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Next generation sequencing surveys Salmonella

Salmonella Typhimurium

Salmonella Typhimurium

Strains of Salmonella bacteria cause over a billion cases of illness worldwide each year, and over 500,000 deaths. Most infection occurs through contaminated food and water. As part of the strategy to find ways to reduce the effects of Salmonella, Dr Arthur Thompson and colleagues at the Institute of Food Research have produced the first extensive and accurate map that shows where in the Salmonella genome genes are switched on and read from. These are called transcriptional start sites (TSSs), and the research has found the TSSs for 78% of the genes in S. Typhimurium.

An accurate map of the TSSs is essential for uncovering new levels of control of the genes used by Salmonella to invade our tissues. The team at the IFR, funded by the Biotechnology and Biological Sciences Research Council, used a novel next-generation sequencing technique called Differential RNA Sequencing (dRNA-seq) to map the precise locations of the TSSs.

“Mapping where the majority of Salmonella genes start to be transcribed from and discovering non-coding RNAs is a major landmark, as this will allow us much greater insight into how the genes that are required for virulence are controlled,” said Dr Thompson.

Since dRNA-seq analyses the entire transcriptome, which is all of the RNA molecules that are transcribed from the genome, the researchers were able to identify many RNA molecules that are not made into proteins. These are called non-coding RNAs and are important in controlling how genes are expressed, in particular the genes involved in making Salmonella pathogenic.

“We discovered striking amounts of non-coding RNA, which represents a new level of virulence gene regulation,” said Dr Thompson. “This exciting discovery is fuelling further research at IFR.”

Salmonella Typhimurium causes severe gastroenteritis in humans, entering our bodies through contaminated food or water and then invading the cells that line our gut. Salmonella uses a specific set of genes to invade the cells. The activation of these genes depends on a signalling molecule, known as ppGpp, but the regulation controlling which genes are turned on, or transcribed, is complex. To get insights into this, the team at IFR also used dRNA-seq to compare the transcriptome of normal S. Typhimurium with that of a mutant that is unable to make ppGpp, they were able to define the extent of the transcriptome Salmonella expresses in response to this signalling model.

The work represents an important resource for future study into Salmonella that researchers can use to understand how this important food borne pathogen adapts and exploits its environment.

Reference: The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression, BMC Genomics 13:25 doi: 10.1186/1471-2164-13-25

 

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