Why a web site of malaria parasite functional genomics is needed?

The genome project of Plasmodium falciparum has been completed and other plasmodia species are on the line. The stage-dependent transcription has also been completed. The challenge of organizing the annotated gene products into functional meaning is the purpose of the website.

The Plasmodium genome contains genes that are expressed during specific stages of the parasite cycle, while other genes may be expressed throughout the entire cycle in the vertebrate host and the mosquito vector. Many gene-encoded proteins are essentially enzymes that participate in various biological functions. Deploying those processes in a useful format may facilitate not only the placement of expressed proteins in the functional context, but also to portray the various co-factors and metabolites that are involved in the activity of each enzyme. The essential advantage of this website is that it is manually curated and continuously updated as new data emerge in the literature.

How do I find my way in the site?

The metabolic pathways of Plasmodium were extracted from the Kyoto University Encyclopedia of Genes and Genomes site (KEGG) that provides the common consent views of biochemistry that are not specific to particular organisms. Each enzyme is linked to the biochemical databases BRENDA (http://www.brenda-enzymes.org), ExPASy ENZYME (http://www.expasy.org/enzyme/), IUBMB reaction schemes http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/ and to KEGG compounds (http://www.genome.jp/dbget-bin/www_bfind?compound), to provide supplementary information. The entries are also linked to PlasmoDB (http://plasmodb.org/) and to P. falciparum in GeneDB (http://www.genedb.org/) allowing direct access to annotated or predicted gene, and to the DeRisi/UCSF transcriptome database (http://malaria.ucsf.edu/). In cases where specific inhibitors were demonstrated to be active against the parasite, they are depicted next to the process that they affect. The site is constructed in a hierarchical pattern that permits logical deepening:

  • Five grouped major functional categories (e.g. biochemistry, physiology)
  • Sub-categories (e.g. Cell-Cell Interactions, Transporters of intracellular membranes)
  • Specific pathways or specific processes
  • Chemical structures of substrates and products or process
  • Names of enzymes or proteins linked to genomic DBs

Each map is linked to other maps thus enabling to verify the origin of a substrate or the fate of a product. In maps of metabolic pathways, clicking on the EC number that appears next to each enzyme connects the site to BRENDA, SWISSPROT ExPASy ENZYME, GeneDB, PlasmoDB and to IUBMB reaction scheme, thus providing:

  1. Direct access to enzyme's name
  2. Details on its catalytic activity and regulation
  3. Reaction mechanisms (when available)
  4. Annotated or predicted gene of Plasmodium falciparum
  5. Stage-dependent transcription

While in these sites, a wealth of additional information can be obtained, such as chemical information, including an interactive view of the structure. Several other sites can be then directly accessed, such as PROSITE that supplies biochemical information on the enzymatic reaction and sequence of the catalytic domain; BRENDA that provides a wealth of information about the enzymatic activity, pH and temperature dependence, kinetic parameters (Km, turnover number), cofactors, effect of metal ions and a list of inhibitors. Each of these details is annotated with the relevant literature. While inside PlasmoDB or GeneDB, all the tools available in this database are available for deeper scrutiny.

Clicking of the name of a metabolite, connects the site to KEGG thus providing its chemical structure and formula as well as every mchemical reaction in which the compound may be participating through different enzymes (http://www.genome.jp/dbget-bin/www_bfind?enzyme).

Next to each enzyme there is a pie that depicts the stage-dependent transcription of the enzyme's coding gene. The pie is constructed as a clock of the 48 hours of the parasite cycle, where red signifies over-transcription and green, under-transcription. Clicking on the pie links to the DeRisi/UCSF transcriptome database (http://malaria.ucsf.edu/comparison/index.php).

Sub-Cellular location of gene products

A loop icon next to a map component indicates that information is available on its sub-cellular location. Pressing on the component name or the EC number opens a menu from which the pictures can be accessed. All existing pictures were collected from the literature and are present with a legend and a link to the original article.

Connection to PubMed

Each map is connected to PubMed with a search string that uses all items that appear on the map. The result is a typical PubMed output that allows for direct retrieval of the publications abstract (when available).

Search the site

The site contains a search engine that allows for searching enzymes by their names (including all synonyms) or EC numbers, other proteins and metabolites by their names or IDs. Pressing on search in the main menu opens the search facility. Choosing an item by browsing the list and pressing the “SEARCH” button, or typing the EC number in the designated windows and pressing the “SEARCH” button, will invoke the map(s) where this item appears. Combined searches can be done through Map Analysis. Thus, you can ask "which are the enzymes of the glycolysis pathway that are also phosphorylated".

Credits

The information for the construction of the metabolic maps has been collected by Prof. Hagai Ginsburg who also designed the maps and keeps them updated. Construction of the website portal with all links and search tools and the construction of the underlying DB were done by Alex Artyomov and Ofir Bar Lev.

Acknowledgments

The Computation Authority of The Hebrew University of Jerusalem, Israel provides the space for this site on its server. The construction of this site received financial support form the UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (TDR) and the National Institute of Allergy and Infectious Diseases (NIAID) through its MR4, the BioMalPar Network of Excellence on Biology and Pathology of the Malaria Parasite and by European Virtual Institute of Malaria Research/European Network of Excellence.