Project description:Gene content in various Enterococcus faecalis strains compared to E. faecalis V583. Strains have been compared to the V583 strain by comparative genomic hybridization using genome-wide PCR-based microarrays representing the V583 genome. Genes have been deemed "present" or "divergent" in the various strains.
Project description:To further investigate the homeostatic response of E. faecalis to Fe exposure, we examine the whole-genome transcriptional response of wild-type (WT) exposed to non toxic Fe excess. This experiment correspond the work titled Transcriptomic response of Enterococcus faecalis to iron excess (work in preparation) A four chip study using total RNA recovered from four separate wild-type cultures of Enterococcus faecalis OG1RF, two controls samples (N medium growth) and two iron samples (N medium gowth with 0.5 mM Fe-NTA). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).
Project description:Analysis of changes in gene expression in Enterococcus faecalis OG1 delta-EF2638 mutant compared to wild-type OG1 strain. The deletion mutant has a growth defect when grown with aeration The mutant presented in this study is described and characterized in Vesic, D. and Kristich, C.J. 2012. A Rex-family transcriptional repressor influnces H2O2 accumulation by Enterococcus faecalis. (submitted for publication) Microarray analysis was done using RNA isolated from two independent cultures of wild-type Enterococcus faecalis OG1 and two independent cultres of Enterococcus faecalis OG1 delta-EF2638 mutant; each RNA sample was subjected to triplicate hybridization (technical replicates) . Microarrays were custom designed to investigate expression of ORFs in Enterococcus faecalis OG1RF genome. The arrays were designed based on the OG1RF annotation generated with the Rapid Annotation Using Subsystem Technology (RAST) server (Aziz et. al. 2008. BMC Genomics 9:75), as described in Frank et al (2012) Infect. Immun. 80:539. The aim was eighteen probe pairs per ORF, each of which is present in triplicate.
Project description:The microarrays experiments was performed with the purpose of identify transcriptional networks activated by copper. This experiment correspond the work tituled Enterococcus faecalis reconfigure the activation of its transcriptional regulatory networks under different copper exposure levels (work in preparation).Mauricio Latorrea,b, Jessica Galloway-Peñac,d,e, Jung Hyeo Rhoc,d, Marko Budinichf, Barbara E. Murrayc,d,e, Alejandro Maassb,f, Mauricio Gonzáleza,b,f*. a INTA, Laboratorio de Bioinformática y Expresión Génica, INTA, Universidad de Chile, Santiago, Chile. b Center for Genome Regulation (Fondap 15090007), University of Chile, Santiago, Chile. c Division of Infectious Disease, Department of Medicine, University of Texas Medical School, Houston, Texas, United States of America. d Center for the Study of Emerging and Reemerging Pathogens, University of Texas Medical School, Houston, Texas, United States of America. e Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston, Texas, United States of America f Mathomics, Center for Mathematical Modeling (UMI2807CNRS), Santiago, Chile. * Corresponding author. Address: El Líbano 5524, Santiago 11, Chile. Fax: +56 (2) 2214030. A eight chip study (two technical replicates) using total RNA recovered from four separate cultures of: Enterococcus faecalis OG1RF (N medium growth), Enterococcus faecalis OG1RF copΔ mutant strain (N medium growth), Enterococcus faecalis OG1RF copΔ mutant low copper treatment (N medium growth + 0.05 mM CuSO4) and Enterococcus faecalis OG1RF copΔ mutant low copper treatment (N medium growth + 0.5 mM CuSO4). Each chip measures the expression level of 3,114 genome genes from Enterococcus faecalis strain V583 (A7980-00-01).
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. Overall design: Comparison of transcriptome data from Enterococcus faecalis growing in BHI broth and monoassociated mice
Project description:The effects of NaCl on transcriptional events were studied by means of genome wide microarrays in Enterococcus faecalis V583. Transcriptional profiles were obtained through time series experiments over periods of 60min.
Project description:Changes in Enterococcus faecalis OG1RF(pCF10) gene expression at 4 hours post-infection in a rabbit model of subdermal abscess formation were studied using RNA-seq analysis. Overall design: Samples consisted of RNA from the input inoculum and RNA collected from the subdermal chambers four hours after inoculation. Two biological replicates were performed.
Project description:Whole Genome Metabolism of "Enterococcus faecalis (strain ATCC 700802 / V583)"
This is a whole genome metabolism model of Enterococcus faecalis (strain ATCC 700802 / V583).
This model has been automatically generated by the SuBliMinaL Toolbox
and libAnnotationSBML using information coming from from KEGG (release 66, April 2013, accessed via the resource's web services interface) and, where relevant, augmented with metabolic pathway information extracted from MetaCyc (version 17.0, March 2013).
This model has been produced by the path2models
project and is currently hosted on BioModels Database
and identified by: BMID000000141416
Other models with the same genus include BMID000000010035 BMID000000010036 BMID000000010037 BMID000000010038 BMID000000010039 BMID000000010040 BMID000000010041 BMID000000010042 BMID000000010043 BMID000000010044 BMID000000010045 BMID000000010046 BMID000000010047 BMID000000010048 BMID000000069302 BMID000000069303 BMID000000069304 BMID000000069305 BMID000000069306 BMID000000069307 BMID000000069308 BMID000000069309 BMID000000069310 BMID000000069311 BMID000000069312 BMID000000069313 BMID000000069314 BMID000000069315 BMID000000069316 BMID000000069317 BMID000000069318 BMID000000069319 BMID000000069320 BMID000000069321 BMID000000069322 BMID000000069323 BMID000000069324 BMID000000069325 BMID000000069326 BMID000000069327 BMID000000069328 BMID000000069329 BMID000000069330 BMID000000069331 BMID000000069332 BMID000000069333 BMID000000069334 BMID000000069335 BMID000000069336 BMID000000069337 BMID000000069338 BMID000000069339 BMID000000069340 BMID000000069341 BMID000000069342 BMID000000069343 BMID000000069344 BMID000000069345 BMID000000069346 BMID000000069347 BMID000000069348 BMID000000069349 BMID000000069350 BMID000000069351 BMID000000069352 BMID000000069353 BMID000000069354 BMID000000069355 BMID000000069356 BMID000000069357 BMID000000069358 BMID000000069359 BMID000000069360 BMID000000069361 BMID000000069362 BMID000000069363 BMID000000069364 BMID000000069365 BMID000000069366 BMID000000069367 BMID000000069368 BMID000000069369 BMID000000069370 BMID000000069371 BMID000000069372 BMID000000141712 BMID000000142199 BMID000000142400 BMID000000142504 BMID000000142649 BMID000000142748 BMID000000142785 BMID000000142790 BMID000000142804 BMID000000142826 .
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
Project description:Emerging antibiotic resistance among clinically relevant bacteria, paired with their ability to form biofilms on medical and technical devices, represents a serious problem in terms of effective and long-term decontamination in health care environments and gives rise to an urgent need for new antimicrobial materials. Here we present the first study of the impact of AGXX®, a novel broad-spectrum antimicrobial surface coating consisting of micro galvanic elements formed by silver and ruthenium, on the transcriptome of the nosocomial pathogen Enterococcus faecalis. E. faecalis was subjected to metal stress by growing it for different periods of time in the presence of AGXX® or silver-coated steel meshes. Subsequently, total RNA was isolated and next-generation RNA sequencing was performed to analyze variations in gene expression levels in the presence of the antimicrobial materials with focus on known stress genes. Exposure to AGXX® had a large impact on the transcriptome of E. faecalis. After 24 minutes almost 1/5 of the E. faecalis genome displayed differential expression. At each time-point the cop operon was strongly up-regulated, providing indirect evidence for the presence of free Ag+-ions. Moreover, exposure to AGXX® induced a broad general stress response in E. faecalis. Genes coding for the chaperones GroEL and GroES as well as the Clp proteases ClpE and ClpB were among the top up-regulated heat shock genes. Furthermore, differential expression of genes coding for thioredoxin, superoxide dismutase and glutathione synthetase indicates a high level of oxidative stress. We postulate a mechanism of action where the combination of Ag+-ions and reactive oxygen species generated by AGXX® results in a synergistic antimicrobial effect, which is superior to that of conventional silver coatings. Gene expression analysis of Enterococcus faecalis 12030 either subjected to metal stress by exposure to an antimicrobial AGXX®- or Ag-coated V2A steel mesh or exposed to an uncoated V2A steel mesh or left untreated performing RNA Sequencing with an Ion ProtonTM Sequencer and subsequent data analysis with a T-REx RNA-Sequencing expression analysis pipeline.