Biological Data: Enhanced

February 17, 2011

BY Bryan Sims

Metabolic engineers within the field of bioenergy are constantly on the lookout for more reliable bioinformatic tools that can help accelerate their research. With help of a three-year, $1.25 million grant from the U.S. DOE, Menlo Park, Calif.-based SRI International intends to make this task easier when it expands its MetaCyc database and enhances its Pathway Tools software. The upgrades are anticipated to give SRI’s bioinformatics tools even greater utility.

MetaCyc, a database that contains 1,500 metabolic pathways and 5,700 enzymes from more than 2,000 organisms within SRI’s BioCyc collection, is an extensive database comprised of experimentally determined, and literature-curated metabolic pathways by a wide range of scientific fields of academia.

Pathway Tools software will draw on data in SRI’s databases to generate alternative pathways to create a target compound from specified feedstocks, according to Ron Caspi, scientific database curator for SRI’s bioinformatics research group.. SRI’s software can also evaluate each pathway’s utility to produce specified target compounds, thereby allowing researchers to quickly identify and evaluate multiple pathways, design effective research protocols and shorten development timeframes.

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According to Caspi, SRI will expand its MetaCyc database to include energy-related metabolic pathways and enzymes associated with lignocellulosic biomass degradation, hydrogen production, biofuel and microalgae oil production. The expansion will allow the Pathway Tools software to recognize bioenergy-related pathways in sequenced microbes. This upgrade will result in more accurate metabolic pathway reconstructions and enable researchers and scientists to develop new ways to produce fuel and other valuable products from biomass and microorganisms.

“In bioenergy today, a lot of the work has to do with genomics because people have realized the power of having the sequenced information and working at the level of an organism rather than a protein here and a protein there,” Caspi says. “So, people have taken the first step and committed tremendous resources into sequencing many of their relevant organisms. The next step is to put it to good use.”

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In addition to enhancing its MetaCyc database, Caspi says that SRI intends to add a new function to Pathway Tools that will aid researchers in metabolic engineering of new or modified pathways. The tool, he adds, would let a researcher specify a starting compound and an end compound, including any desired intermediates.

“It would then scan the metabolic potential of that organism, as well as the large collection of metabolic enzymes available in MetaCyc and come up with potential metabolic routes that connect those two compounds via the desired intermediates,” he says.

The upgrade of SRI’s MetaCyc database, according to Caspi, should be a boon for improved computational approaches that lend themselves to more predictable genomic information access. “I think the [biorefining industry] will find this software very useful,” he says. 

—Bryan Sims

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