New technique used to profile anth...( Scientists at the Georgia Institute ...)

Scientists at the Georgia Institute of Technology have used a new approach, known as RNA-Seq, to profile the gene expression of the bacterium that causes anthrax, Bacillus anthracis. Their study, published March 20, 2009, online by the Journal of Bacteriology, marks the first time any bacterial transcriptomethe complete collection of mRNAs produced by a bacterium as it expresses different geneshas been comprehensively defined, and provides a much more detailed view of how bacteria regulate their gene expression.

"Sequencing a bacterial genome has gotten to be pretty routine, but going to a deeper level and defining the transcriptome has been a much more difficult task," said Nicholas Bergman, assistant professor in the School of Biology at Georgia Tech and senior research scientist in the Electro-Optical Systems Laboratory at the Georgia Tech Research Institute.

"With traditional methods, transcript structure and abundance really have to be determined one gene at a time, and a completely defined transcriptome was out of reach for even the most widely studied species," said Bergman. "The RNA-Seq approach allowed us to get around the limitations of traditional methods so that we can see in a much more detailed way how each of the 5,000+ genes in B. anthracis genome is expressed and regulated."

The RNA-Seq approach works by using a technique known as high throughput sequencing, which counts millions of messenger RNA (mRNA) sequences simultaneously. Although the method was used to define the transcriptomes of several eukaryotic organisms in 2008, applying it to bacteria has been difficult, said Bergman, because bacterial mRNAs have a different structure and cannot be easily separated from the other RNAs in the cell.

To solve this problem, the Georgia Tech team worked with researchers from Life Technologies, a biotechnology tools company, and ultimately developed a set of procedures that can be used to apply RNA-Seq to
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