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Physiological limitations and opportunities in microbial metabolic engineering

Abstract

Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.

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Fig. 1: Cell growth and tolerance to product toxicity or medium conditions.
Fig. 2: Carbon source assimilation.
Fig. 3: Engineering primary metabolism.
Fig. 4: Engineering secondary metabolism.
Fig. 5: The role of subcellular architecture in microbial metabolic engineering.

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Acknowledgements

Work in the laboratory of J.L.A. is supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research Genomic Science Program under award number DE-SC0019363; the US Department of Defense, Air Force Office of Scientific Research (MURI) under award number FA9550-20-1-0241; the NSF CAREER program under award CBET-1751840; The Pew Charitable Trusts; and The Henry & Camille Dreyfus Foundation.

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J.M.L., L.D. and J.L.A. contributed to all aspects of the manuscript, including research, writing and editing.

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Glossary

Bioeconomy

An economy based on the use of biological renewable sources to produce value-added products, such as food, chemicals, materials and energy.

Adaptive laboratory evolution

(ALE). The continuous culturing of an organism under constant selection pressure, yielding microbial strains with improved phenotypes.

Genome shuffling

Methods that enable the recombination of genomes, generating populations with genetic diversity, in which some strains might possess beneficial traits.

Catabolite repression

Regulatory mechanisms that inhibit the use of secondary nutrient sources when a preferred one is present.

Bioreactors

Devices, apparatuses or systems for growing organisms under controlled conditions (for example, temperature, pH, oxygen and nutrient supply) for the synthesis of desired products.

Halophiles

Organisms that thrive in high salt concentrations.

Thermophiles

Organisms that thrive at high temperatures (typically above 45 °C)

Acidophiles

Organisms that can optimally grow at pH 3 or lower.

Alkaliphiles

Organisms that can optimally grow at pH 9 or higher.

Chemoautotrophs

Organisms that can synthesize organic molecules from CO2 using energy and electrons derived from chemicals.

Photoautotrophs

Organisms that can synthesize organic molecules from CO2 using light as an energy source and split water as a source of electrons.

Methylotrophs

Organisms that utilize reduced carbon substrates with no carbon–carbon bonds (for example, methane, methanol and formate) as their sole carbon and energy sources.

Heterotrophs

Organisms that derive their own biomass from organic matter produced by other organisms.

Mixotrophs

Organisms that use both CO2 and organic carbon sources to generate their biomass.

Primary metabolism

Set of enzymatic reactions involved in pathways necessary for growth and development, typically active when nutrients are present in the medium. Primary metabolites, which are essential to sustain cell growth, are synthesized by primary metabolism.

Secondary metabolism

Set of biosynthetic pathways that confer survival advantages on the organism but are not essential for cell growth. Secondary metabolism is typically active during the stationary phase in some microorganisms. Many bioactive compounds, referred to as ‘secondary metabolites’ or ‘natural products’ are synthesized by secondary metabolism.

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Montaño López, J., Duran, L. & Avalos, J.L. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol (2021). https://doi.org/10.1038/s41579-021-00600-0

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