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Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions.

Lavstsen T, Salanti A, Jensen AT, Arnot DE, Theander TG - Malar. J. (2003)

Bottom Line: Two sequences belonging to the var1 and var2 subfamilies formed independent groups.A rif subgroup transcribed towards the centromere was found neighbouring var genes of group A such that the rif and var 5' regions merged.This organization appeared to be unique for the group A var genes The grouping of var genes implies that var gene recombination preferentially occurs within var gene groups and it is speculated that the groups reflect a functional diversification evolved to cope with the varying conditions of transmission and host immune response met by the parasite.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Medical Parasitology at Institute for Medical Microbiology and Immunology, University of Copenhagen, Denmark. thomaslavstsen@vip.cybercity.dk

ABSTRACT

Background: The variant surface antigen family Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. The sequence diversity and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence.

Methods: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains.

Results: var genes can be sub-grouped into three major groups (group A, B and C) and two intermediate groups B/A and B/C representing transitions between the three major groups. The best defined var group, group A, comprises telomeric genes transcribed towards the telomere encoding PfEMP1s with complex domain structures different from the 4-domain type dominant of groups B and C. Two sequences belonging to the var1 and var2 subfamilies formed independent groups. A rif subgroup transcribed towards the centromere was found neighbouring var genes of group A such that the rif and var 5' regions merged. This organization appeared to be unique for the group A var genes

Conclusion: The grouping of var genes implies that var gene recombination preferentially occurs within var gene groups and it is speculated that the groups reflect a functional diversification evolved to cope with the varying conditions of transmission and host immune response met by the parasite.

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Distance tree of 3D7 var gene 500 bp 3' region generated using the p-distance/NJ method. The four dense clusters A through D were supported by both bootstrapping and maximum parsimony (MP) tree (not shown). The relationship of the remaining sequences could not be verified by the MP tree making method. Numbers at the nodes represent bootstrap proportions (BP) on 1000 replicates. The scale bar represents the proportion of different nucleotide compared. PlasmoDB accession numbers are shown. Genes with assigned cluster are collected in figure 7.
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Figure 2: Distance tree of 3D7 var gene 500 bp 3' region generated using the p-distance/NJ method. The four dense clusters A through D were supported by both bootstrapping and maximum parsimony (MP) tree (not shown). The relationship of the remaining sequences could not be verified by the MP tree making method. Numbers at the nodes represent bootstrap proportions (BP) on 1000 replicates. The scale bar represents the proportion of different nucleotide compared. PlasmoDB accession numbers are shown. Genes with assigned cluster are collected in figure 7.

Mentions: Alignments and tree-building (figure 2) of the 500 bp var 3' regions divided most sequences into four clusters (A-D). 13 sequences fell outside these clusters, and the relationship between these sequences could not be confirmed by bootstrapping or comparison the two tree-building methods used.


Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions.

Lavstsen T, Salanti A, Jensen AT, Arnot DE, Theander TG - Malar. J. (2003)

Distance tree of 3D7 var gene 500 bp 3' region generated using the p-distance/NJ method. The four dense clusters A through D were supported by both bootstrapping and maximum parsimony (MP) tree (not shown). The relationship of the remaining sequences could not be verified by the MP tree making method. Numbers at the nodes represent bootstrap proportions (BP) on 1000 replicates. The scale bar represents the proportion of different nucleotide compared. PlasmoDB accession numbers are shown. Genes with assigned cluster are collected in figure 7.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC222925&req=5

Figure 2: Distance tree of 3D7 var gene 500 bp 3' region generated using the p-distance/NJ method. The four dense clusters A through D were supported by both bootstrapping and maximum parsimony (MP) tree (not shown). The relationship of the remaining sequences could not be verified by the MP tree making method. Numbers at the nodes represent bootstrap proportions (BP) on 1000 replicates. The scale bar represents the proportion of different nucleotide compared. PlasmoDB accession numbers are shown. Genes with assigned cluster are collected in figure 7.
Mentions: Alignments and tree-building (figure 2) of the 500 bp var 3' regions divided most sequences into four clusters (A-D). 13 sequences fell outside these clusters, and the relationship between these sequences could not be confirmed by bootstrapping or comparison the two tree-building methods used.

Bottom Line: Two sequences belonging to the var1 and var2 subfamilies formed independent groups.A rif subgroup transcribed towards the centromere was found neighbouring var genes of group A such that the rif and var 5' regions merged.This organization appeared to be unique for the group A var genes The grouping of var genes implies that var gene recombination preferentially occurs within var gene groups and it is speculated that the groups reflect a functional diversification evolved to cope with the varying conditions of transmission and host immune response met by the parasite.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Medical Parasitology at Institute for Medical Microbiology and Immunology, University of Copenhagen, Denmark. thomaslavstsen@vip.cybercity.dk

ABSTRACT

Background: The variant surface antigen family Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. The sequence diversity and organization of the 3D7 PfEMP1 repertoire was investigated on the basis of the complete genome sequence.

Methods: Using two tree-building methods we analysed the coding and non-coding sequences of 3D7 var and rif genes as well as var genes of other parasite strains.

Results: var genes can be sub-grouped into three major groups (group A, B and C) and two intermediate groups B/A and B/C representing transitions between the three major groups. The best defined var group, group A, comprises telomeric genes transcribed towards the telomere encoding PfEMP1s with complex domain structures different from the 4-domain type dominant of groups B and C. Two sequences belonging to the var1 and var2 subfamilies formed independent groups. A rif subgroup transcribed towards the centromere was found neighbouring var genes of group A such that the rif and var 5' regions merged. This organization appeared to be unique for the group A var genes

Conclusion: The grouping of var genes implies that var gene recombination preferentially occurs within var gene groups and it is speculated that the groups reflect a functional diversification evolved to cope with the varying conditions of transmission and host immune response met by the parasite.

Show MeSH
Related in: MedlinePlus