C Kumar, C Anuradha, K Venkateswara Swamy
computational biology, gene ontology, genome analysis, malaria, plasmodium falciparum, vector nt
C Kumar, C Anuradha, K Venkateswara Swamy. Genomic Characterization of Chromosome 1 of Plasmodium falciparum by Computational Methods. The Internet Journal of Microbiology. 2004 Volume 1 Number 2.
Malaria inflicts serious health and economic burdens on many countries throughout the world. The continued emergence of drug-resistant parasites, particularly in
In spite of early progress, malaria is still one of the most serious health problems facing humanity. It affects 300-500 million people causing over 2.5 million deaths annually, mostly in children (WHO Report, 1997). Malaria also poses a particular danger to pregnant woman and may lead to miscarriage or low birth weight of the child. In endemic regions, the disease is recognized as serous impediment to economic and social development (Bowman,
The complete genome sequence of
Since the sequencing of the first two chromosomes of the malaria parasite,
Materials and Methods
Here we present the methodology used for analysis and characterization of chromosome 1 of
Nucleotide sequence of chromosome 1
The complete nucleotide sequence of
Characterization of chromosome 1
DNA sequence of all sub regions were analyzed for the presence of open reading frame (ORF) by submitting the nucleic sequence details to ORF finder online tool available with National Center for Biotechnology Information (http://www.ncbi.nim.nih.gov/orf). The characterization was also made with Vector NTI suite-V.9 (http://www.informaxinc.com/solutions.vectornti) to translate the DNA sequence to protein sequence. Vector NTI is an integrated sequence analysis and data management software package, which allows molecular biologists to analyze, manipulate, construct, store and manage complex biological molecules. Annotation of genes were studied by manual curation of the output of the software which finds genes in microbial DNA, especially the genomes of bacteria and archaea (Salzberg,
Characterization of protein translated from chromosome 1
Pfam and Prosite tools available at http://www.expasy.org were used for characterizing protein sequences. Pfam (Bateman,
Results and Discussion
Characterization of nucleotide sequences (AL031744, AL031745, AL031746 and AL031747) of chromosome1 of
In case of AL031747 nucleotide sequence, the number of predicted genes was 14, the number of restriction sites was approximately 44 and the length of the entire sequence was 66442 base pairs. Based on the restriction site analysis of AL031747 nucleotide sequence has revealed the occurrence of maximum HindIII restriction sites, which can be used in cloning technology (Fig. 2). Sequence analysis using Pfam has also revealed that this particular sequence codes for protein which belongs to the erythrocyte membrane protein PfEMP1 which has been identified as the rosetting ligand of the malaria parasite
In case of AL031745 nucleotide sequence, the number of predicted genes was 136, the number of restriction sites was approximately 54 and the length of the entire sequence was 384550 base pairs. Based on the restriction site analysis of AL031745 nucleotide sequence, it is possible to infer that this sequence has maximum of Bam HI restriction sites (Fig. 3). The Pfam result of predicted ORF from AL_031745 has revealed the presence of bromodomains that are 110 amino acid long domains which are found in many chromatin associated proteins. Bromodomains are found in a variety of mammalian, invertebrate and yeast DNA-binding proteins. In some proteins, the classical bromodomain has diverged to such an extent that parts of the region are either missing or contain an insertion (e.g., mammalian protein HRX,
Another case of AL031746 nucleotide sequence, the number of predicted genes was 17, the number of restriction sites was approximately 40 and the length of the entire sequence was 67975 base pairs. Based on the restriction site analysis of AL031746 nucleotide sequence, it is possible to infer that it has revealed the presence of maximum no of EcoR I restriction sites (Fig.4). Pfam results of the best predicted ORF from AL_031746 has revealed the presence of the ABC transporter transmembrane region of this family represents a unit of six transmembrane helices, which is predicted to function in ATP-binding.
Another case of AL031744 nucleotide sequence, the number of predicted genes was 33, the number of restriction sites was approximately 62and the length of the entire sequence was 124330 base pairs. The restriction site analysis of AL031744 nucleotide sequence has also revealed the presence of maximum of Hind III restriction sites (Fig.5). Best predicted ORF from AL_031744 has revealed that
The presence of the C2 domain, which is a Ca2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking, has revealed that
The presence of Duffy binding domain has revealed that this parasite invade human erythrocytes that express Duffy blood group surface determinants. Duffy is expressed on RBCs (in Duffy-positive individuals), endothelial cells of post capillary venules and Purkinje cells of the cerebellum. On RBCs, the Duffy antigen acts as a receptor for invasion by the malarial parasite; Duffy-negative individuals, whose RBCs do not express the receptor are resistant to such infection. The normal physiological function of Duffy remains unclear (Choe
As the effects of traditional chemotherapy agents decrease as a result of growing parasitic resistance, the global threat of malaria remains a cause for concern.
CSK thanks to DST, New Delhi (DST-FIST program) and UGC-New Delhi for financial support to establish computer networking Lab.