Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii
Abstract
Abstract Background Caldicellulosiruptor bescii , a promising biocatalyst being developed for use in consolidated bioprocessing of lignocellulosic materials to ethanol, grows poorly and has reduced conversion at elevated medium osmolarities. Increasing tolerance to elevated fermentation osmolarities is desired to enable performance necessary of a consolidated bioprocessing (CBP) biocatalyst. Results Two strains of C. bescii showing growth phenotypes in elevated osmolarity conditions were identified. The first strain, ORCB001, carried a deletion of the FapR fatty acid biosynthesis and malonyl-CoA metabolism repressor and had a severe growth defect when grown in high-osmolarity conditions—introduced as the addition of either ethanol, NaCl, glycerol, or glucose to growth media. The second strain, ORCB002, displayed a growth rate over three times higher than its genetic parent when grown in high-osmolarity medium. Unexpectedly, a genetic complement ORCB002 exhibited improved growth, failing to revert the observed phenotype, and suggesting that mutations other than the deleted transcription factor (the fruR/cra gene) are responsible for the growth phenotype observed in ORCB002. Genome resequencing identified several other genomic alterations (three deleted regions, three substitution mutations, one silent mutation, and one frameshift mutation), which may be responsible for the observed increase in osmolarity tolerance in the fruR / cra -deficient strain, includingmore »
- Authors:
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618776
- Alternate Identifier(s):
- OSTI ID: 1606932
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Published Article
- Journal Name:
- Biotechnology for Biofuels
- Additional Journal Information:
- Journal Name: Biotechnology for Biofuels Journal Volume: 13 Journal Issue: 1; Journal ID: ISSN 1754-6834
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Caldicellulosiruptor bescii; Osmotolerance; Fatty acid biosynthesis; dnaK; fapR; fruR/cra
Citation Formats
Sander, Kyle B., Chung, Daehwan, Klingeman, Dawn M., Giannone, Richard J., Rodriguez, Jr., Miguel, Whitham, Jason, Hettich, Robert L., Davison, Brian H., Westpheling, Janet, and Brown, Steven D. Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii. Netherlands: N. p., 2020.
Web. doi:10.1186/s13068-020-01690-3.
Sander, Kyle B., Chung, Daehwan, Klingeman, Dawn M., Giannone, Richard J., Rodriguez, Jr., Miguel, Whitham, Jason, Hettich, Robert L., Davison, Brian H., Westpheling, Janet, & Brown, Steven D. Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii. Netherlands. https://doi.org/10.1186/s13068-020-01690-3
Sander, Kyle B., Chung, Daehwan, Klingeman, Dawn M., Giannone, Richard J., Rodriguez, Jr., Miguel, Whitham, Jason, Hettich, Robert L., Davison, Brian H., Westpheling, Janet, and Brown, Steven D. Fri .
"Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii". Netherlands. https://doi.org/10.1186/s13068-020-01690-3.
@article{osti_1618776,
title = {Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii},
author = {Sander, Kyle B. and Chung, Daehwan and Klingeman, Dawn M. and Giannone, Richard J. and Rodriguez, Jr., Miguel and Whitham, Jason and Hettich, Robert L. and Davison, Brian H. and Westpheling, Janet and Brown, Steven D.},
abstractNote = {Abstract Background Caldicellulosiruptor bescii , a promising biocatalyst being developed for use in consolidated bioprocessing of lignocellulosic materials to ethanol, grows poorly and has reduced conversion at elevated medium osmolarities. Increasing tolerance to elevated fermentation osmolarities is desired to enable performance necessary of a consolidated bioprocessing (CBP) biocatalyst. Results Two strains of C. bescii showing growth phenotypes in elevated osmolarity conditions were identified. The first strain, ORCB001, carried a deletion of the FapR fatty acid biosynthesis and malonyl-CoA metabolism repressor and had a severe growth defect when grown in high-osmolarity conditions—introduced as the addition of either ethanol, NaCl, glycerol, or glucose to growth media. The second strain, ORCB002, displayed a growth rate over three times higher than its genetic parent when grown in high-osmolarity medium. Unexpectedly, a genetic complement ORCB002 exhibited improved growth, failing to revert the observed phenotype, and suggesting that mutations other than the deleted transcription factor (the fruR/cra gene) are responsible for the growth phenotype observed in ORCB002. Genome resequencing identified several other genomic alterations (three deleted regions, three substitution mutations, one silent mutation, and one frameshift mutation), which may be responsible for the observed increase in osmolarity tolerance in the fruR / cra -deficient strain, including a substitution mutation in dnaK , a gene previously implicated in osmoresistance in bacteria. Differential expression analysis and transcription factor binding site inference indicates that FapR negatively regulates malonyl-CoA and fatty acid biosynthesis, as it does in many other bacteria. FruR/Cra regulates neighboring fructose metabolism genes, as well as other genes in global manner. Conclusions Two systems able to effect tolerance to elevated osmolarities in C. bescii are identified. The first is fatty acid biosynthesis. The other is likely the result of one or more unintended, secondary mutations present in another transcription factor deletion strain. Though the locus/loci and mechanism(s) responsible remain unknown, candidate mutations are identified, including a mutation in the dnaK chaperone coding sequence. These results illustrate both the promise of targeted regulatory manipulation for osmotolerance (in the case of fapR ) and the challenges (in the case of fruR/cra ).},
doi = {10.1186/s13068-020-01690-3},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 13,
place = {Netherlands},
year = {Fri Mar 13 00:00:00 EDT 2020},
month = {Fri Mar 13 00:00:00 EDT 2020}
}
https://doi.org/10.1186/s13068-020-01690-3
Web of Science
Works referenced in this record:
Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics
journal, April 2018
- Whitham, Jason M.; Moon, Ji-Won; Rodriguez, Miguel
- Biotechnology for Biofuels, Vol. 11, Issue 1
The global regulatory protein FruR modulates the direction of carbon flow in Escherichia coli
journal, June 1995
- Ramseier, Tom M.; Bledig, Stefan; Michotey, Valerie
- Molecular Microbiology, Vol. 16, Issue 6
In Vitro Binding of the Pleiotropic Transcriptional Regulatory Protein, FruR, to the fru, pps, ace, pts and icd Operons of Escherichia coli and Salmonella typhimurium
journal, November 1993
- Ramseier, Tom M.; Nègre, Didier; Cortay, Jean-Claude
- Journal of Molecular Biology, Vol. 234, Issue 1
Metabolic engineering of a Saccharomyces cerevisiae strain capable of simultaneously utilizing glucose and galactose to produce enantiopure (2R,3R)-butanediol
journal, May 2014
- Lian, Jiazhang; Chao, Ran; Zhao, Huimin
- Metabolic Engineering, Vol. 23
Industrial Robustness: Understanding the Mechanism of Tolerance for the Populus Hydrolysate-Tolerant Mutant Strain of Clostridium thermocellum
journal, October 2013
- Linville, Jessica L.; Rodriguez, Miguel; Land, Miriam
- PLoS ONE, Vol. 8, Issue 10
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
Evaluation of the influence of CO2 on hydrogen production by Caldicellulosiruptor saccharolyticus
journal, June 2009
- Willquist, Karin; Claassen, Pieternel A. M.; van Niel, Ed W. J.
- International Journal of Hydrogen Energy, Vol. 34, Issue 11
Rex in Caldicellulosiruptor bescii : Novel regulon members and its effect on the production of ethanol and overflow metabolites
journal, April 2018
- Sander, Kyle; Chung, Daehwan; Hyatt, Doug
- MicrobiologyOpen, Vol. 8, Issue 2
A kinetic model for quantitative evaluation of the effect of hydrogen and osmolarity on hydrogen production by Caldicellulosiruptor saccharolyticus
journal, January 2011
- Ljunggren, Mattias; Willquist, Karin; Zacchi, Guido
- Biotechnology for Biofuels, Vol. 4, Issue 1
Improving lycopene production in Escherichia coli by engineering metabolic control
journal, May 2000
- Farmer, William R.; Liao, James C.
- Nature Biotechnology, Vol. 18, Issue 5
Cellulosic ethanol production via consolidated bioprocessing at 75 °C by engineered Caldicellulosiruptor bescii
journal, October 2015
- Chung, Daehwan; Cha, Minseok; Snyder, Elise N.
- Biotechnology for Biofuels, Vol. 8, Issue 1
How biotech can transform biofuels
journal, February 2008
- Lynd, Lee R.; Laser, Mark S.; Bransby, David
- Nature Biotechnology, Vol. 26, Issue 2, p. 169-172
Engineering electron metabolism to increase ethanol production in Clostridium thermocellum
journal, January 2017
- Lo, Jonathan; Olson, Daniel G.; Murphy, Sean Jean-Loup
- Metabolic Engineering, Vol. 39
Bacterial responses to osmotic challenges
journal, April 2015
- Wood, Janet M.
- Journal of General Physiology, Vol. 145, Issue 5
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
journal, January 2013
- Novichkov, Pavel S.; Kazakov, Alexey E.; Ravcheev, Dmitry A.
- BMC Genomics, Vol. 14, Issue 1
Evidence for regulation of gluconeogenesis by the fructose phosphotransferase system in Salmonella typhimurium.
journal, January 1987
- Chin, A. M.; Feucht, B. U.; Saier, M. H.
- Journal of Bacteriology, Vol. 169, Issue 2
Methylation by a Unique α-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725
journal, August 2012
- Chung, Daehwan; Farkas, Joel; Huddleston, Jennifer R.
- PLoS ONE, Vol. 7, Issue 8
A thermophile under pressure: Transcriptional analysis of the response of Caldicellulosiruptor saccharolyticus to different H2 partial pressures
journal, February 2013
- Bielen, Abraham A. M.; Verhaart, Marcel R. A.; VanFossen, Amy L.
- International Journal of Hydrogen Energy, Vol. 38, Issue 4
Characterization of FruR as a putative activator of the fructose operon of Spiroplasma citri
journal, April 2001
- Gaurivaud, Patrice; Laigret, Frédéric; Garnier, Monique
- FEMS Microbiology Letters, Vol. 198, Issue 1
Negative Feedback Regulation of Fatty Acid Production Based on a Malonyl-CoA Sensor–Actuator
journal, January 2014
- Liu, Di; Xiao, Yi; Evans, Bradley S.
- ACS Synthetic Biology, Vol. 4, Issue 2
Cyclic AMP-independent catabolite repression in bacteria
journal, May 1996
- H. Saier, Milton
- FEMS Microbiology Letters, Vol. 138, Issue 2-3
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima
journal, January 2013
- Rodionov, Dmitry A.; Rodionova, Irina A.; Li, Xiaoqing
- Frontiers in Microbiology, Vol. 4
Degradation of high loads of crystalline cellulose and of unpretreated plant biomass by the thermophilic bacterium Caldicellulosiruptor bescii
journal, January 2014
- Basen, Mirko; Rhaesa, Amanda M.; Kataeva, Irina
- Bioresource Technology, Vol. 152
Structural basis of lipid biosynthesis regulation in Gram-positive bacteria
journal, August 2006
- Schujman, Gustavo E.; Guerin, Marcelo; Buschiazzo, Alejandro
- The EMBO Journal, Vol. 25, Issue 17
Alterations in Protein Expression Caused by thehha Mutation in Escherichia coli: Influence of Growth Medium Osmolarity
journal, January 1999
- Balsalobre, Carlos; Johansson, Jörgen; Uhlin, Bernt Eric
- Journal of Bacteriology, Vol. 181, Issue 10
Caldicellulosiruptor obsidiansis sp. nov., an Anaerobic, Extremely Thermophilic, Cellulolytic Bacterium Isolated from Obsidian Pool, Yellowstone National Park
journal, December 2009
- Hamilton-Brehm, S. D.; Mosher, J. J.; Vishnivetskaya, T.
- Applied and Environmental Microbiology, Vol. 76, Issue 4, p. 1014-1020
Effect of the FruR Regulator on Transcription of the pts Operon in Escherichia coli
journal, February 1995
- Ryu, Sangryeol; Ramseier, Tom M.; Michotey, Valerie
- Journal of Biological Chemistry, Vol. 270, Issue 6
Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli.
journal, January 1996
- Bledig, S. A.; Ramseier, T. M.; Saier, M. H.
- Journal of bacteriology, Vol. 178, Issue 1
Role of heat shock protein DnaK in osmotic adaptation of Escherichia coli.
journal, January 1991
- Meury, J.; Kohiyama, M.
- Journal of Bacteriology, Vol. 173, Issue 14
The redox-sensing protein Rex, a transcriptional regulator of solventogenesis in Clostridium acetobutylicum
journal, May 2012
- Wietzke, Mandy; Bahl, Hubert
- Applied Microbiology and Biotechnology, Vol. 96, Issue 3
Salt Stress and Hyperosmotic Stress Regulate the Expression of Different Sets of Genes in Synechocystis sp. PCC 6803
journal, January 2002
- Kanesaki, Yu; Suzuki, Iwane; Allakhverdiev, Suleyman I.
- Biochemical and Biophysical Research Communications, Vol. 290, Issue 1
Flavodoxin accumulation contributes to enhanced cyclic electron flow around photosystem I in salt-stressed cells of Synechocystis sp. strain PCC 6803
journal, April 1999
- Hagemann, Martin; Jeanjean, Robert; Fulda, Sabine
- Physiologia Plantarum, Vol. 105, Issue 4
Fructose Utilization in Lactococcus lactis as a Model for Low-GC Gram-Positive Bacteria: Its Regulator, Signal, and DNA-Binding Site
journal, May 2005
- Barriere, C.; Veiga-da-Cunha, M.; Pons, N.
- Journal of Bacteriology, Vol. 187, Issue 11
Membrane fluidity and its roles in the perception of environmental signals
journal, November 2004
- Los, Dmitry A.; Murata, Norio
- Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1666, Issue 1-2
Variations of the Envelope Composition of Bacillus subtilis During Growth in Hyperosmotic Medium
journal, January 1998
- S. López *, , Horaci, Claudia; Ruzal, Sandra M.; Sánchez-Rivas, Carmen
- Current Microbiology, Vol. 36, Issue 1
A Ring to Rule Them All: The Effect of Cyclopropane Fatty Acids on the Fluidity of Lipid Bilayers
journal, April 2015
- Poger, David; Mark, Alan E.
- The Journal of Physical Chemistry B, Vol. 119, Issue 17
Fructose 1-phosphate is the one and only physiological effector of the Cra (FruR) regulator of Pseudomonas putida
journal, January 2014
- Chavarría, Max; Durante-Rodríguez, Gonzalo; Krell, Tino
- FEBS Open Bio, Vol. 4, Issue 1
FapR, a Bacterial Transcription Factor Involved in Global Regulation of Membrane Lipid Biosynthesis
journal, May 2003
- Schujman, Gustavo E.; Paoletti, Luciana; Grossman, Alan D.
- Developmental Cell, Vol. 4, Issue 5
Construction of a Stable Replicating Shuttle Vector for Caldicellulosiruptor Species: Use for Extending Genetic Methodologies to Other Members of This Genus
journal, May 2013
- Chung, Daehwan; Cha, Minseok; Farkas, Joel
- PLoS ONE, Vol. 8, Issue 5, Article No. e62881
Regulons of global transcription factors in Corynebacterium glutamicum
journal, October 2015
- Toyoda, Koichi; Inui, Masayuki
- Applied Microbiology and Biotechnology, Vol. 100, Issue 1
Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes
journal, August 2005
- Munch, R.; Hiller, K.; Grote, A.
- Bioinformatics, Vol. 21, Issue 22
Identification of parallel and divergent optimization solutions for homologous metabolic enzymes
journal, June 2018
- Standaert, Robert F.; Giannone, Richard J.; Michener, Joshua K.
- Metabolic Engineering Communications, Vol. 6
Substrate and product inhibition of hydrogen production by the extreme thermophile,Caldicellulosiruptor saccharolyticus
journal, December 2002
- van Niel, Ed W. J.; Claassen, Pieternel A. M.; Stams, Alfons J. M.
- Biotechnology and Bioengineering, Vol. 81, Issue 3
Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement
journal, January 2013
- Chung, Daehwan; Farkas, Joel; Westpheling, Janet
- Biotechnology for Biofuels, Vol. 6, Issue 1
Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii
journal, November 2012
- Farkas, Joel; Chung, Daehwan; Cha, Minseok
- Journal of Industrial Microbiology & Biotechnology, Vol. 40, Issue 1, p. 41-49