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Title: Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1618706
Alternate Identifier(s):
OSTI ID: 1435314
Grant/Contract Number:  
4000070456; AC05-00OR22725
Resource Type:
Published Article
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Name: Biotechnology for Biofuels Journal Volume: 10 Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
Springer Science + Business Media
Country of Publication:
Netherlands
Language:
English
Subject:
09 BIOMASS FUELS; Clostridium thermocellum; Thermoanaerobacterium saccharolyticum; Redox; Adenylate energy charge; Targeted metabolomics

Citation Formats

Sander, Kyle, Asano, Keiji G., Bhandari, Deepak, Van Berkel, Gary J., Brown, Steven D., Davison, Brian, and Tschaplinski, Timothy J. Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. Netherlands: N. p., 2017. Web. doi:10.1186/s13068-017-0960-4.
Sander, Kyle, Asano, Keiji G., Bhandari, Deepak, Van Berkel, Gary J., Brown, Steven D., Davison, Brian, & Tschaplinski, Timothy J. Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum. Netherlands. doi:10.1186/s13068-017-0960-4.
Sander, Kyle, Asano, Keiji G., Bhandari, Deepak, Van Berkel, Gary J., Brown, Steven D., Davison, Brian, and Tschaplinski, Timothy J. Thu . "Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum". Netherlands. doi:10.1186/s13068-017-0960-4.
@article{osti_1618706,
title = {Targeted redox and energy cofactor metabolomics in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum},
author = {Sander, Kyle and Asano, Keiji G. and Bhandari, Deepak and Van Berkel, Gary J. and Brown, Steven D. and Davison, Brian and Tschaplinski, Timothy J.},
abstractNote = {},
doi = {10.1186/s13068-017-0960-4},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 10,
place = {Netherlands},
year = {2017},
month = {11}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s13068-017-0960-4

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Works referenced in this record:

Glycolysis without pyruvate kinase in Clostridium thermocellum
journal, January 2017


SoNar, a Highly Responsive NAD+/NADH Sensor, Allows High-Throughput Metabolic Screening of Anti-tumor Agents
journal, May 2015


Use of the adenylate energy charge ratio to measure growth state of natural microbial communities.
journal, June 1975

  • Wiebe, W. J.; Bancroft, K.
  • Proceedings of the National Academy of Sciences, Vol. 72, Issue 6
  • DOI: 10.1073/pnas.72.6.2112

Methodology and measurement of adenylate energy charge ratios in environmental samples
journal, January 1978


Genetically encoded fluorescent indicator for imaging NAD+/NADH ratio changes in different cellular compartments
journal, March 2014

  • Bilan, Dmitry S.; Matlashov, Mikhail E.; Gorokhovatsky, Andrey Yu.
  • Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1840, Issue 3
  • DOI: 10.1016/j.bbagen.2013.11.018

Acidic Acetonitrile for Cellular Metabolome Extraction from Escherichia coli
journal, August 2007

  • Rabinowitz, Joshua D.; Kimball, Elizabeth
  • Analytical Chemistry, Vol. 79, Issue 16
  • DOI: 10.1021/ac070470c

Biochemical Issues in Estimation of Cytosolic Free NAD/NADH Ratio
journal, May 2012


Quantitative extraction and estimation of intracellular nicotinamide nucleotides of Escherichia coli
journal, October 1979


Metabolic Profiling of Klebsiella oxytoca: Evaluation of Methods for Extraction of Intracellular Metabolites Using UPLC/Q-TOF-MS
journal, May 2012

  • Park, Changhun; Yun, Seokhun; Lee, Sang Yup
  • Applied Biochemistry and Biotechnology, Vol. 167, Issue 3
  • DOI: 10.1007/s12010-012-9685-9

Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach
journal, July 2008

  • Bennett, Bryson D.; Yuan, Jie; Kimball, Elizabeth H.
  • Nature Protocols, Vol. 3, Issue 8
  • DOI: 10.1038/nprot.2008.107

Metabolic fingerprinting of Lactobacillus paracasei: the optimal quenching strategy
journal, September 2015

  • Jäpelt, Kristina B.; Christensen, Jan H.; Villas-Bôas, Silas G.
  • Microbial Cell Factories, Vol. 14, Issue 1
  • DOI: 10.1186/s12934-015-0322-5

A protocol for the investigation of the intracellular Staphylococcus aureus metabolome
journal, June 2010


Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation
journal, December 2015

  • Sander, Kyle; Wilson, Charlotte M.; Rodriguez, Miguel
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0394-9

Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum
journal, November 2015


Chemically Defined Minimal Medium for Growth of the Anaerobic Cellulolytic Thermophile Clostridium thermocellum
journal, January 1981


Elimination of metabolic pathways to all traditional fermentation products increases ethanol yields in Clostridium thermocellum
journal, November 2015


CO 2 -fixing one-carbon metabolism in a cellulose-degrading bacterium Clostridium thermocellum
journal, October 2016

  • Xiong, Wei; Lin, Paul P.; Magnusson, Lauren
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 46
  • DOI: 10.1073/pnas.1605482113

A novel sensor of NADH/NAD+ redox poise in Streptomyces coelicolor A3(2)
journal, September 2003


Metabolic quenching of Corynebacterium glutamicum: efficiency of methods and impact of cold shock
journal, December 2008

  • Wellerdiek, Max; Winterhoff, Dajana; Reule, Waldemar
  • Bioprocess and Biosystems Engineering, Vol. 32, Issue 5
  • DOI: 10.1007/s00449-008-0280-y

Two-Photon Fluorescence Spectroscopy and Microscopy of NAD(P)H and Flavoprotein
journal, May 2002


The future of NMR-based metabolomics
journal, February 2017


Energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers
journal, November 1968


Strain and bioprocess improvement of a thermophilic anaerobe for the production of ethanol from wood
journal, June 2016

  • Herring, Christopher D.; Kenealy, William R.; Joe Shaw, A.
  • Biotechnology for Biofuels, Vol. 9, Issue 1
  • DOI: 10.1186/s13068-016-0536-8

Glycolytic strategy as a tradeoff between energy yield and protein cost
journal, April 2013

  • Flamholz, A.; Noor, E.; Bar-Even, A.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 24
  • DOI: 10.1073/pnas.1215283110

Imaging Cytosolic NADH-NAD+ Redox State with a Genetically Encoded Fluorescent Biosensor
journal, October 2011


The Free NADH Concentration Is Kept Constant in Plant Mitochondria under Different Metabolic Conditions
journal, February 2006

  • Kasimova, Marina R.; Grigiene, Jurgita; Krab, Klaas
  • The Plant Cell, Vol. 18, Issue 3
  • DOI: 10.1105/tpc.105.039354

Fluorescence quenching of free and bound NADH in HeLa cells determined by hyperspectral imaging and unmixing of cell autofluorescence
journal, January 2017

  • Rehman, Aziz Ul; Anwer, Ayad G.; Gosnell, Martin E.
  • Biomedical Optics Express, Vol. 8, Issue 3
  • DOI: 10.1364/BOE.8.001488

Adenine Nucleotide Ratios and Adenylate Energy Charge in Energy Metabolism
journal, June 1983


Recent progress in consolidated bioprocessing
journal, June 2012

  • Olson, Daniel G.; McBride, John E.; Joe Shaw, A.
  • Current Opinion in Biotechnology, Vol. 23, Issue 3, p. 396-405
  • DOI: 10.1016/j.copbio.2011.11.026

Fluorescence lifetime imaging of free and protein-bound NADH.
journal, February 1992

  • Lakowicz, J. R.; Szmacinski, H.; Nowaczyk, K.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 4
  • DOI: 10.1073/pnas.89.4.1271

Engineering electron metabolism to increase ethanol production in Clostridium thermocellum
journal, January 2017


Sensitive NADH detection in a tumorigenic cell line using a nano-biosensor based on the organic complex formation
journal, November 2016


Sulfide effects on Thalassia testudinum carbon balance and adenylate energy charge
journal, August 2000


Determination of the cytosolic free NAD/NADH ratio in Saccharomyces cerevisiae under steady-state and highly dynamic conditions
journal, July 2008

  • Canelas, André B.; van Gulik, Walter M.; Heijnen, Joseph J.
  • Biotechnology and Bioengineering, Vol. 100, Issue 4
  • DOI: 10.1002/bit.21813

High Ethanol Titers from Cellulose by Using Metabolically Engineered Thermophilic, Anaerobic Microbes
journal, September 2011

  • Argyros, D. Aaron; Tripathi, Shital A.; Barrett, Trisha F.
  • Applied and Environmental Microbiology, Vol. 77, Issue 23, p. 8288-8294
  • DOI: 10.1128/AEM.00646-11

Development and application of a differential method for reliable metabolome analysis in Escherichia coli
journal, March 2009

  • Taymaz-Nikerel, Hilal; de Mey, Marjan; Ras, Cor
  • Analytical Biochemistry, Vol. 386, Issue 1
  • DOI: 10.1016/j.ab.2008.11.018

Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards
journal, January 2005

  • Wu, Liang; Mashego, Mlawule R.; van Dam, Jan C.
  • Analytical Biochemistry, Vol. 336, Issue 2
  • DOI: 10.1016/j.ab.2004.09.001

Levels of Nicotinamide Adenine Dinucleotide and Reduced Nicotinamide Adenine Dinucleotide in Facultative Bacteria and the Effect of Oxygen
journal, January 1972


Leakage of adenylates during cold methanol/glycerol quenching of Escherichia coli
journal, June 2008


Synergistic effect of pyrroloquinoline quinone and graphene nano-interface for facile fabrication of sensitive NADH biosensor
journal, March 2017


Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
journal, June 2009

  • Bennett, Bryson D.; Kimball, Elizabeth H.; Gao, Melissa
  • Nature Chemical Biology, Vol. 5, Issue 8
  • DOI: 10.1038/nchembio.186

Use of NADH fluorescence to determine mitochondrial function in vivo
journal, October 2009

  • Mayevsky, Avraham; Barbiro-Michaely, Efrat
  • The International Journal of Biochemistry & Cell Biology, Vol. 41, Issue 10
  • DOI: 10.1016/j.biocel.2009.03.012

Measured and calculated NAD+/NADH ratios in human erythrocytes
journal, June 1974


Nicotinamide cofactor ratios in engineered strains of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum
journal, April 2016

  • Beri, Dhananjay; Olson, Daniel G.; Holwerda, Evert K.
  • FEMS Microbiology Letters, Vol. 363, Issue 11
  • DOI: 10.1093/femsle/fnw091

Adenylate Energy Charge in Escherichia coli During Growth and Starvation
journal, January 1971


Sampling for Metabolome Analysis of Microorganisms
journal, May 2007

  • Bolten, Christoph J.; Kiefer, Patrick; Letisse, Fabien
  • Analytical Chemistry, Vol. 79, Issue 10
  • DOI: 10.1021/ac0623888

NADH-dependent biosensor in Saccharomyces cerevisiae: principle and validation at the single cell level
journal, October 2014


AMPK Is a Direct Adenylate Charge-Regulated Protein Kinase
journal, June 2011


Simultaneous Analysis of Major Coenzymes of Cellular Redox Reactions and Energy Using ex Vivo 1 H NMR Spectroscopy
journal, April 2016


Single sample extraction protocol for the quantification of NAD and NADH redox states in Saccharomyces cerevisiae
journal, October 2008

  • Sporty, Jennifer L.; Kabir, Md. Mohiuddin; Turteltaub, Kenneth W.
  • Journal of Separation Science, Vol. 31, Issue 18
  • DOI: 10.1002/jssc.200800238

Anoxic metabolism and biochemical production in Pseudomonas putida F1 driven by a bioelectrochemical system
journal, February 2016


A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH
journal, July 1992


Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum
journal, January 2015

  • Biswas, Ranjita; Zheng, Tianyong; Olson, Daniel G.
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0204-4

Elimination of formate production in Clostridium thermocellum
journal, July 2015

  • Rydzak, Thomas; Lynd, Lee R.; Guss, Adam M.
  • Journal of Industrial Microbiology & Biotechnology, Vol. 42, Issue 9
  • DOI: 10.1007/s10295-015-1644-3

Carbohydrate utilization by Clostridium thermocellum: Importance of internal pH in regulating growth
journal, May 1992

  • Nochur, Saraswathy V.; Demain, Arnold L.; Roberts, Mary F.
  • Enzyme and Microbial Technology, Vol. 14, Issue 5
  • DOI: 10.1016/0141-0229(92)90001-5

Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up
journal, March 2015

  • Muhamadali, Howbeer; Xu, Yun; Ellis, David I.
  • Applied and Environmental Microbiology, Vol. 81, Issue 10
  • DOI: 10.1128/AEM.00294-15

Increased levels of ATP and NADH are associated with increased solvent production in continuous cultures of Clostridium acetobutylicum
journal, May 1989

  • Meyer, CharlesL.; Papoutsakis, EleftheriosT.
  • Applied Microbiology and Biotechnology, Vol. 30, Issue 5
  • DOI: 10.1007/BF00263849

Quantitative Evaluation of Intracellular Metabolite Extraction Techniques for Yeast Metabolomics
journal, September 2009

  • Canelas, André B.; ten Pierick, Angela; Ras, Cor
  • Analytical Chemistry, Vol. 81, Issue 17
  • DOI: 10.1021/ac900999t

Lipid production in Yarrowia lipolytica is maximized by engineering cytosolic redox metabolism
journal, January 2017

  • Qiao, Kangjian; Wasylenko, Thomas M.; Zhou, Kang
  • Nature Biotechnology, Vol. 35, Issue 2
  • DOI: 10.1038/nbt.3763

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013

  • Caspi, Ron; Altman, Tomer; Billington, Richard
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1103

Consolidated bioprocessing of cellulose to isobutanol using Clostridium thermocellum
journal, September 2015


Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum
journal, September 2011

  • Amador-Noguez, Daniel; Brasg, Ian A.; Feng, Xiao-Jiang
  • Applied and Environmental Microbiology, Vol. 77, Issue 22
  • DOI: 10.1128/AEM.05374-11

An evaluation of genetically encoded FRET-based biosensors for quantitative metabolite analyses in vivo
journal, December 2014


Fast sampling for quantitative microbial metabolomics
journal, February 2010


Pyruvate Metabolism in Lactococcus lactis Is Dependent upon Glyceraldehyde-3-phosphate Dehydrogenase Activity
journal, July 1999


Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum
journal, August 2011

  • Brown, S. D.; Guss, A. M.; Karpinets, T. V.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 33
  • DOI: 10.1073/pnas.1102444108

Deletion of nfnAB in Thermoanaerobacterium saccharolyticum and Its Effect on Metabolism
journal, June 2015

  • Lo, Jonathan; Zheng, Tianyong; Olson, Daniel G.
  • Journal of Bacteriology, Vol. 197, Issue 18
  • DOI: 10.1128/JB.00347-15