Dataset Information

Optimization of SILAC in human embryonic stem cells

ABSTRACT: We present a fully defined culture system (adapted Essential8 (E8) medium in combination with vitronectin) for human embryonic stem cells (hESC) that can be used for Stable Isotopic Labeling of Amino aCids (SILAC) purposes. Although a complete incorporation of the labels was observed after 4 days in culture, more than 50 % of all mass spectrometry (MS) precursors displayed a conversion of L-arginine (R) to L-proline (P) or L-glumatate (E) of 40 %. To reduce this arginine conversion, E8 medium was modified by adding (1) L-proline, (2) L-ornithine, (3) Nω-hydroxy-nor-L-arginine (Nor-NOHA) acetate or by (4) lowering the arginine concentration. Inhibition of arginine conversion was best obtained by adding 5mM L-ornithine, followed by 3.5 mM L-proline and by lowering arginine concentration to 99.5 µM. No major changes in the proteome (HDMSE data), pluripotency and cell amount could be observed for these adapted Essential8TM media, although sudden cell death was sometimes observed with the use of 99.5 µM L-arginine. In conclusion, we suggest using 5 mM L-ornithine to reduce arginine conversion.

INSTRUMENT(S): Synapt G2-S HDMS, TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Embryonic Stem Cell

SUBMITTER: Ellen Scheerlinck

LAB HEAD: Prof. Dr. Dieter Deforce

PROVIDER: PXD002859 | Pride | 2016-07-15

REPOSITORIES: Pride

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Publications

Assessing the impact of minimizing arginine conversion in fully defined SILAC culture medium in human embryonic stem cells.

Scheerlinck Ellen E Van Steendam Katleen K Daled Simon S Govaert Elisabeth E Vossaert Liesbeth L Meert Paulien P Van Nieuwerburgh Filip F Van Soom Ann A Peelman Luc L De Sutter Petra P Heindryckx Björn B Dhaenens Maarten M Deforce Dieter D

Proteomics 20160912 20

We present a fully defined culture system (adapted Essential8TM [E8TM ] medium in combination with vitronectin) for human embryonic stem cells that can be used for SILAC purposes. Although a complete incorporation of the labels was observed after 4 days in culture, over 90% of precursors showed at least 10% conversion. To reduce this arginine conversion, E8TM medium was modified by adding (1) l-proline, (2) l-ornithine, (3) Nω -hydroxy-nor-l-arginine a ...[more]

PMID: 27392809

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Project description:Most available knowledge on fungal arginine metabolism is derived from studies on Saccharomyces cerevisiae, in which arginine catabolism is initiated by releasing urea via the arginase reaction. Orthologs of the S. cerevisiae genes encoding the first three enzymes in the arginase pathway were cloned from Kluyveromyces lactis and shown to functionally complement the corresponding deletion in S. cerevisiae. Surprisingly, deletion of the single K. lactis arginase gene KlCAR1 did not completely abolish growth on arginine as nitrogen source. Growth rate of mutant strongly increased during serial transfer in shake-flask cultures. A combination of RNAseq-based transcriptome analysis and 13C-15N-based flux analysis was used to elucidate the arginase-independent pathway. Isotopic 13C15N-enrichment in ?-aminobutyrate revealed succinate as the entry point in the TCA cycle of the alternative pathway. Transcript analysis combined with enzyme activity measurements indicated increased expression in the Klcar1? mutant of a guanidinobutyrase (EC.3.5.3.7), an enzyme not previously demonstrated in fungi. Expression of the K. lactis KLLA0F27995g (renamed KlGBU1) encoding guanidinobutyrase enabled S. cerevisiae to use guanidinobutyrate as sole nitrogen source and its deletion in K. lactis almost completely abolish growth on this nitrogen source. Phylogenetic analysis suggests that this enzyme activity is widespread in fungi. The goal of the present study was to characterize arginine catabolism in K. lactis. To this end, CAR1, CAR2 and PRO3 orthologs in K. lactis were identified and functionally analysed by deletion, expression in S. cerevisiae and enzyme activity assays. Since deletion of the arginase gene in K. lactis was found not to completely abolish growth on arginine as a sole nitrogen source, the alternative pathway for arginine catabolism operating in this yeast was studied by a combination of transcriptome analysis, 13C and 15N isotope-based flux analysis and enzyme activity assays in cell extracts. To investigate arginine metabolism in the arginase-negative K. lactis strain, strains GG1632 (Klku80? KlCAR1 reference strain) and IMS0367 (Klcar1? Arg+) were grown in aerobic bioreactor batch cultures on glucose chemically defined medium with arginine as sole nitrogen source. RNA sequencing of samples taken during the exponential phase of growth on glucose-arginine media of the reference strain G1631 and the arginase less strain IMS0367 were compared resulting in the characterization of a new function.

Project description:Analysis of the response to arginine of the Escherichia coli K-12 transcriptome by microarray hybridization and real-time quantitative PCR provides a first coherent quantitative picture of the ArgR-mediated repression of arginine biosynthesis and uptake genes. Transcriptional repression was shown to be the major control mechanism of the biosynthetic genes, leaving only limited room for additional transcriptional or post-transcriptional regulations. The art genes coding for the specific arginine uptake system are subject to ArgR-mediated repression, ; with a strong repression of artJ, coding for the periplasmic binding protein of the system. The hisJQMP genes of the histidine transporter (part of the LAO uptake system) were discovered to be a part of the arginine regulon. Analysis of their control region with reporter gene fusions and electrophoretic mobility shift in the presence of pure ArgR repressor showed the involvement in repression of the ArgR protein and of an ARG box 120 bp upstream of hisJ. No repression of the genes of the AO uptake system was observed. Finally, comparing the time course of arginine repression of gene transcription with the evolution of the specific ; activities of the cognate enzymes showed that while full genetic repression was achieved two minutes after arginine addition, enzyme concentrations were diluted at the rate of cell ; division. This emphasizes the importance of the feedback-inhibition of the first enzymatic ; step of the pathway in controlling the metabolic flow through the biosynthesis in the period following the onset of repression. Experiment Overall Design: 3 groups of 3 replicate samples were analyzed: Experiment Overall Design: (1) Wild type on minimal medium (strain P4X, slides 1753, 1765, 1989), this created a reference condition Experiment Overall Design: (2) Wild type grown in the presence of arginine (strain P4X plus 100Âµg/ml of arginine, slides 1754, 1766, 1990), this gave a list of all the genes repressed by the system: ArgR+arginine Experiment Overall Design: (3) Mutant where no active repressor is present; grown in the presence of arginine (strain P4XB2 (argR-) plus 100Âµg/ml arginine, slides 1992, 1993, 1994). This condition told us which genes are indeed regulated by the system: ArgR+arginine. Those genes are in this case derepressed.

Dataset Information

Optimization of SILAC in human embryonic stem cells

Publications

Assessing the impact of minimizing arginine conversion in fully defined SILAC culture medium in human embryonic stem cells.

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