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Applied Cellular Physiology and Metabolic Engineering

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

  1. Sarah A. Munro1,†,
  2. Leila Choe2,
  3. Stephen H. Zinder3,
  4. Kelvin H. Lee2,
  5. Larry P. Walker1,*

Article first published online: 27 OCT 2011

DOI: 10.1002/btpr.735

Issue

Biotechnology Progress

Biotechnology Progress

Volume 28, Issue 2, pages 312–318, March/April 2012

Additional Information

How to Cite

Munro, S. A., Choe, L., Zinder, S. H., Lee, K. H. and Walker, L. P. (2012), Proteomic and physiological experiments to test Thermotoga neapolitana constraint-based model hypotheses of carbon source utilization. Biotechnol Progress, 28: 312–318. doi: 10.1002/btpr.735

Author Information

  1. 1

    Dept. of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853

  2. 2

    Chemical Engineering Dept. and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711

  3. 3

    Dept. of Microbiology, Cornell University, Ithaca, NY 14853

  1. †

    National Institute of Standards and Technology, Material Measurement Laboratory, Biochemical Science Division, 100 Bureau Drive Gaithersburg, MD 20899

*Dept. of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853

Publication History

  1. Issue published online: 10 APR 2012
  2. Article first published online: 27 OCT 2011
  3. Accepted manuscript online: 3 OCT 2011 11:16AM EST
  4. Manuscript Revised: 19 SEP 2011
  5. Manuscript Received: 23 AUG 2011

Funded by

  • Initiative for Future Agriculture and Food Systems. Grant Number: 2001-52104-11484
  • USDA Cooperative State Research, Education, and Extension Service
  • New York Science Technology and Academic Research Faculty Development Program. Grant Number: C030065

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Keywords:

  • Thermotoga neapolitana;
  • proteomics;
  • two-dimensional protein electrophoresis;
  • constraint-based model;
  • flux balance analysis;
  • ATP conservation;
  • cellotetraose

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. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2012

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