Natural strategies for the spatial optimization of metabolism in synthetic biology

Agapakis, Christina M.; Boyle, Patrick; Silver, Pamela A.

doi:10.1038/nchembio.975

Cited by 361 publications

(287 citation statements)

References 100 publications

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“…However, previous research on microbial consortia was primarily concerned with the study of mixed population stability and dynamic interactions (7)(8)(9)(10)(11), although a few recent studies have reported the engineering of microbial consortia for utilization of simple sugars to make small molecules of central carbon metabolism, such as ethanol and lactate (12,13). Progress was made recently, when a full n-butanol pathway was expressed in two separate E. coli cells to achieve higher production (14) and when a bacterium-yeast coculture was used to address the difficulties of functional reconstitution of a pathway involving prokaryotic and eukaryotic enzymes in a consortium, and thus improved production of complex pharmaceutical molecules (15).…”

Section: -Hydroxybenzoic Acidmentioning

confidence: 99%

Engineering Escherichia coli coculture systems for the production of biochemical products

Zhang

Pereira

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

268

199

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Engineering microbial consortia to express complex biosynthetic pathways efficiently for the production of valuable compounds is a promising approach for metabolic engineering and synthetic biology. Here, we report the design, optimization, and scale-up of an Escherichia coli-E. coli coculture that successfully overcomes fundamental microbial production limitations, such as high-level intermediate secretion and low-efficiency sugar mixture utilization. For the production of the important chemical cis,cis-muconic acid, we show that the coculture approach achieves a production yield of 0.35 g/g from a glucose/xylose mixture, which is significantly higher than reported in previous reports. By efficiently producing another compound, 4-hydroxybenzoic acid, we also demonstrate that the approach is generally applicable for biosynthesis of other important industrial products.metabolic engineering | microbial coculture | muconic acid | 4-hydroxybenzoic acidM etabolic engineering and synthetic biology have made great strides in constructing and optimizing metabolic pathways for biochemical product synthesis in a pure culture (1, 2). There are, however, situations where this approach may be limited, as in the cases where (i) a single host cell cannot provide an optimal environment for the functioning of all pathway enzymes, (ii) biosynthetic efficiency is reduced due to overwhelming metabolic stress from the overexpression of long and complex pathways (3, 4), or (iii) pathway intermediates are secreted yielding undesired byproducts and reducing substrate utilization (5, 6). The above limitations can potentially be overcome through the use of rationally designed microbial coculture systems. Different from previous modular engineering approaches, such coculturebased systems completely modularize and segregate a biosynthetic pathway into two separate cells, each of which carries a portion of the pathway, and thus can be engineered independently to achieve optimal functioning of the combined pathway.The concept of microbial cocultures is not new. However, previous research on microbial consortia was primarily concerned with the study of mixed population stability and dynamic interactions (7-11), although a few recent studies have reported the engineering of microbial consortia for utilization of simple sugars to make small molecules of central carbon metabolism, such as ethanol and lactate (12, 13). Progress was made recently, when a full n-butanol pathway was expressed in two separate E. coli cells to achieve higher production (14) and when a bacterium-yeast coculture was used to address the difficulties of functional reconstitution of a pathway involving prokaryotic and eukaryotic enzymes in a consortium, and thus improved production of complex pharmaceutical molecules (15). Here, we expand the generality of the coculture engineering by demonstrating that microbial cocultures can also be engineered to overcome more universal challenges in metabolic engineering, including high-level intermediate secretion and low-efficiency s...

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Section: -Hydroxybenzoic Acidmentioning

confidence: 99%

Engineering Escherichia coli coculture systems for the production of biochemical products

Zhang

Pereira

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

268

199

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“…To increase the overall reaction efficiency, a spatiotemporal control of the intermediate product is essential. 30 A cellular system optimizes the compartmentalization of metabolic pathways to reduce any significant loss of an intermediate product.…”

Section: Test Of the Microreactorsmentioning

confidence: 99%

Spatial Distance Effect of Bienzymes on the Efficiency of Sequential Reactions in a Microfluidic Reactor Packed with Enzyme-immobilized Microbeads

Heo

2014

ANAL. SCI.

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Recently, microfabrication technology has opened up a new era in the applications of immobilized enzymes. Three different configurations of microfluidic reactors packed with enzyme-bearing microbeads were examined to show that the overall efficiency of coupled enzyme-catalyzed reactions depends on the spatial relationship of two enzymes immobilized on the bead surfaces. The spatial distances of glucose oxidase (GOx) and horseradish peroxidase (HRP) enzymes were controlled by using microbeads as a supporting matrix for immobilizing the two enzymes and packing them in two microfluidic chambers. A microreactor packed with microbeads coimmobilized with the two enzymes showed a better overall reaction efficiency than the other two reactors, where the two enzymes were spatially distant, under a flow condition. These results are ascribed to the reduced diffusional loss of an intermediate product in the bienzyme-coimmobilized microreactor. Furthermore, the inhibition of the GOx enzyme by H2O2, an intermediate product, can be eliminated by quickly converting H2O2 to a final non-inhibiting product in the bienzyme-coimmobilized microreactor.Keywords Microfluidic reactor, sequential enzyme reaction, enzyme immobilization

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“…41 The high level of spatial organization and integration enables the metabolism to be an optimized network of interconnected biological reactions that guide the production, transportation and consumption of nutrients and allows for the maintenance, growth and reproduction of life. Inspired by nature, synthetic biologists are aiming to build biomimetic nano/microfactories for the positional immobilization of multienzymatic cascades with nanoscale precision.…”

Section: Regulating Reaction Pathways For Bioinspired Nanofactoriesmentioning

confidence: 99%

Spatial regulation of synthetic and biological nanoparticles by DNA nanotechnology

Yang

Liu

2015

NPG Asia Mater

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Nanoparticles are among the most fascinating materials because of their unique size-dependent properties. The spatial positioning of the nanoparticles with a nanoscale precision will greatly enhance their potential for use in the fabrication of functional materials and devices. Recently, the development of DNA nanotechnology has enabled the construction of two-and three-dimensional, precisely addressable nanostructures and devices based on DNA sequence design and programmable assembly. Advances in conjugating DNA with nanoparticles can bridge these two technologies and provide scientists with a new tool to study material transportation and energy transfer at a nanometer scale. In this review, we summarize the recent progress in this emerging research field, which includes not only the static arrangements of inorganic nanoparticles but also the dynamic regulation of organic and biological units at a nanometer scale. With the rapid development in this field, new challenges and new possibilities will emerge and bring about fruitful achievements with a significant impact on future work.

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Natural strategies for the spatial optimization of metabolism in synthetic biology

Cited by 361 publications

References 100 publications

Engineering Escherichia coli coculture systems for the production of biochemical products

Engineering Escherichia coli coculture systems for the production of biochemical products

Spatial Distance Effect of Bienzymes on the Efficiency of Sequential Reactions in a Microfluidic Reactor Packed with Enzyme-immobilized Microbeads

Spatial regulation of synthetic and biological nanoparticles by DNA nanotechnology

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