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General Information info

Manuscript title Is the glycolytic flux in Lactococcus lactis primarily controlled by the redox charge? Kinetics of NAD(+) and NADH pools determined in vivo by 13C NMR.
PubMed ID 12011086
Journal The Journal of Biological Chemistry
Year 2002
Authors Ana Rute Neves, Rita Ventura, Nahla Mansour, Claire Shearman, Michael J. Gasson, Christopher Maycock, Ana Ramos and Helena Santos
Affiliations Instituto de Teconcologia Química e Biológica, Universidade Nova de Lisboa and Instituto de Biologia Experimental e Tecnológico, Oeiras, Portugal
Keywords Lactococcus lactis, metabolism of glucose, NMR, in vivo
Full text article Downloadarticle Neves_2002.pdf
Project name PneumoSyS

Experiment Description info

Organism Lactococcus lactis
Strain MG1363
Data type time-series data of metabolites
Data units not specified
Execution date not specified

Experimental Details info

Temperature (0C) 30.0
pH 6.5
Carbon source glucose,
Culture mode batch
Process condition anaerobic
Dilution rate (h-1) not specified
Working volume (L) 0.050
Biomass concentration (g/L) not specified
Medium composition

Chemical-defined medium

General protocol information Sampling method: Cells were harvested in logarithmic growth phase (A 600 = 2.2)

Quenching procedure: Centrifuges, washed, and suspended to a protein concentration of 16,5 mg/ml in 50mM Kpi or Mes/KOA buffer, pH 6,5, for 13C or 31P NMR respectively.

Extraction technique: boiling ethanol

Sample analyzing method: NMR

Methods description - Notes

NMR Experiments - cells were harvested in mid-logarithmic growth phase (A600 = 2.2), centrifuged, washed twice, and suspended to a protein concentration of 16.5 mg/ml in 50 mM KPi or Mes/KOH buffer, pH 6.5, for 13C or 31P NMR experiments, respectively.
Quantification of Products - Lactate, acetoin, acetate, 2,3-butanediol, ethanol, and formate were quantified in NMR sample extracts by 1H NMR [1]. The concentration of minor products (e.g. pyruvate, ethanol, diacetyl) and metabolic intermediates that remained inside the cells (PEP, 3-PGA) was determined from the analysis of 13C spectra of NMR sample extracts as previously described [2]. Intracellular metabolite concentrations were calculated using a value of 2.9 l/mg protein for the intracellular volume of L. lactis [3]. All NMR spectra of living cells were run at 30 °C with a quadruple-nucleus probe head on a Bruker DRX500 spectrometer. Acquisition of 31P NMR and 13C NMR spectra was performed as described by Neves et al. [2]; however, acquisition parameters for 13C NMR were modified as follows: data size, 16,000; recycle delay, 0.3 s; number of transients, 480. Carbon and phosphorus chemical shifts are referenced to the resonances of external methanol or H3PO4 (85%) designated at 49.3 ppm and 0.0 ppm, respectively.

---------References---------
[1] de Vos, W.M (1999). Curr. Opin, Microbiol. 2, 289-295. http://doi.org/dztzb8
[2] Neves, A. R., Ramos, A., Nunes, M. C., Kleerebezem, M., Hugenholtz, J., de Vos, W. M., Almeida, J., and Santos, H. (1999). Biotechnol. Bioeng. 64, 200–212. http://doi.org/fqrv8j
[3] Poolman, B., Smid, E. J., Veldkamp, H., and Konings, W. N. (1987). J. Bacteriol. 169, 1460–1468.

Data file
Downloadmetabolites KIMODATAID37_v1.xlsx
Alternative format(s)
KIMODATAID37_80mM_timeseries.csv
KIMODATAID37_80mM_cometab_timeseries.csv
KIMODATAID37_40mM_timeseries.csv
KIMODATAID37_40mM_cometab_timeseries.csv
KIMODATAID37_20mM_timeseries.csv
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Organism


Related Data: AccessID 53


Submission and curation info

Entered by Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data

Created 2013-04-24 13:08:01 UTC

Updated 2015-07-27 10:39:47 UTC

Version 1

Status (reviewed) 2014-05-01 22:49:12 UTC




Associated Models


Here we can find relevant models associated with Data EntryID 37:

Model
EntryID
Model name Category Model Type Data used for Access Json
23
Authors: Jennifer Levering, Mark W. J. M. Musters, Martijn Bekker, Domenico Bellomo, Tomas Fiedler, Willem M. de Vos, Jeroen Hugenholtz, Bernd Kreikemeyer, Ursula Kummer and Bas Teusink

Original paper: Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach.

glycolysis Lactococcus lactis Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"Department of Modeling of Biological Processes, COS Heidelberg \u2044 BIOQUANT, University of Heidelberg, Germany","article_file_name":null,"authors":"Jennifer Levering, Mark W. J. M. Musters, Martijn Bekker, Domenico Bellomo, Tomas Fiedler, Willem M. de Vos, Jeroen Hugenholtz, Bernd Kreikemeyer, Ursula Kummer and Bas Teusink","biomodels_id":"levering1","category":"Metabolism","combine_archive_content_type":"application/omex+xml","combine_archive_file_name":"COMBINE_KIMOMODELID23.omex","combine_archive_file_size":1068365,"combine_archive_updated_at":"2014-06-30T17:53:53Z","comments":"Original model source: in JWS online database.","control":"2014-03-10T11:18:15Z","dilution_rate":"","id":23,"journal":"FEBS Journal","keywords":"Lactococcus lactis, metabolism of glucose, NMR, in vivo","main_organism":"Lactococcus lactis","manuscript_title":"Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach.","model_name":"glycolysis Lactococcus lactis","model_type":"ordinary differential equations","organism_id":37,"project_name":"","pubmed_id":"22325620","review_journal_id":null,"sbml_file_name":"Levering_2012.pdf","software":"http://www.copasi.org (COPASI)","used_for":"---\n- Model building\n- Model validation\n","year":2012} Administrator KiMoSys
24
Authors: Susana Vinga, Ana R. Neves, Helena Santos, B. W. Brandt and S. A. L. M. Kooijman

Original paper: Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories

DEB L. lactis model Metabolism ordinary differential equations Model building Visto4 {"affiliation":"Instituto de Engenharia de Sistemas e Computadores: Investiga\u00e7\u00e3o e Desenvolvimento (INESC-ID)","article_file_name":null,"authors":"Susana Vinga, Ana R. Neves, Helena Santos, B. W. Brandt and S. A. L. M. Kooijman","biomodels_id":"","category":"Metabolism","combine_archive_content_type":null,"combine_archive_file_name":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"comments":"Archive containing all files to run and plot simulations. Requires MATLAB.","control":"2014-05-15T09:26:26Z","dilution_rate":"","id":24,"journal":"Philosophical transactions of the royal society B","keywords":"Lactococcus lactis, metabolism of glucose, NMR, in vivo","main_organism":"Lactococcus lactis","manuscript_title":"Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories","model_name":"DEB L. lactis model","model_type":"ordinary differential equations","organism_id":37,"project_name":"","pubmed_id":"20921043","review_journal_id":null,"sbml_file_name":"Vinga_2010.pdf","software":"http://www.matlab.com (MATLAB)","used_for":"---\n- Model building\n","year":2010} Administrator KiMoSys
35
Authors: Rafael S. Costa, Andras Hartmann, Paula Gaspar, Ana R. Neves and Susana Vinga

Original paper: An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production

glycolysis Lactococcus lactis for mannitol and 2,3-butanediol production Metabolism ordinary differential equations Model building and Model validation Visto4 {"affiliation":"Instituto de Engenharia de Sistemas e Computadores, Investigac\u00e3o e Desenvolvimento (INESC-ID), R Alves Redol 9, 1000-029 Lisboa, Portugal.","article_file_name":null,"authors":"Rafael S. Costa, Andras Hartmann, Paula Gaspar, Ana R. Neves and Susana Vinga","biomodels_id":"","category":"Metabolism","combine_archive_content_type":null,"combine_archive_file_name":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"comments":" Copasi model file used to produce manuscript figures.","control":"2014-07-21T10:18:41Z","dilution_rate":"\u2014","id":35,"journal":"Molecular BioSystems","keywords":"L. lactis, extended model, mannitol and 2,3-butanediol production, control analysis","main_organism":"Lactococcus lactis","manuscript_title":"An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production","model_name":"glycolysis Lactococcus lactis for mannitol and 2,3-butanediol production","model_type":"ordinary differential equations","organism_id":null,"project_name":"PneumoSyS","pubmed_id":"24413179","review_journal_id":null,"sbml_file_name":"Costa_2014.pdf","software":"http://www.copasi.org (COPASI)","used_for":"---\n- Model building\n- Model validation\n","year":2014} Rafael Costa



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