Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications

Lian, Jiazhang; Mishra, Shekhar; Zhao, Huimin

doi:10.1016/j.ymben.2018.04.011

Title: Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications

Abstract

Metabolic engineering aims to develop efficient cell factories by rewiring cellular metabolism. As one of the most commonly used cell factories, Saccharomyces cerevisiae has been extensively engineered to produce a wide variety of products at high levels from various feedstocks. In this paper, we summarize the recent development of metabolic engineering approaches to modulate yeast metabolism with representative examples. Particularly, we highlight new tools for biosynthetic pathway optimization (i.e. combinatorial transcriptional engineering and dynamic metabolic flux control) and genome engineering (i.e. clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) system based genome engineering and RNA interference assisted genome evolution) to advance metabolic engineering in yeast. Lastly, we also discuss the challenges and perspectives for high throughput metabolic engineering.

Authors:

^[1]; Mishra, Shekhar ^[2]; Zhao, Huimin ^[3]

Zhejiang Univ., Hangzhou (China). Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering; University of Illinois at Urbana-Champaign, Urbana, IL (United States). Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology
University of Illinois at Urbana-Champaign, Urbana, IL (United States). Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology
University of Illinois at Urbana-Champaign, Urbana, IL (United States). Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology and Departments of Chemistry, Biochemistry, and Bioengineering

Publication Date:: Wed Apr 25 00:00:00 EDT 2018

Research Org.:: Center for Advanced Bioenergy and Bioproducts (CABBI), Urbana, IL (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

OSTI Identifier:: 1436581

Grant/Contract Number:: SC0018420; SC0018260

Resource Type:: Accepted Manuscript

Journal Name:: Metabolic Engineering

Additional Journal Information:: Journal Volume: 50; Journal ID: ISSN 1096-7176

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Metabolic engineering; Pathway optimization; Genome engineering; Saccharomyces cerevisiae

Citation Formats


                    Lian, Jiazhang, Mishra, Shekhar, and Zhao, Huimin. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications.  United States: N. p., 2018. 
Web.  doi:10.1016/j.ymben.2018.04.011.

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                    Lian, Jiazhang, Mishra, Shekhar, & Zhao, Huimin. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications.  United States.  https://doi.org/10.1016/j.ymben.2018.04.011

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                    Lian, Jiazhang, Mishra, Shekhar, and Zhao, Huimin. Wed .  
"Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications".  United States.  https://doi.org/10.1016/j.ymben.2018.04.011.  https://www.osti.gov/servlets/purl/1436581.

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@article{osti_1436581,

  title        = {Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications},

  author       = {Lian, Jiazhang and Mishra, Shekhar and Zhao, Huimin},

  abstractNote = {Metabolic engineering aims to develop efficient cell factories by rewiring cellular metabolism. As one of the most commonly used cell factories, Saccharomyces cerevisiae has been extensively engineered to produce a wide variety of products at high levels from various feedstocks. In this paper, we summarize the recent development of metabolic engineering approaches to modulate yeast metabolism with representative examples. Particularly, we highlight new tools for biosynthetic pathway optimization (i.e. combinatorial transcriptional engineering and dynamic metabolic flux control) and genome engineering (i.e. clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated (Cas) system based genome engineering and RNA interference assisted genome evolution) to advance metabolic engineering in yeast. Lastly, we also discuss the challenges and perspectives for high throughput metabolic engineering.},

  doi          = {10.1016/j.ymben.2018.04.011},

  journal      = {Metabolic Engineering},

  number       = ,

  volume       = 50,

  place        = {United States},

  year         = {Wed Apr 25 00:00:00 EDT 2018},

  month        = {Wed Apr 25 00:00:00 EDT 2018}

}

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DOI: 10.1186/s12934-019-1096-y

Metabolic Engineering of Yeast for the Production of 3-Hydroxypropionic Acid
journal, September 2018

Ji, Rong-Yu; Ding, Ying; Shi, Tian-Qiong
Frontiers in Microbiology, Vol. 9
DOI: 10.3389/fmicb.2018.02185

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Title: Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications

Abstract

Citation Formats

Expanding the metabolic engineering toolbox with directed evolution journal, July 2013

Metabolic engineering of Saccharomyces cerevisiae â€ƒfor production of carboxylic acids: current status and challenges journal, December 2009

Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production journal, April 2013

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Systems metabolic engineering: Genome-scale models and beyond journal, February 2010

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Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals journal, February 2014

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Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae journal, March 2015

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Improved vanillin production in baker's yeast through in silico design journal, January 2010

Integration of metabolome data with metabolic networks reveals reporter reactions journal, January 2006

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches journal, April 2009

Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering journal, April 2017

Altered sterol composition renders yeast thermotolerant journal, October 2014

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Engineering biological systems using automated biofoundries journal, July 2017

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Engineering the Saccharomyces cerevisiae β-Oxidation Pathway to Increase Medium Chain Fatty Acid Production as Potential Biofuel journal, January 2014

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Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae journal, January 2016

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Directed evolution: Past, present, and future journal, January 2013

Multiplex Genome Engineering Using CRISPR/Cas Systems journal, January 2013

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Optimization of a Yeast RNA Interference System for Controlling Gene Expression and Enabling Rapid Metabolic Engineering journal, December 2013

Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications journal, September 2013

Metabolic engineering of muconic acid production in Saccharomyces cerevisiae journal, January 2013

Design of synthetic yeast promoters via tuning of nucleosome architecture journal, May 2014

Short Synthetic Terminators for Improved Heterologous Gene Expression in Yeast journal, February 2015

Flux Control at the Malonyl-CoA Node through Hierarchical Dynamic Pathway Regulation in Saccharomyces cerevisiae journal, January 2016

Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae journal, March 2017

Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae journal, June 2017

Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways journal, March 2016

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks journal, July 2017

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems journal, March 2013

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Fully automatized high-throughput enzyme library screening using a robotic platform: Fully Automatized High-Throughput Enzyme Library Screening journal, February 2016

Engineering microbial factories for synthesis of value-added products journal, April 2011

Customized optimization of metabolic pathways by combinatorial transcriptional engineering journal, June 2012

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Diversity-based, model-guided construction of synthetic gene networks with predicted functions journal, April 2009

Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production journal, May 2008

Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform journal, December 2013

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Protein design for pathway engineering journal, February 2014

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Investigating host dependence of xylose utilization in recombinant Saccharomyces cerevisiae strains using RNA-seq analysis journal, January 2013

Metabolic engineering of Saccharomyces cerevisiae to improve 1-hexadecanol production journal, January 2015

Engineering Saccharomyces cerevisiae for high-level synthesis of fatty acids and derived products journal, September 2017

Growth requirements of pyruvate-decarboxylase-negative Saccharomyces cerevisiae journal, May 1999

Expanding the metabolic engineering toolbox with directed evolution
journal, July 2013

Metabolic engineering of Saccharomyces cerevisiae â€ƒfor production of carboxylic acids: current status and challenges
journal, December 2009

Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production
journal, April 2013

Integration of gene expression data into genome-scale metabolic models
journal, October 2004

Diversion of Flux toward Sesquiterpene Production in Saccharomyces cerevisiae by Fusion of Host and Heterologous Enzymes
journal, February 2011

Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass : Adaptive Evolution for Hydrolysates Tolerance in Yeast
journal, July 2013

Kinetic models in industrial biotechnology – Improving cell factory performance
journal, July 2014

Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering
journal, March 2015

Tuning genetic control through promoter engineering
journal, August 2005

Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production
journal, December 2006

Simulation and validation of modelled sphingolipid metabolism in Saccharomyces cerevisiae
journal, January 2005

An endoplasmic reticulum-engineered yeast platform for overproduction of triterpenoids
journal, March 2017

Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
journal, November 2009

Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols
journal, February 2013

Homology-Integrated CRISPR–Cas (HI-CRISPR) System for One-Step Multigene Disruption in Saccharomyces cerevisiae
journal, September 2014

Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision
journal, May 2018

Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes
journal, November 2017

Synthesis of Methyl Halides from Biomass Using Engineered Microbes
journal, May 2009

Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae
journal, January 2009

Metabolic-flux and network analysis in fourteen hemiascomycetous yeasts
journal, April 2005

Systems metabolic engineering: Genome-scale models and beyond
journal, February 2010

Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters
journal, May 2012

Metabolic engineering of Saccharomyces cerevisiae for itaconic acid production
journal, July 2014

Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals
journal, February 2014

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journal, January 2015

Evolutionary Engineering Improves Tolerance for Replacement Jet Fuels in Saccharomyces cerevisiae
journal, March 2015

A comprehensive strategy enabling high-resolution functional analysis of the yeast genome
journal, July 2008

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
journal, November 2005

Improved vanillin production in baker's yeast through in silico design
journal, January 2010

Integration of metabolome data with metabolic networks reveals reporter reactions
journal, January 2006

A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches
journal, April 2009

Centromeric DNA Facilitates Nonconventional Yeast Genetic Engineering
journal, April 2017

Altered sterol composition renders yeast thermotolerant
journal, October 2014

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
journal, August 2013

Engineering biological systems using automated biofoundries
journal, July 2017

Highly efficient Cas9-mediated transcriptional programming
journal, March 2015

Engineering the Saccharomyces cerevisiae β-Oxidation Pathway to Increase Medium Chain Fatty Acid Production as Potential Biofuel
journal, January 2014

Enhancing the copy number of episomal plasmids in Saccharomyces cerevisiae for improved protein production
journal, April 2012

Profiling of Cytosolic and Peroxisomal Acetyl-CoA Metabolism in Saccharomyces cerevisiae
journal, August 2012

Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism
journal, January 2013

Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae
journal, March 2014

Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
journal, January 2016

Lycopene overproduction in Saccharomyces cerevisiae through combining pathway engineering with host engineering
journal, June 2016

Directed evolution: Past, present, and future
journal, January 2013

Multiplex Genome Engineering Using CRISPR/Cas Systems
journal, January 2013

In vivo continuous evolution of genes and pathways in yeast
journal, October 2016

Optimization of a Yeast RNA Interference System for Controlling Gene Expression and Enabling Rapid Metabolic Engineering
journal, December 2013

Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications
journal, September 2013

Metabolic engineering of muconic acid production in Saccharomyces cerevisiae
journal, January 2013

Design of synthetic yeast promoters via tuning of nucleosome architecture
journal, May 2014

Short Synthetic Terminators for Improved Heterologous Gene Expression in Yeast
journal, February 2015

Flux Control at the Malonyl-CoA Node through Hierarchical Dynamic Pathway Regulation in Saccharomyces cerevisiae
journal, January 2016

Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae
journal, March 2017

Enabling Graded and Large-Scale Multiplex of Desired Genes Using a Dual-Mode dCas9 Activator in Saccharomyces cerevisiae
journal, June 2017

Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways
journal, March 2016

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks
journal, July 2017

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
journal, March 2013

Biosynthesis of Taxadiene in Saccharomyces cerevisiae : Selection of Geranylgeranyl Diphosphate Synthase Directed by a Computer-Aided Docking Strategy
journal, October 2014

Effects of overproduction of the catalytic domain of 3-hydroxy-3-methylglutaryl coenzyme A reductase on squalene synthesis in Saccharomyces cerevisiae.
journal, January 1997

Fully automatized high-throughput enzyme library screening using a robotic platform: Fully Automatized High-Throughput Enzyme Library Screening
journal, February 2016

Engineering microbial factories for synthesis of value-added products
journal, April 2011

Customized optimization of metabolic pathways by combinatorial transcriptional engineering
journal, June 2012

Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
journal, June 2004

Diversity-based, model-guided construction of synthetic gene networks with predicted functions
journal, April 2009

Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production
journal, May 2008

Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform
journal, December 2013

The presence of a defective LEU2 gene on 2 mu DNA recombinant plasmids of Saccharomyces cerevisiae is responsible for curing and high copy number
journal, November 1983

Directed evolution of a cellobiose utilization pathway in Saccharomyces cerevisiae by simultaneously engineering multiple proteins
journal, January 2013

Protein design for pathway engineering
journal, February 2014

Harnessing yeast subcellular compartments for the production of plant terpenoids
journal, September 2011

Molecular Characterization of a Heteromeric ATP-Citrate Lyase That Generates Cytosolic Acetyl-Coenzyme A in Arabidopsis
journal, October 2002

Genome-Scale Modeling of the Protein Secretory Machinery in Yeast
journal, May 2013

Investigating glucose and xylose metabolism in Saccharomyces cerevisiae and Scheffersomyces stipitis via ¹³ C metabolic flux analysis
journal, August 2013

Investigating host dependence of xylose utilization in recombinant Saccharomyces cerevisiae strains using RNA-seq analysis
journal, January 2013

Metabolic engineering of Saccharomyces cerevisiae to improve 1-hexadecanol production
journal, January 2015

Engineering Saccharomyces cerevisiae for high-level synthesis of fatty acids and derived products
journal, September 2017

Growth requirements of pyruvate-decarboxylase-negative Saccharomyces cerevisiae
journal, May 1999

Genome-Scale Reconstruction of the Saccharomyces cerevisiae Metabolic Network
journal, February 2003

Complete biosynthesis of opioids in yeast
journal, August 2015

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
journal, December 2016