Next-gen sequencing finds ‘genes of luxury’

For the first time, researchers are able to look at the need for every gene in a bacterial cell in a single experiment. The new method will transform the study of gene activity and the search for weaknesses in bacterial armouries.

Using a newly developed, sequencing method, the team established which genes Salmonella Typhi needs to survive and which are more of a luxury. The results and the method will aid scientists tackling bacterial disease, allowing them to capitalise on the abundance of genomic sequence data from next-generation sequencing technologies.

The team were able to look at almost all the genes in S. Typhi and showed that it needs only 356 genes for survival: 4162 genes were not essential. Knowing which genes are essential to the survival of pathogens, researchers can seek treatments to target those genes.

“We developed a new method that is ten times more powerful than any previous technique,” says Sanger Institute graduate student Gemma Langridge, one of the first authors on the paper. “By combining transposon-induced mutagenesis – a method whereby small chunks of cut-and-paste DNA sequence are inserted into the genome effectively disabling individual genes – and high-throughput sequencing, we have been able to determine which genes are essential for the survival of S. Typhi and which are non-essential.”

“Crucially, our new method allows us to achieve all this in just a single experiment.”

Using the novel method, which the team have named TraDIS (Transposon Directed Insertion site Sequencing), they inserted transposons into the S. Typhi genome to generate more than one million mutants. They then grew the bacteria and used next-generation sequencing to directly identify 370,000 insertion sites in the S. Typhi genome – an average of more than 80 insertion sites per gene. Previous methods produce only a few mutations per gene.

“Sequencing centers such as ours can produce vast amounts of genomic data at a pace unimaginable just a few years ago,” explains Professor Julian Parkhill, Director of Sequencing and head of Pathogen Genomics at the Sanger Institute. “One of our aims is to develop high-throughput research methods that can exploit this explosion of genetic data, to ensure these resources can be used effectively. We can now discover which of all the genes in an organism are essential to its survival or required for growth under special conditions, such as infection. Our new TraDIS method will make a dramatic difference to the ability to carry out such genome-wide research.”