Scientists from the Quadram Institute and University of East Anglia on the Norwich Research Park have developed a new platform technology to study how bacteria survive and grow following exposure to a range of challenging, or stress-inducing conditions. The work which was in collaboration with colleagues from University of Technology in Sydney was used to identify previously unidentified bacterial genes implicated in resistance and sensitivity to the household antimicrobial triclosan.
Triclosan is used extensively in household products such as soaps, mouthwashes, shampoos, cosmetics and toothpastes. A new study, published in the journal Genome Research, deploys this new platform technology to understand how bacteria resist or become more sensitive to exposure to the compound.
TraDIS-Xpress simultaneously assays all of an organism’s genes, identifying those that are essential for growth and those whose up-or down-regulation promotes or inhibits growth under different stresses
Called ‘TraDIS-Xpress’, the new approach builds on the established TraDIS method (Transposon-Directed Insertion-site Sequencing). The platform technology has numerous applications and importantly can be used in the race to find new antimicrobial agents by identifying how drugs like antibiotics act against bacteria. It can also be used to help develop better probiotic bacteria for health promotion, or to understand how to re-engineer bacteria for industrial applications. This study was funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation (UKRI).
In recent years, modern DNA sequencing technology has enabled scientists to identify all the genes in any given bacteria. However, despite this increase in knowledge, the function of many of these genes is still poorly understood, particularly with respect to their role in microbial viability. To address this challenge, the Quadram team, led by the Quadram Institute’s Director Professor Ian Charles and Dr Mark Webber, have developed the new ‘TraDIS-Xpress’ platform.
‘TraDIS-Xpress’ works by simultaneously assaying all the genes in a target organism by combining two fundamental approaches used in bacterial genetics, mutation and gene expression. It then tests the resulting impact of these alterations on survival and growth of the candidate organism. The method introduces small pieces of DNA called transposons into bacterial cells. These also contain a ‘promoter’ and will simultaneously disrupt target gene’s function (mutation) or change how much of a target is produced (expression). The approach can be applied to a wide range of bacteria and used to understand how they are able to survive and grow in any condition of interest.
Prof. Charles and Dr Mark Webber from the Quadram Institute said “We now have a tool which can efficiently assay all the genes in a genome for roles in any given stress situation. Our work on triclosan shows that this platform will help us understand how bacteria work and we hope to use this approach to address important problems such as the fight against antimicrobial resistance and how to produce better ‘good bacteria’ to help protect our health.”
Reference: TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance. Muhammad Yasir, A. Keith Turner, Sarah Bastkowski, David Baker, Andrew J. Page, Andrea Telatin, Minh-Duy Phan, Leigh Monahan, George M. Savva, Aaron Darling, Mark A. Webber, and Ian G. Charles Genome Research doi: 10.1101/gr.254391.119
The basis for the technology is described in a new video produced by the Quadram Institute
TraDIS – Transposon Directed Insertion Site Sequencing from Quadram Institute on Vimeo.