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Why
is a web site of malaria parasite biochemistry 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 in two laboratories. However, as end users of the wealth of
information that gene analysis will provide, we shall have to go back to
basic biochemistry and physiology in order to make full use of this
knowledge.
The Plasmodium genome contains genes
that are expressed during a specific stage of the parasite cycle, while
other genes may be expressed throughout the entire cycle in the vertebrate
host and the mosquito vector. Many gene-coded proteins are essentially
enzymes that participate in various metabolic pathways. Deploying those
pathways in a useful format may facilitate not only the placement of
expressed enzymes in the biochemical context, but also to portray the
various co-factors and metabolites that are involved in the activity of
each enzyme. Metabolic databases have been used to predict the pathways of
several organisms from their genomes. These concepts were at the base of
the construction of this site.
How were the Metabolic Pathways of the Malaria
Parasite constructed?
Although several sites of metabolic
processes are available to the web browser, they are generally loaded with
superfluous information, much of which may not be relevant for malaria
parasites. The purpose of this site was to extract the pertinent
information from the universal sites and to present them in an educative
and informative format.
Very few details of the biochemical
processes that function in Plasmodium spp. are
known. In some investigations the end products of some metabolic pathways
were identified through the use of a radiolabeled
precursor. While such result implicates the presence of a multi-enzyme
pathway, none of the individual enzymes that
are involved has been tested independently. In other cases, the gene coding for an enzyme has been cloned and
sequenced, and its expression in the parasite has been ascertained,
sometimes with useful biochemical information. The maps presented in this
database were constructed based on the present knowledge of parasite
biochemistry and on pathways known to occur in other unicellular
eukaryotes. Most pathways are relevant to the erythrocytic
phase of the parasite cycle. All maps were checked for the presence of enzyme-coding
genes as they are officially annotated in the Plasmodium genome (http://plasmodb.org/). Users
of the site should be aware that not all enzymes and reactions that are
illustrated in the maps have been conclusively shown to operate in
Plasmodium spp. Some genes that code for
essential enzymes have not yet been detected in the genome. All maps have been scrutinized against
annotated and predicted genes in the Plasmodium falciparum
genome. Mostly, annotated genes were accepted, but in some cases
additional bioinformatics and biochemical analysis lead to the
identification of genes. When only few genes are missing from an entire
pathway, they are indicated by the symbol x.When the genes
coding for most of the enzymes of a particular putative pathway, the
pathway is not shown.
Maps of other processes related to parasite
biology
Although
the site was originally constructed to contain metabolic pathways, it has
since been expanded to include, cell-cell interactions (cytoadherence
and rosetting), invasion of the erythrocyte by
the parasite and transport functions. It also contains an artistic
impression of the ultrastructural morphology of
the interaerythrocytic cycle stages and some
details about the morphology of mitochondria and the apicoplast.
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.uni-koeln.de/), ExPASy ENZYME (http://www.expasy.org/enzyme/) and IUBMB
reaction schemes (http://www.chem.qmul.ac.uk/iubmb/enzyme/reaction/), 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 databse (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:
Grouped pathways of major chemical
components or biological process
Specific
pathways or specific process
Chemical
structures of substrates and products or process
Names of
enzymes and their genes or components of process
Each map is linked to other maps thus
enabling to verify the origin of a substrate or the fate of a product. Clicking on the EC number that appears
next to each enzyme, connects the site to BRENDA, SWISSPROT ExPASy ENZYME, PlasmoDB and
to IUBMB reaction scheme, thus providing:
1.
Direct access to enzyme's name
2.
Details on its catalytic activity and
regulation
3.
Gene structure in various organisms
4.
Reaction mechanisms (when available)
5.
Annotated or predicted gene of Plasmodium
falciparum
6.
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 (http://www.genome.jp/kegg/kegg2.html).
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.
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 publication's
abstract (when available). Since Medline covers literature only since 1966,
earlier publications are not included in the bibliographic lists.
Search the site
The site contains a search engine that allows for
searching enzymes by their names or EC numbers, other proteins or
metabolites. Pressing on search in the main menu or in the menu appearing
at the left side of each map, opens the search facility. Choosing an item
by browsing the list and pressing the “GO” button, or typing the EC number
in the designated windows and pressing the “SEARCH” button, will invoke the
map where this item appears.
Credits
The information for the construction of
the metabolic maps has been collected by Prof. Hagai Ginsburg who
also designed the maps. The maps have been reviewed by Dr. Irwin W. Sherman ,
and all scientists who appear on the list of experts (see Contacts. Names
of other experts who have helped in the
preparation of various maps, appear at the bottom of the respective map.
Construction of the site and establishment of the links were done by Assaf Keren, Itamar Levin, Natalia Vikhalevskaya, Elina Vorontsov and Tali and Tzahi Marom.
Acknowledgments
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The Computation Authority of
The Hebrew University of Jerusalem, Israel (http://www.huji.ac.il/huji/eng/info_computers_e.htm), 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 program sponsor the maintenance of this
site. At the present, the maintenance and development of the site is
sponsored by the BioMalPar Network of
Excellence on Biology and Pathology of the Malaria Parasite supported by
a grant (LSHP-CT-2004-503578) in the 6th Framework Programme
of the EU (http://www.biomalpar.org/).
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