skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism

Abstract

Background: Metabolic engineering is a commonly used approach to develop organisms for an industrial function, but engineering aimed at improving one phenotype can negatively impact other phenotypes. This lack of robustness can prove problematic. Cellulolytic bacterium Clostridium thermocellum is able to rapidly ferment cellulose to ethanol and other products. Recently, genes involved in H2 production, including the hydrogenase maturase hydG, were deleted from the chromosome of C. thermocellum. While ethanol yield increased, the growth rate decreased substantially compared to wild type. Results: Addition of 5 mM acetate to the growth medium improved the growth rate in C. thermocellum ΔhydG, whereas wild type remained unaffected. Transcriptomic analysis of the wild type showed essentially no response to the addition of acetate. However, in C. thermocellum ΔhydG, 204 and 56 genes were significantly differentially regulated relative to wild type in the absence and presence of acetate, respectively. Genes Clo1313_0108-0125, which are predicted to encode a sulfate transport system and sulfate assimilatory pathway, were drastically up-regulated in C. thermocellum ΔhydG in presence of added acetate. A similar pattern was seen with proteomics. Further physiological characterization demonstrated an increase in sulfide synthesis and elimination of cysteine consumption in C. thermocellum ΔhydG. In conclusion, sulfur metabolismmore » is perturbed in C. thermocellum ΔhydG, possibly to increase flux through sulfate reduction to act as an electron sink to balance redox reactions.« less

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:
1618660
Alternate Identifier(s):
OSTI ID: 1393809
Grant/Contract Number:  
BioEnergy Science Center; 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; Cellulosic ethanol; Clostridium thermocellum; Redox balance; Metabolic engineering; Sulfate reduction

Citation Formats

Biswas, Ranjita, Wilson, Charlotte M., Giannone, Richard J., Klingeman, Dawn M., Rydzak, Thomas, Shah, Manesh B., Hettich, Robert L., Brown, Steven D., and Guss, Adam M. Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism. Netherlands: N. p., 2017. Web. doi:10.1186/s13068-016-0684-x.
Biswas, Ranjita, Wilson, Charlotte M., Giannone, Richard J., Klingeman, Dawn M., Rydzak, Thomas, Shah, Manesh B., Hettich, Robert L., Brown, Steven D., & Guss, Adam M. Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism. Netherlands. doi:10.1186/s13068-016-0684-x.
Biswas, Ranjita, Wilson, Charlotte M., Giannone, Richard J., Klingeman, Dawn M., Rydzak, Thomas, Shah, Manesh B., Hettich, Robert L., Brown, Steven D., and Guss, Adam M. Tue . "Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism". Netherlands. doi:10.1186/s13068-016-0684-x.
@article{osti_1618660,
title = {Improved growth rate in Clostridium thermocellum hydrogenase mutant via perturbed sulfur metabolism},
author = {Biswas, Ranjita and Wilson, Charlotte M. and Giannone, Richard J. and Klingeman, Dawn M. and Rydzak, Thomas and Shah, Manesh B. and Hettich, Robert L. and Brown, Steven D. and Guss, Adam M.},
abstractNote = {Background: Metabolic engineering is a commonly used approach to develop organisms for an industrial function, but engineering aimed at improving one phenotype can negatively impact other phenotypes. This lack of robustness can prove problematic. Cellulolytic bacterium Clostridium thermocellum is able to rapidly ferment cellulose to ethanol and other products. Recently, genes involved in H2 production, including the hydrogenase maturase hydG, were deleted from the chromosome of C. thermocellum. While ethanol yield increased, the growth rate decreased substantially compared to wild type. Results: Addition of 5 mM acetate to the growth medium improved the growth rate in C. thermocellum ΔhydG, whereas wild type remained unaffected. Transcriptomic analysis of the wild type showed essentially no response to the addition of acetate. However, in C. thermocellum ΔhydG, 204 and 56 genes were significantly differentially regulated relative to wild type in the absence and presence of acetate, respectively. Genes Clo1313_0108-0125, which are predicted to encode a sulfate transport system and sulfate assimilatory pathway, were drastically up-regulated in C. thermocellum ΔhydG in presence of added acetate. A similar pattern was seen with proteomics. Further physiological characterization demonstrated an increase in sulfide synthesis and elimination of cysteine consumption in C. thermocellum ΔhydG. In conclusion, sulfur metabolism is perturbed in C. thermocellum ΔhydG, possibly to increase flux through sulfate reduction to act as an electron sink to balance redox reactions.},
doi = {10.1186/s13068-016-0684-x},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 10,
place = {Netherlands},
year = {2017},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s13068-016-0684-x

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: Growth profle of C. thermocellum strains on minimal medium. a Wild type, b ΔhydG, and c ΔhydG Δech. Symbols: red square, with added acetate; black triangle, without added acetate. Data for “without added acetate” are from [11]

Save / Share:

Works referenced in this record:

Increase in Ethanol Yield via Elimination of Lactate Production in an Ethanol-Tolerant Mutant of Clostridium thermocellum
journal, February 2014


Characterization of the Desulfovibrio desulfuricans ATCC 27774 DsrMKJOP ComplexA Membrane-Bound Redox Complex Involved in the Sulfate Respiratory Pathway
journal, January 2006

  • Pires, Ricardo H.; Venceslau, Sofia S.; Morais, Francisco
  • Biochemistry, Vol. 45, Issue 1
  • DOI: 10.1021/bi0515265

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes
journal, November 2010

  • Biegel, Eva; Schmidt, Silke; González, José M.
  • Cellular and Molecular Life Sciences, Vol. 68, Issue 4
  • DOI: 10.1007/s00018-010-0555-8

Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
journal, June 2006

  • Schwer, B.; Bunkenborg, J.; Verdin, R. O.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 27
  • DOI: 10.1073/pnas.0603968103

End-product induced metabolic shifts in Clostridium thermocellum ATCC 27405
journal, August 2011

  • Rydzak, Thomas; Levin, David B.; Cicek, Nazim
  • Applied Microbiology and Biotechnology, Vol. 92, Issue 1
  • DOI: 10.1007/s00253-011-3511-0

Simultaneous online measurement of sulfide and nitrate in sewers for nitrate dosage optimisation
journal, February 2010

  • Gutierrez, Oriol; Sutherland-Stacey, Luke; Yuan, Zhiguo
  • Water Science and Technology, Vol. 61, Issue 3
  • DOI: 10.2166/wst.2010.901

Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress
journal, January 2012


Microbial Cellulose Utilization: Fundamentals and Biotechnology
journal, September 2002

  • Lynd, L. R.; Weimer, P. J.; van Zyl, W. H.
  • Microbiology and Molecular Biology Reviews, Vol. 66, Issue 3, p. 506-577
  • DOI: 10.1128/MMBR.66.3.506-577.2002

Closing the carbon balance for fermentation by Clostridium thermocellum (ATCC 27405)
journal, January 2012


Reassessment of the Transhydrogenase/Malate Shunt Pathway in Clostridium thermocellum ATCC 27405 through Kinetic Characterization of Malic Enzyme and Malate Dehydrogenase
journal, January 2015

  • Taillefer, M.; Rydzak, T.; Levin, D. B.
  • Applied and Environmental Microbiology, Vol. 81, Issue 7
  • DOI: 10.1128/AEM.03360-14

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


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


IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering
journal, August 2009

  • Ma, Ze-Qiang; Dasari, Surendra; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 8, Issue 8
  • DOI: 10.1021/pr900360j

Identifying promoters for gene expression in Clostridium thermocellum
journal, December 2015


Genetics and Molecular Biology of the Electron Flow for Sulfate Respiration in Desulfovibrio
journal, January 2011


Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
journal, January 2013

  • Wilson, Charlotte M.; Yang, Shihui; Rodriguez, Miguel
  • Biotechnology for Biofuels, Vol. 6, Issue 1
  • DOI: 10.1186/1754-6834-6-131

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

Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli Strain LY180
journal, August 2009

  • Miller, E. N.; Jarboe, L. R.; Turner, P. C.
  • Applied and Environmental Microbiology, Vol. 75, Issue 19
  • DOI: 10.1128/AEM.01187-09

A Targetron System for Gene Targeting in Thermophiles and Its Application in Clostridium thermocellum
journal, July 2013


Redirecting carbon flux through exogenous pyruvate kinase to achieve high ethanol yields in Clostridium thermocellum
journal, January 2013


The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading
journal, October 2014

  • Holwerda, Evert K.; Thorne, Philip G.; Olson, Daniel G.
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/s13068-014-0155-1

MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis
journal, February 2007

  • Tabb, David L.; Fernando, Christopher G.; Chambers, Matthew C.
  • Journal of Proteome Research, Vol. 6, Issue 2
  • DOI: 10.1021/pr0604054

Nitrogen and sulfur requirements for Clostridium thermocellum and Caldicellulosiruptor bescii on cellulosic substrates in minimal nutrient media
journal, February 2013


Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli
journal, July 2013


Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum
journal, January 2012

  • Guss, Adam M.; Olson, Daniel G.; Caiazza, Nicky C.
  • Biotechnology for Biofuels, Vol. 5, Issue 1
  • DOI: 10.1186/1754-6834-5-30

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

Mutant selection and phenotypic and genetic characterization of ethanol-tolerant strains of Clostridium thermocellum
journal, August 2011

  • Shao, Xiongjun; Raman, Babu; Zhu, Mingjun
  • Applied Microbiology and Biotechnology, Vol. 92, Issue 3
  • DOI: 10.1007/s00253-011-3492-z

Proteomic Characterization of Cellular and Molecular Processes that Enable the Nanoarchaeum equitans-Ignicoccus hospitalis Relationship
journal, August 2011


Development of pyrF-Based Genetic System for Targeted Gene Deletion in Clostridium thermocellum and Creation of a pta Mutant
journal, August 2010

  • Tripathi, S. A.; Olson, D. G.; Argyros, D. A.
  • Applied and Environmental Microbiology, Vol. 76, Issue 19, p. 6591-6599
  • DOI: 10.1128/AEM.01484-10

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

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.