trans

18 PARASITE GENOMICS
yield expression level data for the corresponding
genes. Typically, tens of thousands of
SAGE tags are generated and analysed to decipher
which genes they derive from, and the
number of tags per gene indicates relative
expression level.
The ORFeome sets can also be used for protein-based
genomics assays. By expressing the
ORF segments in a yeast two-hybrid vector
system, the ‘interactome’ can be defined. Yeast
two-hybrid analyses require that two proteins
interact (the bait and the prey) in order to rescue
a yeast mutant strain. The interaction
between two parasite proteins can therefore be
assayed, and high-throughput screens allow
the all-versus-all analysis of whole proteomes.
Methods are being developed that permit
immobilization of proteins in active conformations
on high-density arrays, and these will
allow more sensitive assays of protein–protein
interactions.
For parasitology, interest often focuses on
how best to kill the target organism. ORFeome
clone sets can be used to develop medium
throughput vaccine candidacy tests, and to test
drugs in vitro in model transgenic systems
(such as yeast or bacteria). High throughput
screens with nematode parasite proteins in the
model nematode C. elegans are also (theoretically)
possible. To be useful, a drug target must
be essential to the survival of the parasite. While
some parasite systems permit specific knockout
of chosen genes, and thus genetic assays for
their roles, it is hard to prove that a gene is
essential in organisms with no genetics. For
these parasites (such as most nematodes, platyhelminths)
an alternative knockout system may
be available in the phenomenon of doublestranded
RNA-mediated gene knockout (RNAi,
or RNA interference), where endogenous mRNA
is specifically degraded in response to exposure
of the organism to double-stranded RNAs corresponding
to the gene of interest. This process
has been shown to function in all the major
eukaryote lineages, and should be adaptable
for most parasites. It is already a reality in trypanosomatids,
and positive results have been
reported for nematode parasites (A. Aboobaker
and M. Blaxter, unpublished observations).
THE PARASITES AND THEIR
GENOMES
The field of parasite genomics is rapidly
changing. The speed with which genome data
can be acquired will make any simple review
of the current state of parasite genomics date
rapidly. Therefore, below I have indicated the
status of the genome projects, the sorts of data
available, and highlighted some of the striking
research findings that have already emerged.
Each parasite genome project has developed
databases to display and analyse its data.
A core centre for access to parasite genome
data has been established at the European
Bioinformatics Institute, with funding from
the WHO TDR. This www site (http://www.
ebi.ac.uk/parasites/parasite-genome.html;
see Table 1.3) provides access to genome databases
as well as other genomics related sites
for parasites. An excellent collection of review
and primary data papers on parasite genomics
was recently published as a special issue of the
International Journal for Parasitology (volume
30, issue number 4, 2000) and is especially recommended
for readers looking for more detail
on specific genomes.
Parasite genome size and organization
Parasite genomes vary widely in size (from
10 Mb to 5000 Mb) and organization (from
one chromosome to hundreds). There are,
however, several themes that derive from the
phylogenetic disparity of parasitic organisms.
Protozoans tend to have smaller genomes
MOLECULAR BIOLOGY