Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli

Flamholz, Avi I.; Dugan, Eli; Blikstad, Cecilia; Gleizer, Shmuel; Ben-Nissan, Roee; Amram, Shira; Antonovsky, Niv; Ravishankar, Sumedha; Noor, Elad; Bar‐Even, Arren; Milo, Ron; Savage, David F.

doi:10.7554/elife.59882

Cited by 96 publications

(119 citation statements)

References 127 publications

(293 reference statements)

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“…Heterologous expression of a CCM might improve bioconversion, and has been accomplished in E. coli [90]. The β-carboxysome from Synechococcus has been expressed heterologously in E. coli, while the α-carboxysome from Halothiobacillus neapolitanus has been expressed in E. coli and Corynebacterium glutamicum, further demonstrating the plausibility of functional expression of a CCM in C. necator [91][92][93].…”

Section: Discussionmentioning

confidence: 99%

“…SH could be used in a similar way to transform E. coli into a hydrogen bacterium. Furthermore, the carboxysome was recently reconstituted in E. coli and allows this bacterium to grow mixotrophically at ambient concentrations of CO 2 [90]. With further laboratory-directed evolution, it is plausible that combining the CBB cycle with the carboxysome and SH in E. coli could enable autotrophy at ambient concentrations of CO 2 .…”

Section: Roles Of Hydrogenases In C Necatormentioning

confidence: 99%

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Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Panich

Fong

Singer

2021

Trends in Biotechnology

100

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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: Discussionmentioning

confidence: 99%

Section: Roles Of Hydrogenases In C Necatormentioning

confidence: 99%

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Panich

Fong

Singer

2021

Trends in Biotechnology

100

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“…While functional carboxysomes have been assembled, the carboxysomes coalesce to form massive aggregates that are nucleoid-excluded in bacterial cells (135,136) or randomly located within spacious regions of chloroplasts (143). However, a very recent study coexpressed the a-McdAB system with a-carboxysome components of H. neapolitanus in Escherichia coli cells (144). Consistent with the idea that McdA and McdB are both necessary and sufficient for distributing carboxysomes, electron-micrographs show a-carboxysomes distributed across the cell length and along the E. coli nucleoid.…”

Section: The Role Of Liquid-liquid Phase Separation In Carboxysome Positioningmentioning

confidence: 99%

Positioning the Model Bacterial Organelle, the Carboxysome

MacCready

Vecchiarelli

2021

mBio

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Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.

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“…This has inspired researchers to explore whether the dark reaction of photosynthesis can be augmented to support higher productivity by mainly four approaches: i) Enzyme engineering of RuBisCO to increase its activity (Wilson & Whitney, 2017), ii) Implementation of CO2 concentration mechanisms to reduce photorespiration (A. I. Flamholz et al, 2020;Long et al, 2018), iii) Replacing C3 with C4 photosynthesis or with completely new carbon fixation pathways, like the CETCH cycle (Schwander et al, 2016), iv) Installing more efficient pathways for the recycling of phosphoglycolate during photorespiration (South et al, 2019;Trudeau et al, 2018). A more detailed overview of the efforts to improve photosynthesis can be found in (Bar-Even, 2018).…”

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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Functional reconstitution of a bacterial CO2 concentrating mechanism in Escherichia coli

Cited by 96 publications

References 127 publications

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO2

Positioning the Model Bacterial Organelle, the Carboxysome

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

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