TrypanoCyc: A community-led biochemical pathways database for Trypanosoma brucei

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D637-D644

  Shameer, Sanu ^a   Logan Klumpler, Flora J ^b   Vinson, Florence ^a   Cottret, Ludovic ^c   Merlet, Benjamin ^a   Achcar, Fiona ^d   Boshart, Michael ^e   Berriman, Matthew ^b   Breitling, Rainer ^f   Bringaud, Frédéric ^g   Bütikofer, Peter ^h   Cattanach, Amy M ^d   Bannerman Chukualim, Bridget ^b   Creek, Darren J ⁱ   Crouch, Kathryn ^d   De Koning, Harry P ^d   Denise, Hubert ^j   Ebikeme, Charles ^k   Fairlamb, Alan H ^l   Ferguson, Michael A J ^l   Ginger, Michael L ^m   Hertz Fowler, Christiane ⁿ   Kerkhoven, Eduard J ^o   Mäser, Pascal ^p   Michels, Paul A M ^q   Nayak, Archana ^d   Nes, DavidW ^r   Nolan, Derek P ^s   Olsen, Christian ^t   Silva Franco, Fatima ⁿ   Smith, Terry K ^u   Taylor, Martin C ^v   Tielens, Aloysius G M ^w,x   Urbaniak, Michael D ^m   Van Hellemond, Jaap J ^x   Vincent, Isabel M ^d   Wilkinson, Shane R ^y   Wyllie, Susan ^l   Opperdoes, Fred R ^z   Barrett, Michael P ^d   Jourdan, Fabien ^a   more..

^a TOXALIM RESEARCH CENTRE IN FOOD TOXICOLOGY   (France)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c LABORATOIRE DES INTERACTIONS PLANTES MICROORGANISMES LIPM   (France)

^d UNIVERSITY OF GLASGOW   (United Kingdom)

^e UNIVERSITY OF MUNICH   (Germany)

^f UNIVERSITY OF MANCHESTER   (United Kingdom)

^g CNRS   (France)

^h UNIVERSITY OF BERN   (Switzerland)

ⁱ MONASH UNIVERSITY   (Australia)

^j EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^k UNESCO   (France)

^l UNIVERSITY OF DUNDEE   (United Kingdom)

^m LANCASTER UNIVERSITY   (United Kingdom)

ⁿ UNIVERSITY OF LIVERPOOL   (United Kingdom)

^o CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^p SWISS TROPICAL AND PUBLIC HEALTH INSTITUTE   (Switzerland)

^q UNIVERSITY OF EDINBURGH   (United Kingdom)

^r TEXAS TECH UNIVERSITY   (United States)

^s TRINITY COLLEGE DUBLIN   (Ireland)

^t Biomatters Inc   (United States)

^u UNIVERSITY OF ST ANDREWS   (United Kingdom)

^v LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^w UTRECHT UNIVERSITY   (Netherlands)

^x ERASMUS MEDICAL CENTER   (Netherlands)

^y QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^z UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

more..

Author keywords

[No Author keywords available]

Indexed keywords

GLUTATHIONE REDUCTASE; PHOSPHOGLUCONATE DEHYDROGENASE;

AMINO ACID METABOLISM; ARTICLE; BIOCHEMISTRY; CATALYSIS; DATA BASE; ENZYME ACTIVITY; GLYCOLYSIS; LIFE CYCLE; METABOLOMICS; MOLECULAR EVOLUTION; NONHUMAN; PLASTICITY; PRIORITY JOURNAL; PROTEOMICS; SEQUENCE HOMOLOGY; TRANSCRIPTOMICS; TRYPANOCYC DATABASE; TRYPANOSOMA; TRYPANOSOMA BRUCEI; CHEMICAL DATABASE; DATA MINING; GENETICS; INTERNET; METABOLISM; TRYPANOSOMA BRUCEI BRUCEI;

DATA MINING; DATABASES, CHEMICAL; INTERNET; METABOLIC NETWORKS AND PATHWAYS; PROTEOMICS; TRYPANOSOMA BRUCEI BRUCEI;

EID: 84943153611     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku944     Document Type: Article

References (45)

1. Brun, R., Blum, J., Chappuis, F. and Burri, C. (2010) Human African trypanosomiasis. Lancet, 375, 148-59.
2. Barrett, M. P. (2010) Potential new drugs for human African trypanosomiasis: some progress at last. Curr. Opin. Infect. Dis., 23, 603-608.
3. Vincent, I. M., Creek, D. J., Burgess, K., Woods, D. J., Burchmore, R. J. S. and Barrett, M. P. (2012) Untargeted metabolomics reveals a lack of synergy between nifurtimox and eflornithine against Trypanosoma brucei. PLoS Negl. Trop. Dis., 6, e1618.
4. Creek, D. J. and Barrett, M. P. (2014) Determination of antiprotozoal drug mechanisms by metabolomics approaches. Parasitology, 141, 83-92.
5. Achcar, F., Kerkhoven, E. J. and Barrett, M. P. (2014) Trypanosoma brucei: meet the system. Curr. Opin. Microbiol., 20C, 162-169.
6. Cottret, L. and Jourdan, F. (2010) Graph methods for the investigation of metabolic networks in parasitology. Parasitology, 137, 1393-1407.
7. Doyle, M. A., MacRae, J. I., De Souza, D. P., Saunders, E. C., McConville, M. J. and Likić, V. A. (2009) LeishCyc: a biochemical pathways database for Leishmania major. BMC Syst. Biol., 3, 57.
8. Shanmugasundram, A., Gonzalez-Galarza, F. F., Wastling, J. M., Vasieva, O. and Jones, A. R. (2013) Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. Nucleic Acids Res., 41, D706-D713.
9. Thiele, I. and Palsson, Ø. B. (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat. Protoc., 5, 93-121.
10. De Jongh, M., Formsma, K., Boillot, P., Gould, J., Rycenga, M. and Best, A. (2007) Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinform., 8, 139.
11. Whitaker, J. W., Letunic, I., McConkey, G. A. and Westhead, D. R. (2009) metaTIGER: a metabolic evolution resource. Nucleic Acids Res., 37, D531-D538.
12. Agren, R., Liu, L., Shoaie, S., Vongsangnak, W., Nookaew, I. and Nielsen, J. (2013) The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput. Biol., 9, e1002980.
13. May, J. W., James, A. G. and Steinbeck, C. (2013) Metingear: a development environment for annotating genome-scale metabolic models. Bioinformatics, 29, 2213-2215.
14. Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A. et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459-D471.
15. Ginsburg, H. (2006) Progress in in silico functional genomics: the malaria Metabolic Pathways database. Trends. Parasitol., 22, 238-240.
16. Fairlamb, A. H., Blackburn, P., Ulrich, P., Chait, B. T. and Cerami, A. (1985) Trypanothione: a novel bis (glutathionyl) spermidine cofactor for glutathione reductase in trypanosomatids. Science, 227, 1485-1487.
17. Tardif, M., Atteia, A., Specht, M., Cogne, G., Rolland, N., Brugière, S., Hippler, M., Ferro, M., Bruley, C., Peltier, G. et al. (2012) PredAlgo: a new subcellular localization prediction tool dedicated to green algae. Mol. Biol. Evol., 29, 3625-3639.
18. Lamour, N., Rivière, L., Coustou, V., Coombs, G. H., Barrett, M. P. and Bringaud, F. (2005) Proline metabolism in procyclic Trypanosoma brucei is down-regulated in the presence of glucose. J. Biol. Chem., 280, 11902-11910.
19. Michels, P. A., Hannaert, V. and Bringaud, F. (2000) Metabolic aspects of glycosomes in trypanosomatidae - new data and views. Parasitol. Today, 16, 482-489.
20. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res., 42, D199-205.
21. Cottret, L., Wildridge, D., Vinson, F., Barrett, M. P., Charles, H., Sagot, M.-F. and Jourdan, F. (2010) MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res., 38, W132-W137.
22. Berriman, M., Ghedin, E., Hertz-Fowler, C., Blandin, G., Renauld, H., Bartholomeu, D. C., Lennard, N. J., Caler, E., Hamlin, N. E., Haas, B. et al. (2005) The genome of the African trypanosome Trypanosoma brucei. Science, 309, 416-422.
23. Karp, P. D., Latendresse, M. and Caspi, R. (2011) The pathway tools pathway prediction algorithm. Stand. Genomic Sci., 5, 424-429.
24. Thiele, I. and Palsson, B.Ø. (2010) Reconstruction annotation jamborees: a community approach to systems biology. Mol. Syst. Biol., 6, 361.
25. Opperdoes, F. R., Borst, P. and Spits, H. (1977) Particle-bound enzymes in the bloodstream form of Trypanosoma brucei. Eur. J. Bioche., 76, 21-28.
26. Opperdoes, F. R. and Borst, P. (1977) Localization of nine glycolytic enzymes in a microbody-like organelle in Trypanosoma brucei: the glycosome. FEBS Lett., 80, 360-364.
27. Berger, B. J., Dai, W. W., Wang, H., Stark, R. E. and Cerami, A. (1996) Aromatic amino acid transamination and methionine recycling in trypanosomatids. Proc. Natl. Acad. Sci. U. S. A., 93, 4126-4130.
28. Creek, D. J., Chokkathukalam, A., Jankevics, A., Burgess, K. E. V., Breitling, R. and Barrett, M. P. (2012) Stable isotope-assisted metabolomics for network-wide metabolic pathway elucidation. Anal. Chem., 84, 8442-8447.
29. Chavali, A. K., Whittemore, J. D., Eddy, J.a., Williams, K. T. and Papin, J.a. (2008) Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major. Mol. Syst. Biol., 4, 177.
30. Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D. et al. (2013) A community-driven global reconstruction of human metabolism. Nat. Biotechnol., 31, 419-425.
31. Schomburg, I., Chang, A., Ebeling, C., Gremse, M., Heldt, C., Huhn, G. and Schomburg, D. (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res., 32, D431-D433.
32. Schomburg, I., Chang, A., Placzek, S., Söhngen, C., Rother, M., Lang, M., Munaretto, C., Ulas, S., Stelzer, M., Grote, A. et al. (2013) BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res., 41, D764-D772.
33. Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., De Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E. et al. (2012) ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res., 40, W597-W603.
34. McDonald, A. G., Boyce, S. and Tipton, K. F. (2009) ExplorEnz: the primary source of the IUBMB enzyme list. Nucleic Acids Res., 37, D593-D597.
35. The UniProt Consortium (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
36. Aslett, M., Aurrecoechea, C., Berriman, M., Brestelli, J., Brunk, B. P., Carrington, M., Depledge, D. P., Fischer, S., Gajria, B., Gao, X. et al. (2010) TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res., 38, D457-D462.
37. Logan-Klumpler, F. J., De Silva, N., Boehme, U., Rogers, M. B., Velarde, G., McQuillan, J. A., Carver, T., Aslett, M., Olsen, C., Subramanian, S. et al. (2012) GeneDB-an annotation database for pathogens. Nucleic Acids Res., 40, D98-D108.
38. Keseler, I. M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martínez, C., Fulcher, C., Huerta, A. M., Kothari, A., Krummenacker, M. et al. (2013) EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res., 41, D605-D612.
39. Romero, P., Wagg, J., Green, M. L., Kaiser, D., Krummenacker, M. and Karp, P. D. (2005) Computational prediction of human metabolic pathways from the complete human genome. Genome Biol., 6, R2.
40. Zhang, P., Foerster, H., Tissier, C. P., Mueller, L., Paley, S., Karp, P. D. and Rhee, S. Y. (2005) MetaCyc and AraCyc. Metabolic pathway databases for plant research. Plant Physiol., 138, 27-37.
41. Urbaniak, M. D., Guther, M. L. S. and Ferguson, M. A. J. (2012) Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages. PloS One, 7, e36619.
42. Paley, S. M. and Karp, P. D. (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res., 34, 3771-3778.
43. Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B. et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc., 2, 2366-2382.
44. Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A. et al. (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
45. Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S. et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc., 6, 1290-1307.