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Purine and carbohydrate availability drive Enterococcus faecalis fitness in wound infections [dataset 1]

ABSTRACT: Enterococcus faecalis is commonly isolated from different wound types. However, despite its prevalence, the pathogenic mechanisms of E. faecalis during wound infections remain poorly understood. We adopted an in vivo E. faecalis transposon sequencing and RNA sequencing approach to identify fitness determinants that are crucial for replication and persistence of E. faecalis during wound infections in a mouse model. We demonstrated that E. faecalis purine biosynthesis genes are important for replication as purine metabolites are low in wounds during the early phase of wound infections. Furthermore, we found that the E. faecalis MptABCD phosphotransferase system (PTS) involved in the uptake of galactose and mannose, is crucial for E. faecalis persistence in wounds, and that carbohydrate availability changes as the infection progresses. To understand how MptABCD PTS contributes to the reduced fitness observed during E. faecalis wound persistence, we performed an in vitro transcriptomic analysis using the galactose/mannose PTS gene deletion mutant (∆mptD). When mannose was the sole carbohydrate source, shikimate and purine biosynthesis genes in the ∆mptD mutant were downregulated compared to the isogenic wild-type strain, indicating that mannose transport is interconnected with shikimate and purine biosynthesis. Together, our results suggest that dynamic and temporal microenvironment changes at the wound site affects pathogenic requirements and mechanisms of E. faecalis during infections and raise the possibility of inhibiting purine biosynthesis and/or MptABCD PTS to control wound infections.

ORGANISM(S): Enterococcus faecalis

PROVIDER: GSE206749 | GEO | 2023/11/06

REPOSITORIES: GEO

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Purine and carbohydrate availability drive Enterococcus faecalis fitness in wound infections [dataset 2]

Project description:Enterococcus faecalis is commonly isolated from different wound types. However, despite its prevalence, the pathogenic mechanisms of E. faecalis during wound infections remain poorly understood. We adopted an in vivo E. faecalis transposon sequencing and RNA sequencing approach to identify fitness determinants that are crucial for replication and persistence of E. faecalis during wound infections in a mouse model. We demonstrated that E. faecalis purine biosynthesis genes are important for replication as purine metabolites are low in wounds during the early phase of wound infections. Furthermore, we found that the E. faecalis MptABCD phosphotransferase system (PTS) involved in the uptake of galactose and mannose, is crucial for E. faecalis persistence in wounds, and that carbohydrate availability changes as the infection progresses. To understand how MptABCD PTS contributes to the reduced fitness observed during E. faecalis wound persistence, we performed an in vitro transcriptomic analysis using the galactose/mannose PTS gene deletion mutant (∆mptD). When mannose was the sole carbohydrate source, shikimate and purine biosynthesis genes in the ∆mptD mutant were downregulated compared to the isogenic wild-type strain, indicating that mannose transport is interconnected with shikimate and purine biosynthesis. Together, our results suggest that dynamic and temporal microenvironment changes at the wound site affects pathogenic requirements and mechanisms of E. faecalis during infections and raise the possibility of inhibiting purine biosynthesis and/or MptABCD PTS to control wound infections.

2023-11-06 | GSE206750 | GEO

Transcriptome analysis of Enterococcus faecalis towards its adaption to surviving in the mouse intestinal tract

Project description:Enterococcus (E.) faecalis is a commensal in healthy humans, frequently found in a variety of fermented foods, and can serve as a probiotic. However, it has also been recognized as a pathogen causing diseases such as endocarditis, bacteremia and urinary tract infections. As known virulence factors are not limited to clinical isolates but widespread in many strains, additional fitness determinants should influence E. faecalis behavior in the host. We have performed a transcriptomic in vivo study with E. faecalis in the intestine of living mice to identify novel latent and adaptive fitness determinants within E. faecalis. The transcriptomic data derived from E. faecalis strain OG1RF monoassociated with wild type mice provide a first insight in the genes used to live as a commensal in the intestinal tract. Clear changes are observed as compared to growth under laboratory conditions (BHI broth) in the expression of genes involved in energy metabolism (e.g. dhaK and glpK pathway), transport and binding mechanisms (e.g. phosphoenolpyruvate carbohydrate PTS) as well as fatty acid metabolism (fab genes). This knowledge can be used to help explain its persistence in this environment, which is a prerequisite to cause infection in a compromised or inflamed host and possibly develop improved treatment strategies of the so far hard to cure infections.

2016-03-04 | GSE45788 | GEO

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Project description:Enterococcus faecalis (E. faecalis) is a Gram-(+) opportunistic pathogen associated with predominantly nosocomial wound infections. E. faecalis has been shown to suppress or evade immune-mediated clearance by the immune system and promote persistent infection. Here, we sought to interrogate whether E. faecalis infection induces transcriptomic changes in the host at the single-cell resolution using a mouse excisional wound model. Keratinocyte, fibroblast, endothelial and immune cell populations reveal unique clusters in the infected wounds. Cell communication analysis discovered strong ligand-receptor interactions between macrophages and endothelial cells in the infected niche, whilst fibroblast and keratinocytes instruct healing cellular interactions in untreated skin wounds. We also identified differential terminal lineage driving genes, following RNA velocity in each condition. Together, results suggest that E. faecalis infection alters the skin transcriptome, which may help promote the chronicity of bacteria-infected wounds.

2023-12-31 | GSE229257 | GEO

Quantitative proteome analysis of Enterococcus faecalis SK460 during planktonic and biofilm stages

Project description:Enterococcus faecalis is a major nosocomial pathogen frequently isolated from non- healing wound infections. The major factor responsible for the virulence and establishment of infection is its ability to form robust biofilm. This renders the recalcitrant nature of Enterococci towards the current treatment strategies. In the present study, the quantitative proteomic approach is carried out to elucidate the protein expression levels in E. faecalis at planktonic and biofilm stages. This will help to identify biofilm associated pathways in E. faecalis which inturn can be considered as novel targets for biofilm inhibition.

2019-07-12 | PXD010770 | Pride

Ribosome profiling and RNA sequencing reveal genome-wide cellular translation and transcription regulation under osmotic stress in Lactobacillus rhamnosus ATCC 53103

Project description:To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. DEGs involved in the biosynthesis of phenylalanine, tyrosine, and tryptophan, and the phosphotransferase system pathways also were co-regulated at translation and transcription levels, while they showed opposite expression direction at two levels. Moreover, DEGs involved in the two-component system, amino acid metabolism, and pyruvate metabolism pathways were only regulated at the transcription level. And DEGs involved in fructose and mannose metabolism were only regulated at the translation level. The translation efficiency of DEGs involved in the biosynthesis of amino acids was downregulated while in quorum sensing and PTS pathways was upregulated. In addition, the ribosome footprints accumulated in open reading frame regions resulted in impaired translation initiation and elongation under osmotic stress. In summary, L. rhamnosus ATCC 53103 could respond to osmotic stress by translation regulation and control the balance between survival and growth of cells by transcription and translation.

2021-12-15 | GSE188929 | GEO

Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of L. monocytogenes

Project description:Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of Listeria monocytogenes, and their significance for extra- and intracellular growth. Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001)) (supplemented with 10 mM Glucose). Listeria monocytogenes EGD-e possesses 86 pts genes encoding 29 complete and several incomplete PEP-dependent phosphotransferase systems (PTS) for the transport of carbohydrates and sugar alcohols. By a systematic deletion analysis we identified the major PTS involved in glucose, mannose and cellobiose transport, when L. monocytogenes grows in a defined minimal medium in the presence of either of these carbohydrates. Under these conditions two of the four PTSMan and at least one of the five PTSGlc function as glucose transporter with different affinities. Cellobiose is transported (with different efficiencies) mainly by two of the six PTSLac and by a PTSGlc that also transports glucose. One of the PTSMan and both PTSLac are regulated by LevR-homologous PRD containing transcriptional activators, detected with PRD deletion mutants. The growth rates of mutants that are lacking these PTS are drastically reduced compared to the wild-type strain upon growth in a defined medium with low concentrations of glucose and cellobiose, respectively. In contrast, replication of these PTS mutants within epithelial cells or macrophages is as efficient as that of the wild-type strain. Keywords: pts and prd deletion mutants A total of three independently isolated RNA samples from each condition were used for the analysis. PTS Samples: GSM458191-GSM458208 PRD Samples: GSM458209-GSM458214

2010-05-19 | E-GEOD-18363 | biostudies-arrayexpress

Global Analysis of Carbohydrates Utilization of the Alkaline Hemicellulytic Bacteria Bacillus sp. N16-5

Project description:Alkaline hemicellulytic bacteria Bacillus sp. N16-5 has abroad substrate spectrum and exhibits great growth ability on complex carbohydrates. In order to get insight into its carbohydrate utilization mechanism, global transcriptional profiles were separately determined for growth on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan, pectin and carboxymethyl cellulose by using one-color microarrays. Substrate induced gene expression was measured when culture was grown on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan and CMC to mid-logarithmic phase.

2014-06-17 | E-GEOD-38276 | biostudies-arrayexpress

RNA seq of H2O, glucose, mannose or galactose-treated Batrachochytrium salamandrivorans zoospores

Project description:We report RNAseq data from B. salamandrivorans zoospores treated with different carbohydrates (glucose, mannose or galactose, 50 mM) or H2O as a control, for 1 hour. We found a selective upregulation of putative B. salamandrivorans virulence factors during initial contact with carbohydrates and galactose specifically.

2021-10-13 | GSE161129 | GEO

Analysis of global transcriptional response of Mycobacterium tuberculosis H37Rv to the natural compound ethyl p-methoxycinnamate

Project description:Gene expression profiling analysis was performed after exposing M. tuberculosis H37Rv to EPMC for 24 and 48 hours. Significant changes in expression levels were observed in the genome in response to the drug. Analysis of the data carried out by studying the expression pattern at the level of pathways, indicated that several pathways including amino sugar and nucleotide sugar metabolism, linoleic acid metabolism, fructose and mannose metabolism, galactose metabolism, lysine degradation pathways were significantly upregulated upon exposure to EPMC, while the pathways involved primarily in the mycobacterial cell wall biosynthesis - the mycolic acid biosynthesis and D-alanine metabolism were significantly downregulated

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