Data files

Strain MK350 was grown under the same conditions as used when growing cells for microscopy analysis; cells of OD600 = 0.4 were diluted 100-fold in C+Y medium with 0.1 mM ZnCl2 and incubated for 2.5 hours until OD600 = 0.15. Cells were then harvested by centrifugation for 5 min at 6500 x g at 4°C. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit (Promega) as described previously (Slager et al. 2014 Cell). Fragmentation was performed using Covaris instrument, and libraries ...

Supplementary File S2: Kinetic entries for human galactose metabolism. SBML for query: http://sabiork.h-its.org/sabioRestWebServices/searchKineticLaws/sbml?q=Pathway:%22galactose%20metabolism%22%20AND%20Organism:%22homo%20sapiens%22

Kinetic entry 14792 SBML for query http://sabiork.h-its.org/sabioRestWebServices/kineticLaws/14792

L. lactis was grown in rich THY medium, strongly concentrated and glucose-pulsed in a MES buffer. Intracellular metabolite concentration is followed in time.

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.1 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in the model under light growth conditions. In this solution, (i) the photorespiration was set to 0; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set of 0.1 of flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is under-produced in plastid and therefore is additionally imported to cytoplasm. Flux through FQR represents cyclic electron flow through ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.5 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is over-produced in plastid and a surplus is exported to cytoplasm. Flux through FQR ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and ATP transport between plastid and cytoplasm has been set to 0. The last constraint allows finding the ratio between fluxes through FQR (ferredoxin-plastoquinone reductase) and FRN (ferredoxin-NADP oxidoreductase) under which the ATP balance in plastid becomes self-sufficient ...

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set to 0. Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for carbon fixation, therefore plastid imports ATP from cytoplasm.

The solution of Flux Balance Analysis (FBA) represent metabolic flux distribution in the model under dark growth conditions (i.e. constraints)

Flux Balance Analysis (FBA) constraints for light conditions

Flux Balance Analysis (FBA) constraints for dark conditions

The database in ASCII format includes information on compounds and metabolites (trivial name, elemental composition, charge, external database referece, etc) used in the model

The database in ASCII format includes information on gene (gene models in ATG format, gene definition, catalyzed reactions in the model, external database refeneces, locus information, etc) used in the model

The database in ASCII format includes information on transformers [reactions, transport steps, polymerizations] (model's identifier, trivial name, EC number, stoichiometric equation, external database referece, activators, belonging to a pathway, etc) used in the model

The stoichiometric matrix of the multi-compartment metabolic model of growing Arabidopsis thaliana

The ASCII file includes complete information on used transformers / compounds / genes and their inter-connection in the model. The Transformer information includes: Identifier name, Trivial name, Stoichiometric equation, Compartment, EC number, Pathway, Associated genes). The Compound information includes: Identifier name, Trivial name, Kegg ID, Compartment. The Gene information includes: ATG code of the genes whose products participate in transformations accounted in the model, Association with ...

Lactobacillus plantarum JDM1 differentially expressed proteins, comparison between low and high growth rates

Lactobacillus plantarum ATCC 14917 differentially expressed proteins, comparison between low and high growth rates

Lactobacillus plantarum strains WCFS1, NC8, JDM1 and ATCC 14917 amino acid concentrations mM supernatant, high (D=0.4) and low (D=0.05) growth rates

Heterologous Expression of LDH from L.actis (MG1363) in E. coli DH5α. Assessment of kinetic parameters of LDH to include in a catabolic model

Lactobacillus plantarum, 4 strains (WCFS1, NC8, ATCC 14917, JDM1) chemostat experiments low and high growth rates, OD and DW measurements

Lactobacillus plantarum strains WCFS1, NC8, ATCC14917, JDM1. HPLC end products mM measurements (CDM subtracted) and flux calculations, high and low growth rates.

amino acid auxotrophies as determined for S. pyogenes, E. faecalis, L. lactis and L. plantarum (ATCC, NC8, JDM1 and WCFS1) subsequent inoculation (3x) in CDM

Vmaxes E. faecalis from chemostat cultures, D0.05, D0.15 en D0.4 triplicates for every growthrate, measured in in-vivo-like assay (Goel, Teusink, AEM, 2012) glycolytic enzymes + LDH + acetate/EtOH branch

raw data OD600 of amino acid auxotrophy exps S. pyogenes

raw data OD600

Lactobacillus plantarum WCFS1 differentially expressed proteins, comparison between low and high growth rates

Lactobacillus plantarum NC8 differentially expressed proteins, comparison between low and high growth rates