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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
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Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
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Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
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Liu S, Ebel ER, Luniewski A, Zulawinska J, Simpson ML, Kim J, Ene N, Braukmann TWA, Congdon M, Santos W, Yeh E, Guler JL. Direct long read visualization reveals metabolic interplay between two antimalarial drug targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528367. [PMID: 36824743 PMCID: PMC9948948 DOI: 10.1101/2023.02.13.528367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Increases in the copy number of large genomic regions, termed genome amplification, are an important adaptive strategy for malaria parasites. Numerous amplifications across the Plasmodium falciparum genome contribute directly to drug resistance or impact the fitness of this protozoan parasite. During the characterization of parasite lines with amplifications of the dihydroorotate dehydrogenase (DHODH) gene, we detected increased copies of an additional genomic region that encompassed 3 genes (~5 kb) including GTP cyclohydrolase I (GCH1 amplicon). While this gene is reported to increase the fitness of antifolate resistant parasites, GCH1 amplicons had not previously been implicated in any other antimalarial resistance context. Here, we further explored the association between GCH1 and DHODH copy number. Using long read sequencing and single read visualization, we directly observed a higher number of tandem GCH1 amplicons in parasites with increased DHODH copies (up to 9 amplicons) compared to parental parasites (3 amplicons). While all GCH1 amplicons shared a consistent structure, expansions arose in 2-unit steps (from 3 to 5 to 7, etc copies). Adaptive evolution of DHODH and GCH1 loci was further bolstered when we evaluated prior selection experiments; DHODH amplification was only successful in parasite lines with pre-existing GCH1 amplicons. These observations, combined with the direct connection between metabolic pathways that contain these enzymes, lead us to propose that the GCH1 locus is beneficial for the fitness of parasites exposed to DHODH inhibitors. This finding highlights the importance of studying variation within individual parasite genomes as well as biochemical connections of drug targets as novel antimalarials move towards clinical approval.
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Affiliation(s)
- Shiwei Liu
- University of Virginia, Department of Biology, Charlottesville, VA, USA
- Current affiliation: Indiana University School of Medicine, Indianapolis, IN, USA
| | - Emily R. Ebel
- Stanford, Departments of Pediatrics and Microbiology & Immunology, Stanford, CA, USA
| | | | - Julia Zulawinska
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Jane Kim
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | - Nnenna Ene
- University of Virginia, Department of Biology, Charlottesville, VA, USA
| | | | - Molly Congdon
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Webster Santos
- Virginia Tech, Department of Chemistry, Blacksburg, VA, USA
| | - Ellen Yeh
- Stanford University, Departments of Pathology and Microbiology & Immunology, Stanford, CA, USA
| | - Jennifer L. Guler
- University of Virginia, Department of Biology, Charlottesville, VA, USA
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Srisutham S, Madmanee W, Kouhathong J, Sutawong K, Tripura R, Peto TJ, van der Pluijm RW, Callery JJ, Dysoley L, Mayxay M, Newton PN, Pongvongsa T, Hongvanthong B, Day NPJ, White NJ, Dondorp AM, Imwong M. Ten-year persistence and evolution of Plasmodium falciparum antifolate and anti-sulfonamide resistance markers pfdhfr and pfdhps in three Asian countries. PLoS One 2022; 17:e0278928. [PMID: 36525403 PMCID: PMC9757559 DOI: 10.1371/journal.pone.0278928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The amplification of GTP cyclohydrolase 1 (pfgch1) in Plasmodium falciparum has been linked to the upregulation of the pfdhfr and pfdhps genes associated with resistance to the antimalarial drug sulfadoxine-pyrimethamine. During the 1990s and 2000s, sulfadoxine-pyrimethamine was withdrawn from use as first-line treatment in southeast Asia due to clinical drug resistance. This study assessed the temporal and geographic changes in the prevalence of pfdhfr and pfdhps gene mutations and pfgch1 amplification a decade after sulfadoxine-pyrimethamine had no longer been widely used. METHODS A total of 536 P. falciparum isolates collected from clinical trials in Thailand, Cambodia, and Lao PDR between 2008 and 2018 were assayed. Single nucleotide polymorphisms of the pfdhfr and pfdhps genes were analyzed using nested PCR and Sanger sequencing. Gene copy number variations of pfgch1 were investigated using real-time polymerase chain reaction assay. RESULTS Sequences of the pfdhfr and pfdhps genes were obtained from 96% (517/536) and 91% (486/536) of the samples, respectively. There were 59 distinct haplotypes, including single to octuple mutations. The two major haplotypes observed included IRNI-AGEAA (25%) and IRNL-SGKGA (19%). The sextuple mutation IRNL-SGKGA increased markedly over time in several study sites, including Pailin, Preah Vihear, Ratanakiri, and Ubon Ratchathani, whereas IRNI-AGEAA decreased over time in Preah Vihear, Champasak, and Ubon Ratchathani. Octuple mutations were first observed in west Cambodia in 2011 and subsequently in northeast Cambodia, as well as in southern Laos by 2018. Amplification of the pfgch1 gene increased over time across the region, particularly in northeast Thailand close to the border with Laos and Cambodia. CONCLUSION Despite the fact that SP therapy was discontinued in Thailand, Cambodia, and Laos decades ago, parasites retained the pfdhfr and pfdhps mutations. Numerous haplotypes were found to be prevalent among the parasites. Frequent monitoring of pfdhfr and pfdhps in these areas is required due to the relatively rapid evolution of mutation patterns.
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Affiliation(s)
- Suttipat Srisutham
- Faculty of Allied Health Sciences, Department of Clinical Microscopy, Chulalongkorn University, Bangkok, Thailand
| | - Wanassanan Madmanee
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Jindarat Kouhathong
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Kreepol Sutawong
- Buntharik Hospital, Amphoe Buntharik, Ubon Ratchathani, Thailand
| | - Rupam Tripura
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Thomas J. Peto
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Rob W. van der Pluijm
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - James J. Callery
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Lek Dysoley
- Center for Parasitology Entomology and Malaria Control (CNM), Phnom Penh, Cambodia
| | - Mayfong Mayxay
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom,Institute of Research and Education Development, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Paul N. Newton
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Tiengkham Pongvongsa
- Savannakhet Provincial Health Department, Phonsavangnuea Village, Kaysone-Phomvihan District, Savannakhet, Laos
| | - Bouasy Hongvanthong
- Center of Malariology, Parasitology and Entomology, Ministry of Health, Vientiane, Laos
| | - Nicholas P. J. Day
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Nicholas J. White
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Arjen M. Dondorp
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand,Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand,* E-mail:
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Zhao W, Li X, Yang Q, Zhou L, Duan M, Pan M, Qin Y, Li X, Wang X, Zeng W, Zhao H, Sun K, Zhu W, Afrane Y, Amoah LE, Abuaku B, Duah-Quashie NO, Huang Y, Cui L, Yang Z. In vitro susceptibility profile of Plasmodium falciparum clinical isolates from Ghana to antimalarial drugs and polymorphisms in resistance markers. Front Cell Infect Microbiol 2022; 12:1015957. [PMID: 36310880 PMCID: PMC9614232 DOI: 10.3389/fcimb.2022.1015957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Drug resistance in Plasmodium falciparum compromises the effectiveness of antimalarial therapy. This study aimed to evaluate the extent of drug resistance in parasites obtained from international travelers returning from Ghana to guide the management of malaria cases. Eighty-two clinical parasite isolates were obtained from patients returning from Ghana in 2016–2018, of which 29 were adapted to continuous in vitro culture. Their geometric mean IC50 values to a panel of 11 antimalarial drugs, assessed using the standard SYBR Green-I drug sensitivity assay, were 2.1, 3.8, 1.0, 2.7, 17.2, 4.6, 8.3, 8.3, 19.6, 55.1, and 11,555 nM for artemether, artesunate, dihydroartemisinin, lumefantrine, mefloquine, piperaquine, naphthoquine, pyronaridine, chloroquine, quinine, and pyrimethamine, respectively. Except for chloroquine and pyrimethamine, the IC50 values for other tested drugs were below the resistance threshold. The mean ring-stage survival assay value was 0.8%, with four isolates exceeding 1%. The mean piperaquine survival assay value was 2.1%, all below 10%. Mutations associated with chloroquine resistance (pfcrt K76T and pfmdr1 N86Y) were scarce, consistent with the discontinuation of chloroquine a decade ago. Instead, the pfmdr1 86N-184F-1246D haplotype was predominant, suggesting selection by the extensive use of artemether-lumefantrine. No mutations in the pfk13 propeller domain were detected. The pfdhfr/pfdhps quadruple mutant IRNGK associated with resistance to sulfadoxine-pyrimethamine reached an 82% prevalence. In addition, five isolates had pfgch1 gene amplification but, intriguingly, increased susceptibilities to pyrimethamine. This study showed that parasites originating from Ghana were susceptible to artemisinins and the partner drugs of artemisinin-based combination therapies. Genotyping drug resistance genes identified the signature of selection by artemether-lumefantrine. Parasites showed substantial levels of resistance to the antifolate drugs. Continuous resistance surveillance is necessary to guide timely changes in drug policy.
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Affiliation(s)
- Wei Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xinxin Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Qi Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Longcan Zhou
- Department of Infectious Diseases, Shanglin County People’s Hospital, Guangxi, China
| | - Mengxi Duan
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Maohua Pan
- Department of Infectious Diseases, Shanglin County People’s Hospital, Guangxi, China
| | - Yucheng Qin
- Department of Infectious Diseases, Shanglin County People’s Hospital, Guangxi, China
| | - Xiaosong Li
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xun Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Weilin Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Hui Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Kemin Sun
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Wenya Zhu
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yaw Afrane
- Department of Medical Microbiology, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Linda Eva Amoah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benjamin Abuaku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Nancy Odurowah Duah-Quashie
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Yaming Huang
- Department of Protozoan Diseases, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- *Correspondence: Zhaoqing Yang, ; Liwang Cui,
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
- *Correspondence: Zhaoqing Yang, ; Liwang Cui,
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Seevaratnam D, Ansah F, Aniweh Y, Awandare GA, Hall EAH. Analysis and validation of silica-immobilised BST polymerase in loop-mediated isothermal amplification (LAMP) for malaria diagnosis. Anal Bioanal Chem 2022; 414:6309-6326. [PMID: 35657389 PMCID: PMC9163865 DOI: 10.1007/s00216-022-04131-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/04/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022]
Abstract
Bacillus stearothermophilus large fragment (BSTLF) DNA polymerase is reported, isolated on silica via a fused R5 silica-affinity peptide and used in nucleic acid diagnostics. mCherry (mCh), included in the fusion construct, was shown as an efficient fluorescent label to follow the workflow from gene to diagnostic. The R5 immobilisation on silica from cell lysate was consistent with cooperative R5-specific binding of R52-mCh-FL-BSTLF or R52-mCh-H10-BSTLF fusion proteins followed by non-specific protein binding (including E. coli native proteins). Higher R5-binding could be achieved in the presence of phosphate, but phosphate residue reduced loop-mediated isothermal amplification (LAMP) performance, possibly blocking sites on the BSTLF for binding of β- and γ-phosphates of the dNTPs. Quantitative assessment showed that cations (Mg2+ and Mn2+) that complex the PPi product optimised enzyme activity. In malaria testing, the limit of detection depended on Plasmodium species and primer set. For example, 1000 copies of P. knowlesi 18S rRNA could be detected with the P.KNO-LAU primer set with Si-R52-mCh-FL-BSTLF , but 10 copies of P. ovale 18S rRNA could be detected with the P.OVA-HAN primer set using the same enzyme. The Si-immobilised BSTLF outperformed the commercial enzyme for four of the nine Plasmodium LAMP primer sets tested. Si-R52-mCh-FL-BSTLF production was transferred from Cambridge to Accra and set up de novo for a trial with clinical samples. Different detection limits were found, targeting the mitochondrial DNA or the 18S rRNA gene for P. falciparum. The results are discussed in comparison with qPCR and sampling protocol and show that the Si-BSTLF polymerase can be optimised to meet the WHO recommended guidelines.
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7
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Yamauchi M, Hirai M, Tachibana SI, Mori T, Mita T. Fitness of sulfadoxine-resistant Plasmodium berghei harboring a single mutation in dihydropteroate synthase (DHPS). Acta Trop 2021; 222:106049. [PMID: 34273314 DOI: 10.1016/j.actatropica.2021.106049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/30/2021] [Accepted: 07/05/2021] [Indexed: 12/24/2022]
Abstract
Genetic changes conferring drug resistance are generally believed to impose fitness costs to pathogens in the absence of the drug. However, the fitness of resistant parasites against sulfadoxine/pyrimethamine has been inconclusive in Plasmodium falciparum. This is because resistance is conferred by the complex combination of mutations in dihydropteroate synthase (dhps) and dihydrofolate reductase (dhfr), which makes it difficult to separately assess the extent and magnitude of the costs imposed by mutations in dhps and dhfr. To assess the fitness costs imposed by sulfadoxine resistance alone, we generated a transgenic rodent malaria parasite, P. berghei clone harboring an A394G mutation in dhps (PbDHPS-A394G), corresponding to the causative mutation for sulfadoxine resistance in P. falciparum (PfDHPS-A437G). A four-day suppressive test confirmed that the PbDHPS-A394G clone was resistant to sulfadoxine. PbDHPS-A394G and wild-type clones showed similar growth rates and gametocyte production. This observation was confirmed in competitive experiments in which PbDHPS-A394G and wild-type clones were co-infected into mice to directly assess the survival competition between them. In the mosquitoes, there were no significant differences in oocyst production between PbDHPS-A394G and wild-type. These results indicate that the PbDHPS-A394G mutation alters the parasites to sulfadoxine resistance but may not impose fitness disadvantages during the blood stages in mice and oocyst formation in mosquitoes. These results partly explain the persistence of the PfDHPS-A437G mutant in the natural parasite populations.
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8
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Ansah F, Suurbaar J, Darko D, Anabire NG, Blankson SO, Domson BKS, Soulama A, Kpasra P, Chirawurah JD, Amenga-Etego L, Kanyong P, Awandare GA, Aniweh Y. Development of Cooperative Primer-Based Real-Time PCR Assays for the Detection of Plasmodium malariae and Plasmodium ovale. J Mol Diagn 2021; 23:1393-1403. [PMID: 34425259 PMCID: PMC8591562 DOI: 10.1016/j.jmoldx.2021.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/16/2021] [Accepted: 07/14/2021] [Indexed: 11/27/2022] Open
Abstract
Plasmodium malariae and Plasmodium ovale are increasingly gaining public health attention as the global transmission of falciparum malaria is decreasing. However, the absence of reliable Plasmodium species-specific detection tools has hampered accurate diagnosis of these minor Plasmodium species. In this study, SYBR Green-based real-time PCR assays were developed for the detection of P. malariae and P. ovale using cooperative primers that significantly limit the formation and propagation of primers-dimers. Both the P. malariae and P. ovale cooperative primer-based assays had at least 10-fold lower detection limit compared with the corresponding conventional primer-based assays. More important, the cooperative primer-based assays were evaluated in a cross-sectional study using 560 samples obtained from two health facilities in Ghana. The prevalence rates of P. malariae and P. ovale among the combined study population were 18.6% (104/560) and 5.5% (31/560), respectively. Among the Plasmodium-positive cases, P. malariae and P. ovale mono-infections were 3.6% (18/499) and 1.0% (5/499), respectively, with the remaining being co-infections with Plasmodium falciparum. The study demonstrates the public health importance of including detection tools with lower detection limits in routine diagnosis and surveillance of nonfalciparum species. This will be necessary for comprehensively assessing the effectiveness of malaria interventions and control measures aimed toward global malaria elimination.
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Affiliation(s)
- Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Jonathan Suurbaar
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Derrick Darko
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Nsoh G Anabire
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry and Molecular Medicine, School of Medicine, University for Development Studies, Tamale, Ghana
| | - Samuel O Blankson
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Bright K S Domson
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Alamissa Soulama
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Paulina Kpasra
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Jersley D Chirawurah
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Prosper Kanyong
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Flexmedical Solutions Ltd., Eliburn Industrial Park, Livingston, United Kingdom
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.
| | - Yaw Aniweh
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana.
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9
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Khairallah A, Ross CJ, Tastan Bishop Ö. GTP Cyclohydrolase I as a Potential Drug Target: New Insights into Its Allosteric Modulation via Normal Mode Analysis. J Chem Inf Model 2021; 61:4701-4719. [PMID: 34450011 DOI: 10.1021/acs.jcim.1c00898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP into dihydroneopterin triphosphate (DHNP). DHNP is the first intermediate of the folate de novo biosynthesis pathway in prokaryotic and lower eukaryotic microorganisms and the tetrahydrobiopterin (BH4) biosynthesis pathway in higher eukaryotes. The de novo folate biosynthesis provides essential cofactors for DNA replication, cell division, and synthesis of key amino acids in rapidly replicating pathogen cells, such as Plasmodium falciparum (P. falciparum), a causative agent of malaria. In eukaryotes, the product of the BH4 biosynthesis pathway is essential for the production of nitric oxide and several neurotransmitter precursors. An increased copy number of the malaria parasite P. falciparum GCH1 gene has been reported to influence antimalarial antifolate drug resistance evolution, whereas mutations in the human GCH1 are associated with neuropathic and inflammatory pain disorders. Thus, GCH1 stands as an important and attractive drug target for developing therapeutics. The GCH1 intrinsic dynamics that modulate its activity remains unclear, and key sites that exert allosteric effects across the structure are yet to be elucidated. This study employed the anisotropic network model to analyze the intrinsic motions of the GCH1 structure alone and in complex with its regulatory partner protein. We showed that the GCH1 tunnel-gating mechanism is regulated by a global shear motion and an outward expansion of the central five-helix bundle. We further identified hotspot residues within sites of structural significance for the GCH1 intrinsic allosteric modulation. The obtained results can provide a solid starting point to design novel antineuropathic treatments for humans and novel antimalarial drugs against the malaria parasite P. falciparum GCH1 enzyme.
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Affiliation(s)
- Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Caroline J Ross
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
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10
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Kreutzfeld O, Tumwebaze PK, Byaruhanga O, Katairo T, Okitwi M, Orena S, Rasmussen SA, Legac J, Conrad MD, Nsobya SL, Aydemir O, Bailey JA, Duffey M, Cooper RA, Rosenthal PJ. Decreased Susceptibility to Dihydrofolate Reductase Inhibitors Associated With Genetic Polymorphisms in Ugandan Plasmodium falciparum Isolates. J Infect Dis 2021; 225:696-704. [PMID: 34460932 PMCID: PMC8844592 DOI: 10.1093/infdis/jiab435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The Plasmodium falciparum dihydrofolate reductase (PfDHFR) inhibitors pyrimethamine and cycloguanil (the active metabolite of proguanil) have important roles in malaria chemoprevention, but drug resistance challenges their efficacies. A new compound, P218, was designed to overcome resistance, but drug-susceptibility data for P falciparum field isolates are limited. METHODS We studied ex vivo PfDHFR inhibitor susceptibilities of 559 isolates from Tororo and Busia districts, Uganda, from 2016 to 2020, sequenced 383 isolates, and assessed associations between genotypes and drug-susceptibility phenotypes. RESULTS Median half-maximal inhibitory concentrations (IC50s) were 42 100 nM for pyrimethamine, 1200 nM for cycloguanil, 13000 nM for proguanil, and 0.6 nM for P218. Among sequenced isolates, 3 PfDHFR mutations, 51I (100%), 59R (93.7%), and 108N (100%), were very common, as previously seen in Uganda, and another mutation, 164L (12.8%), had moderate prevalence. Increasing numbers of mutations were associated with decreasing susceptibility to pyrimethamine, cycloguanil, and P218, but not proguanil, which does not act directly against PfDHFR. Differences in P218 susceptibilities were modest, with median IC50s of 1.4 nM for parasites with mixed genotype at position 164 and 5.7 nM for pure quadruple mutant (51I/59R/108N/164L) parasites. CONCLUSIONS Resistance-mediating PfDHFR mutations were common in Ugandan isolates, but P218 retained excellent activity against mutant parasites.
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Affiliation(s)
| | | | | | - Thomas Katairo
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Martin Okitwi
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Stephen Orena
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Jennifer Legac
- University of California, San Francisco, California, USA
| | | | - Sam L Nsobya
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | | | | | - Roland A Cooper
- Dominican University of California, San Rafael, California, USA
| | - Philip J Rosenthal
- Correspondence: Philip J. Rosenthal, MD, Department of Medicine, University of California, Box 0811, San Francisco, CA 94143 USA ()
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11
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Liu S, Huckaby AC, Brown AC, Moore CC, Burbulis I, McConnell MJ, Güler JL. Single-cell sequencing of the small and AT-skewed genome of malaria parasites. Genome Med 2021; 13:75. [PMID: 33947449 PMCID: PMC8094492 DOI: 10.1186/s13073-021-00889-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.
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Affiliation(s)
- Shiwei Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Audrey C Brown
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Ian Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
- Current address: Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Jennifer L Güler
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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12
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Nkhoma SC, Ahmed AOA, Zaman S, Porier D, Baker Z, Stedman TT. Dissection of haplotype-specific drug response phenotypes in multiclonal malaria isolates. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2021; 15:152-161. [PMID: 33780700 PMCID: PMC8039770 DOI: 10.1016/j.ijpddr.2021.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 10/28/2022]
Abstract
Natural infections of Plasmodium falciparum, the parasite responsible for the deadliest form of human malaria, often comprise multiple parasite lineages (haplotypes). Multiclonal parasite isolates may exhibit variable phenotypes including different drug susceptibility profiles over time due to the presence of multiple haplotypes. To test this hypothesis, three P. falciparum Cambodian isolates IPC_3445 (MRA-1236), IPC_5202 (MRA-1240) and IPC_6403 (MRA-1285) suspected to be multiclonal were cloned by limiting dilution, and the resulting clones genotyped at 24 highly polymorphic single nucleotide polymorphisms (SNPs). Isolates harbored up to three constituent haplotypes, and exhibited significant variability (p < 0.05) in susceptibility to chloroquine, mefloquine, artemisinin and piperaquine as measured by half maximal drug inhibitory concentration (IC50) assays and parasite survival assays, which measure viability following exposure to pharmacologically relevant concentrations of antimalarial drugs. The IC50 of the most abundant haplotype frequently reflected that of the uncloned parental isolate, suggesting that a single haplotype dominates the antimalarial susceptibility profile and masks the effect of minor frequency haplotypes. These results indicate that phenotypic variability in parasite isolates is often due to the presence of multiple haplotypes. Depending on intended end-use, clinical isolates should be cloned to yield single parasite lineages with well-defined phenotypes and genotypes. The availability of such standardized clonal parasite lineages through NIAID's BEI Resources program will aid research directed towards the development of diagnostics and interventions including drugs against malaria.
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Affiliation(s)
- Standwell C Nkhoma
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA.
| | - Amel O A Ahmed
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Sharmeen Zaman
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Danielle Porier
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Zachary Baker
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA
| | - Timothy T Stedman
- BEI Resources, ATCC, 10801 University Boulevard, Manassas, VA, 20110-2209, USA.
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13
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Turkiewicz A, Manko E, Sutherland CJ, Diez Benavente E, Campino S, Clark TG. Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance. PLoS Genet 2020; 16:e1009268. [PMID: 33382691 PMCID: PMC7774857 DOI: 10.1371/journal.pgen.1009268] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Plasmodium falciparum parasites resistant to antimalarial treatments have hindered malaria disease control. Sulfadoxine-pyrimethamine (SP) was used globally as a first-line treatment for malaria after wide-spread resistance to chloroquine emerged and, although replaced by artemisinin combinations, is currently used as intermittent preventive treatment of malaria in pregnancy and in young children as part of seasonal malaria chemoprophylaxis in sub-Saharan Africa. The emergence of SP-resistant parasites has been predominantly driven by cumulative build-up of mutations in the dihydrofolate reductase (pfdhfr) and dihydropteroate synthetase (pfdhps) genes, but additional amplifications in the folate pathway rate-limiting pfgch1 gene and promoter, have recently been described. However, the genetic make-up and prevalence of those amplifications is not fully understood. We analyse the whole genome sequence data of 4,134 P. falciparum isolates across 29 malaria endemic countries, and reveal that the pfgch1 gene and promoter amplifications have at least ten different forms, occurring collectively in 23% and 34% in Southeast Asian and African isolates, respectively. Amplifications are more likely to be present in isolates with a greater accumulation of pfdhfr and pfdhps substitutions (median of 1 additional mutations; P<0.00001), and there was evidence that the frequency of pfgch1 variants may be increasing in some African populations, presumably under the pressure of SP for chemoprophylaxis and anti-folate containing antibiotics used for the treatment of bacterial infections. The selection of P. falciparum with pfgch1 amplifications may enhance the fitness of parasites with pfdhfr and pfdhps substitutions, potentially threatening the efficacy of this regimen for prevention of malaria in vulnerable groups. Our work describes new pfgch1 amplifications that can be used to inform the surveillance of SP drug resistance, its prophylactic use, and future experimental work to understand functional mechanisms.
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Affiliation(s)
- Anna Turkiewicz
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Emilia Manko
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Colin J. Sutherland
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ernest Diez Benavente
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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14
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Zhang X, Deitsch KW, Kirkman LA. The contribution of extrachromosomal DNA to genome plasticity in malaria parasites. Mol Microbiol 2020; 115:503-507. [PMID: 33103309 DOI: 10.1111/mmi.14632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/19/2020] [Accepted: 10/19/2020] [Indexed: 01/20/2023]
Abstract
Malaria caused by the protozoan parasite Plasmodium falciparum continues to impose significant morbidity and mortality, despite substantial investment into drug and vaccine development and deployment. Underlying the resilience of this parasite is its remarkable ability to undergo genome modifications, thus, providing parasite populations with extensive genetic variability that accelerates selection of drug resistance and limits the efficacy of most vaccines. This genome plasticity is rooted in the mechanisms of DNA repair that parasites employ to maintain genome integrity, a process skewed toward homologous recombination through the evolutionary loss of classical nonhomologous end joining. Repair of DNA double-strand breaks have been shown to enable "shuffling" of antigen-encoding gene sequences to vastly increase antigen diversity and to enable copy number expansion of genes that contribute to drug resistance. The latter phenomenon has been proposed to be a major contributor to the rise of resistance to several classes of antimalarial drugs. In this issue of Molecular Microbiology, McDaniels and colleagues add yet another mechanism that malaria parasites use to reduce drug susceptibility by demonstrating that P. falciparum can maintain expanded arrays of drug resistance cassettes as stably replicating, circular, extrachromosomal DNAs, thus, expanding genome plasticity beyond the parasite's 14 nuclear chromosomes.
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Affiliation(s)
- Xu Zhang
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Laura A Kirkman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA.,Department of Internal Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, USA
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15
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Khairallah A, Tastan Bishop Ö, Moses V. AMBER force field parameters for the Zn (II) ions of the tunneling-fold enzymes GTP cyclohydrolase I and 6-pyruvoyl tetrahydropterin synthase. J Biomol Struct Dyn 2020; 39:5843-5860. [PMID: 32720563 DOI: 10.1080/07391102.2020.1796800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The folate biosynthesis pathway is an essential pathway for cell growth and survival. Folate derivatives serve as a source of the one-carbon units in several intracellular metabolic reactions. Rapidly dividing cells rely heavily on the availability of folate derivatives for their proliferation. As a result, drugs targeting this pathway have shown to be effective against tumor cells and pathogens, but drug resistance against the available antifolate drugs emerged quickly. Therefore, there is a need to develop new treatment strategies and identify alternative metabolic targets. The two de novo folate biosynthesis pathway enzymes, GTP cyclohydrolase I (GCH1) and 6-pyruvoyl tetrahydropterin synthase (PTPS), can provide an alternative strategy to overcome the drug resistance that emerged in the two primary targeted enzymes dihydrofolate reductase and dihydropteroate synthase. Both GCH1 and PTPS enzymes contain Zn2+ ions in their active sites, and to accurately study their dynamic behaviors using all-atom molecular dynamics (MD) simulations, appropriate parameters that can describe their metal sites should be developed and validated. In this study, force field parameters of the GCH1 and PTPS metal centers were generated using quantum mechanics (QM) calculations and then validated through MD simulations to ensure their accuracy in describing and maintaining the Zn2+ ion coordination environment. The derived force field parameters will provide accurate and reliable MD simulations involving these two enzymes for future in-silico identification of drug candidates against the GCH1 and PTPS enzymes. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Vuyani Moses
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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16
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Sugaram R, Suwannasin K, Kunasol C, Mathema VB, Day NPJ, Sudathip P, Prempree P, Dondorp AM, Imwong M. Molecular characterization of Plasmodium falciparum antifolate resistance markers in Thailand between 2008 and 2016. Malar J 2020; 19:107. [PMID: 32127009 PMCID: PMC7055081 DOI: 10.1186/s12936-020-03176-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Resistance to anti-malarials is a major threat to the control and elimination of malaria. Sulfadoxine-pyrimethamine (SP) anti-malarial treatment was used as a national policy for treatment of uncomplicated falciparum malaria in Thailand from 1973 to 1990. In order to determine whether withdrawal of this antifolate drug has led to restoration of SP sensitivity, the prevalence of genetic markers of SP resistance was assessed in historical Thai samples. METHODS Plasmodium falciparum DNA was collected from the Thailand-Myanmar, Thailand-Malaysia and Thailand-Cambodia borders during 2008-2016 (N = 233). Semi-nested PCR and nucleotide sequencing were used to assess mutations in Plasmodium falciparum dihydrofolate reductase (pfdhfr), P. falciparum dihydropteroate synthase (pfdhps). Gene amplification of Plasmodium falcipaurm GTP cyclohydrolase-1 (pfgch1) was assessed by quantitative real-time PCR. The association between pfdhfr/pfdhps mutations and pfgch1 copy numbers were evaluated. RESULTS Mutations in pfdhfr/pfdhsp and pfgch1 copy number fluctuated overtime through the study period. Altogether, 14 unique pfdhfr-pdfhps haplotypes collectively containing quadruple to octuple mutations were identified. High variation in pfdhfr-pfdhps haplotypes and a high proportion of pfgch1 multiple copy number (51% (73/146)) were observed on the Thailand-Myanmar border compared to other parts of Thailand. Overall, the prevalence of septuple mutations was observed for pfdhfr-pfdhps haplotypes. In particular, the prevalence of pfdhfr-pfdhps, septuple mutation was observed in the Thailand-Myanmar (50%, 73/146) and Thailand-Cambodia (65%, 26/40) border. In Thailand-Malaysia border, majority of the pfdhfr-pfdhps haplotypes transaction from quadruple (90%, 9/10) to quintuple (65%, 24/37) during 2008-2016. Within the pfdhfr-pfdhps haplotypes, during 2008-2013 the pfdhps A/S436F mutation was observed only in Thailand-Myanmar border (9%, 10/107), while it was not identified later. In general, significant correlation was observed between the prevalence of pfdhfr I164L (ϕ = 0.213, p-value = 0.001) or pfdhps K540E/N (ϕ = 0.399, p-value ≤ 0.001) mutations and pfgch1 gene amplification. CONCLUSIONS Despite withdrawal of SP as anti-malarial treatment for 17 years, the border regions of Thailand continue to display high prevalence of antifolate and anti-sulfonamide resistance markers in falciparum malaria. Significant association between pfgch1 amplification and pfdhfr (I164L) or pfdhps (K540E) resistance markers were observed, suggesting a compensatory mutation.
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Affiliation(s)
- Rungniran Sugaram
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Rd., Bangkok, 10400, Thailand
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Kanokon Suwannasin
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chanon Kunasol
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vivek Bhakta Mathema
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicholas P J Day
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
- Centre for Tropical Medicine, Churchill Hospital, Oxford, UK
| | - Prayuth Sudathip
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Preecha Prempree
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Arjen M Dondorp
- Division of Vector Borne Diseases, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
- Centre for Tropical Medicine, Churchill Hospital, Oxford, UK
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Rd., Bangkok, 10400, Thailand.
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Valente M, Vidal AE, González-Pacanowska D. Targeting Kinetoplastid and Apicomplexan Thymidylate Biosynthesis as an Antiprotozoal Strategy. Curr Med Chem 2019; 26:4262-4279. [PMID: 30259810 DOI: 10.2174/0929867325666180926154329] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/23/2018] [Accepted: 09/14/2018] [Indexed: 02/04/2023]
Abstract
Kinetoplastid and apicomplexan parasites comprise a group of protozoans responsible for human diseases, with a serious impact on human health and the socioeconomic growth of developing countries. Chemotherapy is the main option to control these pathogenic organisms and nucleotide metabolism is considered a promising area for the provision of antimicrobial therapeutic targets. Impairment of thymidylate (dTMP) biosynthesis severely diminishes the viability of parasitic protozoa and the absence of enzymatic activities specifically involved in the formation of dTMP (e.g. dUTPase, thymidylate synthase, dihydrofolate reductase or thymidine kinase) results in decreased deoxythymidine triphosphate (dTTP) levels and the so-called thymineless death. In this process, the ratio of deoxyuridine triphosphate (dUTP) versus dTTP in the cellular nucleotide pool has a crucial role. A high dUTP/dTTP ratio leads to uracil misincorporation into DNA, the activation of DNA repair pathways, DNA fragmentation and eventually cell death. The essential character of dTMP synthesis has stimulated interest in the identification and development of drugs that specifically block the biochemical steps involved in thymine nucleotide formation. Here, we review the available literature in relation to drug discovery studies targeting thymidylate biosynthesis in kinetoplastid (genera Trypanosoma and Leishmania) and apicomplexan (Plasmodium spp and Toxoplasma gondii) protozoans. The most relevant findings concerning novel inhibitory molecules with antiparasitic activity against these human pathogens are presented herein.
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Affiliation(s)
- María Valente
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Antonio E Vidal
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitologia y Biomedicina "Lopez-Neyra", Consejo Superior de Investigaciones Científicas, Granada, Spain
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18
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Huckaby AC, Granum CS, Carey MA, Szlachta K, Al-Barghouthi B, Wang YH, Guler JL. Complex DNA structures trigger copy number variation across the Plasmodium falciparum genome. Nucleic Acids Res 2019; 47:1615-1627. [PMID: 30576466 PMCID: PMC6393310 DOI: 10.1093/nar/gky1268] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/06/2023] Open
Abstract
Antimalarial resistance is a major obstacle in the eradication of the human malaria parasite, Plasmodium falciparum. Genome amplifications, a type of DNA copy number variation (CNV), facilitate overexpression of drug targets and contribute to parasite survival. Long monomeric A/T tracks are found at the breakpoints of many Plasmodium resistance-conferring CNVs. We hypothesize that other proximal sequence features, such as DNA hairpins, act with A/T tracks to trigger CNV formation. By adapting a sequence analysis pipeline to investigate previously reported CNVs, we identified breakpoints in 35 parasite clones with near single base-pair resolution. Using parental genome sequence, we predicted the formation of stable hairpins within close proximity to all future breakpoint locations. Especially stable hairpins were predicted to form near five shared breakpoints, establishing that the initiating event could have occurred at these sites. Further in-depth analyses defined characteristics of these 'trigger sites' across the genome and detected signatures of error-prone repair pathways at the breakpoints. We propose that these two genomic signals form the initial lesion (hairpins) and facilitate microhomology-mediated repair (A/T tracks) that lead to CNV formation across this highly repetitive genome. Targeting these repair pathways in P. falciparum may be used to block adaptation to antimalarial drugs.
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Affiliation(s)
- Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Claire S Granum
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Maureen A Carey
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, VA 22908, USA.,Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Basel Al-Barghouthi
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.,Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Jennifer L Guler
- Department of Biology, University of Virginia, Charlottesville, VA 22908, USA.,Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
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19
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Patil GB, Lakhssassi N, Wan J, Song L, Zhou Z, Klepadlo M, Vuong TD, Stec AO, Kahil SS, Colantonio V, Valliyodan B, Rice JH, Piya S, Hewezi T, Stupar RM, Meksem K, Nguyen HT. Whole-genome re-sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad-based resistance to soybean cyst nematode. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1595-1611. [PMID: 30688400 PMCID: PMC6662113 DOI: 10.1111/pbi.13086] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 05/19/2023]
Abstract
Soybean cyst nematode (SCN) is the most devastating plant-parasitic nematode. Most commercial soybean varieties with SCN resistance are derived from PI88788. Resistance derived from PI88788 is breaking down due to narrow genetic background and SCN population shift. PI88788 requires mainly the rhg1-b locus, while 'Peking' requires rhg1-a and Rhg4 for SCN resistance. In the present study, whole genome re-sequencing of 106 soybean lines was used to define the Rhg haplotypes and investigate their responses to the SCN HG-Types. The analysis showed a comprehensive profile of SNPs and copy number variations (CNV) at these loci. CNV of rhg1 (GmSNAP18) only contributed towards resistance in lines derived from PI88788 and 'Cloud'. At least 5.6 copies of the PI88788-type rhg1 were required to confer SCN resistance, regardless of the Rhg4 (GmSHMT08) haplotype. However, when the GmSNAP18 copies dropped below 5.6, a 'Peking'-type GmSHMT08 haplotype was required to ensure SCN resistance. This points to a novel mechanism of epistasis between GmSNAP18 and GmSHMT08 involving minimum requirements for copy number. The presence of more Rhg4 copies confers resistance to multiple SCN races. Moreover, transcript abundance of the GmSHMT08 in root tissue correlates with more copies of the Rhg4 locus, reinforcing SCN resistance. Finally, haplotype analysis of the GmSHMT08 and GmSNAP18 promoters inferred additional levels of the resistance mechanism. This is the first report revealing the genetic basis of broad-based resistance to SCN and providing new insight into epistasis, haplotype-compatibility, CNV, promoter variation and its impact on broad-based disease resistance in plants.
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Affiliation(s)
- Gunvant B. Patil
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Jinrong Wan
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Li Song
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | | | - Tri D. Vuong
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Adrian O. Stec
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Sondus S. Kahil
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Babu Valliyodan
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - J. Hollis Rice
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Sarbottam Piya
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Robert M. Stupar
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Henry T. Nguyen
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
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20
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Osei M, Ansah F, Matrevi SA, Asante KP, Awandare GA, Quashie NB, Duah NO. Amplification of GTP-cyclohydrolase 1 gene in Plasmodium falciparum isolates with the quadruple mutant of dihydrofolate reductase and dihydropteroate synthase genes in Ghana. PLoS One 2018; 13:e0204871. [PMID: 30265714 PMCID: PMC6162080 DOI: 10.1371/journal.pone.0204871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/14/2018] [Indexed: 11/19/2022] Open
Abstract
Sulfadoxine-pyrimethamine (SP) is used as malaria chemoprophylaxis for pregnant women and children in Ghana. Plasmodium falciparum resistance to SP is linked to mutations in the dihydropteroate synthase gene (pfdhps), dihydrofolate reductase gene (pfdhfr) and amplification of GTP cyclohydrolase 1 (pfgch1) gene. The pfgch1 duplication is associated with pfdhfr L164, a crucial mutant for high level pyrimethamine resistance which is rare in Ghana. The presence of amplified pfgch1 in Ghanaian isolates could be an indicator of the evolution of the L164 mutant. This study therefore determined the pfgch1 copy number variations and SP resistance mutations in clinical isolates from Ghana. One hundred and ninety-two (192) blood samples collected from children aged ≤14 years with uncomplicated malaria in 2013-14 and 2015-16 were used. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the pfgch1 copy number and nested PCR-Sanger sequencing used to detect mutations in pfdhps and pfdhfr genes. Twelve parasites (6.3%) harbored double copies of the pfgch1 gene out of the 192 samples. Of the 12, 75% had the pfdhfr I51-R59-N108, 92% had the pfdhps G437 mutant, 8% had the pfdhps E540 and 67% had the SP resistance haplotype IRNG. No L164 was detected in samples with amplified pfgch1. The rare T108 mutant associated with cycloguanil resistance showed predominance (60%) over N108 in the 2015-16 isolates. The observation of parasites with increased copy number of pfgch1 gene is indicative of the future evolution of the rare quadruple pfdhfr mutant, I51-R59-N108-L164, in Ghanaian parasites. Mutant pfdhps isolates also had increased gch1 copy number suggestive that it may also facilitate sulphadoxine resistance. The selection of parasites with pfgch1 gene amplification will enhance the sustenance and persistence of parasites with SP resistance in the country. Policy makers need to begin the search for a replacement chemoprophylaxis drug for malaria vulnerable groups in Ghana.
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Affiliation(s)
- Musah Osei
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Sena A. Matrevi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | | | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra, Ghana
| | - Neils B. Quashie
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
- Centre for Tropical Clinical Pharmacology and Therapeutics, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Nancy O. Duah
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
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21
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Pathogenic Nocardia cyriacigeorgica and Nocardia nova Evolve To Resist Trimethoprim-Sulfamethoxazole by both Expected and Unexpected Pathways. Antimicrob Agents Chemother 2018; 62:AAC.00364-18. [PMID: 29686152 DOI: 10.1128/aac.00364-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/15/2018] [Indexed: 12/12/2022] Open
Abstract
Nocardia spp. are Gram-positive opportunistic pathogens that affect largely immunocompromised patients, leading to serious pulmonary or systemic infections. Combination therapy using the folate biosynthesis pathway inhibitors trimethoprim (TMP) and sulfamethoxazole (SMX) is commonly used as an antimicrobial therapy. Not surprisingly, as antibiotic therapies for nocardiosis can extend for many months, resistance to TMP-SMX has emerged. Using experimental evolution, we surveyed the genetic basis of adaptation to TMP-SMX across 8 strains of Nocardia nova and 2 strains of Nocardia cyriacigeorgica By employing both continuous experimental evolution to provide longitudinal information on the order of changes and characterization of resistant endpoint isolates, we observe changes that are consistent with modifications of two enzymes of the folate biosynthesis pathway: dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) (FolP), with the mutations often being clustered near the active site of the enzymes. While changes to DHFR and DHPS might be expected, we also noted that mutations in a previously undescribed homolog of DHPS (DHPS2 or FolP2) that was annotated as being "nonfunctional" were also sufficient to generate TMP-SMX resistance, which serves as a cautionary tale for the use of automated annotation by investigators and for the future discovery of drugs against this genus. Additionally, folP2 overlapped glucosyl-3-phosphoglycerate synthase. Remarkably, an adaptive frameshift mutation within the overlapping region resulted in a new in-frame fusion to the downstream gene to produce a potentially new bifunctional enzyme. How a single potentially bifunctional DHPS2 enzyme might confer resistance is unclear. However, it highlights the unexpected ways in which adaptive evolution finds novel solutions for selection.
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22
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Fastman Y, Assaraf S, Rose M, Milrot E, Basore K, Arasu BS, Desai SA, Elbaum M, Dzikowski R. An upstream open reading frame (uORF) signals for cellular localization of the virulence factor implicated in pregnancy associated malaria. Nucleic Acids Res 2018; 46:4919-4932. [PMID: 29554358 PMCID: PMC6007598 DOI: 10.1093/nar/gky178] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/17/2022] Open
Abstract
Plasmodium falciparum, the causative agent of the deadliest form of human malaria, alternates expression of variable antigens, encoded by members of a multi-copy gene family named var. In var2csa, the var gene implicated in pregnancy-associated malaria, translational repression is regulated by a unique upstream open reading frame (uORF) found only in its 5' UTR. Here, we report that this translated uORF significantly alters both transcription and posttranslational protein trafficking. The parasite can alter a protein's destination without any modifications to the protein itself, but instead by an element within the 5' UTR of the transcript. This uORF-dependent localization was confirmed by single molecule STORM imaging, followed by fusion of the uORF to a reporter gene which changes its cellular localization from cytoplasmic to ER-associated. These data point towards a novel regulatory role of uORF in protein trafficking, with important implications for the pathology of pregnancy-associated malaria.
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Affiliation(s)
- Yair Fastman
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel - Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shany Assaraf
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel - Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Miriam Rose
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel - Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Elad Milrot
- Electron Microscopy Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Katherine Basore
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - B Sivanandam Arasu
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Sanjay A Desai
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Michael Elbaum
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, The Institute for Medical Research Israel - Canada, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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23
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Simam J, Rono M, Ngoi J, Nyonda M, Mok S, Marsh K, Bozdech Z, Mackinnon M. Gene copy number variation in natural populations of Plasmodium falciparum in Eastern Africa. BMC Genomics 2018; 19:372. [PMID: 29783949 PMCID: PMC5963192 DOI: 10.1186/s12864-018-4689-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in the laboratory have revealed their important role in parasite fitness phenotypes such as red cell invasion, transmissibility and cytoadherence. Studies of natural parasite populations indicate that CNVs are also common in the field and thus may facilitate adaptation of the parasite to its local environment. RESULTS In a survey of 183 fresh field isolates from three populations in Eastern Africa with different malaria transmission intensities, we identified 94 CNV loci using microarrays. All CNVs had low population frequencies (minor allele frequency < 5%) but each parasite isolate carried an average of 8 CNVs. Nine CNVs showed high levels of population differentiation (FST > 0.3) and nine exhibited significant clines in population frequency across a gradient in transmission intensity. The clearest example of this was a large deletion on chromosome 9 previously reported only in laboratory-adapted isolates. This deletion was present in 33% of isolates from a population with low and highly seasonal malaria transmission, and in < 9% of isolates from populations with higher transmission. Subsets of CNVs were strongly correlated in their population frequencies, implying co-selection. CONCLUSIONS These results support the hypothesis that CNVs are the target of selection in natural populations of P. falciparum. Their environment-specific patterns observed here imply an important role for them in conferring adaptability to the parasite thus enabling it to persist in its highly diverse ecological environment.
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Affiliation(s)
| | - Martin Rono
- KEMRI-Wellcome Trust Research Program, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Pwani University Bioscience Research Centre, Pwani University, Kilifi, Kenya
| | - Joyce Ngoi
- KEMRI-Wellcome Trust Research Program, Kilifi, Kenya
| | - Mary Nyonda
- Department of Microbiology and Molecular Medicine, Medical Faculty, University of Geneva, Geneva, Switzerland
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University, New York, USA
| | - Kevin Marsh
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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24
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Abstract
It is rare to come across an Aesop’s fable in respectable journals. It might catch scientists outside the malaria field by surprise to learn that the famous story of “The Boy Who Cried Wolf” has been repeatedly compared to the threat from artemisinin-resistant malaria parasites, including the two latest reports on the rise of a specific haplotype in Cambodia and Thailand, sensationally dubbed “Super Malaria” by the media [1, 2]. The comparison to a children’s tale should not negate the fact that malaria drug resistance is one of the most pressing threats to the global public health community. Here, the findings leading to this contentious discourse will be delineated in order to provide a perspective. Possible solutions will be presented to stimulate further research and discussion to solve one of the greatest public health challenges of our lifetime.
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Affiliation(s)
- Thanat Chookajorn
- Genomics and Evolutionary Medicine Unit (GEM), Center of Excellence in Malaria Research, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- * E-mail:
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25
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Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases. Future Med Chem 2018; 10:935-959. [PMID: 29629843 DOI: 10.4155/fmc-2017-0168] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.
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26
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Hamilton WL, Claessens A, Otto TD, Kekre M, Fairhurst RM, Rayner JC, Kwiatkowski D. Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Res 2017; 45:1889-1901. [PMID: 27994033 PMCID: PMC5389722 DOI: 10.1093/nar/gkw1259] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/01/2016] [Indexed: 01/31/2023] Open
Abstract
For reasons that remain unknown, the Plasmodium falciparum genome has an exceptionally high AT content compared to other Plasmodium species and eukaryotes in general - nearly 80% in coding regions and approaching 90% in non-coding regions. Here, we examine how this phenomenon relates to genome-wide patterns of de novo mutation. Mutation accumulation experiments were performed by sequential cloning of six P. falciparum isolates growing in human erythrocytes in vitro for 4 years, with 279 clones sampled for whole genome sequencing at different time points. Genome sequence analysis of these samples revealed a significant excess of G:C to A:T transitions compared to other types of nucleotide substitution, which would naturally cause AT content to equilibrate close to the level seen across the P. falciparum reference genome (80.6% AT). These data also uncover an extremely high rate of small indel mutation relative to other species, primarily associated with repetitive AT-rich sequences, in addition to larger-scale structural rearrangements focused in antigen-coding var genes. In conclusion, high AT content in P. falciparum is driven by a systematic mutational bias and ultimately leads to an unusual level of microstructural plasticity, raising the question of whether this contributes to adaptive evolution.
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Affiliation(s)
- William L Hamilton
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0SP, UK
| | - Antoine Claessens
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Medical Research Council Unit The Gambia, Atlantic Road, Fajara, P.O. Box 273, Banjul, The Gambia.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Thomas D Otto
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Mihir Kekre
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Julian C Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Dominic Kwiatkowski
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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27
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Costa GL, Amaral LC, Fontes CJF, Carvalho LH, de Brito CFA, de Sousa TN. Assessment of copy number variation in genes related to drug resistance in Plasmodium vivax and Plasmodium falciparum isolates from the Brazilian Amazon and a systematic review of the literature. Malar J 2017; 16:152. [PMID: 28420389 PMCID: PMC5395969 DOI: 10.1186/s12936-017-1806-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/07/2017] [Indexed: 12/29/2022] Open
Abstract
Background Parasite resistance to anti-malarials represents a great obstacle for malaria elimination. The majority of studies have investigated the association between single-nucleotide polymorphisms (SNPs) and drug resistance; however, it is becoming clear that the copy number variation (CNV) is also associated with this parasite phenotype. To provide a baseline for molecular surveillance of anti-malarial drug resistance in the Brazilian Amazon, the present study characterized the genetic profile of both markers in the most common genes associated with drug resistance in Plasmodium falciparum and Plasmodium vivax isolates. Additionally, these data were compared to data published elsewhere applying a systematic review of the literature published over a 20-year time period. Methods The genomic DNA of 67 patients infected by P. falciparum and P. vivax from three Brazilian States was obtained between 2002 and 2012. CNV in P. falciparum multidrug resistance gene-1 (pfmdr1), GTP cyclohydrolase 1 (pfgch1) and P. vivax multidrug resistance gene-1 (pvmdr1) were assessed by real-time PCR assays. SNPs in the pfmdr1 and pfcrt genes were assessed by PCR–RFLP. A literature search for studies that analysed CNP in the same genes of P. falciparum and P. vivax was conducted between May 2014 and March 2017 across four databases. Results All analysed samples of P. falciparum carried only one copy of pfmdr1 or pfgch1. Although the pfcrt K76T polymorphism, a determinant of CQ resistance, was present in all samples genotyped, the pfmdr1 N86Y was absent. For P. vivax isolates, an amplification rate of 20% was found for the pvmdr1 gene. The results of the study are in agreement with the low amplification rates for pfmdr1 gene evidenced in the Americas and Africa, while higher rates have been described in Southeast Asia. For P. vivax, very low rates of amplification for pvmdr1 have been described worldwide, with exceptions in French Guiana, Cambodia, Thailand and Brazil. Conclusions The present study was the first to evaluate gch1 CNV in P. falciparum isolates from Brazil, showing an absence of amplification of this gene more than 20 years after the withdrawal of the Brazilian antifolates therapeutic scheme. Furthermore, the rate of pvmdr1 amplification was significantly higher than that previously reported for isolates circulating in Northern Brazil. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-1806-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel Luíz Costa
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Lara Cotta Amaral
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | | | - Luzia Helena Carvalho
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Cristiana Ferreira Alves de Brito
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Taís Nóbrega de Sousa
- Molecular Biology and Malaria Immunology Research Group, Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil.
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28
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Jovel IT, Björkman A, Roper C, Mårtensson A, Ursing J. Unexpected selections of Plasmodium falciparum polymorphisms in previously treatment-naïve areas after monthly presumptive administration of three different anti-malarial drugs in Liberia 1976-78. Malar J 2017; 16:113. [PMID: 28288632 PMCID: PMC5347173 DOI: 10.1186/s12936-017-1747-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 02/21/2017] [Indexed: 01/08/2023] Open
Abstract
Background To assess the effect on malaria prevalence, village specific monthly administrations of pyrimethamine, chlorproguanil, chloroquine or placebo were given to children in four previously treatment-naïve Liberian villages, 1976–78. Plasmodium falciparum in vivo resistance developed to pyrimethamine only. Selection of molecular markers of P. falciparum resistance after 2 years of treatment are reported. Methods Blood samples were collected from 191 study children in a survey in 1978. Polymorphisms in pfcrt, pfmdr1, pfdhfr, pfdhps, pfmrp1 and pfnhe1 genes were determined using PCR-based methods. Results Pfcrt 72–76 CVIET was found in one chloroquine village sample, all remaining samples had pfcrt CVMNK. Pfmdr1 N86 prevalence was 100%. A pfmdr1 T1069ACT→ACG synonymous polymorphism was found in 30% of chloroquine village samples and 3% of other samples (P = 0.008). Variations in pfnhe1 block I were found in all except the chloroquine treated village (P < 0.001). Resistance associated pfdhfr 108N prevalence was 2% in the pyrimethamine village compared to 45–65% elsewhere, including the placebo village (P = 0.001). Conclusions Chloroquine treatment possibly resulted in the development of pfcrt 72–76 CVIET. Selection of pfmdr1 T1069ACG and a pfnhe1 block 1 genotypes indicates that chloroquine treatment exerted a selective pressure on P. falciparum. Pyrimethamine resistance associated pfdhfr 108N was present prior to the introduction of any drug. Decreased pfdhfr 108N frequency concurrent with development of pyrimethamine resistance suggests a non-pfdhfr polymorphisms mediated resistance mechanism. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-1747-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irina T Jovel
- Malaria Research, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Anders Björkman
- Malaria Research, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health Unit, Uppsala University, Uppsala, Sweden
| | - Johan Ursing
- Malaria Research, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Danderyds Hospital, Stockholm, Sweden
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Ravenhall M, Benavente ED, Mipando M, Jensen ATR, Sutherland CJ, Roper C, Sepúlveda N, Kwiatkowski DP, Montgomery J, Phiri KS, Terlouw A, Craig A, Campino S, Ocholla H, Clark TG. Characterizing the impact of sustained sulfadoxine/pyrimethamine use upon the Plasmodium falciparum population in Malawi. Malar J 2016; 15:575. [PMID: 27899115 PMCID: PMC5129638 DOI: 10.1186/s12936-016-1634-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/23/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malawi experienced prolonged use of sulfadoxine/pyrimethamine (SP) as the front-line anti-malarial drug, with early replacement of chloroquine and delayed introduction of artemisinin-based combination therapy. Extended use of SP, and its continued application in pregnancy is impacting the genomic variation of the Plasmodium falciparum population. METHODS Whole genome sequence data of P. falciparum isolates covering 2 years of transmission within Malawi, alongside global datasets, were used. More than 745,000 SNPs were identified, and differences in allele frequencies between countries assessed, as well as genetic regions under positive selection determined. RESULTS Positive selection signals were identified within dhps, dhfr and gch1, all components of the parasite folate pathway associated with SP resistance. Sitting predominantly on a dhfr triple mutation background, a novel copy number increase of ~twofold was identified in the gch1 promoter. This copy number was almost fixed (96.8% frequency) in Malawi samples, but found at less than 45% frequency in other African populations, and distinct from a whole gene duplication previously reported in Southeast Asian parasites. CONCLUSIONS SP resistance selection pressures have been retained in the Malawian population, with known resistance dhfr mutations at fixation, complemented by a novel gch1 promoter duplication. The effects of the duplication on the fitness costs of SP variants and resistance need to be elucidated.
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Affiliation(s)
- Matt Ravenhall
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ernest Diez Benavente
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Mwapatsa Mipando
- Department of Physiology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Anja T. R. Jensen
- Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | - Colin J. Sutherland
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Cally Roper
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Nuno Sepúlveda
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Centre for Statistics and Applications of University of Lisbon, Lisbon, Portugal
| | | | - Jacqui Montgomery
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Kamija S. Phiri
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Anja Terlouw
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Alister Craig
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Harold Ocholla
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- School of Public Health and Family Medicine, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
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Witkowski B, Duru V, Khim N, Ross LS, Saintpierre B, Beghain J, Chy S, Kim S, Ke S, Kloeung N, Eam R, Khean C, Ken M, Loch K, Bouillon A, Domergue A, Ma L, Bouchier C, Leang R, Huy R, Nuel G, Barale JC, Legrand E, Ringwald P, Fidock DA, Mercereau-Puijalon O, Ariey F, Ménard D. A surrogate marker of piperaquine-resistant Plasmodium falciparum malaria: a phenotype-genotype association study. THE LANCET. INFECTIOUS DISEASES 2016; 17:174-183. [PMID: 27818097 PMCID: PMC5266792 DOI: 10.1016/s1473-3099(16)30415-7] [Citation(s) in RCA: 257] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/26/2016] [Accepted: 09/30/2016] [Indexed: 11/30/2022]
Abstract
Background Western Cambodia is the epicentre of Plasmodium falciparum multidrug resistance and is facing high rates of dihydroartemisinin–piperaquine treatment failures. Genetic tools to detect the multidrug-resistant parasites are needed. Artemisinin resistance can be tracked using the K13 molecular marker, but no marker exists for piperaquine resistance. We aimed to identify genetic markers of piperaquine resistance and study their association with dihydroartemisinin–piperaquine treatment failures. Methods We obtained blood samples from Cambodian patients infected with P falciparum and treated with dihydroartemisinin–piperaquine. Patients were followed up for 42 days during the years 2009–15. We established in-vitro and ex-vivo susceptibility profiles for a subset using piperaquine survival assays. We determined whole-genome sequences by Illumina paired-reads sequencing, copy number variations by qPCR, RNA concentrations by qRT-PCR, and protein concentrations by immunoblotting. Fisher’s exact and non-parametric Wilcoxon rank-sum tests were used to identify significant differences in single-nucleotide polymorphisms or copy number variants, respectively, for differential distribution between piperaquine-resistant and piperaquine-sensitive parasite lines. Findings Whole-genome exon sequence analysis of 31 culture-adapted parasite lines associated amplification of the plasmepsin 2–plasmepsin 3 gene cluster with in-vitro piperaquine resistance. Ex-vivo piperaquine survival assay profiles of 134 isolates correlated with plasmepsin 2 gene copy number. In 725 patients treated with dihydroartemisinin–piperaquine, multicopy plasmepsin 2 in the sample collected before treatment was associated with an adjusted hazard ratio (aHR) for treatment failure of 20·4 (95% CI 9·1–45·5, p<0·0001). Multicopy plasmepsin 2 predicted dihydroartemisinin–piperaquine failures with 0·94 (95% CI 0·88–0·98) sensitivity and 0·77 (0·74–0·81) specificity. Analysis of samples collected across the country from 2002 to 2015 showed that the geographical and temporal increase of the proportion of multicopy plasmepsin 2 parasites was highly correlated with increasing dihydroartemisinin–piperaquine treatment failure rates (r=0·89 [95% CI 0·77–0·95], p<0·0001, Spearman’s coefficient of rank correlation). Dihydroartemisinin–piperaquine efficacy at day 42 fell below 90% when the proportion of multicopy plasmepsin 2 parasites exceeded 22%. Interpretation Piperaquine resistance in Cambodia is strongly associated with amplification of plasmepsin 2–3, encoding haemoglobin-digesting proteases, regardless of the location. Multicopy plasmepsin 2 constitutes a surrogate molecular marker to track piperaquine resistance. A molecular toolkit combining plasmepsin 2 with K13 and mdr1 monitoring should provide timely information for antimalarial treatment and containment policies. Funding Institut Pasteur in Cambodia, Institut Pasteur Paris, National Institutes of Health, WHO, Agence Nationale de la Recherche, Investissement d’Avenir programme, Laboratoire d’Excellence Integrative “Biology of Emerging Infectious Diseases”.
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Affiliation(s)
- Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia; Malaria Translational Research Unit, Institut Pasteur, Paris, France; Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Valentine Duru
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Nimol Khim
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia; Malaria Translational Research Unit, Institut Pasteur, Paris, France; Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Leila S Ross
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Johann Beghain
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Sophy Chy
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Saorin Kim
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Sopheakvatey Ke
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Nimol Kloeung
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Rotha Eam
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Chanra Khean
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Malen Ken
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Kaknika Loch
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Anthony Bouillon
- Malaria Translational Research Unit, Institut Pasteur, Paris, France; Institut Pasteur in Cambodia, Phnom Penh, Cambodia; Structural Microbiology Unit, Biology of Malaria Targets Group, Department of Structural Biology and Chemistry and CNRS, UMR3528, Institut Pasteur, Paris, France
| | - Anais Domergue
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia
| | - Laurence Ma
- Plate-forme Génomique, Département Génomes et Génétique, Institut Pasteur, Paris, France
| | - Christiane Bouchier
- Plate-forme Génomique, Département Génomes et Génétique, Institut Pasteur, Paris, France
| | - Rithea Leang
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Rekol Huy
- National Center for Parasitology, Entomology and Malaria Control, Phnom Penh, Cambodia
| | - Grégory Nuel
- Laboratoire de Mathématiques Appliquées (MAP5) UMR CNRS 8145, Université Paris Descartes, Paris, France
| | - Jean-Christophe Barale
- Malaria Translational Research Unit, Institut Pasteur, Paris, France; Institut Pasteur in Cambodia, Phnom Penh, Cambodia; Structural Microbiology Unit, Biology of Malaria Targets Group, Department of Structural Biology and Chemistry and CNRS, UMR3528, Institut Pasteur, Paris, France
| | - Eric Legrand
- Malaria Translational Research Unit, Institut Pasteur, Paris, France; Institut Pasteur in Cambodia, Phnom Penh, Cambodia; Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Pascal Ringwald
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - David A Fidock
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Frédéric Ariey
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France; Institut Cochin Inserm U1016, Université Paris-Descartes, Sorbonne Paris Cité, and Laboratoire de Parasitologie-Mycologie, Hôpital Cochin, Paris, France
| | - Didier Ménard
- Malaria Molecular Epidemiology Unit, Institut Pasteur in Cambodia, Phnom Penh, Cambodia; Malaria Translational Research Unit, Institut Pasteur, Paris, France; Institut Pasteur in Cambodia, Phnom Penh, Cambodia.
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31
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Miles A, Iqbal Z, Vauterin P, Pearson R, Campino S, Theron M, Gould K, Mead D, Drury E, O'Brien J, Ruano Rubio V, MacInnis B, Mwangi J, Samarakoon U, Ranford-Cartwright L, Ferdig M, Hayton K, Su XZ, Wellems T, Rayner J, McVean G, Kwiatkowski D. Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum. Genome Res 2016; 26:1288-99. [PMID: 27531718 PMCID: PMC5052046 DOI: 10.1101/gr.203711.115] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 06/28/2016] [Indexed: 12/14/2022]
Abstract
The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired.
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Affiliation(s)
- Alistair Miles
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Zamin Iqbal
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Paul Vauterin
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Richard Pearson
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Susana Campino
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Michel Theron
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Kelda Gould
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Daniel Mead
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Eleanor Drury
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | | | | | - Bronwyn MacInnis
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Jonathan Mwangi
- Department of Biochemistry, Medical School, Mount Kenya University, 01000 Thika, Kenya; Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Upeka Samarakoon
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Lisa Ranford-Cartwright
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Michael Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Karen Hayton
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Xin-Zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Thomas Wellems
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland 20892-9806, USA
| | - Julian Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Gil McVean
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom; Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom
| | - Dominic Kwiatkowski
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, United Kingdom; Malaria Programme, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
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32
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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Host Mitochondrial Association Evolved in the Human Parasite Toxoplasma gondii via Neofunctionalization of a Gene Duplicate. Genetics 2016; 203:283-98. [PMID: 26920761 PMCID: PMC4858780 DOI: 10.1534/genetics.115.186270] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/14/2016] [Indexed: 01/30/2023] Open
Abstract
In Toxoplasma gondii, an intracellular parasite of humans and other animals, host mitochondrial association (HMA) is driven by a gene family that encodes multiple mitochondrial association factor 1 (MAF1) proteins. However, the importance of MAF1 gene duplication in the evolution of HMA is not understood, nor is the impact of HMA on parasite biology. Here we used within- and between-species comparative analysis to determine that the MAF1 locus is duplicated in T. gondii and its nearest extant relative Hammondia hammondi, but not another close relative, Neospora caninum. Using cross-species complementation, we determined that the MAF1 locus harbors multiple distinct paralogs that differ in their ability to mediate HMA, and that only T. gondii and H. hammondi harbor HMA+ paralogs. Additionally, we found that exogenous expression of an HMA+ paralog in T. gondii strains that do not normally exhibit HMA provides a competitive advantage over their wild-type counterparts during a mouse infection. These data indicate that HMA likely evolved by neofunctionalization of a duplicate MAF1 copy in the common ancestor of T. gondii and H. hammondi, and that the neofunctionalized gene duplicate is selectively advantageous.
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34
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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] [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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Ogbunugafor CB, Hartl D. A pivot mutation impedes reverse evolution across an adaptive landscape for drug resistance in Plasmodium vivax. Malar J 2016; 15:40. [PMID: 26809718 PMCID: PMC4727274 DOI: 10.1186/s12936-016-1090-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 01/10/2016] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The study of reverse evolution from resistant to susceptible phenotypes can reveal constraints on biological evolution, a topic for which evolutionary theory has relatively few general principles. The public health catastrophe of antimicrobial resistance in malaria has brought these constraints on evolution into a practical realm, with one proposed solution: withdrawing anti-malarial medication use in high resistance settings, built on the assumption that reverse evolution occurs readily enough that populations of pathogens may revert to their susceptible states. While past studies have suggested limits to reverse evolution, there have been few attempts to properly dissect its mechanistic constraints. METHODS Growth rates were determined from empirical data on the growth and resistance from a set of combinatorially complete set of mutants of a resistance protein (dihydrofolate reductase) in Plasmodium vivax, to construct reverse evolution trajectories. The fitness effects of individual mutations were calculated as a function of drug environment, revealing the magnitude of epistatic interactions between mutations and genetic backgrounds. Evolution across the landscape was simulated in two settings: starting from the population fixed for the quadruple mutant, and from a polymorphic population evenly distributed between double mutants. RESULTS A single mutation of large effect (S117N) serves as a pivot point for evolution to high resistance regions of the landscape. Through epistatic interactions with other mutations, this pivot creates an epistatic ratchet against reverse evolution towards the wild type ancestor, even in environments where the wild type is the most fit of all genotypes. This pivot mutation underlies the directional bias in evolution across the landscape, where evolution towards the ancestor is precluded across all examined drug concentrations from various starting points in the landscape. CONCLUSIONS The presence of pivot mutations can dictate dynamics of evolution across adaptive landscape through epistatic interactions within a protein, leaving a population trapped on local fitness peaks in an adaptive landscape, unable to locate ancestral genotypes. This irreversibility suggests that the structure of an adaptive landscape for a resistance protein should be understood before considering resistance management strategies. This proposed mechanism for constraints on reverse evolution corroborates evidence from the field indicating that phenotypic reversal often occurs via compensatory mutation at sites independent of those associated with the forward evolution of resistance. Because of this, molecular methods that identify resistance patterns via single SNPs in resistance-associated markers might be missing signals for resistance and compensatory mutation throughout the genome. In these settings, whole genome sequencing efforts should be used to identify resistance patterns, and will likely reveal a more complicated genomic signature for resistance and susceptibility, especially in settings where anti-malarial medications have been used intermittently. Lastly, the findings suggest that, given their role in dictating the dynamics of evolution across the landscape, pivot mutations might serve as future targets for therapy.
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Affiliation(s)
- C Brandon Ogbunugafor
- Department of Biology, University of Vermont, Burlington, VT, USA.
- Vermont Complex Systems Center, The University of Vermont, Burlington, VT, USA.
| | - Daniel Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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36
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Cheeseman IH, Miller B, Tan JC, Tan A, Nair S, Nkhoma SC, De Donato M, Rodulfo H, Dondorp A, Branch OH, Mesia LR, Newton P, Mayxay M, Amambua-Ngwa A, Conway DJ, Nosten F, Ferdig MT, Anderson TJC. Population Structure Shapes Copy Number Variation in Malaria Parasites. Mol Biol Evol 2015; 33:603-20. [PMID: 26613787 PMCID: PMC4760083 DOI: 10.1093/molbev/msv282] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
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Affiliation(s)
- Ian H Cheeseman
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Becky Miller
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - John C Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Asako Tan
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
| | - Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Marcos De Donato
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Hectorina Rodulfo
- Lab. Genetica Molecular, IIBCAUDO, Universidad De Oriente, Cumana, Venezuela
| | - Arjen Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Oralee H Branch
- Division of Parasitology, Department of Microbiology, New York University School of Medicine
| | - Lastenia Ruiz Mesia
- Laboratorio De Investigaciones De Productos Naturales Y Antiparasitarios, Universidad Nacional De La Amazonia Peruana, Iquitos, Peru
| | - Paul Newton
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR
| | | | - David J Conway
- Medical Research Council Unit, Fajara, Banjul, The Gambia Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - François Nosten
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Churchill Hospital, University of Oxford, Oxford, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Michael T Ferdig
- The Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX
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Flannery EL, Wang T, Akbari A, Corey VC, Gunawan F, Bright AT, Abraham M, Sanchez JF, Santolalla ML, Baldeviano GC, Edgel KA, Rosales LA, Lescano AG, Bafna V, Vinetz JM, Winzeler EA. Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes. ACS Infect Dis 2015; 1:367-79. [PMID: 26719854 DOI: 10.1021/acsinfecdis.5b00049] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the mechanisms of drug resistance in Plasmodium vivax, the parasite that causes the most widespread form of human malaria, is complicated by the lack of a suitable long-term cell culture system for this parasite. In contrast to P. falciparum, which can be more readily manipulated in the laboratory, insights about parasite biology need to be inferred from human studies. Here we analyze the genomes of parasites within 10 human P. vivax infections from the Peruvian Amazon. Using next-generation sequencing we show that some P. vivax infections analyzed from the region are likely polyclonal. Despite their polyclonality we observe limited parasite genetic diversity by showing that three or fewer haplotypes comprise 94% of the examined genomes, suggesting the recent introduction of parasites into this geographic region. In contrast we find more than three haplotypes in putative drug-resistance genes, including the gene encoding dihydrofolate reductase-thymidylate synthase and the P. vivax multidrug resistance associated transporter, suggesting that resistance mutations have arisen independently. Additionally, several drug-resistance genes are located in genomic regions with evidence of increased copy number. Our data suggest that whole genome sequencing of malaria parasites from patients may provide more insight about the evolution of drug resistance than genetic linkage or association studies, especially in geographical regions with limited parasite genetic diversity.
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Affiliation(s)
| | | | | | | | | | | | | | - Juan F. Sanchez
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Meddly L. Santolalla
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - G. Christian Baldeviano
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Kimberly A. Edgel
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Luis A. Rosales
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
| | - Andrés G. Lescano
- U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Avenida Venezuela Cuadra 36 S/N, Centro Médico
Naval, Lima Callao 02, Peru
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38
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Ukaegbu UE, Zhang X, Heinberg AR, Wele M, Chen Q, Deitsch KW. A Unique Virulence Gene Occupies a Principal Position in Immune Evasion by the Malaria Parasite Plasmodium falciparum. PLoS Genet 2015; 11:e1005234. [PMID: 25993442 PMCID: PMC4437904 DOI: 10.1371/journal.pgen.1005234] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/21/2015] [Indexed: 12/13/2022] Open
Abstract
Mutually exclusive gene expression, whereby only one member of a multi-gene family is selected for activation, is used by the malaria parasite Plasmodium falciparum to escape the human immune system and perpetuate long-term, chronic infections. A family of genes called var encodes the chief antigenic and virulence determinant of P. falciparum malaria. var genes are transcribed in a mutually exclusive manner, with switching between active genes resulting in antigenic variation. While recent work has shed considerable light on the epigenetic basis for var gene activation and silencing, how switching is controlled remains a mystery. In particular, switching seems not to be random, but instead appears to be coordinated to result in timely activation of individual genes leading to sequential waves of antigenically distinct parasite populations. The molecular basis for this apparent coordination is unknown. Here we show that var2csa, an unusual and highly conserved var gene, occupies a unique position within the var gene switching hierarchy. Induction of switching through the destabilization of var specific chromatin using both genetic and chemical methods repeatedly led to the rapid and exclusive activation of var2csa. Additional experiments demonstrated that these represent "true" switching events and not simply de-silencing of the var2csa promoter, and that activation is limited to the unique locus on chromosome 12. Combined with translational repression of var2csa transcripts, frequent "default" switching to this locus and detection of var2csa untranslated transcripts in non-pregnant individuals, these data suggest that var2csa could play a central role in coordinating switching, fulfilling a prediction made by mathematical models derived from population switching patterns. These studies provide the first insights into the mechanisms by which var gene switching is coordinated as well as an example of how a pharmacological agent can disrupt antigenic variation in Plasmodium falciparum.
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Affiliation(s)
- Uchechi E. Ukaegbu
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Xu Zhang
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- Key Laboratory of Zoonosis, College of Veterinary Medicine, Jilin University, Xi An Da Lu, Changchun, China
| | - Adina R. Heinberg
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Mamadou Wele
- University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Qijun Chen
- Key Laboratory of Zoonosis, College of Veterinary Medicine, Jilin University, Xi An Da Lu, Changchun, China
| | - Kirk W. Deitsch
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
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DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum. Microbiol Mol Biol Rev 2015; 78:469-86. [PMID: 25184562 DOI: 10.1128/mmbr.00059-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Research into the complex genetic underpinnings of the malaria parasite Plasmodium falciparum is entering a new era with the arrival of site-specific genome engineering. Previously restricted only to model systems but now expanded to most laboratory organisms, and even to humans for experimental gene therapy studies, this technology allows researchers to rapidly generate previously unattainable genetic modifications. This technological advance is dependent on DNA double-strand break repair (DSBR), specifically homologous recombination in the case of Plasmodium. Our understanding of DSBR in malaria parasites, however, is based largely on assumptions and knowledge taken from other model systems, which do not always hold true in Plasmodium. Here we describe the causes of double-strand breaks, the mechanisms of DSBR, and the differences between model systems and P. falciparum. These mechanisms drive basic parasite functions, such as meiosis, antigen diversification, and copy number variation, and allow the parasite to continually evolve in the contexts of host immune pressure and drug selection. Finally, we discuss the new technologies that leverage DSBR mechanisms to accelerate genetic investigations into this global infectious pathogen.
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40
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Heinberg A, Kirkman L. The molecular basis of antifolate resistance in Plasmodium falciparum: looking beyond point mutations. Ann N Y Acad Sci 2015; 1342:10-8. [PMID: 25694157 DOI: 10.1111/nyas.12662] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drugs that target the folate-synthesis pathway have a long history of effectiveness against a variety of pathogens. As antimalarials, the antifolates were safe and well tolerated, but resistance emerged quickly and has persisted even with decreased drug pressure. The primary determinants of resistance in Plasmodium falciparum are well-described point mutations in the enzymes dihydropteroate synthase and dihydrofolate reductase targeted by the combination sulfadoxine-pyrimethamine. Recent work has highlighted the contributions of additional parasite adaptation to antifolate resistance. In fact, the evolution of antifolate-resistant parasites is multifaceted and complex. Gene amplification of the first enzyme in the parasite folate synthesis pathway, GTP-cyclohydrolase, is strongly associated with resistant parasites and potentially contributes to persistence of resistant parasites. Further understanding of how parasites adjust flux through the folate pathway is important to the further development of alternative agents targeting this crucial synthesis pathway.
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41
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Cook DE, Bayless AM, Wang K, Guo X, Song Q, Jiang J, Bent AF. Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode. PLANT PHYSIOLOGY 2014; 165:630-647. [PMID: 24733883 PMCID: PMC4044848 DOI: 10.1104/pp.114.235952] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/19/2014] [Indexed: 05/18/2023]
Abstract
Copy number variation of kilobase-scale genomic DNA segments, beyond presence/absence polymorphisms, can be an important driver of adaptive traits. Resistance to Heterodera glycines (Rhg1) is a widely utilized quantitative trait locus that makes the strongest known contribution to resistance against soybean cyst nematode (SCN), Heterodera glycines, the most damaging pathogen of soybean (Glycine max). Rhg1 was recently discovered to be a complex locus at which resistance-conferring haplotypes carry up to 10 tandem repeat copies of a 31-kb DNA segment, and three disparate genes present on each repeat contribute to SCN resistance. Here, we use whole-genome sequencing, fiber-FISH (fluorescence in situ hybridization), and other methods to discover the genetic variation at Rhg1 across 41 diverse soybean accessions. Based on copy number variation, transcript abundance, nucleic acid polymorphisms, and differentially methylated DNA regions, we find that SCN resistance is associated with multicopy Rhg1 haplotypes that form two distinct groups. The tested high-copy-number Rhg1 accessions, including plant introduction (PI) 88788, contain a flexible number of copies (seven to 10) of the 31-kb Rhg1 repeat. The identified low-copy-number Rhg1 group, including PI 548402 (Peking) and PI 437654, contains three copies of the Rhg1 repeat and a newly identified allele of Glyma18g02590 (a predicted α-SNAP [α-soluble N-ethylmaleimide-sensitive factor attachment protein]). There is strong evidence for a shared origin of the two resistance-conferring multicopy Rhg1 groups and subsequent independent evolution. Differentially methylated DNA regions also were identified within Rhg1 that correlate with SCN resistance. These data provide insights into copy number variation of multigene segments, using as the example a disease resistance trait of high economic importance.
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Affiliation(s)
- David E Cook
- Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)
| | - Adam M Bayless
- Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)
| | - Kai Wang
- Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)
| | - Xiaoli Guo
- Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)
| | - Qijian Song
- Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)
| | - Jiming Jiang
- Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)
| | - Andrew F Bent
- Department of Plant Pathology (D.E.C., A.M.B., X.G., A.F.B.) and Department of Horticulture (K.W., J.J.), University of Wisconsin, Madison, Wisconsin 53706; andSoybean Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland 20705 (Q.S.)
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Biochemical and functional characterization of Plasmodium falciparum GTP cyclohydrolase I. Malar J 2014; 13:150. [PMID: 24745605 PMCID: PMC4005822 DOI: 10.1186/1475-2875-13-150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/17/2013] [Indexed: 12/12/2022] Open
Abstract
Background Antifolates are currently in clinical use for malaria preventive therapy and treatment. The drugs kill the parasites by targeting the enzymes in the de novo folate pathway. The use of antifolates has now been limited by the spread of drug-resistant mutations. GTP cyclohydrolase I (GCH1) is the first and the rate-limiting enzyme in the folate pathway. The amplification of the gch1 gene found in certain Plasmodium falciparum isolates can cause antifolate resistance and influence the course of antifolate resistance evolution. These findings showed the importance of P. falciparum GCH1 in drug resistance intervention. However, little is known about P. falciparum GCH1 in terms of kinetic parameters and functional assays, precluding the opportunity to obtain the key information on its catalytic reaction and to eventually develop this enzyme as a drug target. Methods Plasmodium falciparum GCH1 was cloned and expressed in bacteria. Enzymatic activity was determined by the measurement of fluorescent converted neopterin with assay validation by using mutant and GTP analogue. The genetic complementation study was performed in ∆folE bacteria to functionally identify the residues and domains of P. falciparum GCH1 required for its enzymatic activity. Plasmodial GCH1 sequences were aligned and structurally modeled to reveal conserved catalytic residues. Results Kinetic parameters and optimal conditions for enzymatic reactions were determined by the fluorescence-based assay. The inhibitor test against P. falciparum GCH1 is now possible as indicated by the inhibitory effect by 8-oxo-GTP. Genetic complementation was proven to be a convenient method to study the function of P. falciparum GCH1. A series of domain truncations revealed that the conserved core domain of GCH1 is responsible for its enzymatic activity. Homology modelling fits P. falciparum GCH1 into the classic Tunnelling-fold structure with well-conserved catalytic residues at the active site. Conclusions Functional assays for P. falciparum GCH1 based on enzymatic activity and genetic complementation were successfully developed. The assays in combination with a homology model characterized the enzymatic activity of P. falciparum GCH1 and the importance of its key amino acid residues. The potential to use the assay for inhibitor screening was validated by 8-oxo-GTP, a known GTP analogue inhibitor.
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43
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Kümpornsin K, Modchang C, Heinberg A, Ekland EH, Jirawatcharadech P, Chobson P, Suwanakitti N, Chaotheing S, Wilairat P, Deitsch KW, Kamchonwongpaisan S, Fidock DA, Kirkman LA, Yuthavong Y, Chookajorn T. Origin of robustness in generating drug-resistant malaria parasites. Mol Biol Evol 2014; 31:1649-60. [PMID: 24739308 DOI: 10.1093/molbev/msu140] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Biological robustness allows mutations to accumulate while maintaining functional phenotypes. Despite its crucial role in evolutionary processes, the mechanistic details of how robustness originates remain elusive. Using an evolutionary trajectory analysis approach, we demonstrate how robustness evolved in malaria parasites under selective pressure from an antimalarial drug inhibiting the folate synthesis pathway. A series of four nonsynonymous amino acid substitutions at the targeted enzyme, dihydrofolate reductase (DHFR), render the parasites highly resistant to the antifolate drug pyrimethamine. Nevertheless, the stepwise gain of these four dhfr mutations results in tradeoffs between pyrimethamine resistance and parasite fitness. Here, we report the epistatic interaction between dhfr mutations and amplification of the gene encoding the first upstream enzyme in the folate pathway, GTP cyclohydrolase I (GCH1). gch1 amplification confers low level pyrimethamine resistance and would thus be selected for by pyrimethamine treatment. Interestingly, the gch1 amplification can then be co-opted by the parasites because it reduces the cost of acquiring drug-resistant dhfr mutations downstream in the same metabolic pathway. The compensation of compromised fitness by extra GCH1 is an example of how robustness can evolve in a system and thus expand the accessibility of evolutionary trajectories leading toward highly resistant alleles. The evolution of robustness during the gain of drug-resistant mutations has broad implications for both the development of new drugs and molecular surveillance for resistance to existing drugs.
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Affiliation(s)
- Krittikorn Kümpornsin
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Charin Modchang
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, ThailandBiophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Adina Heinberg
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY
| | - Eric H Ekland
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY
| | | | - Pornpimol Chobson
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Nattida Suwanakitti
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sastra Chaotheing
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Prapon Wilairat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kirk W Deitsch
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY
| | - Sumalee Kamchonwongpaisan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NYDivision of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY
| | - Laura A Kirkman
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NYDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thanat Chookajorn
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, ThailandCenter of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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44
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Rosenthal PJ. The interplay between drug resistance and fitness in malaria parasites. Mol Microbiol 2013; 89:1025-38. [PMID: 23899091 DOI: 10.1111/mmi.12349] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2013] [Indexed: 12/01/2022]
Abstract
Controlling the spread of antimalarial drug resistance, especially resistance of Plasmodium falciparum to artemisinin-based combination therapies, is a high priority. Available data indicate that, as with other microorganisms, the spread of drug-resistant malaria parasites is limited by fitness costs that frequently accompany resistance. Resistance-mediating polymorphisms in malaria parasites have been identified in putative drug transporters and in target enzymes. The impacts of these polymorphisms on parasite fitness have been characterized in vitro and in animal models. Additional insights have come from analyses of samples from clinical studies, both evaluating parasites under different selective pressures and determining the clinical consequences of infection with different parasites. With some exceptions, resistance-mediating polymorphisms lead to malaria parasites that, compared with wild type, grow less well in culture and in animals, and are replaced by wild type when drug pressure diminishes in the clinical setting. In some cases, the fitness costs of resistance may be offset by compensatory mutations that increase virulence or changes that enhance malaria transmission. However, not enough is known about effects of resistance mediators on parasite fitness. A better appreciation of the costs of fitness-mediating mutations will facilitate the development of optimal guidelines for the treatment and prevention of malaria.
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Affiliation(s)
- Philip J Rosenthal
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
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45
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Mita T, Ohashi J, Venkatesan M, Marma ASP, Nakamura M, Plowe CV, Tanabe K. Ordered accumulation of mutations conferring resistance to sulfadoxine-pyrimethamine in the Plasmodium falciparum parasite. J Infect Dis 2013; 209:130-9. [PMID: 23922363 DOI: 10.1093/infdis/jit415] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Monitoring the prevalence of drug resistant Plasmodium falciparum is essential for effective malaria control. Resistance to pyrimethamine and sulfadoxine increases as mutations accumulate in the parasite genes encoding dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps), respectively. Although parasites are exposed to these antifolate drugs simultaneously, it remains virtually unknown whether dhfr and dhps mutations accumulate along interrelated paths. METHODS We investigated the order of step-wise accumulation in dhfr and dhps by cumulative analyses using binomial tests in 575 P. falciparum isolates obtained from 7 countries in Asia and Melanesia. RESULTS An initial step in the accumulation of mutations preferentially occurred in dhfr (2 mutations), followed by 1 mutation in dhps. In a subsequent step, mutations were estimated separately for 5 dhfr/dhps-resistant lineages identified using 12 microsatellites flanking dhfr and dhps. Among these lineages, we found 3 major mutational paths, each of which follows a unique stepwise trajectory to produce the most highly resistant form with 4 mutations in dhfr and 3 in dhps. CONCLUSIONS The ordered accumulation of mutations in dhfr and dhps elucidated here will assist in predicting the status and progression of antifolate resistance in malaria-endemic regions where antifolate drugs are used for intermittent preventive treatment.
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Affiliation(s)
- Toshihiro Mita
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Tokyo, Japan
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46
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Salcedo-Sora JE, Ward SA. The folate metabolic network of Falciparum malaria. Mol Biochem Parasitol 2013; 188:51-62. [PMID: 23454873 DOI: 10.1016/j.molbiopara.2013.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 02/04/2013] [Accepted: 02/11/2013] [Indexed: 01/07/2023]
Abstract
The targeting of key enzymes in the folate pathway continues to be an effective chemotherapeutic approach that has earned antifolate drugs a valuable position in the medical pharmacopoeia. The successful therapeutic use of antifolates as antimalarials has been a catalyst for ongoing research into the biochemistry of folate and pterin biosynthesis in malaria parasites. However, our understanding of the parasites folate metabolism remains partial and patchy, especially in relation to the shikimate pathway, the folate cycle, and folate salvage. A sizeable number of potential folate targets remain to be characterised. Recent reports on the parasite specific transport of folate precursors that would normally be present in the human host awaken previous hypotheses on the salvage of folate precursors or by-products. As the parasite progresses through its life-cycle it encounters very contrasting host cell environments that present radically different metabolic milieus and biochemical challenges. It would seem probable that as the parasite encounters differing environments it would need to modify its biochemistry. This would be reflected in the folate homeostasis in Plasmodium. Recent drug screening efforts and insights into folate membrane transport substantiate the argument that folate metabolism may still offer unexplored opportunities for therapeutic attack.
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Affiliation(s)
- J Enrique Salcedo-Sora
- Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
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