phosphates other than LPA. In silico analysis suggest that Phm8p is a soluble protein with no transmembrane domain. Site-directed mutational studies revealed that aspartate residues in a DXDXT motif are important for the catalysis. These findings indicated that LPA plays a direct role in phosphate starvation. This is the first report of the identification and characterization of magnesium-dependent soluble LPA phosphatase.
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Affiliation(s)
- Venky Sreedhar Reddy
- Lipid Laboratory, Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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Tyson T, Reardon W, Browne JA, Burnell AM. Gene induction by desiccation stress in the entomopathogenic nematode Steinernema carpocapsae reveals parallels with drought tolerance mechanisms in plants. Int J Parasitol 2007; 37:763-76. [PMID: 17306805 DOI: 10.1016/j.ijpara.2006.12.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 12/13/2006] [Accepted: 12/17/2006] [Indexed: 01/03/2023]
Abstract
The dauer juvenile (DJ) stage of the insect parasitic nematode Steinernema carpocapsae is the only stage in the life cycle which is capable of surviving outside its host and it is adapted for tolerating environmental stresses and for host finding. We have isolated 45 unique expressed sequence tags (ESTs) that are up-regulated in response to desiccation in S. carpocapsae DJs. The majority of these ESTs were co-expressed in response to desiccation and osmotic stress and were generally not induced in response to heat and cold stress. Thirty-two ESTs showed similarity to known sequences. Among these were sequences which encode putative signalling molecules or transcription factors, sequences which detoxify reactive oxygen species, two C-type lectin sequences, ESTs which encode membrane-associated proteins and seven distinct late embryogenic abundant (LEA) sequences. We also isolated 13 novel ESTs. These data show that the molecular response to desiccation stress in entomopathogenic nematode DJs is complex and parallels many of the adaptive changes which occur in drought tolerant plants during exposure to desiccation and osmotic stress. A notable feature of the desiccation response of plants is the number and diversity of hydrophilic LEA proteins synthesised in response to desiccation. All of the LEA sequences detected in animals to date, including those reported in this study, belong to LEA3 group. We show that S. carpocapsae expresses several novel sequences which encode putative hydrophilic and natively unfolded proteins. It is likely that these novel and putative proteins play an important role in desiccation tolerance, possibly by carrying out analogous roles in nematodes to those carried out by the other LEA protein classes in plants.
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Affiliation(s)
- Trevor Tyson
- Institute of Bioengineering and Agroecology, Biology Department, National University of Ireland Maynooth, Maynooth Co, Kildare, Ireland
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Abstract
Organisms are exposed to epoxide-containing compounds from both exogenous and endogenous sources. In mammals, the hydration of these compounds by various epoxide hydrolases (EHs) can not only regulate their genotoxicity but also, for lipid-derived epoxides, their endogenous roles as chemical mediators. Recent findings suggest that the EHs as a family represent novel drug discovery targets for regulation of blood pressure, inflammation, cancer progression, and the onset of several other diseases. Knowledge of the EH mechanism provides a solid foundation for the rational design of inhibitors, and this review summarizes the current understanding of the catalytic mechanism of the EHs. Although the overall EH mechanism is now known, the molecular basis of substrate selectivity, possible allosteric regulation, and many fine details of the catalytic mechanism remain to be solved. Finally, recent development in the design of EH inhibitors and the EH biological role are discussed.
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Affiliation(s)
- Christophe Morisseau
- Department of Entomology and U.C. Davis Cancer Center, University of California, Davis, California 95616, USA
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Wang W, Roach PJ. Glycogen and related polysaccharides inhibit the laforin dual-specificity protein phosphatase. Biochem Biophys Res Commun 2005; 325:726-30. [PMID: 15541350 DOI: 10.1016/j.bbrc.2004.10.083] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Indexed: 11/21/2022]
Abstract
Lafora disease, a progressive myoclonus epilepsy, is an autosomal recessive disease caused in approximately 80% of cases by mutation of the EPM2A gene, which encodes a dual specificity protein phosphatase called laforin. In addition to its phosphatase domain, laforin contains an N-terminal carbohydrate-binding domain (CBD). Mouse laforin was expressed as an N-terminally polyHis tagged protein in Escherichia coli and purified close to homogeneity. The enzyme was active towards p-nitrophenylphosphate (50-80mmol/min/mg, K(m) 4.5mM) with maximal activity at pH 4.5. Laforin binds to glycogen, as previously shown, and caused potent inhibition, half maximally at approximately 1mug/ml. Less branched glucose polymers, amylopectin and amylose, were even more potent, with half maximal inhibition at 10 and 100ng/ml, respectively. With all polysaccharides, however, inhibition was incomplete and laforin retained 20-30% of its native activity at high polysaccharide concentrations. Glucose and short oligosaccharides did not affect activity. Substitution of Trp32 in the CBD by Gly, a mutation found in a patient, caused only a 30% decrease in laforin activity but abolished binding to and inhibition by glycogen, indicating that impaired glycogen binding is sufficient to cause Lafora disease.
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Affiliation(s)
- Wei Wang
- Department of Biochemistry and Molecular Biology, Center for Diabetes Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Newman JW, Morisseau C, Harris TR, Hammock BD. The soluble epoxide hydrolase encoded by EPXH2 is a bifunctional enzyme with novel lipid phosphate phosphatase activity. Proc Natl Acad Sci U S A 2003; 100:1558-63. [PMID: 12574510 PMCID: PMC149871 DOI: 10.1073/pnas.0437724100] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The gene EPXH2 encodes for the soluble epoxide hydrolase (sEH), an enzyme involved in the regulation of cardiovascular and renal physiology containing two distinct domains connected via a proline-rich linker. The C-terminal domain containing the EH catalytic activity has been well studied. In contrast, a function for the N-terminal domain, which has high homology to the haloacid dehalogenase family of phosphatases, has not been definitively reported. In this study we describe the N-terminal domain as a functional phosphatase unaffected by a number of classic phosphatase inhibitors. Assuming a functional association between these catalytic activities, dihydroxy lipid phosphates were rationalized as potential endogenous substrates. A series of phosphorylated hydroxy lipids were therefore synthesized and found to be excellent substrates for the human sEH. The best substrate tested was the monophosphate of dihydroxy stearic acid (threo-910-phosphonoxy-hydroxy-octadecanoic acid) with K(m) = 21 +/- 0.3 microM, V(Max) = 338 +/- 12 nmol x min(-1) x mg(-1), and k(cat) = 0.35 +/- 0.01 s(-1). Therefore dihydroxy lipid phosphates are possible candidates for the endogenous substrates of the sEH N-terminal domain, which would represent a novel branch of fatty acid metabolism with potential signaling functions.
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Affiliation(s)
- John W Newman
- Department of Entomology and University of California Davis Cancer Center, University of California, One Shields Avenue, Davis, CA 95616, USA
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