Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production
Abstract
Metabolic engineering efforts that harness living organisms to produce natural products and other useful chemicals face inherent difficulties because the maintenance of life processes often runs counter to our desire to maximize important production metrics. These challenges are particularly problematic for commodity chemical manufacturing where cost is critical. A cell-free approach, where biochemical pathways are built by mixing desired enzyme activities outside of cells, can obviate problems associated with cell-based methods. Yet supplanting cell-based methods of chemical production will require the creation of self-sustaining, continuously operating systems where input biomass is converted into desired products at high yields, productivities, and titers. We call the field of designing and implementing reliable and efficient enzyme systems that replace cellular metabolism, synthetic biochemistry.
- Publication Date:
- Research Org.:
- Univ. of California, Los Angeles, CA (United States)
- Sponsoring Org.:
- USDOE Advanced Research Projects Agency - Energy (ARPA-E); USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1593509
- Alternate Identifier(s):
- OSTI ID: 1799020
- Grant/Contract Number:
- AR0000556; FC02-02ER63421
- Resource Type:
- Published Article
- Journal Name:
- Trends in Biotechnology
- Additional Journal Information:
- Journal Name: Trends in Biotechnology Journal Volume: 38 Journal Issue: 7; Journal ID: ISSN 0167-7799
- Publisher:
- Elsevier
- Country of Publication:
- Netherlands
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; metabolic engineering; enzyme cascade; cascade biocatalysis; multienzyme systems; biofuel; biomanufacturing; green chemistry; natural products; commodity chemical
Citation Formats
Bowie, James U., Sherkhanov, Saken, Korman, Tyler P., Valliere, Meaghan A., Opgenorth, Paul H., and Liu, Hongjiang. Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production. Netherlands: N. p., 2020.
Web. doi:10.1016/j.tibtech.2019.12.024.
Bowie, James U., Sherkhanov, Saken, Korman, Tyler P., Valliere, Meaghan A., Opgenorth, Paul H., & Liu, Hongjiang. Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production. Netherlands. https://doi.org/10.1016/j.tibtech.2019.12.024
Bowie, James U., Sherkhanov, Saken, Korman, Tyler P., Valliere, Meaghan A., Opgenorth, Paul H., and Liu, Hongjiang. Wed .
"Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production". Netherlands. https://doi.org/10.1016/j.tibtech.2019.12.024.
@article{osti_1593509,
title = {Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production},
author = {Bowie, James U. and Sherkhanov, Saken and Korman, Tyler P. and Valliere, Meaghan A. and Opgenorth, Paul H. and Liu, Hongjiang},
abstractNote = {Metabolic engineering efforts that harness living organisms to produce natural products and other useful chemicals face inherent difficulties because the maintenance of life processes often runs counter to our desire to maximize important production metrics. These challenges are particularly problematic for commodity chemical manufacturing where cost is critical. A cell-free approach, where biochemical pathways are built by mixing desired enzyme activities outside of cells, can obviate problems associated with cell-based methods. Yet supplanting cell-based methods of chemical production will require the creation of self-sustaining, continuously operating systems where input biomass is converted into desired products at high yields, productivities, and titers. We call the field of designing and implementing reliable and efficient enzyme systems that replace cellular metabolism, synthetic biochemistry.},
doi = {10.1016/j.tibtech.2019.12.024},
journal = {Trends in Biotechnology},
number = 7,
volume = 38,
place = {Netherlands},
year = {Wed Jul 01 00:00:00 EDT 2020},
month = {Wed Jul 01 00:00:00 EDT 2020}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.tibtech.2019.12.024
https://doi.org/10.1016/j.tibtech.2019.12.024
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 53 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Optimization of a blueprint for in vitro glycolysis by metabolic real-time analysis
journal, March 2011
- Bujara, Matthias; Schümperli, Michael; Pellaux, René
- Nature Chemical Biology, Vol. 7, Issue 5
Synthetic and systems biology for microbial production of commodity chemicals
journal, April 2016
- Chubukov, Victor; Mukhopadhyay, Aindrila; Petzold, Christopher J.
- npj Systems Biology and Applications, Vol. 2, Issue 1
A synthetic biochemistry module for production of bio-based chemicals from glucose
journal, April 2016
- Opgenorth, Paul H.; Korman, Tyler P.; Bowie, James U.
- Nature Chemical Biology, Vol. 12, Issue 6
Simplified in Vitro and in Vivo Bioaccess to Prenylated Compounds
journal, April 2019
- Couillaud, Julie; Rico, Juan; Rubini, Alyssa
- ACS Omega, Vol. 4, Issue 4
In vitro metabolic engineering for the production of α-ketoglutarate
journal, March 2017
- Beer, Barbara; Pick, André; Sieber, Volker
- Metabolic Engineering, Vol. 40
Hydrogenesis in hyperthermophilic microorganisms: Implications for biofuels
journal, November 2008
- Chou, Chung-Jung; Jenney, Francis E.; Adams, Michael W.W.
- Metabolic Engineering, Vol. 10, Issue 6, p. 394-404
Biotechnological Development of a Practical Synthesis of Ethyl ( S )-2-Ethoxy-3-( p -methoxyphenyl)propanoate (EEHP): Over 100-Fold Productivity Increase from Yeast Whole Cells to Recombinant Isolated Enzymes
journal, September 2011
- Bechtold, Matthias; Brenna, Elisabetta; Femmer, Christian
- Organic Process Research & Development, Vol. 16, Issue 2
An Artificial Pathway for Isoprenoid Biosynthesis Decoupled from Native Hemiterpene Metabolism
journal, January 2019
- Lund, Sean; Hall, Rachael; Williams, Gavin J.
- ACS Synthetic Biology, Vol. 8, Issue 2
Developmental strategies and regulation of cell-free enzyme system for ethanol production: a molecular prospective
journal, October 2014
- Khattak, Waleed Ahmad; Ullah, Muhammad Wajid; Ul-Islam, Mazhar
- Applied Microbiology and Biotechnology, Vol. 98, Issue 23
A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system
journal, July 2017
- Opgenorth, Paul H.; Korman, Tyler P.; Iancu, Liviu
- Nature Chemical Biology, Vol. 13, Issue 9
Metabolite damage and repair in metabolic engineering design
journal, November 2017
- Sun, Jiayi; Jeffryes, James G.; Henry, Christopher S.
- Metabolic Engineering, Vol. 44
High-yield hydrogen production from biomass by in vitro metabolic engineering: Mixed sugars coutilization and kinetic modeling
journal, April 2015
- Rollin, Joseph A.; Martin del Campo, Julia; Myung, Suwan
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 16
Improved strategies for electrochemical 1,4-NAD(P)H2 regeneration: A new era of bioreactors for industrial biocatalysis
journal, January 2018
- Morrison, Clifford S.; Armiger, William B.; Dodds, David R.
- Biotechnology Advances, Vol. 36, Issue 1
Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR
journal, October 2019
- Klöpfer, Kai; Hagn, Franz
- Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 114-115
In vitro production of n-butanol from glucose
journal, November 2013
- Krutsakorn, Borimas; Honda, Kohsuke; Ye, Xiaoting
- Metabolic Engineering, Vol. 20
Production of biofuels and biochemicals by in vitro synthetic biosystems: Opportunities and challenges
journal, November 2015
- Zhang, Yi-Heng Percival
- Biotechnology Advances, Vol. 33, Issue 7
Cell free biosynthesis of isoprenoids from isopentenol
journal, September 2019
- Ward, Valerie C. A.; Chatzivasileiou, Alkiviadis Orfefs; Stephanopoulos, Gregory
- Biotechnology and Bioengineering, Vol. 116, Issue 12
Metabolic engineering for the microbial production of 1,3-propanediol
journal, October 2003
- Nakamura, Charles E; Whited, Gregory M
- Current Opinion in Biotechnology, Vol. 14, Issue 5, p. 454-459
Enzymatic production of biohydrogen: Biotechnology
journal, June 2000
- Woodward, Jonathan; Orr, Mark; Cordray, Kimberley
- Nature, Vol. 405, Issue 6790, p. 1014-1015
The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis
journal, June 2019
- Clomburg, James M.; Qian, Shuai; Tan, Zaigao
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 26
Two-step pathway for isoprenoid synthesis
journal, December 2018
- Chatzivasileiou, Alkiviadis Orfefs; Ward, Valerie; Edgar, Steven McBride
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 2
Engineering the third wave of biocatalysis
journal, May 2012
- Bornscheuer, U. T.; Huisman, G. W.; Kazlauskas, R. J.
- Nature, Vol. 485, Issue 7397
Assembly and multiple gene expression of thermophilic enzymes in Escherichia coli for in vitro metabolic engineering : Multiple Expression of Thermophilic Enzymes
journal, September 2014
- Ninh, Pham Huynh; Honda, Kohsuke; Sakai, Takaaki
- Biotechnology and Bioengineering, Vol. 112, Issue 1
Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism
journal, March 2018
- Lin, Paul P.; Jaeger, Alec J.; Wu, Tung-Yun
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 14
Two-phase partitioning bioreactors in fermentation technology
journal, November 2001
- Malinowski, Janusz J.
- Biotechnology Advances, Vol. 19, Issue 7
A mass spectrometry approach for the identification and localization of small aldehyde modifications of proteins
journal, May 2018
- Afonso, Catarina B.; Sousa, Bebiana C.; Pitt, Andrew R.
- Archives of Biochemistry and Biophysics, Vol. 646
Substrate channeling and enzyme complexes for biotechnological applications
journal, November 2011
- Zhang, Y. -H. Percival
- Biotechnology Advances, Vol. 29, Issue 6
Lysate of engineered Escherichia coli supports high-level conversion of glucose to 2,3-butanediol
journal, November 2015
- Kay, Jennifer E.; Jewett, Michael C.
- Metabolic Engineering, Vol. 32
Development of a commercial scale process for production of 1,4-butanediol from sugar
journal, December 2016
- Burgard, Anthony; Burk, Mark J.; Osterhout, Robin
- Current Opinion in Biotechnology, Vol. 42
Nanodiscs in Membrane Biochemistry and Biophysics
journal, February 2017
- Denisov, Ilia G.; Sligar, Stephen G.
- Chemical Reviews, Vol. 117, Issue 6
GPCR–styrene maleic acid lipid particles (GPCR–SMALPs): their nature and potential
journal, April 2016
- Wheatley, Mark; Charlton, Jack; Jamshad, Mohammed
- Biochemical Society Transactions, Vol. 44, Issue 2
Principles of Protein Stability and Their Application in Computational Design
journal, June 2018
- Goldenzweig, Adi; Fleishman, Sarel J.
- Annual Review of Biochemistry, Vol. 87, Issue 1
Recent advances in systems metabolic engineering tools and strategies
journal, October 2017
- Chae, Tong Un; Choi, So Young; Kim, Je Woong
- Current Opinion in Biotechnology, Vol. 47
Directed evolution of enzyme stability
journal, June 2005
- Eijsink, Vincent G. H.; Gåseidnes, Sigrid; Borchert, Torben V.
- Biomolecular Engineering, Vol. 22, Issue 1-3
Stabilizing membrane proteins
journal, August 2001
- Bowie, J.
- Current Opinion in Structural Biology, Vol. 11, Issue 4
An Overview of Bioinspired and Biomimetic Self-Repairing Materials
journal, March 2019
- Speck, Olga; Speck, Thomas
- Biomimetics, Vol. 4, Issue 1
Transforming biochemical engineering with cell-free biology
journal, December 2011
- Swartz, James R.
- AIChE Journal, Vol. 58, Issue 1
An integrated cell-free metabolic platform for protein production and synthetic biology
journal, October 2008
- Jewett, Michael C.; Calhoun, Kara A.; Voloshin, Alexei
- Molecular Systems Biology, Vol. 4, Issue 1, Article No. 220
‘Nothing of chemistry disappears in biology’: the Top 30 damage-prone endogenous metabolites
journal, June 2016
- Lerma-Ortiz, Claudia; Jeffryes, James G.; Cooper, Arthur J. L.
- Biochemical Society Transactions, Vol. 44, Issue 3
Efficient multi-enzyme-catalyzed CDP-choline production driven by an ATP donor module
journal, October 2016
- Liu, Yingmiao; Wang, Junzhi; Xu, Chongmao
- Applied Microbiology and Biotechnology, Vol. 101, Issue 4
Synthetic non-oxidative glycolysis enables complete carbon conservation
journal, September 2013
- Bogorad, Igor W.; Lin, Tzu-Shyang; Liao, James C.
- Nature, Vol. 502, Issue 7473
Alleviating monoterpene toxicity using a two-phase extractive fermentation for the bioproduction of jet fuel mixtures in Saccharomyces cerevisiae
journal, May 2012
- Brennan, Timothy C. R.; Turner, Christopher D.; Krömer, Jens O.
- Biotechnology and Bioengineering, Vol. 109, Issue 10
Rewriting yeast central carbon metabolism for industrial isoprenoid production
journal, September 2016
- Meadows, Adam L.; Hawkins, Kristy M.; Tsegaye, Yoseph
- Nature, Vol. 537, Issue 7622
A synthetic biochemistry platform for cell free production of monoterpenes from glucose
journal, May 2017
- Korman, Tyler P.; Opgenorth, Paul H.; Bowie, James U.
- Nature Communications, Vol. 8, Issue 1
Emerging Enzymes for ATP Regeneration in Biocatalytic Processes
journal, January 2015
- Andexer, Jennifer N.; Richter, Michael
- ChemBioChem, Vol. 16, Issue 3
Recent developments in pyridine nucleotide regeneration
journal, August 2003
- van der Donk, Wilfred A.; Zhao, Huimin
- Current Opinion in Biotechnology, Vol. 14, Issue 4
A high-energy-density sugar biobattery based on a synthetic enzymatic pathway
journal, January 2014
- Zhu, Zhiguang; Kin Tam, Tsz; Sun, Fangfang
- Nature Communications, Vol. 5, Issue 1
Yeast cell-free enzyme system for bio-ethanol production at elevated temperatures
journal, March 2014
- Khattak, Waleed Ahmad; Ul-Islam, Mazhar; Ullah, Muhammad Wajid
- Process Biochemistry, Vol. 49, Issue 3
A synthetic biochemistry molecular purge valve module that maintains redox balance
journal, June 2014
- Opgenorth, Paul H.; Korman, Tyler P.; Bowie, James U.
- Nature Communications, Vol. 5, Issue 1
Dynamic metabolic control: towards precision engineering of metabolism
journal, January 2018
- Liu, Di; Mannan, Ahmad A.; Han, Yichao
- Journal of Industrial Microbiology & Biotechnology, Vol. 45, Issue 7
An in vitro synthetic biology platform for the industrial biomanufacturing of myo-inositol from starch: Biomanufacturing by In Vitro Synthetic Biology
journal, May 2017
- You, Chun; Shi, Ting; Li, Yunjie
- Biotechnology and Bioengineering, Vol. 114, Issue 8
In vitro metabolic engineering of hydrogen production at theoretical yield from sucrose
journal, July 2014
- Myung, Suwan; Rollin, Joseph; You, Chun
- Metabolic Engineering, Vol. 24
Regeneration of cofactors for use in biocatalysis
journal, December 2003
- Zhao, Huimin; van der Donk, Wilfred A.
- Current Opinion in Biotechnology, Vol. 14, Issue 6
Challenges in Engineering Microbes for Biofuels Production
journal, February 2007
- Stephanopoulos, Gregory
- Science, Vol. 315, Issue 5813, p. 801-804
Building a Thermostable Membrane Protein
journal, March 2000
- Zhou, Yufeng; Bowie, James U.
- Journal of Biological Chemistry, Vol. 275, Issue 10
Cell-Free Metabolic Engineering: Production of Chemicals by Minimized Reaction Cascades
journal, October 2012
- Guterl, Jan-Karl; Garbe, Daniel; Carsten, Jörg
- ChemSusChem, Vol. 5, Issue 11
Cell-free synthetic biology: Thinking outside the cell
journal, May 2012
- Hodgman, C. Eric; Jewett, Michael C.
- Metabolic Engineering, Vol. 14, Issue 3
Diverse Bacterial Microcompartment Organelles
journal, September 2014
- Chowdhury, C.; Sinha, S.; Chun, S.
- Microbiology and Molecular Biology Reviews, Vol. 78, Issue 3
A cell-free platform for the prenylation of natural products and application to cannabinoid production
journal, February 2019
- Valliere, Meaghan A.; Korman, Tyler P.; Woodall, Nicholas B.
- Nature Communications, Vol. 10, Issue 1
A synthetic pathway for the fixation of carbon dioxide in vitro
journal, November 2016
- Schwander, Thomas; Schada von Borzyskowski, Lennart; Burgener, Simon
- Science, Vol. 354, Issue 6314
A review of beetle hindwings: Structure, mechanical properties, mechanism and bioinspiration
journal, June 2019
- Sun, Jiyu; Liu, Chao; Bhushan, Bharat
- Journal of the Mechanical Behavior of Biomedical Materials, Vol. 94
Mimicking theEscherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis
journal, January 2004
- Jewett, Michael C.; Swartz, James R.
- Biotechnology and Bioengineering, Vol. 86, Issue 1
A synthetic biochemistry system for the in vitro production of isoprene from glycolysis intermediates : Production of Isoprene from Glycolysis Intermediates
journal, March 2014
- Korman, Tyler P.; Sahachartsiri, Bobby; Li, Dan
- Protein Science, Vol. 23, Issue 5
Cell-free synthetic biology for in vitro prototype engineering
journal, June 2017
- Moore, Simon J.; MacDonald, James T.; Freemont, Paul S.
- Biochemical Society Transactions, Vol. 45, Issue 3
High-Yield Hydrogen Production from Starch and Water by a Synthetic Enzymatic Pathway
journal, May 2007
- Zhang, Y.-H. Percival; Evans, Barbara R.; Mielenz, Jonathan R.
- PLoS ONE, Vol. 2, Issue 5, Article No. e456
An artificial synthetic pathway for acetoin, 2,3-butanediol, and 2-butanol production from ethanol using cell free multi-enzyme catalysis
journal, January 2018
- Zhang, Liaoyuan; Singh, Raushan; D., Sivakumar
- Green Chemistry, Vol. 20, Issue 1
Biosynthesis of D-xylulose 5-phosphate from D-xylose and polyphosphate through a minimized two-enzyme cascade: Biosynthesis of D-Xylulose 5-Phosphate
journal, September 2015
- Kim, Jae-Eung; Zhang, Y. -H. Percival
- Biotechnology and Bioengineering, Vol. 113, Issue 2
Five hard truths for synthetic biology
journal, January 2010
- Kwok, Roberta
- Nature, Vol. 463, Issue 7279
Expanding biological applications using cell-free metabolic engineering: An overview
journal, November 2018
- Swartz, James R.
- Metabolic Engineering, Vol. 50
Structure and function of the radical enzyme ribonucleotide reductase
journal, November 2001
- Eklund, Hans; Uhlin, Ulla; Färnegårdh, Mathias
- Progress in Biophysics and Molecular Biology, Vol. 77, Issue 3
CO2 fixation for malate synthesis energized by starch via in vitro metabolic engineering
journal, September 2019
- Shi, Ting; Liu, Shan; Zhang, Yi-Heng P. Job
- Metabolic Engineering, Vol. 55
High-Yield Production of Dihydrogen from Xylose by Using a Synthetic Enzyme Cascade in a Cell-Free System
journal, March 2013
- Martín del Campo, Julia S.; Rollin, Joseph; Myung, Suwan
- Angewandte Chemie International Edition, Vol. 52, Issue 17
O 2 sensitivity and H 2 production activity of hydrogenases—A review
journal, August 2019
- Lu, Yuan; Koo, Jamin
- Biotechnology and Bioengineering, Vol. 116, Issue 11
Into new territory: improved microbial synthesis through engineering of the essential metabolic network
journal, April 2016
- Lynch, Michael D.
- Current Opinion in Biotechnology, Vol. 38