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Reduced and specialized: The genome of the parasite E. cuniculi
By Birgit Reinert


French researchers have sequenced the genome of Encephalitozoon cuniculi, a parasite that has retained a very small and specialized set of genes during its evolution. In fact, the genome is so reduced and adapted to a parasitic lifestyle that researchers are wondering how such an organism could maintain one of the most sophisticated infection mechanisms in biology.

Infection by parasites. A scanning electron micrograph of Encephalitozoon cuniculi spores inside a human host cell.

The answer may be in the genome. The E. cuniculi sequence is a useful tool for identifying genes that are involved in energy metabolism and related to the variety of infections the parasite can cause in humans. Through comparative studies, the researchers are also expecting to identify shared genes in other major infectious organisms such as the malaria-causing Plasmodium.

The E. cuniculi genome is only 2.9 million base pairs long—less than 0.1 percent the size of the human genome—and organized into 11 chromosomes. "This genome is a mere shadow of those found in other eukaryotes (organisms with nucleated cells), " writes Patrick J. Keeling, of University of British Columbia, in Vancouver, in a News and Views article accompanying the study in Nature. Despite being one of the smallest and most primitive eukaryotic cells, "the genome is a treasure trove of information on the powerful reductive forces that shape these unusual parasites," Keeling writes.

The researchers predicted biological functions for about half of the genes they identified in E. cuniculi. Many of the genes are shorter than their counterparts in other organisms, which is reflected in the compact size of the genome. And in accordance with the parasitic nature of E. cuniculi, genes for biosynthetic pathways and a variety of cellular processes are missing in the genome.

Distribution of predicted E. cuniculi proteins among functional groups.

The parasite E. cuniculi belongs to a group of single-celled organisms called microsporidia, which have only recently been classified as a unique group. Microsporidia are found throughout the animal world, including humans, and they survive by living inside other cells. In humans, the parasites cause a variety of diseases such as diarrhea and respiratory symptoms such as bronchitis, pneumonia, or sinusitis.

The sequencing was a collaborative project between Genoscope, France's National Sequencing Center in Paris, and a team led by Christian P. Vivarès, of the Université Blaise Pascal in Aubière, France. Vivarès will present the findings at the Burroughs Wellcome Fund Symposium on the Evolution of Protist Parasites during the 14th Meeting of the International Society for Evolutionary Protistology (ISEP) in Vancouver in 2002.

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Katinka, M.D. et al. Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450-453 (November 22, 2001).
Keeling, P.J. Parasites go the full monty. Nature 414, 401-402 (November 22, 2001).

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