In Silico analysis of malaria parasite databanks for specific genes and motifs associated with immune evasion

Abstract

In Silica analysis of available biological data is a powerful tool for not only the identification of new genes, but also to study evolutionary relationships and regulatory mechanisms. In this study, a number of bioinformatic tools and techniques were applied on the available sequence data of the malaria parasite, Plasmodium falciparum. In Silica techniques were used for the identification of a genomic sequence tag (GST) matching the facilitated glucose transporter family as assessed by BLAST. The open reading frame encoding the fUll-length glucose transporter gene was subsequently assembled from contig sequences of chromosome 2 of the malaria parasite. The frequency of occurrence of di-, tri- and tetranucleotide sequences in both the coding and non-coding regions of chromosome 2 of P. falciparum was also exhaustively analysed. The relative abundance (observed, compared to expected values) of these oligonucleotide sequences, normalised for the nucleotide base composition, was calculated as an odds ratio and compared to those of other organisms. These relative abundancies are referred to as the organism's genomic signature. The CC•GG and CG-dinucleotides exhibited the highest and the lowest odds ratios, respectively. These genome signatures were shown to be constrained by the codon preference and amino acid abundancies. A number of genes with genomic signatures differing significantly from the average signature were also identified and were deduced to be acquired by lateral transfer from unidentified sources. A definite association between interspaced TGCA tetranucleotides and polymorphic traits of the FC27 allele of merozoite surface antigen 2 (MSA-2) was shown. The observed switching and deletion of a limited number of identical nucleotide sequences of several alleles interspersed between direct repeats, provided clues to potential mechanisms employed by the parasite to affect antigenic polymorphism. The identification of a number of motifs for intragenic (homologous) recombination led us to propose a mechanism by which the parasite achieves antigenic variation in single copy genes. These results have profound implications for the design of candidate anti-malarial vaccines, microsatellite typing and characterisation of proteins mediating these recombination events.