Serratia marcescens subsp. marcescens Db11
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Project description:Opportunistic pathogen that causes multiple hospital-acquired infections
| PRJNA31 | ENA
Project description:Opportunistic pathogen that causes multiple hospital-acquired infections
| PRJNA21073 | ENA
Project description:Serratia marcescens (S. marcescens), an opportunistic human pathogen, has been identified as a major cause of nosocomial infection and outbreaks. The purpose of this analysis is to examine the S. marcescens (ATCC 13880) protein profile using a high resolution mass spectrometry (MS). S. marcescens ATCC 13880 strain was grown in Luria-Bertani broth and the protein extracted underwent trypsin digestion followed by simple reverse phase liquid chromatography fractionation. Peptide fractions were then analyzed using Orbitrap Fusion Mass Spectrometry and raw MS data was processed using Proteome Discoverer software. The proteomic study identified 2,541 unique protein groups, corresponding to approximately 54% of the measured protein-coding genes. Bioinformatics analysis of these identified proteins demonstrated their involvement in biological processes such as cell wall organization, caperone-mediated protein folding and ATP binding. To our knowledge, this is the first high-performance S.marcescens proteomics analysis (ATCC 13880). These novel observations provide a key baseline molecular profile of the S. marcescens proteome which will prove to be helpful for the future research in understanding the host-pathogen interactions during infection, elucidating the mechanism of multidrug resistance and for developing novel diagnostic markers or vaccine for the disease.
2020-06-17 | PXD011776 | Pride
Project description:Whole genome sequencing of Serratia marcescens sakuensis, an opportunistic pathogen
| PRJDB2620 | ENA
Project description:Whole genome sequencing of Serratia marcescens subsp. marcescens, an opportunistic pathogen
| PRJDB2327 | ENA
Project description:Candida albicans is a ubiquitous opportunistic pathogen that is the most prevalent cause of hospital-acquired fungal infections. In mammalian hosts, C. albicans is engulfed by phagocytes that attack the pathogen with DNA-damaging reactive oxygen species (ROS). Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 is important for yeast model organisms to survive DNA damage and maintain genome integrity. To assess the importance of Rtt109 for C. albicans pathogenicity, we deleted the predicted homologue of Rtt109 in the clinical C. albicans isolate, SC5314. C. albicans rtt109 -/- mutant cells lack acetylated H3K56 (H3K56ac) and are hypersensitive to genotoxic agents. Additionally, rtt109 -/- mutant cells constitutively display increased H2A S129 phosphorylation and elevated DNA repair gene expression, consistent with endogenous DNA damage.
2010-01-04 | GSE18936 | GEO
Project description:Regulatory RNAs (sRNAs) are now considered as major players in many physiological and adaptive responses in pathogenic bacteria. sRNAs have been extensively studied in Gram-negative bacteria, but less information is available in Gram-positive pathogens. There is a spread of multidrug-resistant (MDR) opportunistic organisms, grouped as “ESKAPE” pathogens, which comprise enterococci, a leading cause of hospital-acquired infections and outbreaks with emergence of MDR isolates, especially vancomycin-resistant Enterococcus faecium (VREF). Note that no information about sRNA expression is known in this major opportunistic pathogen. By transcriptomic and genomic analyses using E. faecium Aus0004 reference strain, 249 transcribed IGRs, including sRNA candidates, were detected and, using a series of cut-offs, this set was lowered down to 54 sRNAs while 7 that were predicted based on comparative sequence analysis. RNA-seq was performed with and without subinhibitory concentrations (SIC) of daptomycin, a cyclic lipopeptide antibiotic used for VREF infections. Under daptomycin SIC exposure, 260 genes (9.1% of the genome) had a significant alteration of expression including 80 upregulated genes and 180 downregulated genes. Among the repressed genes, a large proportion (55%) coded for proteins involved in carbohydrate and transport metabolism. Also, we focused on the 9 sRNAs exhibiting the highest expression, and all of them were confirmed as expressed along bacterial growth by Northern blots and qPCR. Out of these 9 sRNAs, four had significantly lower or higher expression in the presence of daptomycin SIC, and therefore responded to antibiotic exposure. Finally, we also tested the expression of these 9 sRNAs in a collection of isogenic Aus0004 mutants with increasing levels of daptomycin resistance, and we observed by qPCR that some sRNAs had a significantly modified expression in daptomycin resistance mutants. It highlights the significant implication of some of the E. faecium sRNAs in the early steps of the development of daptomycin resistance. This is the first experimental genome-wide sRNA identification in Gram-positive E. faecium, a leading cause of hospital acquired infections.
2017-02-16 | GSE94924 | GEO
Project description:In order to identify mRNA and sRNAs associated with the RNA-binding protein Hfq in Serratia marcescens strain Db10, Hfq-bound RNA was immunoprecipitated from a strain encoding an Hfq-3FLAG fusion protein at the normal location and sequenced, in parallel with the wild type strain (no fusion) as negative control. Additionally global transcriptional start site mapping was performed on total RNA, with or without TEX treatment, isolated from wild type Serratia marcescens. The data was used to identify regions of mRNA and sRNAs associated with Hfq in this organism. Associated work in Serratia marcescens Db10, an opportunistic bacterial pathogen, has shown that Hfq is essential for virulence in several models and exerts a wide-ranging impact on the transcriptome and, particularly, genes encoding virulence factors.
2022-02-19 | GSE78185 | GEO
Project description:Candida albicans is a ubiquitous opportunistic pathogen that is the most prevalent cause of hospital-acquired fungal infections. In mammalian hosts, C. albicans is engulfed by phagocytes that attack the pathogen with DNA-damaging reactive oxygen species (ROS). Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 is important for yeast model organisms to survive DNA damage and maintain genome integrity. To assess the importance of Rtt109 for C. albicans pathogenicity, we deleted the predicted homologue of Rtt109 in the clinical C. albicans isolate, SC5314. C. albicans rtt109 -/- mutant cells lack acetylated H3K56 (H3K56ac) and are hypersensitive to genotoxic agents. Additionally, rtt109 -/- mutant cells constitutively display increased H2A S129 phosphorylation and elevated DNA repair gene expression, consistent with endogenous DNA damage. Four independent pairs of biological replicate samples were analyzed to compare RNA levels in wild-type and rtt109 -/- cells. Two experiments were performed: first, in unperturbed cells grown in YPD and second, in cells exposed to H2O2. To account for dye effects, two of the four samples for each experiment were analyzed using Cy3 labeling of the wild-type sample and Cy5 labeling of the mutant sample; the dyes were swapped for the other two biological replicates.
2010-05-16 | E-GEOD-18936 | biostudies-arrayexpress