Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

Campodonico, Miguel A.; Andrews, Bárbara A.; Asenjo, Juan A.; Palsson, Bernhard Ø.; Feist, Adam M.

doi:10.1016/j.ymben.2014.07.009

Cited by 158 publications

(136 citation statements)

References 91 publications

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“…The authors verified the effectiveness of their proportional flux forcing modeling method by identifying manipulation targets for enhancing free fatty acid production in Escherichia coli (Ip et al 2014). Campodonico et al (2014) developed a more efficient algorithm, the GEM pathway predictor, which optimizes the computational process and introduces reaction specification analysis. Owing to its novel features, the GEM pathway predictor algorithm combined with a growth-coupled strain design method enabled the synthetic pathway design of 20 chemicals and predicted all feasible pathways with theoretical yields in E. coli.…”

Section: Gem-guided Metabolic Engineeringmentioning

confidence: 97%

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

Liu

Shin

et al. 2014

Appl Microbiol Biotechnol

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Metabolic engineering facilitates the rational development of recombinant bacterial strains for metabolite overproduction. Building on enormous advances in system biology and synthetic biology, novel strategies have been established for multivariate optimization of metabolic networks in ensemble, spatial, and dynamic manners such as modular pathway engineering, compartmentalization metabolic engineering, and metabolic engineering guided by genome-scale metabolic models, in vitro reconstitution, and systems and synthetic biology. Herein, we summarize recent advances in novel metabolic engineering strategies. Combined with advancing kinetic models and synthetic biology tools, more efficient new strategies for improving cellular properties can be established and applied for industrially important biochemical production.

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Section: Gem-guided Metabolic Engineeringmentioning

confidence: 97%

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

Liu

Shin

et al. 2014

Appl Microbiol Biotechnol

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“…Perhaps, the most promising future is a fully replicated fossil fuel, i.e., a mixture structurally and chemically identical to the fossil fuels that are currently under use, which is a mixture of aliphatic n-and iso-alkanes of various chain lengths [99]. Also, a more complete metabolic atlas of E. coli is needed, and recent eforts have mapped the metabolic lux from this bacterium further [100].…”

Section: Genetic Engineering and Synthetic Biology Of E Colimentioning

confidence: 99%

<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology

Idalia¹,

Bernardo²

2017

≪i>Escherichia Coli

32
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23
0

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Without a doubt, in the past 20 or so years, we have achieved the power of biology in diferent ways. In the present, we have many tools for developing novel technologies and applications for organism modiications that ultimately let us know many aspects of organisms' biology and, therefore, apply that knowledge for technological purposes. Of all the model organisms and tools for genetic modiication available, Escherichia coli stands out as a model organism and what we would like to call "molecular biologist tool box." In the present chapter, we aim to review our current knowledge regarding genetic modiications and tools for modifying E. coli to generate plasmid vectors, single and multiple gene knockouts, whole genome editing, biosensor generation and applications and synthetic gene circuits and genomes.

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“…Several examples of in silico strategies for the reengineering of naturally occurring enzymes into novel biocatalysts are shown by the work of (1) Cho et al (2010), who predicted novel enzyme activities on the basis of physicochemical properties of substrate/product pairs, (2) Brunk et al (2012), who predicted novel enzyme activity within a biosynthetic pathway (Henry et al 2010) on the basis of 3D protein structural characteristics and molecular dynamics simulations (Fig. 4), and (3) Campodonico et al (2014), who predicted enzyme similarity on the basis of enzyme commission classification. In certain cases, a comprehensive assessment was performed for 20 predicted heterologous pathways in E. coli (Campodonico et al 2014).…”

Section: Increased Substrate Specificitymentioning
confidence: 99%

“…4), and (3) Campodonico et al (2014), who predicted enzyme similarity on the basis of enzyme commission classification. In certain cases, a comprehensive assessment was performed for 20 predicted heterologous pathways in E. coli (Campodonico et al 2014). …”

Section: Increased Substrate Specificitymentioning
confidence: 99%

The Need for Integrated Approaches in Metabolic Engineering
Lechner
¹
,
Brunk
²
,
Keasling
³

2016
Cold Spring Harb Perspect Biol
47
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31
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This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must be considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes. CURRENT APPROACHES IN METABOLIC ENGINEERING AND THEIR LIMITATIONS

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Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path

Cited by 158 publications

References 91 publications

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

Toward metabolic engineering in the context of system biology and synthetic biology: advances and prospects

<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology

The Need for Integrated Approaches in Metabolic Engineering

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