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A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number.

Mok BW, Ribacke U, Sherwood E, Wahlgren M - Malar. J. (2008)

Bottom Line: The n-gene transcription levels were found to correlate to the number of n-gene copies.Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome.In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden. bobo.mok@ki.se

ABSTRACT

Background: Segmental duplications (SD) have been found in genomes of various organisms, often accumulated at the ends of chromosomes. It has been assumed that the sequence homology in-between the SDs allow for ectopic interactions that may contribute to the emergence of new genes or gene variants through recombinatorial events.

Methods: In silico analysis of the 3D7 Plasmodium falciparum genome, conducted to investigate the subtelomeric compartments, led to the identification of subtelomeric SDs. Sequence variation and copy number polymorphisms of the SDs were studied by DNA sequencing, real-time quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The levels of transcription and the developmental expression of copy number variant genes were investigated by qPCR.

Results: A block of six genes of >10 kilobases in size, including var, rif, pfmc-2tm and three hypothetical genes (n-, o- and q-gene), was found duplicated in the subtelomeric regions of chromosomes 1, 2, 3, 6, 7, 10 and 11 (SD1). The number of SD1 per genome was found to vary from 4 to 8 copies in between different parasites. The intragenic regions of SD1 were found to be highly conserved across ten distinct fresh and long-term cultivated P. falciparum. Sequence variation was detected in a approximately 23 amino-acid long hypervariable region of a surface-exposed loop of PFMC-2TM. A hypothetical gene within SD1, the n-gene, encoding a PEXEL/VTS-containing two-transmembrane protein was found expressed in ring stage parasites. The n-gene transcription levels were found to correlate to the number of n-gene copies. Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome. In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

Conclusion: Plasmodium falciparum carries multiple sequence conserved SDs in the otherwise highly variable subtelomeres of its chromosomes. The uniqueness of the SDs amongst plasmodium species, and the conserved nature of the genes within, is intriguing and suggests an important role of the SD to P. falciparum.

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Temporal and relative transcript abundance of the n-gene in 3D7, FCR3 and 7G8. The transcript levels of the n-gene, in relation to the endogenous control gene seryl-tRNA synthetase, were measured during 8–28 hours post invasion. Data was log2 transformed and plotted at four-hour intervals for each particular parasite.
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Figure 5: Temporal and relative transcript abundance of the n-gene in 3D7, FCR3 and 7G8. The transcript levels of the n-gene, in relation to the endogenous control gene seryl-tRNA synthetase, were measured during 8–28 hours post invasion. Data was log2 transformed and plotted at four-hour intervals for each particular parasite.

Mentions: In order to investigate the impact of gene dosage on transcription levels, n-gene transcription was investigated for three parasites with varying numbers of SD1s. 3D7AH1, FCR3 and 7G8 parasites were harvested at 4-hour intervals from eight to 28 hours post-invasion and relative mRNA levels were studied by qPCR. The maximum level of transcription of the n-gene was found in ring-stage parasites, which coincides with previous transcription data [43,44]. A clear transcriptional difference was observed when comparing 3D7AH1 and 7G8, which carry eight and five copies in the genome, respectively, but similar level of transcription was found for 3D7AH1 and FCR3, although the latter carries fewer copies of the n-gene (Figure 5).


A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number.

Mok BW, Ribacke U, Sherwood E, Wahlgren M - Malar. J. (2008)

Temporal and relative transcript abundance of the n-gene in 3D7, FCR3 and 7G8. The transcript levels of the n-gene, in relation to the endogenous control gene seryl-tRNA synthetase, were measured during 8–28 hours post invasion. Data was log2 transformed and plotted at four-hour intervals for each particular parasite.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2279139&req=5

Figure 5: Temporal and relative transcript abundance of the n-gene in 3D7, FCR3 and 7G8. The transcript levels of the n-gene, in relation to the endogenous control gene seryl-tRNA synthetase, were measured during 8–28 hours post invasion. Data was log2 transformed and plotted at four-hour intervals for each particular parasite.
Mentions: In order to investigate the impact of gene dosage on transcription levels, n-gene transcription was investigated for three parasites with varying numbers of SD1s. 3D7AH1, FCR3 and 7G8 parasites were harvested at 4-hour intervals from eight to 28 hours post-invasion and relative mRNA levels were studied by qPCR. The maximum level of transcription of the n-gene was found in ring-stage parasites, which coincides with previous transcription data [43,44]. A clear transcriptional difference was observed when comparing 3D7AH1 and 7G8, which carry eight and five copies in the genome, respectively, but similar level of transcription was found for 3D7AH1 and FCR3, although the latter carries fewer copies of the n-gene (Figure 5).

Bottom Line: The n-gene transcription levels were found to correlate to the number of n-gene copies.Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome.In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77 Stockholm, Sweden. bobo.mok@ki.se

ABSTRACT

Background: Segmental duplications (SD) have been found in genomes of various organisms, often accumulated at the ends of chromosomes. It has been assumed that the sequence homology in-between the SDs allow for ectopic interactions that may contribute to the emergence of new genes or gene variants through recombinatorial events.

Methods: In silico analysis of the 3D7 Plasmodium falciparum genome, conducted to investigate the subtelomeric compartments, led to the identification of subtelomeric SDs. Sequence variation and copy number polymorphisms of the SDs were studied by DNA sequencing, real-time quantitative PCR (qPCR) and fluorescent in situ hybridization (FISH). The levels of transcription and the developmental expression of copy number variant genes were investigated by qPCR.

Results: A block of six genes of >10 kilobases in size, including var, rif, pfmc-2tm and three hypothetical genes (n-, o- and q-gene), was found duplicated in the subtelomeric regions of chromosomes 1, 2, 3, 6, 7, 10 and 11 (SD1). The number of SD1 per genome was found to vary from 4 to 8 copies in between different parasites. The intragenic regions of SD1 were found to be highly conserved across ten distinct fresh and long-term cultivated P. falciparum. Sequence variation was detected in a approximately 23 amino-acid long hypervariable region of a surface-exposed loop of PFMC-2TM. A hypothetical gene within SD1, the n-gene, encoding a PEXEL/VTS-containing two-transmembrane protein was found expressed in ring stage parasites. The n-gene transcription levels were found to correlate to the number of n-gene copies. Fragments of SD1 harbouring two or three of the SD1-genes (o-gene, pfmc-2tm, q-gene) were also found in the 3D7 genome. In addition a related second SD, SD2, of approximately 55% sequence identity to SD1 was found duplicated in a fresh clinical isolate but was only present in a single copy in 3D7 and in other P. falciparum lines or clones.

Conclusion: Plasmodium falciparum carries multiple sequence conserved SDs in the otherwise highly variable subtelomeres of its chromosomes. The uniqueness of the SDs amongst plasmodium species, and the conserved nature of the genes within, is intriguing and suggests an important role of the SD to P. falciparum.

Show MeSH
Related in: MedlinePlus