New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

Santos-Merino, María; Singh, Amit K.; Ducat, Daniel C.

doi:10.3389/fbioe.2019.00033

Title: New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

Abstract

Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.

Authors:: Santos-Merino, María; Singh, Amit K.; Ducat, Daniel C.

Publication Date:: Wed Feb 27 00:00:00 EST 2019

Research Org.:: Michigan State Univ., East Lansing, MI (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1496889

Alternate Identifier(s):: OSTI ID: 1610156

Grant/Contract Number:: FG02-91ER20021

Resource Type:: Published Article

Journal Name:: Frontiers in Bioengineering and Biotechnology

Additional Journal Information:: Journal Name: Frontiers in Bioengineering and Biotechnology Journal Volume: 7; Journal ID: ISSN 2296-4185

Publisher:: Frontiers Research Foundation

Country of Publication:: Switzerland

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; cyanobacteria; metabolic engineering; synthetic biology; genome scale models; photosynthesis

Citation Formats


                    Santos-Merino, María, Singh, Amit K., and Ducat, Daniel C. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering.  Switzerland: N. p., 2019. 
Web.  doi:10.3389/fbioe.2019.00033.

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                    Santos-Merino, María, Singh, Amit K., & Ducat, Daniel C. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering.  Switzerland.  https://doi.org/10.3389/fbioe.2019.00033

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                    Santos-Merino, María, Singh, Amit K., and Ducat, Daniel C. Wed .  
"New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering".  Switzerland.  https://doi.org/10.3389/fbioe.2019.00033.

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@article{osti_1496889,

  title        = {New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering},

  author       = {Santos-Merino, María and Singh, Amit K. and Ducat, Daniel C.},

  abstractNote = {Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.},

  doi          = {10.3389/fbioe.2019.00033},

  journal      = {Frontiers in Bioengineering and Biotechnology},

  number       = ,

  volume       = 7,

  place        = {Switzerland},

  year         = {Wed Feb 27 00:00:00 EST 2019},

  month        = {Wed Feb 27 00:00:00 EST 2019}

}

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Title: New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering

Abstract

Citation Formats

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Dynamic Localization of the Cyanobacterial Circadian Clock Proteins
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Metabolic model of Synechococcus sp. PCC 7002: Prediction of flux distribution and network modification for enhanced biofuel production
journal, August 2016

Cpf1 Is A Versatile Tool for CRISPR Genome Editing Across Diverse Species of Cyanobacteria
journal, December 2016

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journal, August 2017

Metabolic engineering of cyanobacteria for the synthesis of commodity products
journal, June 2015

Toward systems metabolic engineering in cyanobacteria: Opportunities and bottlenecks
journal, May 2013

Standardization in synthetic biology: an engineering discipline coming of age
journal, September 2017

Evidence for an NIH shift in oxidation of naphthalene by the marine cyanobacterium Oscillatoria sp. strain JCM.
journal, January 1992

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
journal, August 2003

Reconstruction and verification of a genome-scale metabolic model for Synechocystis sp. PCC6803
journal, September 2011

Metabolic engineering of the pentose phosphate pathway for enhanced limonene production in the cyanobacterium Synechocysti s sp. PCC 6803
journal, December 2017

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 2000

Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803
journal, October 2012

High-Frequency Gene Replacement in Cyanobacteria Using a Heterologous rps12 Gene
journal, March 2004

Cyanobacteria and microalgae: A positive prospect for biofuels
journal, November 2011

CRISPR-Cas9 for the genome engineering of cyanobacteria and succinate production
journal, November 2016

Sustained photosynthetic conversion of CO₂ to ethylene in recombinant cyanobacterium Synechocystis 6803
journal, January 2012

Rerouting Carbon Flux To Enhance Photosynthetic Productivity
journal, February 2012

Limitation of Photosynthesis by Carbon Metabolism: II. O
journal, August 1986

Exploring native genetic elements as plug-in tools for synthetic biology in the cyanobacterium Synechocystis sp. PCC 6803
journal, March 2018

Streamlining recombination-mediated genetic engineering by validating three neutral integration sites in Synechococcus sp. PCC 7002
journal, June 2017

Three factors underlying incorrect in silico predictions of essential metabolic genes
journal, February 2008

Use of filamentous cyanobacteria for biodegradation of organic pollutants.
journal, January 1995

Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803
journal, January 2011

Circadian gating of cell division in cyanobacteria growing with average doubling times of less than 24 hours.
journal, September 1996

Developing a Cas9‐based tool to engineer native plasmids in Synechocystis sp. PCC 6803
journal, June 2018

Gene replacement in cyanobacteria mediated by a dominant streptomycin-sensitive rps12 gene that allows selection of mutants free from drug resistance markers
journal, August 2001

Efficient Multiplex Genome Editing Induces Precise, and Self-Ligated Type Mutations in Tomato Plants
journal, July 2018

Precise and reliable gene expression via standard transcription and translation initiation elements
journal, March 2013

Cyanobacterial Evolution: Fresh Insight into Ancient Questions
journal, March 2015

MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks
journal, January 2012

Transformation in the cyanobacterium Synechocystis sp. 6803
journal, April 1982

Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria
journal, October 2015

Theophylline-Dependent Riboswitch as a Novel Genetic Tool for Strict Regulation of Protein Expression in Cyanobacterium Synechococcus elongatus PCC 7942
journal, September 2013

Cyanobacterial conversion of carbon dioxide to 2,3-butanediol
journal, January 2013

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators
journal, August 2010

The plasticity of cyanobacterial carbon metabolism
journal, December 2017

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803
journal, June 2013

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction
journal, October 2016

Effects of overexpressing photosynthetic carbon flux control enzymes in the cyanobacterium Synechocystis PCC 6803
journal, November 2016

Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction
journal, December 2015

Modeling and analysis of flux distribution and bioproduct formation in Synechocystis sp. PCC 6803 using a new genome-scale metabolic reconstruction
journal, November 2017

Cyanobacteria: Promising biocatalysts for sustainable chemical production
journal, October 2017

Genetic tools for cyanobacteria
journal, January 2002

Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942
journal, August 2014

MetaCyc: a multiorganism database of metabolic pathways and enzymes
journal, January 2006

Identification of Functional Differences in Metabolic Networks Using Comparative Genomics and Constraint-Based Models
journal, April 2012

Isobutanol production as an alternative metabolic sink to rescue the growth deficiency of the glycogen mutant of Synechococcus elongatus PCC 7942
journal, March 2014

Flux balance analysis of photoautotrophic metabolism: Uncovering new biological details of subsystems involved in cyanobacterial photosynthesis
journal, April 2017

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models
journal, September 2016

A tightly inducible riboswitch system in <i>Synechocystis</i> sp. PCC 6803
journal, January 2016

Circadian orchestration of gene expression in cyanobacteria.
journal, June 1995

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

Cyanobacteria as a Platform for Biofuel Production
journal, January 2013

Riboswitch engineering — making the all-important second and third steps
journal, February 2015

Genetic tools for advancement of Synechococcus sp. PCC 7002 as a cyanobacterial chassis
journal, November 2016

Synthetic Biology Toolbox for Controlling Gene Expression in the Cyanobacterium Synechococcus sp. strain PCC 7002
journal, September 2014

Correction: Bottom-Up Engineering of Biological Systems through Standard Bricks: A Modularity Study on Basic Parts and Devices
journal, October 2012

Grand Challenges in Synthetic Biology to be Accomplished
journal, January 2013

A glutamine riboswitch is a key element for the regulation of glutamine synthetase in cyanobacteria
journal, August 2018

Metabolism of monocrotophos and quinalphos by algae isolated from soil
journal, August 1987

Oxidation of Naphthalene by Cyanobacteria and Microalgae
journal, February 1980

Cyanobacteria: Photoautotrophic Microbial Factories for the Sustainable Synthesis of Industrial Products
journal, January 2015

CRISPR-Based Technologies for Metabolic Engineering in Cyanobacteria
journal, October 2018

Algal oxidation of aromatic hydrocarbons: Formation of 1-naphthol from naphthalene by Agmenellum quadruplicatum, strain PR-6
journal, May 1979

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
journal, November 2010

Flipping Riboswitches
journal, July 2006

Engineered cyanobacteria: Teaching an old bug new tricks
journal, May 2011

Flux balance analysis indicates that methane is the lowest cost feedstock for microbial cell factories
journal, December 2017

Sink regulation of photosynthesis
journal, July 2001

Nitrogen Control in Cyanobacteria
journal, January 2001

Computational metabolic engineering strategies for growth-coupled biofuel production by Synechocystis
journal, December 2016

A Genetic Toolbox for Modulating the Expression of Heterologous Genes in the Cyanobacterium Synechocystis sp. PCC 6803
journal, August 2017

Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing
journal, May 2018

Programming cells by multiplex genome engineering and accelerated evolution
journal, July 2009

A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production
journal, July 2015

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis
journal, December 2016

Installing extra bicarbonate transporters in the cyanobacterium Synechocystis sp. PCC6803 enhances biomass production
journal, May 2015

The Bacillus BioBrick Box 2.0: expanding the genetic toolbox for the standardized work with Bacillus subtilis
journal, November 2017