Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Emma Holden

PROVIDER: E-MTAB-12353 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

Project description: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.

2023-08-31 | E-MTAB-13250 | 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

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

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

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 E. coli in different concentrations of the antibiotics trimethoprim and sulfamethoxazole

Project description:To assay every gene in the E. coli genome to identify those that contribute to increased or decreased susceptibility to the antibiotics trimethoprim and sulfamethoxazole. This will help to define more accurately those bacterial cell mechanisms that contribute to these phenomena and provide information that will contribute to the development of new antibiotics, or compounds or known antibiotics that synergise with those already in clinical use. Thus, this set of experiments confirmed that AZT, widely known for its antiviral activity, acts synergistically with trimehoprim.

2020-10-19 | E-MTAB-9305 | biostudies-arrayexpress

Comparison of Tn-seq of Escherichia coli using B-2163 and MFDpir as donor strains.

Project description:To perform Tn-seq experiments random distribution of the transposon in the genome of the recipient cells is essential. In case transposon is delivered into the host cell by conjugation, donor may affect the distribution of the transposon in the genome of the recipient cell. Here, we provide two Tn-seq performed with two different donor strains. FX371 corresponds the Tn-seq using E. coli B-2163 as donor strain. FX442 corresponds to the Tn-seq using E. coli MFDpir as donor strain.

2020-11-12 | E-MTAB-9713 | biostudies-arrayexpress

Tn-seq of Vibrio cholerae in presence of 0.2% of L-arabinose

Project description:In presence of high concentrations of L-arabinose, Vibrio cholerae enters into a non-proliferative state. In V. cholerae, when L-arabinose in present into the media, it is incorporated and metabolized through the galactose pathway. In the present datasets we show that in presence of L-arabinose, transposon insertions in the galactose pathway confer a resistance to the detrimental effect of L-arabinose.

2020-11-16 | E-MTAB-9747 | biostudies-arrayexpress

Mapping the cellular and molecular landscape of cardiac non-myocytes in murine type-2 diabetes

Project description:Here we define key single-cell transcriptional alterations within cardiac non-myocytes, from ventricles of spontaneously type-2 diabetic (db/db) and control (db/h) mouse hearts ([B6.BKS(D)-Lepr<db>/J], stock #000697). The cell preparation sequenced consisted of metabolically active, live and nucleated non-myocyte cells, which were depleted of endothelial cells. The objective of this experiment was to develop a framework for understanding the dynamics of cardiac cell networks in murine type-2 diabetes, as a resource for future mechanistic studies.

2022-11-29 | E-MTAB-11940 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data