BY FRANK JACKSON III
JAN 27, 2011

A map of nearly 30,000 new microbial genes shows the path to enzymes that could provide improvements in biofuels, federal researchers are reporting.

The microbes are easy to find – they are located in a cow’s rumen – the animal’s preliminary digestive chamber.

Instead of using engineering approaches to optimize break down of biomass, the mapping vastly expands researchers’ genetic understanding of the microbes, enabling the use of natural organisms in communities that are already optimized for breaking down biomass.

The U.S. Department of Energy Joint Genome Institute released the research Thursday. The large-scale mapping capabilities provided by the DOE allowed researchers – including then postdoctoral fellow Matthias Hess – to map 270 billion new DNA letters and compile them into a genome of about two million genes.

Of those, 27,775 show markers for enzymes specific to breaking down cellulose sugars in plants. “One of the neat things,” Hess said, “is that we established a catalog of enzymes that we are interested in, which will be available Friday for anyone to access.”

Genes were classified as having enzymatic capabilities of biomass degradation by short stretches on the gene that had been identified as characteristics of other biomass degrading genes. The genetic understanding of the breakdown of biomass is an integral component of industrial advances in biofuel production.

“If we’re going to take these enzymes and use them on an industrial level, we need to be able to mass produce them. To do that, you actually need the gene that produces the enzyme,” said Garret Suen, professor of bacteriology at the University of Wisconsin-Madison.

One of the goals of the DOE is to generate second-generation biofuels such as ethanol, said Suen. To do so, complex sugars, such as cellulose, must be broken down by enzymes into simple sugars, such as glucose. Glucose is then converted into biofuel. “It’s the basic starting unit that people want to capitalize on,” he said.

In the past, said Hess, now a professor of molecular biosciences at Washington State University in Richland, microbes had to be cultivated and then sequenced. “The big advantage here is that you can now tap into this large amount of genes that can potentially degrade biomass,” he said.

In a cow's rumen, plant fiber is broken down into usable material, and has been studied for the past 40-50 years. “Now we have all this sequencing power, 200 times more than before…now we see the larger picture,” Hess said.

The larger picture is comprised of a complex community of microbes in the rumen, some of which have yet to be discovered. Hess said that there is an understanding of how some microbes work, and certain steps involved in the process of breaking down complex sugars into simple ones. However, the overall process is still unknown.

“Nature is so much more complex than we can, at this point, understand,” he said.

Researchers do understand, however, that the enzymes work together. Capturing all the genes in the system allows researchers to detect enzyme groups that work in tandem to break down biomass, whereas alone those enzymes would be unable to do so with the same efficiency. “We’re looking for things to boost the efficiency of the enzymes. You can think of it as an additive,” Suen said.

The Renewable Fuel Standard – a federal mandate outlined in the Energy Policy Act of 2005 –established a minimum requirement for biofuel consumption: an increase to 7.5 billion gallons by 2012. “If you can increase the efficiency of even one of those enzymes by 1 percent, think of the increase, in terms of the gallons of ethanol that is needed. It is quite a lot,” Suen said.

For such advances to be made and marketed, collaborations between the industry and academia must increase. “The industrial conversation of biomass into biofuel is a complex process,” Hess said, adding that the responsibility for the creation of such connections falls upon the industry.

Read full article on http://news.medill.northwestern.edu/