Listeria monocytogenes transcriptomics
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PROVIDER: PRJEB32036 | ENA |
REPOSITORIES: ENA
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Project description:Listeria monocytogenes strains classify into at least three distinct phylogenetic lineages. Correlations exist between lineage classification and source of bacterial isolation, e.g., human clinical and food isolates usually classify into either lineage I or II, however, human clinical isolates are over-represented in lineage I while food isolates are over-represented in lineage II. σB, a transcriptional regulator previously demonstrated to contribute to environmental stress response and virulence in L. monocytogenes lineage II strains, was hypothesized to provide differential capabilities for L. monocytogenes survival in various niches (e.g., food vs. human clinical). To determine if σB contributions to stress response and virulence differ across diverse L. monocytogenes strains, ΔsigB mutations were created in strains from lineages I, II, IIIA, and IIIB. Paired parent and ΔsigB mutant strains were tested for acid and oxidative stress survival, Caco-2 cell invasion efficiency, and virulence using the guinea pig listeriosis infection model. Parent and ΔsigB mutant strain transcriptomes were compared using whole-genome expression microarrays. σB contributed to virulence in each strain. However, while σB contributed significantly to acid and oxidative stress survival and Caco-2 cell invasion in lineage I, II, and IIIB strains, σB contributions were not significant for these phenotypes in the lineage IIIA strain. A core set of 63 genes was positively regulated by σB in all four strains; different total numbers of genes were positively regulated by σB in each strain. Our results suggest that σB universally contributes to L. monocytogenes virulence, but specific σB-regulated stress response phenotypes vary among strains.
2010-06-01 | GSE21427 | GEO
Project description:The aim of this study is to contribute to the understanding of L. monocytogenes virulence and survival capabilities using global gene expression profiling by means of DNA macroarrays. Keywords: strain comparison; correlation between expression and behaviour
2006-07-03 | GSE3247 | GEO
Project description:Listeria monocytogenes strains classify into at least three distinct phylogenetic lineages. Correlations exist between lineage classification and source of bacterial isolation, e.g., human clinical and food isolates usually classify into either lineage I or II, however, human clinical isolates are over-represented in lineage I while food isolates are over-represented in lineage II. σB, a transcriptional regulator previously demonstrated to contribute to environmental stress response and virulence in L. monocytogenes lineage II strains, was hypothesized to provide differential capabilities for L. monocytogenes survival in various niches (e.g., food vs. human clinical). To determine if σB contributions to stress response and virulence differ across diverse L. monocytogenes strains, ΔsigB mutations were created in strains from lineages I, II, IIIA, and IIIB. Paired parent and ΔsigB mutant strains were tested for acid and oxidative stress survival, Caco-2 cell invasion efficiency, and virulence using the guinea pig listeriosis infection model. Parent and ΔsigB mutant strain transcriptomes were compared using whole-genome expression microarrays. σB contributed to virulence in each strain. However, while σB contributed significantly to acid and oxidative stress survival and Caco-2 cell invasion in lineage I, II, and IIIB strains, σB contributions were not significant for these phenotypes in the lineage IIIA strain. A core set of 63 genes was positively regulated by σB in all four strains; different total numbers of genes were positively regulated by σB in each strain. Our results suggest that σB universally contributes to L. monocytogenes virulence, but specific σB-regulated stress response phenotypes vary among strains.
2010-06-01 | E-GEOD-21427 | biostudies-arrayexpress
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:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator CtsR, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DctsR log phase cells were compared to both wt and ictsR-mcsA log phase cells grown with 0.5mM IPTG to identify CtsR-dependent genes.We identified 62 CtsR-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression either between ΔctsR and wt or between ΔctsR and ictsR-mcsA. Keywords: Listeria monocytogenes, CtsR regulon, log phase
2007-10-14 | GSE7514 | GEO
Project description:Clinical Listeria monocytogenes isolates in Miyagi
| PRJDB9929 | ENA
Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes. We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression between ΔhrcA and wt. Combined with microarray analysis, Hidden Markov Model searches show HrcA directly repress at least 8 genes. Keywords: Listeria monocytogenes, HrcA regulon, stationary phase
2007-11-03 | GSE7517 | GEO
Project description:The stationary phase stress response transcriptome of the human bacterial pathogen Listeria monocytogenes was defined using RNA sequencing (RNA-Seq) with the Illumina Genome Analyzer. Specifically, bacterial transcriptomes were compared between stationary phase cells of L. monocytogenes 10403S and an otherwise isogenic DsigB mutant, which does not express the alternative sigma factor σB, a major regulator of genes contributing to stress response. Keywords: Transcriptome and differential expression analyses
2010-01-05 | GSE15651 | GEO
Project description:Full title: Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes: Implications for its niche adaptation, pathogenesis, and evolution Listeria monocytogenes is a foodborne bacterial pathogen well known for adaptability to diverse environmental and host niches, and a high fatality rate among infected, immuno-compromised individuals. Three genetic lineages have been identified within this species. Strains of genetic lineages I and II account for more than ninety percent of foodborne disease outbreaks worldwide, whereas strains from genetic lineage III are rarely implicated in human infectious for unknown, yet intriguing, reasons. Here we have probed the genomic diversity of 26 L. monocytogenes strains using both whole-genome sequences and a novel 385,000 probe pan-genome microarray, fully tiling the genomes of 20 representative strains. Using these methods to identify genes highly conserved in lineages I and II but rare in lineage III, we have identified 86 genes and 8 small RNAs that play roles in bacterial stress resistance, pathogenicity, and niche, potentially explaining the predominance of L. monocytogenes lineages I and II in foodborne disease outbreaks. Extending gene content analysis to all lineages revealed a L. monocytogenes core genome of approximately 2,350 genes (80% of each individual genome) and a pan-genomic reservoir of >4,000 unique genes. Combined gene content data from both sequences and arrays was used to reconstruct an informative phylogeny for the L. monocytogenes species that confirms three distinct lineages and describes the relationship of 9 new lineage III genomes. Comparative analysis of 18 fully sequenced L. monocytogenes lineage I and II genomes shows a high level of genomic conservation and synteny, indicative of a closed pan-genome, with moderate domain shuffling and sequence drift associated with bacteriophages is present in all lineages. In contrast with lineages I and II, notable genomic diversity and characteristics of an open pan-genome were observed in the lineage III genomes, including many strain-specific genes and a more complex conservation pattern. This indicates that the L. monocytogenes pan-genome has not yet been fully sampled by genome sequencing, and additional sequencing of lineage III genomes is necessary to survey the full diversity of this intriguing species and reveal its mechanisms for adaptability and virulence.
2010-04-06 | GSE20367 | GEO
Project description:Listeria monocytogenes Hangzhou isolates from different sources
| PRJNA475406 | ENA