Differential RNA-Seq (dRNA-seq) of Staphylococcus epidermidis PS2 and PS10 isolates
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ABSTRACT:
ORGANISM(S): Staphylococcus epidermidis
PROVIDER: GSE126097 | GEO | 2019/02/05
REPOSITORIES: GEO
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Project description:Background. During infection, pneumococci exist mainly in sessile biofilms rather than in planktonic form, except during sepsis. However, relatively little is known about how biofilms contribute to pneumococcal pathogenesis. Methods. We performed a biofilm assay and mouse infection experiments on opaque and transparent variants of a clinical serotype 19F strain. Results. After 4 days incubation, scanning electron microscopy revealed that opaque biofilm bacteria produced an extracellular matrix, whereas the transparent variant did not. The opaque biofilm-derived bacteria translocated from the nasopharynx to the lungs and brain of mice, and showed 100-fold greater in vitro adherence to A549 cells. Microarray analysis of planktonic and sessile bacteria from transparent and opaque variants showed differential gene expression in two operons: the lic operon, involved in choline uptake, and in the two-component system, ciaRH. Mutants of these genes did not form an extracellular matrix, could not translocate from the nasopharynx to the lungs or the brain, and adhered poorly to A549 cells. Conclusions. We conclude that only the opaque phenotype is able to form extracellular matrix, and that the lic operon and ciaRH contribute to this process. We propose that during infection, extracellular matrix formation enhances the ability of pneumococci to cause invasive disease. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-117
2011-04-20 | E-BUGS-117 | biostudies-arrayexpress
Project description:This study is focused on understanding the molecular basis of protein- and polysaccharide intercellular adhesin (PIA)- mediated biofilm formation by S. epidermidis in PCs. Comparative transcriptomic analysis of S. epidermidis PIA- biofilm positive (AZ22, AZ39) and PIA+ biofilm positive (ST02) strains was performed using a RNAseq approach. Pathway enrichment analysis revealed cellular component GO term (AZ22), two KEGG pathways (AZ39), and two molecular function GO term and 8 KEGG pathways (ST02) were enriched. Remarkably, glutamate biosynthesis and tricarboxylic acid cycle (TCA) genes were upregulated in AZ22 and AZ39, respectively whereas arginine deiminase (ADI) pathway genes were downregulated in ST02. Moreover, genes conferring resistance against antimicrobial peptides (AMPs) and antibiotics such as lysostaphin, fusidic acid and tetracycline were upregulated, thus implying their increased resistance in S. epidermidis grown in PCs. Notably, expression of genes conferring resistance against aminoglycoside (in AZ22) and methicillin (in AZ39 and ST02) were downregulated. This study provided an overview, how biofilm-mediated virulence, antibiotic resistance and metabolic pathways are interlinked and reprogrammed during biofilm maturation in PCs which will be intriguing in development of novel preventive strategies against S. epidermidis transfusion-transmitted infections.
2020-07-14 | GSE154352 | GEO
Project description:Differential RNA-Seq (dRNA-seq) of Staphylococcus epidermidis PS2 and PS10 isolates
| PRJNA521019 | ENA
Project description:Pseudomonas aeruginosa infections for individuals with Cystic Fibrosis (CF), result in high morbidity and mortality, with premature death often occurring. These infections are complicated by the formation of biofilms in the sputum. Antibiotic therapy is stymied by antibiotic resistance of the biofilm matrix, making novel anti-biofilm strategies highly desirable. Within the P. aeruginosa biofilm, the redox factor pyocyanin enhances biofilm integrity by intercalating with extracellular DNA. The antioxidant glutathione (GSH) reacts with pyocyanin to disrupt intercalation. This study investigated GSH disruption by assaying the physiological effects of GSH and DNase I on biofilms of clinical CF isolates grown in artificial CF sputum media (ASMDM+). Confocal scanning laser microscopy showed that 2mM GSH alone or combined with DNase I significantly disrupted the immature (24 hour) biofilms of Australian Epidemic Strain (AES) isogens AES-1R and AES-1M. GSH alone greatly disrupted the mature (72 hour) biofilm of AES-1R, resulting in significant differential expression of 587 genes, as evidenced by RNA-sequencing. Upregulated systems included cyclic diguanylate and pyoverdine biosynthesis, the Type VI secretion system, nitrate metabolism and translational machinery. Physiochemical biofilm disruption with GSH revealed a metabolically active cellular physiology distinct from either mature or dispersed biofilm physiology. RNA-seq results were validated by biochemical assay and qPCR. Biofilms of a range of CF isolates disrupted with GSH and DNase I were significantly more susceptible to ciprofloxacin, and increased antibiotic effectiveness was achieved at 10mM GSH. This study demonstrated that GSH alone or with DNase I represent effective anti-biofilm treatments when combined with appropriate antibiotics.
2016-02-01 | GSE75334 | GEO
Project description:Biofilm formation is considered the most important factor involved in pathogenicity of Staphylococcus epidermidis.We investigated the role of two-component signal transduction system (TCS) srrAB, which was up-regulated under micro-aerobic condition, in the growth and biofilm formation of S. epidermidis.AsrrA-deficient mutant (M-bM-^HM-^FsrrA) derived from S. epidermidis1457 (SE1457), exhibited dramatic reduction in growth and biofilm formation underboth aerobic and micro-aerobic conditions, and more sensitive to several different types of antimicrobial agents, H2O2 and SDS. In New Zealand Rabbit model of S. epidermidis biofilm infection, M-bM-^HM-^FsrrA hardly formed biofilm compared to that of SE1457. Phenotypic alteration was restored to the wide-type levelwhen srrAB were complemented into M-bM-^HM-^FsrrA. Further study found that the initial adherence capacity and production of polysaccharide intercellular adhesion (PIA) in M-bM-^HM-^FsrrA were decreased, while extracellular DNA (eDNA) was increased. Transcriptional Analysisby qRT-PCR demonstrated that expression level of icaRin M-bM-^HM-^FsrrA was up-regulated compared to that of SE1457 under aerobic condition, while down-regulated under micro-aerobic condition;icaA and altE were down-regulated under both conditions. Expression of genes involved in respiratory metabolism, such as qoxB(quinol oxidase polypeptide II), ctaA(heme A synthase), and pfl(pyruvate formatelyase), etc. were down-regulated in M-bM-^HM-^FsrrAunder both conditions. Electrophoretic mobility shift assay (EMSA) revealed that phosphorylated SrrA bound to the promoter regions of icaR, icaA, atlE, qoxB,ctaA, andpflB just like binding its own promoter region srr. Taken together, our results demonstrate that srrAB may provide a mechanistic link between respiratory metabolism, environmental signals, and regulation of biofilm formation in S. epidermidis. Microarrays covering different S. epidermidis genomes were used to assess the impact of the two component system srrAB on growth and biofilm formation, by comparing WT with srrA mutant transcriptomes
2014-11-21 | E-GEOD-47101 | biostudies-arrayexpress
Project description:Biofilm formation is considered the most important factor involved in pathogenicity of Staphylococcus epidermidis.We investigated the role of two-component signal transduction system (TCS) srrAB, which was up-regulated under micro-aerobic condition, in the growth and biofilm formation of S. epidermidis.AsrrA-deficient mutant (∆srrA) derived from S. epidermidis1457 (SE1457), exhibited dramatic reduction in growth and biofilm formation underboth aerobic and micro-aerobic conditions, and more sensitive to several different types of antimicrobial agents, H2O2 and SDS. In New Zealand Rabbit model of S. epidermidis biofilm infection, ∆srrA hardly formed biofilm compared to that of SE1457. Phenotypic alteration was restored to the wide-type levelwhen srrAB were complemented into ∆srrA. Further study found that the initial adherence capacity and production of polysaccharide intercellular adhesion (PIA) in ∆srrA were decreased, while extracellular DNA (eDNA) was increased. Transcriptional Analysisby qRT-PCR demonstrated that expression level of icaRin ∆srrA was up-regulated compared to that of SE1457 under aerobic condition, while down-regulated under micro-aerobic condition;icaA and altE were down-regulated under both conditions. Expression of genes involved in respiratory metabolism, such as qoxB(quinol oxidase polypeptide II), ctaA(heme A synthase), and pfl(pyruvate formatelyase), etc. were down-regulated in ∆srrAunder both conditions. Electrophoretic mobility shift assay (EMSA) revealed that phosphorylated SrrA bound to the promoter regions of icaR, icaA, atlE, qoxB,ctaA, andpflB just like binding its own promoter region srr. Taken together, our results demonstrate that srrAB may provide a mechanistic link between respiratory metabolism, environmental signals, and regulation of biofilm formation in S. epidermidis.
2014-11-21 | GSE47101 | GEO
Project description:Biofilms are matrix-encased microbial communities that increase the environmental fitness and infectivity of many human pathogens including Vibrio cholerae. Biofilm matrix assembly is essential for biofilm formation and function. Known components of the V. cholerae biofilm matrix are the polysaccharide VPS, matrix proteins RbmA, RbmC, Bap1, and extracellular DNA, but the majority of the protein composition is uncharacterized. This study comprehensively analyzed the biofilm matrix proteome and revealed the presence of outer membrane proteins (OMPs). Outer membrane vesicles (OMVs) were also present in the V. cholerae biofilm matrix and were associated with OMPs and many biofilm matrix proteins suggesting that they participate in biofilm matrix assembly. Consistent with this, OMVs had the capability to alter biofilm structural properties depending on their composition. OmpU was the most prevalent OMP in the matrix, and its absence altered biofilm architecture by increasing VPS production. Using single-cell force spectroscopy, we further showed that OmpU, the matrix proteins RbmA, RbmC, and Bap1, and VPS contribute to cell-surface adhesion forces, which are critical for biofilm formation. Our findings provide new insights into the molecular mechanisms underlying biofilm matrix assembly in V. cholerae, which may open up new opportunities to develop inhibitors that specifically alter biofilm matrix properties and, thus, affect either the environmental survival or pathogenesis of Vibrio cholerae.
2023-07-14 | MSV000092446 | MassIVE
Project description:Biofilms are matrix-encased microbial communities that increase the environmental fitness and infectivity of many human pathogens including Vibrio cholerae. Biofilm matrix assembly is essential for biofilm formation and function. Known components of the V. cholerae biofilm matrix are the polysaccharide VPS, matrix proteins RbmA, RbmC, Bap1, and extracellular DNA, but the majority of the protein composition is uncharacterized. This study comprehensively analyzed the biofilm matrix proteome and revealed the presence of outer membrane proteins (OMPs). Outer membrane vesicles (OMVs) were also present in the V. cholerae biofilm matrix and were associated with OMPs and many biofilm matrix proteins suggesting that they participate in biofilm matrix assembly. Consistent with this, OMVs had the capability to alter biofilm structural properties depending on their composition. OmpU was the most prevalent OMP in the matrix, and its absence altered biofilm architecture by increasing VPS production. Single-cell force spectroscopy revealed that proteins critical for biofilm formation, OmpU, the matrix proteins RbmA, RbmC, Bap1, and VPS, contribute to cell-surface adhesion forces at differing efficiency, with VPS showing the highest efficiency whereas Bap1 showing the lowest efficiency. Our findings provide new insights into the molecular mechanisms underlying biofilm matrix assembly in V. cholerae, which may provide new opportunities to develop inhibitors that specifically alter biofilm matrix properties and, thus, affect either the environmental survival or pathogenesis of V. cholerae.
2023-12-12 | MSV000093650 | MassIVE
Project description:The study is about the role of Bacteroides thetaiotaomicron in the human gut microbiota, specifically its ability to form biofilms in response to bile salts. The study found that bile induces the expression of certain efflux pumps, and inhibiting these pumps impairs biofilm formation. Among the induced pumps, the BipABC pump is crucial for biofilm formation as it is involved in the efflux of magnesium, which affects the biofilm's extracellular matrix and structure. This discovery sheds light on how intestinal chemical cues, like bile salts, regulate biofilm formation in B. thetaiotaomicron, a significant gut symbiont.
2024-03-19 | E-MTAB-13460 | biostudies-arrayexpress
Project description:Staphylococcus aureus is a medically important pathogen that exhibit high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development we constructed and characterized codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control cellular metabolic status by altering carbon flow through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of eDNA into the biofilm matrix while disrupting codY resulted in a robust structured biofilm tethered together with eDNA and PIA. Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and neglects eDNA release in the double mutant. Compared to inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, codY ccpA mutant produced higher amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Overall, results of this study suggest that interplay between CodY and CcpA modulates central metabolism to optimize growth on preferred carbon sources while repressing virulence gene expression until nutrient limitation requires scavenging nutrients from the host.
2022-05-25 | ST002187 | MetabolomicsWorkbench