A framework for the identification of promising bio-based chemicals
Abstract
Recent progress in metabolic engineering and synthetic biology enables the use of microorganisms for the production of chemicals (“bio-based chemicals”). Yet, it is still unclear which chemicals have the highest economic prospect. Because of this, we develop a framework for the identification of such promising ones. Specifically, we first develop a genome-scale constraintbased metabolic modeling approach, which is used to identify a candidate pool of 209 chemicals (together with the estimated yield, productivity and residence time for each) from the intersection of the High-Production-Volume (HPV) chemicals and the KEGG and MetaCyc databases. Second, we design three screening criteria based on a chemical’s profit margin, market volume and market size. The total process cost, including the downstream separation cost, is systematically incorporated into the evaluation. Third, given the three aforementioned criteria, we identify 32 products as economically promising if the maximum yields can be achieved, and 22 products if the maximum productivities can be achieved. The breakeven titer that renders zero profit margin for each product is also presented. Comparisons between extracellular and intracellular production, as well as E. coli and S. cerevisiae systems are also discussed. The proposed framework provides important guidance for future studies in the production of bio-basedmore »
- Authors:
-
- Univ. of Wisconsin, Madison, WI (United States)
- Publication Date:
- Research Org.:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1506073
- Grant/Contract Number:
- SC0018409; FC02–07ER64494
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Biotechnology and Bioengineering
- Additional Journal Information:
- Journal Volume: 115; Journal Issue: 9; Journal ID: ISSN 0006-3592
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; bio‐based chemicals; value‐added chemicals; HPV chemicals; bio‐conversion; flux balance analysis; biorefinery
Citation Formats
Wu, Wenzhao, Long, Matthew R., Zhang, Xiaolin, Reed, Jennifer L., and Maravelias, Christos T. A framework for the identification of promising bio-based chemicals. United States: N. p., 2018.
Web. doi:10.1002/bit.26779.
Wu, Wenzhao, Long, Matthew R., Zhang, Xiaolin, Reed, Jennifer L., & Maravelias, Christos T. A framework for the identification of promising bio-based chemicals. United States. https://doi.org/10.1002/bit.26779
Wu, Wenzhao, Long, Matthew R., Zhang, Xiaolin, Reed, Jennifer L., and Maravelias, Christos T. Mon .
"A framework for the identification of promising bio-based chemicals". United States. https://doi.org/10.1002/bit.26779. https://www.osti.gov/servlets/purl/1506073.
@article{osti_1506073,
title = {A framework for the identification of promising bio-based chemicals},
author = {Wu, Wenzhao and Long, Matthew R. and Zhang, Xiaolin and Reed, Jennifer L. and Maravelias, Christos T.},
abstractNote = {Recent progress in metabolic engineering and synthetic biology enables the use of microorganisms for the production of chemicals (“bio-based chemicals”). Yet, it is still unclear which chemicals have the highest economic prospect. Because of this, we develop a framework for the identification of such promising ones. Specifically, we first develop a genome-scale constraintbased metabolic modeling approach, which is used to identify a candidate pool of 209 chemicals (together with the estimated yield, productivity and residence time for each) from the intersection of the High-Production-Volume (HPV) chemicals and the KEGG and MetaCyc databases. Second, we design three screening criteria based on a chemical’s profit margin, market volume and market size. The total process cost, including the downstream separation cost, is systematically incorporated into the evaluation. Third, given the three aforementioned criteria, we identify 32 products as economically promising if the maximum yields can be achieved, and 22 products if the maximum productivities can be achieved. The breakeven titer that renders zero profit margin for each product is also presented. Comparisons between extracellular and intracellular production, as well as E. coli and S. cerevisiae systems are also discussed. The proposed framework provides important guidance for future studies in the production of bio-based chemicals. It is also flexible in that the databases, yield estimations, and criteria can be modified to customize the screening.},
doi = {10.1002/bit.26779},
journal = {Biotechnology and Bioengineering},
number = 9,
volume = 115,
place = {United States},
year = {2018},
month = {6}
}
Web of Science
Works referenced in this record:
Metabolic engineering approaches for production of biochemicals in food and medicinal plants
journal, April 2014
- Wilson, Sarah A.; Roberts, Susan C.
- Current Opinion in Biotechnology, Vol. 26
Metabolic assessment of E. coli as a Biofactory for commercial products
journal, May 2016
- Zhang, Xiaolin; Tervo, Christopher J.; Reed, Jennifer L.
- Metabolic Engineering, Vol. 35
A systems engineering perspective on process integration in industrial biotechnology: Process integration in industrial biotechnology
journal, November 2014
- Kiss, Anton A.; Grievink, Johan; Rito-Palomares, Marco
- Journal of Chemical Technology & Biotechnology, Vol. 90, Issue 3
Connecting extracellular metabolomic measurements to intracellular flux states in yeast
journal, January 2009
- Mo, Monica L.; Palsson, Bernhard Ø; Herrgård, Markus J.
- BMC Systems Biology, Vol. 3, Issue 1
Automated Generation and Optimal Selection of Biofuel-Gasoline Blends and Their Synthesis Routes
journal, May 2013
- Marvin, W. Alex; Rangarajan, Srinivas; Daoutidis, Prodromos
- Energy & Fuels, Vol. 27, Issue 6
Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
journal, August 2008
- Jankowski, Matthew D.; Henry, Christopher S.; Broadbelt, Linda J.
- Biophysical Journal, Vol. 95, Issue 3
Production Rate-Dependent Key Performance Indicators for a Systematic Design of Biochemical Downstream Processes
journal, January 2016
- Brandt, Katrin; Schembecker, Gerhard
- Chemical Engineering & Technology, Vol. 39, Issue 2
Growth of wildtype and mutant E. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides
journal, August 2010
- Thakur, Chandar S.; Brown, Margaret E.; Sama, Jacob N.
- Applied Microbiology and Biotechnology, Vol. 88, Issue 3
The future of metabolic engineering and synthetic biology: Towards a systematic practice
journal, May 2012
- Yadav, Vikramaditya G.; De Mey, Marjan; Giaw Lim, Chin
- Metabolic Engineering, Vol. 14, Issue 3
KEGG: new perspectives on genomes, pathways, diseases and drugs
journal, November 2016
- Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao
- Nucleic Acids Research, Vol. 45, Issue D1
A superstructure representation, generation, and modeling framework for chemical process synthesis
journal, June 2016
- Wu, WenZhao; Henao, Carlos A.; Maravelias, Christos T.
- AIChE Journal, Vol. 62, Issue 9
Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution
journal, October 1991
- Mavrovouniotis, Michael L.
- Biotechnology and Bioengineering, Vol. 38, Issue 7
Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models
journal, July 2013
- Hamilton, Joshua J.; Dwivedi, Vivek; Reed, Jennifer L.
- Biophysical Journal, Vol. 105, Issue 2
A framework for efficient large scale equation-oriented flowsheet optimization
journal, January 2015
- Dowling, Alexander W.; Biegler, Lorenz T.
- Computers & Chemical Engineering, Vol. 72
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
journal, November 2015
- Caspi, Ron; Billington, Richard; Ferrer, Luciana
- Nucleic Acids Research, Vol. 44, Issue D1
Production of biofuels and biochemicals: in need of an ORACLE
journal, August 2010
- Miskovic, Ljubisa; Hatzimanikatis, Vassily
- Trends in Biotechnology, Vol. 28, Issue 8
A roadmap for the synthesis of separation networks for the recovery of bio-based chemicals: Matching biological and process feasibility
journal, December 2016
- Yenkie, Kirti M.; Wu, WenZhao; Clark, Ryan L.
- Biotechnology Advances, Vol. 34, Issue 8
A novel framework for simultaneous separation process and product design
journal, May 2004
- Eden, M. R.; Jørgensen, S. B.; Gani, R.
- Chemical Engineering and Processing: Process Intensification, Vol. 43, Issue 5
Metabolic Engineering: Past and Future
journal, June 2013
- Woolston, Benjamin M.; Edgar, Steven; Stephanopoulos, Gregory
- Annual Review of Chemical and Biomolecular Engineering, Vol. 4, Issue 1
Bio-based production of C2-C6 platform chemicals
journal, July 2012
- Jang, Yu-Sin; Kim, Byoungjin; Shin, Jae Ho
- Biotechnology and Bioengineering, Vol. 109, Issue 10
Bioseparations
journal, January 2004
- Lightfoot, E. N.; Moscariello, J. S.
- Biotechnology and Bioengineering, Vol. 87, Issue 3
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
journal, October 2003
- Burgard, Anthony P.; Pharkya, Priti; Maranas, Costas D.
- Biotechnology and Bioengineering, Vol. 84, Issue 6
Surrogate-based superstructure optimization framework
journal, June 2010
- Henao, Carlos A.; Maravelias, Christos T.
- AIChE Journal, Vol. 57, Issue 5
Biomass in the manufacture of industrial products—the use of proteins and amino acids
journal, March 2007
- Scott, Elinor; Peter, Francisc; Sanders, Johan
- Applied Microbiology and Biotechnology, Vol. 75, Issue 4
Biotechnology—a sustainable alternative for chemical industry
journal, November 2005
- Gavrilescu, Maria; Chisti, Yusuf
- Biotechnology Advances, Vol. 23, Issue 7-8
A Framework for the Systematic Design of Hybrid Separation Processes
journal, June 2008
- Marquardt, Wolfgang; Kossack, Sven; Kraemer, Korbinian
- Chinese Journal of Chemical Engineering, Vol. 16, Issue 3
Metabolic engineering under uncertainty. I: Framework development
journal, March 2006
- Wang, L.; Hatzimanikatis, V.
- Metabolic Engineering, Vol. 8, Issue 2
Constraint-based models predict metabolic and associated cellular functions
journal, January 2014
- Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A.
- Nature Reviews Genetics, Vol. 15, Issue 2
Opportunities for yeast metabolic engineering: Lessons from synthetic biology
journal, February 2011
- Krivoruchko, Anastasia; Siewers, Verena; Nielsen, Jens
- Biotechnology Journal, Vol. 6, Issue 3
KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999
- Ogata, H.; Goto, S.; Sato, K.
- Nucleic Acids Research, Vol. 27, Issue 1
KEGG as a reference resource for gene and protein annotation
journal, October 2015
- Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki
- Nucleic Acids Research, Vol. 44, Issue D1
The biomass objective function
journal, June 2010
- Feist, Adam M.; Palsson, Bernhard O.
- Current Opinion in Microbiology, Vol. 13, Issue 3
k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
journal, February 2014
- Chowdhury, Anupam; Zomorrodi, Ali R.; Maranas, Costas D.
- PLoS Computational Biology, Vol. 10, Issue 2
A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
journal, January 2011
- Orth, Jeffrey D.; Conrad, Tom M.; Na, Jessica
- Molecular Systems Biology, Vol. 7, Issue 1
A review of separation technologies in current and future biorefineries
journal, August 2008
- Huang, Hua-Jiang; Ramaswamy, Shri; Tschirner, U. W.
- Separation and Purification Technology, Vol. 62, Issue 1
Simultaneous Optimization Model for Multicomponent Separation
journal, January 1994
- Novak, Zorka; Kravanja, Zdravko; Grossmann, Ignacio E.
- Computers & Chemical Engineering, Vol. 18
Genome-scale microbial in silico models: the constraints-based approach
journal, April 2003
- Price, Nathan D.; Papin, Jason A.; Schilling, Christophe H.
- Trends in Biotechnology, Vol. 21, Issue 4
Expanding the metabolic engineering toolbox more options to engineer cells
journal, March 2007
- Tyo, Keith E.; Alper, Hal S.; Stephanopoulos, Gregory N.
- Trends in Biotechnology, Vol. 25, Issue 3, p. 132-137
Editorial overview: Chemical biotechnology: Interdisciplinary concepts for modern biotechnological production of biochemicals and biofuels
journal, December 2015
- Bornscheuer, Uwe T.; Nielsen, Alex Toftgaard
- Current Opinion in Biotechnology, Vol. 35
Equations and calculations for fermentations of butyric acid bacteria
journal, March 2000
- Papoutsakis, Eleftherios Terry
- Biotechnology and Bioengineering, Vol. 67, Issue 6
Innovation at the intersection of synthetic and systems biology
journal, October 2012
- Lanza, Amanda M.; Crook, Nathan C.; Alper, Hal S.
- Current Opinion in Biotechnology, Vol. 23, Issue 5
Top value platform chemicals: bio-based production of organic acids
journal, December 2015
- Becker, Judith; Lange, Anna; Fabarius, Jonathan
- Current Opinion in Biotechnology, Vol. 36
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
journal, May 2010
- Feist, Adam M.; Zielinski, Daniel C.; Orth, Jeffrey D.
- Metabolic Engineering, Vol. 12, Issue 3, p. 173-186
OptStrain: A computational framework for redesign of microbial production systems
journal, November 2004
- Pharkya, P.
- Genome Research, Vol. 14, Issue 11
Design and optimization of energy efficient complex separation networks
journal, September 2010
- Ruiz, Gerardo J.; Kim, Seon B.; Moon, Jeonghwa
- Computers & Chemical Engineering, Vol. 34, Issue 9
A superstructure-based framework for bio-separation network synthesis
journal, January 2017
- Wu, Wenzhao; Yenkie, Kirti; Maravelias, Christos T.
- Computers & Chemical Engineering, Vol. 96
Catalytic conversion of biomass-derived feedstocks into olefins and aromatics with ZSM-5: the hydrogen to carbon effective ratio
journal, January 2011
- Zhang, Huiyan; Cheng, Yu-Ting; Vispute, Tushar P.
- Energy & Environmental Science, Vol. 4, Issue 6, p. 2297-2307
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
journal, September 2010
- Chandrasekaran, Sriram; Price, Nathan D.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 41
Systems biology as a foundation for genome-scale synthetic biology
journal, October 2006
- Barrett, Christian L.; Kim, Tae Yong; Kim, Hyun Uk
- Current Opinion in Biotechnology, Vol. 17, Issue 5
Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries
journal, March 2012
- Hong, Kuk-Ki; Nielsen, Jens
- Cellular and Molecular Life Sciences, Vol. 69, Issue 16
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
journal, January 2010
- Schellenberger, Jan; Park, Junyoung O.; Conrad, Tom M.
- BMC Bioinformatics, Vol. 11, Issue 1
Metabolic engineering of yeast for production of fuels and chemicals
journal, June 2013
- Nielsen, Jens; Larsson, Christer; van Maris, Antonius
- Current Opinion in Biotechnology, Vol. 24, Issue 3
A review of process synthesis
journal, May 1981
- Nishida, Naonori; Stephanopoulos, George; Westerberg, A. W.
- AIChE Journal, Vol. 27, Issue 3
An Economic Impact Analysis of the US Biobased Products Industry: A Report to the Congress of the United States of America
journal, August 2015
- Golden, Jay S.; Handfield, Robert B.; Daystar, Jesse
- Industrial Biotechnology, Vol. 11, Issue 4
Developing new platform chemicals: what is required for a new bio-based molecule to become a platform chemical in the bioeconomy?
journal, January 2017
- Bomtempo, José-Vitor; Chaves Alves, Flavia; de Almeida Oroski, Fabio
- Faraday Discuss., Vol. 202
Synthesis of nanogel–protein conjugates
journal, January 2013
- Matsumoto, Nicholas M.; González-Toro, Daniella C.; Chacko, Reuben T.
- Polymer Chemistry, Vol. 4, Issue 8
Synthesis of optimal process flowsheets by an infeasible decomposition technique in the presence of functional non-convexities
journal, October 1975
- Stephanopoulos, George; Westerberg, Arthur W.
- The Canadian Journal of Chemical Engineering, Vol. 53, Issue 5
Engineering synergy in biotechnology
journal, April 2014
- Nielsen, Jens; Fussenegger, Martin; Keasling, Jay
- Nature Chemical Biology, Vol. 10, Issue 5
Design of integrated biorefineries
journal, October 2015
- Kokossis, A. C.; Tsakalova, M.; Pyrgakis, K.
- Computers & Chemical Engineering, Vol. 81
Beyond Petrochemicals: The Renewable Chemicals Industry
journal, October 2011
- Vennestrøm, P. N. R.; Osmundsen, C. M.; Christensen, C. H.
- Angewandte Chemie International Edition, Vol. 50, Issue 45
The model organism as a system: integrating 'omics' data sets
journal, March 2006
- Joyce, Andrew R.; Palsson, Bernhard Ø.
- Nature Reviews Molecular Cell Biology, Vol. 7, Issue 3
Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals
journal, November 2015
- Jullesson, David; David, Florian; Pfleger, Brian
- Biotechnology Advances, Vol. 33, Issue 7
A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation
journal, July 2010
- Nicolaou, Sergios A.; Gaida, Stefan M.; Papoutsakis, Eleftherios T.
- Metabolic Engineering, Vol. 12, Issue 4
Model-Based Design of Tailor-Made Biofuels
journal, February 2016
- Dahmen, Manuel; Marquardt, Wolfgang
- Energy & Fuels, Vol. 30, Issue 2
Works referencing / citing this record:
A market‐driven algorithm for the assessment of promising bio‐based chemicals
journal, September 2019
- Helal, Agustín; Kreimerman, Roberto; Gutiérrez, Soledad
- AIChE Journal, Vol. 65, Issue 12
Streamlined assessment of membrane permeability and its application to membrane engineering of Escherichia coli for octanoic acid tolerance
journal, February 2019
- Santoscoy, Miguel C.; Jarboe, Laura R.
- Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 6
Solvent system for effective near-term production of hydroxymethylfurfural (HMF) with potential for long-term process improvement
journal, January 2019
- Motagamwala, Ali Hussain; Huang, Kefeng; Maravelias, Christos T.
- Energy & Environmental Science, Vol. 12, Issue 7
Synthesis and analysis of separation processes for extracellular chemicals generated from microbial conversions
journal, October 2019
- Wu, Wenzhao; Yenkie, Kirti M.; Maravelias, Christos T.
- BMC Chemical Engineering, Vol. 1, Issue 1