Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph
Abstract
Synthetic methylotrophy aims to develop non-native methylotrophic microorganisms to utilize methane or methanol to produce chemicals and biofuels. We report two complimentary strategies to further engineer a previously engineered methylotrophic E. coli strain for improved methanol utilization. First, we demonstrate improved methanol assimilation in the presence of small amounts of yeast extract by expressing the non-oxidative pentose phosphate pathway (PPP) from Bacillus methanolicus. Second, we demonstrate improved co-utilization of methanol and glucose by deleting the phosphoglucose isomerase gene (pgi), which rerouted glucose carbon flux through the oxidative PPP. Both strategies led to significant improvements in methanol assimilation as determined by 13C-labeling in intracellular metabolites. As a result, introduction of an acetone-formation pathway in the pgi-deficient methylotrophic E. coli strain led to improved methanol utilization and acetone titers during glucose fed-batch fermentation.
- Authors:
-
- Univ. of Delaware, Newark, DE (United States)
- Publication Date:
- Research Org.:
- Univ. of Delaware, Newark, DE (United States)
- Sponsoring Org.:
- USDOE Advanced Research Projects Agency - Energy (ARPA-E)
- OSTI Identifier:
- 1411402
- Alternate Identifier(s):
- OSTI ID: 1703839
- Grant/Contract Number:
- AR0000432
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Metabolic Engineering
- Additional Journal Information:
- Journal Volume: 45; Journal Issue: C; Journal ID: ISSN 1096-7176
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Synthetic methylotrophy; Methanol; Escherichia coli; Pentose phosphate pathway; Phosphoglucose isomerase
Citation Formats
Bennett, R. Kyle, Gonzalez, Jacqueline E., Whitaker, W. Brian, Antoniewicz, Maciek R., and Papoutsakis, Eleftherios T. Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph. United States: N. p., 2017.
Web. doi:10.1016/j.ymben.2017.11.016.
Bennett, R. Kyle, Gonzalez, Jacqueline E., Whitaker, W. Brian, Antoniewicz, Maciek R., & Papoutsakis, Eleftherios T. Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph. United States. https://doi.org/10.1016/j.ymben.2017.11.016
Bennett, R. Kyle, Gonzalez, Jacqueline E., Whitaker, W. Brian, Antoniewicz, Maciek R., and Papoutsakis, Eleftherios T. Tue .
"Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph". United States. https://doi.org/10.1016/j.ymben.2017.11.016. https://www.osti.gov/servlets/purl/1411402.
@article{osti_1411402,
title = {Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph},
author = {Bennett, R. Kyle and Gonzalez, Jacqueline E. and Whitaker, W. Brian and Antoniewicz, Maciek R. and Papoutsakis, Eleftherios T.},
abstractNote = {Synthetic methylotrophy aims to develop non-native methylotrophic microorganisms to utilize methane or methanol to produce chemicals and biofuels. We report two complimentary strategies to further engineer a previously engineered methylotrophic E. coli strain for improved methanol utilization. First, we demonstrate improved methanol assimilation in the presence of small amounts of yeast extract by expressing the non-oxidative pentose phosphate pathway (PPP) from Bacillus methanolicus. Second, we demonstrate improved co-utilization of methanol and glucose by deleting the phosphoglucose isomerase gene (pgi), which rerouted glucose carbon flux through the oxidative PPP. Both strategies led to significant improvements in methanol assimilation as determined by 13C-labeling in intracellular metabolites. As a result, introduction of an acetone-formation pathway in the pgi-deficient methylotrophic E. coli strain led to improved methanol utilization and acetone titers during glucose fed-batch fermentation.},
doi = {10.1016/j.ymben.2017.11.016},
journal = {Metabolic Engineering},
number = C,
volume = 45,
place = {United States},
year = {2017},
month = {12}
}
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Figure 1: Strategies to enhance synthetic methylotrophy. (A): Methanol is oxidized by the mdh-encoded MDH to formaldehyde, which is assimilated via the ribulose monophosphate (RuMP) pathway (hps, phi) to F6P upon reacting with Ru5P (green). Deletion of frmA eliminates formaldehyde dissimilation to CO2 to conserve methanol carbon. The heterologous non-oxidativemore »
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Works referenced in this record:
Parallel labeling experiments for pathway elucidation and 13C metabolic flux analysis
journal, December 2015
- Antoniewicz, Maciek R.
- Current Opinion in Biotechnology, Vol. 36
Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements
journal, July 2006
- Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
- Metabolic Engineering, Vol. 8, Issue 4
Elementary metabolite units (EMU): A novel framework for modeling isotopic distributions
journal, January 2007
- Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
- Metabolic Engineering, Vol. 9, Issue 1
Measuring Deuterium Enrichment of Glucose Hydrogen Atoms by Gas Chromatography/Mass Spectrometry
journal, April 2011
- Antoniewicz, Maciek R.; Kelleher, Joanne K.; Stephanopoulos, Gregory
- Analytical Chemistry, Vol. 83, Issue 8
Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol
journal, May 2007
- Antoniewicz, M.; Kraynie, D.; Laffend, L.
- Metabolic Engineering, Vol. 9, Issue 3
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants the Keio collection
journal, February 2006
- Baba, Tomoya; Ara, Takeshi; Hasegawa, Miki
- Molecular Systems Biology, Vol. 2, Article No. 2006.0008
Overflow metabolism in Escherichia coli results from efficient proteome allocation
journal, December 2015
- Basan, Markus; Hui, Sheng; Okano, Hiroyuki
- Nature, Vol. 528, Issue 7580
Expression of Clostridium acetobutylicumATCC 824 Genes in Escherichia coli for Acetone Production and Acetate Detoxification
journal, March 1998
- Bermejo, Lourdes L.; Welker, Neil E.; Papoutsakis, Eleftherios T.
- Applied and Environmental Microbiology, Vol. 64, Issue 3
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
journal, November 2013
- Espah Borujeni, Amin; Channarasappa, Anirudh S.; Salis, Howard M.
- Nucleic Acids Research, Vol. 42, Issue 4
Plasmid-Dependent Methylotrophy in Thermotolerant Bacillus methanolicus
journal, February 2004
- Brautaset, T.; Jakobsen, O. M.; Flickinger, M. C.
- Journal of Bacteriology, Vol. 186, Issue 5, p. 1229-1238
Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene
journal, November 2010
- Charusanti, Pep; Conrad, Tom M.; Knight, Eric M.
- PLoS Genetics, Vol. 6, Issue 11
Growth dynamics of a methylotroph (Methylomonas L3) in continuous cultures. I. Fast transients induced by methanol pulses and methanol accumulation
journal, January 1987
- Chu, I-Ming; Papoutsakis, Eleftherios Terry
- Biotechnology and Bioengineering, Vol. 29, Issue 1, p. 55-64
Integrated 13 C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli
journal, March 2015
- Crown, Scott B.; Long, Christopher P.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 28
Optimal tracers for parallel labeling experiments and 13C metabolic flux analysis: A new precision and synergy scoring system
journal, November 2016
- Crown, Scott B.; Long, Christopher P.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 38
Metabolic construction strategies for direct methanol utilization in Saccharomyces cerevisiae
journal, December 2017
- Dai, Zhongxue; Gu, Honglian; Zhang, Shangjie
- Bioresource Technology, Vol. 245
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
journal, May 2000
- Datsenko, K. A.; Wanner, B. L.
- Proceedings of the National Academy of Sciences, Vol. 97, Issue 12, p. 6640-6645
Maintenance of broad-host-range incompatibility group P and group Q plasmids and transposition of Tn5 in Bartonella henselae following conjugal plasmid transfer from Escherichia coli.
journal, January 1997
- Dehio, C.; Meyer, M.
- Journal of Bacteriology, Vol. 179, Issue 2
Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli
journal, January 2017
- Englaender, Jacob A.; Jones, J. Andrew; Cress, Brady F.
- ACS Synthetic Biology, Vol. 6, Issue 4
Correction of13C Mass Isotopomer Distributions for Natural Stable Isotope Abundance
journal, March 1996
- Fernandez, Charles A.; Rosiers, Christine Des; Previs, Stephen F.
- Journal of Mass Spectrometry, Vol. 31, Issue 3
Identification and validation of reference genes to study the gene expression in Gluconacetobacter diazotrophicus grown in different carbon sources using RT-qPCR
journal, October 2012
- Galisa, Péricles S.; da Silva, Helder A. P.; Macedo, Aline V. M.
- Journal of Microbiological Methods, Vol. 91, Issue 1
Molecular Basis of Formaldehyde Detoxification: CHARACTERIZATION OF TWO S-FORMYLGLUTATHIONE HYDROLASES FROM ESCHERICHIA COLI, FrmB AND YeiG
journal, March 2006
- Gonzalez, Claudio F.; Proudfoot, Michael; Brown, Greg
- Journal of Biological Chemistry, Vol. 281, Issue 20
Tracing metabolism from lignocellulosic biomass and gaseous substrates to products with stable-isotopes
journal, February 2017
- Gonzalez, Jacqueline E.; Antoniewicz, Maciek R.
- Current Opinion in Biotechnology, Vol. 43
Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis
journal, January 2017
- Gonzalez, Jacqueline E.; Long, Christopher P.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 39
Rethinking biological activation of methane and conversion to liquid fuels
journal, April 2014
- Haynes, Chad A.; Gonzalez, Ramon
- Nature Chemical Biology, Vol. 10, Issue 5
Formaldehyde incorporation by a new methylotroph (L3).
journal, January 1978
- Hirt, W.; Papoutsakis, E.; Krug, E.
- Applied and Environmental Microbiology, Vol. 36, Issue 1
Responses of the Central Metabolism in Escherichia coli to Phosphoglucose Isomerase and Glucose-6-Phosphate Dehydrogenase Knockouts
journal, December 2003
- Hua, Q.; Yang, C.; Baba, T.
- Journal of Bacteriology, Vol. 185, Issue 24
Upregulated Transcription of Plasmid and Chromosomal Ribulose Monophosphate Pathway Genes Is Critical for Methanol Assimilation Rate and Methanol Tolerance in the Methylotrophic Bacterium Bacillus methanolicus
journal, April 2006
- Jakobsen, O. M.; Benichou, A.; Flickinger, M. C.
- Journal of Bacteriology, Vol. 188, Issue 8, p. 3063-3072
Construction of CoA-dependent 1-butanol synthetic pathway functions under aerobic conditions in Escherichia coli
journal, June 2015
- Kataoka, Naoya; Vangnai, Alisa S.; Pongtharangkul, Thunyarat
- Journal of Biotechnology, Vol. 204
Parallel labeling experiments with [U-13C]glucose validate E. coli metabolic network model for 13C metabolic flux analysis
journal, September 2012
- Leighty, Robert W.; Antoniewicz, Maciek R.
- Metabolic Engineering, Vol. 14, Issue 5
Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate
journal, August 2015
- Leßmeier, Lennart; Pfeifenschneider, Johannes; Carnicer, Marc
- Applied Microbiology and Biotechnology, Vol. 99, Issue 23
Quantifying Biomass Composition by Gas Chromatography/Mass Spectrometry
journal, September 2014
- Long, Christopher P.; Antoniewicz, Maciek R.
- Analytical Chemistry, Vol. 86, Issue 19
13C metabolic flux analysis of microbial and mammalian systems is enhanced with GC-MS measurements of glycogen and RNA labeling
journal, November 2016
- Long, Christopher P.; Au, Jennifer; Gonzalez, Jacqueline E.
- Metabolic Engineering, Vol. 38
Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism
journal, September 2016
- Long, Christopher P.; Gonzalez, Jacqueline E.; Sandoval, Nicholas R.
- Metabolic Engineering, Vol. 37
A modified pathway for the production of acetone in Escherichia coli
journal, January 2013
- May, Antje; Fischer, Ralf-Jörg; Maria Thum, Simone
- Metabolic Engineering, Vol. 15
Measuring the Composition and Stable-Isotope Labeling of Algal Biomass Carbohydrates via Gas Chromatography/Mass Spectrometry
journal, April 2016
- McConnell, Brian O.; Antoniewicz, Maciek R.
- Analytical Chemistry, Vol. 88, Issue 9
Metabolic engineering ofClostridium acetobutylicum ATCC 824 for increased solvent production by enhancement of acetone formation enzyme activities using a synthetic acetone operon
journal, November 1993
- Mermelstein, Lee D.; Papoutsakis, Eleftherios T.; Petersen, Daniel J.
- Biotechnology and Bioengineering, Vol. 42, Issue 9
Engineering Escherichia coli for methanol conversion
journal, March 2015
- Müller, Jonas E. N.; Meyer, Fabian; Litsanov, Boris
- Metabolic Engineering, Vol. 28, p. 190-201
Improvement of pCVD442, a suicide plasmid for gene allele exchange in bacteria
journal, May 2004
- Philippe, Nadège; Alcaraz, Jean-Pierre; Coursange, Evelyne
- Plasmid, Vol. 51, Issue 3
Determination of rpoA as the most suitable internal control to study stress response in C. jejuni by RT-qPCR and application to oxidative stress
journal, February 2009
- Ritz, M.; Garenaux, A.; Berge, M.
- Journal of Microbiological Methods, Vol. 76, Issue 2
Sort-Seq Approach to Engineering a Formaldehyde-Inducible Promoter for Dynamically Regulated Escherichia coli Growth on Methanol
journal, May 2017
- Rohlhill, Julia; Sandoval, Nicholas R.; Papoutsakis, Eleftherios T.
- ACS Synthetic Biology, Vol. 6, Issue 8, p. 1584-1595
Automated design of synthetic ribosome binding sites to control protein expression
journal, October 2009
- Salis, Howard M.; Mirsky, Ethan A.; Voigt, Christopher A.
- Nature Biotechnology, Vol. 27, Issue 10, p. 946-950
A new alcohol dehydrogenase, reactive towards methanol, from Bacillus stearothermophilus
journal, June 1988
- Sheehan, M. C.; Bailey, C. J.; Dowds, B. C. A.
- Biochemical Journal, Vol. 252, Issue 3
Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13 C metabolic flux analysis
journal, January 2012
- Usui, Yuki; Hirasawa, Takashi; Furusawa, Chikara
- Microbial Cell Factories, Vol. 11, Issue 1
Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase
journal, January 2010
- Valgepea, Kaspar; Adamberg, Kaarel; Nahku, Ranno
- BMC Systems Biology, Vol. 4, Issue 1
Overflow Metabolism in Escherichia coli during Steady-State Growth: Transcriptional Regulation and Effect of the Redox Ratio
journal, May 2006
- Vemuri, G. N.; Altman, E.; Sangurdekar, D. P.
- Applied and Environmental Microbiology, Vol. 72, Issue 5
A Toolbox of Diverse Promoters Related to Methanol Utilization: Functionally Verified Parts for Heterologous Pathway Expression in Pichia pastoris
journal, December 2015
- Vogl, Thomas; Sturmberger, Lukas; Kickenweiz, Thomas
- ACS Synthetic Biology, Vol. 5, Issue 2
Engineering the biological conversion of methanol to specialty chemicals in Escherichia coli
journal, January 2017
- Whitaker, W. Brian; Jones, J. Andrew; Bennett, R. Kyle
- Metabolic Engineering, Vol. 39
Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization
journal, June 2015
- Whitaker, William B.; Sandoval, Nicholas R.; Bennett, Robert K.
- Current Opinion in Biotechnology, Vol. 33
Metabolic Engineering of Corynebacterium glutamicum for Methanol Metabolism
journal, January 2015
- Witthoff, Sabrina; Schmitz, Katja; Niedenführ, Sebastian
- Applied and Environmental Microbiology, Vol. 81, Issue 6, p. 2215-2225
Metabolic Burden: Cornerstones in Synthetic Biology and Metabolic Engineering Applications
journal, August 2016
- Wu, Gang; Yan, Qiang; Jones, J. Andrew
- Trends in Biotechnology, Vol. 34, Issue 8
Characterization and evolution of an activator-independent methanol dehydrogenase from Cupriavidus necator N-1
journal, February 2016
- Wu, Tung-Yun; Chen, Chang-Ting; Liu, Jessica Tse-Jin
- Applied Microbiology and Biotechnology, Vol. 100, Issue 11
ePathBrick: A Synthetic Biology Platform for Engineering Metabolic Pathways in E. coli
journal, May 2012
- Xu, Peng; Vansiri, Amerin; Bhan, Namita
- ACS Synthetic Biology, Vol. 1, Issue 7
Quantifying Reductive Carboxylation Flux of Glutamine to Lipid in a Brown Adipocyte Cell Line
journal, March 2008
- Yoo, Hyuntae; Antoniewicz, Maciek R.; Stephanopoulos, Gregory
- Journal of Biological Chemistry, Vol. 283, Issue 30
Promoters and transcripts for genes involved in methanol oxidation in Methylobacterium extorquens AM1
journal, April 2003
- Zhang, Meng; Lidstrom, Mary E.
- Microbiology, Vol. 149, Issue 4
Novel reference genes for quantifying transcriptional responses of Escherichia coli to protein overexpression by quantitative PCR
journal, January 2011
- Zhou, Kang; Zhou, Lihan; Lim, Qing
- BMC Molecular Biology, Vol. 12, Issue 1
Works referencing / citing this record:
Growth of E. coli on formate and methanol via the reductive glycine pathway
journal, February 2020
- Kim, Seohyoung; Lindner, Steffen N.; Aslan, Selçuk
- Nature Chemical Biology, Vol. 16, Issue 5
Biological conversion of methane to chemicals and fuels: technical challenges and issues
journal, February 2018
- Hwang, In Yeub; Nguyen, Anh Duc; Nguyen, Thu Thi
- Applied Microbiology and Biotechnology, Vol. 102, Issue 7
Methanol-essential growth of Escherichia coli
journal, April 2018
- Meyer, Fabian; Keller, Philipp; Hartl, Johannes
- Nature Communications, Vol. 9, Issue 1
Methanol fermentation increases the production of NAD(P)H-dependent chemicals in synthetic methylotrophic Escherichia coli
journal, January 2019
- Wang, Xin; Wang, Xuelin; Lu, Xiaolu
- Biotechnology for Biofuels, Vol. 12, Issue 1
C1 Compound Biosensors: Design, Functional Study, and Applications
journal, May 2019
- Lee, Jin-Young; Sung, Bong Hyun; Oh, So-Hyung
- International Journal of Molecular Sciences, Vol. 20, Issue 9
Engineering Artificial Fusion Proteins for Enhanced Methanol Bioconversion
journal, October 2018
- Fan, Liwen; Wang, Yu; Tuyishime, Philibert
- ChemBioChem, Vol. 19, Issue 23
Improving formaldehyde consumption drives methanol assimilation in engineered E. coli
journal, June 2018
- Woolston, Benjamin M.; King, Jason R.; Reiter, Michael
- Nature Communications, Vol. 9, Issue 1
Charting the Metabolic Landscape of the Facultative Methylotroph Bacillus methanolicus
journal, October 2020
- Delépine, Baudoin; López, Marina Gil; Carnicer, Marc
- mSystems, Vol. 5, Issue 5
Methanol-essential growth of Escherichia coli
text, January 2018
- Meyer, Fabian; Keller, Philipp; Hartl, Johannes
- ETH Zurich
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