دورية أكاديمية
أعرض في EDS

A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on (13)C mass isotopologue profiles under non-steady-state conditions.

التفاصيل البيبلوغرافية
العنوان: A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on (13)C mass isotopologue profiles under non-steady-state conditions.
المؤلفون: Moseley HN; Department of Chemistry and Center for Regulatory & Environmental Analytical Metabolomics (CREAM), University of Louisville, Louisville, KY 40292, USA., Lane AN, Belshoff AC, Higashi RM, Fan TW
المصدر: BMC biology [BMC Biol] 2011 May 31; Vol. 9, pp. 37. Date of Electronic Publication: 2011 May 31.
نوع المنشور: Evaluation Study; Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة: English
بيانات الدورية: Publisher: BioMed Central Country of Publication: England NLM ID: 101190720 Publication Model: Electronic Cited Medium: Internet ISSN: 1741-7007 (Electronic) Linking ISSN: 17417007 NLM ISO Abbreviation: BMC Biol Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [London] : BioMed Central, c2003-
مواضيع طبية MeSH: Biosynthetic Pathways*, Glucose/*metabolism , Isotope Labeling/*methods , Metabolomics/*methods , Uridine Diphosphate N-Acetylglucosamine/*biosynthesis, Algorithms ; Carbon Isotopes/chemistry ; Cell Line, Tumor ; Cyclotrons ; Fourier Analysis ; Humans ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Ribose/metabolism ; Uracil/metabolism
مستخلص: Background: Stable isotope tracing is a powerful technique for following the fate of individual atoms through metabolic pathways. Measuring isotopic enrichment in metabolites provides quantitative insights into the biosynthetic network and enables flux analysis as a function of external perturbations. NMR and mass spectrometry are the techniques of choice for global profiling of stable isotope labeling patterns in cellular metabolites. However, meaningful biochemical interpretation of the labeling data requires both quantitative analysis and complex modeling. Here, we demonstrate a novel approach that involved acquiring and modeling the timecourses of (13)C isotopologue data for UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) synthesized from [U-(13)C]-glucose in human prostate cancer LnCaP-LN3 cells. UDP-GlcNAc is an activated building block for protein glycosylation, which is an important regulatory mechanism in the development of many prominent human diseases including cancer and diabetes.
Results: We utilized a stable isotope resolved metabolomics (SIRM) approach to determine the timecourse of (13)Cincorporation from [U-(13)C]-glucose into UDP-GlcNAc in LnCaP-LN3 cells. (13)CPositional isotopomers and isotopologues of UDP-GlcNAc were determined by high resolution NMR and Fourier transform-ion cyclotron resonance-mass spectrometry. A novel simulated annealing/genetic algorithm, called 'Genetic Algorithm for Isotopologues in Metabolic Systems' (GAIMS) was developed to find the optimal solutions to a set of simultaneous equations that represent the isotopologue compositions, which is a mixture of isotopomer species. The best model was selected based on information theory. The output comprises the timecourse of the individual labeled species, which was deconvoluted into labeled metabolic units, namely glucose, ribose, acetyl and uracil. The performance of the algorithm was demonstrated by validating the computed fractional 13C enrichment in these subunits against experimental data. The reproducibility and robustness of the deconvolution were verified by replicate experiments, extensive statistical analyses, and cross-validation against NMR data.
Conclusions: This computational approach revealed the relative fluxes through the different biosynthetic pathways of UDP-GlcNAc, which comprises simultaneous sequential and parallel reactions, providing new insight into the regulation of UDP-GlcNAc levels and O-linked protein glycosylation. This is the first such analysis of UDP-GlcNAc dynamics, and the approach is generally applicable to other complex metabolites comprising distinct metabolic subunits, where sufficient numbers of isotopologues can be unambiguously resolved and accurately measured.
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معلومات مُعتمدة: 1R01CA101199-01 United States CA NCI NIH HHS; 5P20RR018733 United States RR NCRR NIH HHS; R01CA118434-01A2 United States CA NCI NIH HHS; R21CA133668-01 United States CA NCI NIH HHS
المشرفين على المادة: 0 (Carbon Isotopes)
528-04-1 (Uridine Diphosphate N-Acetylglucosamine)
56HH86ZVCT (Uracil)
681HV46001 (Ribose)
IY9XDZ35W2 (Glucose)
تواريخ الأحداث: Date Created: 20110602 Date Completed: 20110927 Latest Revision: 20211020
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC3126751
DOI: 10.1186/1741-7007-9-37
PMID: 21627825
قاعدة البيانات: MEDLINE
الوصف
تدمد:1741-7007
DOI:10.1186/1741-7007-9-37