Ontology highlight
ABSTRACT:
PROVIDER: PRJNA554767 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9691140_1.fastq.gz | Fastqsanger.gz | |||
| SRR9691140_2.fastq.gz | Fastqsanger.gz | |||
| SRR9691150_1.fastq.gz | Fastqsanger.gz | |||
| SRR9691150_2.fastq.gz | Fastqsanger.gz | |||
| SRR9691141_1.fastq.gz | Fastqsanger.gz |
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Project description:Listeria monocytogenes is a food-borne pathogen and the causative agent of listeriosis, an infection which typically arises through the consumption of contaminated foodstuffs. L. monocytogenes is a psychotrophic and facultatively anaerobic; properties which permit growth under refrigeration conditions and within modified atmosphere packaging. Through transcriptional changes L. monocytogenes is able to mount adaptive responses against stressors. Such responses typically cross protect against subsequent stresses.
2016-12-30 | GSE84879 | GEO
Project description:Peracetic acid (PAA), a strong oxidizing agent, has been widely used as a disinfectant in food processing settings as it does not produce harmful chlorinated by-products. In the present study, the transcriptional response of Listeria monocytogenes to 2.5 ppm of PAA was assessed using RNA-sequencing (RNA-seq). Our analysis revealed 12 differentially expressed genes, of which 9 were up-regulated (ohrR, ohrA, rpsN, lmo0637, lmo1973, fur, lmo2492, zurM, and lmo1007), and 3 were down-regulated (argG, lmo0604, lmo2156) in PAA treated samples compared to the control samples. A non-coding small RNA (rli32) was also found to be down-regulated. In detail, the organic peroxide toxicity protection (OhrA-OhrR) system, the metal homeostasis genes fur and zurM, the SbrE-regulated lmo0636-lmo0637 operon and a carbohydrate phosphotransferase system (PTS) operon component were induced under exposure of L. monocytogenes to PAA. Hence, this study identified key elements involved in the primary response of L. monocytogenes to oxidative stress caused by PAA. The investigation of the molecular mechanism of PAA response in L. monocytogenes is of utmost importance for the food industry, as this response can be induced in food-processing environments, as a result of inadequate rinsing during the disinfection process, that lead to PAA residues at low concentrations.
2024-10-04 | GSE269393 | GEO
Project description:Persistence of Listeria monocytogenes in retail deli environments is a serious food safety issue, potentially leading to cross-contamination of ready-to-eat foods such as deli meats, salads, and cheeses. We previously discovered strong evidence of L. monocytogenes persistence in delis across multiple states. We hypothesized that this was correlated with isolates’ innate characteristics, such as biofilm-forming capacity or gene differences.We further chose four isolates for RNA-sequencing analysis and compared their global biofilm transcriptome to their global planktonic transcriptome. Analysis of biofilm vs planktonic gene expression did not show the expected differences in gene expression patterns. Overall, L. monocytogenes persistence in the deli environment is likely a matter of poor sanitation and/or facility design, rather than isolates’ biofilm-forming capacity, sanitizer tolerance, or genomic content
2021-06-11 | GSE176617 | GEO
Project description:Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site (TSS) maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. Our data revealed conservation across most transcripts, but significant divergence between the species in a subset of non-coding RNAs. In L. monocytogenes we identified 113 sRNAs and 70 asRNAs, significantly increasing the repertoire of non coding RNAs in this species. Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 5M-bM-^@M-^Y UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such lasRNA/operon structure, termed "excludon", might represent a novel form of regulation in bacteria. Construction of consensus TSS-maps in Listeria monocytogenes and Listeria innocua by applying 5'-end sequencing on samples in different conditions and genetic backgrounds.
2012-05-01 | E-GEOD-36060 | biostudies-arrayexpress
Project description:In several gram-positive bacterial genera including Bacillus, Staphylococcus, and Listeria, sigma B (σB) has been identified as a stress-responsive alternative sigma factor responsible for initiating transcription of genes (the σB regulon) involved in response to stress-inducing environmental conditions. In L. monocytogenes, a foodborne pathogen of considerable threat to public health and the food industry, σB is involved in regulation of stress response and virulence gene expression. We have defined the σB regulon in L. monocytogenes during early stationary phase and under salt stress (0.3M NaCl) conditions using whole-genome microarrays, identifying 168 genes that generated ≥2.0-fold higher signals in the parental strain 10403S than in an isogenic sigB null mutant (ΔsigB), categorized into nine functional groups including stress-response genes (12), virulence genes (5), and genes related to transport (26) and metabolism (45). To gain a broader biological perspective of the σB stress response system, we applied these microarrays to Listeria innocua under the same environmental conditions. Our studies revealed 64 candidates in the L. innocua σB regulon with ≥2.0-fold higher signals in the parent than in a ΔsigB mutant; 49 of the 64 genes overlap with the L. monocytogenes σB regulon, indicating extensive overlap in σB-controlled genes between the two species. Further transcriptional analysis using TaqMan quantitative real time RT-PCR was performed for selected genes that displayed contrasting fold changes among the four microarray data sets (two stress conditions per species). We report novel members of the L. monocytogenes σB regulon, as well as the initial definition of the L. innocua σB regulon. Our comparative studies of the σB stress response systems in L. monocytogenes and L. innocua revealed features of the σB regulon that are conserved and unique to the two species. Keywords: Listeria monocytogenes, Listeria innocua, SigB regulon, salt stress, stationary phase
2007-11-29 | GSE7492 | GEO
Project description:The SOS response is a conserved pathway that is activated under certain stress conditions and is regulated by the repressor LexA and the activator RecA. The food-borne pathogen Listeria monocytogenes contains RecA and LexA homologs, but their roles in Listeria have not been established. In this study, we identified the SOS regulon in L. monocytogenes by comparing the transcription profiles of the wild-type strain and the ΔrecA mutant strain after exposure to the DNA damaging agent mitomycinC (MMC). The SOS response is an inducible pathway involved in DNA repair, restart of stalled replication forks, and in induction of genetic variation in stressed and stationary phase cells. It is regulated by LexA and RecA. LexA is an autoregulatory repressor which binds to a consensus sequence in the promoter region of the SOS response genes, thereby repressing transcription. A consensus LexA binding motif for L. monocytogenes has not been identified thus far. Generally, the SOS response is induced under circumstances in which single stranded DNA accumulates in the cell. This results in activation of RecA, which in turn stimulates cleavage of LexA, and ultimately in the induction of the SOS response. Keywords: stress response, loop design, SOS response, mitomycin c, listeria monocytogenes, RecA, LexA
2009-11-25 | GSE12634 | GEO
Project description:The formation of Listeria monocytogenes biofilms contributes to persistent contamination in food processing facilities. A microarray comparison of L. monocytogenes between the transcriptome of the strong biofilm forming strain (Bfms) Scott A and the weak biofilm forming (Bfmw) strain F2365 was conducted to identify genes potentially involved in biofilm formation. Among 951 genes with significant difference in expression between the two strains, a GntR-family response regulator encoding gene (LMOf2365_0414), designated lbrA, was found to be highly expressed in Scott A relative to F2365. A Scott A lbrA-deletion mutant, designated AW3, formed biofilm to a much lesser extent as compared to the parent strain by a rapid attachment assay and scanning electron microscopy. Complementation with lbrA from Scott A restored the Bfms phenotype in the AW3 derivative. A second microarray assessment using the lbrA deletion mutant AW3 and the wild type Scott A revealed a total of 304 genes with expression significantly different between the two strains, indicating the potential regulatory role of LbrA in L. monocytogenes. A cloned copy of Scott A lbrA was unable to confer enhanced biofilm forming potential in F2365, suggesting that additional factors contributed to weak biofilm formation by F2365. Findings from the study may lead to new strategies to modulate biofilm formation. Two comparisons were performed between 1) strong biofilm former Listeria monocytogenes strain ScottA versus weak biofilm former Listeria monocytogenes strain F2365; 2) Listeria monocytogenes ScottA LbrA deletion mutant strain versus Listeria monocytogenes ScottA. Four replicates were loaded for the first comparison and two replicates were loaded for the second comparison.
2012-09-06 | E-GEOD-40598 | biostudies-arrayexpress
Project description:Listeria monocytogenes is a food-borne pathogen which causes listeriosis. It is an intracellular parasite invading the epithelial cells where it escapes from the vacuole into the host cytoplasm to replicate, using actin-based motility to move within and between cells. The intracellular life cycle is well documented whereas the time spent in the lumen of the intestine is poorly understood. The aim of this study was to investigate the mechanism by which L. monocytogenes adapts to the environment of the small intestine prior to invasion. Specifically, to determine if the PrfA regulon, that encodes the virulence factors of L. monocytogenes, is switched on by signals within the intestinal lumen. L. monocytogenes were grown under aerobic or microaerobic conditions with glucose or glycerol as carbon source.
2023-11-24 | E-MTAB-12856 | biostudies-arrayexpress
Project description:The foodborne pathogen Listeria monocytogenes has the ability to develop biofilm in food-processing environment, which becomes a major concern for the food safety. PrfA, a key transcriptional activator that regulates most of the known listerial virulence gene expression, has been shown to promote L. monocytogenes biofilm formation. In this study, the whole genome microarray was used to identify differentially expressed genes associated with the putative interaction between biofilm formation and PrfA in L. monocytogenes. Comparative transcriptome analyses indicated over 21.9% of the L. monocytogenes EGDe genes (627 out of 2857 predicted) were altered in their expression in biofilm cells relative to planktonic cell populations. These genes were classed into different functional categories which cover most of the biochemical functions encountered in bacterial cells, especially involved in ion transport, DNA repair, and cell wall biosynthesis based on significant enrichment of GO terms. Among them, 185 genes were identified to be associated with PrfA and biofilm formation by comparison of the whole gene expression profiles of L. monocytogenes EGDe and its M-NM-^TprfA mutant. The expression tendency of these PrfA-associated and biofilm-specific genes were mainly opposite in M-NM-^TprfA biofilm, and most of them are involved in phage-related function, membrane bioenergetics, and cell wall. Our results indicated that L. monocytogenes biofilm formation is probably controlled by the complex regulation network involved variable genes required for the different biological pathways. This regulatory network is modified in the prfA deletion mutant in order to maintain its stable biofilm lifestyle. Gene expression of planktonic cells and biofilm cells in Listeria monocytogenes EGDe and prfA isogenic deletion strain EGDeM-NM-^TprfA with cultivated in MEM and BHI for 48 hours, were mesasued using Agilent Listeria monocytogenes customized whole-genome microarray 8x15 array. Three replicates.
2013-05-01 | E-GEOD-43052 | biostudies-arrayexpress