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Synthetic biology of cyanobacteria: unique challenges and opportunities.

Berla BM, Saha R, Immethun CM, Maranas CD, Moon TS, Pakrasi HB - Front Microbiol (2013)

Bottom Line: Synthetic biology tools can help unlock cyanobacteria's potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli.While these organisms may in many cases be more difficult to work with as "chassis" strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a "green E. coli." In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria.Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

View Article: PubMed Central - PubMed

Affiliation: Department of Energy, Environmental, and Chemical Engineering, Washington University St. Louis, MO, USA.

ABSTRACT
Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria's potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as "chassis" strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a "green E. coli." In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

No MeSH data available.


Using fluxomics and genome scale models to link genotype to metabolic phenotype. From an annotated genome sequence, a stoichiometric model of metabolism can be constructed. That model can be solved via either prediction of an optimal flux phenotype (FBA) or measurement of actual flux phenotype (13C-MFA). These results can help suggest modifications for altering the phenotype of the cell in a desired manner. In this way, a synthetic biologist can design new strains, build them using genetic modification methods, and test their phenotypes before designing new modifications in an iterative fashion.
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Figure 3: Using fluxomics and genome scale models to link genotype to metabolic phenotype. From an annotated genome sequence, a stoichiometric model of metabolism can be constructed. That model can be solved via either prediction of an optimal flux phenotype (FBA) or measurement of actual flux phenotype (13C-MFA). These results can help suggest modifications for altering the phenotype of the cell in a desired manner. In this way, a synthetic biologist can design new strains, build them using genetic modification methods, and test their phenotypes before designing new modifications in an iterative fashion.

Mentions: A primary aim of cyanobacterial synthetic biology is the production of particular metabolites as biofuels or platform chemicals. As such, better understanding the metabolic phenotypes of wild-type and synthetic strains is a critical aim. While cyanobacterial metabolomics have been recently reviewed (Schwarz et al., 2013), here we describe recent progress in genome-scale modeling and fluxomics of cyanobacteria. These approaches can help guide the creation of synthetic strains with desirable metabolic phenotypes such as biofuel overproduction via in silico prediction or in vivo measurement of metabolic fluxes (See Figure 3). Specific to cyanobacterial systems, we highlight a number of challenges including complexity of modeling the photosynthetic metabolism and performing flux balance analysis (FBA), poor annotations of important metabolic pathways, and unavailability of in vivo gene essentiality information for most cyanobacteria. Finally, we focus on recent advancements in this area.


Synthetic biology of cyanobacteria: unique challenges and opportunities.

Berla BM, Saha R, Immethun CM, Maranas CD, Moon TS, Pakrasi HB - Front Microbiol (2013)

Using fluxomics and genome scale models to link genotype to metabolic phenotype. From an annotated genome sequence, a stoichiometric model of metabolism can be constructed. That model can be solved via either prediction of an optimal flux phenotype (FBA) or measurement of actual flux phenotype (13C-MFA). These results can help suggest modifications for altering the phenotype of the cell in a desired manner. In this way, a synthetic biologist can design new strains, build them using genetic modification methods, and test their phenotypes before designing new modifications in an iterative fashion.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3755261&req=5

Figure 3: Using fluxomics and genome scale models to link genotype to metabolic phenotype. From an annotated genome sequence, a stoichiometric model of metabolism can be constructed. That model can be solved via either prediction of an optimal flux phenotype (FBA) or measurement of actual flux phenotype (13C-MFA). These results can help suggest modifications for altering the phenotype of the cell in a desired manner. In this way, a synthetic biologist can design new strains, build them using genetic modification methods, and test their phenotypes before designing new modifications in an iterative fashion.
Mentions: A primary aim of cyanobacterial synthetic biology is the production of particular metabolites as biofuels or platform chemicals. As such, better understanding the metabolic phenotypes of wild-type and synthetic strains is a critical aim. While cyanobacterial metabolomics have been recently reviewed (Schwarz et al., 2013), here we describe recent progress in genome-scale modeling and fluxomics of cyanobacteria. These approaches can help guide the creation of synthetic strains with desirable metabolic phenotypes such as biofuel overproduction via in silico prediction or in vivo measurement of metabolic fluxes (See Figure 3). Specific to cyanobacterial systems, we highlight a number of challenges including complexity of modeling the photosynthetic metabolism and performing flux balance analysis (FBA), poor annotations of important metabolic pathways, and unavailability of in vivo gene essentiality information for most cyanobacteria. Finally, we focus on recent advancements in this area.

Bottom Line: Synthetic biology tools can help unlock cyanobacteria's potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli.While these organisms may in many cases be more difficult to work with as "chassis" strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a "green E. coli." In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria.Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

View Article: PubMed Central - PubMed

Affiliation: Department of Energy, Environmental, and Chemical Engineering, Washington University St. Louis, MO, USA.

ABSTRACT
Photosynthetic organisms, and especially cyanobacteria, hold great promise as sources of renewably-produced fuels, bulk and specialty chemicals, and nutritional products. Synthetic biology tools can help unlock cyanobacteria's potential for these functions, but unfortunately tool development for these organisms has lagged behind that for S. cerevisiae and E. coli. While these organisms may in many cases be more difficult to work with as "chassis" strains for synthetic biology than certain heterotrophs, the unique advantages of autotrophs in biotechnology applications as well as the scientific importance of improved understanding of photosynthesis warrant the development of these systems into something akin to a "green E. coli." In this review, we highlight unique challenges and opportunities for development of synthetic biology approaches in cyanobacteria. We review classical and recently developed methods for constructing targeted mutants in various cyanobacterial strains, and offer perspective on what genetic tools might most greatly expand the ability to engineer new functions in such strains. Similarly, we review what genetic parts are most needed for the development of cyanobacterial synthetic biology. Finally, we highlight recent methods to construct genome-scale models of cyanobacterial metabolism and to use those models to measure properties of autotrophic metabolism. Throughout this paper, we discuss some of the unique challenges of a diurnal, autotrophic lifestyle along with how the development of synthetic biology and biotechnology in cyanobacteria must fit within those constraints.

No MeSH data available.