An orthogonal metabolic framework for one-carbon utilization

Chou, Alexander; Lee, Seung Hwan; Zhu, Fayin; Clomburg, James M.; González, Ramón

doi:10.1038/s42255-021-00453-0

Cited by 44 publications

(54 citation statements)

References 66 publications

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“…The developed JST07 extract can be adapted for use for iPROBE prototyping of a wide range of biosynthetic pathways that use CoA ester intermediates and start with acetyl-CoA or pyruvate (e.g., isoprenoids, fatty acids, cannabinoids, polyketides). Additionally it has the potential to enable faster optimization of recently established CoA ester dependent new-to-nature/synthetic pathways like CETCH 33 and FORCE 34 . Second, by using this approach, we were able to tailor r-BOX to produce a single product at high selectivity.…”

Section: Discussionmentioning

confidence: 99%

Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria

Vögeli

Schulz

Garg

et al. 2022

Preprint

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Carbon-negative synthesis of biochemical products has the potential to mitigate global CO2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimized and implemented r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screened 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generated designer strains for the selective production of butanoic acid (4.9 +/- 0.1 gL-1), hexanoic acid (3.06 +/- 0.03 gL-1) and 1-hexanol (1.0 +/- 0.1 gL-1) at the best performance reported to date in this bacterium. We also generated Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL-1 in a 1.5-L continuous fermentation. Our strategy enables optimization of rBOX derived products for biomanufacturing and industrial biotechnology.

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Section: Discussionmentioning

confidence: 99%

Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria

Vögeli

Schulz

Garg

et al. 2022

Preprint

Self Cite

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“…Therefore, it is also attractive to design synthetic routes using novel enzymes and novel combinations of well-studied enzymes. Well-designed synthetic routes can be superior to natural ones in: 1) circumventing the limitations of natural pathways, for example, the use of oxygen-tolerant enzymes makes rGlyP also functional in aerobic conditions ( Bang and Lee, 2018 ; Bang et al, 2020 ); 2) simplifying the metabolic pathway using less enzymes ( Xiao et al, 2022 ); 3) bypassing the host metabolism and regulations using orthogonal designs ( Chou et al, 2021 ); 4) achieving higher efficiency ( Schwander et al, 2016 ; Cai et al, 2021 ) or making the pathway more thermodynamically favourable ( Siegel et al, 2015 ).…”

Section: Metabolic Engineering Of Microbes To Use Next-generation Fee...mentioning

confidence: 99%

“…To overcome the technological challenges, researchers in metabolic engineering and synthetic biology have intelligently engineered and evolved microorganisms in laboratories to make best use of NGFs. For C1 feedstocks, current efforts are mainly spared on how to assimilate them faster and better into biomass and central metabolism of both naturally occurring microbes (e.g., chemoorganoautotrophs, methylotrophs) or synthetic model microbes, e.g., Escherichia coli ( Antonovsky et al, 2016 ; Yu and Liao, 2018 ; Gleizer et al, 2019 ; Chen F. Y.-H. et al, 2020 ; Chou et al, 2021 ) and yeasts ( Espinosa et al, 2020 ; Gassler et al, 2020 ). In contrast, industrial workhorse microbes can readily use C2 feedstocks without sophisticated genetic engineering or prolonged adaptive laboratory evolution (ALE).…”

Section: Introductionmentioning

confidence: 99%

Microbial Utilization of Next-Generation Feedstocks for the Biomanufacturing of Value-Added Chemicals and Food Ingredients

Zhang

Ottenheim

Weingarten

et al. 2022

Front. Bioeng. Biotechnol.

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Global shift to sustainability has driven the exploration of alternative feedstocks beyond sugars for biomanufacturing. Recently, C1 (CO2, CO, methane, formate and methanol) and C2 (acetate and ethanol) substrates are drawing great attention due to their natural abundance and low production cost. The advances in metabolic engineering, synthetic biology and industrial process design have greatly enhanced the efficiency that microbes use these next-generation feedstocks. The metabolic pathways to use C1 and C2 feedstocks have been introduced or enhanced into industrial workhorses, such as Escherichia coli and yeasts, by genetic rewiring and laboratory evolution strategies. Furthermore, microbes are engineered to convert these low-cost feedstocks to various high-value products, ranging from food ingredients to chemicals. This review highlights the recent development in metabolic engineering, the challenges in strain engineering and bioprocess design, and the perspectives of microbial utilization of C1 and C2 feedstocks for the biomanufacturing of value-added products.

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“…At the same time, synthetic biotechnology was also employed to construct engineered bacteria by introducing the heterogeneous CO 2 fixation–related gene for carbon neutrality. Computational analysis was also another powerful tool to identify and design pathways with a more favorable thermodynamic driving force for CO 2 fixation ( Satanowski et al, 2020 ; Chou et al, 2021 ). Beyond that, electrically driven microbial and enzyme engineering was also suitable for CO 2 fixation with high efficiency.…”

Section: Conclusion and Perspectivementioning

confidence: 99%

Applications of Synthetic Biotechnology on Carbon Neutrality Research: A Review on Electrically Driven Microbial and Enzyme Engineering

Zhuang

Zhang

Xiao

et al. 2022

Front. Bioeng. Biotechnol.

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With the advancement of science, technology, and productivity, the rapid development of industrial production, transportation, and the exploitation of fossil fuels has gradually led to the accumulation of greenhouse gases and deterioration of global warming. Carbon neutrality is a balance between absorption and emissions achieved by minimizing carbon dioxide (CO2) emissions from human social productive activity through a series of initiatives, including energy substitution and energy efficiency improvement. Then CO2 was offset through forest carbon sequestration and captured at last. Therefore, efficiently reducing CO2 emissions and enhancing CO2 capture are a matter of great urgency. Because many species have the natural CO2 capture properties, more and more scientists focus their attention on developing the biological carbon sequestration technique and further combine with synthetic biotechnology and electricity. In this article, the advances of the synthetic biotechnology method for the most promising organisms were reviewed, such as cyanobacteria, Escherichia coli, and yeast, in which the metabolic pathways were reconstructed to enhance the efficiency of CO2 capture and product synthesis. Furthermore, the electrically driven microbial and enzyme engineering processes are also summarized, in which the critical role and principle of electricity in the process of CO2 capture are canvassed. This review provides detailed summary and analysis of CO2 capture through synthetic biotechnology, which also pave the way for implementing electrically driven combined strategies.

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An orthogonal metabolic framework for one-carbon utilization

Cited by 44 publications

References 66 publications

Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria

Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria

Microbial Utilization of Next-Generation Feedstocks for the Biomanufacturing of Value-Added Chemicals and Food Ingredients

Applications of Synthetic Biotechnology on Carbon Neutrality Research: A Review on Electrically Driven Microbial and Enzyme Engineering

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