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Genomes and Genome Projects of Protozoan Parasites Curr. Issues Mol. Biol. (2003) 5: 61-74. Genomes of Protozoan Parasites 61 Genomes and Genome Projects of Protozoan Parasites Klaus Ersfeld other projects (Table 1) are at various stages of progress, but the reasoning and motivations for genomic research is School of Biological Sciences, 2.205 Stopford Building, virtually identical between all of them (Tarleton and University of Manchester, Oxford Road, Manchester M13 Kissinger, 2001). 9PT, UK. The Plasmodium falciparum genome Abstract More than 1 billion people are estimated to carry malaria- causing parasites at any one time. The annual mortality Protozoan parasites are causing some of the most rate is between 0.5-3 million people. A massive increase devastating diseases world-wide. It has now been in population, a deterioration in public health services and recognised that a major effort is needed to be able to infrastructures and the problems associated with now control or eliminate these diseases. Genome projects widespread drug resistance has led to a re-emergence of for the most important protozoan parasites have been malaria as one of the most serious diseases world-wide initiated in the hope that the read-out of these projects (http://www.who.int/tdr/diseases/malaria/default.htm). After will help to understand the biology of the parasites a period of optimism, mainly due to the relatively successful and identify new targets for urgently needed drugs. reduction of the malaria-transmitting mosquitoes with the Here, I will review the current status of protozoan pesticide DDT, more people die know of the disease than parasite genome projects, present findings obtained 40 years ago (Guerin et al., 2002a; Miller and Greenwood, as a result of the availability of genomic data and 2002). An important factor contributing to the failure to discuss the potential impact of genome information reduce the burden of this disease is the ever decreasing on disease control. number of drugs that are still effective in treatment. Chloroquine, once the most important anti-malaria drug, Introduction is almost useless due to the spread of resistance parasite populations in virtually all endemic areas. Likewise, The resurgence of infectious diseases world-wide has been resistances are now observed for every anti-malaria drug a major impetus in increasing research activities. The World with the exception of artemisinin derivatives (Wellems and Health Organisation (http://www.who.int/tdr/) has identified Plowe, 2001; Wellems, 2002). Projects to develop ten major, yet neglected, infectious diseases (African vaccines, a strategy probably more appropriate in areas trypanosomiasis, Chagas disease, dengue fever, lymphatic were continuous drug supplies are difficult to maintain, have filariasis, leishmaniasis, leprosy, malaria, onchocerciasis, so-far failed (Richie and Saul, 2002). Therefore, after a schistosomiasis, and tuberculosis) that are the focus of period of four decades of relative stagnation in malaria intense efforts to control or even eradicate the organisms research, it has been recognised that a massive effort at that cause these diseases. Four diseases of this list are all levels is required to control this disease. Inspired by the caused by protozoan parasites (African trypanosomiasis, successfully initiated large-scale genome projects (human Chagas disease, leishmaniasis, and malaria), causing more and yeast) and the rapid completion of the first genomes than 1.3 million deaths annually, possibly as many as 4 of pathogenic bacteria (Haemophilus influenzae and million. It is anticipated that the genome information of these Mycoplasma genitalium in 1995) the Plasmodium parasites will be a major contributing factor in the translation falciparum genome project consortium was founded in 1996 of basic research into applications pertinent to disease with the objective to sequence the entire genome of control (Hoffman, 2000). In contrast to the human genome Plasmodium falciparum, the most dangerous of the four project, data of parasite genomes are immediately released malaria-causing Plasmodium species (Dame et al., 1996; into the public domain. It is hoped that the free access and Hoffman et al., 1997). The major motivation and justification dissemination of the data will de-monopolise research and for this project was the prospect that the complete genome will lead to a strong involvement of research communities information would be the basis for a catalogue of new drug in developing countries where these diseases are most and vaccine candidates. prevalent (Varmus, 2002). Initiatives involving the genome The genome of P. falciparum is approximately 23 x research centres world-wide have been founded around 106 bp in size, comparable to the size of other protozoan 1996/97 and as a first major landmark in their combined parasites (see Table 1). It consists of 14 chromosomes, efforts the complete genome sequence of the most ranging from 0.6 - 3.5 x 106 bp (Gardner, 2001). important of these parasites, Plasmodium falciparum, has Chromosomes, with the exception of 6,7 and 8, can be recently been published (Gardner et al., 2002a). In this resolved by pulsed-field gel electrophoresis and therefore, review I illustrate the scientific framework of genome given also the technical and computational limitations at projects using three representative parasites (African the beginning of the project, a whole chromosome shotgun trypanosomes, Leishmania and Plasmodium). Several sequencing strategy was used to sequence the genome. A major technical challenge was the extremely high A/T- *For correspondence. Email [email protected]. content of the genome. On average it is 80.6% but can © 2003 Caister Academic Press 62 Ersfeld Table 1. Current genome projects of protozoan parasites. Parasite Disease Genome No. of Website size (Mb) genes Apicomplexa Plasmodium falciparum Malignant tertian malaria 23 5268 http://www.sanger.ac.uk/Projects/P_falciparum/who&what.shtml Plasmodium vivax Benign tertian malaria 35-40 http://www.tigr.org/tdb/e2k1/pva1/intro.shtml Plasmodium yoelii Rodent malaria 23 5878 http://www.tigr.org/tdb/e2k1/pya1/ Plasmodium chabaudi Rodent malaria http://www.sanger.ac.uk/Projects/P_chabaudi/ Plasmodium berghei Rodent malaria 25-27 http://www.lumc.nl/1040/research/malaria/model.html Plasmodium knowlesi Malaria of monkeys (Macaca spp.) http://www.sanger.ac.uk/Projects/P_knowlesi/ Toxoplasma gondii Aquired or congenital toxoplasmosis 80 http://www.toxodb.org/links.shtml Theileria annulata Theileriosis in domestic ruminants 10 http://www.sanger.ac.uk/Projects/T_annulata/ Theileria parva East coast fever in ruminants 9 http://www.tigr.org/tdb/e2k1/tpa1/ Eimeria tenella Coccidiosis in poultry 60 http://www.iah.bbsrc.ac.uk/eimeria/ Babesia bovis Redwater fever in cattle 9.4 http://www.sanger.ac.uk/Projects/B_bovis/ Cryptosporidium parvum Cryptosporidiosis 10 http://www.mrc-lmb.cam.ac.uk/happy/CRYPTO/cryptogenome.html Kinetoplastida Trypanosoma brucei Sleeping sickness 35 80001 http://parsun1.path.cam.ac.uk/ Trypanosoma cruzi Chagas disease 40 http://www.dbbm.fiocruz.br/genome/tcruzi/tcruzi.html Leishmania major Cutaneous leishmaniasis 34 80001 http://www.genedb.org/genedb/leish/index.jsp Others Giardia lamblia Giardiasis 12 http://jbpc.mbl.edu/Giardia-HTML/index2.html Entamoeba histolytica Intestinal amoebiasis 20 http://www.lshtm.ac.uk/itd/units/pmbbu/enta/home.htm Caenorhabditis elegans 100 19000 http://www.sanger.ac.uk/Projects/C_elegans/ Saccharomyces cerevisiae 12 6275 http://mips.gsf.de/proj/yeast/CYGD/db/index.html 1 Estimated by extrapolation from the gene number on already finished chromosomes or contigs rise to more 90% in introns and intergenic regions. In some between different species of Plasmodium (Scherf et al., regions, short 2-3 kb imperfect tandem repeats that are 2001). The divergence of genes involved in antigenic assigned as putative centromeres, the A/T content is higher variation between species makes comparative genomics/ than 97%. This unusual base composition makes both proteomics with respect to host-parasite interactions less sequencing and assembly difficult and is one of the reasons useful than was hoped for (Doolittle, 2002). Nevertheless, why sequencing the whole genome has taken a laboratory models of malaria will be of great use to comparatively long time. New software and improved functionally characterise and exploit genomic information sequencing tools had do be developed to overcome this in the future (Carlton and Carucci, 2002). major obstacle. Optical mapping techniques were used to The mosquito Anopheles gambiae is the most support the assembly of sequence data into large contigs important vector for transmission of malaria parasites (but (Lai et al., 1999). In 1998 and 1999, respectively, the by no means the only one - there are about 60 other sequences of chromosomes 3 and 2 were published and mosquito species capable of malaria transmission) in 2002 the entire genome sequence was published (Spielman and D’Antonio, 2001). The major interest in the (Gardner et al., 1998; Bowman et al., 1999; Gardner et al., Anopheles genome will focus on the specific features of 2002a; Gardner et al., 2002b; Hall et al., 2002; Hyman et the insect enabling co-existence with the parasite (De al., 2002). At the same time both the genome sequence of Gregorio and Lemaitre, 2002). Firstly, comparison with the the model rodent malaria parasite Plasmodium yoelii yoelii genome of Drosophila melongaster, also of the order and the sequence of the genome of the insect vector of P.
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