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Harnessing the power of microbial autotrophy

Key Points

  • Autotrophic microorganisms have the potential to efficiently convert CO2 into a wide range of chemicals and biofuels, which is a promising sustainable avenue for future biotechnology. Natural autotrophs have evolved to use energy sources, that is, light (photoautotrophs) and/or inorganic electron donors such as hydrogen (chemolithoautotrophs), to convert CO2 into biomass. However, natural autotrophs are generally not yet suitable for industrial applications, owing to low autotrophic product yields and productivities, and because of poorly developed genetic tools.

  • A few natural autotrophs with limited genetic toolboxes, including some photoautotrophic cyanobacteria and some promising chemolithoautotrophs, are being engineered towards autotrophic cell factories. This includes the introduction of heterologous pathways for products of interest and the engineering of autotrophic systems and pathways to improve their efficiency under industrial conditions.

  • Some autotrophic systems, such as partial or complete CO2 fixation pathways and simple photosystems, have been transplanted into heterotrophic model microorganisms. Transplantation of CO2 fixation pathways into heterotrophs has already led to higher mixotrophic product yields.

  • Biochemical and computational analyses have uncovered the large diversity of natural and synthetic CO2 fixation pathways. This large repertoire of pathways includes pathways that are more ATP-efficient and have potentially faster kinetics than the ubiquitous Calvin cycle. However, these promising CO2 fixations pathways have not yet been successfully introduced into heterotrophic or autotrophic cell factories. Future attempts to establish these pathways will benefit from synthetic biology approaches, involving rational pathway design, enzyme engineering and modularization, in combination with indispensable laboratory evolution approaches.

  • Natural photosystems have been improved by genetic engineering to a limited extend so far, and there is a large potential to further improve their light-harvesting and energy conversion efficiency. Current photovoltaic solar cells are much more efficient at light-harvesting than the biological process of photosynthesis. Based on this notion, record-breaking solar-to-product efficiencies have been recently achieved by bio-inorganic hybrid systems that carry out microbial electrosynthesis. These systems consist of the photovoltaic solar-cell driven electrocatalytic production of electron donors (for example, hydrogen), which is integrated with chemolithoautotrophic microorganisms that convert electron donors into products.

Abstract

Autotrophic microorganisms convert CO2 into biomass by deriving energy from light or inorganic electron donors. These CO2-fixing microorganisms have a large, but so far only partially realized, potential for the sustainable production of chemicals and biofuels. Productivities have been improved in autotrophic hosts through the introduction of production pathways and the modification of autotrophic systems by genetic engineering. In addition, approaches are emerging in which CO2 fixation pathways and energy-harvesting systems are transplanted into heterotrophic model microorganisms. Alternative promising concepts are hybrid production systems of autotrophs and heterotrophs, and bio-inorganic hybrids of autotrophic microorganisms with electrocatalysts or light-harvesting semiconductor materials. In this Review, we discuss recent advances and bottlenecks for engineering microbial autotrophy and explore novel strategies that will pave the way towards improved microbial autotrophic production platforms.

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Figure 1: Production platforms that are based on different types of microbial trophic metabolism.
Figure 2: Key examples of engineering towards autotrophic microbial production platforms.
Figure 3: Balancing supply and demand for CO2 fixation pathways.
Figure 4: Proposed workflow for engineering autotrophic cell factories.

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Acknowledgements

N.J.C. was supported by the internal Systems Biology program at Wageningen University, The Netherlands (grant KB-17-003.02-024). The authors acknowledge support from the Netherlands Organization of Scientific Research (NWO) through grants in the TOP (grant 714.015.001 to J.v.d.O.), Gravitation (grant SIAM 024.002.002 to W.M.d.V.) and Spinoza (W.M.d.V.) programmes, as well as from the European Union through European Research Council grants 323009 (W.M.d.V) and 250172 (D.Z.S.), the 7th Framework Programme (FP7) project Sustainable Polymers from Algae Sugars and Hydrocarbons (SPLASH; grant 311956 to V.A.P.M.d.S.) and the Horizon 2020 (H2020) project EmpowerPutida (grant 635536 to V.A.P.M.d.S.).

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Supplementary information

Supplementary information S1 (box)

Natural CO2 fixation pathways. (PDF 225 kb)

Supplementary information S2 (box)

Two examples of promising synthetic CO2 fixation cycles. (PDF 137 kb)

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Glossary

Autotrophs

Organisms that require only CO2 as a carbon source for growth.

Heterotrophs

Organisms that require organic substrates as a carbon source for growth.

Mixotrophs

Organisms that use both CO2 and an organic carbon source for growth (that is, the combination of autotrophic and heterotrophic processes in one organism).

Microbial cell factories

Microbial cells that produce compounds of interest under industrial conditions.

Synthetic biology principles

Principles that are borrowed from other engineering fields that can be applied for the engineering of biological systems, such as modularization and standardization.

Chemolithoautotrophs

Autotrophic microorganisms that use reduced inorganic compounds (such as H2 or NH3) as an energy source.

Electrocatalysis

Electrochemical processes in which electrical energy drives the conversion of water into H2 or other reduced compounds (such as formate or carbon monoxide) and O2.

Chassis

A concept in synthetic biology of a well-characterized, possibly streamlined, microbial host that acts as a platform to introduce heterologous systems.

Transformation efficiency

The efficiency of introducing extracellular DNA into microbial cells.

Photoautotrophs

Autotrophic organisms that use light as an energy source (for example, cyanobacteria, algae or plants).

Reducing power

Low potential electron donors (such as NAD(P)H or reduced ferredoxin) that can be used as electron donors in metabolic pathways.

Acetogens

Anaerobic microorganisms that produce acetate from H2 and CO2 or CO.

Nanowires

Thin artificial or microbial wires that can transport electrons; for example, between microorganisms or between a microorganism and an electrode.

Diazotrophic

Organisms that can fix N2 into, for example, NH4.

Ferredoxin

Iron–sulfur proteins that have key roles as metabolic electron carriers.

Carboxylase

An enzyme that catalyses the incorporation of CO2 into an organic molecule.

Photorespiration

Pathways that re-assimilate 2-phosphoglycolate, which results from ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) oxygenase side-activity, into central metabolism.

Bacterial microcompartments

Organelles found in bacteria that consist of a protein shell that encloses enzymes and other proteins.

Synthetic scaffolds

Synthetic biomolecular constructs that are based on nucleic acid or protein backbones to colocalize enzymes to improve their functionality.

Proton-pumping rhodopsins

Photosystems with a retinal pigment that can use light energy to pump protons across membranes.

Photosynthetic reaction centres

Photosystems with chlorophyll pigments containing reaction centres that use light energy to excite electrons.

Light-harvesting antennae

Pigment systems that absorb light and channel the energy of excited electrons towards the reaction centres of photosystems.

Cytochromes

Haem-containing proteins that have key roles as metabolic electron carriers in processes such as respiration.

Gibbs free energy of reactions

The thermodynamic potential of a reaction; reactions are only feasible for negative Gibbs free energy changes, the more negative the Gibbs free energy change the more thermodynamically favourable the reaction is.

Refactoring

The reorganization of native gene systems that encode a module such that they are better amenable for transplantation and engineering; for example, by removing native genetic regulatory elements and by clustering genes that are usually spread in their native state.

Allosteric regulation

The regulation of enzymatic activity by small molecules (for example, products) through interactions at allosteric non-catalytic sites of an enzyme.

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Claassens, N., Sousa, D., dos Santos, V. et al. Harnessing the power of microbial autotrophy. Nat Rev Microbiol 14, 692–706 (2016). https://doi.org/10.1038/nrmicro.2016.130

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