Goodall, E.C., Robinson, A., Johnston, I.G., Jabbari, S., Turner, K.A., Cunningham, A.F., Lund, P.A., Cole, J.A. and Henderson, I.R., 2018. The essential genome of Escherichia coli K-12. mBio, 9 e02096 (2018)
Bacteria cause diseases, and are developing resistance to the drugs we use to kill them. Anti-microbial resistance (AMR) is one of the most pressing global health challenges facing society. In the immense scientific endeavour of creating new, effective treatments for bacterial infections, fundamental biological knowledge about how bacteria live and proliferate is of vital importance.
One way we can obtain this knowledge is by discovering what cellular machinery that bacteria need to survive and proliferate. A common (and famous) bacterium called Escherichia coli (E. coli) has over 4000 protein-coding genes, but we're not really sure which of these genes is essential for the bacterium, and how many provide some non-essential "added value". If we can learn which genes are essential for bacteria, we have a more specific set of targets to shoot for in designing new drugs and therapies.
So -- how can we find out which genes are essential for E. coli? One neat way involves a new experimental approach called transposon-directed insertion site sequencing (TraDIS). Transposons are elements of DNA that can be inserted into a bacterial genome -- when they are inserted into part of the genome that codes for a gene, they prevent that gene being properly expressed, effectively removing it from the bacterium. TraDIS, in essence, takes a large population of bacteria and inserts one transposon into a random position in each bacterium. The population is then left to evolve for some time. After that time, we look at the genomes of bacteria within the surviving population, and see exactly where transposon insertions have been retained in some living bacteria.
The idea is that any bacteria in the population that have a transposon inserted into an essential gene will die. As such a gene is essential, it's required for survival, and a transposon preventing its expression will kill the bacterium. Therefore, if some bacteria in a population retain an insertion in gene X and survive, it follows that gene X is not essential. Conversely, if we see a large region of the genome within which no insertions are retained in the final population, it is likely that that region corresponds to an essential gene.
There's some mathematical subtlety in the "it is likely". Depending on how many transposon insertions originally occur, and the length of the genome, some regions without insertions may occur just by chance. We did a bit of maths to work out how unlikely it is to see an insertion-free region of a given length arise by chance; and, by extension, how likely it is that a gene identified by this analysis is indeed essential for the bacterium. However, the maths was only one part of this project -- it was first and foremost an experimental tour de force by our excellent collaborators. We jointly provided a new atlas of essential genes in E. coli, provide a new way of reasoning about the powerful TraDIS technique, and provide several new insights into bacterial physiology and biochemistry. The work is freely available in the journal mBio here. Iain
Bacteria cause diseases, and are developing resistance to the drugs we use to kill them. Anti-microbial resistance (AMR) is one of the most pressing global health challenges facing society. In the immense scientific endeavour of creating new, effective treatments for bacterial infections, fundamental biological knowledge about how bacteria live and proliferate is of vital importance.
One way we can obtain this knowledge is by discovering what cellular machinery that bacteria need to survive and proliferate. A common (and famous) bacterium called Escherichia coli (E. coli) has over 4000 protein-coding genes, but we're not really sure which of these genes is essential for the bacterium, and how many provide some non-essential "added value". If we can learn which genes are essential for bacteria, we have a more specific set of targets to shoot for in designing new drugs and therapies.
So -- how can we find out which genes are essential for E. coli? One neat way involves a new experimental approach called transposon-directed insertion site sequencing (TraDIS). Transposons are elements of DNA that can be inserted into a bacterial genome -- when they are inserted into part of the genome that codes for a gene, they prevent that gene being properly expressed, effectively removing it from the bacterium. TraDIS, in essence, takes a large population of bacteria and inserts one transposon into a random position in each bacterium. The population is then left to evolve for some time. After that time, we look at the genomes of bacteria within the surviving population, and see exactly where transposon insertions have been retained in some living bacteria.
A stylised representation of the E. coli genome and the positions within it where we found transposons to have been retained (corresponding to non-essential genes).
The idea is that any bacteria in the population that have a transposon inserted into an essential gene will die. As such a gene is essential, it's required for survival, and a transposon preventing its expression will kill the bacterium. Therefore, if some bacteria in a population retain an insertion in gene X and survive, it follows that gene X is not essential. Conversely, if we see a large region of the genome within which no insertions are retained in the final population, it is likely that that region corresponds to an essential gene.
There's some mathematical subtlety in the "it is likely". Depending on how many transposon insertions originally occur, and the length of the genome, some regions without insertions may occur just by chance. We did a bit of maths to work out how unlikely it is to see an insertion-free region of a given length arise by chance; and, by extension, how likely it is that a gene identified by this analysis is indeed essential for the bacterium. However, the maths was only one part of this project -- it was first and foremost an experimental tour de force by our excellent collaborators. We jointly provided a new atlas of essential genes in E. coli, provide a new way of reasoning about the powerful TraDIS technique, and provide several new insights into bacterial physiology and biochemistry. The work is freely available in the journal mBio here. Iain
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