Typically, the DNA that makes up an organism's genome is transcribed into RNA, which is then translated into protein. Not all RNA is translated into protein, but research in recent decades has shown that even untranslated, or noncoding, RNA can play an important regulatory role. Cossart's group previously identified pieces of noncoding RNA that regulate Listeria's virulence. Suspecting that such a system of regulation might be widespread in the bacterial world, they set out to investigate Listeria's transcriptional program more systematically.

The gene chip company Affymetrix built them a set of tiling arrays, or arrays of DNA probes that correspond to overlapping stretches of the Listeria genome. Led by postdoc Alejandro Toledo-Arana, researchers from Cossart's lab and the labs of Jörgen Johansson (Umeá University, Sweden) and Marc Lecuit (Pasteur) used these arrays to analyze RNA extracted from Listeria that had been grown under different conditions. Specifically, they compared bacteria grown in broth with bacteria extracted from the intestine of Listeria-inoculated mice and with bacteria from inoculated samples of human blood. They also compared wild-type bacteria with bacteria genetically altered to lack known virulence factors.

They identified several previously unknown regulatory mechanisms, including two noncoding RNAs that contribute to Listeria's virulence and around 40 riboswitches—RNA structures that regulate protein production. Their work also revealed that Listeria's transcriptional program changes dramatically between its soil-dwelling and intestinal modes. As it arrives in the gut, some gene activity is turned up while other gene activity is turned down. For example, one protein, SigB, switches on a series of genes needed for Listeria to adapt to the mouse gut, whereas a different protein, PrfA, switches on genes needed for survival and replication in human blood.

Similar regulatory mechanisms will almost certainly turn up in other bacteria, Cossart says. While researchers go hunting for them, she has gone back to her model to fill in more gaps in knowledge. For example, with Lecuit and others, she has largely worked out the mechanisms Listeria uses to cross two of three internal barriers. Now she wants to nail the third: how it penetrates the blood-brain barrier. The more she knows about her model, she reasons, the more useful it will be—not only in the perpetual war against bacteria that make humans sick, but against all agents of infectious disease.

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