New technology will help crack E. Coli’s gene code


New York : E. coli has remained a mystery for long as a fourth of the roughly 4,000 genes it carries are unknown to researchers. But ‘GIANT-Coli,’ short for genetic interaction analysis technology for E. coli, a new technique, has the potential to speed up the discovery of new gene functions and help crack its code, says a new study.

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The principle behind this technique is to track interaction among genes that produces observable effects, and helping identify gene functions. Harmless E. coli strains are found in many animals and human intestines, but some can cause diseases.

The use of GIANT-Coli has already allowed researchers to identify some previously unknown genetic interactions in E. coli , said Deborah Siegele, a biology professor at Texas A&M University.

Siegele and her co-workers at the University of California San Francisco, Nara Institute of Science Technology and Purdue University have devised this method that allows rapid and large-scale studies of the E. coli genes.

To study genetic interaction, researchers need to use what they call double-mutant strains. GIANT-Coli allows large-scale generation of these double-mutant strains (high-throughput generation). And this is the first time that a high-throughput generation method for double mutants of E. coli has been developed.

Why is it so important to know the E. coli better? “Much of what we know about other bacteria, including the more dangerous ones like Vibrio cholerae, comes from our knowledge of E. coli,” said Siegele. “The E. coli is a model organism.”

Siegele said that GIANT-Coli can be developed to study genetic interactions in other bacteria, and because some proteins are conserved from bacteria to humans, perhaps some of the results can even be extrapolated to gene function in humans.

Moreover, Siegele pointed out that the method has obvious application in medicine because understanding gene functions in harmful bacteria will help develop better treatment approaches.

The new method has been detailed in the current online issue of Nature Methods.