Endogenous Superoxide Is a Key Effector of the Oxygen Sensitivity of a Model Obligate Anaerobe
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. -
Rewiring Hydrogenase-Dependent Redox Circuits in Cyanobacteria
Rewiring hydrogenase-dependent redox circuits in cyanobacteria Daniel C. Ducata,b, Gairik Sachdevac, and Pamela A. Silvera,b,1 aDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115; bWyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115; and cSchool of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 Edited by David Baker, University of Washington, Seattle, WA, and approved January 26, 2011 (received for review October 26, 2010) þ þ − ↔ Hydrogenases catalyze the reversible reaction 2H 2e H2 The hydrogen production capacity of a variety of cyanobacter- with an equilibrium constant that is dependent on the reducing ial and algal species has been surveyed (8–10), and the highest potential of electrons carried by their redox partner. To examine rates of hydrogen evolution are typically observed in algae the possibility of increasing the photobiological production of and some nitrogen-fixing cyanobacteria. Algal species frequently hydrogen within cyanobacterial cultures, we expressed the [FeFe] possess [FeFe]-hydrogenases that accept low-potential electrons hydrogenase, HydA, from Clostridium acetobutylicum in the non- from ferredoxins that are, in turn, linked to the light reactions of nitrogen-fixing cyanobacterium Synechococcus elongatus sp. 7942. photosynthesis (11). Nitrogen-fixing microorganisms, including We demonstrate that the heterologously expressed hydrogenase is many cyanobacteria (12), produce hydrogen gas as a byproduct functional in vitro and in -
The Genetic Basis of Energy Conservation in the Sulfate-Reducing Bacterium Desulfovibrio Alaskensis G20
Lawrence Berkeley National Laboratory Recent Work Title The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Permalink https://escholarship.org/uc/item/7b44z00f Journal Frontiers in microbiology, 5(OCT) ISSN 1664-302X Authors Price, Morgan N Ray, Jayashree Wetmore, Kelly M et al. Publication Date 2014 DOI 10.3389/fmicb.2014.00577 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH ARTICLE published: 31 October 2014 doi: 10.3389/fmicb.2014.00577 The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20 Morgan N. Price 1*, Jayashree Ray 1, Kelly M. Wetmore 1, Jennifer V. Kuehl 1, Stefan Bauer 2, Adam M. Deutschbauer 1 and Adam P.Arkin 1,2,3* 1 Physical Biosciences Division, Lawrence Berkeley Lab, Berkeley, CA, USA 2 Energy Biosciences Institute, University of California, Berkeley, CA, USA 3 Department of Bioengineering, University of California, Berkeley, CA, USA Edited by: Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but Thomas E. Hanson, University of it remains unclear how reducing sulfate yields energy. To determine the genetic basis Delaware, USA of energy conservation, we measured the fitness of thousands of pooled mutants of Reviewed by: Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors Caroline M. Plugge, Wageningen University, Netherlands and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is Ulrike Kappler, University of required whenever substrate-level phosphorylation is not possible. The uncharacterized Queensland, Australia complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may *Correspondence: perform an electron bifurcation to generate more reduced ferredoxin from NADH Morgan N. -
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. -
Microbial Bioenergy: Hydrogen Production Microbial Bioenergy: Hydrogen Production
Advances in Photosynthesis and Respiration 38 Including Bioenergy and Related Processes Davide Zannoni Roberto De Philippis Editors Microbial BioEnergy: Hydrogen Production Microbial BioEnergy: Hydrogen Production Different Ways for BioHydrogen Production The four possible ways for producing H2 , by exploiting microbial activities, are shown here. Biophotolysis : H2 production by microalgae (through H 2 -ase) or Cyanobacteria (through H2 -ase or N 2 -ase) by using low potential reductants derived from either water or stored sugars via the photosynthetic machinery. Photofermentation : H2 production by anoxygenic photosynthetic bacteria (through N2 -ase) by using reductants obtained from the oxidation of organic compounds as well as solar energy used through photosynthesis. Dark fermentation : H2 production by mesophilic or thermophilic chemoheterotrophic bacteria (through H2 -ase) by using reductants and energy obtained from the oxidation of organic compounds. Microbial Electrolysis Cell (MEC): H2 production by means of cathodic proton reduction with applied potential exploiting the low redox potential produced by exoelectrogenic bacteria at the anode. This fi gure is adapted from Fig. 1.3 in Chap. 1 of this book. Advances in Photosynthesis and Respiration Including Bioenergy and Related Processes VOLUME 38 Series Editors: GOVINDJEE * ( University of Illinois at Urbana- Champaign , IL , U.S.A ) THOMAS D. SHARKEY ( Michigan State University , East Lansing , MI , U.S.A ) * Founding Series Editor Advisory Editors: Elizabeth AINSWORTH, United States Department of Agriculture , Urbana , IL , U.S.A. Basanti BISWAL, Sambalpur University , Jyoti Vihar , Odisha , India Robert E. BLANKENSHIP, Washington University , St Louis , MO , U.S.A. Ralph BOCK, Max Planck Institute of Molecular Plant Physiology , Postdam - Golm , Germany Julian J. -
Methanogens: Pushing the Boundaries of Biology
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Biochemistry -- Faculty Publications Biochemistry, Department of 12-14-2018 Methanogens: pushing the boundaries of biology Nicole R. Buan Follow this and additional works at: https://digitalcommons.unl.edu/biochemfacpub Part of the Biochemistry Commons, Biotechnology Commons, and the Other Biochemistry, Biophysics, and Structural Biology Commons This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Biochemistry -- Faculty Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Emerging Topics in Life Sciences (2018) 2 629–646 https://doi.org/10.1042/ETLS20180031 Review Article Methanogens: pushing the boundaries of biology Nicole R. Buan Department of Biochemistry, University of Nebraska-Lincoln, 1901 Vine St., Lincoln, NE 68588-0664, U.S.A. Correspondence: Nicole R. Buan ([email protected]) Downloaded from https://portlandpress.com/emergtoplifesci/article-pdf/2/4/629/484198/etls-2018-0031c.pdf by University of Nebraska Libraries user on 11 February 2020 Methanogens are anaerobic archaea that grow by producing methane gas. These microbes and their exotic metabolism have inspired decades of microbial physiology research that continues to push the boundary of what we know about how microbes conserve energy to grow. The study of methanogens has helped to elucidate the thermodynamic and bioener- getics basis of life, contributed our understanding of evolution and biodiversity, and has garnered an appreciation for the societal utility of studying trophic interactions between environmental microbes, as methanogens are important in microbial conversion of biogenic carbon into methane, a high-energy fuel. -
(12) United States Patent (10) Patent No.: US 7927,859 B2 San Et Al
USOO7927859B2 (12) United States Patent (10) Patent No.: US 7927,859 B2 San et al. (45) Date of Patent: Apr. 19, 2011 (54) HIGH MOLARSUCCINATEYIELD FOREIGN PATENT DOCUMENTS BACTERIA BY INCREASING THE WO WO99.06532 * 2/1999 INTRACELLULAR NADHAVAILABILITY WO WO 2007 OO1982 1, 2007 OTHER PUBLICATIONS (75) Inventors: Ka-Yiu San, Houston, TX (US); George N. Bennett, Houston, TX (US); Ailen Branden et al. Introduction to Protein Structure, Garland Publishing Inc., New York, p. 247, 1991.* Sánchez, Houston, TX (US) ExPASy. Formate Dehydrogenase.* Vemuri et al. Effects of growth mode and pyruvate carboxylase on (73) Assignee: Rice University, Houston, TX (US) Succinic acid production by metabolically engineered strains of Escherichia coli. Appl Environ Microbiol. Apr. 2002:68(4): 1715 (*) Notice: Subject to any disclaimer, the term of this 27.3 patent is extended or adjusted under 35 Goodbye et al. Cloning and sequence analysis of the fermentative alcohol-dehydrogenase-encoding gene of Escherichia coli. Gene. U.S.C. 154(b) by 791 days. Dec. 21, 1989;85(1):209-14.* Datsenko et al. One-step inactivation of chromosomal genes in (21) Appl. No.: 10/923,635 Escherichia coli K-12 using PCR products. Proc Natl AcadSci USA. Jun. 6, 2000:97(12):6640-5.* (22) Filed: Aug. 20, 2004 Berrios-Rivera et al. Metabolic engineering of Escherichia coli: increase of NADHavailability by overexpressing an NAD(+)-depen (65) Prior Publication Data dent formate dehydrogenase. Metab Eng. Jul. 2002;4(3):217-29.* Gupta et al. Escherichia coli derivatives lacking both alcohol US 2005/OO42736A1 Feb. 24, 2005 dehydrogenase and phosphotransacetylase grow anaerobically by lactate fermentation. -
Opportunistic Interactions on Fe0 Between Methanogens and Acetogens 2 from a Climate Lake
bioRxiv preprint doi: https://doi.org/10.1101/556704; this version posted December 6, 2020. 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-NC-ND 4.0 International license. 1 Opportunistic interactions on Fe0 between methanogens and acetogens 2 from a climate lake 3 Paola Andrea Palacios 1 and Amelia-Elena Rotaru1* 4 1Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark 5 * Correspondence: 6 Amelia-Elena Rotaru 7 [email protected] 8 Keywords: microbial influenced corrosion, acetogens, methanogens, interspecies interactions, 9 iron corrosion, Clostridium, Methanosarcinales, Methanothermobacter. 10 Abstract 11 Microbial-induced corrosion has been extensively studied in pure cultures. However, Fe0 corrosion 12 by complex environmental communities, and especially the interplay between microbial 13 physiological groups, is still poorly understood. In this study, we combined experimental physiology 14 and metagenomics to explore Fe0-dependent microbial interactions between physiological groups 15 enriched from anoxic climate lake sediments. Then, we investigated how each physiological group 16 interacts with Fe0. We offer evidence for a new interspecies interaction during Fe0 corrosion. We 17 showed that acetogens enhanced methanogenesis but were negatively impacted by methanogens 18 (opportunistic microbial interaction). Methanogens were positively impacted by acetogens. In the 19 metagenome of the corrosive community, the acetogens were mostly represented by Clostridium and 20 Eubacterium, the methanogens by 21 Methanosarcinales, Methanothermobacter and Methanobrevibacter. Within the corrosive 22 community, acetogens and methanogens produced acetate and methane concurrently, however at 0 23 rates that cannot be explained by abiotic H2-buildup at the Fe surface. -
NAD+-Dependent Formate Dehydrogenase from Plants
reVIeWS NAD+-dependent Formate Dehydrogenase from Plants A.A. Alekseeva1,2,3, S.S. Savin2,3, V.I. Tishkov1,2,3,* 1Chemistry Department, Lomonosov Moscow State University 2Innovations and High Technologies MSU Ltd 3Bach Institute of Biochemistry, Russian Academy of Sciences *E-mail: [email protected] Received 05.08.2011 Copyright © 2011 Park-media, Ltd. This is an open access article distributed under the Creative Commons Attribution License,which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT NAD+-dependent formate dehydrogenase (FDH, EC 1.2.1.2) widely occurs in nature. FDH consists of two identical subunits and contains neither prosthetic groups nor metal ions. This type of FDH was found in different microorganisms (including pathogenic ones), such as bacteria, yeasts, fungi, and plants. As opposed to microbiological FDHs functioning in cytoplasm, plant FDHs localize in mitochondria. Formate dehydrogenase activity was first discovered as early as in 1921 in plant; however, until the past decade FDHs from plants had been considerably less studied than the enzymes from microorganisms. This review summarizes the recent results on studying the physiological role, properties, structure, and protein engineering of plant formate dehy- drogenases. KEYWORDS plant formate dehydrogenase; physiological role; properties; structure; expression; Escherichia coli; protein engineering. ABBREVIATIONS FDH – formate dehydrogenase; PseFDH, CboFDH – formate dehydrogenases from -
Hydrogenase and Ferredoxin:NADP -Oxidoreductase (FNR)
Photosynthetic electron partitioning between [FeFe]- hydrogenase and ferredoxin:NADPþ-oxidoreductase (FNR) enzymes in vitro Iftach Yacobya,1, Sergii Pochekailova, Hila Toporikb, Maria L. Ghirardic, Paul W. Kingc,1, and Shuguang Zhanga,1 aCenter for Biomedical Engineering NE47-379, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139-4307; cBiosciences Center, National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401-3305; and bDepartment of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel Edited by Alan R. Fersht, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom, and approved April 28, 2011 (receivedfor review March 5, 2011) Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its commercialization. Here we provide evi- dence that, under the anaerobic conditions that support hydrogen production, there is a significant loss of photosynthetic electrons toward NADPH production in vitro. To elucidate the basis for com- petition, we bioengineered a ferredoxin-hydrogenase fusion and characterized hydrogen production kinetics in the presence of Fd, ferredoxin:NADPþ-oxidoreductase (FNR), and NADPþ. Replacing the hydrogenase with a ferredoxin-hydrogenase fusion switched the bias of electron transfer from FNR to hydrogenase and resulted in an increased rate of hydrogen photoproduction. These results suggest a new direction for improvement of biohydrogen produc- tion and a means to further resolve the mechanisms that control partitioning of photosynthetic electron transport. -
Ferredoxin: the Central Hub Connecting Photosystem I to Cellular Metabolism
DOI: 10.1007/s11099-018-0793-9 PHOTOSYNTHETICA 56 (1): 279-293, 2018 REVIEW Ferredoxin: the central hub connecting photosystem I to cellular metabolism J. MONDAL* and B.D. BRUCE*,**,+ Department of Biochemistry, Cellular and Molecular Biology*, Graduate School of Genome Science and Technology**, University of Tennessee at Knoxville, Knoxville, Tennessee, USA Abstract Ferredoxin (Fd) is a small soluble iron-sulfur protein essential in almost all oxygenic photosynthetic organisms. It contains a single [2Fe-2S] cluster coordinated by four cysteine ligands. It accepts electrons from the stromal surface of PSI and facilitates transfer to a myriad of acceptors involved in diverse metabolic processes, including generation of NADPH via Fd-NADP-reductase, cyclic electron transport for ATP synthesis, nitrate reduction, nitrite reductase, sulfite reduction, hydrogenase and other reductive reactions. Fd serves as the central hub for these diverse cellular reactions and is integral to complex cellular metabolic networks. We describe advances on the central role of Fd and its evolutionary role from cyanobacteria to algae/plants. We compare structural diversity of Fd partners to understand this orchestrating role and shed light on how Fd dynamically partitions between competing partner proteins to enable the optimum transfer of PSI-derived electrons to support cell growth and metabolism. Additional key words: cellular metabolism; electron transfer; ferredoxin; global interaction; oxidation-reduction. Introduction The discovery of Fd is itself an interesting achievement (Fd). Dan Arnon and collaborators were the first to investi- in the history of biochemistry. Its role in the cellular gate the role of Fd in photosynthesis as described over 50 oxidation-reduction processes is essential in organisms years ago (Tagawa and Arnon 1962).