A framework for the identification of promising bio-based chemicals

Wu, Wenzhao; Long, Matthew R.; Zhang, Xiaolin; Reed, Jennifer L.; Maravelias, Christos T.

doi:10.1002/bit.26779

Title: 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 »« less

Authors:

^[1]; Long, Matthew R. ^[1]; Zhang, Xiaolin ^[1]; Reed, Jennifer L. ^[1];

^[1]

Univ. of Wisconsin, Madison, WI (United States)

Publication Date:: 2018-06-25

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.

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                    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

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                    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.

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@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}

}

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Title: A framework for the identification of promising bio-based chemicals

Abstract

Citation Formats

Metabolic engineering approaches for production of biochemicals in food and medicinal plants journal, April 2014

Metabolic assessment of E. coli as a Biofactory for commercial products journal, May 2016

A systems engineering perspective on process integration in industrial biotechnology: Process integration in industrial biotechnology journal, November 2014

Connecting extracellular metabolomic measurements to intracellular flux states in yeast journal, January 2009

Automated Generation and Optimal Selection of Biofuel-Gasoline Blends and Their Synthesis Routes journal, May 2013

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks journal, August 2008

Production Rate-Dependent Key Performance Indicators for a Systematic Design of Biochemical Downstream Processes journal, January 2016

Growth of wildtype and mutant E. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides journal, August 2010

The future of metabolic engineering and synthetic biology: Towards a systematic practice journal, May 2012

KEGG: new perspectives on genomes, pathways, diseases and drugs journal, November 2016

A superstructure representation, generation, and modeling framework for chemical process synthesis journal, June 2016

Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution journal, October 1991

Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models journal, July 2013

A framework for efficient large scale equation-oriented flowsheet optimization journal, January 2015

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases journal, November 2015

Production of biofuels and biochemicals: in need of an ORACLE journal, August 2010

A roadmap for the synthesis of separation networks for the recovery of bio-based chemicals: Matching biological and process feasibility journal, December 2016

A novel framework for simultaneous separation process and product design journal, May 2004

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Bioseparations journal, January 2004

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization journal, October 2003

Surrogate-based superstructure optimization framework journal, June 2010

Biomass in the manufacture of industrial products—the use of proteins and amino acids journal, March 2007

Biotechnology—a sustainable alternative for chemical industry journal, November 2005

A Framework for the Systematic Design of Hybrid Separation Processes journal, June 2008

Metabolic engineering under uncertainty. I: Framework development journal, March 2006

Constraint-based models predict metabolic and associated cellular functions journal, January 2014

Opportunities for yeast metabolic engineering: Lessons from synthetic biology journal, February 2011

KEGG: Kyoto Encyclopedia of Genes and Genomes journal, January 1999

KEGG as a reference resource for gene and protein annotation journal, October 2015

The biomass objective function journal, June 2010

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design journal, February 2014

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011 journal, January 2011

A review of separation technologies in current and future biorefineries journal, August 2008

Simultaneous Optimization Model for Multicomponent Separation journal, January 1994

Genome-scale microbial in silico models: the constraints-based approach journal, April 2003

Expanding the metabolic engineering toolbox more options to engineer cells journal, March 2007

Editorial overview: Chemical biotechnology: Interdisciplinary concepts for modern biotechnological production of biochemicals and biofuels journal, December 2015

Equations and calculations for fermentations of butyric acid bacteria journal, March 2000

Innovation at the intersection of synthetic and systems biology journal, October 2012

Top value platform chemicals: bio-based production of organic acids journal, December 2015

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli journal, May 2010

OptStrain: A computational framework for redesign of microbial production systems journal, November 2004

Design and optimization of energy efficient complex separation networks journal, September 2010

A superstructure-based framework for bio-separation network synthesis journal, January 2017

Catalytic conversion of biomass-derived feedstocks into olefins and aromatics with ZSM-5: the hydrogen to carbon effective ratio journal, January 2011

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis journal, September 2010

Systems biology as a foundation for genome-scale synthetic biology journal, October 2006

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries journal, March 2012

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions journal, January 2010

Metabolic engineering of yeast for production of fuels and chemicals journal, June 2013

A review of process synthesis journal, May 1981

An Economic Impact Analysis of the US Biobased Products Industry: A Report to the Congress of the United States of America journal, August 2015

Developing new platform chemicals: what is required for a new bio-based molecule to become a platform chemical in the bioeconomy? journal, January 2017

Synthesis of nanogel–protein conjugates journal, January 2013

Synthesis of optimal process flowsheets by an infeasible decomposition technique in the presence of functional non-convexities journal, October 1975

Engineering synergy in biotechnology journal, April 2014

Design of integrated biorefineries journal, October 2015

Beyond Petrochemicals: The Renewable Chemicals Industry journal, October 2011

The model organism as a system: integrating 'omics' data sets journal, March 2006

Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals journal, November 2015

A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation journal, July 2010

Model-Based Design of Tailor-Made Biofuels journal, February 2016

A market‐driven algorithm for the assessment of promising bio‐based chemicals journal, September 2019

Streamlined assessment of membrane permeability and its application to membrane engineering of Escherichia coli for octanoic acid tolerance journal, February 2019

Solvent system for effective near-term production of hydroxymethylfurfural (HMF) with potential for long-term process improvement journal, January 2019

Synthesis and analysis of separation processes for extracellular chemicals generated from microbial conversions journal, October 2019

Metabolic engineering approaches for production of biochemicals in food and medicinal plants
journal, April 2014

Metabolic assessment of E. coli as a Biofactory for commercial products
journal, May 2016

A systems engineering perspective on process integration in industrial biotechnology: Process integration in industrial biotechnology
journal, November 2014

Connecting extracellular metabolomic measurements to intracellular flux states in yeast
journal, January 2009

Automated Generation and Optimal Selection of Biofuel-Gasoline Blends and Their Synthesis Routes
journal, May 2013

Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks
journal, August 2008

Production Rate-Dependent Key Performance Indicators for a Systematic Design of Biochemical Downstream Processes
journal, January 2016

Growth of wildtype and mutant E. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides
journal, August 2010

The future of metabolic engineering and synthetic biology: Towards a systematic practice
journal, May 2012

KEGG: new perspectives on genomes, pathways, diseases and drugs
journal, November 2016

A superstructure representation, generation, and modeling framework for chemical process synthesis
journal, June 2016

Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution
journal, October 1991

Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models
journal, July 2013

A framework for efficient large scale equation-oriented flowsheet optimization
journal, January 2015

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
journal, November 2015

Production of biofuels and biochemicals: in need of an ORACLE
journal, August 2010

A roadmap for the synthesis of separation networks for the recovery of bio-based chemicals: Matching biological and process feasibility
journal, December 2016

A novel framework for simultaneous separation process and product design
journal, May 2004

Metabolic Engineering: Past and Future
journal, June 2013

Bio-based production of C2-C6 platform chemicals
journal, July 2012

Bioseparations
journal, January 2004

Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
journal, October 2003

Surrogate-based superstructure optimization framework
journal, June 2010

Biomass in the manufacture of industrial products—the use of proteins and amino acids
journal, March 2007

Biotechnology—a sustainable alternative for chemical industry
journal, November 2005

A Framework for the Systematic Design of Hybrid Separation Processes
journal, June 2008

Metabolic engineering under uncertainty. I: Framework development
journal, March 2006

Constraint-based models predict metabolic and associated cellular functions
journal, January 2014

Opportunities for yeast metabolic engineering: Lessons from synthetic biology
journal, February 2011

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999

KEGG as a reference resource for gene and protein annotation
journal, October 2015

The biomass objective function
journal, June 2010

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
journal, February 2014

A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011
journal, January 2011

A review of separation technologies in current and future biorefineries
journal, August 2008

Simultaneous Optimization Model for Multicomponent Separation
journal, January 1994

Genome-scale microbial in silico models: the constraints-based approach
journal, April 2003

Expanding the metabolic engineering toolbox more options to engineer cells
journal, March 2007

Editorial overview: Chemical biotechnology: Interdisciplinary concepts for modern biotechnological production of biochemicals and biofuels
journal, December 2015

Equations and calculations for fermentations of butyric acid bacteria
journal, March 2000

Innovation at the intersection of synthetic and systems biology
journal, October 2012

Top value platform chemicals: bio-based production of organic acids
journal, December 2015

Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
journal, May 2010

OptStrain: A computational framework for redesign of microbial production systems
journal, November 2004

Design and optimization of energy efficient complex separation networks
journal, September 2010

A superstructure-based framework for bio-separation network synthesis
journal, January 2017

Catalytic conversion of biomass-derived feedstocks into olefins and aromatics with ZSM-5: the hydrogen to carbon effective ratio
journal, January 2011

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
journal, September 2010

Systems biology as a foundation for genome-scale synthetic biology
journal, October 2006

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries
journal, March 2012

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
journal, January 2010

Metabolic engineering of yeast for production of fuels and chemicals
journal, June 2013

A review of process synthesis
journal, May 1981

An Economic Impact Analysis of the US Biobased Products Industry: A Report to the Congress of the United States of America
journal, August 2015

Developing new platform chemicals: what is required for a new bio-based molecule to become a platform chemical in the bioeconomy?
journal, January 2017

Synthesis of nanogel–protein conjugates
journal, January 2013

Synthesis of optimal process flowsheets by an infeasible decomposition technique in the presence of functional non-convexities
journal, October 1975

Engineering synergy in biotechnology
journal, April 2014

Design of integrated biorefineries
journal, October 2015

Beyond Petrochemicals: The Renewable Chemicals Industry
journal, October 2011

The model organism as a system: integrating 'omics' data sets
journal, March 2006

Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals
journal, November 2015

A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation
journal, July 2010

Model-Based Design of Tailor-Made Biofuels
journal, February 2016

A market‐driven algorithm for the assessment of promising bio‐based chemicals
journal, September 2019

Streamlined assessment of membrane permeability and its application to membrane engineering of Escherichia coli for octanoic acid tolerance
journal, February 2019

Solvent system for effective near-term production of hydroxymethylfurfural (HMF) with potential for long-term process improvement
journal, January 2019

Synthesis and analysis of separation processes for extracellular chemicals generated from microbial conversions
journal, October 2019