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Adaptive copy number evolution in malaria parasites.

Nair S, Miller B, Barends M, Jaidee A, Patel J, Mayxay M, Newton P, Nosten F, Ferdig MT, Anderson TJ - PLoS Genet. (2008)

Bottom Line: The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP.These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function.More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

View Article: PubMed Central - PubMed

Affiliation: Southwest Foundation for Biomedical Research (SFBR), San Antonio, TX, USA.

ABSTRACT
Copy number polymorphism (CNP) is ubiquitous in eukaryotic genomes, but the degree to which this reflects the action of positive selection is poorly understood. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP. We provide compelling evidence that gch1 CNP is an adaptive consequence of selection by antifolate drugs, which target enzymes downstream in this pathway. (1) We compared gch1 CNP in parasites from Thailand (strong historical antifolate selection) with those from neighboring Laos (weak antifolate selection). Two percent of chromosomes had amplified copy number in Laos, while 72% carried multiple (2-11) copies in Thailand, and differentiation exceeded that observed at 73 synonymous SNPs. (2) We found five amplicon types containing one to greater than six genes and spanning 1 to >11 kb, consistent with parallel evolution and strong selection for this gene amplification. gch1 was the only gene occurring in all amplicons suggesting that this locus is the target of selection. (3) We observed reduced microsatellite variation and increased linkage disequilibrium (LD) in a 900-kb region flanking gch1 in parasites from Thailand, consistent with rapid recent spread of chromosomes carrying multiple copies of gch1. (4) We found that parasites bearing dhfr-164L, which causes high-level resistance to antifolate drugs, carry significantly (p = 0.00003) higher copy numbers of gch1 than parasites bearing 164I, indicating functional association between genes located on different chromosomes but linked in the same biochemical pathway. These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function. More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

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The folate biosynthesis pathway of P. falciparum.The steps catalyzed by gch1, dhfr and dhps are highlighted. The positions at which antifolate drugs (Pyrimethamine (PYR) and Sulfadoxine (SDX)) target the pathway are marked. Abbreviations: pyruvoyltetrahydropterin synthase (ptps), hydroxymethyldihydropterin pyrophosphokinase (pppk), dihydrofolate synthase (dhfs). Modified from [18].
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pgen-1000243-g001: The folate biosynthesis pathway of P. falciparum.The steps catalyzed by gch1, dhfr and dhps are highlighted. The positions at which antifolate drugs (Pyrimethamine (PYR) and Sulfadoxine (SDX)) target the pathway are marked. Abbreviations: pyruvoyltetrahydropterin synthase (ptps), hydroxymethyldihydropterin pyrophosphokinase (pppk), dihydrofolate synthase (dhfs). Modified from [18].

Mentions: The first cGH study of P. falciparum in 16 laboratory isolates revealed a particularly interesting CNP containing GTP-cyclohydrolase I (gch1) [12]. This gene encodes the first and rate limiting enzyme in the folate metabolism pathway (Figure 1) [18],[19]. Two key enzymes in later stages of this pathway–dihydrofolate reductase (dhfr) (chr. 4) and dihydropteroate synthase (dhps) (chr. 8)–are targets of the antifolate drugs pyrimethamine and sulfadoxine, which are combined in the drug Fansidar (Roche). This drug replaced chloroquine as the first-line treatment against malaria in many countries, but resistance has spread rapidly where it has been deployed. Specific point mutations (N51I, C59R, S108N, I164L) in parasite dhfr alter the binding of pyrimethamine to the enzyme's active site [20]. In addition to causing resistance, mutations in dhfr reduce enzyme efficacy and carry adverse fitness effects [21],[22],[but see 23]. Similarly, mutations in dhps (S436A/F, A437G, K540E, A581G, and A613T/S) underlie resistance to sulfadoxine [20]. Kidgell et al [12] speculated that increased gene dosage might play a compensatory role in antifolate resistance by increasing flux in the pathway to compensate for reduced efficacy of dhfr and/or dhps genes bearing resistance mutations.


Adaptive copy number evolution in malaria parasites.

Nair S, Miller B, Barends M, Jaidee A, Patel J, Mayxay M, Newton P, Nosten F, Ferdig MT, Anderson TJ - PLoS Genet. (2008)

The folate biosynthesis pathway of P. falciparum.The steps catalyzed by gch1, dhfr and dhps are highlighted. The positions at which antifolate drugs (Pyrimethamine (PYR) and Sulfadoxine (SDX)) target the pathway are marked. Abbreviations: pyruvoyltetrahydropterin synthase (ptps), hydroxymethyldihydropterin pyrophosphokinase (pppk), dihydrofolate synthase (dhfs). Modified from [18].
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570623&req=5

pgen-1000243-g001: The folate biosynthesis pathway of P. falciparum.The steps catalyzed by gch1, dhfr and dhps are highlighted. The positions at which antifolate drugs (Pyrimethamine (PYR) and Sulfadoxine (SDX)) target the pathway are marked. Abbreviations: pyruvoyltetrahydropterin synthase (ptps), hydroxymethyldihydropterin pyrophosphokinase (pppk), dihydrofolate synthase (dhfs). Modified from [18].
Mentions: The first cGH study of P. falciparum in 16 laboratory isolates revealed a particularly interesting CNP containing GTP-cyclohydrolase I (gch1) [12]. This gene encodes the first and rate limiting enzyme in the folate metabolism pathway (Figure 1) [18],[19]. Two key enzymes in later stages of this pathway–dihydrofolate reductase (dhfr) (chr. 4) and dihydropteroate synthase (dhps) (chr. 8)–are targets of the antifolate drugs pyrimethamine and sulfadoxine, which are combined in the drug Fansidar (Roche). This drug replaced chloroquine as the first-line treatment against malaria in many countries, but resistance has spread rapidly where it has been deployed. Specific point mutations (N51I, C59R, S108N, I164L) in parasite dhfr alter the binding of pyrimethamine to the enzyme's active site [20]. In addition to causing resistance, mutations in dhfr reduce enzyme efficacy and carry adverse fitness effects [21],[22],[but see 23]. Similarly, mutations in dhps (S436A/F, A437G, K540E, A581G, and A613T/S) underlie resistance to sulfadoxine [20]. Kidgell et al [12] speculated that increased gene dosage might play a compensatory role in antifolate resistance by increasing flux in the pathway to compensate for reduced efficacy of dhfr and/or dhps genes bearing resistance mutations.

Bottom Line: The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP.These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function.More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

View Article: PubMed Central - PubMed

Affiliation: Southwest Foundation for Biomedical Research (SFBR), San Antonio, TX, USA.

ABSTRACT
Copy number polymorphism (CNP) is ubiquitous in eukaryotic genomes, but the degree to which this reflects the action of positive selection is poorly understood. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP. We provide compelling evidence that gch1 CNP is an adaptive consequence of selection by antifolate drugs, which target enzymes downstream in this pathway. (1) We compared gch1 CNP in parasites from Thailand (strong historical antifolate selection) with those from neighboring Laos (weak antifolate selection). Two percent of chromosomes had amplified copy number in Laos, while 72% carried multiple (2-11) copies in Thailand, and differentiation exceeded that observed at 73 synonymous SNPs. (2) We found five amplicon types containing one to greater than six genes and spanning 1 to >11 kb, consistent with parallel evolution and strong selection for this gene amplification. gch1 was the only gene occurring in all amplicons suggesting that this locus is the target of selection. (3) We observed reduced microsatellite variation and increased linkage disequilibrium (LD) in a 900-kb region flanking gch1 in parasites from Thailand, consistent with rapid recent spread of chromosomes carrying multiple copies of gch1. (4) We found that parasites bearing dhfr-164L, which causes high-level resistance to antifolate drugs, carry significantly (p = 0.00003) higher copy numbers of gch1 than parasites bearing 164I, indicating functional association between genes located on different chromosomes but linked in the same biochemical pathway. These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function. More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

Show MeSH
Related in: MedlinePlus