Purification and Characterization of Chorismate Synthase from Euglena Gracilis'
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Part One Amino Acids As Building Blocks
Part One Amino Acids as Building Blocks Amino Acids, Peptides and Proteins in Organic Chemistry. Vol.3 – Building Blocks, Catalysis and Coupling Chemistry. Edited by Andrew B. Hughes Copyright Ó 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN: 978-3-527-32102-5 j3 1 Amino Acid Biosynthesis Emily J. Parker and Andrew J. Pratt 1.1 Introduction The ribosomal synthesis of proteins utilizes a family of 20 a-amino acids that are universally coded by the translation machinery; in addition, two further a-amino acids, selenocysteine and pyrrolysine, are now believed to be incorporated into proteins via ribosomal synthesis in some organisms. More than 300 other amino acid residues have been identified in proteins, but most are of restricted distribution and produced via post-translational modification of the ubiquitous protein amino acids [1]. The ribosomally encoded a-amino acids described here ultimately derive from a-keto acids by a process corresponding to reductive amination. The most important biosynthetic distinction relates to whether appropriate carbon skeletons are pre-existing in basic metabolism or whether they have to be synthesized de novo and this division underpins the structure of this chapter. There are a small number of a-keto acids ubiquitously found in core metabolism, notably pyruvate (and a related 3-phosphoglycerate derivative from glycolysis), together with two components of the tricarboxylic acid cycle (TCA), oxaloacetate and a-ketoglutarate (a-KG). These building blocks ultimately provide the carbon skeletons for unbranched a-amino acids of three, four, and five carbons, respectively. a-Amino acids with shorter (glycine) or longer (lysine and pyrrolysine) straight chains are made by alternative pathways depending on the available raw materials. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Microbial Production of Methyl Anthranilate, a Grape Flavor Compound
Microbial production of methyl anthranilate, a grape flavor compound Zi Wei Luoa,b,1, Jae Sung Choa,b,1, and Sang Yup Leea,b,c,d,2 aMetabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Institute for the BioCentury, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; bSystems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; cBioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea; and dBioInformatics Research Center, Korea Advanced Institute of Science and Technology, 34141 Daejeon, Republic of Korea Contributed by Sang Yup Lee, April 5, 2019 (sent for review March 6, 2019; reviewed by Jay D. Keasling and Blaine A. Pfeifer) Methyl anthranilate (MANT) is a widely used compound to give While these biotransformation procedures are considered more grape scent and flavor, but is currently produced by petroleum-based natural and ecofriendly compared with chemical synthesis, their processes. Here, we report the direct fermentative production of actual use is limited due to low yields, long reaction times, and MANT from glucose by metabolically engineered Escherichia coli and formation of byproducts (5). In addition, the chemical and bio- Corynebacterium glutamicum strains harboring a synthetic plant- transformation processes mentioned -
Davidge JBC Supplementary.Pdf
promoting access to White Rose research papers Universities of Leeds, Sheffield and York http://eprints.whiterose.ac.uk/ White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/7923/ (includes links to Main Article, Supplementary Material and Figures) Published paper Davidge, K.S., Sanguinetti, G., Yee, C.H., Cox, A.G., McLeod, C.W., Monk, C.E., Mann, B.E., Motterlini, R. and Poole, R.K. (2009) Carbon monoxide-releasing antibacterial molecules target respiration and global transcriptional regulators. Journal of Biological Chemistry, 284 (7). pp. 4516-4524. http://dx.doi.org/10.1074/jbc.M808210200 Supplementary Material White Rose Research Online [email protected] Supplementary Material Carbon monoxide-releasing antibacterial molecules target respiration and global transcriptional regulators Kelly S Davidge, Guido Sanguinetti, Chu Hoi Yee, Alan G Cox, Cameron W McLeod, Claire E Monk, Brian E Mann, Roberto Motterlini and Robert K Poole Contents Page Number Supplementary Figure S1 3 Inhibition by CORM-3 of E. coli cultures grown in defined medium anaerobically and aerobically Supplementary Figure S2 4 Viability assays showing survival of anaerobically and aerobically E. coli in defined growth medium Supplementary Figure S3 5 Reaction of terminal oxidases in vivo on addition of RuCl2(DMSO)4 to intact cells in a dual-wavelength spectrophotometer Supplementary Figure S4 6 CORM-3 generates carbonmonoxycytochrome bd in vivo and depresses synthesis of cytochrome bo' Supplementary Figure S5 7 Expression of spy-lacZ activity -
Production of Muconic Acid in Plants T ⁎ Aymerick Eudesa,B, , Roland Berthomieua,C, Zhangying Haoa,B, Nanxia Zhaoa,D, ⁎ Veronica Teixeira Benitesa,E, Edward E.K
Metabolic Engineering 46 (2018) 13–19 Contents lists available at ScienceDirect Metabolic Engineering journal homepage: www.elsevier.com/locate/meteng Production of muconic acid in plants T ⁎ Aymerick Eudesa,b, , Roland Berthomieua,c, Zhangying Haoa,b, Nanxia Zhaoa,d, ⁎ Veronica Teixeira Benitesa,e, Edward E.K. Baidooa,e, Dominique Loquéa,b,f,g, a Joint BioEnergy Institute, EmeryStation East, 5885 Hollis St, 4th Floor, Emeryville, CA 94608, USA b Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA c Ecole Polytechnique, Université Paris-Saclay, Palaiseau 91120, France d Department of Bioengineering, Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, USA e Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA f Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA g Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France ARTICLE INFO ABSTRACT Keywords: Muconic acid (MA) is a dicarboxylic acid used for the production of industrially relevant chemicals such as Muconic acid adipic acid, terephthalic acid, and caprolactam. Because the synthesis of these polymer precursors generates Salicylic acid toxic intermediates by utilizing petroleum-derived chemicals and corrosive catalysts, the development of al- Catechol ternative strategies for the bio-based production of MA has garnered significant interest. Plants produce organic Shikimate carbon skeletons by harvesting carbon dioxide and energy from the sun, and therefore represent advantageous Plastid hosts for engineered metabolic pathways towards the manufacturing of chemicals. -
Insensitive 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthaset LISA M
JOURNAL OF BACTERIOLOGY, Nov. 1990, p. 6581-6584 Vol. 172, No. 11 0021-9193/90/116581-04$02.00/0 Copyright X 1990, American Society for Microbiology Cloning of an aroF Allele Encoding a Tyrosine- Insensitive 3-Deoxy-D-arabino-Heptulosonate 7-Phosphate Synthaset LISA M. WEAVER AND KLAUS M. HERRMANN* Department ofBiochemistry, Purdue University, West Lafayette, Indiana 47907 Received 9 May 1990/Accepted 10 August 1990 In Escherichia coli, genes aroF+, aroG+, and aroH+ encode isoenzymes of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthases that are feedback inhibited by tyrosine, phenylalanine, and tryptophan, respectively. A single base pair change in aroF causes a Pro-148-to-Leu-148 substitution and results in a tyrosine-insensitive enzyme. In bacteria and plants, the aromatic amino acids phenyl- plasmid, designated pLW22, contained an 8-kb insert that alanine, tyrosine, and tryptophan are synthesized via the hybridized to the 714-bp DdeI (Fig. 1) aroF probe (6, 11). shikimate pathway (7, 13). The first enzyme of this pathway Digestion of pLW22 with HindIII-BglII gave a 950-bp frag- is 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) ment that hybridized to the probe. This result was unex- synthase (EC 4.1.2.15). In Escherichia coli, the three un- pected, since the corresponding wild-type fragment is 1.8 kb linked genes aroF+, aroG+, and aroH+ (1) encode three in size. Subsequent detailed restriction analysis and hybrid- isoenzymes of DAHP synthase that are sensitive to tyrosine, ization of pLW22 with the 796-bp DdeI (Fig. 1) aroF probe phenylalanine, and tryptophan, respectively (2). -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
Advancing a Systems Cell-Free Metabolic Engineering Approach to Natural Product Synthesis and Discovery
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2020 Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery Benjamin Mohr University of Tennessee Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Mohr, Benjamin, "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery. " PhD diss., University of Tennessee, 2020. https://trace.tennessee.edu/utk_graddiss/6837 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Benjamin Mohr entitled "Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Energy Science and Engineering. Mitchel Doktycz, Major Professor We have read this dissertation and recommend its acceptance: Jennifer Morrell-Falvey, Dale Pelletier, Michael Simpson, Robert Hettich Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Advancing a systems cell-free metabolic engineering approach to natural product synthesis and discovery A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Benjamin Pintz Mohr December 2019 c by Benjamin Pintz Mohr, 2019 All Rights Reserved. -
8.2 Shikimic Acid Pathway
CHAPTER 8 © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORAromatic SALE OR DISTRIBUTION and NOT FOR SALE OR DISTRIBUTION Phenolic Compounds © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION CHAPTER OUTLINE Overview Synthesis and Properties of Polyketides 8.1 8.5 Synthesis of Chalcones © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 8.2 Shikimic Acid Pathway Synthesis of Flavanones and Derivatives NOT FOR SALE ORPhenylalanine DISTRIBUTION and Tyrosine Synthesis NOT FOR SALESynthesis OR DISTRIBUTION and Properties of Flavones Tryptophan Synthesis Synthesis and Properties of Anthocyanidins Synthesis and Properties of Isofl avonoids Phenylpropanoid Pathway 8.3 Examples of Other Plant Polyketide Synthases Synthesis of Trans-Cinnamic Acid Synthesis and Activity of Coumarins Lignin Synthesis Polymerization© Jonesof Monolignols & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC Genetic EngineeringNOT FOR of Lignin SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Natural Products Derived from the 8.4 Phenylpropanoid Pathway Natural Products from Monolignols © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION 119 © Jones & Bartlett Learning, LLC. -
Genetic Characterisaton of Rhodococcus Rhodochrous ATCC
The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town Genetic characterization of Rhodococcus rhodochrous ATCC BAA-870 with emphasis on nitrile hydrolysing enzymes n ow Joni Frederick A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy in the Departmentty of of MolecularCape and T Cell Biology, Universitysi of Cape Town er UnivSupervisor: Professor B. T. Sewell Co-supervisor: Professor D. Brady February 2013 Keywords Nitrile hydrolysis Biocatalysis Rhodococcus rhodochrous ATCC BAA-870 Genome sequencing Nitrilase Nitrile hydratase n ow ty of Cape T si er Univ ii Keywords Abstract Rhodococcus rhodochrous ATCC BAA-870 (BAA-870) had previously been isolated on selective media for enrichment of nitrile hydrolysing bacteria. The organism was found to have a wide substrate range, with activity against aliphatics, aromatics, and aryl aliphatics, and enantioselectivity towards beta substituted nitriles and beta amino nitriles, compounds that have potential applications in the pharmaceutical industry. This makes R. rhodochrous ATCC BAA-870 potentially a versatile biocatalyst for the synthesis of a broad range of compounds with amide and carboxylic acid groups that can be derived from structurally related nitrile precursors. The selectivity of biocatalysts allows for high product yields and better atom economyn than non- selective chemical methods of performing this reaction, suchow as acid or base hydrolysis. -
Crystal Structure of Chorismate Synthase: a Novel FMN-Binding Protein Fold and Functional Insights
doi:10.1016/j.jmb.2003.12.072 J. Mol. Biol. (2004) 336, 903–915 Crystal Structure of Chorismate Synthase: A Novel FMN-binding Protein Fold and Functional Insights Hyung Jun Ahn, Hye-Jin Yoon, Byung Il Lee and Se Won Suh* Department of Chemistry Chorismate synthase catalyzes the conversion of 5-enolpyruvylshikimate College of Natural Sciences 3-phosphate to chorismate in the shikimate pathway, which represents Seoul National University an attractive target for discovering antimicrobial agents and herbicides. Seoul 151-0742, South Korea Chorismate serves as a common precursor for the synthesis of aromatic amino acids and many aromatic compounds in microorganisms and plants. Chorismate synthase requires reduced FMN as a cofactor but the catalyzed reaction involves no net redox change. Here, we have deter- mined the crystal structure of chorismate synthase from Helicobacter pylori in both FMN-bound and FMN-free forms. It is a tetrameric enzyme, with each monomer possessing a novel “b-a-b sandwich fold”. Highly con- served regions, including several flexible loops, cluster together around the bound FMN to form the active site. The unique FMN-binding site is formed largely by a single subunit, with a small contribution from a neighboring subunit. The isoalloxazine ring of the bound FMN is signifi- cantly non-planar. Our structure illuminates the essential functional roles played by the cofactor. q 2004 Elsevier Ltd. All rights reserved. Keywords: aroC; chorismate synthase; FMN-binding protein; Helicobacter *Corresponding author pylori; shikimate -
Molecular Targets for Antifungals in Amino Acid and Protein Biosynthetic Pathways
Amino Acids https://doi.org/10.1007/s00726-021-03007-6 REVIEW ARTICLE Molecular targets for antifungals in amino acid and protein biosynthetic pathways Aleksandra Kuplińska1 · Kamila Rząd1 Received: 1 March 2021 / Accepted: 17 May 2021 © The Author(s) 2021 Abstract Fungi cause death of over 1.5 million people every year, while cutaneous mycoses are among the most common infections in the world. Mycoses vary greatly in severity, there are long-term skin (ringworm), nail or hair infections (tinea capitis), recurrent like vaginal candidiasis or severe, life-threatening systemic, multiorgan infections. In the last few years, increas- ing importance is attached to the health and economic problems caused by fungal pathogens. There is a growing need for improvement of the availability of antifungal drugs, decreasing their prices and reducing side efects. Searching for novel approaches in this respect, amino acid and protein biosynthesis pathways appear to be competitive. The route that leads from amino acid biosynthesis to protein folding and its activation is rich in enzymes that are descriptive of fungi. Blocking the action of those enzymes often leads to avirulence or growth inhibition. In this review, we want to trace the principal processes of fungi vitality. We present the data of genes encoding enzymes involved in amino acid and protein biosynthesis, potential molecular targets in antifungal chemotherapy, and describe the impact of inhibitors on fungal organisms. Keywords Antifungal targets · Amino acid biosynthesis · Protein biosynthesis · Candida · Aspergillus · Plant pathogens Introduction is approximately 30–55% and 50–100% for aspergillosis (Brown et al. 2012; Verweij et al. 2016; Haidar and Singh Invasive fungal mycoses may afect over 300 million peo- 2018).