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Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?

Nature Reviews Microbiology volume 7, pages 715–723 (2009)Cite this article

Key Points

  • The ideal organism for biofuel production will possess high substrate use and processing capacities, fast and deregulated pathways of sugar transport, good tolerances to inhibitors and product, and high metabolic fluxes and will produce a single fermentation product. It is unclear whether such an organism will be engineered using a native isolated strain or a recombinant model organism as the starting point.

  • Ethanol and other alternative, next-generation biofuels all rely on the application of metabolic engineering principles to create an industrially relevant organism.

  • The discovery of additional diverse pathways through bioprospecting methods and new strain isolation will certainly improve prospects for further optimizing microorganisms and play an important part in developing biofuel production systems.

  • Advances in synthetic biology provide a valuable technology, enabling better diversification of the biofuel-type molecules that are produced in standard model organisms.

  • The divergent and often competing metabolic pathways that are required for the conversion of the relevant carbohydrates increase the challenge of finding or engineering one such superior organism. Therefore, it is important to consider the potential of using multiple engineered organisms to accomplish the goal of biofuels production.

  • The future of bioprocessing (whether biofuels or other chemicals) will be faced with the choice between exploiting innate cellular capacity and importing biosynthetic potential.

Abstract

The ideal microorganism for biofuel production will possess high substrate utilization and processing capacities, fast and deregulated pathways for sugar transport, good tolerance to inhibitors and product, and high metabolic fluxes and will produce a single fermentation product. It is unclear whether such an organism will be engineered using a native, isolated strain or a recombinant, model organism as the starting point. The choice between engineering natural function and importing biosynthetic capacity is affected by current progress in metabolic engineering and synthetic biology. This Review highlights some of the factors influencing the above decision, in light of current advances.

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Figure 1: Biofuel production by microorganisms.
Figure 2: Two routes to xylose assimilation.

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Acknowledgements

We acknowledge support from the Department of Energy (grant number: DE-FC36-07G017058), the National Science Foundation (grant number: CBET-0730238) and the Camille and Henry Dreyfus New Faculty Award.

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Authors and Affiliations

  1. Department of Chemical Engineering, The University of Texas at Austin, 1 University Station, Austin, C0400, 78712, Texas, USA

    Hal Alper

  2. Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56–469, Cambridge, 02139, Massachusetts, USA

    Gregory Stephanopoulos

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Correspondence to Gregory Stephanopoulos.

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DATABASES

Entrez Genome Project

Clostridium acetobutylicum

Clostridium phytofermentans

Clostridium thermocellum

Corynebacterium glutamicum

Escherichia coli

Saccharomyces cerevisiae

Zymomonas mobilis

FURTHER INFORMATION

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Glossary

Biomass

Raw plant material or agricultural waste typically composed of polymers of sugars and lignin.

Gasification

The thermal conversion of biomass into carbon monoxide and hydrogen through high temperature processing.

Syn gas

The carbon monoxide and hydrogen gas formed during gasification. Also known as synthesis gas.

Aqueous-phase reforming

A low-temperature, liquid- phase catalytic process that is used to convert biomass sugars into hydrocarbons through the formation of hydrogen gas.

Biomass utilization

The process of converting biomass into fuels and chemicals, including any physical, chemical, enzymatic or cell-based application.

Synthetic biology

The use of DNA synthesis and recombinant DNA technologies to design and construct novel functions and genetic circuits de novo.

Consolidated bioprocessing

An approach whereby the four major steps of biomass utilization (enzyme production, biomass hydrolysis, hexose fermentation and pentose fermentation) take place in a single step.

Lignocellulose

Plant biomass that is composed of the sugar polymers (cellulose and hemicellulose) and lignin (which is often composed of hydrophobic and aromatic molecules).

Bioprospecting

Searching for and borrowing useful genes from other organisms to confer a specifcally confer a specifically desired phenotype technology.

Isoprenoid

A chemically diverse and flexible polymer of the 5-carbon isoprene group that is found naturally in all living organisms.

Xylose fermentation capacity

The ability of a cell to convert xylose (a highly abundant, but often difficult to ferment, five-carbon sugar found in hemicellulose) into a biofuel.

Lycopene

A carotenoid (specific type of isoprenoid) that is a 40-carbon molecule formed by the condensation of isoprene units.

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Alper, H., Stephanopoulos, G. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?. Nat Rev Microbiol 7, 715–723 (2009). https://doi.org/10.1038/nrmicro2186

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