Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats

Niklaus Fankhauser¹ , Tien-Minh Nguyen-Ha¹ , Joël Adler² and Pascal Mäser¹

¹University of Bern, Institute of Cell Biology, Baltzerstrasse 4, CH-3012 Bern, Switzerland

²Pädagogische Hochschule Bern, Gertrud Woker Strasse 5, CH-3012 Bern, Switzerland

author email corresponding author email

Proteome Science 2007, 5:20doi:10.1186/1477-5956-5-20


Published:	20 December 2007

Abstract

Background

Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms.

Results

We have developed Reptile http://reptile.unibe.ch webcite, a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites.

Conclusion

Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at http://genomics.unibe.ch/dora webcite.