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TrypanoCyc – a metabolic pathway database for Trypanosoma brucei

Background

Trypanosoma brucei (T. brucei) is a single celled parasite, subspecies of which are causative agents of African sleeping sickness in humans and nagana in domestic animals. Sleeping sickness is endemic in about 36 countries in Sub-Saharan Africa and is threatening over 60 million people. Disease prevention is a priority, as few effective drugs are available. Currently, there are only four drugs used as treatment: Pentamidine, Suramin. Melarsoprol and Eflornithine, though they have poor safety profiles, challenging treatment regimes and lack in efficacy. There is therefore a great need in identifying novel therapeutics for the treatment of sleeping sickness and fortunately, efforts have intensified over recent years. One such development has been the availability of the Pathway Tools Software [1]. We have used this production software to set up TrypanoCyc, a metabolic pathway database for T. brucei http://www.genedb.org/tmp/.

Methods/results

Based on the available genome annotation, Pathologic assigned proteins to reactions and pathways. The Pathway hole filler algorithm was subsequently used to identify missing enzyme annotations in the T. brucei genome. Further manual refinement included enzymes and pathways previously identified in the literature but unique to T. brucei (e.g. GPI Biosynthetic pathway) and thus not present as 'generic' pathways in the tool. A total of 178 pathways were identified comprising 1112 enzymes, 341 of which represented additional annotations to proteins with no previous functional assignments.

In order to determine potential drug targets, we performed chokepoint analyses of the metabolic network of T. brucei. We define a "chokepoint reaction" as a reaction that either uniquely consumes a specific substrate or uniquely produces a specific product in the TrypanoCyc metabolic network. We expect the inhibition of an enzyme that consumes a unique substrate to result in the accumulation of the unique substrate (potentially toxic to the cell) and the inhibition of an enzyme that produces a unique product to result in the starvation of the unique product (potentially crippling essential cell functions).

  1. 168

    enzymes were identified as choke point enzymes and this set included almost all of the drug targets of currently used and proposed drugs (e.g. trypanothione pathway – Figure 1) against sleeping sickness.

Figure 1
figure1

A graphical overview of TrypanoCyc: Trypanothione pathway (coloured green) and biopterin pathway (coloured red) in graphical overview diagram of TrypanoCyc.

Conclusion

TrypanoCyc, a database of metabolic pathways for T. brucei will remain an invaluable resource for detailed analyses of the metabolic network of the parasite T. brucei and related species. The database will continually be updated with new reactions and pathways identified from Literature and refinement of chokepoint analyses to identify potential drug targets would be a priority.

References

  1. 1.

    Karp P, Paley S, Romero P: The Pathway Tools software. Bioinformatics 2002, 18(1):S225-S2232.

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Correspondence to Bridget Chukualim.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Chukualim, B., Peters, N., Fowler, C.H. et al. TrypanoCyc – a metabolic pathway database for Trypanosoma brucei. BMC Bioinformatics 9, P5 (2008). https://doi.org/10.1186/1471-2105-9-S10-P5

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Keywords

  • Metabolic Network
  • Suramin
  • Pentamidine
  • Unique Product
  • Potential Drug Target