Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium

Trends in Parasitology

Volumn 25, Issue 1, 2009, Pages 37-43

  Ginsburg, Hagai ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

6 PHOSPHOFRUCTOKINASE; GALACTOSE 1 PHOSPHATE URIDYLYLTRANSFERASE; GENE PRODUCT; HEXOKINASE; ORNITHINE OXOACID AMINOTRANSFERASE; TERPENOID;

CATALYSIS; DATA BASE; FUNCTIONAL GENOMICS; GENE SEQUENCE; GLYCOLYSIS; METABOLISM; NONHUMAN; PLASMODIUM FALCIPARUM; PROTOZOAL GENETICS; REVIEW;

ANIMALS; COMPUTER SIMULATION; GENOME, PROTOZOAN; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; PLASMODIUM;

PLASMODIUM FALCIPARUM;

EID: 58149119607     PISSN: 14714922     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pt.2008.08.012     Document Type: Review

References (33)

1. Berriman M. Data mining parasite genomes. Parasitology 128 Suppl. 1 (2004) S23-S31
2. Sammut S.J., et al. Pfam 10 years on: 10,000 families and still growing. Brief. Bioinform 9 (2008) 210-219
3. Kriventseva E.V., et al. Clustering and analysis of protein families. Curr. Opin. Struct. Biol. 11 (2001) 334-339
4. Harris M.A., et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32 (2004) D258-D261
5. Kanehisa M. The KEGG database. Novartis. Found. Symp. 247 (2002) 91-103 119-128, 244-252
6. Anon. (2001) PlasmoDB: an integrative database of the Plasmodium falciparum genome. Tools for accessing and analyzing finished and unfinished sequence data. The Plasmodium Genome Database Collaborative. Nucleic Acids Res. 29, 66-69.
7. Kissinger J.C., et al. The Plasmodium genome database. Nature 419 (2002) 490-492
8. Hertz-Fowler C., et al. GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res. 32 (2004) D339-D343
9. Aslett M., et al. Integration of tools and resources for display and analysis of genomic data for protozoan parasites. Int. J. Parasitol. 35 (2005) 481-493
10. Gardner M.J., et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419 (2002) 498-511
11. Lu F., et al. cDNA sequences reveal considerable gene prediction inaccuracy in the Plasmodium falciparum genome. BMC Genomics 8 (2007) 255
12. Ginsburg H. Progress in in silico functional genomics: the malaria Metabolic Pathways database. Trends Parasitol. 22 (2006) 238-240
13. Li L., et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13 (2003) 2178-2189
14. McConkey G.A. Targeting the shikimate pathway in the malaria parasite Plasmodium falciparum. Antimicrob. Agents Chemother. 43 (1999) 175-177
15. Scheibel L.W. Plasmodial metabolism and related organellar function during various stages of the life cycle: carbohydrates. In: Wernsdorfer W.H., and McGregor I. (Eds). Malaria: Principles and Practices of Malariology (1988), Churchill Livingston 199-212
16. Sherman I.W. Biochemistry of Plasmodium (malarial parasites). Microbiol. Rev. 43 (1979) 453-493
17. Pfaller M.A., et al. Plasmodium falciparum: stage-specific lactate production in synchronized cultures. Exp. Parasitol. 54 (1982) 391-396
18. Atamna H., et al. Hexose-monophosphate shunt activity in intact Plasmodium falciparum infected erythrocytes and in free parasites. Mol. Biochem. Parasitol. 67 (1994) 79-89
19. Müller S., et al. Thiol-based redox metabolism of protozoan parasites. Trends Parasitol. 19 (2003) 320-328
20. Gengenbacher M., et al. Vitamin B6 biosynthesis by the malaria parasite Plasmodium falciparum: biochemical and structural insights. J. Biol. Chem. 281 (2006) 3633-3641
21. Wang P., et al. Genetic and metabolic analysis of folate salvage in the human malaria parasite Plasmodium falciparum. Mol. Biochem. Parasitol. 135 (2004) 77-87
22. Dittrich S., et al. An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites. Mol. Microbiol. 67 (2007) 609-618
23. Green M.L., and Karp P.D. The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res. 34 (2006) 3687-3697
24. Caspi R., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 36 (2008) D623-D631
25. Green M.L., and Karp P.D. Using genome-context data to identify specific types of functional associations in pathway/genome databases. Bioinformatics 23 (2007) i205-i211
26. Karp P.D., et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33 (2005) 6083-6089
27. Green M.L., and Karp P.D. A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. BMC Bioinformatics 5 (2004) 76
28. Jomaa H., et al. Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. Science 285 (1999) 1573-1576
29. Divo A.A., et al. Nutritional requirements of Plasmodium falciparum in culture I. Exogenously supplied dialayzable components necessary for continuous growth. J. Protozool 32 (1985) 59-64
30. Zarchin S., et al. Digestion of the host erythrocyte by malaria parasites is the primary target for quinoline-containing antimalarials. Biochem. Pharmacol. 35 (1986) 2435-2442
31. Pinney J.W., et al. metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella. Nucleic Acids Res. 33 (2005) 1399-1409
32. Pinney J.W., et al. Metabolic reconstruction and analysis for parasite genomes. Trends Parasitol. 23 (2007) 548-554
33. Claudel-Renard C., et al. Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res. 31 (2003) 6633-6639