LeishCyc: a biochemical pathways database for Leishmania major.
BACKGROUND
Leishmania spp. are sandfly transmitted protozoan parasites that cause a spectrum of diseases in more than 12 million people worldwide. Much research is now focusing on how these parasites adapt to the distinct nutrient environments they encounter in the digestive tract of the sandfly vector and the phagolysosome compartment of mammalian macrophages. While data mining and annotation of the genomes of three Leishmania species has provided an initial inventory of predicted metabolic components and associated pathways, resources for integrating this information into metabolic networks and incorporating data from transcript, protein, and metabolite profiling studies is currently lacking. The development of a reliable, expertly curated, and widely available model of Leishmania metabolic networks is required to facilitate systems analysis, as well as discovery and prioritization of new drug targets for this important human pathogen.


METHODS
The LeishCyc database was initially built from the genome sequence of Leishmania major (v5.2), based on the annotation published by the Wellcome Trust Sanger Institute. LeishCyc was manually curated to remove errors, correct automated predictions, and add information from the literature. The ongoing curation is based on public sources, literature searches, and our own experimental and bioinformatics studies. In a number of instances we have improved on the original genome annotation, and, in some ambiguous cases, collected relevant information from the literature in order to help clarify gene or protein annotation in the future. All genes in LeishCyc are linked to the corresponding entry in GeneDB (Wellcome Trust Sanger Institute).


CONCLUSIONS
The LeishCyc database describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the evolving information about Leishmania biochemical networks and is a tool for analysis, interpretation, and visualization of Leishmania Omics data (transcriptomics, proteomics, metabolomics) in the context of metabolic pathways. LeishCyc is the first such database for the Trypanosomatidae family, which includes a number of other important human parasites. Flexible query/visualization capabilities are provided by the Pathway Tools software and its Web interface. The LeishCyc database is made freely available over the Internet http://www.leishcyc.org.
Doyle
Maria A
MA
Department of Biochemistry and Molecular Biology, University of Melbourne, VIC, Australia. doym@unimelb.edu.au
MacRae
James I
JI
De Souza
David P
DP
Saunders
Eleanor C
EC
McConville
Malcolm J
MJ
Likić
Vladimir A
VA
D000818:Animals; D016208:Databases, Factual; D018503:Genome, Protozoan; D006801:Humans; D018320:Leishmania major / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D055432:Metabolomics; D010963:Plasmodium falciparum / Q000187:drug effects / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D040901:Proteomics; D015800:Protozoan Proteins / Q000378:metabolism
D015800:Protozoan Proteins