Synthetic Methanol and Formate Assimilation Via Modular Engineering and Selection Strategies
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Harnessing Escherichia Coli for Bio-Based Production of Formate
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.06.425572; this version posted January 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Harnessing Escherichia coli for bio‐based production of formate under pressurized H2 and CO2 gases. Magali Roger1,2, Tom C. Reed2 and Frank Sargent2* 1 Aix Marseille University, CNRS, Bioenergetics and Protein Engineering (BIP UMR7281), 31 Chemin Joseph Aiguier, CS70071, 13042 Marseille Cedex 09, France. 2 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, England, UK *For Correspondence: Prof Frank Sargent FRSE, Division of Plant & Microbial Biology, School of Natural & Environmental Sciences, Newcastle University, Devonshire Building, Kensington Terrace, Newcastle upon Tyne NE2 4BF, England, United Kingdom. T: +44 191 20 85138. E: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.06.425572; this version posted January 6, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. ABSRACT Escherichia coli is gram‐negative bacterium that is a workhorse of the biotechnology industry. The organism has a flexible metabolism and can perform a mixed‐acid fermentation under anaerobic conditions. Under these conditions E. coli synthesises a formate hydrogenlyase isoenzyme (FHL‐1) that can generate molecular hydrogen and carbon dioxide from formic acid. -
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 -
Analysis of the Impact of Silver Ions on Creatine Amidinohydrolase
ActaBIOMATERIALIA Acta Biomaterialia 1 (2005) 183–191 www.actamat-journals.com A stable three enzyme creatinine biosensor. 2. Analysis of the impact of silver ions on creatine amidinohydrolase Jason A. Berberich b,1, Lee Wei Yang a, Ivet Bahar a, Alan J. Russell b,* a Center for Computational Biology & Bioinformatics and Department of Molecular Genetics & Biochemistry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA b Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA Received 11 October 2004; received in revised form 26 November 2004; accepted 28 November 2004 Abstract The enzyme creatine amidinohydrolase is a clinically important enzyme used in the determination of creatinine in blood and urine. Continuous use biosensors are becoming more important in the clinical setting; however, long-use creatinine biosensors have not been commercialized due to the complexity of the three-enzyme creatinine biosensor and the lack of stability of its components. This paper, the second in a series of three, describes the immobilization and stabilization of creatine amidinohydrolase. Creatine amidinohydrolase modified with poly(ethylene glycol) activated with isocyanate retains significant activity after modification. The enzyme was successfully immobilized into hydrophilic polyurethanes using a reactive prepolymer strategy. The immobilized enzyme retained significant activity over a 30 day period at 37 °C and was irreversibly immobilized into the polymer. Despite being stabilized in the polymer, the enzyme remained highly sensitive to silver ions which were released from the amperometric electrodes. Computational analysis of the structure of the protein using the Gaussian network model suggests that the silver ions bind tightly to a cysteine residue preventing normal enzyme dynamics and catalysis. -
Supplementary Materials
Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented. -
Differential Gene Expression in Tomato Fruit and Colletotrichum
Barad et al. BMC Genomics (2017) 18:579 DOI 10.1186/s12864-017-3961-6 RESEARCH Open Access Differential gene expression in tomato fruit and Colletotrichum gloeosporioides during colonization of the RNAi–SlPH tomato line with reduced fruit acidity and higher pH Shiri Barad1,2, Noa Sela3, Amit K. Dubey1, Dilip Kumar1, Neta Luria1, Dana Ment1, Shahar Cohen4, Arthur A. Schaffer4 and Dov Prusky1* Abstract Background: The destructive phytopathogen Colletotrichum gloeosporioides causes anthracnose disease in fruit. During host colonization, it secretes ammonia, which modulates environmental pH and regulates gene expression, contributing to pathogenicity. However, the effect of host pH environment on pathogen colonization has never been evaluated. Development of an isogenic tomato line with reduced expression of the gene for acidity, SlPH (Solyc10g074790.1.1), enabled this analysis. Total RNA from C. gloeosporioides colonizing wild-type (WT) and RNAi– SlPH tomato lines was sequenced and gene-expression patterns were compared. Results: C. gloeosporioides inoculation of the RNAi–SlPH line with pH 5.96 compared to the WT line with pH 4.2 showed 30% higher colonization and reduced ammonia accumulation. Large-scale comparative transcriptome analysis of the colonized RNAi–SlPH and WT lines revealed their different mechanisms of colonization-pattern activation: whereas the WT tomato upregulated 13-LOX (lipoxygenase), jasmonic acid and glutamate biosynthesis pathways, it downregulated processes related to chlorogenic acid biosynthesis II, phenylpropanoid biosynthesis and hydroxycinnamic acid tyramine amide biosynthesis; the RNAi–SlPH line upregulated UDP-D-galacturonate biosynthesis I and free phenylpropanoid acid biosynthesis, but mainly downregulated pathways related to sugar metabolism, such as the glyoxylate cycle and L-arabinose degradation II. -
Enzymatic Conversion of CO2 to Methanol
Verónica Catarina Ferreira Amado Licenciada em Bioquímica “One-pot” enzymatic conversion of CO2 to methanol Dissertação para obtenção do Grau de Mestre em Biotecnologia Orientador: Susana Barreiros, Professora Associada com Agregação Universidade Nova de Lisboa Co-orientador: Alexandre Paiva, Investigador Doutorado Universidade Nova de Lisboa Júri: Presidente: Prof. Doutor Carlos Alberto Gomes Salgueiro Arguente: Doutora Ana Sofia Diogo Ferreira Vogal: Prof. Doutora Susana Filipe Barreiros Setembro de 2013 i ii “One-pot” enzymatic conversion of CO2 to methanol Copyright Verónica Catarina Ferreira Amado, FCT/UNL, UNL A Faculdade de Ciências e Tecnologia e a Universidade Nova de Lisboa têm o direito, perpétuo e sem limites geográficos, de arquivar e publicar esta dissertação através de exemplares impressos reproduzidos em papel ou de forma digital, ou por qualquer outro meio conhecido ou que venha a ser inventado, e de a divulgar através de repositórios científicos e de admitir a sua cópia e distribuição com objetivos educativos ou de investigação, não comerciais, desde que seja dado crédito ao autor e editor. iii iv Ao meu irmão Rafael v AGRADECIMENTOS Gostaria de agradecer a todos aqueles que me apoiaram nesta jornada e que, de algum modo contribuíram para a realização desta tese. Quero expressar a mais sincera gratidão aos meus orientadores. Em primeiro lugar à minha orientadora Prof. Doutora Susana Barreiros por todo o interesse e entusiasmo que demonstrou no meu trabalho, por todas as críticas científicas que tanto o enriqueceram, e por estar sempre disponível para discutir o mesmo. Gostaria de agradecer também ao meu co-orientador o Doutor Alexandre Paiva pela paciência, concelhos dados, discussão de ideias e alternativas, pelo espírito crítico sempre incisivo em pontos fulcrais e também pelos momentos de descontracção. -
Enzyme Immobilization for Use in Biofuel Cells and Sensors
(19) & (11) EP 2 343 766 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 13.07.2011 Bulletin 2011/28 H01M 8/16 (2006.01) C12Q 1/00 (2006.01) (21) Application number: 10179649.8 (22) Date of filing: 21.11.2003 (84) Designated Contracting States: (72) Inventors: AT BE BG CH CY CZ DE DK EE ES FI FR GB GR • Minteer, Shelly, D. HU IE IT LI LU MC NL PT RO SE SI SK TR Pacific, MO 63069 (US) Designated Extension States: • Akers, Niki, L. AL LT LV MK St Louis, MO 63129 (US) • Moore, Christine, M. (30) Priority: 27.11.2002 US 429829 P St Louis, MO 63125 (US) 10.07.2003 US 486076 P 11.07.2003 US 617452 (74) Representative: Smaggasgale, Gillian Helen W.P. Thompson & Co (62) Document number(s) of the earlier application(s) in 55 Drury Lane accordance with Art. 76 EPC: London WC2B 5SQ (GB) 03812443.4 / 1 565 957 Remarks: (71) Applicant: ST. LOUIS UNIVERSITY This application was filed on 24-09-2010 as a St. Louis, MO 63110-0250 (US) divisional application to the application mentioned under INID code 62. (54) Enzyme immobilization for use in biofuel cells and sensors (57) Disclosed are bioanodes comprising a quater- cleotide. The ion conducting polymer membrane lies jux- nary ammonium treated Nation(R) polymer membrane taposed to a polymethylene green redox polymer mem- and a dehydrogenase incorporated within the treated Na- brane, which serves to electro-oxidize the reduced ade- tion(R) polymer. The dehydrogenase catalyzes the oxi- nine dinucleotide. -
University of Groningen Physiology and Biochemistry of Primary Alcohol
University of Groningen Physiology and biochemistry of primary alcohol oxidation in the gram-positive bacteria "amycolatopsis methanolica" and "bacillus methanolicus" Hektor, Harm Jan IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 1997 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Hektor, H. J. (1997). Physiology and biochemistry of primary alcohol oxidation in the gram-positive bacteria "amycolatopsis methanolica" and "bacillus methanolicus". s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 30-09-2021 Chapter 2 Formaldehyde dismutase activities in Gram-positive bacteria oxidizing methanol L.V. -
Recent Progress in the Microbial Production of Pyruvic Acid
fermentation Review Recent Progress in the Microbial Production of Pyruvic Acid Neda Maleki 1 and Mark A. Eiteman 2,* 1 Department of Food Science, Engineering and Technology, University of Tehran, Karaj 31587-77871, Iran; [email protected] 2 School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602, USA * Correspondence: [email protected]; Tel.: +1-706-542-0833 Academic Editor: Gunnar Lidén Received: 10 January 2017; Accepted: 6 February 2017; Published: 13 February 2017 Abstract: Pyruvic acid (pyruvate) is a cellular metabolite found at the biochemical junction of glycolysis and the tricarboxylic acid cycle. Pyruvate is used in food, cosmetics, pharmaceutical and agricultural applications. Microbial production of pyruvate from either yeast or bacteria relies on restricting the natural catabolism of pyruvate, while also limiting the accumulation of the numerous potential by-products. In this review we describe research to improve pyruvate formation which has targeted both strain development and process development. Strain development requires an understanding of carbohydrate metabolism and the many competing enzymes which use pyruvate as a substrate, and it often combines classical mutation/isolation approaches with modern metabolic engineering strategies. Process development requires an understanding of operational modes and their differing effects on microbial growth and product formation. Keywords: auxotrophy; Candida glabrata; Escherichia coli; fed-batch; metabolic engineering; pyruvate; pyruvate dehydrogenase 1. Introduction Pyruvic acid (pyruvate at neutral pH) is a three carbon oxo-monocarboxylic acid, also known as 2-oxopropanoic acid, 2-ketopropionic acid or acetylformic acid. Pyruvate is biochemically located at the end of glycolysis and entry into the tricarboxylic acid (TCA) cycle (Figure1). -
Fumarate Respiration of Wolinella Succinogenes: Enzymology, Energetics and Coupling Mechanism
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1553 (2002) 23^38 www.bba-direct.com Review Fumarate respiration of Wolinella succinogenes: enzymology, energetics and coupling mechanism Achim Kro«ger a;*, Simone Biel a,Jo«rg Simon a, Roland Gross a, Gottfried Unden b, C. Roy D. Lancaster c a Institut fu«r Mikrobiologie, Johann Wolfgang Goethe-Universita«t, Marie-Curie-Str. 9, D-60439 Frankfurt am Main, Germany b Institut fu«r Mikrobiologie und Weinforschung, Johannes Gutenberg-Universita«t, D-55099 Mainz, Germany c Max-Planck-Institut fu«r Biophysik, Heinrich-Ho¡mann-Str. 7, D-60528 Frankfurt am Main, Germany Received 10 May 2001; received in revised form 27 August 2001; accepted 12 October 2001 Abstract Wolinella succinogenes performs oxidative phosphorylation with fumarate instead of O2 as terminal electron acceptor and H2 or formate as electron donors. Fumarate reduction by these donors (`fumarate respiration') is catalyzed by an electron transport chain in the bacterial membrane, and is coupled to the generation of an electrochemical proton potential (vp) across the bacterial membrane. The experimental evidence concerning the electron transport and its coupling to vp generation is reviewed in this article. The electron transport chain consists of fumarate reductase, menaquinone (MK) and either hydrogenase or formate dehydrogenase. Measurements indicate that the vp is generated exclusively by MK reduction with H2 or formate; MKH2 oxidation by fumarate appears to be an electroneutral process. However, evidence derived from the crystal structure of fumarate reductase suggests an electrogenic mechanism for the latter process. -
Original Article Compensatory Upregulation of Aldo-Keto Reductase 1B10 to Protect Hepatocytes Against Oxidative Stress During Hepatocarcinogenesis
Am J Cancer Res 2019;9(12):2730-2748 www.ajcr.us /ISSN:2156-6976/ajcr0097527 Original Article Compensatory upregulation of aldo-keto reductase 1B10 to protect hepatocytes against oxidative stress during hepatocarcinogenesis Yongzhen Liu1, Jing Zhang1, Hui Liu1, Guiwen Guan1, Ting Zhang1, Leijie Wang1, Xuewei Qi1, Huiling Zheng1, Chia-Chen Chen1, Jia Liu1, Deliang Cao2, Fengmin Lu3, Xiangmei Chen1 1State Key Laboratory of Natural and Biomimetic Drugs, Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P. R. China; 2Department of Medical Microbiology, Immunology and Cell Biology, Simmons Cancer Institute at Southern Illinois University School of Medicine, 913 N, Rutledge Street, Springfield, IL 62794, USA; 3Peking University People’s Hospital, Peking University Hepatology Institute, Beijing 100044, P. R. China Received May 26, 2019; Accepted November 15, 2019; Epub December 1, 2019; Published December 15, 2019 Abstract: Aldo-keto reductase 1B10 (AKR1B10), a member of aldo-keto reductase superfamily, contributes to detox- ification of xenobiotics and metabolization of physiological substrates. Although increased expression of AKR1B10 was found in hepatocellular carcinoma (HCC), the role of AKR1B10 in the development of HCC remains unclear. This study aims to illustrate the role of AKR1B10 in hepatocarcinogenesis based on its intrinsic oxidoreduction abilities. HCC cell lines with AKR1B10 overexpression or knockdown were treated with doxorubicin or hydrogen peroxide to determinate the influence of aberrant AKR1B10 expression on cells’ response to oxidative stress. Using Akr1b8 (the ortholog of human AKR1B10) knockout mice, diethylnitrosamine (DEN) induced liver injury, chronic inflammation and hepatocarcinogenesis were explored. Clinically, the pattern of serum AKR1B10 relevant to disease progres- sion was investigated in a patient cohort with chronic hepatitis B (n=30), liver cirrhosis (n=30) and HCC (n=40). -
Polyol Pathway Links Glucose Metabolism to the Aggressiveness
Published OnlineFirst January 17, 2018; DOI: 10.1158/0008-5472.CAN-17-2834 Cancer Metabolism and Chemical Biology Research Polyol Pathway Links Glucose Metabolism to the Aggressiveness of Cancer Cells Annemarie Schwab1, Aarif Siddiqui1, Maria Eleni Vazakidou1, Francesca Napoli1, Martin Bottcher€ 2, Bianca Menchicchi3, Umar Raza4, Ozge€ Saatci4, Angela M. Krebs5, Fulvia Ferrazzi6, Ida Rapa7, Katja Dettmer-Wilde8, Maximilian J. Waldner3, Arif B. Ekici6, Suhail Ahmed Kabeer Rasheed9, Dimitrios Mougiakakos2, Peter J. Oefner8, Ozgur Sahin4, Marco Volante7, Florian R. Greten10, Thomas Brabletz5, and Paolo Ceppi1 Abstract Cancer cells alter their metabolism to support their malig- sequencing confirmed a profound alteration of EMT in PP- nant properties. In this study, we report that the glucose- deficient cells, revealing a strong repression of TGFb signature transforming polyol pathway (PP) gene aldo-keto-reductase- genes. Excess glucose was found to promote EMT through 1-member-B1 (AKR1B1) strongly correlates with epithelial-to- autocrine TGFb stimulation, while PP-deficient cells were mesenchymal transition (EMT). This association was con- refractory to glucose-induced EMT. These data show that PP firmed in samples from lung cancer patients and from an represents a molecular link between glucose metabolism, can- EMT-driven colon cancer mouse model with p53 deletion. In cer differentiation, and aggressiveness, and may serve as a novel vitro, mesenchymal-like cancer cells showed increased AKR1B1 therapeutic target. levels, and AKR1B1 knockdown was sufficient to revert EMT. An Significance: A glucose-transforming pathway in TGFb-driven equivalent level of EMT suppression was measured by targeting epithelial-to-mesenchymal transition provides novel mecha- the downstream enzyme sorbitol-dehydrogenase (SORD), fur- nistic insights into the metabolic control of cancer differenti- ther pointing at the involvement of the PP.