Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator

Claassens, Nico J.; Bordanaba‐Florit, Guillermo; Cotton, Charles A. R.; Maria, Alberto De; Finger-Bou, Max; Friedeheim, Lukas; Giner-Laguarda, Natalia; Munar-Palmer, Martí; Newell, William R.; Scarinci, Giovanni; Verbunt, Jari; Vries, Stijn T. de; Yilmaz, Suzan; Bar‐Even, Arren

doi:10.1016/j.ymben.2020.08.004

Cited by 100 publications

(67 citation statements)

References 46 publications

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“…The lac promoter is active as a constitutive promoter in the absence of LacY, LacI, or the lac operator [71]. Other constitutive promoters that have been used in C. necator include P tac and P trc derivatives, P cat , and P j5 , derivatives of P j5 [71,72,[74][75][76]. In addition, the Larabinose-inducible (P bad ) promoter from E. coli and a synthetic anhydrotetracycline inducible promoter are functional in C. necator, [77,78].…”

Section: Synthetic Biology Tools For C Necatormentioning

confidence: 99%

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Panich

Fong

Singer

2021

Trends in Biotechnology

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Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO 2 to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO 2 emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO 2 to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO 2 . Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO 2 . Mitigation of Atmospheric CO 2 with BioconversionSatisfying current and future global energy demand while allowing favorable environmental outcomes will require innovative solutions in the fuel sector. Although portions of the transportation infrastructure can be electrified (such as automobile transport), energy-dense carbon-based fuels will continue to be required for aviation, long-distance trucking, rocketry, maritime shipping, and industrial operations. Petroleum-based fuels are finite, given that BP and the International Energy Agency (IEA) project that petroleum sources are likely to be depleted between 2050 and 2070 using current oil extraction technologies i-iii . Climate change caused by an increase in CO 2 (and CH 4 ) levels in Earth's atmosphere has brought cataclysmic weather events and has decimated ocean habitats in recent years, a trend that will likely continue through our lifetimes given that CO 2 is being emitted into the atmosphere at a rate of ≈32 billion tons of CO 2 per year [1-6] iv . Therefore, sustainable and economically viable bioconversion of CO 2 to fuels and commodity chemicals should be realized within the next decade. A small but significant mitigation of anthropogenic CO 2 release can be achieved by using CO 2 from atmospheric air as a feedstock to produce biofuels in microorganisms: if 10% of global aviation fuel (accounting for~2.6% of total CO 2 emissions [7]) were replaced with Sustainable Aviation Fuels (SAFs) from Cupriavidus necator at a titer of 1 g/l and assuming 90 g/l biomass accumulation [8],~500 000 tons of sustainable fuel per year could be produced from recycled CO 2 (at a carbon density of 0.8 kg/l). In addition, the accumulated biomass would sequester~80 million tons of CO 2 per year (mitigating ≈0.25% of emissions).CO 2 is an ideal feedstock for the production of biofuels because it is an inexpensive, nontoxic, and abundant starting material (≈850 billion tons of CO 2 are currently present in the atmosphere). Furthermore, CO 2 is noncompetitive with the global food supply chain. Technoeconomic analysis indicates that CO 2 -derived biofuel production could be a US$10-250 billion industry by 2030 v . However, CO 2 is dilute in the atmosphere (≈0.04% CO 2 by volume) and ...

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Section: Synthetic Biology Tools For C Necatormentioning

confidence: 99%

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Panich

Fong

Singer

2021

Trends in Biotechnology

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“…As this is one of the key reactions and we also did not find a value for the forward kinetic constant, this standard deviation has a crucial impact on the total estimation of pathway specific activity. In vivo the rGlyP will only work with high CO2 concentration (Claassens et al, 2020;Kim et al, 2020) which also does not match with the results of the analysis here. All in all, the estimation for the rGlyP are therefore not completely trustworthy which stresses how urgently kinetic data for this system is needed to make accurate predictions.…”

Section: Comparison Of Pathway Specific Activities and Efficiencies Omentioning

confidence: 62%

“…Additionally, multiple optimized artificial pathways for C1-assimilation have been proposed and their basic working principle could be shown (Chou et al, 2019;He et al, 2020;Siegel et al, 2015). Among them, the Reductive Glycine Pathway (rGlyP) that was developed by the group of Arren Bar-Even and others, shines as it is the most efficient aerobic formate-dependent pathway and the only pathway to be integrated in vivo to support growth with C1-compounds as the sole carbon and energy source (Claassens et al, 2020;Kim et al, 2020). This work is dedicated to Arren Bar-Even, a visionary in pathway design and metabolic engineering, who passed away far too early in the zenith of his scientific achievements.…”

Section: Introductionmentioning

confidence: 99%

In-depth computational analysis of natural and artificial carbon fixation pathways

Löwe

Kremling

2021

Preprint

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In the recent years, engineering new-to-nature CO2 and C1 fixing metabolic pathways made a leap forward. These new, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway “better” than another.In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their ATP-efficiency and specific activity considering the kinetics and thermodynamics of the reactions. Beside natural pathways, this included the artificial Reductive Glycine Pathway, the CETCH cycle and two completely new cycles with superior stoichiometry: The Reductive Citramalyl-CoA cycle and the 2-Hydroxyglutarate-Reverse Tricarboxylic Acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways and missing kinetic data was sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway specific activities.We found that the Reductive Glycine Pathway, the CETCH cycle and the new Reductive Citramalyl-CoA cycle were predicted to have higher ATP-efficiencies and specific activities than the natural cycles. The Calvin Cycle performed better than previously thought, however. It can be concluded that the weaker overall characteristics in the design of the Calvin Cycle might be compensated by other benefits like robustness, low nutrient demand and a good compatibility with the host’s physiological requirements. Nevertheless, the artificial carbon fixation cycles hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.

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“…introduced into E.coli 20,21,22,23 for autotrophic growth on formate and CO 2 . At the same time, part of this pathway was successfully transferred into Saccharomyces cerevisiae 24 , Cupriavidus necator 25 and Clostridium pasteurianum 26 . However, the flux of rGP is quite low, which limits the growth of microorganism.…”

Section: Introductionmentioning

confidence: 99%

Stand-alone lipoylated H-protein of the glycine cleavage system enables glycine cleavage and the synthesis of glycine from one-carbon compounds in vitro

Zhang

et al. 2021

Preprint

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H-protein, one of the four component proteins (H, T, P and L) of glycine cleavage system (GCS), is generally considered a shuttle protein interacting with the other three GCS-proteins via a lipoyl swinging arm. We report that without P-, T- and L-proteins, lipoylated H-protein (Hlip) enables GCS reactions in both glycine cleavage and synthesis directions in vitro. This apparent catalytic activity is closely related to the cavity on the H-protein surface where the lipoyl arm is attached. Heating or mutation of selected residues in the cavity destroys or reduces the stand-alone activity of Hlip, which can be restored by adding the other three GCS-proteins. Systematic study of the Hlip-catalyzed overall GCS reactions and the individual reaction steps provides a first step towards understanding the stand-alone function of Hlip. The results in this work provide some inspiration for further understanding the mechanism of the GCS and give some interesting implications on the evolution of the GCS.

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Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator

Cited by 100 publications

References 46 publications

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

In-depth computational analysis of natural and artificial carbon fixation pathways

Stand-alone lipoylated H-protein of the glycine cleavage system enables glycine cleavage and the synthesis of glycine from one-carbon compounds in vitro

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