Tools
ToolsPage, Andrew J., Bastkowski, Sarah, Yasir, Muhammad, Turner, A Keith, Le Viet, Thanh, Savva, George M, Webber, Mark A and Charles, Ian G (2020) AlbaTraDIS:Comparative analysis of large datasets from parallel transposon mutagenesis experiments. PLoS Computational Biology, 16 (7). ISSN 1553-734X
Preview |
PDF (Published_Version)
- Published Version
Available under License Creative Commons Attribution. Download (1MB) | Preview |
Abstract
Bacteria need to survive in a wide range of environments. Currently, there is an incomplete understanding of the genetic basis for mechanisms underpinning survival in stressful conditions, such as the presence of anti-microbials. Transposon directed insertion-site sequencing (TraDIS) is a powerful tool to identify genes and networks which are involved in survival and fitness under a given condition by simultaneously assaying the fitness of millions of mutants, thereby relating genotype to phenotype and contributing to an understanding of bacterial cell biology. A recent refinement of this approach allows the roles of essential genes in conditional stress survival to be inferred by altering their expression. These advancements combined with the rapidly falling costs of sequencing now allows comparisons between multiple experiments to identify commonalities in stress responses to different conditions. This capacity however poses a new challenge for analysis of multiple data sets in conjunction. To address this analysis need, we have developed 'AlbaTraDIS'; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes. AlbaTraDIS can identify genes which are up or down regulated, or inactivated, between multiple conditions, producing a filtered list of genes for further experimental validation as well as several accompanying data visualisations. We demonstrate the utility of our new approach by applying it to identify genes used by Escherichia coli to survive in a wide range of different concentrations of the biocide Triclosan. AlbaTraDIS identified all well characterised Triclosan resistance genes, including the primary target, fabI. A number of new loci were also implicated in Triclosan resistance and the predicted phenotypes for a selection of these were validated experimentally with results being consistent with predictions. AlbaTraDIS provides a simple and rapid method to analyse multiple transposon mutagenesis data sets allowing this technology to be used at large scale. To our knowledge this is the only tool currently available that can perform these tasks. AlbaTraDIS is written in Python 3 and is available under the open source licence GNU GPL 3 from https://github.com/quadram-institute-bioscience/albatradis.
| Item Type: | Article |
|---|---|
| Faculty \ School: | Faculty of Science > School of Biological Sciences Faculty of Medicine and Health Sciences > School of Health Sciences Faculty of Medicine and Health Sciences > Norwich Medical School |
| UEA Research Groups: | Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 13 Aug 2020 23:58 |
| Last Modified: | 03 Dec 2023 03:12 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/76435 |
| DOI: | 10.1371/journal.pcbi.1007980 |
Downloads
Downloads per month over past year
Actions (login required)
 |
View Item |