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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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TraDIS-Xpress finds mechanisms of action and synergies of a novel lipid IVA biosynthesis inhibitor

ABSTRACT: We used TraDIS-Xpress to determine the mechanism of action of a novel antimicrobial compound. We found that it inhibits lipid IVA biosynthesis in both Escherichia coli and Salmonella enterica serovar Typhimurium. We also were able to determine mechanisms of synergy with colistin, through ATP biosynthesis and the BasSR signalling system.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium

SUBMITTER: emma holden

PROVIDER: E-MTAB-13250 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Investigating Biofilm Formation Mechanisms in Salmonella on Fresh Produce Using TraDIS-Xpress

Project description:This study investigates the mechanisms employed by Salmonella to colonise and establish itself on fresh produce at critical timepoints following infection. We established an alfalfa infection model and compared the findings to those obtained from glass surfaces. Our research revealed dynamic changes in the pathways associated with biofilm formation over time, with distinct plant-specific and glass-specific mechanisms for biofilm formation, alongside the identification of shared genes playing pivotal roles in both contexts.

2023-11-24 | E-MTAB-13495 | biostudies-arrayexpress

Genome wide analysis of genes involved in efflux function and regulation within Escherichia coli and Salmonella enterica serovar Typhimurium

Project description:Expression of efflux pumps is a key feature of most cells which are resistant to multiple antibiotics. This study used TraDIS-Xpress, a genome wide transposon mutagenesis technology to identify genes in Escherichia coli and Salmonella Typhimurium involved in drug efflux and its regulation. We exposed mutant libraries to the canonical efflux substrate acriflavine in the presence and absence of the efflux inhibitor phenylalanine-arginine β-naphthylamide. Comparisons between conditions identified efflux specific and drug specific responses. Known efflux associated genes were easily identified including: AcrAB-TolC, MarA, RamA and SoxS confirming specificity of the response. Further genes encoding cell envelope maintenance enzymes and products involved with stringent response activation, DNA housekeeping, respiration and glutathione biosynthesis were also identified as affecting efflux activity in both species. We identified a conserved set of pathways crucial for efflux activity in these experimental conditions which expands the list of genes known to impact efflux efficacy.

2022-11-12 | E-MTAB-12353 | biostudies-arrayexpress

LoRTIS: A long read method for analysis of large transposon mutant libraries

Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.

2022-05-30 | E-MTAB-11351 | biostudies-arrayexpress

TraDIS-Xpress to determine E. coli response to Piperacillin and Tazobactam separately and in combination

Project description:Found how E. coli responds to the commonly prescribed antibiotic-inhibitor combination piperacillin and tazobactam, separately and in combination. TraDIS-Xpress was performed following the protocol outlined by Yasir et al 2020 Genome Research. The results suggest tazobactam triggers the activity of multidrug efflux systems that have been previously seen to confer clinical resistance to multiple classes of antibiotics.

2023-08-31 | E-MTAB-13226 | biostudies-arrayexpress

Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli

Project description:Most bacteria can form biofilms, which typically have a life cycle from cells initially attaching to a surface before aggregation and growth produces biomass and an extracellular matrix before finally cells disperse. To maximise fitness at each stage of this life cycle, and given the different events taking place within a biofilm, temporal regulation of gene expression is essential. We recently described the genes required for optimal fitness over time during biofilm formation in Escherichia coli using a massively parallel transposon mutagenesis approach called TraDIS-Xpress. We have now repeated this study in Salmonella enterica serovar Typhimurium to determine the similarities and differences in biofilm formation through time between these species. This work deepens understanding of the core requirements for biofilm formation in the Enterobacteriaceae whilst also identifying some genes with specialised roles in biofilm formation in each species.

2022-05-27 | E-MTAB-11765 | biostudies-arrayexpress

TraDIS-Xpress analysis of gene functions in Escherichia coli

Project description:This experiment was conducted to understand the gene functions of Escherichia coli in different concentrations of induction of Isopropyl β-D-1-thiogalactopyranoside (IPTG). Experiments were performed with no induction, or with induction using 0.2mM or 1 mM of IPTG.

2022-06-09 | E-MTAB-11808 | biostudies-arrayexpress

TraDIS-Xpress analysis of colistin stress responses in Escherichia coli

Project description:In past, resistance mechanisms have been identified by analysis of resistant isolates or defined mutants. Recently, high-throughput transposon mutagenesis coupled with sequencing (TraDIS-Xpress) is another approach proving useful for elucidating the roles of genes involved in the overall cellular response to a particular stress. In this study, we used TraDIS-Xpress to determine the role played by genes following exposure to colistin stress. Approximately 10^7 cells from the mutant library were inoculated into LB broth at a range of doubling concentrations of colistin ( 0.25 x MIC, 0.5 x MIC, 1 x MIC, 2 X MIC). Experiments were performed with no induction, or with induction using 0.2 or 1 mM of Isopropyl β-D-1-thiogalactopyranoside (IPTG). All experiments were performed in duplicate.

2022-06-09 | E-MTAB-11807 | biostudies-arrayexpress

Identification of Campylobacter jejuni and Campylobacter coli genes contributing to aerobic stress response using TraDIS analysis

Project description:The experiment aimed to find how Campylobacter responds to oxidative stress using hydrogen peroxide. This was done by using previously made TraDIS libraries (https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02835-8) and putting them under oxidative stress. The strains used were C. jejuni 11168, C. coli 15-537360 and C. coli CCN182.

2023-09-14 | E-MTAB-13336 | biostudies-arrayexpress

Transposon sequencing of E. coli in planktonic culture and in biofilms to determine the essentiality of genes throughout the biofilm life cycle

Project description:Biofilms undergo a life cycle where cells attach to a surface, grow and produce a structured community before dispersing to seed biofilms in new environments. Progression through this life cycle requires controlled temporal gene expression to maximise fitness at each stage. Previous studies have focused on the essential genome for the formation of a mature biofilm, but here we present an insight into the genes involved at different stages of biofilm formation. We used TraDIS-Xpress (a massively parallel transposon mutagenesis using transposon-located promoters to assay expression of all genes in the genome) to determine how gene essentiality and expression affects the fitness of E. coli growing as a biofilm on glass beads after 12, 24 and 48 hours. An E. coli transposon mutant library of approximately 800,000 unique mutants was grown on glass beads, and a planktonic sample was taken alongside this at each time point to compare gene essentiality and expression at each time point.

2021-06-09 | E-MTAB-9873 | biostudies-arrayexpress

Whole genome TraDIS-Xpress assay to determine gene roles during growth of Escherichia coli in competition with Pseudomonas aeruginosa, in the presence or absence of glucose

Project description:The aim of the experiment was to assay every gene in the Escherichia coli genome to identify those that contribute to competition with Pseudomonas aeruginosa. A library of transposon-insertion mutants was grown overnight either alone or together with an equal starting number of P. aeruginosa cells. The experiment was also conducted in the presence or absence of glucose to interrogate the effect of a plentiful supply of carbon source. DNA sequencing was then used to reveal the locations of the transposons in every mutant. By comparing the numbers of each mutant between conditions, information can be gained about the relative fitness of that mutant under the conditions tested.

2023-10-31 | E-MTAB-13391 | biostudies-arrayexpress

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