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Ponsuwanna P, Kochakarn T, Bunditvorapoom D, Kümpornsin K, Otto TD, Ridenour C, Chotivanich K, Wilairat P, White NJ, Miotto O, Chookajorn T. Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites. Malar J 2016; 15:51. [PMID: 26821618 PMCID: PMC4731938 DOI: 10.1186/s12936-016-1097-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/12/2016] [Indexed: 11/25/2022] Open
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. Conclusion 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. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1097-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patrath Ponsuwanna
- Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Theerarat Kochakarn
- Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
| | - Duangkamon Bunditvorapoom
- Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Bangkok, Thailand. .,Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Krittikorn Kümpornsin
- Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Thomas D Otto
- Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
| | - Chase Ridenour
- Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Kesinee Chotivanich
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Prapon Wilairat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
| | - Nicholas J White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. .,Wellcome Trust Sanger Institute, Hinxton, UK. .,Medical Research Council (MRC) Centre for Genomics and Global Health, University of Oxford, Oxford, UK.
| | - Thanat Chookajorn
- Genomic and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Ponsuwanna P, Kümpornsin K, Chookajorn T. Genome-wide prediction of the polymorphic Ser gene family in Tetrahymena thermophila based on motif analysis. PLoS One 2014; 9:e105201. [PMID: 25133747 PMCID: PMC4136848 DOI: 10.1371/journal.pone.0105201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 07/21/2014] [Indexed: 11/18/2022] Open
Abstract
Even though antigenic variation is employed among parasitic protozoa for host immune evasion, Tetrahymena thermophila, a free-living ciliate, can also change its surface protein antigens. These cysteine-rich glycosylphosphatidylinositol (GPI)-linked surface proteins are encoded by a family of polymorphic Ser genes. Despite the availability of T. thermophila genome, a comprehensive analysis of the Ser family is limited by its high degree of polymorphism. In order to overcome this problem, a new approach was adopted by searching for Ser candidates with common motif sequences, namely length-specific repetitive cysteine pattern and GPI anchor site. The candidate genes were phylogenetically compared with the previously identified Ser genes and classified into subtypes. Ser candidates were often found to be located as tandem arrays of the same subtypes on several chromosomal scaffolds. Certain Ser candidates located in the same chromosomal arrays were transcriptionally expressed at specific T. thermophila developmental stages. These Ser candidates selected by the motif analysis approach can form the foundation for a systematic identification of the entire Ser gene family, which will contribute to the understanding of their function and the basis of T. thermophila antigenic variation.
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Affiliation(s)
- Patrath Ponsuwanna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Krittikorn Kümpornsin
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanat Chookajorn
- Center of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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Chookajorn T, Ponsuwanna P, Cui L. Mutually exclusive var gene expression in the malaria parasite: multiple layers of regulation. Trends Parasitol 2008; 24:455-61. [PMID: 18771955 DOI: 10.1016/j.pt.2008.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 07/15/2008] [Accepted: 07/16/2008] [Indexed: 02/05/2023]
Abstract
As a major factor in Plasmodium falciparum malaria pathogenesis, the var gene family has been the focus of extensive research, which has contributed to our current understanding of Plasmodium antigenic variation. In recent years, sophisticated molecular tools have enabled the generation of interesting data regarding the regulation of mutually exclusive var expression. Although their results are still inconclusive, these studies have demonstrated the existence of multiple layers of control over gene activation, silencing, memory and 'counting'. This review attempts to summarize recent findings and dissect the different layers of var regulation.
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Affiliation(s)
- Thanat Chookajorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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