A three-level problem-centric strategy for selecting NMR precursor labeling and analytes

Metabolic Engineering

Volumn 8, Issue 5, 2006, Pages 491-507

  Ghosh, Soumitra ^a   Grossmann, Ignacio E ^a   Ataai, Mohammad M ^b   Domach, Michael M ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b University of Pittsburgh   (United States)

Author keywords

E. coli; Global optimization; Metabolic flux analysis; Non linear programming; Nuclear magnetic resonance

Indexed keywords

COST BENEFIT ANALYSIS; DATA ACQUISITION; ESCHERICHIA COLI; HIERARCHICAL SYSTEMS; METABOLISM; NONLINEAR PROGRAMMING;

GLOBAL OPTIMIZATION; METABOLIC FLUX ANALYSIS; PRECURSOR LABELING;

NUCLEAR MAGNETIC RESONANCE;

ANALYTIC METHOD; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; COST BENEFIT ANALYSIS; INSTRUMENT; METABOLIC ENGINEERING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PREDICTION; PRIORITY JOURNAL; PROBLEM IDENTIFICATION; PROBLEM SOLVING; QUANTITATIVE ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; ISOTOPE LABELING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, BIOLOGICAL;

EID: 33747766257     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2006.05.001     Document Type: Article

References (19)

1. Fell, and Wagner. The small world of metabolism. Nat. Biotechnol. 18 (2000) 1121-1122
2. 13C constraints. Anal. Biochem. 325 2 (2004) 308-316
3. Forbes N.S., Clark D.S., and Blanch H.W. Using isotopomer path tracing to quantify metabolic fluxes in pathway models containing reversible reactions. Biotech. Bioeng. 74 3 (2001) 196-211
4. Ghosh S., Zhu T., Grossmann I.E., Ataai M.M., and Domach M.M. Closing the loop between feasible flux scenario identification for construct evaluation and resolution of realized fluxes via NMR. Comput. Chem. Eng. 29 (2005) 459-466
5. Goel A., Lee J.W., Domach M.M., and Ataai M.M. Suppressed acid formation by co-feeding glucose and citrate in Bacillus cultures: Emergence of pyruvate kinase as a potential metabolic engineering site. Biotechnol. Prog. 11 (1995) 380-386
6. Lee S., Phalakornkule C., Ataai M.M., Domach M.M., and Grossmann I.E. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput. Chem. Eng. 24 (2000) 711-716
7. Lehninger A.L. Biochemistry. sixth printing (1972), Worth Publishers, New York p. 93
8. Majewski R.A., and Domach M.M. Effect of Regulatory Mechanism on Hyperbolic Reaction Network Properties. Biotechnol. Bioeng. 36 (1989) 166-178
9. Mollney M., Wiechert W., Kownatzki D., and de Graaf A.A. Bidirectional reaction steps in metabolic networks IV: optimal design of isotopomer labeling experiments. Biotechnol. Bioeng. 66 2 (1999) 86-103
10. 13C NMR evidence for pyruvate kinase flux attenuation underlying suppressed acid formation in B. subtilis. Biotechnol. Prog. 16 (2000) 169-175
11. Phalakornkule C., Lee S., Zhu T., Koepsel R., Ataai M.M., Grossmann I.E., and Domach M.M. A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering. Metab. Eng. 3 (2001) 124-137
12. Saaty T.L. Fundamentals of Decision Making and Priority Theory. second ed. (2000), RWS Publications, Pittsburgh, PA
13. Sahinidis, N.V., Tawarmalani, M., 2002. GAMS/BARON 5.0-Global Optimization of Mixed-Integer Nonlinear Programs.
14. Schmidt K., Carlsen M., Nielsen J., and Villadsen J. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55 (1997) 831-840
15. Schmidt K., Carlsen M., Nielsen J., and Villadsen J. Quantitative analysis of metabolic fluxs in E. coli, using 2-dimensional NMR spectroscopy and complete isotopomer models. J. Biotechnol. 71 (1999) 175-189
16. Siddiquee K.A., Arauzo-Bravo M.J., and Shimuzu K. Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in E. coli. FEMS Microbiol. Lett. 235 1 (2004) 25-33
17. Tempest D.W., and Meers J.L. Influence of environment on the content and composition of microbial free amino acid pools. J. Gen. Microbiol. 64 (1970) 171-185
18. Zhu T., Phalakornkule C., Koepsel R.R., Domach M.M., and Ataai M.M. Cell growth and by-product formation in a pyruvate kinase mutant of E. coli. Biotechnol. Prog. 17 (2001) 624-628
19. Zhu T., Phalakorkule C., Ghosh S., Grossmann I.E., Koepsel R.R., Ataai M.M., and Domach M.M. A metabolic network analysis and NMR experiment design tool with user interface-driven model construction for depth-first search analysis. Metab. Eng. 5 (2003) 74-85