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Lee J, Kim TI, Lê HG, Yoo WG, Kang JM, Ahn SK, Myint MK, Lin K, Kim TS, Na BK. Genetic diversity of Plasmodium vivax and Plasmodium falciparum lactate dehydrogenases in Myanmar isolates. Malar J 2020; 19:60. [PMID: 32019541 PMCID: PMC7001217 DOI: 10.1186/s12936-020-3134-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/22/2020] [Indexed: 12/25/2022] Open
Abstract
Background Plasmodium lactate dehydrogenase (pLDH) is a major target in diagnosing the erythrocytic stage of malaria parasites because it is highly expressed during blood-stage parasites and is distinguished from human LDH. Rapid diagnostic tests (RDTs) for malaria use pLDH as a target antigen; however, genetic variations in pLDH within the natural population threaten the efficacy of pLDH-based RDTs. Methods Genetic polymorphisms of Plasmodium vivax LDH (PvLDH) and Plasmodium falciparum LDH (PfLDH) in Myanmar isolates were analysed by nucleotide sequencing analysis. Genetic polymorphisms and the natural selection of PvLDH and PfLDH were analysed using DNASTAR, MEGA6, and DnaSP ver. 5.10.00 programs. The genetic diversity and natural selection of global PvLDH and PfLDH were also analysed. The haplotype network of global PvLDH and PfLDH was constructed using NETWORK ver. 5.0.0.3. Three-dimensional structures of PvLDH and PfLDH were built with YASARA Structure ver. 18.4.24 and the impact of mutations on structural change and stability was evaluated with SDM ver. 2, CUPSAT and MAESTROweb. Results Forty-nine PvLDH and 52 PfLDH sequences were obtained from Myanmar P. vivax and P. falciparum isolates. Non-synonymous nucleotide substitutions resulting in amino acid changes were identified in both Myanmar PvLDH and PfLDH. Amino acid changes were also identified in the global PvLDH and PfLDH populations, but they did not produce structural alterations in either protein. Low genetic diversity was observed in global PvLDH and PfLDH, which may be maintained by a strong purifying selection. Conclusion This study extends knowledge for genetic diversity and natural selection of global PvLDH and PfLDH. Although amino acid changes were observed in global PvLDH and PfLDH, they did not alter the conformational structures of the proteins. These suggest that PvLDH and PfLDH are genetically well-conserved in global populations, which indicates that they are suitable antigens for diagnostic purpose and attractive targets for drug development.
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Affiliation(s)
- Jinyoung Lee
- Department of Tropical Medicine and Inha Research Institute for Medical Science, Inha University School of Medicine, Incheon, Republic of Korea
| | - Tae Im Kim
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,Planning and Management Division, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea
| | - Hương Giang Lê
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Won Gi Yoo
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, 06974, Republic of Korea
| | - Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Seong-Kyu Ahn
- Department of Tropical Medicine and Inha Research Institute for Medical Science, Inha University School of Medicine, Incheon, Republic of Korea
| | - Moe Kyaw Myint
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin, Myanmar
| | - Khin Lin
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin, Myanmar
| | - Tong-Soo Kim
- Department of Tropical Medicine and Inha Research Institute for Medical Science, Inha University School of Medicine, Incheon, Republic of Korea.
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea. .,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
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Ahmad A, Verma AK, Krishna S, Sharma A, Singh N, Bharti PK. Plasmodium falciparum glutamate dehydrogenase is genetically conserved across eight malaria endemic states of India: Exploring new avenues of malaria elimination. PLoS One 2019; 14:e0218210. [PMID: 31199842 PMCID: PMC6568416 DOI: 10.1371/journal.pone.0218210] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/28/2019] [Indexed: 02/04/2023] Open
Abstract
Accurate and timely diagnosis is very critical for management, control and elimination of the malaria. Malaria rapid diagnostic tests (RDTs) have improved the diagnosis and management of malaria in remote areas, community and places where microscopy is not available for diagnosis. According to WHO report 2018, Plasmodium falciparum malaria constitutes more than 50% of malaria cases in India. Most of the RDTs used for diagnosis of falciparum malaria today employ HRP2 as a target antigen. However, low density parasitemia and deletion of hrp-2 gene in P. falciparum leads to false negative results and necessitates the development of alternative/ new or improved RDT for malaria diagnosis. We have analysed the genetic diversity and homology modelling of Pfgdh (glutamate dehydrogenase), ldh (lactate dehydrogenase) and aldolase genes in P. falciparum isolates from the eight endemic states of India to assess their potential as antigen for RDT development. We observed negligible sequence diversity in Pfgdh in comparison to the low level of diversity in ldh and aldolase gene. No structural or functional changes were observed in modelling studies and all three genes were under negative purifying selection pressure. The highly conserved nature of pfgdh gene suggests that GDH could be a potential target molecule for Pan/Pf diagnostic test for malaria.
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Affiliation(s)
- Amreen Ahmad
- ICMR-National Institute of Research in Tribal Health (NIRTH), Garha, Jabalpur, India
| | - Anil Kumar Verma
- ICMR-National Institute of Research in Tribal Health (NIRTH), Garha, Jabalpur, India
| | - Sri Krishna
- ICMR-National Institute of Research in Tribal Health (NIRTH), Garha, Jabalpur, India
| | - Anjana Sharma
- Department of P. G. Studies and Research in Biological Science, Rani Durgavati University, Pachpedi, Jabalpur, Madhya Pradesh, India
| | - Neeru Singh
- ICMR-National Institute of Research in Tribal Health (NIRTH), Garha, Jabalpur, India
| | - Praveen Kumar Bharti
- ICMR-National Institute of Research in Tribal Health (NIRTH), Garha, Jabalpur, India
- * E-mail:
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Simpalipan P, Pattaradilokrat S, Harnyuttanakorn P. Global sequence diversity of the lactate dehydrogenase gene in Plasmodium falciparum. Malar J 2018; 17:16. [PMID: 29316927 PMCID: PMC5761093 DOI: 10.1186/s12936-017-2157-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Antigen-detecting rapid diagnostic tests (RDTs) have been recommended by the World Health Organization for use in remote areas to improve malaria case management. Lactate dehydrogenase (LDH) of Plasmodium falciparum is one of the main parasite antigens employed by various commercial RDTs. It has been hypothesized that the poor detection of LDH-based RDTs is attributed in part to the sequence diversity of the gene. To test this, the present study aimed to investigate the genetic diversity of the P. falciparum ldh gene in Thailand and to construct the map of LDH sequence diversity in P. falciparum populations worldwide. METHODS The ldh gene was sequenced for 50 P. falciparum isolates in Thailand and compared with hundreds of sequences from P. falciparum populations worldwide. Several indices of molecular variation were calculated, including the proportion of polymorphic sites, the average nucleotide diversity index (π), and the haplotype diversity index (H). Tests of positive selection and neutrality tests were performed to determine signatures of natural selection on the gene. Mean genetic distance within and between species of Plasmodium ldh was analysed to infer evolutionary relationships. RESULTS Nucleotide sequences of P. falciparum ldh could be classified into 9 alleles, encoding 5 isoforms of LDH. L1a was the most common allelic type and was distributed in P. falciparum populations worldwide. Plasmodium falciparum ldh sequences were highly conserved, with haplotype and nucleotide diversity values of 0.203 and 0.0004, respectively. The extremely low genetic diversity was maintained by purifying selection, likely due to functional constraints. Phylogenetic analysis inferred the close genetic relationship of P. falciparum to malaria parasites of great apes, rather than to other human malaria parasites. CONCLUSIONS This study revealed the global genetic variation of the ldh gene in P. falciparum, providing knowledge for improving detection of LDH-based RDTs and supporting the candidacy of LDH as a therapeutic drug target.
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Affiliation(s)
- Phumin Simpalipan
- Zoology Ph.D. Programme, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Sittiporn Pattaradilokrat
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
- Veterinary Parasitology Research Group, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330 Thailand
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Wen YZ, Lun ZR, Zhu XQ, Hide G, Lai DH. Further evidence from SSCP and ITS DNA sequencing support Trypanosoma evansi and Trypanosoma equiperdum as subspecies or even strains of Trypanosoma brucei. INFECTION GENETICS AND EVOLUTION 2016; 41:56-62. [PMID: 27016375 DOI: 10.1016/j.meegid.2016.03.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 10/22/2022]
Abstract
The subgenus Trypanozoon includes three species Trypanosoma brucei, Trypanosoma evansi and Trypanosoma equiperdum, which are morphologically identical and indistinguishable even using some molecular methods. In this study, PCR-based single strand conformation polymorphism (PCR-SSCP) was used to analyze the ribosomal DNA of the Trypanozoon species. Data indicate different patterns of ITS2 fragments between T. brucei, T. evansi and T. equiperdum by SSCP. Furthermore, analysis of total ITS sequences within these three members of the subgenus Trypanozoon showed a high degree of homology using phylogenetic analysis but were polyphyletic in haplotype networks. These data provide novel nuclear evidence to further support the notion that T. evansi and T. equiperdum should be subspecies or even strains of T. brucei.
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Affiliation(s)
- Yan-Zi Wen
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zhao-Rong Lun
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China; State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China; Ecosystems & Environment Centre, School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK; Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Geoff Hide
- Ecosystems & Environment Centre, School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK; Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, Salford M5 4WT, UK
| | - De-Hua Lai
- Center for Parasitic Organisms, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
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