title: Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites.
abstract: BACKGROUND
  Malaria parasites have evolved a series of intricate mechanisms to survive and propagate within host red blood cells. Intra-erythrocytic parasitism requires these organisms to digest haemoglobin and detoxify iron-bound haem. These tasks are executed by haemoglobin-specific proteases and haem biocrystallization factors that are components of a large multi-subunit complex. Since haemoglobin processing machineries are functionally and genetically linked to the modes of action and resistance mechanisms of several anti-malarial drugs, an understanding of their evolutionary history is important for drug development and drug resistance prevention.
  
  
  METHODS
  Maximum likelihood trees of genetic repertoires encoding haemoglobin processing machineries within Plasmodium species, and with the representatives of Apicomplexan species with various host tropisms, were created. Genetic variants were mapped onto existing three-dimensional structures. Genome-wide single nucleotide polymorphism data were used to analyse the selective pressure and the effect of these mutations at the structural level.
  
  
  RESULTS
  Recent expansions in the falcipain and plasmepsin repertoires are unique to human malaria parasites especially in the Plasmodium falciparum and P. reichenowi lineage. Expansion of haemoglobin-specific plasmepsins occurred after the separation event of Plasmodium species, but the other members of the plasmepsin family were evolutionarily conserved with one copy for each sub-group in every Apicomplexan species. Haemoglobin-specific falcipains are separated from invasion-related falcipain, and their expansions within one specific locus arose independently in both P. falciparum and P. vivax lineages. Gene conversion between P. falciparum falcipain 2A and 2B was observed in artemisinin-resistant strains. Comparison between the numbers of non-synonymous and synonymous mutations suggests a strong selective pressure at falcipain and plasmepsin genes. The locations of amino acid changes from non-synonymous mutations mapped onto protein structures revealed clusters of amino acid residues in close proximity or near the active sites of proteases.
  
  
  CONCLUSIONS
  A high degree of polymorphism at the haemoglobin processing genes implicates an imposition of selective pressure. The identification in recent years of functional redundancy of haemoglobin-specific proteases makes them less appealing as potential drug targets, but their expansions, especially in the human malaria parasite lineages, unequivocally point toward their functional significance during the independent and repetitive adaptation events in malaria parasite evolutionary history.
authors.affiliation: Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. patrath.pons@gmail.com.
authors.forename: Patrath
authors.initials: P
authors.lastname: Ponsuwanna
authors.affiliation: Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. faith1114@gmail.com.|Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand. faith1114@gmail.com.
authors.forename: Theerarat
authors.initials: T
authors.lastname: Kochakarn
authors.affiliation: Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. duangkamon.bun@mahidol.edu.|Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand. duangkamon.bun@mahidol.edu.|Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. duangkamon.bun@mahidol.edu.
authors.forename: Duangkamon
authors.initials: D
authors.lastname: Bunditvorapoom
authors.affiliation: Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. krittikorn.kum@student.mahidol.edu.
authors.forename: Krittikorn
authors.initials: K
authors.lastname: Kümpornsin
authors.affiliation: Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK. tdo@sanger.ac.uk.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Otto
authors.affiliation: Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. chase.ridenour@gmail.com.
authors.forename: Chase
authors.initials: C
authors.lastname: Ridenour
authors.affiliation: Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. nok@tropmedres.ac.|Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. nok@tropmedres.ac.
authors.forename: Kesinee
authors.initials: K
authors.lastname: Chotivanich
authors.affiliation: Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand. prapon.wil@mahidol.ac.th.
authors.forename: Prapon
authors.initials: P
authors.lastname: Wilairat
authors.affiliation: Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. nickwdt@tropmedres.ac.|Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK. nickwdt@tropmedres.ac.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: White
authors.affiliation: Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. olivo@tropmedres.ac.|Wellcome Trust Sanger Institute, Hinxton, UK. olivo@tropmedres.ac.|Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, UK. olivo@tropmedres.ac.
authors.forename: Olivo
authors.initials: O
authors.lastname: Miotto
authors.affiliation: Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. thanat.cho@mahidol.edu.
authors.forename: Thanat
authors.initials: T
authors.lastname: Chookajorn
mesh_terms: D000818:Animals; D003546:Cysteine Endopeptidases / Q000378:metabolism; D019143:Evolution, Molecular; D055106:Genome-Wide Association Study; D006418:Heme / Q000378:metabolism; D006454:Hemoglobins / Q000378:metabolism*; D010802:Phylogeny; D010961:Plasmodium / Q000145:classification* / Q000201:enzymology*; D010963:Plasmodium falciparum / Q000201:enzymology; D016133:Polymerase Chain Reaction; D015800:Protozoan Proteins / Q000378:metabolism*
chemical_list: D006454:Hemoglobins; D015800:Protozoan Proteins; D006418:Heme; D003546:Cysteine Endopeptidases; C099607:falcipain
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