Salmonella genome SCV sequencing
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ABSTRACT:
PROVIDER: PRJEB12856 | ENA |
REPOSITORIES: ENA
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Project description:Salmonella is a human and animal pathogen causing gastro-enteric diseases worldwide. The key feature of Salmonella infection is its entry into intestinal epithelial cells within a Salmonella-Containing Vacuole (SCV). This original compartment is distinct from empty macropinosomes formed around the infection site. A few minutes after its formation, the SCV increases in size through fusions with the surrounding macropinosomes. On the opposite, Salmonella induces the formation of elongated tubules leading to SCV membrane and volume loss. Later, the SCV can mature into a vacuolar pathogen niche, or be ruptured releasing Salmonella in the host cytosol where the bacteria hyper-replicates. Here, we describe how size control of the early SCV is the main contributor to its stability and consequently determines the Salmonella intracellular niche and growth. We identify the SNAREs required for increasing the SCV size through fusions. We show that this fusion promotes the maintenance of the SCV integrity and the establishment of a vacuolar niche
2020-01-09 | PXD012825 | Pride
Project description:Salmonella Typhimurium (S. Typhimurium) is an enteric bacterium capable of invading a wide range of host cell types and adopting different intracellular lifestyles for survival. Host endocytic trafficking and autophagy have been implied to regulate the S. Typhimurium subcellular localization and survival. To reveal alternative host regulators on S. Typhimurium lifestyle, we combined a novel fluorescent reporter, Salmonella Intracellular Analyzer (SINA) with haploid forward genetic screening. This identified transcription factor c-MYC as a negative regulator of S. Typhimurium cytosolic lifestyle via stabilizing the Salmonella-containing vacuole (SCV). We further confirmed that c-MYC downstream regulated LC3 acts to maintain SCV stability and limits S. Typhimurium cytosolic lifestyle. We demonstrated that LC3 is recruited to the SCV prior to the endomembrane damage marker Galectin 3, and it regulates SCV stability independent of the autophagosome adaptor NDP52. The LC3 processing enzymes ATG3 and ATG4 reciprocally act on SCV stability, where the loss of LC3-PE conjugation in the absence of ATG3 limits SCV damages. We further identified the dosage-dependent function of the S. Typhimurium effector SopF in mediating SCV stability by actively avoiding LC3 recruitment to the proximity of the SCV to reduce its catastrophic rupture and host cell death. Altogether, we offer insights on the significance of cellular transcription profile in the determination of S. Typhimurium pathophysiology as well as the underlying host-evasion strategy of S. Typhimurium.
2022-09-25 | GSE161812 | GEO
Project description:To better understand transcriptional changes in the SCV, RNA-seq analyses were conducted by comparing a SCV mutant to the wild-type. Transcriptomic profiling identified more than 1000 genes indicating a significant reprograming of gene expression in the SCV mutant. In accordance with observed phenotypes, genes involved in metabolism functions, motility and phenazine production were downregulated; whereas, oxidative stress and iron uptake genes were significantly upregulated. A total of 5 samples were analyzed in AB medium + 2% casamino acids, Pseudomonas chlororaphis wild type strain (3 replicates); Pseudomonas chlororaphis SCV mutant (2 replicates).
2014-11-25 | E-GEOD-51293 | biostudies-arrayexpress
Project description:To better understand transcriptional changes in the SCV, RNA-seq analyses were conducted by comparing a SCV mutant to the wild-type. Transcriptomic profiling identified more than 1000 genes indicating a significant reprograming of gene expression in the SCV mutant. In accordance with observed phenotypes, genes involved in metabolism functions, motility and phenazine production were downregulated; whereas, oxidative stress and iron uptake genes were significantly upregulated.
2014-11-25 | GSE51293 | GEO
Project description:Salmonella enterica serovar Typhimurium (S. Typhimurium) is a zoonotic pathogen that causes diarrheal disease in humans and animals. During salmonellosis, S. Typhimurium colonizes epithelial cells lining the gastrointestinal tract. S. Typhimurium has an unusual lifestyle in epithelial cells that begins within an endocytic-derived Salmonella-containing vacuole (SCV), followed by escape into the cytosol, epithelial cell lysis and bacterial release. The cytosol is a more permissive environment than the SCV and supports rapid bacterial growth. The physicochemical conditions encountered by S. Typhimurium within the cytosol, and the bacterial genes required for cytosolic colonization, remain unknown. Here we have exploited the parallel colonization strategies of S. Typhimurium in epithelial cells to decipher the two niche-specific bacterial virulence programs. By combining a population-based RNA-seq approach with single-cell microscopic analysis, we identified bacterial genes/sRNAs with cytosol-specific or vacuole-specific expression signatures. Using these genes/sRNAs as environmental biosensors, we defined that Salmonella is exposed to iron and manganese deprivation and oxidative stress in the cytosol and zinc and magnesium deprivation in the SCV. Furthermore, iron availability was critical for optimal S. Typhimurium replication in the cytosol, as well as entC, fepB, soxS and sitA-mntH. Virulence genes that are typically associated with extracellular bacteria, namely Salmonella pathogenicity island 1 (SPI1) and SPI4, had a cytosolic-specific expression profile. Our study reveals that the cytosolic and vacuolar S. Typhimurium virulence gene programs are unique to, and tailored for, residence within distinct intracellular compartments. Therefore, this archetypical vacuole-adapted pathogen requires extensive transcriptional reprogramming to successfully colonize the mammalian cytosol.
2021-06-30 | GSE179103 | GEO
Project description:Salmonella nitra genome sequencing
| PRJEB2121 | ENA
Project description:Salmonella enterica genome sequencing
| PRJNA294295 | ENA
Project description:Salmonella enterica serovar Typhimurium is a rod-shaped Gram-negative bacterium. It is a leading cause of gastroenteritis and public health problem. In the environment, it interacts with protozoa, particular amoeba, however the interactions between Salmonella and these eukaryotic microbes have not been addressed in detail. We and others recently described that S. Typhimurium is able to survive in the model amoeba Dictyostelium discoideum requiring the Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2, respectively)-encoded type three secretion systems (T3SSs). In this work, we investigated the role of two particular effector proteins, SopB and SifA that are secreted by either one of the T3SSs. SopB and SifA are involved in the remodelling of the intracellular compartment that contains Salmonella (Salmonella-containing vacuole, SCV) in other cellular models. We combined genetic and proteomics analysis to investigate the roles of SopB and SifA during infections of D. discoideum. We identified over 1,000 proteins per sample performing proteomics on fractions enriched in SCVs from amoeba cells infected with wild-type, sopB or sifA S. Typhimurium. Among them, we observed several Rho GTPases, guanine nucleotide exchange factors and motor proteins. Finally, we decided to evaluate if the changes observed in the proteome from the SCV of wild-type and mutants affect the intracellular survival of S. Typhimurium. These finding suggest that Salmonella exploits this route to survive intracellularly, a process that requires SopB and/or SifA effectors. To our knowledge this is the first proteomic description of the Salmonella intracellular compartment in D. discoideum.
2020-09-23 | PXD014955 | Pride
Project description:Comparative genome hybridization (CGH) of 35 Salmonella bongori strains and 16 Salmonella spp strains belonging to SarC collection
2010-12-31 | E-TABM-931 | biostudies-arrayexpress
Project description:We have observed that for a number of S. aureus strains as they switch to a SCV lifestyle there is the formation of an extracellular matrix. We focused our analysis on one strain, WCH-SK2. For bacterial survival in the host, the combination of low nutrients and the prolonged timeframe forms a stress that selects for a specific cell-type from the population. In this context, we used steady-state growth conditions with low nutrients and a controlled low growth rate, for a prolonged time and with methylglyoxal. These conditions induced S. aureus WCH-SK2 into a stable SCV cell-type, they did not revert after sub-culturing. Methods: Transcriptomic profiles of wild-type (WT) and SCV were generated in continuous culture in the presence of stress (high and low level of methylglyoxal). Results: Analysis revealed these cells possessed a metabolic and surface profile that was different from previously described SCVs or biofilm cells. The extracellular matrix was protein and extracellular DNA; but not polysaccharide. The SCV cells induced expression of certain surface proteins (such as Ebh) and lantibiotic synthesis while down-regulating factors that stimulates immune response (leucocidin, capsule, carotenoid). We also studied further their genetic characteristics. They possessed an increased viability in the presence of antibiotics compared to their non-SCV form. Their stability implied there had been genetic changes, we determined the whole genome sequence of WCH-SK2 and its stable SCV forms at a single base resolution, employing Single Molecular Real-Time (SMRT) sequencing that also enables the methylome to be determined. The genetic features of this isolate have been identified; the SCCmec type, the pathogenicity and genetic islands and virulence factors. The comparison has identified a set of genetic changes that occurred in the stable SCV form; most notably to the global regulator MgrA and the phosphoserine phosphatase RsbU (part of the regulatory pathway of the sigma factor SigB). There was a shift in the methylation across the genome. Conclusions: Our data reveal a cell heterogeneity within a S. aureus population and using conditions that resemble long-term survival in the host has identified a previously unnoticed S. aureus cell-type, with a distinctive metabolic and molecular profile. The results from this study represent a unique identification of a suite of epigenetic, genetic and transcriptional factors that are implicated in the switch in S. aureus to its persistent SCV form
2014-12-02 | GSE63750 | GEO