A New Exploration of Extracting and Purifying the Coenzyme F420 from Natural Sludge
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Reduction by the Methylreductase System in Methanobacterium Bryantii WILLIAM B
JOURNAL OF BACTERIOLOGY, Jan. 1987, p. 87-92 Vol. 169, No. 1 0021-9193/87/010087-06$02.00/0 Copyright © 1987, American Society for Microbiology Inhibition by Corrins of the ATP-Dependent Activation and CO2 Reduction by the Methylreductase System in Methanobacterium bryantii WILLIAM B. WHITMAN'* AND RALPH S. WOLFE2 Department of Microbiology, University of Georgia, Athens, Georgia 30602,1 and Department of Microbiology, University ofIllinois, Urbana, Illinois 618012 Received 1 August 1986/Accepted 28 September 1986 Corrins inhibited the ATP-dependent activation of the methylreductase system and the methyl coenzyme M-dependent reduction of CO2 in extracts of Methanobacterium bryantii resolved from low-molecular-weight factors. The concentrations of cobinamides and cobamides required for one-half of maximal inhibition of the ATP-depen4ent activation were between 1 and 5 ,M. Cobinamides were more inhibitory at lower concentra- tiops than cobamides. Deoxyadenosylcobalamin was not inhibitory at concentrations up to 25 ,uM. The inhibition of CO2 reduction was competitive with respect to CO2. The concentration of methylcobalamin required for one-half of maximal inhibition was 5 ,M. Other cobamideg inhibited at similar concentrations, but diaquacobinami4e inhibited at lower concentrations. With respect to their affinities and specificities for corrins, inhibition of both the ATP-dependent activation'and CO2 reduction closely resembled the corrin- dependent activation of the methylreductase described in similar extracts (W. B. Whitman and R. S. Wolfe, J. Bacteriol. 164:165-172, 1985). However, whether the multiple effects of corrins are due to action at a single site is unknown. The effect of corrins (cobamides and cobinamides) on in CO2 reduction. -
The Wolfe Cycle Comes Full Circle
The Wolfe cycle comes full circle Rudolf K. Thauer1 Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany n 1988, Rouvière and Wolfe (1) H - ΔμNa+ 2 CO2 suggested that methane formation + MFR from H and CO by methanogenic + 2H+ *Fd + H O I 2 2 ox 2 archaea could be a cyclical process. j O = Indirect evidence indicated that the CoB-SH + CoM-SH fi *Fd 2- a rst step, the reduction of CO2 to for- red R mylmethanofuran, was somehow coupled + * H MPT 2 H2 Fdox 4 to the last step, the reduction of the het- h erodisulfide (CoM-S-S-CoB) to coenzyme CoM-S-S-CoB b MFR M (CoM-SH) and coenzyme B (CoB-SH). H Over 2 decades passed until the coupling C 4 10 mechanism was unraveled in 2011: Via g flavin-based electron bifurcation, the re- CoB-SH duction of CoM-S-S-CoB with H provides 2 H+ the reduced ferredoxin (Fig. 1h) required c + Purines for CO2 reduction to formylmethanofuran ΔμNa + H MPT 4 f H O (2) (Fig. 1a). However, one question still 2 remained unanswered: How are the in- termediates replenished that are removed CoM-SH for the biosynthesis of cell components H Methionine d from CO2 (orange arrows in Fig. 1)? This Acetyl-CoA e anaplerotic (replenishing) reaction has F420 F420H2 recently been identified by Lie et al. (3) as F420 F420H2 the sodium motive force-driven reduction H i of ferredoxin with H2 catalyzed by the i energy-converting hydrogenase EhaA-T H2 (green arrow in Fig. -
Annotation Guidelines for Experimental Procedures
Annotation Guidelines for Experimental Procedures Developed By Mohammed Alliheedi Robert Mercer Version 1 April 14th, 2018 1- Introduction and background information What is rhetorical move? A rhetorical move can be defined as a text fragment that conveys a distinct communicative goal, in other words, a sentence that implies an author’s specific purpose to readers. What are the types of rhetorical moves? There are several types of rhetorical moves. However, we are interested in 4 rhetorical moves that are common in the method section of a scientific article that follows the Introduction Methods Results and Discussion (IMRaD) structure. 1- Description of a method: It is concerned with a sentence(s) that describes experimental events (e.g., “Beads with bound proteins were washed six times (for 10 min under rotation at 4°C) with pulldown buffer and proteins harvested in SDS-sample buffer, separated by SDS-PAGE, and analyzed by autoradiography.” (Ester & Uetz, 2008)). 2- Appeal to authority: It is concerned with a sentence(s) that discusses the use of standard methods, protocols, and procedures. There are two types of this move: - A reference to a well-established “standard” method (e.g., the use of a method like “PCR” or “electrophoresis”). - A reference to a method that was previously described in the literature (e.g., “Protein was determined using fluorescamine assay [41].” (Larsen, Frandesn and Treiman, 2001)). 3- Source of materials: It is concerned with a sentence(s) that lists the source of biological materials that are used in the experiment (e.g., “All microalgal strains used in this study are available at the Elizabeth Aidar Microalgae Culture Collection, Department of Marine Biology, Federal Fluminense University, Brazil.” (Larsen, Frandesn and Treiman, 2001)). -
Untargetted Metabolomic Exploration of the Mycobacterium Tuberculosis Stress Response to Cinnamon Essential Oil
biomolecules Article Untargetted Metabolomic Exploration of the Mycobacterium tuberculosis Stress Response to Cinnamon Essential Oil Elwira Sieniawska 1,* , Rafał Sawicki 2 , Joanna Golus 2 and Milen I. Georgiev 3,4 1 Chair and Department of Pharmacognosy, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland 2 Chair and Department of Biochemistry and Biotechnology, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland; [email protected] (R.S.); [email protected] (J.G.) 3 Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 139 Ruski Blvd., 4000 Plovdiv, Bulgaria; [email protected] 4 Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria * Correspondence: [email protected] Received: 6 January 2020; Accepted: 24 February 2020; Published: 26 February 2020 Abstract: The antimycobacterial activity of cinnamaldehyde has already been proven for laboratory strains and for clinical isolates. What is more, cinnamaldehyde was shown to threaten the mycobacterial plasma membrane integrity and to activate the stress response system. Following promising applications of metabolomics in drug discovery and development we aimed to explore the mycobacteria response to cinnamaldehyde within cinnamon essential oil treatment by untargeted liquid chromatography–mass spectrometry. The use of predictive metabolite pathway analysis and description of produced lipids enabled the evaluation of the stress symptoms shown by bacteria. This study suggests that bacteria exposed to cinnamaldehyde could reorganize their outer membrane as a physical barrier against stress factors. They probably lowered cell wall permeability and inner membrane fluidity, and possibly redirected carbon flow to store energy in triacylglycerols. Being a reactive compound, cinnamaldehyde may also contribute to disturbances in bacteria redox homeostasis and detoxification mechanisms. -
Towards Kinetic Modeling of Global Metabolic Networks with Incomplete Experimental Input on Kinetic Parameters
Towards Kinetic Modeling of Global Metabolic Networks with Incomplete Experimental Input on Kinetic Parameters Ping Ao 1,2 , Lik Wee Lee 1, Mary E. Lidstrom 3,4 , Lan Yin 5, and Xiaomei Zhu 6 1 Department of Mechanical Engineering , University of Washington , Seattle , WA 98195, USA 2 Department of Physics , University of Washington , Seattle , WA 98195, USA 3 Department of Microbiology , University of Washington , Seattle , WA 98195, USA 4 Department of Chemical Engineering , University of Washington , Seattle , WA 98195, USA 5 School of Physics , Peking University , 100871 Beijing , PR China 6 GeneMath , 5525 27 th Ave . N .E., Seattle , WA 98105, USA Abstract: This is the first report on a systematic method for constructing a large scale kinetic metabolic model and its initial application to the modeling of central metabolism of Methylobacterium extorquens AM1, a methylotrophic and environmental important bacterium. Its central metabolic network includes formaldehyde metabolism, serine cycle, citric acid cycle, pentose phosphate pathway, gluconeogensis, PHB synthesis and acetyl-CoA conversion pathway, respiration and energy metabolism. Through a systematic and consistent procedure of finding a set of parameters in the physiological range we overcome an outstanding difficulty in large scale kinetic modeling: the requirement for a massive number of enzymatic reaction parameters. We are able to construct the kinetic model based on general biological considerations and incomplete experimental kinetic parameters. Our method consists of -
Recycling of Vitamin B12 and NAD+ Within the Pdu Microcompartment of Salmonella Enterica Shouqiang Cheng Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2010 Recycling of vitamin B12 and NAD+ within the Pdu microcompartment of Salmonella enterica Shouqiang Cheng Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Cheng, Shouqiang, "Recycling of vitamin B12 and NAD+ within the Pdu microcompartment of Salmonella enterica" (2010). Graduate Theses and Dissertations. 11713. https://lib.dr.iastate.edu/etd/11713 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. + Recycling of vitamin B12 and NAD within the Pdu microcompartment of Salmonella enterica by Shouqiang Cheng A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Biochemistry Program of Study Committee: Thomas A. Bobik, Major Professor Alan DiSpirito Basil Nikolau Reuben Peters Gregory J. Phillips Iowa State University Ames, Iowa 2010 Copyright © Shouqiang Cheng, 2010. All rights reserved. ii Table of contents Abstract............................................................................................................................. -
Supplemental Methods
Supplemental Methods: Sample Collection Duplicate surface samples were collected from the Amazon River plume aboard the R/V Knorr in June 2010 (4 52.71’N, 51 21.59’W) during a period of high river discharge. The collection site (Station 10, 4° 52.71’N, 51° 21.59’W; S = 21.0; T = 29.6°C), located ~ 500 Km to the north of the Amazon River mouth, was characterized by the presence of coastal diatoms in the top 8 m of the water column. Sampling was conducted between 0700 and 0900 local time by gently impeller pumping (modified Rule 1800 submersible sump pump) surface water through 10 m of tygon tubing (3 cm) to the ship's deck where it then flowed through a 156 µm mesh into 20 L carboys. In the lab, cells were partitioned into two size fractions by sequential filtration (using a Masterflex peristaltic pump) of the pre-filtered seawater through a 2.0 µm pore-size, 142 mm diameter polycarbonate (PCTE) membrane filter (Sterlitech Corporation, Kent, CWA) and a 0.22 µm pore-size, 142 mm diameter Supor membrane filter (Pall, Port Washington, NY). Metagenomic and non-selective metatranscriptomic analyses were conducted on both pore-size filters; poly(A)-selected (eukaryote-dominated) metatranscriptomic analyses were conducted only on the larger pore-size filter (2.0 µm pore-size). All filters were immediately submerged in RNAlater (Applied Biosystems, Austin, TX) in sterile 50 mL conical tubes, incubated at room temperature overnight and then stored at -80oC until extraction. Filtration and stabilization of each sample was completed within 30 min of water collection. -
Hydrogenases of Methanogens
ANRV413-BI79-18 ARI 27 April 2010 21:0 Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H2 Storage Rudolf K. Thauer, Anne-Kristin Kaster, Meike Goenrich, Michael Schick, Takeshi Hiromoto, and Seigo Shima Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany; email: [email protected] Annu. Rev. Biochem. 2010. 79:507–36 Key Words First published online as a Review in Advance on H2 activation, energy-converting hydrogenase, complex I of the March 17, 2010 respiratory chain, chemiosmotic coupling, electron bifurcation, The Annual Review of Biochemistry is online at reversed electron transfer biochem.annualreviews.org This article’s doi: Abstract 10.1146/annurev.biochem.030508.152103 Most methanogenic archaea reduce CO2 with H2 to CH4. For the Copyright c 2010 by Annual Reviews. activation of H2, they use different [NiFe]-hydrogenases, namely All rights reserved energy-converting [NiFe]-hydrogenases, heterodisulfide reductase- 0066-4154/10/0707-0507$20.00 associated [NiFe]-hydrogenase or methanophenazine-reducing by University of Texas - Austin on 06/10/13. For personal use only. [NiFe]-hydrogenase, and F420-reducing [NiFe]-hydrogenase. The energy-converting [NiFe]-hydrogenases are phylogenetically related Annu. Rev. Biochem. 2010.79:507-536. Downloaded from www.annualreviews.org to complex I of the respiratory chain. Under conditions of nickel limitation, some methanogens synthesize a nickel-independent [Fe]- hydrogenase (instead of F420-reducing [NiFe]-hydrogenase) and by that reduce their nickel requirement. The [Fe]-hydrogenase harbors a unique iron-guanylylpyridinol cofactor (FeGP cofactor), in which a low-spin iron is ligated by two CO, one C(O)CH2-, one S-CH2-, and a sp2-hybridized pyridinol nitrogen. -
Methane Utilization in Methylomicrobium Alcaliphilum 20ZR: a Systems Approach Received: 8 September 2017 Ilya R
www.nature.com/scientificreports OPEN Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach Received: 8 September 2017 Ilya R. Akberdin1,2, Merlin Thompson1, Richard Hamilton1, Nalini Desai3, Danny Alexander3, Accepted: 22 January 2018 Calvin A. Henard4, Michael T. Guarnieri4 & Marina G. Kalyuzhnaya1 Published: xx xx xxxx Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confrmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. The computational framework of C1-metabolism in methanotrophic bacteria can represent an efcient tool for metabolic engineering or ecosystem modeling. Climate change concerns linked to increasing concentrations of anthropogenic methane have spiked inter- est in biological methane utilization as a novel platform for improving ecological and human well-being1–4. -
Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane
Supporting Information for Manuscript Submitted to Archaea Community and Proteomic Analysis of Anaerobic Consortia Converting Tetramethylammonium to Methane Wei-Yu Chen1, Lucia Kraková2, Jer-Horng Wu1*, Domenico Pangallo2, Lenka Jeszeová2, Bing Liu3, Hidenari Yasui3 , 1Department of Environmental Engineering, National Cheng Kung University, No.1, University Road, East District, Tainan City 701, Taiwan (ROC) 2Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 84551 Bratislava, Slovakia 3Faculty of Environmental Engineering, The University of Kitakyushu, 1-1, Hibikino, Wakamatsu, Kitakyushu, Japan 808-0135 1 Table S1 Annotation of proteins related to the conversion of methylamines by the methanogens in the CMJP sample analyzed in this study. Relative Coverage Peptides Accession Organism gene Annotation abundance (%) (#) (%) A0A0E3SIM3 Methanosarcina barkeri 3 MSBR3_0618 Dimethylamine:corrinoid methyltransferase 17.13 21 1.39 A0A0E3Q5F5 Methanosarcina vacuolata Z-761 MSVAZ_1366 Methanol methyltransferase corrinoid protein 12.94 15 0.28 A0A0E3P0I6 Methanosarcina siciliae T4/M MSSIT_0113 Monomethylamine:corrinoid methyltransferase 23.58 20 0.48 A0A0E3WTL8 Methanosarcina lacustris Z-7289 MSLAZ_3204 Monomethylamine:corrinoid methyltransferase 15.94 9 0.24 A0A0E3KRC1 Methanosarcina thermophila CHTI-55 MSTHC_1357 Monomethylamine:corrinoid methyltransferase 18.12 10 0.22 A0A0E3WT78 Methanosarcina lacustris Z-7289 MSLAZ_2479 Dimethylamine methyltransferase corrinoid protein 25.00 11 0.13 A0A0E3Q3C8 Methanosarcina vacuolata -
Sequencing, Assembly, and Annotation of the Kaistella Koreensis Genome and Comparison to Closely Related Organisms
Sequencing, Assembly, and Annotation of the Kaistella koreensis Genome and Comparison to Closely Related Organisms Presented to the faculty of Lycoming College in partial fulfillment of the requirements for Departmental Honors in Biology by Timothy Hostelley Lycoming College April 22, 2013 Approved by: (Signature) (Signature) (Signature) (Signature) Abstract Advances in DNA sequencing technology have made DNA sequencing cheaper and more efficient. As a result, there has been an enormous increase in the number of genomes being sequenced. The sequence data can be assembled into complete genomes and annotated in order to reveal information about the organism’s physiology. In this study the DNA of the bacterium Kaistella koreensis was sequenced and assembled into 578 contigs, these contigs were then uploaded to Rapid Annotation Using Subsystems Technology for annotation in order to compute the Average Nucleotide Identity between K. koreensis and closely related organisms in order to dispute the reclassification of K. koreensis as Chryseobacterium koreense. Phenotypic tests including Biolog GenII, API ZYM, and Fatty Acid Methyl Ester analysis were also done in order to supplement the ambiguous results of the ANI. The results of these tests reveal a number of significant differences between K. koreensis and its closest related neighbors that suggests that K. koreensis does not belong in the Chryseobacterium genus or the closely related Lycomia genus. Instead, K. koreensis should be reclassified back to its original classification in the Kaistella genus. This would dispute the proposal made by Kämpfer et al. to reclassify Kaistella koreensis into the Chryseobacterium genus. 1 Introduction DNA sequencing has rapidly evolved from the earliest sequencing efforts using only whole genome shotgun-cloning based sequencing of the 1990’s, to the further advances in Sanger sequencing in the early 2000’s. -
Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium Formicicum NEIL L
JOURNAL OF BACTERIOLOGY, Feb. 1986, p. 405-411 Vol. 165, No. 2 0021-9193/86/020405-07$02.00/0 Copyright (C 1986, American Society for Microbiology Composition of the Coenzyme F420-Dependent Formate Dehydrogenase from Methanobacterium formicicum NEIL L. SCHAUERt AND JAMES G. FERRY* Department of Anaerobic Microbiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061 Received 16 August 1985/Accepted 19 November 1985 The coenzyme F420-dependent formate dehydrogenase from Methanobacterium formicicum was purified to electrophoretic homogeneity by anoxic procedures which included the addition o(f azide, flavin adenine dinucleotide (FAD), glycerol, and 2-mercaptoethanol to all buffer solutions to stabilize iictivity. The enzyme contains, in approximate miolar ratios, 1 FAD molecule and 1 molybdenum, 2 zinc, 21 to 24 iron, and 25 to 29 Downloaded from inorganic sulfur atoms. Denaturation of the enzyme released a molybdopterin cofactor. The enzyme has a molecular weight of 177,000 and consists of one each of two different subunits, giving the composition olol. The molecular weight of the a-subunit is 85,000, and that of the ,-subunit is 53,000. The UV-visible spectrum is typical of nonheme iron-sulfur flavoprotein. Reduction of the enzyme facilitated dissociation of FAD, and the FAD-depleted enzyme was unable to reduce coenzyme F420. Preincubation of the FAD-depleted enzyme with FAD restored coenzyme F420-dependent activity. The methanogenic bacteria are phylogenetically distant Cells were harvested in the late log phase at an optical density from eubacteria and eucaryotes (10). Consistent with this of 3.0 to 4.5 (550 nm, 1-cm light path).