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BESC proteomic analysis of Yellowstone thermophile could aid cellulosic biofuel production

The study of proteins (proteomics) of thermophilic bacteria first found in Yellowstone’s hot springs are furthering efforts at the Department of Energy’s BioEnergy Science Center (BESC) toward developing commercially viable ethanol production from crops such as switchgrass.

The current production of ethanol generally relies on the use of expensive enzymes that break down complex plant materials to yield sugars that are fermented into ethanol. One suggested cheaper alternative is consolidated bioprocessing (CBP, e.g., earlier post), a process that allows simultaneous enzyme production, biomass hydrolysis and fermentation through the use of a cellulolytic, hemicellulolytic, and ethanologenic microbe or a microbial consortium.

The BESC study focused on Caldicellulosiruptor obsidiansis, a naturally occurring bacterium discovered by BESC scientists in a Yellowstone National Park hot spring. The microorganism, which thrives at extremely high temperatures, breaks down organic material such as sticks and leaves in its natural environment, and scientists hope to transfer this capability to biofuel production tanks.

In a paper featured on the cover of the ACS Journal of Proteome Research, the BESC team conducted a comparative analysis of proteins from C. obsidiansis grown on four different carbon sources, ranging from a simple sugar to more complex substrates such as pure cellulose and finally to switchgrass. The succession of carbon substrates allowed researchers to compare how the organism processes increasingly complex materials.

The researchers found that growth on switchgrass prompted the organism to express an expanded set of proteins that deal specifically with the hemicellulose content of the plant, including hemicellulose-targeted glycosidases and extracellular solute-binding proteins. Acting together, these two sub-systems work to break down the plant material and import the resulting sugars into the cell.

The scientists went on to show that once inside the cell, the organism “switches on” certain enzymes involved in pentose metabolism in order to further process these hemicellulose-derived sugars into usable energy.

By comparing how C. obsidiansis reacted to switchgrass, relative to pure cellulose, we were able to pinpoint the specific proteins and enzymes that are important to plant cell wall deconstruction—a major roadblock to the production of advanced biofuels.

—Richard Giannone, Oak Ridge National Laboratory, coauthor on a BESC proteomics study

The team’s measurement of the full complement and abundance of C. obsidiansis proteins can now be combined with other technologies such as genomics, transcriptomics and metabolomics in order to obtain a 360-degree, system-wide view of the organism. Instead of studying discrete proteins, these systems biology-type approaches provide more thorough insight into the day-to-day operations of bioenergy-relevant organisms and thus better equip researchers to make recommendations about their use in ethanol production.

One goal for us at the BioEnergy Science Center is to take these ‘omic’ technologies and integrate the data so we can draw definitive conclusions about a system.

—Richard Giannone

BESC is one of three DOE Bioenergy Research Centers established by the DOE’s Office of Science in 2007. The centers support multidisciplinary, multi-institutional research teams pursuing the fundamental scientific breakthroughs needed to make production of cellulosic biofuels, or biofuels from nonfood plant fiber, cost-effective on a national scale. The three centers are coordinated at ORNL, Lawrence Berkeley National Laboratory and the University of Wisconsin-Madison in partnership with Michigan State University.


  • Adriane Lochner, Richard J. Giannone, Martin Keller, Garabed Antranikian, David E. Graham, and Robert L. Hettich (2011) Label-free Quantitative Proteomics for the Extremely Thermophilic Bacterium Caldicellulosiruptor obsidiansis Reveal Distinct Abundance Patterns upon Growth on Cellobiose, Crystalline Cellulose, and Switchgrass. Journal of Proteome Research (12), 5302-5314 doi: 10.1021/pr200536j



They have tried jungle rot fungus, mushrooms that eat wood and other of natures cellulose eating organisms, if they keep at it they just might find or make something that does a good job.


The biologists try to find or make a bug or set of bugs to take plant-stuff apart and make it into ethanol. Meanwhile, the chemical engineers have a water-based process which does the job but requires a fair amount of process heat.

It's a horserace.


To use existing natural bugs and improve them may be a smart way to break down biomass and make bio-fuels more affordable. That's probably how crude oil and NG were made.


It is all solar energy, where plants and organisms over millions of years or a more current account system. We have used 100 million years of fossil fuel in 100 years, we can not keep doing this, obviously.


The world will certainly learn how to better convert and use clean solar energy before we run out of fossil fuel. Our grandchildren (pr their children) will have to visit museums to see our glorious ICEVs.

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