Proteomic and physiological experiments to test Thermotoga neapolitana constraint-based model hypotheses of carbon source utilization

Sarah A. Munro, Leila Choe, Stephen H. Zinder, Kelvin H. Lee, Larry P. Walker

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Constraint-based models of biochemical reaction networks require experimental validation to test model-derived hypotheses and iteratively improve the model. Physiological and proteomic analysis of Thermotoga neapolitana growth on cellotetraose was conducted to identify gene products related to growth on cellotetraose to improve a constraint-based model of T. neapolitana central carbon metabolism with incomplete cellotetraose pathways. In physiological experiments comparing cellotetraose to cellobiose and glucose as growth substrates, product formation yields on cellotetraose, cellobiose, and glucose were similar; however cell yields per mol carbon consumed were higher on cellotetraose than on cellobiose or glucose. Proteomic analysis showed increased expression of several proteins from cells grown on cellotetraose compared with glucose cell cultures, including cellobiose phosphorylase (CTN_0783), endo-1,4-β-glucosidase (CTN_1106), and an ATP-binding protein (CTN_1296). The CTN_1296 gene product should be evaluated further for participation in cellotetraose metabolism and is included as one of two hypothetical gene-protein-reaction associations in the T. neapolitana constraint-based model to reinstate cellotetraose metabolism in model simulations.

Original languageEnglish (US)
Pages (from-to)312-318
Number of pages7
JournalBiotechnology Progress
Volume28
Issue number2
DOIs
StatePublished - Mar 1 2012
Externally publishedYes

Keywords

  • ATP conservation
  • Cellotetraose
  • Constraint-based model
  • Flux balance analysis
  • Proteomics
  • Thermotoga neapolitana
  • Two-dimensional protein electrophoresis

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