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Ding H, Dong Y, Deng Y, Xu Y, Liu Y, Wu J, Chen M, Zhang C, Liu L, Lin Y. Molecular surveillance of chloroquine resistance in Plasmodium vivax isolates from malaria cases in Yunnan Province of China using pvcrt-o gene polymorphisms. Malar J 2023; 22:338. [PMID: 37940956 PMCID: PMC10631137 DOI: 10.1186/s12936-023-04776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The efficacy of chloroquine treatment for vivax malaria has been rarely evaluated due to a lack of an appropriate testing method. The objective of this study was to conduct molecular monitoring of chloroquine resistance in Plasmodium vivax strains from vivax malaria patients in Yunnan Province, focusing on the analysis of polymorphism in the P. vivax chloroquine resistance transporter protein orthologous gene (pvcrt-o). METHODS In accordance with the principles of a cohort study, blood samples were collected from malaria cases diagnosed with a P. vivax mono-infection in Yunnan Province from 2020 to 2022. Segmental PCR was used to amplify the whole pvcrt-o gene in the blood samples and their products were subsequently sequenced. The sequencing data were arranged to obtain the full coding DNA sequence (CDS) as well as the gene's promoter region sequences. The CDSs were aligned with the reference sequence (XM_001613407.1) of the P. vivax SalI isolate to identify the mutant loci. RESULTS From a total of 375 blood samples taken from vivax malaria cases, 272 both whole gene CDSs (1272-1275 bp) and promoter DNA sequences (707 bp) of pvcrt-o gene were obtained. Among the whole CDSs, there were 7 single nucleotide polymorphic sites in which c.7 A>G was the minor allele frequency (MAF) site with 4.4% (12/272) detection rate. The mutation detection rate showed a significant decrease from 9.8% (10/102) in 2020 to 1.1% (1/92) in 2021 and 1.3% (1/78) in 2022, indicating statistical significance (χ2 = 11.256, P < 0.05). Among the identified 12 haplotypes, the majority of which were wild type (75.7%; 206/272). These four mutant haplotypes (Hap_3, Hap_5, Hap_9, and Hap_10) were classified as "K10 insertion type" and accounted for 12.1% (33/272). The detection rate of Hap_3 increased from 1.0% (1/102) in 2020 to 13.0% (12/92) in 2021 and 14.1% (11/78) in 2022, indicating statistical significance. A total of 23.8% (65/272) of the samples exhibited 14 bp (bp) deletions in the promoter region, occurring most frequently in the wild type haplotype (Hap_1) samples at a rate of 28.6% (59/206). CONCLUSIONS In recent years in Yunnan Province, a notable proportion of vivax malaria patients are infected by P. vivax strains with a "K10 insertion" and partial sequence deletions in the promoter region of the pvcrt-o gene, necessitating vigilance.
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Affiliation(s)
- Hongyun Ding
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Ying Dong
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China.
| | - Yan Deng
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Yanchun Xu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Yan Liu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Jing Wu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Mengni Chen
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Canglin Zhang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Yunnan International Joint Laboratory of Tropical Infectious Diseases, Yunnan Institute of Parasitic Diseases Control, Pu'er, 665000, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yingkun Lin
- Center for Disease Control and Prevention, Dehong, 678499, China.
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Abstract
In eukaryotic organisms, noncoding RNAs (ncRNAs) have been implicated as important regulators of multifaceted biological processes, including transcriptional, posttranscriptional, and epigenetic regulation of gene expression. In recent years, it is becoming clear that protozoan parasites encode diverse ncRNA transcripts; however, little is known about their cellular functions. Recent advances in high-throughput “omic” studies identified many novel long ncRNAs (lncRNAs) in apicomplexan parasites, some of which undergo splicing, polyadenylation, and encode small proteins. To date, only a few of them are characterized, leaving a big gap in our understanding regarding their origin, mode of action, and functions in parasite biology. In this review, we focus on lncRNAs of the human malaria parasite Plasmodium falciparum and highlight their cellular functions and possible mechanisms of action.
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Affiliation(s)
- Karina Simantov
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Manish Goyal
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ron Dzikowski
- Department of Microbiology & Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
- * E-mail:
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Akoniyon OP, Adewumi TS, Maharaj L, Oyegoke OO, Roux A, Adeleke MA, Maharaj R, Okpeku M. Whole Genome Sequencing Contributions and Challenges in Disease Reduction Focused on Malaria. BIOLOGY 2022; 11:587. [PMID: 35453786 PMCID: PMC9027812 DOI: 10.3390/biology11040587] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/11/2022]
Abstract
Malaria elimination remains an important goal that requires the adoption of sophisticated science and management strategies in the era of the COVID-19 pandemic. The advent of next generation sequencing (NGS) is making whole genome sequencing (WGS) a standard today in the field of life sciences, as PCR genotyping and targeted sequencing provide insufficient information compared to the whole genome. Thus, adapting WGS approaches to malaria parasites is pertinent to studying the epidemiology of the disease, as different regions are at different phases in their malaria elimination agenda. Therefore, this review highlights the applications of WGS in disease management, challenges of WGS in controlling malaria parasites, and in furtherance, provides the roles of WGS in pursuit of malaria reduction and elimination. WGS has invaluable impacts in malaria research and has helped countries to reach elimination phase rapidly by providing required information needed to thwart transmission, pathology, and drug resistance. However, to eliminate malaria in sub-Saharan Africa (SSA), with high malaria transmission, we recommend that WGS machines should be readily available and affordable in the region.
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Affiliation(s)
- Olusegun Philip Akoniyon
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Taiye Samson Adewumi
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Leah Maharaj
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Olukunle Olugbenle Oyegoke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Alexandra Roux
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Matthew A. Adeleke
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
| | - Rajendra Maharaj
- Office of Malaria Research, South African Medical Research Council, Cape Town 7505, South Africa;
| | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4041, South Africa; (O.P.A.); (T.S.A.); (L.M.); (O.O.O.); (A.R.); (M.A.A.)
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Na BK, Kim TS, Lin K, Baek MC, Chung DI, Hong Y, Goo YK. Genetic polymorphism of vir genes of Plasmodium vivax in Myanmar. Parasitol Int 2020; 80:102233. [PMID: 33144194 DOI: 10.1016/j.parint.2020.102233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 09/10/2020] [Accepted: 09/25/2020] [Indexed: 02/03/2023]
Abstract
The Plasmodium vivax variant proteins encoded by vir genes are highly polymorphic antigens and are considered as one of key proteins of P. vivax for host immune evasion via antigenic variations. Because genetic diversity of these antigens is a critical hurdle in the development of an effective vaccine, understanding the genetic nature of the vir genes in natural population is important. In this study, we selected four vir genes (vir 4, vir 12, vir 21, and vir 27) previously used for genetic analysis in several studies and evaluated the genetic polymorphisms and phylogenetic relationship of these 4 vir genes in Myanmar P. vivax population. Taken all genetic diversity values, the vir 12 (S = 168, H = 17, Hd = 0.854, Tajima's D value = 2.91524) was the most genetically diverse gene and the vir 4 (S = 9, H = 4, Hd = 0.744, Tajima's D value = -0.49151) was the most conserved gene. All phylogenetic trees showed two clades, and vir 4 and 12 haplotypes from Myanmar were clustered in a distinct clade with those from India and Republic of Korea. These results confirmed the pattern of high genetic polymorphism of vir genes and provided information on vir gene for further functional research and studies focused toward the practical use of vir genes.
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Affiliation(s)
- Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727, Republic of Korea
| | - Tong-Soo Kim
- Department of Tropical Medicine, Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon 22212, Republic of Korea
| | - Khin Lin
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin, Myanmar
| | - Moon-Chang Baek
- Department of Molecular Medicine, CMRI, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Dong-Il Chung
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Yeonchul Hong
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Youn-Kyoung Goo
- Department of Parasitology and Tropical Medicine, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea.
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Benelli G, Maggi F, Pavela R, Murugan K, Govindarajan M, Vaseeharan B, Petrelli R, Cappellacci L, Kumar S, Hofer A, Youssefi MR, Alarfaj AA, Hwang JS, Higuchi A. Mosquito control with green nanopesticides: towards the One Health approach? A review of non-target effects. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:10184-10206. [PMID: 28755145 DOI: 10.1007/s11356-017-9752-4] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 07/10/2017] [Indexed: 05/27/2023]
Abstract
The rapid spread of highly aggressive arboviruses, parasites, and bacteria along with the development of resistance in the pathogens and parasites, as well as in their arthropod vectors, represents a huge challenge in modern parasitology and tropical medicine. Eco-friendly vector control programs are crucial to fight, besides malaria, the spread of dengue, West Nile, chikungunya, and Zika virus, as well as other arboviruses such as St. Louis encephalitis and Japanese encephalitis. However, research efforts on the control of mosquito vectors are experiencing a serious lack of eco-friendly and highly effective pesticides, as well as the limited success of most biocontrol tools currently applied. Most importantly, a cooperative interface between the two disciplines is still lacking. To face this challenge, we have reviewed a wide number of promising results in the field of green-fabricated pesticides tested against mosquito vectors, outlining several examples of synergy with classic biological control tools. The non-target effects of green-fabricated nanopesticides, including acute toxicity, genotoxicity, and impact on behavioral traits of mosquito predators, have been critically discussed. In the final section, we have identified several key challenges at the interface between "green" nanotechnology and classic biological control, which deserve further research attention.
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Affiliation(s)
- Giovanni Benelli
- Department of Agriculture, Food and Environment, University of Pisa, via del Borghetto 80, 56124, Pisa, Italy.
| | - Filippo Maggi
- School of Pharmacy, University of Camerino, Via Sant'Agostino 1, 62032, Camerino, Italy
| | - Roman Pavela
- Crop Research Institute, Drnovska 507, 16106, Prague 6, Czech Republic
| | - Kadarkarai Murugan
- Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632 115, India
| | - Marimuthu Govindarajan
- Unit of Vector Control, Phytochemistry and Nanotechnology, Department of Zoology, Annamalai University, Annamalainagar, Tamil Nadu, 608 002, India
| | - Baskaralingam Vaseeharan
- Nanobiosciences and Nanopharmacology Division, Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi, Tamil Nadu, 630004, India
| | - Riccardo Petrelli
- School of Pharmacy, University of Camerino, Via Sant'Agostino 1, 62032, Camerino, Italy
| | - Loredana Cappellacci
- School of Pharmacy, University of Camerino, Via Sant'Agostino 1, 62032, Camerino, Italy
| | - Suresh Kumar
- Department of Medical Microbiology and Parasitology, 43400, Serdang, Malaysia
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Mohammad Reza Youssefi
- Department of Veterinary Parasitology, Babol-Branch, Islamic Azad University, Babol, Iran
| | - Abdullah A Alarfaj
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Jiang-Shiou Hwang
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Akon Higuchi
- Department of Chemical and Materials Engineering, National Central University, Taoyuan, 32001, Taiwan
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Bourgard C, Albrecht L, Kayano ACAV, Sunnerhagen P, Costa FTM. Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics. Front Cell Infect Microbiol 2018; 8:34. [PMID: 29473024 PMCID: PMC5809496 DOI: 10.3389/fcimb.2018.00034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022] Open
Abstract
During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp. biology and host-parasite interactions. Among the several parasite species that cause human malaria, the neglected Plasmodium vivax presents great research challenges, as in vitro culturing is not yet feasible and functional assays are heavily limited. Therefore, there are gaps in our P. vivax biology knowledge that affect decisions for control policies aiming to eradicate vivax malaria in the near future. In this review, we provide a snapshot of key discoveries already achieved in P. vivax sequencing projects, focusing on developments, hurdles, and limitations currently faced by the research community, as well as perspectives on future vivax malaria research.
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Affiliation(s)
- Catarina Bourgard
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Letusa Albrecht
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil.,Laboratory of Regulation of Gene Expression, Instituto Carlos Chagas, Curitiba, Brazil
| | - Ana C A V Kayano
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
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Yeoh LM, Goodman CD, Mollard V, McFadden GI, Ralph SA. Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates. BMC Genomics 2017; 18:734. [PMID: 28923023 PMCID: PMC5604118 DOI: 10.1186/s12864-017-4100-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/31/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The clinical symptoms of malaria are caused by the asexual replication of Plasmodium parasites in the blood of the vertebrate host. To spread to new hosts, however, the malaria parasite must differentiate into sexual forms, termed gametocytes, which are ingested by a mosquito vector. Sexual differentiation produces either female or male gametocytes, and involves significant morphological and biochemical changes. These transformations prepare gametocytes for the rapid progression to gamete formation and fertilisation, which occur within 20 min of ingestion. Here we present the transcriptomes of asexual, female, and male gametocytes in P. berghei, and a comprehensive statistically-based differential-expression analysis of the transcriptional changes that underpin this sexual differentiation. RESULTS RNA-seq analysis revealed numerous differences in the transcriptomes of female and male gametocytes compared to asexual stages. Overall, there is net downregulation of transcripts in gametocytes compared to asexual stages, with this trend more marked in female gametocytes. Our analysis identified transcriptional changes in previously-characterised gametocyte-specific pathways, which validated our approach. We also detected many previously-unreported female- and male-specific pathways and genes. Transcriptional biases in stage and gender were then used to investigate sex-specificity and sexual dimorphism of Plasmodium in an evolutionary context. Sex-related gene expression is well conserved between Plasmodium species, but relatively poorly conserved in related organisms outside this genus. This pattern of conservation is most evident in genes necessary for both male and female gametocyte formation. However, this trend is less pronounced for male-specific genes, which are more highly conserved outside the genus than genes specific to female development. CONCLUSIONS We characterised the transcriptional changes that are integral to the development of the female and male sexual forms of Plasmodium. These differential-expression patterns provide a vital insight into understanding the gender-specific characteristics of this essential stage that is the primary target for treatments that block parasite transmission. Our results also offer insight into the evolution of sex genes through Alveolata, and suggest that many Plasmodium sex genes evolved within the genus. We further hypothesise that male gametocytes co-opted pre-existing cellular machinery in their evolutionary history, whereas female gametocytes evolved more through the development of novel, parasite-specific pathways.
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Affiliation(s)
- Lee M Yeoh
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia.,School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | | | - Vanessa Mollard
- School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | - Geoffrey I McFadden
- School of BioSciences, The University of Melbourne, Parkville, 3010, Australia.
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia.
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Castillo AI, Andreína Pacheco M, Escalante AA. Evolution of the merozoite surface protein 7 (msp7) family in Plasmodium vivax and P. falciparum: A comparative approach. INFECTION GENETICS AND EVOLUTION 2017; 50:7-19. [PMID: 28163236 DOI: 10.1016/j.meegid.2017.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 01/17/2023]
Abstract
Malaria parasites (genus Plasmodium) are a diverse group found in many species of vertebrate hosts. These parasites invade red blood cells in a complex process comprising several proteins, many encoded by multigene families, one of which is merozoite surface protein 7 (msp7). In the case of Plasmodium vivax, the most geographically widespread human-infecting species, differences in the number of paralogs within multigene families have been previously explained, at least in part, as potential adaptations to the human host. To explore this in msp7, we studied its orthologs in closely related nonhuman primate parasites; investigating both paralog evolutionary history and genetic polymorphism. The emerging patterns were then compared with the human parasite Plasmodium falciparum. We found that the evolution of the msp7 family is consistent with a birth-and-death model, where duplications, pseudogenizations, and gene loss events are common. However, all paralogs in P. vivax and P. falciparum had orthologs in their closely related species in non-human primates indicating that the ancestors of those paralogs precede the events leading to their origins as human parasites. Thus, the number of paralogs cannot be explained as an adaptation to human hosts. Although there is no functional information for msp7 in P. vivax, we found evidence for purifying selection in the genetic polymorphism of some of its paralogs as well as their orthologs in closely related non-human primate parasites. We also found evidence indicating that a few of P. vivax's paralogs may have diverged from their orthologs in non-human primates by episodic positive selection. Hence, they may had been under selection when the lineage leading to P. vivax diverged from the Asian non-human primates and switched into Homininae. All these lines of evidence suggest that msp7 is functionally important in P. vivax.
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Affiliation(s)
| | - M Andreína Pacheco
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA, USA
| | - Ananias A Escalante
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA, USA.
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Benelli G. Green synthesized nanoparticles in the fight against mosquito-borne diseases and cancer-a brief review. Enzyme Microb Technol 2016; 95:58-68. [PMID: 27866627 DOI: 10.1016/j.enzmictec.2016.08.022] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022]
Abstract
Nanobiomedicine and parasitology are facing a number of key challenges, which mostly deal with the paucity of effective preventive and curative tools against mosquito-borne diseases and cancer. In this scenario, the employ of botanical and invertebrate extracts as reducing, stabilizing and capping agents for the synthesis of nanoparticles is advantageous over chemical and physical methods, since it is one-pot, cheap, and does not require high pressure, energy, temperature, or the use of highly toxic chemicals. Considering the overlooked connection between mosquito vector activity and the spread of cancer in USA, this review focused on the current knowledge available about green synthesized nanoparticles with efficacy against mosquito-borne diseases and cancer. Green fabricated metal nanoparticles showed antiplasmodial activity that often encompasses the efficacy of currently marked drugs for malaria treatment. They have been also reported as growth inhibitors against dengue virus (serotype DEN-2), with moderate cytotoxicity on mammalian cells. However, this feature is strongly dependent to the botanical agents employed during nanosynthesis. In addition, green nanoparticles have been successfully used to reduce mosquito young instar populations in the field. The final section focuses on some issues for future research, with special reference to the chemical standardization of the botanical extracts used for nanosynthesis and the potential effects on green fabricated nanoparticles on non-target organisms.
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Affiliation(s)
- Giovanni Benelli
- Insect Behavior Group, Department of Agriculture, Food and Environment, University of Pisa, via del Borghetto 80, 56124 Pisa, Italy; The BioRobotics Institute, Sant'Anna School of Advanced Studies, Viale Rinaldo Piaggio 34, 56025 Pontedera, Italy.
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Hoo R, Zhu L, Amaladoss A, Mok S, Natalang O, Lapp SA, Hu G, Liew K, Galinski MR, Bozdech Z, Preiser PR. Integrated analysis of the Plasmodium species transcriptome. EBioMedicine 2016; 7:255-66. [PMID: 27322479 PMCID: PMC4909483 DOI: 10.1016/j.ebiom.2016.04.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/09/2016] [Accepted: 04/11/2016] [Indexed: 01/18/2023] Open
Abstract
The genome sequence available for different Plasmodium species is a valuable resource for understanding malaria parasite biology. However, comparative genomics on its own cannot fully explain all the species-specific differences which suggests that other genomic aspects such as regulation of gene expression play an important role in defining species-specific characteristics. Here, we developed a comprehensive approach to measure transcriptional changes of the evolutionary conserved syntenic orthologs during the intraerythrocytic developmental cycle across six Plasmodium species. We show significant transcriptional constraint at the mid-developmental stage of Plasmodium species while the earliest stages of parasite development display the greatest transcriptional variation associated with critical functional processes. Modeling of the evolutionary relationship based on changes in transcriptional profile reveal a phylogeny pattern of the Plasmodium species that strictly follows its mammalian hosts. In addition, the work shows that transcriptional conserved orthologs represent potential future targets for anti-malaria intervention as they would be expected to carry out key essential functions within the parasites. This work provides an integrated analysis of orthologous transcriptome, which aims to provide insights into the Plasmodium evolution thereby establishing a framework to explore complex pathways and drug discovery in Plasmodium species with broad host range. Comparison of variations in mRNA abundance across six different Plasmodium species. Transcriptional conservation and divergence of Plasmodium syntenic orthologs. Pattern of Plasmodium transcriptome evolution are established. Transcriptionally conserved orthologs represent attractive intervention targets.
Malaria remains a major public health concern despite global efforts in the fight against this disease. The intraerythrocytic stage of the malaria parasites is currently in the spotlight for anti-malarial intervention and vaccine targets. The primary goal of this study is to generate a comprehensive and directly comparable transcriptome dataset across multiple Plasmodium species originating from different hosts. We establish that specific pathways and intraerythrocytic stages are more transcriptionally diverged than others, reflecting transcriptional evolutionary diversity. We further propose a panel of transcriptionally conserved genes as potential drug targets.
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Affiliation(s)
- Regina Hoo
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Lei Zhu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Anburaj Amaladoss
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Sachel Mok
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Onguma Natalang
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Stacey A Lapp
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Guangan Hu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Kingsley Liew
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore.
| | - Peter R Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore.
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11
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Arnot DE, Jensen ATR. Antigenic Variation and the Genetics and Epigenetics of the PfEMP1 Erythrocyte Surface Antigens in Plasmodium falciparum Malaria. ADVANCES IN APPLIED MICROBIOLOGY 2016; 74:77-96. [PMID: 21459194 DOI: 10.1016/b978-0-12-387022-3.00007-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
How immunity to malaria develops remains one of the great unresolved issues in bio-medicine and resolution of its various paradoxes is likely to be the key to developing effective malaria vaccines. The basic epidemiological observations are; under conditions of intense natural transmission, humans do become immune to P. falciparum malaria, but this is a slow process requiring multiple disease episodes which many, particularly young children, do not survive. Adult survivors are immune to the symptoms of malaria, and unless pregnant, can control the growth of most or all new inoculations. Sterile immunity is not achieved and chronic parasitization of apparently healthy adults is the norm. In this article, we analyse the best understood malaria "antigenic variation" system, that based on Plasmodium falciparum's PfEMP1-type cytoadhesion antigens, and critically review recent literature on the function and control of this multi-gene family of parasite variable surface antigens.
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Affiliation(s)
- David E Arnot
- Centre for Medical Parasitology, Department of International Health, Immunology and Microbiology, Faculty of Health Sciences, University of Copenhagen, CSS Oester Farimagsgade 5, Copenhagen K, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), CSS Oester Farimagsgade 5, Copenhagen K, Denmark; Institute of Immunology and Infection Research, School of Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
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12
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Declining malaria, rising of dengue and Zika virus: insights for mosquito vector control. Parasitol Res 2016; 115:1747-54. [DOI: 10.1007/s00436-016-4971-z] [Citation(s) in RCA: 342] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 02/22/2016] [Indexed: 12/21/2022]
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13
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Lima-Junior JDC, Pratt-Riccio LR. Major Histocompatibility Complex and Malaria: Focus on Plasmodium vivax Infection. Front Immunol 2016; 7:13. [PMID: 26858717 PMCID: PMC4728299 DOI: 10.3389/fimmu.2016.00013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/12/2016] [Indexed: 01/13/2023] Open
Abstract
The importance of host and parasite genetic factors in malaria resistance or susceptibility has been investigated since the middle of the last century. Nowadays, of all diseases that affect man, malaria still plays one of the highest levels of selective pressure on human genome. Susceptibility to malaria depends on exposure profile, epidemiological characteristics, and several components of the innate and adaptive immune system that influences the quality of the immune response generated during the Plasmodium lifecycle in the vertebrate host. But it is well known that the parasite's enormous capacity of genetic variation in conjunction with the host genetics polymorphism is also associated with a wide spectrum of susceptibility degrees to complicated or severe forms of the disease. In this scenario, variations in genes of the major histocompatibility complex (MHC) associated with host resistance or susceptibility to malaria have been identified and used as markers in host-pathogen interaction studies, mainly those evaluating the impact on the immune response, acquisition of resistance, or increased susceptibility to infection or vulnerability to disease. However, due to the intense selective pressure, number of cases, and mortality rates, the majority of the reported associations reported concerned Plasmodium falciparum malaria. Studies on the MHC polymorphism and its association with Plasmodium vivax, which is the most widespread Plasmodium and the most prevalent species outside the African continent, are less frequent but equally important. Despite punctual contributions, there are accumulated evidences of human genetic control in P. vivax infection and disease. Herein, we review the current knowledge in the field of MHC and derived molecules (HLA Class I, Class II, TNF-α, LTA, BAT1, and CTL4) regarding P. vivax malaria. We discuss particularly the results of P. vivax studies on HLA class I and II polymorphisms in relation to host susceptibility, naturally acquired immune response against specific antigens and the implication of this knowledge to overcome the parasite immune evasion. Finally, the potential impact of such polymorphisms on the development of vaccine candidate antigens against P. vivax will be studied.
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14
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Yu X, Korkmaz T, Lilburn TG, Cai H, Gu J, Wang Y. Heavy path mining of protein-protein associations in the malaria parasite. Methods 2015; 83:63-70. [PMID: 25861922 DOI: 10.1016/j.ymeth.2015.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 01/17/2023] Open
Abstract
Annotating and understanding the function of proteins and other elements in a genome can be difficult in the absence of a well-studied and evolutionarily close relative. The causative agent of malaria, one of the oldest and most deadly global infectious diseases, is a good example of this problem. The burden of malaria is huge and there is a pressing need for new, more effective antimalarial strategies. However, techniques such as homology-dependent annotation transfer are severely impaired in this parasite because there are no well-understood close relatives. To circumvent this approach we developed a network-based method that uses a heavy path network-mining algorithm. We uncovered the protein-protein associations that are implicated in important cellular processes including genome integrity, DNA repair, transcriptional regulation, invasion, and pathogenesis, thus demonstrating the utility of this method. The URL of the source code for super-sequence mining method is http://www.cs.utsa.edu/~korkmaz/research/heavy-path-mining/.
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Affiliation(s)
- Xinran Yu
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Turgay Korkmaz
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | | | - Hong Cai
- Department of Biology, South Texas for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | - Jianying Gu
- Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA.
| | - Yufeng Wang
- Department of Biology, South Texas for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA.
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15
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Chen Y, Chan CK, Kerishnan JP, Lau YL, Wong YL, Gopinath SC. Identification of circulating biomarkers in sera of Plasmodium knowlesi-infected malaria patients--comparison against Plasmodium vivax infection. BMC Infect Dis 2015; 15:49. [PMID: 25656928 PMCID: PMC4336705 DOI: 10.1186/s12879-015-0786-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/27/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Plasmodium knowlesi was identified as the fifth major malaria parasite in humans. It presents severe clinical symptoms and leads to mortality as a result of hyperparasitemia in a short period of time. This study aimed to improve the current understanding of P. knowlesi and identify potential biomarkers for knowlesi malaria. METHODS In the present study, we have employed two-dimensional gel electrophoresis-coupled immunoblotting techniques and mass spectrometry to identify novel circulating markers in sera from P. knowlesi-infected patients. Specifically, we have compared serum protein profiles from P. knowlesi-infected patients against those of healthy or P. vivax-infected individuals. RESULTS We identified several immunoreactive proteins in malarial-infected subjects, including alpha-2-HS glycoprotein (AHSG), serotransferrin (TF), complement C3c (C3), hemopexin (HPX), zinc-2-alpha glycoprotein (ZAG1), apolipoprotein A1 (Apo-A1), haptoglobin (HAP), and alpha-1-B-glycoprotein (A1BG). However, only TF and HPX displayed enhanced antigenicity and specificity, suggesting that they might represent valid markers for detecting P. knowlesi infection. Additionally, six P. knowlesi-specific antigens were identified (K15, K16, K28, K29, K30, and K38). Moreover, although HAP antigenicity was observed during P. vivax infection, it was undetectable in P. knowlesi-infected subjects. CONCLUSIONS We have demonstrated the application of immunoproteomics approach to identify potential candidate biomarkers for knowlesi malaria infection.
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Affiliation(s)
- Yeng Chen
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
| | - Choon K Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Penang, Malaysia.
| | - Jesinda P Kerishnan
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yee L Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yin-Ling Wong
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Subash Cb Gopinath
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Institute of Nano Electronic Engineering (INEE), & School of Bioprocess Engineering, Universiti Malaysia Perlis, Kangar, Perlis, Malaysia.
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16
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Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B, Hoeijmakers WAM, Religa AA, Robertson L, Sanders M, Ogun SA, Cunningham D, Erhart A, Billker O, Khan SM, Stunnenberg HG, Langhorne J, Holder AA, Waters AP, Newbold CI, Pain A, Berriman M, Janse CJ. A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol 2014; 12:86. [PMID: 25359557 PMCID: PMC4242472 DOI: 10.1186/s12915-014-0086-0] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/10/2014] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function. RESULTS We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the 'Plasmodium interspersed repeat genes' (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family. CONCLUSIONS Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
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Affiliation(s)
- Thomas D Otto
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Ulrike Böhme
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Andrew P Jackson
- />Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Martin Hunt
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Blandine Franke-Fayard
- />Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wieteke A M Hoeijmakers
- />Department of Molecular Biology, Science faculty, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Agnieszka A Religa
- />Institute of Infection, Immunity & Inflammation, School of Medical, Veterinary & Life Sciences, & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, Scotland UK
| | | | - Mandy Sanders
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Solabomi A Ogun
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Deirdre Cunningham
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Annette Erhart
- />Unit of Malariology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Oliver Billker
- />Wellcome Trust Sanger Institute, Hinxton, Cambridge UK
| | - Shahid M Khan
- />Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hendrik G Stunnenberg
- />Department of Molecular Biology, Science faculty, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Jean Langhorne
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Anthony A Holder
- />Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London UK
| | - Andrew P Waters
- />Institute of Infection, Immunity & Inflammation, School of Medical, Veterinary & Life Sciences, & Wellcome Centre for Molecular Parasitology, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, Scotland UK
| | - Chris I Newbold
- />Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- />Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford UK
| | - Arnab Pain
- />Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | | | - Chris J Janse
- />Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
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Hughes GL, Rivero A, Rasgon JL. Wolbachia can enhance Plasmodium infection in mosquitoes: implications for malaria control? PLoS Pathog 2014; 10:e1004182. [PMID: 25187984 PMCID: PMC4154766 DOI: 10.1371/journal.ppat.1004182] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Grant L. Hughes
- The Huck Institutes of The Life Sciences, The Center for Infectious Disease Dynamics and the Department of Entomology, Pennsylvania State University, State College, Pennsylvania, United States of America
| | - Ana Rivero
- Maladies Infectieuses et Vecteurs: Écologie, Génétique, Évolution et Contrôle, MIVEGEC (UMR CNRS-UM1-UM2 5290, IRD 224), Montpellier, France
| | - Jason L. Rasgon
- The Huck Institutes of The Life Sciences, The Center for Infectious Disease Dynamics and the Department of Entomology, Pennsylvania State University, State College, Pennsylvania, United States of America
- * E-mail:
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18
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Ponts N, Fu L, Harris EY, Zhang J, Chung DWD, Cervantes MC, Prudhomme J, Atanasova-Penichon V, Zehraoui E, Bunnik EM, Rodrigues EM, Lonardi S, Hicks GR, Wang Y, Le Roch KG. Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum. Cell Host Microbe 2014; 14:696-706. [PMID: 24331467 DOI: 10.1016/j.chom.2013.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/18/2013] [Accepted: 10/21/2013] [Indexed: 01/13/2023]
Abstract
Cytosine DNA methylation is an epigenetic mark in most eukaryotic cells that regulates numerous processes, including gene expression and stress responses. We performed a genome-wide analysis of DNA methylation in the human malaria parasite Plasmodium falciparum. We mapped the positions of methylated cytosines and identified a single functional DNA methyltransferase (Plasmodium falciparum DNA methyltransferase; PfDNMT) that may mediate these genomic modifications. These analyses revealed that the malaria genome is asymmetrically methylated and shares common features with undifferentiated plant and mammalian cells. Notably, core promoters are hypomethylated, and transcript levels correlate with intraexonic methylation. Additionally, there are sharp methylation transitions at nucleosome and exon-intron boundaries. These data suggest that DNA methylation could regulate virulence gene expression and transcription elongation. Furthermore, the broad range of action of DNA methylation and the uniqueness of PfDNMT suggest that the methylation pathway is a potential target for antimalarial strategies.
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Affiliation(s)
- Nadia Ponts
- Department of Cell Biology and Neuroscience, University of California, 900 University Avenue, Riverside, CA 92521, USA; INRA, UR1264-MycSA, 71 Avenue E. Bourlaux, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Lijuan Fu
- Department of Chemistry, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Elena Y Harris
- Department of Computer Science and Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Jing Zhang
- Department of Chemistry, University of California, 900 University Avenue, Riverside, CA 92521, USA; School of Chemistry & Materials Science, Shaanxi Normal University, 199 South Chang'an Road, Xi'an 710062, China
| | - Duk-Won D Chung
- Department of Cell Biology and Neuroscience, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Michael C Cervantes
- Department of Cell Biology and Neuroscience, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Jacques Prudhomme
- Department of Cell Biology and Neuroscience, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | | | - Enric Zehraoui
- INRA, UR1264-MycSA, 71 Avenue E. Bourlaux, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Evelien M Bunnik
- Department of Cell Biology and Neuroscience, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Elisandra M Rodrigues
- Department of Cell Biology and Neuroscience, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Glenn R Hicks
- Center for Plant Cell Biology and Department of Botany & Plant Sciences, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Karine G Le Roch
- Department of Cell Biology and Neuroscience, University of California, 900 University Avenue, Riverside, CA 92521, USA.
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19
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Identification of a vir-orthologous immune evasion gene family from primate malaria parasites. Parasitology 2014; 141:641-5. [PMID: 24477117 DOI: 10.1017/s003118201300214x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The immune evasion gene family of malaria parasites encodes variant surface proteins that are expressed at the surface of infected erythrocytes and help the parasite in evading the host immune response by means of antigenic variation. The identification of Plasmodium vivax vir orthologous immune evasion gene family from primate malaria parasites would provide new insight into the evolution of virulence and pathogenesis. Three vir subfamilies viz. vir-B, vir-D and vir-G were successfully PCR amplified from primate malaria parasites, cloned and sequenced. DNA sequence analysis confirmed orthologues of vir-D subfamily in Plasmodium cynomolgi, Plasmodium simium, Plasmodium simiovale and Plasmodium fieldi. The identified vir-D orthologues are 1-9 distinct members of the immune evasion gene family which have 68-83% sequence identity with vir-D and 71.2-98.5% sequence identity within the members identified from primate malaria parasites. The absence of other vir subfamilies among primate malaria parasites reflects the limitations in the experimental approach. This study clearly identified the presence of vir-D like sequences in four species of Plasmodium infecting primates that would be useful in understanding the evolution of virulence in malaria parasites.
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Prajapati SK, Joshi H, Carlton JM, Rizvi MA. Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India. PLoS Negl Trop Dis 2013; 7:e2425. [PMID: 24069480 PMCID: PMC3777877 DOI: 10.1371/journal.pntd.0002425] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/01/2013] [Indexed: 11/18/2022] Open
Abstract
The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.
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Affiliation(s)
- Surendra K Prajapati
- Molecular Biology Division, National Institute of Malaria Research, New Delhi, India
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21
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Neafsey DE. Genome sequencing sheds light on emerging drug resistance in malaria parasites. Nat Genet 2013; 45:589-90. [PMID: 23715326 DOI: 10.1038/ng.2648] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum in Southeast Asia are gradually becoming resistant to artemesinin, a standard first-line treatment for malaria. Whole-genome sequencing offers a chance to better understand and perhaps undermine the parasite's evolutionary response to this drug.
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Frech C, Chen N. Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis. BMC Genomics 2013; 14:427. [PMID: 23805789 PMCID: PMC3747859 DOI: 10.1186/1471-2164-14-427] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/19/2013] [Indexed: 11/10/2022] Open
Abstract
Background Plasmodium parasites, the causative agents of malaria, express many variant antigens on cell surfaces. Variant surface antigens (VSAs) are typically organized into large subtelomeric gene families that play critical roles in virulence and immune evasion. Many important aspects of VSA function and evolution remain obscure, impeding our understanding of virulence mechanisms and vaccine development. To gain further insights into VSA function and evolution, we comparatively classified and examined known VSA gene families across seven Plasmodium species. Results We identified a set of ultra-conserved orthologs within the largest Plasmodium gene family pir, which should be considered as high-priority targets for experimental functional characterization and vaccine development. Furthermore, we predict a lipid-binding domain in erythrocyte surface-expressed PYST-A proteins, suggesting a role of this second largest rodent parasite gene family in host cholesterol salvage. Additionally, it was found that PfMC-2TM proteins carry a novel and putative functional domain named MC-TYR, which is conserved in other P. falciparum gene families and rodent parasites. Finally, we present new conclusive evidence that the major Plasmodium VSAs PfEMP1, SICAvar, and SURFIN are evolutionarily linked through a modular and structurally conserved intracellular domain. Conclusion Our comparative analysis of Plasmodium VSA gene families revealed important functional and evolutionary insights, which can now serve as starting points for further experimental studies.
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Affiliation(s)
- Christian Frech
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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Galinski MR, Meyer EVS, Barnwell JW. Plasmodium vivax: modern strategies to study a persistent parasite's life cycle. ADVANCES IN PARASITOLOGY 2013; 81:1-26. [PMID: 23384620 DOI: 10.1016/b978-0-12-407826-0.00001-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plasmodium vivax has unique attributes to support its survival in varying ecologies and climates. These include hypnozoite forms in the liver, an invasion preference for reticulocytes, caveola-vesicle complex structures in the infected erythrocyte membrane and rapidly forming and circulating gametocytes. These characteristics make this species very different from P. falciparum. Plasmodium cynomolgi and other related simian species have identical biology and can serve as informative models of P. vivax infections. Plasmodium vivax and its model parasites can be grown in non-human primates (NHP), and in short-term ex vivo cultures. For P. vivax, in the absence of in vitro culture systems, these models remain highly relevant side by side with human clinical studies. While post-genomic technologies allow for greater exploration of P. vivax-infected blood samples from humans, these come with restrictions. Two advantages of NHP models are that infections can be experimentally tailored to address hypotheses, including genetic manipulation. Also, systems biology approaches can capitalise on computational biology combined with set experimental infection periods and protocols, which may include multiple sampling times, different types of samples, and the broad use of "omics" technologies. Opportunities for research on vivax malaria are increasing with the use of existing and new methodological strategies in combination with modern technologies.
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Affiliation(s)
- Mary R Galinski
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA.
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24
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Arango EM, Samuel R, Agudelo OM, Carmona-Fonseca J, Maestre A, Yanow SK. Genotype comparison of Plasmodium vivax and Plasmodium falciparum clones from pregnant and non-pregnant populations in North-west Colombia. Malar J 2012. [PMID: 23181896 PMCID: PMC3519599 DOI: 10.1186/1475-2875-11-392] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Placental malaria is the predominant pathology secondary to malaria in pregnancy, causing substantial maternal and infant morbidity and mortality in tropical areas. While it is clear that placental parasites are phenotypically different from those in the peripheral circulation, it is not known whether unique genotypes are associated specifically with placental infection or perhaps more generally with pregnancy. In this study, genetic analysis was performed on Plasmodium vivax and Plasmodium falciparum parasites isolated from peripheral and placental blood in pregnant women living in North-west Colombia, and compared with parasites causing acute malaria in non-pregnant populations. METHODS A total of 57 pregnant women at delivery with malaria infection confirmed by real-time PCR in peripheral or placental blood were included, as well as 50 pregnant women in antenatal care and 80 men or non-pregnant women with acute malaria confirmed by a positive thick smear for P. vivax or P. falciparum. Five molecular markers per species were genotyped by nested PCR and capillary electrophoresis. Genetic diversity and the fixation index FST per species and study group were calculated and compared. RESULTS Almost all infections at delivery were asymptomatic with significantly lower levels of infection compared with the groups with acute malaria. Expected heterozygosity for P. vivax molecular markers ranged from 0.765 to 0.928 and for P. falciparum markers ranged from 0.331 to 0.604. For P. vivax infections, the genetic diversity was similar amongst the four study groups and the fixation index from each pairwise comparison failed to show significant genetic differentiation. For P. falciparum, no genetic differentiation was observed between placental and peripheral parasites from the same woman at delivery, but the parasites isolated at delivery showed significant genetic differentiation compared with parasites isolated from subjects with acute malaria. CONCLUSIONS In North-west Colombia, P. vivax parasites have high genetic diversity that is equivalent in pregnant and non-pregnant populations as well as in symptomatic and asymptomatic infections. For P. falciparum, the overall genetic diversity is lower, with specific genotypes associated with asymptomatic infections at delivery.
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Affiliation(s)
- Eliana M Arango
- Grupo Salud y Comunidad, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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GUPTA BHAVNA, SRIVASTAVA NALINI, DAS APARUP. Inferring the evolutionary history of IndianPlasmodium vivaxfrom population genetic analyses of multilocus nuclear DNA fragments. Mol Ecol 2012; 21:1597-616. [DOI: 10.1111/j.1365-294x.2012.05480.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Morbidity in the marshes: Using spatial epidemiology to investigate skeletal evidence for malaria in Anglo-Saxon England (AD 410-1050). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2011; 147:301-11. [DOI: 10.1002/ajpa.21648] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 10/29/2011] [Indexed: 12/21/2022]
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Abstract
The development of an effective malaria vaccine has taken many decades, but there is now a good chance that the first malaria vaccine will be licensed within the next few years. However, this vaccine (RTS,S) will not be fully effective, and more efficacious, second-generation vaccines will be needed. Good progress is being made in the development of potential vaccines directed at each of the three main stages of the parasite's life cycle, with a variety of different approaches, but many challenges remain, e.g. overcoming the problem of polymorphism in many key parasite antigens. It is likely vaccines that are effective enough to block transmission, and thus contribute to increasing drives towards malaria elimination, will need to contain antigens from different stages of the parasite's life cycle.
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Affiliation(s)
- B M Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
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28
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Mu J, Seydel KB, Bates A, Su XZ. Recent Progress in Functional Genomic Research in Plasmodium falciparum. Curr Genomics 2011; 11:279-86. [PMID: 21119892 PMCID: PMC2930667 DOI: 10.2174/138920210791233081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 02/22/2010] [Accepted: 03/09/2010] [Indexed: 02/02/2023] Open
Abstract
With the completion and near completion of many malaria parasite genome-sequencing projects, efforts are now being directed to a better understanding of gene functions and to the discovery of vaccine and drug targets. Inter- and intraspecies comparisons of the parasite genomes will provide invaluable insights into parasite evolution, virulence, drug resistance, and immune invasion. Genome-wide searches for loci under various selection pressures may lead to discovery of genes conferring drug resistance or encoding for protective antigens. In addition, the Plasmodium falciparum genome sequence provides the basis for the development of various microarrays to monitor gene expression and to detect nucleotide substitution and deletion/amplification. Genome-wide profiling of the parasite proteome, chromatin modification, and nucleosome position also depend on availability of the parasite genome. In this brief review, we will highlight some recent advances and studies in characterizing gene function and related phenotype in P. falciparum that were made possible by the genome sequence, particularly the development of a genome-wide diversity map and various high-throughput genotyping methods for genome-wide association studies (GWAS).
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Affiliation(s)
- Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Costa CHN, Peters NC, Maruyama SR, de Brito EC, de Miranda Santos IKF. Vaccines for the leishmaniases: proposals for a research agenda. PLoS Negl Trop Dis 2011; 5:e943. [PMID: 21468307 PMCID: PMC3066138 DOI: 10.1371/journal.pntd.0000943] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | | | - Nathan C. Peters
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sandra Regina Maruyama
- Laboratory of Immunoparasitology, Department of Biochemistry and Immunology, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, Brazil
| | - Eldo Cardoso de Brito
- Natan Portella Institute for Tropical Diseases, Federal University of Piauí, Teresina, Brazil
| | - Isabel Kinney Ferreira de Miranda Santos
- Laboratory of Immunoparasitology, Department of Biochemistry and Immunology, Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, Brazil
- National Center for Genetic Resources and Biotechnology, Brazilian Enterprise for Agricultural Research, Brasília, Brazil
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Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes. Proc Natl Acad Sci U S A 2010; 107:20045-50. [PMID: 21037109 DOI: 10.1073/pnas.1003776107] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plasmodium vivax causes 25-40% of malaria cases worldwide, yet research on this human malaria parasite has been neglected. Nevertheless, the recent publication of the P. vivax reference genome now allows genomics and systems biology approaches to be applied to this pathogen. We show here that whole-genome analysis of the parasite can be achieved directly from ex vivo-isolated parasites, without the need for in vitro propagation. A single isolate of P. vivax obtained from a febrile patient with clinical malaria from Peru was subjected to whole-genome sequencing (30× coverage). This analysis revealed over 18,261 single-nucleotide polymorphisms (SNPs), 6,257 of which were further validated using a tiling microarray. Within core chromosomal genes we find that one SNP per every 985 bases of coding sequence distinguishes this recent Peruvian isolate, designated IQ07, from the reference Salvador I strain obtained in 1972. This full-genome sequence of an uncultured P. vivax isolate shows that the same regions with low numbers of aligned sequencing reads are also highly variable by genomic microarray analysis. Finally, we show that the genes containing the largest ratio of nonsynonymous-to-synonymous SNPs include two AP2 transcription factors and the P. vivax multidrug resistance-associated protein (PvMRP1), an ABC transporter shown to be associated with quinoline and antifolate tolerance in Plasmodium falciparum. This analysis provides a data set for comparative analysis with important potential for identifying markers for global parasite diversity and drug resistance mapping studies.
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31
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Single nucleotide polymorphisms, putatively neutral DNA markers and population genetic parameters in Indian Plasmodium vivax isolates. Parasitology 2010; 137:1721-30. [DOI: 10.1017/s0031182010000533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SUMMARYWith a view to developing putatively neutral markers based on Single Nucleotide Polymorphisms (SNPs) in the human malaria parasite, Plasmodium vivax, we utilized the published whole genome sequence information of P. falciparum and P. vivax to find a ~200 kb conserved syntenic region between these two species. We have selected 27 non-coding DNA fragments (in introns and intergenic regions) of variable length (300–750 bp) in P. vivax in this syntenic region. PCR of P. vivax isolates of a population sample from India could successfully amplify 17 fragments. Subsequently, DNA sequencing and sequence analysis confirmed the polymorphic status of only 11 fragments. Altogether, 18 SNPs were detected and 2 different measures of nucleotide diversity showed variable patterns across different fragments; in general, introns were less variable than the intergenic regions. All 11 polymorphic fragments were found to be evolving according to a neutral equilibrium model and thus could be utilized as putatively neutral markers for population genetic studies in P. vivax. Different molecular population genetics parameters were also estimated, providing initial insight into the population genetics of Indian P. vivax.
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Souza-Neiras WC, Storti-Melo LM, Cassiano GC, Couto VSCA, Couto AARA, Soares IS, Carvalho LH, Cunha MG, Póvoa MM, Herrera S, Herrera MA, Rossit ARM, Carareto CMA, Machado RLD. Plasmodium vivax circumsporozoite genotypes: a limited variation or new subspecies with major biological consequences? Malar J 2010; 9:178. [PMID: 20573199 PMCID: PMC2908638 DOI: 10.1186/1475-2875-9-178] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 06/23/2010] [Indexed: 12/02/2022] Open
Abstract
Background Plasmodium vivax circumsporozoite variants have been identified in several geographical areas. The real implication of the genetic variation in this region of the P. vivax genome has been questioned for a long time. Although previous studies have observed significant association between VK210 and the Duffy blood group, we present here that evidences of this variation are limited to the CSP central portion. Methods The phylogenetic analyses were accomplished starting from the amplification of conserved domains of 18 SSU RNAr and Cyt B. The antibodies responses against the CSP peptides, MSP-1, AMA-1 and DBP were detected by ELISA, in plasma samples of individuals infected with two P. vivax CS genotypes: VK210 and P. vivax-like. Results These analyses of the two markers demonstrate high similarity among the P. vivax CS genotypes and surprisingly showed diversity equal to zero between VK210 and P. vivax-like, positioning these CS genotypes in the same clade. A high frequency IgG antibody against the N- and C-terminal regions of the P. vivax CSP was found as compared to the immune response to the R- and V- repetitive regions (p = 0.0005, Fisher's Exact test). This difference was more pronounced when the P. vivax-like variant was present in the infection (p = 0.003, Fisher's Exact test). A high frequency of antibody response against MSP-1 and AMA-1 peptides was observed for all P. vivax CS genotypes in comparison to the same frequency for DBP. Conclusions This results target that the differences among the P. vivax CS variants are restrict to the central repeated region of the protein, mostly nucleotide variation with important serological consequences.
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Affiliation(s)
- Wanessa C Souza-Neiras
- Departamento de Biologia, Universidade Estadual Paulista Júlio Mesquita Filho, São José do Rio Preto, São Paulo State, Brazil.
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Malaria parasite genome scan: insights into antimalarial resistance. Parasitol Res 2010; 107:495-9. [PMID: 20499094 DOI: 10.1007/s00436-010-1917-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 05/07/2010] [Indexed: 10/19/2022]
Abstract
Genome scan and genotype-phenotype association study offer excellent opportunities to unearth drug/vaccine targets in human pathogens including malaria parasites. A recently conducted such study in worldwide isolates in the most devastating malaria parasite Plasmodium falciparum has reported important genomic information on genetic basis of antimalarial resistance. Several unknown genes were also found to be under strong influence of natural selection. The findings provide important insights into the malaria parasite genome evolution in general and to use this information to develop more focused malaria control strategies, in particular.
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Pacheco MA, Ryan EM, Poe AC, Basco L, Udhayakumar V, Collins WE, Escalante AA. Evidence for negative selection on the gene encoding rhoptry-associated protein 1 (RAP-1) in Plasmodium spp. INFECTION GENETICS AND EVOLUTION 2010; 10:655-61. [PMID: 20363375 DOI: 10.1016/j.meegid.2010.03.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 11/18/2022]
Abstract
Assessing how natural selection, negative or positive, operates on genes with low polymorphism is challenging. We investigated the genetic diversity of orthologous genes encoding the rhoptry-associated protein 1 (RAP-1), a low polymorphic protein of malarial parasites that is involved in erythrocyte invasion. We applied evolutionary genetic methods to study the polymorphism in RAP-1 from Plasmodium falciparum (n=32) and Plasmodium vivax (n=6), the two parasites responsible for most human malaria morbidity and mortality, as well as RAP-1 orthologous in closely related malarial species found in non-human primates (NHPs). Overall, genes encoding RAP-1 are highly conserved in all Plasmodium spp. included in this investigation. We found no evidence for natural selection, positive or negative, acting on the gene encoding RAP-1 in P. falciparum or P. vivax. However, we found evidence that the orthologous genes in non-human primate parasites (Plasmodium cynomolgi, Plasmodium inui, and Plasmodium knowlesi) are under purifying (negative) selection. We discuss the importance of considering negative selection while studying genes encoding proteins with low polymorphism and how selective pressures may differ among orthologous genes in closely related malarial parasites species.
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Affiliation(s)
- M Andreína Pacheco
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287-4501, United States
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Cox FE. History of the discovery of the malaria parasites and their vectors. Parasit Vectors 2010; 3:5. [PMID: 20205846 PMCID: PMC2825508 DOI: 10.1186/1756-3305-3-5] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 02/01/2010] [Indexed: 11/10/2022] Open
Abstract
Malaria is caused by infection with protozoan parasites belonging to the genus Plasmodium transmitted by female Anopheles species mosquitoes. Our understanding of the malaria parasites begins in 1880 with the discovery of the parasites in the blood of malaria patients by Alphonse Laveran. The sexual stages in the blood were discovered by William MacCallum in birds infected with a related haematozoan, Haemoproteus columbae, in 1897 and the whole of the transmission cycle in culicine mosquitoes and birds infected with Plasmodium relictum was elucidated by Ronald Ross in 1897. In 1898 the Italian malariologists, Giovanni Battista Grassi, Amico Bignami, Giuseppe Bastianelli, Angelo Celli, Camillo Golgi and Ettore Marchiafava demonstrated conclusively that human malaria was also transmitted by mosquitoes, in this case anophelines. The discovery that malaria parasites developed in the liver before entering the blood stream was made by Henry Shortt and Cyril Garnham in 1948 and the final stage in the life cycle, the presence of dormant stages in the liver, was conclusively demonstrated in 1982 by Wojciech Krotoski. This article traces the main events and stresses the importance of comparative studies in that, apart from the initial discovery of parasites in the blood, every subsequent discovery has been based on studies on non-human malaria parasites and related organisms.
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Affiliation(s)
- Francis Eg Cox
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT UK.
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Ponts N, Harris EY, Prudhomme J, Wick I, Eckhardt-Ludka C, Hicks GR, Hardiman G, Lonardi S, Le Roch KG. Nucleosome landscape and control of transcription in the human malaria parasite. Genome Res 2010; 20:228-38. [PMID: 20054063 DOI: 10.1101/gr.101063.109] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In eukaryotic cells, chromatin reorganizes within promoters of active genes to allow the transcription machinery and various transcription factors to access DNA. In this model, promoter-specific transcription factors bind DNA to initiate the production of mRNA in a tightly regulated manner. In the case of the human malaria parasite, Plasmodium falciparum, specific transcription factors are apparently underrepresented with regards to the size of the genome, and mechanisms underlying transcriptional regulation are controversial. Here, we investigate the modulation of DNA accessibility by chromatin remodeling during the parasite infection cycle. We have generated genome-wide maps of nucleosome occupancy across the parasite erythrocytic cycle using two complementary assays--the formaldehyde-assisted isolation of regulatory elements to extract protein-free DNA (FAIRE) and the MNase-mediated purification of mononucleosomes to extract histone-bound DNA (MAINE), both techniques being coupled to high-throughput sequencing. We show that chromatin architecture undergoes drastic upheavals throughout the parasite's cycle, contrasting with targeted chromatin reorganization usually observed in eukaryotes. Chromatin loosens after the invasion of the red blood cell and then repacks prior to the next cycle. Changes in nucleosome occupancy within promoter regions follow this genome-wide pattern, with a few exceptions such as the var genes involved in virulence and genes expressed at early stages of the cycle. We postulate that chromatin structure and nucleosome turnover control massive transcription during the erythrocytic cycle. Our results demonstrate that the processes driving gene expression in Plasmodium challenge the classical eukaryotic model of transcriptional regulation occurring mostly at the transcription initiation level.
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Affiliation(s)
- Nadia Ponts
- Department of Cell Biology and Neuroscience, University of California, Riverside, California 92521, USA
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Jerlström-Hultqvist J, Ankarklev J, Svärd SG. Is human giardiasis caused by two different Giardia species? Gut Microbes 2010; 1:379-82. [PMID: 21468219 PMCID: PMC3056102 DOI: 10.4161/gmic.1.6.13608] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 09/08/2010] [Accepted: 09/13/2010] [Indexed: 02/03/2023] Open
Abstract
We have recently sequenced the genome of the human Giardia intestinalis assemblage B isolate GS.1 comparisons to the earlier sequenced genome of the human assemblage A isolate WB showed that the average amino acid identity in 4,300 orthologous proteins was only 78%. Here we discuss these results in the light of new genome sequencing data from the hoofed-animal assemblage E (isolate P15, isolated from a pig) and further characterization of assemblage A and B isolates from humans. There is a highly conserved set of core genes (4,557 genes, 91% of genome) common to all isolates. The largest genomic differences are found in variable, Giardia-specific gene families and a large number of chromosomal rearrangements were detected, even between different chromosomes. Surprisingly, the assemblage E and A isolates are more similar at the amino-acid level than the two human isolates are to each other. This strengthens our earlier data suggesting that humans are infected by two different species of Giardia.
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Evolutionary genetic insights into Plasmodium falciparum functional genes. Parasitol Res 2009; 106:349-55. [PMID: 19902252 DOI: 10.1007/s00436-009-1668-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 10/20/2009] [Indexed: 10/20/2022]
Abstract
Complex and rapidly evolving behavior of the human malaria parasite Plasmodium falciparum have always been mysterious to the evolutionary biologists, as the parasite is the most virulent and now becoming the most prevalent malaria parasite species across the globe. With the availability of complete genome sequence of P. falciparum, better understanding of the genome design and evolution could be possible. We herein utilized the available information of all known functional genes from whole genome of P. falciparum and investigate the differential mode of gene evolution. The study comparing P. falciparum functional genes with Plasmodium vivax revealed about 82% of genes to be conserved in the later species and the rest, 18% to be totally unique to P. falciparum. Genetic architectural pattern of functional genes shows absence of introns in about a half of the conserved genes, whereas almost all unique genes have introns. Similarly, distribution of intron number and length were also observed to be different for conserved and unique genes of P. falciparum. Statistically significant positive correlations between total intron length and gene lengths were detected in 11 chromosomes for unique genes, whereas only in three chromosomes for conserved genes. Preference of intron presence in some P. falciparum genes were also detected which provide functional relevance of introns. The study provides, for the first time, a detail evolutionary analysis of functional genes of a devastating malaria parasite. The marked differences in organization of introns between the unique and conserved genes in P. falciparum, and the contribution of introns to genome complexity are some of the hallmarks of the study.
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Sartorello R, Amaya MJ, Nathanson MH, Garcia CRS. The plasmodium receptor for activated C kinase protein inhibits Ca(2+) signaling in mammalian cells. Biochem Biophys Res Commun 2009; 389:586-92. [PMID: 19748487 DOI: 10.1016/j.bbrc.2009.09.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 09/04/2009] [Indexed: 11/28/2022]
Abstract
Plasmodium falciparum, the most lethal malarial parasite, expresses an ortholog for the protein kinase C (PKC) activator RACK1. However, PKC has not been identified in this parasite, and the mammalian RACK1 can interact with the inositol 1,4,5-trisphosphate receptor (InsP3R). Therefore we investigated whether the Plasmodium ortholog PfRACK also can affect InsP3R-mediated Ca(2+) signaling in mammalian cells. GFP-tagged PfRACK and endogenous RACK1 were expressed in a similar distribution within cells. PfRACK inhibited agonist-induced Ca(2+) signals in cells expressing each isoform of the InsP3R, and this effect persisted when expression of endogenous RACK1 was reduced by siRNA. PfRACK also inhibited Ca(2+) signals induced by photorelease of caged InsP3. These findings provide evidence that PfRACK directly inhibits InsP3-mediated Ca(2+) signaling in mammalian cells. Interference with host cell signaling pathways to subvert the host intracellular milieu may be an important mechanism for parasite survival.
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Affiliation(s)
- Robson Sartorello
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil.
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Key gaps in the knowledge of Plasmodium vivax, a neglected human malaria parasite. THE LANCET. INFECTIOUS DISEASES 2009; 9:555-66. [PMID: 19695492 DOI: 10.1016/s1473-3099(09)70177-x] [Citation(s) in RCA: 469] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Franzén O, Jerlström-Hultqvist J, Castro E, Sherwood E, Ankarklev J, Reiner DS, Palm D, Andersson JO, Andersson B, Svärd SG. Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species? PLoS Pathog 2009; 5:e1000560. [PMID: 19696920 PMCID: PMC2723961 DOI: 10.1371/journal.ppat.1000560] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 07/27/2009] [Indexed: 01/05/2023] Open
Abstract
Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16× coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species. Giardia intestinalis is a major contributor to the enormous burden of diarrheal diseases with 250 million symptomatic infections per year, and it is part of the WHO neglected disease initiative. Nonetheless, there is poor insight into how Giardia causes disease; it is not invasive, secretes no known toxin and both the duration and symptoms of giardiasis are highly variable. Currently, there are seven defined variants (assemblages) of G. intestinalis, with only assemblages A and B being known to infect humans. Although assemblage B is the most prevalent worldwide, it is inconclusive whether the various genotypes are associated with different disease outcomes. We have used the 454 sequencing technology to sequence the first assemblage B isolate, and the genome was compared to the earlier sequenced assemblage A isolate. Large genetic differences were detected in genes involved in survival of the parasite during infections. The genomic differences between assemblage A and B can explain some of the observed biological and clinical differences between the two assemblages. Our data suggest that assemblage A and B Giardia can be two different species. The identification of genomic differences between assemblages is indeed very important for further studies of the disease and in the development of new methods for diagnosis and treatment of giardiasis.
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Affiliation(s)
- Oscar Franzén
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Elsie Castro
- Centre for Microbiological Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Ellen Sherwood
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Johan Ankarklev
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
| | - David S. Reiner
- The Burnham Institute for Medical Research, La Jolla, California, United States of America
| | - Daniel Palm
- Centre for Microbiological Preparedness, Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Jan O. Andersson
- Department of Evolution, Genomics and Systematics, EBC, Uppsala University, Uppsala, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Staffan G. Svärd
- Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden
- * E-mail:
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Zarlenga DS, Gasbarre LC. From parasite genomes to one healthy world: Are we having fun yet? Vet Parasitol 2009; 163:235-49. [PMID: 19560277 DOI: 10.1016/j.vetpar.2009.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In 1990, the Human Genome Sequencing Project was established. This laid the ground work for an explosion of sequence data that has since followed. As a result of this effort, the first complete genome of an animal, Caenorhabditis elegans was published in 1998. The sequence of Drosophila melanogaster was made available in March, 2000 and in the following year, working drafts of the human genome were generated with the completed sequence (92%) being released in 2003. Recent advancements and next-generation technologies have made sequencing common place and have infiltrated every aspect of biological research, including parasitology. To date, sequencing of 32 apicomplexa and 24 nematode genomes are either in progress or near completion, and over 600k nematode EST and 200k apicomplexa EST submissions fill the databases. However, the winds have shifted and efforts are now refocusing on how best to store, mine and apply these data to problem solving. Herein we tend not to summarize existing X-omics datasets or present new technological advances that promise future benefits. Rather, the information to follow condenses up-to-date-applications of existing technologies to problem solving as it relates to parasite research. Advancements in non-parasite systems are also presented with the proviso that applications to parasite research are in the making.
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Affiliation(s)
- Dante S Zarlenga
- USDA, ARS, ANRI Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA.
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Seventy-five years of Resochin in the fight against malaria. Parasitol Res 2009; 105:609-27. [PMID: 19593586 DOI: 10.1007/s00436-009-1524-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 06/08/2009] [Indexed: 12/17/2022]
Abstract
The four different forms of human malaria have threatened humanity since time immemorial and to this day, they exact a death toll of one to three million people annually. Synthetic anti-malarial agents have been in development since early 1900. Perhaps the most successful and widely used drug, Resochin (chloroquine), was discovered 75 years ago; for a long time, it was the drug of choice and to this day, it is still used in many regions of the world as a reliable treatment against simpler forms of malaria. In regions where it has not been in use against malaria tropica for quite some time due to the development of resistances, it has regained some of its efficacy. This review traces the discovery and the mechanism of action of this substance, illustrates the significance of malaria today, and underlines the need for controlled and reliable therapeutic measures.
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