Adaptive Copy Number Evolution in Malaria Parasites

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.

[1]  J. E. Hyde,et al.  An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites , 2007, Molecular Microbiology.

[2]  D. Hartl,et al.  A portrait of copy-number polymorphism in Drosophila melanogaster , 2007, Proceedings of the National Academy of Sciences.

[3]  P. Kassner,et al.  Significant gene content variation characterizes the genomes of inbred mouse strains. , 2007, Genome research.

[4]  Ira M. Hall,et al.  Recurrent DNA copy number variation in the laboratory mouse , 2007, Nature Genetics.

[5]  Pardis C Sabeti,et al.  Genome-wide detection and characterization of positive selection in human populations , 2007, Nature.

[6]  Fernando A. Villanea,et al.  Diet and the evolution of human amylase gene copy number variation , 2007, Nature Genetics.

[7]  P. Nilsson,et al.  Genome wide gene amplifications and deletions in Plasmodium falciparum. , 2007, Molecular and biochemical parasitology.

[8]  X. Su,et al.  Genetic linkage and association analyses for trait mapping in Plasmodium falciparum , 2007, Nature Reviews Genetics.

[9]  Conner I. Sandefur,et al.  Pyrimethamine-resistant dihydrofolate reductase enzymes of Plasmodium falciparum are not enzymatically compromised in vitro. , 2007, Molecular and biochemical parasitology.

[10]  E. Eichler,et al.  Mutational and selective effects on copy-number variants in the human genome , 2007, Nature Genetics.

[11]  E. Neidle,et al.  Double trouble: medical implications of genetic duplication and amplification in bacteria. , 2007, Future microbiology.

[12]  P. Newton,et al.  Diagnosis and management of malaria by rural community health providers in the Lao People's Democratic Republic (Laos) , 2007, Tropical medicine & international health : TM & IH.

[13]  E. Eichler,et al.  Population Stratification of a Common APOBEC Gene Deletion Polymorphism , 2007, PLoS genetics.

[14]  R. Redon,et al.  Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes , 2007, Science.

[15]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[16]  J. Roth,et al.  Multiple pathways of selected gene amplification during adaptive mutation , 2006, Proceedings of the National Academy of Sciences.

[17]  F. Nosten,et al.  Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites. , 2006, Molecular biology and evolution.

[18]  D. Fidock,et al.  Decreasing pfmdr1 copy number in plasmodium falciparum malaria heightens susceptibility to mefloquine, lumefantrine, halofantrine, quinine, and artemisinin. , 2006, The Journal of infectious diseases.

[19]  R. Redon,et al.  Copy number variation: new insights in genome diversity. , 2006, Genome research.

[20]  Junjun Zhang,et al.  Hotspots for copy number variation in chimpanzees and humans. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[21]  O. Berg,et al.  Reducing the fitness cost of antibiotic resistance by amplification of initiator tRNA genes. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Caleb Webber,et al.  Bias of Selection on Human Copy-Number Variants , 2006, PLoS genetics.

[23]  Mayfong Mayxay,et al.  Geographical distribution of selected and putatively neutral SNPs in Southeast Asian malaria parasites. , 2005, Molecular biology and evolution.

[24]  P. Newton,et al.  Selection strength and hitchhiking around two anti-malarial resistance genes , 2005, Proceedings of the Royal Society B: Biological Sciences.

[25]  B. Rovin,et al.  The Influence of CCL3L1 Gene-Containing Segmental Duplications on HIV-1/AIDS Susceptibility , 2005, Science.

[26]  B. Sharp,et al.  Intercontinental Spread of Pyrimethamine-Resistant Malaria , 2004, Science.

[27]  R. Price,et al.  Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number , 2004, The Lancet.

[28]  D. Balding,et al.  Identifying adaptive genetic divergence among populations from genome scans , 2004, Molecular ecology.

[29]  Jakob C. Mueller,et al.  Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity , 2004, Bioinform..

[30]  X. Su,et al.  Genetic and biochemical aspects of drug resistance in malaria parasites. , 2004, Current drug targets. Infectious disorders.

[31]  D. Roos,et al.  Fitness effects of DHFR‐TS mutations associated with pyrimethamine resistance in apicomplexan parasites , 2003, Molecular microbiology.

[32]  M. Ouellette,et al.  Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays. , 2003, Nucleic acids research.

[33]  P. Newton,et al.  A selective sweep driven by pyrimethamine treatment in southeast asian malaria parasites. , 2003, Molecular biology and evolution.

[34]  Jane Fridlyand,et al.  Shaping of tumor and drug-resistant genomes by instability and selection , 2003, Oncogene.

[35]  M. Shriver,et al.  Interrogating a high-density SNP map for signatures of natural selection. , 2002, Genome research.

[36]  Pardis C Sabeti,et al.  Detecting recent positive selection in the human genome from haplotype structure , 2002, Nature.

[37]  F. Nosten,et al.  Rapid genotyping of loci involved in antifolate drug resistance in Plasmodium falciparum by primer extension. , 2002, International journal for parasitology.

[38]  J. Kublin,et al.  Plasmodium falciparum crossresistance between trimethoprim and pyrimethamine , 2001, The Lancet.

[39]  T. Yoneyama,et al.  GTP cyclohydrolase I feedback regulatory protein-dependent and -independent inhibitors of GTP cyclohydrolase I. , 2001, Archives of biochemistry and biophysics.

[40]  J. T. Williams,et al.  Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. , 2000, Molecular biology and evolution.

[41]  Markus Schuelke,et al.  An economic method for the fluorescent labeling of PCR fragments , 2000, Nature Biotechnology.

[42]  X. Su,et al.  Twelve microsatellite markers for characterization of Plasmodium falciparum from finger-prick blood samples , 1999, Parasitology.

[43]  D. Conway,et al.  High recombination rate in natural populations of Plasmodium falciparum. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[44]  O. Doumbo,et al.  Mutations in Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase and epidemiologic patterns of pyrimethamine-sulfadoxine use and resistance. , 1997, The Journal of infectious diseases.

[45]  W. Sirawaraporn,et al.  Antifolate-resistant mutants of Plasmodium falciparum dihydrofolate reductase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[46]  W. G. Hill,et al.  Estimation of numbers of malaria clones in blood samples , 1995, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[47]  N. White,et al.  Antimalarial drug resistance: the pace quickens. , 1992, The Journal of antimicrobial chemotherapy.

[48]  T. Harinasuta,et al.  The current status of drug resistance in malaria. , 1987, International journal for parasitology.

[49]  M. Nei.  Molecular Evolutionary Genetics , 1987 .

[50]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[51]  G. McVean,et al.  Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome , 2007, Nature Genetics.

[52]  Pardis C Sabeti,et al.  A genome-wide map of diversity in Plasmodium falciparum , 2007, Nature Genetics.

[53]  Yingyao Zhou,et al.  A Systematic Map of Genetic Variation in Plasmodium falciparum , 2006 .

[54]  P. Newton,et al.  A selective sweep driven by pyrimethamine treatment in SE Asian malaria , 2003 .

[55]  J. Goudet.  FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Updated from Goudet (1995) , 2001 .

[56]  O. Doumbo,et al.  P. falciparum dihydrofolate reductase and dihydropteroate synthase mutations: epidemiology and role in clinical resistance to antifolates. , 1998, Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy.

[57]  Xavier Estivill,et al.  Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies , 2022 .