Computational tools for the synthetic design of biochemical pathways

Medema, Marnix H.; Raaphorst, Renske van; Takano, Eriko; Breitling, Rainer

doi:10.1038/nrmicro2717

Cited by 209 publications

(125 citation statements)

References 112 publications

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“…Some computational prediction tools are involved in changing the metabolic pathway by using knockouts or by adding new catalytic enzymes, and this may help in increasing biofuel production. One important tool for the prediction of metabolic pathway is From Metabolite to Metabolite (FMM)-freely available software (Medema et al, 2012). It compiles the KEGG map and KEGG ligand data to obtain a combined pathway.…”

Section: Optimization Of Production Pathways and Hostmentioning

confidence: 99%

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

et al. 2017

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The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools' development and application should focus on unexplored non-conventional yeast species.

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Section: Optimization Of Production Pathways and Hostmentioning

confidence: 99%

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

et al. 2017

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“…By way of comparison, TeseleGen estimates that direct DNA synthesis of the same 240 constructs would cost $540,000 at current prices. Although peer-reviewed data are not yet available to evaluate the TeseleGen claims, it is clear that these kinds of improvements in model-driven synthetic biology [other recent advances are reviewed in (Koeppl 2011) (Blount et al 2012), (Medema et al 2012) and (Shiue and Prather 2012)] will reduce the number of cycles of design, construction and analysis needed to engineer systems that meet performance goals.…”

Section: Progress Toward Design-driven Synthetic Biologymentioning

confidence: 99%

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

Carothers

2013

Syst Synth Biol

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Many of the synthetic biological devices, pathways and systems that can be engineered are multi-use, in the sense that they could be used both for commerciallyimportant applications and to help meet global health needs. The on-going development of models and simulation tools for assembling component parts into functionally-complex devices and systems will enable successful engineering with much less trial-and-error experimentation and laboratory infrastructure. As illustrations, I draw upon recent examples from my own work and the broader Keasling research group at the University of California Berkeley and the Joint BioEnergy Institute, of which I was formerly a part. By combining multi-use synthetic biology research agendas with advanced computer-aided design tool creation, it may be possible to more rapidly engineer safe and effective synthetic biology technologies that help address a wide range of global health problems.

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“…Several recent reviews describe and compare the different drag and drop tools developed for the synthetic biology community in the last few years [Alterovitz et al 2009;Marchisio et al 2009;Clancy et al 2010;MacDonald et al 2011;Medema et al 2012]. All of these tools have the same goal, i.e.…”

Section: Drag and Drop Toolsmentioning

confidence: 99%

Synthetic Biology and Microdevices

Venken

Marchal

Vanderleyden

2013

J. Emerg. Technol. Comput. Syst.

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Recent developments demonstrate that the combination of microbiology with micro-and nanoelectronics is a successful approach to develop new miniaturized sensing devices and other technologies. In the last decade, there is a shift from the optimization of the abiotic components, e.g. the chip, to the improvement of the processing capabilities of cells through genetic engineering. The synthetic biology approach will not only give rise to systems with new functionalities, but will also improve the robustness and speed of their response towards applied signals. To this end, the development of new genetic circuits has to be guided by computational design methods that enable to tune and optimize the circuit response. As the successful design of genetic circuits is highly dependent on the quality and reliability of its composing elements, intense characterization of standard biological parts will be crucial for an efficient rational design process in the development of new genetic circuits. Microengineered devices can thereby offer a new analytical approach for the study of complex biological parts and systems. By summarizing the recent techniques in creating new synthetic circuits and in integrating biology with microdevices, this review aims at emphasizing the power of combining synthetic biology with microfluidics and microelectronics.

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Computational tools for the synthetic design of biochemical pathways

Cited by 209 publications

References 112 publications

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

Design-driven, multi-use research agendas to enable applied synthetic biology for global health

Synthetic Biology and Microdevices

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