Handling uncertainty in dynamic models: the pentose phosphate pathway in trypanosoma brucei

Kerkhoven, E. J. et al. (2013) Handling uncertainty in dynamic models: the pentose phosphate pathway in trypanosoma brucei. PLoS Computational Biology, 9(12), e1003371. (doi: 10.1371/journal.pcbi.1003371) (PMID:24339766) (PMCID:PMC3854711)

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Dynamic models of metabolism can be useful in identifying potential drug targets, especially in unicellular organisms. A model of glycolysis in the causative agent of human African trypanosomiasis, Trypanosoma brucei, has already shown the utility of this approach. Here we add the pentose phosphate pathway (PPP) of T. brucei to the glycolytic model. The PPP is localized to both the cytosol and the glycosome and adding it to the glycolytic model without further adjustments leads to a draining of the essential bound-phosphate moiety within the glycosome. This phosphate “leak” must be resolved for the model to be a reasonable representation of parasite physiology. Two main types of theoretical solution to the problem could be identified: (i) including additional enzymatic reactions in the glycosome, or (ii) adding a mechanism to transfer bound phosphates between cytosol and glycosome. One example of the first type of solution would be the presence of a glycosomal ribokinase to regenerate ATP from ribose 5-phosphate and ADP. Experimental characterization of ribokinase in T. brucei showed that very low enzyme levels are sufficient for parasite survival, indicating that other mechanisms are required in controlling the phosphate leak. Examples of the second type would involve the presence of an ATP:ADP exchanger or recently described permeability pores in the glycosomal membrane, although the current absence of identified genes encoding such molecules impedes experimental testing by genetic manipulation. Confronted with this uncertainty, we present a modeling strategy that identifies robust predictions in the context of incomplete system characterization. We illustrate this strategy by exploring the mechanism underlying the essential function of one of the PPP enzymes, and validate it by confirming the model predictions experimentally.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Alibu, Dr Vincent and Achcar, Dr Fiona and Burchmore, Dr Richard and Breitling, Professor Rainer and Kerkhoven, Mr Eduard and Barrett, Professor Michael
Authors: Kerkhoven, E. J., Achcar, F., Alibu, V. P., Burchmore, R. J., Gilbert, I. H., Trybiło, M., Driessen, N. N., Gilbert, D., Breitling, R., Bakker, B. M., and Barrett, M.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
Journal Name:PLoS Computational Biology
Publisher:Public Library of Science
ISSN (Online):1553-7358
Copyright Holders:Copyright © 2013 The Authors
First Published:First published in PLoS Computational Biology 9(12):e1003371
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
371796The Wellcome Centre for Molecular Parasitology ( Core Support )Andrew WatersWellcome Trust (WELLCOME)085349/Z/08/ZIII - PARASITOLOGY
617461Can marine calcifying organisms use proteomic responses to adpat to anthropogenic global change? (ISSF Catalyst Fund)Richard BurchmoreWellcome Trust (WELLCOME)097821/Z/11/ZIII - PARASITOLOGY