Structure and Function of Biotin-Dependent Carboxylases
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Adaptive Laboratory Evolution Enhances Methanol Tolerance and Conversion in Engineered Corynebacterium Glutamicum
ARTICLE https://doi.org/10.1038/s42003-020-0954-9 OPEN Adaptive laboratory evolution enhances methanol tolerance and conversion in engineered Corynebacterium glutamicum Yu Wang 1, Liwen Fan1,2, Philibert Tuyishime1, Jiao Liu1, Kun Zhang1,3, Ning Gao1,3, Zhihui Zhang1,3, ✉ ✉ 1234567890():,; Xiaomeng Ni1, Jinhui Feng1, Qianqian Yuan1, Hongwu Ma1, Ping Zheng1,2,3 , Jibin Sun1,3 & Yanhe Ma1 Synthetic methylotrophy has recently been intensively studied to achieve methanol-based biomanufacturing of fuels and chemicals. However, attempts to engineer platform micro- organisms to utilize methanol mainly focus on enzyme and pathway engineering. Herein, we enhanced methanol bioconversion of synthetic methylotrophs by improving cellular tolerance to methanol. A previously engineered methanol-dependent Corynebacterium glutamicum is subjected to adaptive laboratory evolution with elevated methanol content. Unexpectedly, the evolved strain not only tolerates higher concentrations of methanol but also shows improved growth and methanol utilization. Transcriptome analysis suggests increased methanol con- centrations rebalance methylotrophic metabolism by down-regulating glycolysis and up- regulating amino acid biosynthesis, oxidative phosphorylation, ribosome biosynthesis, and parts of TCA cycle. Mutations in the O-acetyl-L-homoserine sulfhydrylase Cgl0653 catalyzing formation of L-methionine analog from methanol and methanol-induced membrane-bound transporter Cgl0833 are proven crucial for methanol tolerance. This study demonstrates the importance of -
Lipid Deposition and Metabolism in Local and Modern Pig Breeds: a Review
animals Review Lipid Deposition and Metabolism in Local and Modern Pig Breeds: A Review Klavdija Poklukar 1 , Marjeta Candek-Potokarˇ 1,2 , Nina Batorek Lukaˇc 1 , Urška Tomažin 1 and Martin Škrlep 1,* 1 Agricultural Institute of Slovenia, Ljubljana SI-1000, Slovenia; [email protected] (K.P.); [email protected] (M.C.-P.);ˇ [email protected] (N.B.L.); [email protected] (U.T.) 2 University of Maribor, Faculty of Agriculture and Life Sciences, HoˇceSI-2311, Slovenia * Correspondence: [email protected]; Tel.: +386-(0)1-280-52-34 Received: 17 February 2020; Accepted: 29 February 2020; Published: 3 March 2020 Simple Summary: Intensive selective breeding and genetic improvement of relatively few pig breeds led to the abandonment of many low productive local pig breeds. However, local pig breeds are more highly adapted to their specific environmental conditions and feeding resources, and therefore present a valuable genetic resource. They are able to deposit more fat and have a distinct lipogenic capacity, along with a better fatty acid composition than modern breeds. Physiological, biochemical and genetic mechanisms responsible for the differences between fatty and lean breeds are still not fully clarified. The present paper highlights important associations to better understand the underlying mechanisms of lipid deposition in subcutaneous and intramuscular fat between fatty and lean breeds. Abstract: Modern pig breeds, which have been genetically improved to achieve fast growth and a lean meat deposition, differ from local pig breeds with respect to fat deposition, fat specific metabolic characteristics and various other properties. The present review aimed to elucidate the mechanisms underlying the differences between fatty local and modern lean pig breeds in adipose tissue deposition and lipid metabolism, taking into consideration morphological, cellular, biochemical, transcriptomic and proteomic perspectives. -
Engineering Alcohol Oxidases for Substrate Scope and Their Application in Flow and Cascade Biocatalysis
ENGINEERING ALCOHOL OXIDASES FOR SUBSTRATE SCOPE AND THEIR APPLICATION IN FLOW AND CASCADE BIOCATALYSIS Rachel Heath, University of Manchester [email protected] Matthew Thompson, EnginZyme Jeremy Ramsden, University of Manchester Sebastian Cosgrove, University of Manchester William Finnigan, University of Manchester Nicholas Turner, University of Manchester Key Words: oxidation, primary alcohol, secondary alcohol, high-throughput screening, thermostability Alcohol oxidases have significant advantages over alcohol dehydrogenases (ADHs) for biocatalytic oxidation of alcohols: they don’t require addition of (expensive) nicotinamide cofactors (or a recycling system for cofactor regeneration) and the catalytic reaction is irreversible. Although alcohol oxidases generate hydrogen peroxide when they turn over, this issue can be alleviated by addition of catalase, which, not only removes the peroxide, but also creates more oxygen for cofactor regeneration. Alcohol oxidases are perceived to have a limited substrate scope preventing their wider use in synthesis. Thus, we present the engineering of two alcohol oxidases for increased substrate scope, one for the selective oxidation of primary alcohols and one for secondary alcohol oxidation. Arthrobacter chlorophenolicus choline oxidase and Streptomyces hygroscopicus cholesterol oxidase were selected as the primary and secondary alcohol oxidase, respectively. Examination of crystal structures of homologous alcohol oxidases revealed positions in the active site and entrance channel to target for saturation mutagenesis. Libraries were screened using a high-throughput assay based on the detection of hydrogen peroxide using hexanol as the substrate for evolution of choline oxidase and cyclohexanol for evolution of cholesterol oxidase. Mutations from positive hits were combined and, in these cases, resulted in variants with further improvements in both kcat and conversion to the carbonyl in biotransformations. -
Solarbio Catalogue with PRICES
CAS Name Grade Purity Biochemical Reagent Biochemical Reagent 75621-03-3 C8390-1 3-((3-Cholamidopropyl)dimethylammonium)-1-propanesulfonateCHAPS Ultra Pure Grade 1g 75621-03-3 C8390-5 3-((3-Cholamidopropyl)dimethylammonium)-1-propanesulfonateCHAPS 5g 57-09-0 C8440-25 Cetyl-trimethyl Ammonium Bromide CTAB High Pure Grade ≥99.0% 25g 57-09-0 C8440-100 Cetyl-trimethyl Ammonium Bromide CTAB High Pure Grade ≥99.0% 100g 57-09-0 C8440-500 Cetyl-trimethyl Ammonium Bromide CTAB High Pure Grade ≥99.0% 500g E1170-100 0.5M EDTA (PH8.0) 100ml E1170-500 0.5M EDTA (PH8.0) 500ml 6381-92-6 E8030-100 EDTA disodium salt dihydrate EDTA Na2 Biotechnology Grade ≥99.0% 100g 6381-92-6 E8030-500 EDTA disodium salt dihydrate EDTA Na2 Biotechnology Grade ≥99.0% 500g 6381-92-6 E8030-1000 EDTA disodium salt dihydrate EDTA Na2 Biotechnology Grade ≥99.0% 1kg 6381-92-6 E8030-5000 EDTA disodium salt dihydrate EDTA Na2 Biotechnology Grade ≥99.0% 5kg 60-00-4 E8040-100 Ethylenediaminetetraacetic acid EDTA Ultra Pure Grade ≥99.5% 100g 60-00-4 E8040-500 Ethylenediaminetetraacetic acid EDTA Ultra Pure Grade ≥99.5% 500g 60-00-4 E8040-1000 Ethylenediaminetetraacetic acid EDTA Ultra Pure Grade ≥99.5% 1kg 67-42-5 E8050-5 Ethylene glycol-bis(2-aminoethylether)-N,N,NEGTA′,N′-tetraacetic acid Ultra Pure Grade ≥97.0% 5g 67-42-5 E8050-10 Ethylene glycol-bis(2-aminoethylether)-N,N,NEGTA′,N′-tetraacetic acid Ultra Pure Grade ≥97.0% 10g 50-01-1 G8070-100 Guanidine Hydrochloride Guanidine HCl ≥98.0%(AT) 100g 50-01-1 G8070-500 Guanidine Hydrochloride Guanidine HCl ≥98.0%(AT) 500g 56-81-5 -
Targeting Demyelination and Virtual Hypoxia with High-Dose Biotin As a Treatment for Progressive Multiple Sclerosis
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Neuropharmacology 110 (2016) 644e653 Contents lists available at ScienceDirect Neuropharmacology journal homepage: www.elsevier.com/locate/neuropharm Invited review Targeting demyelination and virtual hypoxia with high-dose biotin as a treatment for progressive multiple sclerosis * Fred eric Sedel a, , Delphine Bernard a, Donald M. Mock b, c, Ayman Tourbah d a MedDay Pharmaceuticals, ICM-Brain and Spine Institute-IPEPs, Groupe Hospitalier Pitie Salp^etriere, 47 Boulevard de l'Hopital, 75013 Paris, France b Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA c Department of Pediatrics, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA d Department of Neurology and FacultedeMedecine de Reims, CHU de Reims, URCA, 45 Rue Cognacq Jay, 51092 Reims Cedex, France article info abstract Article history: Progressive multiple sclerosis (MS) is a severely disabling neurological condition, and an effective Received 7 April 2015 treatment is urgently needed. Recently, high-dose biotin has emerged as a promising therapy for affected Received in revised form individuals. Initial clinical data have shown that daily doses of biotin of up to 300 mg can improve 24 July 2015 objective measures of MS-related disability. In this article, we review the biology of biotin and explore Accepted 18 August 2015 the properties of this ubiquitous coenzyme that may explain the encouraging responses seen in patients Available online 5 September 2015 with progressive MS. The gradual worsening of neurological disability in patients with progressive MS is caused by progressive axonal loss or damage. -
Purification and Some Properties of Alcohol Oxidase from Alkane-Grown Candida Tropicalis
Biochem. J. (1992) 282, 325-331 (Printed in Great Britain) 325 Purification and some properties of alcohol oxidase from alkane-grown Candida tropicalis Francis M. DICKINSON and Catherine WADFORTH Department of Applied Biology, University of Hull, Cottingham Road, Hull HU6 7RX, U.K. Alcohol oxidase was purified to homogeneity from membrane fractions obtained from alkane-grown Candida tropicalis. The enzyme appears to be a dimer ofequal-sized subunits of Mr 70000. The purified enzyme is photosensitive and contains flavin-type material which is released by a combination of boiling and proteolytic digestion. The identity of the flavin material is not yet known, but it is not FMN, FAD or riboflavin. The enzyme is most active with dodecan-l-ol, but other long-chain alcohols are also attacked. The enzyme shows a weak, but significant activity towards long-chain aldehydes. Detailed kinetic studies with decan-1-ol as substrate suggest a group-transfer (Ping-Pong)-type mechanism of catalysis. INTRODUCTION portions of this culture were inoculated into each of six 3-litre conical flasks containing 500 ml of minimal salts Work from this laboratory has shown that growth of the yeast medium, which contained (g/l) KH2PO4, 7.0; Na2HPO4, 2.0; MgSO4, 1.5; yeast Candida tropicalis on long-chain alkane substrates induces the extract, 1.5; CaCI2, 0.1; FeCl2, 0.008; ZnSO4, 0.0001; synthesis of a long-chain-specific alcohol oxidase (Kemp et al., diammonium tartrate, 15; in distilled water at pH 6.5. The 1988). The enzyme presumably catalyses one of the steps in the pathway in which alkanes undergo monoterminal oxidation carbon source was hexadecane (1 %). -
Metabolic Enzyme Expression Highlights a Key Role for MTHFD2 and the Mitochondrial Folate Pathway in Cancer
ARTICLE Received 1 Nov 2013 | Accepted 17 Dec 2013 | Published 23 Jan 2014 DOI: 10.1038/ncomms4128 Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer Roland Nilsson1,2,*, Mohit Jain3,4,5,6,*,w, Nikhil Madhusudhan3,4,5, Nina Gustafsson Sheppard1,2, Laura Strittmatter3,4,5, Caroline Kampf7, Jenny Huang8, Anna Asplund7 & Vamsi K. Mootha3,4,5 Metabolic remodeling is now widely regarded as a hallmark of cancer, but it is not clear whether individual metabolic strategies are frequently exploited by many tumours. Here we compare messenger RNA profiles of 1,454 metabolic enzymes across 1,981 tumours spanning 19 cancer types to identify enzymes that are consistently differentially expressed. Our meta- analysis recovers established targets of some of the most widely used chemotherapeutics, including dihydrofolate reductase, thymidylate synthase and ribonucleotide reductase, while also spotlighting new enzymes, such as the mitochondrial proline biosynthetic enzyme PYCR1. The highest scoring pathway is mitochondrial one-carbon metabolism and is centred on MTHFD2. MTHFD2 RNA and protein are markedly elevated in many cancers and correlated with poor survival in breast cancer. MTHFD2 is expressed in the developing embryo, but is absent in most healthy adult tissues, even those that are proliferating. Our study highlights the importance of mitochondrial compartmentalization of one-carbon metabolism in cancer and raises important therapeutic hypotheses. 1 Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, 17176 Stockholm, Sweden. 2 Center for Molecular Medicine, Karolinska Institutet, 17176 Stockholm, Sweden. 3 Broad Institute, Cambridge, Massachusetts 02142, USA. 4 Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA. -
Generate Metabolic Map Poster
Authors: Zheng Zhao, Delft University of Technology Marcel A. van den Broek, Delft University of Technology S. Aljoscha Wahl, Delft University of Technology Wilbert H. Heijne, DSM Biotechnology Center Roel A. Bovenberg, DSM Biotechnology Center Joseph J. Heijnen, Delft University of Technology An online version of this diagram is available at BioCyc.org. Biosynthetic pathways are positioned in the left of the cytoplasm, degradative pathways on the right, and reactions not assigned to any pathway are in the far right of the cytoplasm. Transporters and membrane proteins are shown on the membrane. Marco A. van den Berg, DSM Biotechnology Center Peter J.T. Verheijen, Delft University of Technology Periplasmic (where appropriate) and extracellular reactions and proteins may also be shown. Pathways are colored according to their cellular function. PchrCyc: Penicillium rubens Wisconsin 54-1255 Cellular Overview Connections between pathways are omitted for legibility. Liang Wu, DSM Biotechnology Center Walter M. van Gulik, Delft University of Technology L-quinate phosphate a sugar a sugar a sugar a sugar multidrug multidrug a dicarboxylate phosphate a proteinogenic 2+ 2+ + met met nicotinate Mg Mg a cation a cation K + L-fucose L-fucose L-quinate L-quinate L-quinate ammonium UDP ammonium ammonium H O pro met amino acid a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar a sugar K oxaloacetate L-carnitine L-carnitine L-carnitine 2 phosphate quinic acid brain-specific hypothetical hypothetical hypothetical hypothetical -
ACACB Knockout 293T Cell Lysate
Leader in Biomolecular Solutions for Life Science ACACB Knockout 293T Cell Lysate Catalog No.: RM02031 Basic Information Background Catalog No. Acetyl-CoA carboxylase (ACC) is a complex multifunctional enzyme system. ACC is a biotin- RM02031 containing enzyme which catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, the rate- limiting step in fatty acid synthesis. ACC-beta is thought to control fatty acid oxidation by Category means of the ability of malonyl-CoA to inhibit carnitine-palmitoyl-CoA transferase I, the rate- Cell Lysate limiting step in fatty acid uptake and oxidation by mitochondria. ACC-beta may be involved in the regulation of fatty acid oxidation, rather than fatty acid biosynthesis. There is evidence for the presence of two ACC-beta isoforms. [provided by RefSeq, Jul 2008] Description ACACB Knockout 293T Cell Line is engineered from 293T cell line with CRISPR/Cas9 technology. Allele-1:1bp insertion in exon1 Allele-2:94bp deletion in exon1 Gene Information Product Information Gene Symbol Parental Cell line Amount Genotype ACACB 293T 50μL, 2μg/μL. Homozygous knockout Species Packaging Human 1 vial parental cell Lysate and 1 vial knockout cell Lysate Gene ID Shipping Conditions 32 4℃ Swiss Prot Application O00763 Western Blot Synonyms Storage ACC2, ACCB, HACC275 Lysate is stable for 12 months when stored at -20℃. Minimizing freeze-thaw cycles. Protocol Contact To be used as WB control. Lysate is supplied in 1× SDS sample buffer (2% SDS, 60 mM Tris-HCl pH 6.8, 10% Glycerol, 0.02% Bromophenol blue, 60 mM beta-mercaptoethanol). 400-999-6126 Lysate should be boiled for 3 - 5 minutes before loading onto gel. -
Alcohol Oxidase from Hansenula Polymorpha
Alcohol Oxidase from Hansenula polymorpha Catalog Number A0438 Storage Temperature –20 C CAS RN 9073-63-6 Molecular mass:6 670 kDa (octomer, gel filtration) EC 1.1.3.13 Synonym: Alcohol:oxygen oxidoreductase Alcohol oxidase is a homooctomeric flavoprotein with eight equal subunits of 83 kDa; each of which contains Product Description a flavin adenine dinucleotide (FAD) molecule.6 Alcohol oxidase catalyzes the oxidation of short-chain, primary, aliphatic alcohols to the respective aldehydes. Cofactor:4 FAD, one molecule/subunit 7 RCH2OH + O2 RCHO + H2O2 Isoelectric point: 6.1 The enzyme has the highest affinity for methanol with pH Range:8 6.7–9.8 the affinity decreasing with increasing chain length of the alkyl (R) group. pH Optimum:8 8.5 5 Alcohol oxidase plays a major role in the metabolism of Ki (mM): methanol resulting in the formation of formaldehyde and methanol 6,500 has been detected in several genera of yeasts, such as Candida, Pichia, and Hansenula, that utilize methanol Inhibitors:3,8 as a sole carbon and energy source.1,2 1,4-butynediol (irreversible) 4-hydroxy-2- butynal Primarily localized in the peroxisome, alcohol oxidase cyclopropanol has also been found in the cytoplasm. Monomers are cyclopropanone (suicide substrate) synthesized in the cytosol and assembled into octomers formaldehyde, H2O2 (5–10 mM) in the peroxisome. Octomerization is thought to be hydroxylamine, KBr, KCN chaparone mediated.3 Alcohol oxidase is of interest for sodium azide, urea the study of protein translocation into peroxisomes.4 This product is purified from Hansenula polymorpha 4,5 KM (mM): and is supplied as an orange vacuum-dried powder. -
In Vitro Silencing of Acetyl-Coa Carboxylase Beta (ACACB) Gene Reduces Cholesterol Synthesis in Knockdown Chicken Myoblast Cells
In vitro Silencing of Acetyl-CoA Carboxylase beta (ACACB) Gene Reduces Cholesterol Synthesis in Knockdown Chicken Myoblast Cells G. Sushma College of veterinary Science, Hyderabad, India P. Jaya Laxmi PV Narasimha Rao Telangana Veterinary University: Sri PV Narasimha Rao Telangana State Veterinary University S.T. Viroji Rao PV Narasimha Rao Telangana Veterinary University: Sri PV Narasimha Rao Telangana State Veterinary University R.M.V. Prasad PV Narasimha Rao Telangana Veterinary University: Sri PV Narasimha Rao Telangana State Veterinary University M. Kanakachari Directorate of Poultry Research Ch. Shiva Prasad College of Veterinary Science, Korutla, Telangana, India A. Rajendra Prasad Directorate of Poultry Research D. Divya Directorate of Poultry Research Tarun Kumar Bhattacharya ( [email protected] ) Directorate of Poultry Research https://orcid.org/0000-0003-4502-1852 Research Article Keywords: Chicken, fatty acid metabolism, ACACB, shRNA, myoblast cell culture, gene silencing. Posted Date: June 18th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-502942/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/22 Abstract The poultry industry provides cost-effective, healthy, and protein-enriched food for the growing population and achieving the nutritional security to the country. Excessive abdominal and subcutaneous fat deposition is one of the major setbacks to the poultry industry that reduces carcass yield and feed eciency. In chicken abdominal fat constitutes 20% of total body fat which make up 2–3% of live weight of the bird. In fatty acid metabolism, acetyl-CoA Carboxylase (ACC) is one of the key enzymes with two isoforms i.e. -
Metabolic Network Construction Based on the Genome of The
San Jose State University SJSU ScholarWorks Master's Theses Master's Theses and Graduate Research Fall 2013 Metabolic Network Construction Based on the Genome of the Marine Diatom Thalassiosira Pseudonana and the Analysis of Genome-wide Transcriptome Data to Investigate Triacylglyceride Accumulation Karen Parker San Jose State University Follow this and additional works at: https://scholarworks.sjsu.edu/etd_theses Recommended Citation Parker, Karen, "Metabolic Network Construction Based on the Genome of the Marine Diatom Thalassiosira Pseudonana and the Analysis of Genome-wide Transcriptome Data to Investigate Triacylglyceride Accumulation" (2013). Master's Theses. 4400. DOI: https://doi.org/10.31979/etd.mved-nx78 https://scholarworks.sjsu.edu/etd_theses/4400 This Thesis is brought to you for free and open access by the Master's Theses and Graduate Research at SJSU ScholarWorks. It has been accepted for inclusion in Master's Theses by an authorized administrator of SJSU ScholarWorks. For more information, please contact [email protected]. METABOLIC NETWORK CONSTRUCTION BASED ON THE GENOME OF THE MARINE DIATOM THALASSIOSIRA PSEUDONANA AND THE ANALYSIS OF GENOME-WIDE TRANSCRIPTOME DATA TO INVESTIGATE TRIACYLGLYCERIDE ACCUMULATION A Thesis Presented to The Faculty of Moss Landing Marine Labs San José State University In Partial Fulfillment of the Requirements for the Degree Master of Science By Karen R. Parker December 2013 © 2013 Karen R. Parker ALL RIGHTS RESERVED The Designated Thesis Committee Approves the Thesis Titled METABOLIC NETWORK CONSTRUCTION BASED ON THE GENOME OF THE MARINE DIATOM THALASSIOSIRA PSEUDONANA AND THE ANALYSIS OF GENOME-WIDE TRANSCRIPTOME DATA TO INVESTIGATE TRIACYLGLYCERIDE ACCUMULATION By Karen R. Parker APPPROVED FOR MOSS LANDING MARINE LABS SAN JOSÉ STATE UNIVERSITY December 2013 Dr.