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PubMed2025

Common food preservatives induce an oxidative stress response in Salmonella enterica serovar Typhimurium.

Despite their frequent use, the mechanisms of action of common food preservatives are poorly understood. As there is a drive to develop alternative preservatives, understanding the mechanisms of action of current preservatives can inform the development of novel food preservatives to ensure their efficacy. Here, we used TraDIS-Xpress, a large-scale, genome-wide unbiased screen to determine the mechanisms of action of common food preservatives by determining the genes that affect preservative susceptibility in Salmonella enterica serovar Typhimurium. We identified genes associated with central metabolism and oxidative stress responses that were important for all four preservatives. Formate dehydrogenase activity and synthesis was crucial for survival in the presence of both sodium chloride and potassium chloride. We found some preservative-specific effects on pathogen susceptibility, for example, LPS synthesis which improved survival upon exposure to sodium nitrite but harmed survival when exposed to sodium chloride or potassium chloride. This research expands our understanding of how some current preservatives act and can inform the effective use of preservatives in current and emerging food products to ensure high standards of food safety.

Salmonella typhimurium↗

PubMed2026

Disruption of efflux activity reduces biofilm formation through multiple pathways.

Free-swimming bacteria must undergo large-scale changes in gene expression to form structured, aggregated biofilm communities. These regulatory changes are susceptible to environmental stimuli such as exposure to antimicrobials, which can affect adhesion, biofilm matrix production, pathogenicity and multidrug susceptibility. Previously, we found that genetic or chemical inactivation of efflux activity in Escherichia coli and Salmonella Typhimurium disrupts biofilm formation with a wide range of pathways sensitive to efflux inhibition, including reduced expression of csgD, a major regulator of biofilm matrix production. How the regulatory networks controlling efflux activity and biofilm formation overlap and how perturbing efflux impacts biofilm formation is still unclear. To address this, we used a combination of directed evolution experiments and large-scale functional genomics screens (TraDIS-Xpress) to identify the genes and pathways affecting efflux activity and biofilm formation in Salmonella enterica serovar Typhimurium and E. coli. This work describes the landscape of pathways linking efflux activity and biofilm formation. Whilst no singular gene or pathway was found to control the link between the two phenotypes, we propose changes in membrane potential following efflux inactivation are sensed through multiple response regulators that each in turn contribute to repression of biofilm development. These include the two-component signal transduction system EnvZ-OmpR and AraC/XylS family transcriptional regulators, RamA and MarA, which have extensive overlapping regulons and demonstrate high degrees of functional redundancy. This work deepens our understanding of the regulatory networks governing efflux activity and biofilm formation in Enterobacteriaceae and highlights the level of overlapping regulation and functional redundancy between them.

Salmonella typhimurium↗

PubMed1979

Investigations of the F conjugation gene traI:traI mutants and lambdatraI transducing phages.

A series of traI point and deletion mutants of Flac, and a traM mutant, were characterised. Complementation tests with an amber Flac traI mutant confirmed their genotypes, and in addition all the traI mutants, but not the traM mutant, were complemented by pRS31 (PSC101 traDI) and EDlambda109 (lambdatraI). Judging from the efficiencies of plating of F-specific phages, none of the mutations affected pilus formation. The traI products of F and of the F-like plasmid R1 were interchangeable with each other but not with that of R100, while the traM product of F could not be replaced by those of R1 or of R100. Neither traI nor traM were needed for conjugal transfer of ColE1. Three lambda transducing phages carrying traI were isolated by in vivo or in vitro techniques, and characterised by genetic complementation tests, by analysis of the fragments produced by restriction endonucleases, and by measurement of heteroduplex molecules. The genetic structures together with the sizes and F coordinates, of the transfer regions carried by the phages were thereby determined. Comparison of the proteins synthesised in UV-irradiated cells by one of the lambdatraI phages with those made by a derivative carrying an amber traI mutation, allowed the traI product to be identified as a protein of molecular weight 174,000. In addition, the molecular weights of the traD (84,000), traS (18,000), and traT (25,000) products made by the lambdatraSTD1 phage EDlambda107 were measured. The possible roles of the traI and traM products in conjugation are discussed.

Coliphages↗

PubMed2026

Applications of transposon-insertion sequencing for understanding bacterial physiology.

Transposon-insertion sequencing (Tn-seq) couples transposon mutagenesis with next-generation sequencing to identify the transposon insertion site for thousands of mutants in parallel. It is a powerful technology with a myriad of uses beyond the identification of essential genes required for a cell to grow and divide. Tn-seq is particularly useful as a high-throughput method to assign function to function-unknown genes, which have increased steadily with the abundance of newly sequenced bacterial genomes. Tn-seq has now been adapted for use in over 100 bacterial species. Here, we summarize the applications of Tn-seq for querying bacterial physiology and discuss some of the possible applications for the future.

DNA Transposable Elements↗

PubMed2026

Genome-wide identification of conditionally essential genes for growth in the presence of sulfamethoxazole and trimethoprim in sulfamethoxazole- and trimethoprim-resistant Escherichia coli.

UNLABELLED: Resistance to sulfonamides (SULs) and trimethoprim (TMP) in Escherichia coli threatens their clinical relevance. Beyond known resistance mechanisms, little is understood about the cellular responses that enable resistant E. coli to grow under these antibiotic stresses. This study aimed to identify genes that support bacterial growth under SUL and TMP stress. Two saturated transposon mutant libraries were constructed in resistant E. coli MG1655 harboring either dfrA1 or sul2. They were grown with and without 1/2 and 1/4 minimum inhibitory concentration (MIC) of sulfamethoxazole (SMX) or TMP, and mutant depletion was assessed via transposon-directed insertion-site sequencing. At 1/2 MIC, 36 and 89 genes were identified as conditionally essential during SMX and TMP exposure, while 5 and 2 genes were classified as conditionally essential at 1/4 MIC. Genes identified as conditionally essential at 1/4 MIC were also important at 1/2 MIC. Conditionally essential genes belonged to lipopolysaccharide biosynthesis, peptidoglycan metabolism, energy production, membrane integrity, phosphate metabolism, and stress responses, highlighting the role of these factors in maintaining cell stability under SMX and TMP stress. Validation with 10 conditionally essential genes (apaH, mtn, surA, waaO, nlpI, prc, wzxE, fadR, degP, and tpiA) showed that deletion mutants indeed exhibited growth defects and two- to eightfold reductions in MIC under antibiotic stresses compared to their parent strains. This study highlights cellular responses to SMX and TMP under antibiotic stress, and it has identified a list of genes whose products may serve as potential helper drug targets to resensitize resistant E. coli to SMX and TMP treatments. IMPORTANCE: Sulfonamides (SULs) and trimethoprim (TMP) are broad-spectrum antimicrobials. They are commonly used to treat infections in both humans and animals. Resistance against SUL and TMP is widespread in pathogenic bacteria, and there is a need to overcome this problem. One possibility is to target the cellular mechanism by which the resistant bacteria adapt to growth in the presence of the antimicrobials. In this study, we identify the genes, besides the resistance genes, which enable resistant Escherichia coli to grow in the presence of SUL and TMP. We further show that knocking out many of these genes attenuates the resistant E. coli for growth during SUL and/or TMP stress, irrespective of which SUL- or TMP-resistant gene the bacteria carry. The gene products of these genes may serve as potential helper drug targets to resensitize resistant E. coli to sulfamethoxazole and TMP treatments.

Escherichia coli↗