A reconstruction of the cellular metabolism of the opportunistic human pathogen Enterococcus faecalis V583 represented as stoichiometric model and analysed using constraint-based modelling approaches
Organism: Enterococcus faecalis
Model type: Linear equations
Model format: SBML
Execution or visualisation environment: Not specified
Model image: No image specified
Institutions: University of Heidelberg
Roles: Project Coordinator
Ursula Kummer is heading the dept. "Modeling of Biological Processes" at the University of Heidelberg.
Roles: Vice Coordinator
Expertise: genome-scale modeling, enzyme kinetics, Metabolic Pathway Analysis and Engineering Microbial Physiology Modeling of Biological Networks Industrial Systems Biotechnology White Biotech..., dynamics and control of biological networks
Since August 2008 I am professor in Systems Biology at the VU University Amsterdam. My Systems Bioinformatics group focusses on systems biology with a special focus on integrative bioinformatics. It aims at forming bridges between the classical bottom-up approaches in systems biology and the more data-driven approaches in classical bioinformatics. We combine experimental, modeling and theoretical approaches to study cellular physiology, with an emphasis on metabolic networks.
I am working on a kinetic model of the central metabolism as well as on a genome wide model of Streptococcus pyogenes.
Roles: Not specified
Tools: gel-based and gel-free proteomics, 2-D Gel Electrophoresis, bacterial chemostat culture, Mutant and Strain Construction, qRT-PCR, molecular biological techniques (RNA/DNA techniques, Chromatography
Professor in biotechnology at the Dept. Chemistry, Biotechnology and Food Science. I am heading "Laboratory of microbial gene technology and food microbiology" that consists of approximately 20 members (staff members, technicians,and students). During the last 20 years my research has been focused on lactica acid bacteria with a focus on bacteriocins of lactic acid bacteria.These studies have included purification and chemical and genetic characterization of such peptides followed by biosynthesis
Challenge: Comparative analyses, as demonstrated by comparative genomics and bioinformatics, are extremely powerful for (i) transfer of information from (experimentally) well-studied organisms to the other organisms, and (ii) when coupled to functional and phenotypic information, insight in the relative importance of components to the observed differences and simalities. The central principle of this proposal is that important aspects of the functional differences between organisms derive not
Snapshots: No snapshots
Studies: Comparative modeling and phosphate dependence flux distributions and glu..., Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis and L...., Reconstructing the metabolic pathways of S. pyogenes and E. faecalis fro..., Study of the physiological characterization of three lactic acid bacteri...
Assays: BIOLOG substrate utilization assay, Genome-Scale Model Enterococcus faecalis V583, Genome-scale model of Streptococcus pyogenes, Global sensitivity analysis, Glucose pulsed L. lactis, Glucose pulsed S. pyogenes, Kinetics of L-lactate dehydrogenase from L. lactis, Kinetics of L-lactate dehydrogenase from S. pyogenes, E. faecalis, and L..., Maximal specific growth rates of the three lactic acid bacteria and thei..., Model of L. lactis glycolysis, Physiological characterization of Lactic acid bacteria grown in C-limite..., Regulation of the activity of lactate dehydrogenases from four lactic ac...
The reconstruction of the metabolic networks is done by sequence comparison with already annotated genomes of L. lactis, L. plantarum, B. subtilis and E. coli
Person responsible: Not available
Snapshots: No snapshots
Metabolic network of Enterococcus faecalis including primary metabolism, polysaccharide metabolism, purine and pyrimidine biosoynthesis, teichoic acid biosynthesis, fatty acid and phospholipid bioynthesis, amino acid metabolism, vitamins and cofactors
Investigation: Investigation of glycolysis and pyruvate branch...
SOPs: No SOPs
Data files: No Data files
Date Published: 19th Dec 2014
Journal: Appl Environ Microbiol
PubMed ID: 25527553
Citation: Appl Environ Microbiol. 2015 Mar 1;81(5):1622-33. doi: 10.1128/AEM.03279-14. Epub 2014 Dec 19.