Journal of Natural Sciences Research www.iiste.org ISSN 2224-3186 (Paper) ISSN 2225-0921 (Online) Vol.5, No.7, 2015 145 PfEMP1 DBLα Sequence Tags in Genomic DNA of P. falciparum Field Isolates from Two Malaria Endemic Sites in Kenya Francis W. Makokha 1,2,4* Sabah A. Omar 4 Francis T. Kimani 4 Gabriel Magoma 4 Rahma Udu 4,6 Edwin Too 4 Nathan Shaviya 5 Charity Hungu 4 1.Directorate of Research and Development, Mount Kenya, P.O Box 342-01000, Thika, Kenya 2.Institute of Tropical Medicine and Infectious Diseases, Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000-00200, Nairobi Kenya 3.Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O Box 62000- 00200, Nairobi Kenya 4.Centre for Biotechnology and Research Development, Kenya Medical Research Institute, P.O Box 54840- 00200, Nairobi, Kenya 5.Masinde Muliro University of Science and Technology, Department of Biomedical Sciences, P.O 190-50100, Kakamega, Kenya 6.Department of Biochemistry, Pwani University, P.O Box 185-80108, Kilifi, Kenya Email: makokhafw@gmail.com Abstract Background Malaria caused by Plasmodium falciparum remains a major cause of childhood morbidity and mortality in sub- Saharan Africa. PfEMP1 protein, coded for by a family of about sixty variant var genes, is a parasite protein found on infected erythrocyte membrane. PfEMP1 protein mediates cytoadherence of infected erythrocytes on endothelial cells which may lead to severe symptoms of malaria. Although PCR amplification of the whole gene is difficult due to high variability, primers targeting the DBLα domain have been designed and used to study pfemp1 genes. This objective of this study was to establish the distribution of DBLα sequence tags in isolates of Plasmodium falciparum from two malaria endemic sites in Kenya. Methods DNA extracted from field isolates collected from Mbita (Western Kenya) and Tiwi (Coastal region) was used to isolate and amplify DBLα domain sequence tags of pfemp1 by PCR. PCR products were sequenced by 454 next generation sequencing. After assembly, the translated protein sequences (GenBank KP085750-KP087726) were then aligned in Mega 5.2 and classified into cys/PoLV groups based on the number of cysteine residues and the motifs at PoLV1 and PoLV2 within the sequence tag. Six sequence groups were found in sequences from both endemic sites. Group 4 sequences were the most prevalent (57.35% and 57.07% in isolates from Mbita and Tiwi respectively) in the isolates from both sites. Sequence tags from Tiwi had a higher proportion of cys2 (group 1 and 2) than sequences from Mbita although individual group 2 sequence tags were slightly higher in Mbita tags. Similarly the proportion of groups 5 and 6 sequence tags was higher in sequence tags from Tiwi than those from Mbita. Conclusion In conclusion, the frequency of the different cyc/PoLV groups of DBLα sequence tags at both endemic sites follow almost similar pattern with group four sequence tags being the majority among the sequence tags isolated from patient isolates from both study sites. However, in the absence of expression data, the impact of this genomic distribution pattern on malaria pathology remains unknown. Key Words: Malaria, PfEMP1, cys/PoLV, DBLα, var, Sequence tags Background Plasmodium falciparum expresses parasite proteins that are exported to the infected erythrocyte surface. These proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1) (1–3) are encoded by a family of genes known as var. Each haploid genome contains approximately 60 var genes, with only one gene being expressed at any given time (4). The family of the 60 var genes is classified into three subgroups based on semi- conserved upstream sequences and the direction of transcription. Group A and B var genes are associated with telomeric regions of chromosomes and are transcribed towards the telomere. The third group, group C is associated with internal var clusters (5–9). Studies have demonstrated that the var genes have both functional and clinical significance. Expressing of group A var genes is associated with severe malaria symptoms. Group A var genes also do not bind host receptors CD36 and intracellular adhesion molecule1 (ICAM1) (7). Further these genes tend to be abundantly expressed in patients whose immunity to malaria is naïve, especially young infants. Group A var genes have been predominantly associated to cerebral malaria and have been found in patient