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BioFiles Volume 5, Number 5 — Enzymes and Reagents for Alternative Energy

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Table of Contents



Robert Gates
Robert Gates

Leveraging nature's metabolic strategies for tomorrow's energy resources.

Although most of the world's population understands that carbon dioxide is the predominant end product of energy production from combustible fuels, most of us forget that the "raw material" for most of our combustible fuel sources is also atmospheric carbon dioxide. Photosynthetic carbon dioxide fixation is most often the first step in the synthesis of both our renewable fuels and non-renewable fossil fuels. Even much of our hydrogen production is an indirect product of carbon dioxide fixation as it is often derived from fossil fuels.

The basic differences between nonrenewable fossil fuels and our "new generation" renewable fuels is time, energy input and mass. Our non-renewable fuels, such as petroleum and coal required thousands of years of collection of solar energy to power carbon fixation for the biosynthesis of enormous amounts of biomass. That biomass then underwent millions of years of anaerobic decomposition to yield today's fossil fuels. In our attempt to circumvent or speed up this process, we are finding natural "renewable analogs" to some of our fossil fuels, i.e., ethanol and butanol to replace or supplement gasoline and fatty acid esters to replace diesel.

However, we have not advanced far enough in our manufacturing technology to divest ourselves of the need for biological systems to do the complicated work for us. Current processes for ethanol production rely on plants to fix carbon dioxide, synthesize a "common currency" molecule such as glucose, and then needlessly polymerize this glucose into starch or cellulose. Then we often rely on microbial and enzymatic hydrolysis of these biopolymers to give back glucose and then ferment it to yield ethanol. Sugarcane ethanol employs a slightly simpler path via sucrose.

Our challenge for the future may be to find the "straightest metabolic line" between carbon dioxide and ethanol, butanol, fatty acids or even hydrogen. The ideal route to ethanol production might be to devise an enzymatic or cellular system to fix carbon dioxide and take the direct route from ribose-1,5-bis-phosphate to pyruvate to ethanol and bypass glucose biosynthesis, polymerization and depolymerization. We have included the Nicholson/IUBMB Metabolic Pathway chart on the following pages illustrating the specific pathways related to carbon dioxide fixation and glucose, cellulose, pectin, starch, lignin and ethanol production highlighted in yellow.

Enzymes and their metabolic pathways enter the energy equation from other directions. Microbial strains are being discovered that can ferment cellulosic biomass to yield hydrogen. Some photosynthetic microbes, such as algae, are capable of splitting water to produce hydrogen utilizing solar energy. Hydrogenases are being targeted not only for hydrogen production but also for the oxidation of H2 in fuel cells. Immobilized enzyme-based fuel cell batteries can utilize multi-enzyme systems that mimic in vivo glycolytic and Krebs Cycle pathways. Immobilized enzymes are also being studied for the sequestration of carbon dioxide emissions.

Engineering organisms and enzyme systems to maximize biofuel production could require insertion of exogenous enzymatic pathways from various organisms into a new host. In addition, alternative metabolic pathways such as the mevalonate and isoprenoid pathways are being studied as sources of biofuel.

This issue of BioFiles is devoted to how Sigma-Aldrich enzymes and reagents are involved in many of these areas of research. As summarized above and illustrated below, many of these areas require an understanding of metabolic pathways and enzymatic processes.

Todays fuel sources originate primarily from the biosythesis of hydrocarbons originating from photosynthetic carbon dioxide fixation. The combustion of these fuels results in production of carbon dioxide. Ideally, this might someday be a "closed-CO2-loop" system with solar power as the only energy input. Many of the structures shown are basic examples of simple unbranched molecules intended to represent heterogeneous mixtures.


  1. S. Atsumi, J. C. Liao, Metabolic Engineering for Advanced Biofuels Production from Escherichia coli, Curr. Opin. Biotechnol., 19, 414–419 (2008).
  2. H. Alper, G. Stephanopoulos, Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?, Nature Reviews, Microbiology, 7, 715–723 (2009).
  3. P. P. Peralta-Yahya, J. D. Keasling, Advanced biofuel production in microbes, Biotechnol. J., 5, 147–162 (2010).
  4. J. M. Clomburg, R. Gonzalez, Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology, Appl. Microbiol. Biotechnpl., 86, 419–434 (2010).
  5. D. Klein-Marcuschamer, V. G. Yadav, A. Ghaderi, G. Stephanopoulos, De Novo Metabolic Engineering and the Promise of Synthetic DNA, Adv. Biochem. Eng. Biotechnol. in press (2010).
  6. J. L. Fortman, S. Chhabra, A. Mukhopadhyay, H. Chou, T. S. Lee, E. Steen, J. D. Keasling, Biofuel alternatives to ethanol: pumping the microbial well, Trends in Biotechnol., 26, 375–381 (2010).
  7. D. B. Levin, R. Islam, N. Cicek, R. Sparling, Hydrogen production by Clostridium thermocellum 27405 from cellulosic biomass substrates., Int. J. Hydrogen Energy, 31, 1496–1503 (2006).
  8. M. L. Ghirardi, S. Kosourov, A. Tsygankov1, A. Rubin, M. Seibert, Cyclic Photobiological Algal H2-Production, Proceedings of the 2002 U. S. DOE Hydrogen Program Review.
  9. A. A. Karyakin, S. V. Morozov, E. E. Karyakina, N. A. Zorin V. V. Perelygin, S. Cosnie, Hydrogenase Electrodes for Fuel Cells, International Hydrogenases Conference 2004.

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