Scientists Identify Thousands of Proteins Associated with the Deadliest
Form of Malaria
By Jason Socrates Bardi
Two scientists at The Scripps Research Institute (TSRI) led a collaborative
effort involving 18 researchers at half a dozen laboratories in the United
States and Great Britain to determine the "proteome" of the most deadly
form of the malaria pathogen Plasmodium falciparum.
This study, in the current issue of the journal Nature, accompanies
an article detailing the completion of a major six-year $17.9-million
genome-sequencing effort involving 185 researchers from the United Kingdom,
the United States, and Australia that sequenced the entire Plasmodium
"This is the first instance that I know of where these proteomics studies
have gone along side-by-side with the genome sequencing project," says
TSRI Cell Biology Professor John Yates, who was the lead scientist involved
in the proteomics effort, which identified the proteins in the single-celled
Plasmodium that cause malaria.
These efforts will pay huge dividends in global healthcare if even a
few of the newly identified proteins lead to the development of new malaria
vaccinesand Yates and his colleagues found a total of more than
"We don't exactly know the function of well over half of the proteins
identifiedwe just know that they are there," says Laurence Florens,
who is a research associate at TSRI and the lead author of the study.
Malaria is a nasty and often fatal disease, which may lead to kidney
failure, seizures, permanent neurological damage, coma, and death. There
are four types of Plasmodium parasites that cause the disease, of which
falciparum is the most deadly.
Knowing which proteins are expressed by Plasmodium falciparum
should help scientists understand how the pathogen causes malaria and,
with luck, how to thwart it. That was the goal of the proteomics approach
taken by Florens and Yates.
Where "genomics" maps the DNA sequence and genes in an organism like
Plasmodium falciparum, "proteomics" adds the topographical information
to that map by identifying which genes are actually expressed as proteins
in the Plasmodium falciparum cells.
More importantly, Florens and Yates also sought to identify which proteins
are expressed at which stages of the organism's lifecycle. This was no
small task. Plasmodium falciparum has at least ten distinct stages
in its lifecycle, and there is no way of telling which are expressed at
each distinct stage of the pathogen's lifecycle simply by looking at the
But Florens and Yates were able to figure out which proteins were expressed
during four different stages (sporozoites, merozoites, trophozoites, and
gametocytes) and, thus, which might make good vaccine targets.
Mass Spectrometry and Malaria
The process was basically to take samples of a single isolate of Plasmodium
falciparum and grow three of the four different stages in blood in
a way that allowed samples to be purified. The fourth stage, the sporozoites,
had to be hand-dissected from mosquito salivary glands.
In purifying the samples, Yates and Florens first separated the soluble
proteins from the membrane-bound proteins, then digested them (chopped
into smaller "peptide" pieces with enzymes), and resolved them using liquid
chromatography combined with tandem mass spectrometry.
The instrument detects the pieces and uses sophisticated software that
Yates and his colleagues developed previously to search a database of
predicted genes to reconstruct most of the proteins in the sample. This
technique was particularly useful in this context because it allowed a
very large background "noise" of mosquito and human proteins to be subtracted
out. The peptides that come from the Plasmodium can be distinguished
from those that come from the mosquito or the human.
Furthermore, using the technique, Florens and Yates were able to show
not only which genes were expressed in each stage of the Plasmodium
falciparum life cycle, but which proteins were membrane-associated,
and which were inside the cellimportant pieces of information for
One unexpected finding was that a lot of the proteins that were expressed
in particular stages "co-localized" in chromosomal gene clusters possibly
under the control of common regulatory elements.
Promoters are regions of DNA in front of a gene that "turn on" that
gene like a switch and cause it to be expressed as protein. Normally,
any given gene will have its own promoter. But Florens and Yates found
many different clusters of genes that become expressed together and might
be under the control of a single promoter. Florens and Yates believe that
this is one of the ways that the pathogen is able to thrive in two different
organisms (mosquitoes and humans).
"The switching between stages is something that happens very fast,"
says Florens, "and [the pathogen] needs a mechanism to express many genes
The article, "A proteomic view of the Plasmodium falciparum life
cycle" was authored by Laurence Florens, Michael P. Washburn, J. Dale
Raine, Robert M. Anthony, Munira Grainger, J. David Haynes, J. Kathleen
Moch, Nemone Muster, John B. Sacci, David L. Tabb, Adam A. Witney, Dirk
Wolters, Yimin Wu, Malcolm J. Gardner, Anthony A. Holder, Robert E. Sinden,
John R. Yates, and Daniel J. Carucci and appears in the October 3, 2002
issue of the journal Nature.
This work was supported by the Office of Naval Research, the U.S. Army
Medical Research and Material Command, and the National Institutes of
The authors of the paper are affiliated with the following institutions:
The Scripps Research Institute; Syngenta Research & Technology; the Imperial
College of Science, Technology & Medicine; the Naval Medical Research
Center; the National Institute for Medical Research; the American Type
Culture Collection; and The Institute for Genomic Research.
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