2 c methyl d erythritol 4 phosphate mep  (Echelon Biosciences)


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    Echelon Biosciences 2 c methyl d erythritol 4 phosphate mep
    2 C Methyl D Erythritol 4 Phosphate Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mep  (Echelon Biosciences)


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    Echelon Biosciences mep
    Michaelis-Menten plot of reaction velocity as a function of A) <t>MEP</t> concentration and <t>B)</t> <t>CTP</t> concentration. The solid line represents the nonlinear least-squares best fit of the data to the Michaelis-Menten equation. Each assay was performed in duplicate. The R 2 value for each plot is indicated. Kinetic parameters derived from the plots are listed in .
    Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Francisella tularensis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase: Kinetic Characterization and Phosphoregulation"

    Article Title: Francisella tularensis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase: Kinetic Characterization and Phosphoregulation

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0020884

    Michaelis-Menten plot of reaction velocity as a function of A) MEP concentration and B) CTP concentration. The solid line represents the nonlinear least-squares best fit of the data to the Michaelis-Menten equation. Each assay was performed in duplicate. The R 2 value for each plot is indicated. Kinetic parameters derived from the plots are listed in .
    Figure Legend Snippet: Michaelis-Menten plot of reaction velocity as a function of A) MEP concentration and B) CTP concentration. The solid line represents the nonlinear least-squares best fit of the data to the Michaelis-Menten equation. Each assay was performed in duplicate. The R 2 value for each plot is indicated. Kinetic parameters derived from the plots are listed in .

    Techniques Used: Concentration Assay, Derivative Assay

    Enzyme assays were performed with the indicated divalent cations at a fixed MEP (200 µM) and CTP (200 µM) concentration. Relative enzyme activity reveals the strict preference of the enzyme for Mg +2 . Each assay was performed in duplicate.
    Figure Legend Snippet: Enzyme assays were performed with the indicated divalent cations at a fixed MEP (200 µM) and CTP (200 µM) concentration. Relative enzyme activity reveals the strict preference of the enzyme for Mg +2 . Each assay was performed in duplicate.

    Techniques Used: Concentration Assay, Activity Assay

    Enzyme assays were performed with the identified nucleotide at either 200 µM or 400 µM, as indicated. The assays contained a fixed MEP (200 µM) concentration. Each assay was performed in duplicate. Relative enzyme activity reveals the preference of the enzyme for CTP.
    Figure Legend Snippet: Enzyme assays were performed with the identified nucleotide at either 200 µM or 400 µM, as indicated. The assays contained a fixed MEP (200 µM) concentration. Each assay was performed in duplicate. Relative enzyme activity reveals the preference of the enzyme for CTP.

    Techniques Used: Concentration Assay, Activity Assay

    A) Intrinsic fluorescence spectra of MEP cytidylyltransferase and two mutant derivatives. Wildtype and mutant (T141D and T141E) proteins were adjusted to 5 µM in 0.1 M Tris pH 7.5, 1 mM NaCl and analyzed using an excitation wavelength of 290 nm. The emission spectra was measured from 310 to 400 nm. The Em λ max of all three proteins was detected at 320 nm. Identical spectra indicate little structural change in the protein globular fold accompanies the introduction of either Asp or Glu. B) The relative activity of wildtype MEP cytidylyltransferase and the T141D and T141E mutants. Assays were performed in duplicate with 200 µM MEP and 200 µM CTP.
    Figure Legend Snippet: A) Intrinsic fluorescence spectra of MEP cytidylyltransferase and two mutant derivatives. Wildtype and mutant (T141D and T141E) proteins were adjusted to 5 µM in 0.1 M Tris pH 7.5, 1 mM NaCl and analyzed using an excitation wavelength of 290 nm. The emission spectra was measured from 310 to 400 nm. The Em λ max of all three proteins was detected at 320 nm. Identical spectra indicate little structural change in the protein globular fold accompanies the introduction of either Asp or Glu. B) The relative activity of wildtype MEP cytidylyltransferase and the T141D and T141E mutants. Assays were performed in duplicate with 200 µM MEP and 200 µM CTP.

    Techniques Used: Fluorescence, Mutagenesis, Activity Assay

    2 c methyl d erythritol 4 phosphate mep  (Echelon Biosciences)


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    Echelon Biosciences 2 c methyl d erythritol 4 phosphate mep
    2 C Methyl D Erythritol 4 Phosphate Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    c methyl d erythritol 4 phosphate mep  (Echelon Biosciences)


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    Echelon Biosciences c methyl d erythritol 4 phosphate mep
    Expression of isoprene synthase ( isp S) in E. coli. Strains carrying the empty plasmid pCOLA, the plasmid containing isp S (pCOLA::IspS) or the plasmid containing isp S and idi (pCOLA::IspS-idi) are compared. a Influence on E. coli growth. E. coli carrying the empty plasmid shows normal exponential growth kinetics. b Influence on MEP pathway intermediate concentrations. The concentration is shown relative to wild-type bacteria carrying the empty vector pCOLA. The data represent the mean of biological triplicates ( \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$\overline{\varvec{x}}$$\end{document} x ¯ ± SE; n = 3). c The MEP pathway in E. coli . The metabolite DXP is also a precursor for the synthesis of vitamin B 6 and thiamin. Ispoprene can be synthesized through the heterologous expression of isp S (shown in red). DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase
    C Methyl D Erythritol 4 Phosphate Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis"

    Article Title: Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis

    Journal: Microbial Cell Factories

    doi: 10.1186/s12934-019-1235-5

    Expression of isoprene synthase ( isp S) in E. coli. Strains carrying the empty plasmid pCOLA, the plasmid containing isp S (pCOLA::IspS) or the plasmid containing isp S and idi (pCOLA::IspS-idi) are compared. a Influence on E. coli growth. E. coli carrying the empty plasmid shows normal exponential growth kinetics. b Influence on MEP pathway intermediate concentrations. The concentration is shown relative to wild-type bacteria carrying the empty vector pCOLA. The data represent the mean of biological triplicates ( \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$\overline{\varvec{x}}$$\end{document} x ¯ ± SE; n = 3). c The MEP pathway in E. coli . The metabolite DXP is also a precursor for the synthesis of vitamin B 6 and thiamin. Ispoprene can be synthesized through the heterologous expression of isp S (shown in red). DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase
    Figure Legend Snippet: Expression of isoprene synthase ( isp S) in E. coli. Strains carrying the empty plasmid pCOLA, the plasmid containing isp S (pCOLA::IspS) or the plasmid containing isp S and idi (pCOLA::IspS-idi) are compared. a Influence on E. coli growth. E. coli carrying the empty plasmid shows normal exponential growth kinetics. b Influence on MEP pathway intermediate concentrations. The concentration is shown relative to wild-type bacteria carrying the empty vector pCOLA. The data represent the mean of biological triplicates ( \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\overline{\varvec{x}}$$\end{document} x ¯ ± SE; n = 3). c The MEP pathway in E. coli . The metabolite DXP is also a precursor for the synthesis of vitamin B 6 and thiamin. Ispoprene can be synthesized through the heterologous expression of isp S (shown in red). DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase

    Techniques Used: Expressing, Plasmid Preparation, Concentration Assay, Synthesized

    Metabolic characterization of the MEP pathway in E. coli expressing isoprene synthase and isopentenyl pyrophosphate isomerase from a plasmid. The intracellular metabolite concentrations, secretion rate of metabolites and isoprene production rate are plotted against dxs expression. The expression strength of dxs was modulated by randomization of its ribosome-binding site. DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase
    Figure Legend Snippet: Metabolic characterization of the MEP pathway in E. coli expressing isoprene synthase and isopentenyl pyrophosphate isomerase from a plasmid. The intracellular metabolite concentrations, secretion rate of metabolites and isoprene production rate are plotted against dxs expression. The expression strength of dxs was modulated by randomization of its ribosome-binding site. DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase

    Techniques Used: Expressing, Plasmid Preparation, Binding Assay

    mep  (Echelon Biosciences)


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    Echelon Biosciences mep
    Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    m mep  (Echelon Biosciences)


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    Echelon Biosciences m mep
    <t>1R,3S-MMV008138</t> inhibits isoprenoid biosynthesis in malaria parasites. <t>MEP</t> metabolites [deoxyxylulose phosphate (DOXP, upstream from IspD) and methylerythritol cyclic diphosphate (MEcPP, downstream from IspD)] were quantified by LC-MS/MS from P. falciparum parasites, following treatment with the indicated agents: fosmidomycin, positive control (known DXR inhibitor); 1S,3R-MMV008138, inactive diastereomer; and 1R,3S-MMV008138, active diastereomer whose antiparasitic effects are relieved by cotreatment with downstream isoprenoid IPP. Data are normalized to untreated controls and represent three independent biological replicates. Below is shown a schematic of the selected MEP pathway enzymes and metabolites, including DOXP and MEcPP.
    M Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Plasmodium IspD (2-C-Methyl-D-erythritol 4-Phosphate Cytidyltransferase), an Essential and Druggable Antimalarial Target"

    Article Title: Plasmodium IspD (2-C-Methyl-D-erythritol 4-Phosphate Cytidyltransferase), an Essential and Druggable Antimalarial Target

    Journal: ACS infectious diseases

    doi: 10.1021/id500047s

    1R,3S-MMV008138 inhibits isoprenoid biosynthesis in malaria parasites. MEP metabolites [deoxyxylulose phosphate (DOXP, upstream from IspD) and methylerythritol cyclic diphosphate (MEcPP, downstream from IspD)] were quantified by LC-MS/MS from P. falciparum parasites, following treatment with the indicated agents: fosmidomycin, positive control (known DXR inhibitor); 1S,3R-MMV008138, inactive diastereomer; and 1R,3S-MMV008138, active diastereomer whose antiparasitic effects are relieved by cotreatment with downstream isoprenoid IPP. Data are normalized to untreated controls and represent three independent biological replicates. Below is shown a schematic of the selected MEP pathway enzymes and metabolites, including DOXP and MEcPP.
    Figure Legend Snippet: 1R,3S-MMV008138 inhibits isoprenoid biosynthesis in malaria parasites. MEP metabolites [deoxyxylulose phosphate (DOXP, upstream from IspD) and methylerythritol cyclic diphosphate (MEcPP, downstream from IspD)] were quantified by LC-MS/MS from P. falciparum parasites, following treatment with the indicated agents: fosmidomycin, positive control (known DXR inhibitor); 1S,3R-MMV008138, inactive diastereomer; and 1R,3S-MMV008138, active diastereomer whose antiparasitic effects are relieved by cotreatment with downstream isoprenoid IPP. Data are normalized to untreated controls and represent three independent biological replicates. Below is shown a schematic of the selected MEP pathway enzymes and metabolites, including DOXP and MEcPP.

    Techniques Used: Liquid Chromatography with Mass Spectroscopy, Positive Control

    Inhibition of PfIspD by 1R,3S-MMV008138 is competitive with CTP but not MEP. (a) Kinetic parameters with respect to the CTP substrate. Each data point represents mean ± SEM from at least three independent experiments. (b) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of CTP substrate concentrations, for illustrative purposes only. (c) Kinetic parameters with respect to the MEP substrate. Each data point represents the mean ± SEM from at least three independent experiments. (d) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of MEP substrate concentrations, for illustrative purposes only.
    Figure Legend Snippet: Inhibition of PfIspD by 1R,3S-MMV008138 is competitive with CTP but not MEP. (a) Kinetic parameters with respect to the CTP substrate. Each data point represents mean ± SEM from at least three independent experiments. (b) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of CTP substrate concentrations, for illustrative purposes only. (c) Kinetic parameters with respect to the MEP substrate. Each data point represents the mean ± SEM from at least three independent experiments. (d) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of MEP substrate concentrations, for illustrative purposes only.

    Techniques Used: Inhibition, Activity Assay

    4 diphosphocytidyl 2 c methyl d erythritol 2 phosphate  (Echelon Biosciences)


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    Echelon Biosciences 4 diphosphocytidyl 2 c methyl d erythritol 2 phosphate
    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, <t>4-diphosphocytidyl-2-C-methyl-</t> d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans
    4 Diphosphocytidyl 2 C Methyl D Erythritol 2 Phosphate, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite"

    Article Title: Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    Journal: Microbial Cell Factories

    doi: 10.1186/s12934-015-0381-7

    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans
    Figure Legend Snippet: Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans

    Techniques Used:

    MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)
    Figure Legend Snippet: MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)

    Techniques Used: Over Expression, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

    2 c methyl d erythritol 2 4 cyclodiphosphate mecpp  (Echelon Biosciences)


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    Echelon Biosciences 2 c methyl d erythritol 2 4 cyclodiphosphate mecpp
    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, <t>4-diphosphocytidyl-2-C-methyl-</t> d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol <t>2,4-cyclodiphosphate</t> synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans
    2 C Methyl D Erythritol 2 4 Cyclodiphosphate Mecpp, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite"

    Article Title: Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    Journal: Microbial Cell Factories

    doi: 10.1186/s12934-015-0381-7

    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans
    Figure Legend Snippet: Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans

    Techniques Used:

    MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)
    Figure Legend Snippet: MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)

    Techniques Used: Over Expression, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

    2 c methyl d erythritol 4 phosphate mep  (Echelon Biosciences)


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    Echelon Biosciences 2 c methyl d erythritol 4 phosphate mep
    MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), <t>2-C-methyl-</t> d <t>-erythritol-4-phosphate</t> (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)
    2 C Methyl D Erythritol 4 Phosphate Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite"

    Article Title: Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    Journal: Microbial Cell Factories

    doi: 10.1186/s12934-015-0381-7

    MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)
    Figure Legend Snippet: MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)

    Techniques Used: Over Expression, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

    mep  (Echelon Biosciences)


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    Echelon Biosciences mep
    The <t>MEP</t> pathway for the synthesis of isoprenoids is specifically inhibited by FSM. FSM competitively inhibits PfDXR and indirectly inhibits PfIspD . <t>Abbreviations:</t> <t>DOXP,</t> 1-deoxy-D-xylulose 5-phosphate; MEP, 2-C-methylerythritol 4-phosphate; CDP-ME, 4-diphosphocytidyl-2-C-methylerythritol; CDP-MEP, 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; MEcPP, 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl pyrophosphate; DXR, DOXP reductase; IspD, CDP-ME synthase; IspE, CDP-ME kinase; IspF, MEcPP synthase.
    Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "A sugar phosphatase regulates the methylerythritol phosphate (MEP) pathway in malaria parasites"

    Article Title: A sugar phosphatase regulates the methylerythritol phosphate (MEP) pathway in malaria parasites

    Journal: Nature communications

    doi: 10.1038/ncomms5467

    The MEP pathway for the synthesis of isoprenoids is specifically inhibited by FSM. FSM competitively inhibits PfDXR and indirectly inhibits PfIspD . Abbreviations: DOXP, 1-deoxy-D-xylulose 5-phosphate; MEP, 2-C-methylerythritol 4-phosphate; CDP-ME, 4-diphosphocytidyl-2-C-methylerythritol; CDP-MEP, 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; MEcPP, 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl pyrophosphate; DXR, DOXP reductase; IspD, CDP-ME synthase; IspE, CDP-ME kinase; IspF, MEcPP synthase.
    Figure Legend Snippet: The MEP pathway for the synthesis of isoprenoids is specifically inhibited by FSM. FSM competitively inhibits PfDXR and indirectly inhibits PfIspD . Abbreviations: DOXP, 1-deoxy-D-xylulose 5-phosphate; MEP, 2-C-methylerythritol 4-phosphate; CDP-ME, 4-diphosphocytidyl-2-C-methylerythritol; CDP-MEP, 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; MEcPP, 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate; IPP, isopentenyl pyrophosphate; DMAPP, dimethylallyl pyrophosphate; DXR, DOXP reductase; IspD, CDP-ME synthase; IspE, CDP-ME kinase; IspF, MEcPP synthase.

    Techniques Used:

    (a) Schematic of PfHAD1 variants found in FSM R strains. Six of the alleles result in premature stop codons. Five alleles produce full-length protein. N70S is a nondeleterious allele reported from sequenced clinical and laboratory isolates. Conserved active site motifs are shown as black boxes . (b) Overall structure of PfHAD1 with the core domain in blue, cap domain in green, and polymorphic residues mapped in yellow. Residues W130 and Y148 are located in the hydrophobic inner region of the cap domain. Residues T26 and A60 are located in the hydrophobic inner region of the core domain. Residue G30 is located in the substrate-binding site. (c) The backbone carbonyl oxygen of Asp-29 and the side chains of Asp-27 and Asp-238 coordinate a magnesium ion to form the active site. The side chains of Asp-29, Thr-61, and Lys-215 coordinate a chloride ion, and are correctly positioned to coordinate a phosphate group upon substrate binding. These activesite residues are conserved in PfHAD1 homologs from organisms possessing the MEP pathway. Alignment was produced in T-Coffee using default parameters. Accession codes for NCBI protein sequences: E. coli YidA, EOU46719; M. tuberculosis Rv3813c, NP_218330; C. reinhardtii FER_156463, ADF43173; A. thaliana At2g25870, ABO38782.
    Figure Legend Snippet: (a) Schematic of PfHAD1 variants found in FSM R strains. Six of the alleles result in premature stop codons. Five alleles produce full-length protein. N70S is a nondeleterious allele reported from sequenced clinical and laboratory isolates. Conserved active site motifs are shown as black boxes . (b) Overall structure of PfHAD1 with the core domain in blue, cap domain in green, and polymorphic residues mapped in yellow. Residues W130 and Y148 are located in the hydrophobic inner region of the cap domain. Residues T26 and A60 are located in the hydrophobic inner region of the core domain. Residue G30 is located in the substrate-binding site. (c) The backbone carbonyl oxygen of Asp-29 and the side chains of Asp-27 and Asp-238 coordinate a magnesium ion to form the active site. The side chains of Asp-29, Thr-61, and Lys-215 coordinate a chloride ion, and are correctly positioned to coordinate a phosphate group upon substrate binding. These activesite residues are conserved in PfHAD1 homologs from organisms possessing the MEP pathway. Alignment was produced in T-Coffee using default parameters. Accession codes for NCBI protein sequences: E. coli YidA, EOU46719; M. tuberculosis Rv3813c, NP_218330; C. reinhardtii FER_156463, ADF43173; A. thaliana At2g25870, ABO38782.

    Techniques Used: Binding Assay, Produced

    Displayed are the means ± SEM of enzyme activity from at least three independent experiments. Substrate abbreviations are as follows: fru1P, fructose 1-phosphate; glc2P, glycerol 2-phosphate; man6P, mannose 6-phosphate; glu6P, glucose 6-phosphate; ribu5P, ribulose 5-phosphate; DOXP, 1-deoxy-D-xylulose 5-phosphate; rib5P, ribose 5-phosphate; gly3P, glyceraldehyde 3-phosphate; fru6P, fructose 6-phosphate; ery4P, erythrose 4-phosphate; 2drib5P, deoxyribose 5-phosphate; MEP, 2-C-methylerythritol 4-phosphate; DHAP, dihydroxyacetone phosphate; glu1P, glucose 1-phosphate; fru1,6bisP, fructose 1,6-bisphosphate; sedo7P, sedoheptulose 7-phosphate; gal1P, galactose 1-phosphate; 2-PGA, 2-phosphoglyceric acid; sorb6P, sorbitol 6-phosphate; tre6P, trehalose 6-phosphate; PEP, phosphoenolpyruvate; gln1P, glucosamine 1-phosphate; 3-PGA, 3-phosphoglyceric acid; man1P, mannose 1-phosphate; FSM, fosmidomycin.
    Figure Legend Snippet: Displayed are the means ± SEM of enzyme activity from at least three independent experiments. Substrate abbreviations are as follows: fru1P, fructose 1-phosphate; glc2P, glycerol 2-phosphate; man6P, mannose 6-phosphate; glu6P, glucose 6-phosphate; ribu5P, ribulose 5-phosphate; DOXP, 1-deoxy-D-xylulose 5-phosphate; rib5P, ribose 5-phosphate; gly3P, glyceraldehyde 3-phosphate; fru6P, fructose 6-phosphate; ery4P, erythrose 4-phosphate; 2drib5P, deoxyribose 5-phosphate; MEP, 2-C-methylerythritol 4-phosphate; DHAP, dihydroxyacetone phosphate; glu1P, glucose 1-phosphate; fru1,6bisP, fructose 1,6-bisphosphate; sedo7P, sedoheptulose 7-phosphate; gal1P, galactose 1-phosphate; 2-PGA, 2-phosphoglyceric acid; sorb6P, sorbitol 6-phosphate; tre6P, trehalose 6-phosphate; PEP, phosphoenolpyruvate; gln1P, glucosamine 1-phosphate; 3-PGA, 3-phosphoglyceric acid; man1P, mannose 1-phosphate; FSM, fosmidomycin.

    Techniques Used: Activity Assay

    PfHAD1 (blue arrows) may dephosphorylate intermediates of glycolysis. Loss of PfHAD1 may increase local levels of sugar phosphates and increase substrate availability to the apicoplast MEP pathway (green). Use of PEP as a substrate is unlikely, given poor PfHAD1 activity against this substrate in vitro . Green reactions and substrates are part of the MEP pathway. PfiTPT and PfoTPT are transporters responsible for import of PEP and DHAP into the apicoplast , . The conversion of PEP and DHAP into pyruvate and gly3P, respectively, are catalyzed by apicoplast-localized pyruvate kinase (PK) and triosephosphate isomerase (TPI) .
    Figure Legend Snippet: PfHAD1 (blue arrows) may dephosphorylate intermediates of glycolysis. Loss of PfHAD1 may increase local levels of sugar phosphates and increase substrate availability to the apicoplast MEP pathway (green). Use of PEP as a substrate is unlikely, given poor PfHAD1 activity against this substrate in vitro . Green reactions and substrates are part of the MEP pathway. PfiTPT and PfoTPT are transporters responsible for import of PEP and DHAP into the apicoplast , . The conversion of PEP and DHAP into pyruvate and gly3P, respectively, are catalyzed by apicoplast-localized pyruvate kinase (PK) and triosephosphate isomerase (TPI) .

    Techniques Used: Activity Assay, In Vitro

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    Echelon Biosciences 2 c methyl d erythritol 4 phosphate mep
    2 C Methyl D Erythritol 4 Phosphate Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Echelon Biosciences mep
    Michaelis-Menten plot of reaction velocity as a function of A) <t>MEP</t> concentration and <t>B)</t> <t>CTP</t> concentration. The solid line represents the nonlinear least-squares best fit of the data to the Michaelis-Menten equation. Each assay was performed in duplicate. The R 2 value for each plot is indicated. Kinetic parameters derived from the plots are listed in .
    Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Echelon Biosciences c methyl d erythritol 4 phosphate mep
    Expression of isoprene synthase ( isp S) in E. coli. Strains carrying the empty plasmid pCOLA, the plasmid containing isp S (pCOLA::IspS) or the plasmid containing isp S and idi (pCOLA::IspS-idi) are compared. a Influence on E. coli growth. E. coli carrying the empty plasmid shows normal exponential growth kinetics. b Influence on MEP pathway intermediate concentrations. The concentration is shown relative to wild-type bacteria carrying the empty vector pCOLA. The data represent the mean of biological triplicates ( \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$\overline{\varvec{x}}$$\end{document} x ¯ ± SE; n = 3). c The MEP pathway in E. coli . The metabolite DXP is also a precursor for the synthesis of vitamin B 6 and thiamin. Ispoprene can be synthesized through the heterologous expression of isp S (shown in red). DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase
    C Methyl D Erythritol 4 Phosphate Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Echelon Biosciences m mep
    <t>1R,3S-MMV008138</t> inhibits isoprenoid biosynthesis in malaria parasites. <t>MEP</t> metabolites [deoxyxylulose phosphate (DOXP, upstream from IspD) and methylerythritol cyclic diphosphate (MEcPP, downstream from IspD)] were quantified by LC-MS/MS from P. falciparum parasites, following treatment with the indicated agents: fosmidomycin, positive control (known DXR inhibitor); 1S,3R-MMV008138, inactive diastereomer; and 1R,3S-MMV008138, active diastereomer whose antiparasitic effects are relieved by cotreatment with downstream isoprenoid IPP. Data are normalized to untreated controls and represent three independent biological replicates. Below is shown a schematic of the selected MEP pathway enzymes and metabolites, including DOXP and MEcPP.
    M Mep, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Echelon Biosciences 4 diphosphocytidyl 2 c methyl d erythritol 2 phosphate
    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, <t>4-diphosphocytidyl-2-C-methyl-</t> d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans
    4 Diphosphocytidyl 2 C Methyl D Erythritol 2 Phosphate, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Echelon Biosciences 2 c methyl d erythritol 2 4 cyclodiphosphate mecpp
    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, <t>4-diphosphocytidyl-2-C-methyl-</t> d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol <t>2,4-cyclodiphosphate</t> synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans
    2 C Methyl D Erythritol 2 4 Cyclodiphosphate Mecpp, supplied by Echelon Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Michaelis-Menten plot of reaction velocity as a function of A) MEP concentration and B) CTP concentration. The solid line represents the nonlinear least-squares best fit of the data to the Michaelis-Menten equation. Each assay was performed in duplicate. The R 2 value for each plot is indicated. Kinetic parameters derived from the plots are listed in .

    Journal: PLoS ONE

    Article Title: Francisella tularensis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase: Kinetic Characterization and Phosphoregulation

    doi: 10.1371/journal.pone.0020884

    Figure Lengend Snippet: Michaelis-Menten plot of reaction velocity as a function of A) MEP concentration and B) CTP concentration. The solid line represents the nonlinear least-squares best fit of the data to the Michaelis-Menten equation. Each assay was performed in duplicate. The R 2 value for each plot is indicated. Kinetic parameters derived from the plots are listed in .

    Article Snippet: MEP cytidylyltransferase activity was evaluated using a coupled-enzyme colorimetric assay, derived from that originally described by Bernal et al . To determine the apparent K M for 2-C-methyl-D-erythritol 4-phosphate (MEP), the assay (200 µL) was performed using 2.5 µM IspD, 100 mM Tris pH 8.0, 1 mM MgCl 2 , 1 mM DTT, 0.2 mM CTP, 100 mU/mL inorganic pyrophosphatase, and varying concentrations of MEP (Echelon Biosciences, Salt Lake City, UT).

    Techniques: Concentration Assay, Derivative Assay

    Enzyme assays were performed with the indicated divalent cations at a fixed MEP (200 µM) and CTP (200 µM) concentration. Relative enzyme activity reveals the strict preference of the enzyme for Mg +2 . Each assay was performed in duplicate.

    Journal: PLoS ONE

    Article Title: Francisella tularensis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase: Kinetic Characterization and Phosphoregulation

    doi: 10.1371/journal.pone.0020884

    Figure Lengend Snippet: Enzyme assays were performed with the indicated divalent cations at a fixed MEP (200 µM) and CTP (200 µM) concentration. Relative enzyme activity reveals the strict preference of the enzyme for Mg +2 . Each assay was performed in duplicate.

    Article Snippet: MEP cytidylyltransferase activity was evaluated using a coupled-enzyme colorimetric assay, derived from that originally described by Bernal et al . To determine the apparent K M for 2-C-methyl-D-erythritol 4-phosphate (MEP), the assay (200 µL) was performed using 2.5 µM IspD, 100 mM Tris pH 8.0, 1 mM MgCl 2 , 1 mM DTT, 0.2 mM CTP, 100 mU/mL inorganic pyrophosphatase, and varying concentrations of MEP (Echelon Biosciences, Salt Lake City, UT).

    Techniques: Concentration Assay, Activity Assay

    Enzyme assays were performed with the identified nucleotide at either 200 µM or 400 µM, as indicated. The assays contained a fixed MEP (200 µM) concentration. Each assay was performed in duplicate. Relative enzyme activity reveals the preference of the enzyme for CTP.

    Journal: PLoS ONE

    Article Title: Francisella tularensis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase: Kinetic Characterization and Phosphoregulation

    doi: 10.1371/journal.pone.0020884

    Figure Lengend Snippet: Enzyme assays were performed with the identified nucleotide at either 200 µM or 400 µM, as indicated. The assays contained a fixed MEP (200 µM) concentration. Each assay was performed in duplicate. Relative enzyme activity reveals the preference of the enzyme for CTP.

    Article Snippet: MEP cytidylyltransferase activity was evaluated using a coupled-enzyme colorimetric assay, derived from that originally described by Bernal et al . To determine the apparent K M for 2-C-methyl-D-erythritol 4-phosphate (MEP), the assay (200 µL) was performed using 2.5 µM IspD, 100 mM Tris pH 8.0, 1 mM MgCl 2 , 1 mM DTT, 0.2 mM CTP, 100 mU/mL inorganic pyrophosphatase, and varying concentrations of MEP (Echelon Biosciences, Salt Lake City, UT).

    Techniques: Concentration Assay, Activity Assay

    A) Intrinsic fluorescence spectra of MEP cytidylyltransferase and two mutant derivatives. Wildtype and mutant (T141D and T141E) proteins were adjusted to 5 µM in 0.1 M Tris pH 7.5, 1 mM NaCl and analyzed using an excitation wavelength of 290 nm. The emission spectra was measured from 310 to 400 nm. The Em λ max of all three proteins was detected at 320 nm. Identical spectra indicate little structural change in the protein globular fold accompanies the introduction of either Asp or Glu. B) The relative activity of wildtype MEP cytidylyltransferase and the T141D and T141E mutants. Assays were performed in duplicate with 200 µM MEP and 200 µM CTP.

    Journal: PLoS ONE

    Article Title: Francisella tularensis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase: Kinetic Characterization and Phosphoregulation

    doi: 10.1371/journal.pone.0020884

    Figure Lengend Snippet: A) Intrinsic fluorescence spectra of MEP cytidylyltransferase and two mutant derivatives. Wildtype and mutant (T141D and T141E) proteins were adjusted to 5 µM in 0.1 M Tris pH 7.5, 1 mM NaCl and analyzed using an excitation wavelength of 290 nm. The emission spectra was measured from 310 to 400 nm. The Em λ max of all three proteins was detected at 320 nm. Identical spectra indicate little structural change in the protein globular fold accompanies the introduction of either Asp or Glu. B) The relative activity of wildtype MEP cytidylyltransferase and the T141D and T141E mutants. Assays were performed in duplicate with 200 µM MEP and 200 µM CTP.

    Article Snippet: MEP cytidylyltransferase activity was evaluated using a coupled-enzyme colorimetric assay, derived from that originally described by Bernal et al . To determine the apparent K M for 2-C-methyl-D-erythritol 4-phosphate (MEP), the assay (200 µL) was performed using 2.5 µM IspD, 100 mM Tris pH 8.0, 1 mM MgCl 2 , 1 mM DTT, 0.2 mM CTP, 100 mU/mL inorganic pyrophosphatase, and varying concentrations of MEP (Echelon Biosciences, Salt Lake City, UT).

    Techniques: Fluorescence, Mutagenesis, Activity Assay

    Expression of isoprene synthase ( isp S) in E. coli. Strains carrying the empty plasmid pCOLA, the plasmid containing isp S (pCOLA::IspS) or the plasmid containing isp S and idi (pCOLA::IspS-idi) are compared. a Influence on E. coli growth. E. coli carrying the empty plasmid shows normal exponential growth kinetics. b Influence on MEP pathway intermediate concentrations. The concentration is shown relative to wild-type bacteria carrying the empty vector pCOLA. The data represent the mean of biological triplicates ( \documentclass[12pt]{minimal} 				\usepackage{amsmath} 				\usepackage{wasysym}  				\usepackage{amsfonts}  				\usepackage{amssymb}  				\usepackage{amsbsy} 				\usepackage{mathrsfs} 				\usepackage{upgreek} 				\setlength{\oddsidemargin}{-69pt} 				\begin{document}$$\overline{\varvec{x}}$$\end{document} x ¯ ± SE; n = 3). c The MEP pathway in E. coli . The metabolite DXP is also a precursor for the synthesis of vitamin B 6 and thiamin. Ispoprene can be synthesized through the heterologous expression of isp S (shown in red). DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase

    Journal: Microbial Cell Factories

    Article Title: Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis

    doi: 10.1186/s12934-019-1235-5

    Figure Lengend Snippet: Expression of isoprene synthase ( isp S) in E. coli. Strains carrying the empty plasmid pCOLA, the plasmid containing isp S (pCOLA::IspS) or the plasmid containing isp S and idi (pCOLA::IspS-idi) are compared. a Influence on E. coli growth. E. coli carrying the empty plasmid shows normal exponential growth kinetics. b Influence on MEP pathway intermediate concentrations. The concentration is shown relative to wild-type bacteria carrying the empty vector pCOLA. The data represent the mean of biological triplicates ( \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\overline{\varvec{x}}$$\end{document} x ¯ ± SE; n = 3). c The MEP pathway in E. coli . The metabolite DXP is also a precursor for the synthesis of vitamin B 6 and thiamin. Ispoprene can be synthesized through the heterologous expression of isp S (shown in red). DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase

    Article Snippet: The following standards for the quantification of MEP pathway intermediates were supplied by Echelon Biosciences (Salt Lake City, UT, USA): 2- C -methyl- d -erythritol 4-phosphate (MEP), 1-deoxy- d -xylulose 5-phosphate (DXP), isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP).

    Techniques: Expressing, Plasmid Preparation, Concentration Assay, Synthesized

    Metabolic characterization of the MEP pathway in E. coli expressing isoprene synthase and isopentenyl pyrophosphate isomerase from a plasmid. The intracellular metabolite concentrations, secretion rate of metabolites and isoprene production rate are plotted against dxs expression. The expression strength of dxs was modulated by randomization of its ribosome-binding site. DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase

    Journal: Microbial Cell Factories

    Article Title: Investigation of the methylerythritol 4-phosphate pathway for microbial terpenoid production through metabolic control analysis

    doi: 10.1186/s12934-019-1235-5

    Figure Lengend Snippet: Metabolic characterization of the MEP pathway in E. coli expressing isoprene synthase and isopentenyl pyrophosphate isomerase from a plasmid. The intracellular metabolite concentrations, secretion rate of metabolites and isoprene production rate are plotted against dxs expression. The expression strength of dxs was modulated by randomization of its ribosome-binding site. DXP 1-deoxy- d -xylulose 5-phosphate, MEP 2- C -methyl- d -erythritol 4-phosphate, MEcPP 2- C -methyl- d -erythritol 2,4-cyclopyrophosphate, ME-CDP 4-diphosphocytidyl-2- C -methylerythritol, MEP-CDP 4-diphosphocytidyl-2- C -methyl- d -erythritol 2-phosphate, HMBPP 4-hydroxy-3-methyl-but-2-enyl pyrophosphate, IPP isopentenyl pyrophosphate, DMAPP dimethylallyl pyrophosphate, GAP glyceraldehyde 3-phosphate, Dxs DXP synthase, Dxr DXP reductoisomerase, IspD MEP cytidylyltransferase, IspE ME-CDP kinase, IspF MEcPP synthase, IspG HMBPP synthase, IspH HMBPP reductase, Idi isopentenyl diphosphate isomerase, IspS isoprene synthase

    Article Snippet: The following standards for the quantification of MEP pathway intermediates were supplied by Echelon Biosciences (Salt Lake City, UT, USA): 2- C -methyl- d -erythritol 4-phosphate (MEP), 1-deoxy- d -xylulose 5-phosphate (DXP), isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP).

    Techniques: Expressing, Plasmid Preparation, Binding Assay

    1R,3S-MMV008138 inhibits isoprenoid biosynthesis in malaria parasites. MEP metabolites [deoxyxylulose phosphate (DOXP, upstream from IspD) and methylerythritol cyclic diphosphate (MEcPP, downstream from IspD)] were quantified by LC-MS/MS from P. falciparum parasites, following treatment with the indicated agents: fosmidomycin, positive control (known DXR inhibitor); 1S,3R-MMV008138, inactive diastereomer; and 1R,3S-MMV008138, active diastereomer whose antiparasitic effects are relieved by cotreatment with downstream isoprenoid IPP. Data are normalized to untreated controls and represent three independent biological replicates. Below is shown a schematic of the selected MEP pathway enzymes and metabolites, including DOXP and MEcPP.

    Journal: ACS infectious diseases

    Article Title: Plasmodium IspD (2-C-Methyl-D-erythritol 4-Phosphate Cytidyltransferase), an Essential and Druggable Antimalarial Target

    doi: 10.1021/id500047s

    Figure Lengend Snippet: 1R,3S-MMV008138 inhibits isoprenoid biosynthesis in malaria parasites. MEP metabolites [deoxyxylulose phosphate (DOXP, upstream from IspD) and methylerythritol cyclic diphosphate (MEcPP, downstream from IspD)] were quantified by LC-MS/MS from P. falciparum parasites, following treatment with the indicated agents: fosmidomycin, positive control (known DXR inhibitor); 1S,3R-MMV008138, inactive diastereomer; and 1R,3S-MMV008138, active diastereomer whose antiparasitic effects are relieved by cotreatment with downstream isoprenoid IPP. Data are normalized to untreated controls and represent three independent biological replicates. Below is shown a schematic of the selected MEP pathway enzymes and metabolites, including DOXP and MEcPP.

    Article Snippet: IC 50 assays contained 50 μ M CTP (Sigma), 500 μ M MEP (Echelon Biosciences), 0.1% DMSO (vehicle for 1 R ,3 S -MMV008138), and 0.2 mM MESG.

    Techniques: Liquid Chromatography with Mass Spectroscopy, Positive Control

    Inhibition of PfIspD by 1R,3S-MMV008138 is competitive with CTP but not MEP. (a) Kinetic parameters with respect to the CTP substrate. Each data point represents mean ± SEM from at least three independent experiments. (b) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of CTP substrate concentrations, for illustrative purposes only. (c) Kinetic parameters with respect to the MEP substrate. Each data point represents the mean ± SEM from at least three independent experiments. (d) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of MEP substrate concentrations, for illustrative purposes only.

    Journal: ACS infectious diseases

    Article Title: Plasmodium IspD (2-C-Methyl-D-erythritol 4-Phosphate Cytidyltransferase), an Essential and Druggable Antimalarial Target

    doi: 10.1021/id500047s

    Figure Lengend Snippet: Inhibition of PfIspD by 1R,3S-MMV008138 is competitive with CTP but not MEP. (a) Kinetic parameters with respect to the CTP substrate. Each data point represents mean ± SEM from at least three independent experiments. (b) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of CTP substrate concentrations, for illustrative purposes only. (c) Kinetic parameters with respect to the MEP substrate. Each data point represents the mean ± SEM from at least three independent experiments. (d) Lineweaver–Burk double-reciprocal plots of wild-type PfIspD activity over a range of MEP substrate concentrations, for illustrative purposes only.

    Article Snippet: IC 50 assays contained 50 μ M CTP (Sigma), 500 μ M MEP (Echelon Biosciences), 0.1% DMSO (vehicle for 1 R ,3 S -MMV008138), and 0.2 mM MESG.

    Techniques: Inhibition, Activity Assay

    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans

    Journal: Microbial Cell Factories

    Article Title: Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    doi: 10.1186/s12934-015-0381-7

    Figure Lengend Snippet: Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans

    Article Snippet: 1-Deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 4-diphosphocytidyl-2-C-methyl- d -erythritol 2-phosphate (CDP-MEP, synthesis kit), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP) and farnesyl pyrophosphate (FPP) were purchased from Echelon Biosciences (Salt Lake City, UT, USA).

    Techniques:

    MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)

    Journal: Microbial Cell Factories

    Article Title: Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    doi: 10.1186/s12934-015-0381-7

    Figure Lengend Snippet: MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)

    Article Snippet: 1-Deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 4-diphosphocytidyl-2-C-methyl- d -erythritol 2-phosphate (CDP-MEP, synthesis kit), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP) and farnesyl pyrophosphate (FPP) were purchased from Echelon Biosciences (Salt Lake City, UT, USA).

    Techniques: Over Expression, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy

    Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans

    Journal: Microbial Cell Factories

    Article Title: Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    doi: 10.1186/s12934-015-0381-7

    Figure Lengend Snippet: Quantitative proteomics comparison of Seq + and MG1655* during lycopene production. a Selective Reaction Monitoring (SRM) proteomics for all MEP and lycopene production pathway enzymes measured in this study. b Lycopene biosynthesis pathway in E. coli . Shown are all enzymes involved in the formation of lycopene from glyceraldehyde-3-phosphate (GA3P) and pyruvate (PYR), as well as reactions competing for either isopentenyl pyrophosphate (IPP), dimethylallyl-pyrophosphate (DMAPP) or farnesyl-pyrophosphate (FPP). Peptides for MiaA and IspU were obtained but did not match our quality criteria and were excluded from this study. c Gene Set Enrichment Analysis of differentially expressed genes in the lycopene production phase. Up- or down-regulated proteins are shown for the Δ rpoS strain MG1655* relative to Seq + . Abbreviations: MEP pathway: Dxs, 1-deoxyxylulose-5-phosphate synthase; Dxr, 1-deoxy- d -xylulose-5-phosphate reductoisomerasease; IspD, 4-diphosphocytidyl-2-C-methyl- d -erythritol synthase; IspE, 4-diphosphocytidyl-2-C-methyl- d -erythritol kinase; IspF, 2-C-methyl- d -erythritol 2,4-cyclodiphosphate synthase; IspG, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase; IspH, hydroxymethylbutenyl diphosphate reductase; Idi, isopentenyl diphosphate isomerase. Competing pathways: IspA, farnesyl pyrophosphate synthase; IspB, octaprenyl diphosphate synthase; IspU, undecaprenyl diphosphate synthase; MiaA, tRNA(i 6 A37) synthase. pAC-LYC04: Idi(pLYC) from H. pluvialis ; CrtE, geranylgeranyl diphosphate synthase from P. agglomerans ; CrtB, phytoene synthase from P. agglomerans ; CrtI, phytoene desaturase from P. agglomerans

    Article Snippet: 1-Deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 4-diphosphocytidyl-2-C-methyl- d -erythritol 2-phosphate (CDP-MEP, synthesis kit), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP) and farnesyl pyrophosphate (FPP) were purchased from Echelon Biosciences (Salt Lake City, UT, USA).

    Techniques:

    MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)

    Journal: Microbial Cell Factories

    Article Title: Systems analysis of methylerythritol-phosphate pathway flux in E. coli : insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite

    doi: 10.1186/s12934-015-0381-7

    Figure Lengend Snippet: MEP pathway flux is not affected by RpoS. a Intracellular MEP pathway metabolite pools during lycopene production in MG1655* and Seq + with dxs overexpression. Glyceraldehyde-3phosphate (GA3P), dihydroxyacetone-phosphate (DHAP), pyruvate (PYR), 1-deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP)/dimethylallyl pyrophosphate (DMAPP; no chromatographic separation of IPP and DMAPP) and farnesyl pyrophosphate (FPP) were quantified using liquid chromatography tandem mass spectrometry (LC–MS/MS). 4-Diphosphocytidyl-2-C-methyl- d -erythritol-2-phosphate (CDP-MEP) was below detection level in all samples. b Isoprene production in the two strains harboring pT-ispS(L70R)

    Article Snippet: 1-Deoxy- d -xylulose 5-phosphate (DXP), 2-C-methyl- d -erythritol-4-phosphate (MEP), 4-diphosphocytidyl-2-C-methylerythritol (CDP-ME), 4-diphosphocytidyl-2-C-methyl- d -erythritol 2-phosphate (CDP-MEP, synthesis kit), 2-C-methyl- d -erythritol-2,4-cyclodiphosphate (MEcPP), (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), isopentenyl pyrophosphate (IPP), dimethylallyl pyrophosphate (DMAPP) and farnesyl pyrophosphate (FPP) were purchased from Echelon Biosciences (Salt Lake City, UT, USA).

    Techniques: Over Expression, Liquid Chromatography, Mass Spectrometry, Liquid Chromatography with Mass Spectroscopy