401
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Affiliation(s)
- Karine Frénal
- Department of Microbiology and Molecular Medicine, Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
- * E-mail:
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Centre Médical Universitaire, University of Geneva, Geneva, Switzerland
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402
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MacPherson CR, Scherf A. Flexible guide-RNA design for CRISPR applications using Protospacer Workbench. Nat Biotechnol 2015; 33:805-6. [PMID: 26121414 DOI: 10.1038/nbt.3291] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Cameron Ross MacPherson
- 1] Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France. [2] CNRS, ERL 9195, Paris, France. [3] INSERM, Unit U1201, Paris, France
| | - Artur Scherf
- 1] Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France. [2] CNRS, ERL 9195, Paris, France. [3] INSERM, Unit U1201, Paris, France
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403
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CRISPR/Cas9-Induced Disruption of Paraflagellar Rod Protein 1 and 2 Genes in Trypanosoma cruzi Reveals Their Role in Flagellar Attachment. mBio 2015. [PMID: 26199333 PMCID: PMC4513075 DOI: 10.1128/mbio.01012-15] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Trypanosoma cruzi is the etiologic agent of Chagas disease, and current methods for its genetic manipulation have been highly inefficient. We report here the use of the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated gene 9) system for disrupting genes in the parasite by three different strategies. The utility of the method was established by silencing genes encoding the GP72 protein, which is required for flagellar attachment, and paraflagellar rod proteins 1 and 2 (PFR1, PFR2), key components of the parasite flagellum. We used either vectors containing single guide RNA (sgRNA) and Cas9, separately or together, or one vector containing sgRNA and Cas9 plus donor DNA for homologous recombination to rapidly generate mutant cell lines in which the PFR1, PFR2, and GP72 genes have been disrupted. We demonstrate that genome editing of these endogenous genes in T. cruzi is successful without detectable toxicity of Cas9. Our results indicate that PFR1, PFR2, and GP72 contribute to flagellar attachment to the cell body and motility of the parasites. Therefore, CRISPR/Cas9 allows efficient gene disruption in an almost genetically intractable parasite and suggest that this method will improve the functional analyses of its genome. Trypanosoma cruzi is the agent of Chagas disease, which affects millions of people worldwide. Vaccines to prevent this disease are not available, and drug treatments are not completely effective. The study of the biology of this parasite through genetic approaches will make possible the development of new preventive or treatment options. Previous attempts to use the CRISPR/Cas9 in T. cruzi found a detectable but low frequency of Cas9-facilitated homologous recombination and fluorescent marker swap between exogenous genes, while Cas9 was toxic to the cells. In this report, we describe new approaches that generate complete disruption of an endogenous gene without toxicity to the parasites and establish the relevance of several proteins for flagellar attachment and motility.
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404
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Abstract
The prokaryotic CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9, an RNA-guided endonuclease, has been shown to mediate efficient genome editing in a wide variety of organisms. In the present study, the CRISPR-Cas9 system has been adapted to Leishmania donovani, a protozoan parasite that causes fatal human visceral leishmaniasis. We introduced the Cas9 nuclease into L. donovani and generated guide RNA (gRNA) expression vectors by using the L. donovani rRNA promoter and the hepatitis delta virus (HDV) ribozyme. It is demonstrated within that L. donovani mainly used homology-directed repair (HDR) and microhomology-mediated end joining (MMEJ) to repair the Cas9 nuclease-created double-strand DNA break (DSB). The nonhomologous end-joining (NHEJ) pathway appears to be absent in L. donovani. With this CRISPR-Cas9 system, it was possible to generate knockouts without selection by insertion of an oligonucleotide donor with stop codons and 25-nucleotide homology arms into the Cas9 cleavage site. Likewise, we disrupted and precisely tagged endogenous genes by inserting a bleomycin drug selection marker and GFP gene into the Cas9 cleavage site. With the use of Hammerhead and HDV ribozymes, a double-gRNA expression vector that further improved gene-targeting efficiency was developed, and it was used to make precise deletion of the 3-kb miltefosine transporter gene (LdMT). In addition, this study identified a novel single point mutation caused by CRISPR-Cas9 in LdMT (M381T) that led to miltefosine resistance, a concern for the only available oral antileishmanial drug. Together, these results demonstrate that the CRISPR-Cas9 system represents an effective genome engineering tool for L. donovani. Leishmania donovani is the causative agent of fatal visceral leishmaniasis. To understand Leishmania infection and pathogenesis and identify new drug targets for control of leishmaniasis, more-efficient ways to manipulate this parasite genome are required. In this study, we have implemented CRISPR-Cas9 genome-editing technology in L. donovani. Both single- and dual-gRNA expression vectors were developed using a strong RNA polymerase I promoter and ribozymes. With this system, it was possible to generate loss-of-function insertion and deletion mutations and introduce drug selection markers and the GFP sequence precisely into the L. donovani genome. These methods greatly improved the ability to manipulate this parasite genome and will help pave the way for high-throughput functional analysis of Leishmania genes. This study further revealed that double-stranded DNA breaks created by CRISPR-Cas9 were repaired by the homology-directed repair (HDR) pathway and microhomology-mediated end joining (MMEJ) in Leishmania.
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405
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Mitcheson DF, Tobin AB, Alam MM. Applying chemical genetic tools to the study of phospho-signalling pathways in malaria parasites. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1650-6. [PMID: 26143498 DOI: 10.1016/j.bbapap.2015.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/25/2015] [Accepted: 06/30/2015] [Indexed: 12/27/2022]
Abstract
Until very recently there has been very little information about the phospho-signalling pathways in apicomplexan parasites including the most virulent species of human malaria parasite, Plasmodium falciparum. With the advancement of mass spectrometry-based phosphoproteomics and the development of chemical genetic approaches to target specific parasite protein kinases, the complexity of the essential role played by phosphorylation in maintaining the viability of apicomplexan parasites is now being revealed. This review will describe these recent advances and will discuss how these approaches can be used to validate parasite protein kinases as drug targets and to determine the on- and off-target action of protein kinase inhibitors. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases.
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Affiliation(s)
- Deborah F Mitcheson
- Department of Cell Physiology and Pharmacology, University of Leicester, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Andrew B Tobin
- MRC Toxicology Unit, University of Leicester, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - Mahmood M Alam
- MRC Toxicology Unit, University of Leicester, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK.
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406
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Philip N, Waters AP. Conditional Degradation of Plasmodium Calcineurin Reveals Functions in Parasite Colonization of both Host and Vector. Cell Host Microbe 2015; 18:122-31. [PMID: 26118994 PMCID: PMC4509507 DOI: 10.1016/j.chom.2015.05.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/29/2015] [Accepted: 05/27/2015] [Indexed: 12/01/2022]
Abstract
Functional analysis of essential genes in the malarial parasite, Plasmodium, is hindered by lack of efficient strategies for conditional protein regulation. We report the development of a rapid, specific, and inducible chemical-genetic tool in the rodent malaria parasite, P. berghei, in which endogenous proteins engineered to contain the auxin-inducible degron (AID) are selectively degraded upon adding auxin. Application of AID to the calcium-regulated protein phosphatase, calcineurin, revealed functions in host and vector stages of parasite development. Whereas depletion of calcineurin in late-stage schizonts demonstrated its critical role in erythrocyte attachment and invasion in vivo, stage-specific depletion uncovered roles in gamete development, fertilization, and ookinete-to-oocyst and sporozoite-to-liver stage transitions. Furthermore, AID technology facilitated concurrent generation and phenotyping of transgenic lines, allowing multiple lines to be assessed simultaneously with significant reductions in animal use. This study highlights the broad applicability of AID for functional analysis of proteins across the Plasmodium life cycle. Calcineurin regulates colonization of host cells across the Plasmodium life cycle Calcineurin regulates male gametogenesis AID technology is broadly applicable to study protein function in Plasmodium Multiplexing of AID technology results in substantially reduced animal use
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Affiliation(s)
- Nisha Philip
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
| | - Andrew P Waters
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
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407
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Diagana TT. Supporting malaria elimination with 21st century antimalarial agent drug discovery. Drug Discov Today 2015; 20:1265-70. [PMID: 26103616 DOI: 10.1016/j.drudis.2015.06.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/27/2015] [Accepted: 06/15/2015] [Indexed: 12/26/2022]
Abstract
The burden of malaria has been considerably reduced over recent years. However, to achieve disease elimination, drug discovery for the next generation needs to focus on blocking disease transmission and on targeting the liver-stage forms of the parasite. Properties of the 'ideal' new antimalarial drug and the key scientific and technological advances that have led to recent progress in antimalarial drug discovery are reviewed. Using these advances, Novartis has built a robust pipeline of next-generation antimalarials. The preclinical and clinical development of two candidate drugs: KAE609 and KAF156, provide a framework for the path to breakthrough treatments that could be taking us a step closer to the vision of malaria elimination.
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Affiliation(s)
- Thierry T Diagana
- Novartis Institute for Tropical Diseases, 10 Biopolis Road, #05-01 Chromos, Singapore 138670, Singapore.
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408
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Sollelis L, Ghorbal M, MacPherson CR, Martins RM, Kuk N, Crobu L, Bastien P, Scherf A, Lopez-Rubio JJ, Sterkers Y. First efficient CRISPR-Cas9-mediated genome editing inLeishmaniaparasites. Cell Microbiol 2015; 17:1405-12. [DOI: 10.1111/cmi.12456] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Lauriane Sollelis
- University of Montpellier; Faculty of Medicine; Laboratory of Parasitology-Mycology; Paris France
- CNRS - 5290; IRD 224 - University of Montpellier (UMR ‘MiVEGEC’); Paris France
| | - Mehdi Ghorbal
- University of Montpellier; Faculty of Medicine; Laboratory of Parasitology-Mycology; Paris France
- CNRS - 5290; IRD 224 - University of Montpellier (UMR ‘MiVEGEC’); Paris France
| | - Cameron Ross MacPherson
- Institut Pasteur - INSERM U1201 - CNRS ERL9195; “Biology of Host-Parasite Interactions” Unit; Paris France
| | - Rafael Miyazawa Martins
- Institut Pasteur - INSERM U1201 - CNRS ERL9195; “Biology of Host-Parasite Interactions” Unit; Paris France
| | - Nada Kuk
- University of Montpellier; Faculty of Medicine; Laboratory of Parasitology-Mycology; Paris France
| | - Lucien Crobu
- CNRS - 5290; IRD 224 - University of Montpellier (UMR ‘MiVEGEC’); Paris France
| | - Patrick Bastien
- University of Montpellier; Faculty of Medicine; Laboratory of Parasitology-Mycology; Paris France
- CNRS - 5290; IRD 224 - University of Montpellier (UMR ‘MiVEGEC’); Paris France
- CHRU (Centre Hospitalier Universitaire de Montpellier); Department of Parasitology-Mycology; Montpellier France
| | - Artur Scherf
- Institut Pasteur - INSERM U1201 - CNRS ERL9195; “Biology of Host-Parasite Interactions” Unit; Paris France
| | - Jose-Juan Lopez-Rubio
- University of Montpellier; Faculty of Medicine; Laboratory of Parasitology-Mycology; Paris France
- CNRS - 5290; IRD 224 - University of Montpellier (UMR ‘MiVEGEC’); Paris France
| | - Yvon Sterkers
- University of Montpellier; Faculty of Medicine; Laboratory of Parasitology-Mycology; Paris France
- CNRS - 5290; IRD 224 - University of Montpellier (UMR ‘MiVEGEC’); Paris France
- CHRU (Centre Hospitalier Universitaire de Montpellier); Department of Parasitology-Mycology; Montpellier France
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409
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Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics 2015; 16:454. [PMID: 26070627 PMCID: PMC4465157 DOI: 10.1186/s12864-015-1603-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2015] [Indexed: 11/21/2022] Open
Abstract
Background The human malaria parasite Plasmodium falciparum has a complex and multi-stage life cycle that requires extensive and precise gene regulation to allow invasion and hijacking of host cells, transmission, and immune escape. To date, the regulatory elements orchestrating these critical parasite processes remain largely unknown. Yet it is becoming increasingly clear that long non-coding RNAs (lncRNAs) could represent a missing regulatory layer across a broad range of organisms. Results To investigate the regulatory capacity of lncRNA in P. falciparum, we harvested fifteen samples from two time-courses. Our sample set profiled 56 h of P. falciparum blood stage development. We then developed and validated strand-specific, non-polyA-selected RNA sequencing methods, and pursued the first assembly of P. falciparum strand-specific transcript structures from RNA sequencing data. This approach enabled the annotation of over one thousand lncRNA transcript models and their comprehensive global analysis: coding prediction, periodicity, stage-specificity, correlation, GC content, length, location relative to annotated transcripts, and splicing. We validated the complete splicing structure of three lncRNAs with compelling properties. Non-polyA-selected deep sequencing also enabled the prediction of hundreds of intriguing P. falciparum circular RNAs, six of which we validated experimentally. Conclusions We found that a subset of lncRNAs, including all subtelomeric lncRNAs, strongly peaked in expression during invasion. By contrast, antisense transcript levels significantly dropped during invasion. As compared to neighboring mRNAs, the expression of antisense-sense pairs was significantly anti-correlated during blood stage development, indicating transcriptional interference. We also validated that P. falciparum produces circRNAs, which is notable given the lack of RNA interference in the organism, and discovered that a highly expressed, five-exon antisense RNA is poised to regulate P. falciparum gametocyte development 1 (PfGDV1), a gene required for early sexual commitment events. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1603-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kate M Broadbent
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA.
| | - Jill C Broadbent
- FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
| | - Ulf Ribacke
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA. .,Department of Cell and Molecular Biology, BMC, Uppsala University, Uppsala, Sweden.
| | - Dyann Wirth
- Broad Institute, Cambridge, Massachusetts, USA. .,Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA.
| | - John L Rinn
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA.
| | - Pardis C Sabeti
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA. .,Broad Institute, Cambridge, Massachusetts, USA. .,FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA. .,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.
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410
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Lack of Artemisinin Resistance in Plasmodium falciparum in Uganda Based on Parasitological and Molecular Assays. Antimicrob Agents Chemother 2015; 59:5061-4. [PMID: 26033725 DOI: 10.1128/aac.00921-15] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 05/29/2015] [Indexed: 11/20/2022] Open
Abstract
We evaluated markers of artemisinin resistance in Plasmodium falciparum isolated in Kampala in 2014. By standard in vitro assays, all isolates were highly sensitive to dihydroartemisinin (DHA). By the ring-stage survival assay, after a 6-h DHA pulse, parasitemia was undetectable in 40 of 43 cultures at 72 h. Two of 53 isolates had nonsynonymous K13-propeller gene polymorphisms but did not have the mutations associated with resistance in Asia. Thus, we did not see evidence for artemisinin resistance in Uganda.
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411
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Implications of Glutathione Levels in the Plasmodium berghei Response to Chloroquine and Artemisinin. PLoS One 2015; 10:e0128212. [PMID: 26010448 PMCID: PMC4444287 DOI: 10.1371/journal.pone.0128212] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/23/2015] [Indexed: 11/19/2022] Open
Abstract
Malaria is one of the most devastating parasitic diseases worldwide. Plasmodium drug resistance remains a major challenge to malaria control and has led to the re-emergence of the disease. Chloroquine (CQ) and artemisinin (ART) are thought to exert their anti-malarial activity inducing cytotoxicity in the parasite by blocking heme degradation (for CQ) and increasing oxidative stress. Besides the contribution of the CQ resistance transporter (PfCRT) and the multidrug resistant gene (pfmdr), CQ resistance has also been associated with increased parasite glutathione (GSH) levels. ART resistance was recently shown to be associated with mutations in the K13-propeller protein. To analyze the role of GSH levels in CQ and ART resistance, we generated transgenic Plasmodium berghei parasites either deficient in or overexpressing the gamma-glutamylcysteine synthetase gene (pbggcs) encoding the rate-limiting enzyme in GSH biosynthesis. These lines produce either lower (pbggcs-ko) or higher (pbggcs-oe) levels of GSH than wild type parasites. In addition, GSH levels were determined in P. berghei parasites resistant to CQ and mefloquine (MQ). Increased GSH levels were detected in both, CQ and MQ resistant parasites, when compared to the parental sensitive clone. Sensitivity to CQ and ART remained unaltered in both pgggcs-ko and pbggcs-oe parasites when tested in a 4 days drug suppressive assay. However, recrudescence assays after the parasites have been exposed to a sub-lethal dose of ART showed that parasites with low levels of GSH are more sensitive to ART treatment. These results suggest that GSH levels influence Plasmodium berghei response to ART treatment.
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412
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Flaherty BR, Wang Y, Trope EC, Ho TG, Muralidharan V, Kennedy EJ, Peterson DS. The Stapled AKAP Disruptor Peptide STAD-2 Displays Antimalarial Activity through a PKA-Independent Mechanism. PLoS One 2015; 10:e0129239. [PMID: 26010880 PMCID: PMC4444124 DOI: 10.1371/journal.pone.0129239] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/06/2015] [Indexed: 11/19/2022] Open
Abstract
Drug resistance poses a significant threat to ongoing malaria control efforts. Coupled with lack of a malaria vaccine, there is an urgent need for the development of new antimalarials with novel mechanisms of action and low susceptibility to parasite drug resistance. Protein Kinase A (PKA) has been implicated as a critical regulator of pathogenesis in malaria. Therefore, we sought to investigate the effects of disrupted PKA signaling as a possible strategy for inhibition of parasite replication. Host PKA activity is partly regulated by a class of proteins called A Kinase Anchoring Proteins (AKAPs), and interaction between HsPKA and AKAP can be inhibited by the stapled peptide Stapled AKAP Disruptor 2 (STAD-2). STAD-2 was tested for permeability to and activity against Plasmodium falciparum blood stage parasites in vitro. The compound was selectively permeable only to infected red blood cells (iRBC) and demonstrated rapid antiplasmodial activity, possibly via iRBC lysis (IC50 ≈ 1 μM). STAD-2 localized within the parasite almost immediately post-treatment but showed no evidence of direct association with PKA, indicating that STAD-2 acts via a PKA-independent mechanism. Furosemide-insensitive parasite permeability pathways in the iRBC were largely responsible for uptake of STAD-2. Further, peptide import was highly specific to STAD-2 as evidenced by low permeability of control stapled peptides. Selective uptake and antiplasmodial activity of STAD-2 provides important groundwork for the development of stapled peptides as potential antimalarials. Such peptides may also offer an alternative strategy for studying protein-protein interactions critical to parasite development and pathogenesis.
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Affiliation(s)
- Briana R. Flaherty
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Yuxiao Wang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
| | - Edward C. Trope
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, United States of America
| | - Tienhuei G. Ho
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
| | - Vasant Muralidharan
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (EK); David Peterson: (DP)
| | - David S. Peterson
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (EK); David Peterson: (DP)
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413
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de Koning-Ward TF, Gilson PR, Crabb BS. Advances in molecular genetic systems in malaria. Nat Rev Microbiol 2015; 13:373-87. [DOI: 10.1038/nrmicro3450] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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414
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Asada M, Yahata K, Hakimi H, Yokoyama N, Igarashi I, Kaneko O, Suarez CE, Kawazu SI. Transfection of Babesia bovis by Double Selection with WR99210 and Blasticidin-S and Its Application for Functional Analysis of Thioredoxin Peroxidase-1. PLoS One 2015; 10:e0125993. [PMID: 25962142 PMCID: PMC4427477 DOI: 10.1371/journal.pone.0125993] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/27/2015] [Indexed: 11/28/2022] Open
Abstract
Genetic manipulation is an essential technique to analyze gene function; however, limited methods are available for Babesia bovis, a causative pathogen of the globally important cattle disease, bovine babesiosis. To date, two stable transfection systems have been developed for B. bovis, using selectable markers blasticidin-S deaminase (bsd) or human dihydrofolate reductase (hdhfr). In this work, we combine these two selectable markers in a sequential transfection system. Specifically, a parent transgenic B. bovis line which episomally expresses green fluorescent protein (GFP) and human dihydrofolate reductase (hDHFR), was transfected with a plasmid encoding a fusion protein consisting of red fluorescent protein (RFP) and blasticidin-S deaminase (BSD). Selection with WR99210 and blasticidin-S resulted in the emergence of parasites double positive for GFP and RFP. We then applied this method to complement gene function in a parasite line in which thioredoxin peroxidase-1 (Bbtpx-1) gene was knocked out using hDHFR as a selectable marker. A plasmid was constructed harboring both RFP-BSD and Bbtpx-1 expression cassettes, and transfected into a Bbtpx-1 knockout (KO) parasite. Transfectants were independently obtained by two transfection methods, episomal transfection and genome integration. Complementation of Bbtpx-1 resulted in full recovery of resistance to nitrosative stress, via the nitric oxide donor sodium nitroprusside, which was impaired in the Bbtpx-1 KO parasites. In conclusion, we developed a sequential transfection method in B. bovis and subsequently applied this technique in a gene complementation study. This method will enable broader genetic manipulation of Babesia toward enhancing our understanding of the biology of this parasite.
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Affiliation(s)
- Masahito Asada
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto, Nagasaki, Japan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Japan
| | - Kazuhide Yahata
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Hassan Hakimi
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto, Nagasaki, Japan
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Japan
| | - Naoaki Yokoyama
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Japan
| | - Ikuo Igarashi
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Japan
| | - Osamu Kaneko
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto, Nagasaki, Japan
| | - Carlos E. Suarez
- Program in Vector-Borne Diseases, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America
- Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, Washington, United States of America
- * E-mail: E-mail: (CES); (S-IK)
| | - Shin-ichiro Kawazu
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Japan
- * E-mail: E-mail: (CES); (S-IK)
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415
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Mbengue A, Bhattacharjee S, Pandharkar T, Liu H, Estiu G, Stahelin RV, Rizk SS, Njimoh DL, Ryan Y, Chotivanich K, Nguon C, Ghorbal M, Lopez-Rubio JJ, Pfrender M, Emrich S, Mohandas N, Dondorp AM, Wiest O, Haldar K. A molecular mechanism of artemisinin resistance in Plasmodium falciparum malaria. Nature 2015; 520:683-7. [PMID: 25874676 PMCID: PMC4417027 DOI: 10.1038/nature14412] [Citation(s) in RCA: 401] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 03/19/2015] [Indexed: 11/08/2022]
Abstract
Artemisinins are the cornerstone of anti-malarial drugs. Emergence and spread of resistance to them raises risk of wiping out recent gains achieved in reducing worldwide malaria burden and threatens future malaria control and elimination on a global level. Genome-wide association studies (GWAS) have revealed parasite genetic loci associated with artemisinin resistance. However, there is no consensus on biochemical targets of artemisinin. Whether and how these targets interact with genes identified by GWAS, remains unknown. Here we provide biochemical and cellular evidence that artemisinins are potent inhibitors of Plasmodium falciparum phosphatidylinositol-3-kinase (PfPI3K), revealing an unexpected mechanism of action. In resistant clinical strains, increased PfPI3K was associated with the C580Y mutation in P. falciparum Kelch13 (PfKelch13), a primary marker of artemisinin resistance. Polyubiquitination of PfPI3K and its binding to PfKelch13 were reduced by the PfKelch13 mutation, which limited proteolysis of PfPI3K and thus increased levels of the kinase, as well as its lipid product phosphatidylinositol-3-phosphate (PI3P). We find PI3P levels to be predictive of artemisinin resistance in both clinical and engineered laboratory parasites as well as across non-isogenic strains. Elevated PI3P induced artemisinin resistance in absence of PfKelch13 mutations, but remained responsive to regulation by PfKelch13. Evidence is presented for PI3P-dependent signalling in which transgenic expression of an additional kinase confers resistance. Together these data present PI3P as the key mediator of artemisinin resistance and the sole PfPI3K as an important target for malaria elimination.
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Affiliation(s)
- Alassane Mbengue
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Souvik Bhattacharjee
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Trupti Pandharkar
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Haining Liu
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Guillermina Estiu
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Robert V Stahelin
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA [3] Department of Biochemistry &Molecular Biology, Indiana University School of Medicine-South Bend, 143 Raclin-Carmichael Hall, 1234 Notre Dame Avenue, South Bend, Indiana 46617, USA
| | - Shahir S Rizk
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Dieudonne L Njimoh
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA [3] Departmen of. Biochemistry and Molecular Biology, Faculty of Science University of Buea, P.O. Box 63 Buea, Southwest region, Cameroon
| | - Yana Ryan
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Kesinee Chotivanich
- Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand
| | - Chea Nguon
- National Center for Parasitology, Entomology and Malaria Control, 12302 Phnom Penh, Monivong Blvd, Phnom Penh 12302, Cambodia
| | - Mehdi Ghorbal
- CNRS 5290/IRD 224/University Montpellier 1&2 ("MiVEGEC"), Montpellier, France
| | | | - Michael Pfrender
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Scott Emrich
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, Indiana 46556. USA
| | | | - Arjen M Dondorp
- 1] Faculty of Tropical Medicine, Mahidol University, 420/6 Ratchawithi Road, Ratchathewi, Bangkok 10400, Thailand [2] Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN. UK
| | - Olaf Wiest
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA [3] Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Kasturi Haldar
- 1] Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana 46556, USA [2] Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
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416
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Dogovski C, Xie SC, Burgio G, Bridgford J, Mok S, McCaw JM, Chotivanich K, Kenny S, Gnädig N, Straimer J, Bozdech Z, Fidock DA, Simpson JA, Dondorp AM, Foote S, Klonis N, Tilley L. Targeting the cell stress response of Plasmodium falciparum to overcome artemisinin resistance. PLoS Biol 2015; 13:e1002132. [PMID: 25901609 PMCID: PMC4406523 DOI: 10.1371/journal.pbio.1002132] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 03/16/2015] [Indexed: 11/30/2022] Open
Abstract
Successful control of falciparum malaria depends greatly on treatment with artemisinin combination therapies. Thus, reports that resistance to artemisinins (ARTs) has emerged, and that the prevalence of this resistance is increasing, are alarming. ART resistance has recently been linked to mutations in the K13 propeller protein. We undertook a detailed kinetic analysis of the drug responses of K13 wild-type and mutant isolates of Plasmodium falciparum sourced from a region in Cambodia (Pailin). We demonstrate that ART treatment induces growth retardation and an accumulation of ubiquitinated proteins, indicative of a cellular stress response that engages the ubiquitin/proteasome system. We show that resistant parasites exhibit lower levels of ubiquitinated proteins and delayed onset of cell death, indicating an enhanced cell stress response. We found that the stress response can be targeted by inhibiting the proteasome. Accordingly, clinically used proteasome inhibitors strongly synergize ART activity against both sensitive and resistant parasites, including isogenic lines expressing mutant or wild-type K13. Synergy is also observed against Plasmodium berghei in vivo. We developed a detailed model of parasite responses that enables us to infer, for the first time, in vivo parasite clearance profiles from in vitro assessments of ART sensitivity. We provide evidence that the clinical marker of resistance (delayed parasite clearance) is an indirect measure of drug efficacy because of the persistence of unviable parasites with unchanged morphology in the circulation, and we suggest alternative approaches for the direct measurement of viability. Our model predicts that extending current three-day ART treatment courses to four days, or splitting the doses, will efficiently clear resistant parasite infections. This work provides a rationale for improving the detection of ART resistance in the field and for treatment strategies that can be employed in areas with ART resistance. Resistance to artemisinin antimalarial drugs is jeopardizing malaria control. This study shows that proteasome-mediated stress responses can be targeted to overcome artemisinin resistance and suggests alternate therapeutic regimens and monitoring strategies. Resistance to artemisinin antimalarials, some of the most effective antimalarial drugs, has emerged in Southeast Asia, jeopardizing malaria control. We have undertaken a detailed study of artemisinin-sensitive and-resistant strains of Plasmodium falciparum, the parasite responsible for malaria, taken directly from the field in a region where resistance is developing. We compared these strains to lab strains engineered with either mutant or wild-type resistance alleles. We demonstrate that in sensitive P. falciparum, artemisinin induces growth retardation and accumulation of ubiquitinated proteins, indicating that the drugs activate the cellular stress response. Resistant parasites, on the other hand, exhibit reduced protein ubiquitination and delayed onset of cell death following drug exposure. We show that proteasome inhibitors strongly synergize artemisinin activity, offering a means of overcoming artemisinin resistance. We have developed a detailed model of parasite responses and have modelled in vivo clearance profiles. Our data indicate that extending artemisinin treatment from the standard three-day treatment to a four-day treatment will clear resistant parasites, thus preserving the use of this critical therapy in areas experiencing artemisinin resistance.
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Affiliation(s)
- Con Dogovski
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stanley C Xie
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gaetan Burgio
- John Curtin School of Medical Research, the Australian National University, Canberra, Australian Capital Territory, Australia; Australian School of Advanced Medicine, Macquarie University, Sydney, New South Wales, Australia
| | - Jess Bridgford
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sachel Mok
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - James M McCaw
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia; Murdoch Childrens Research Institute, Royal Childrens Hospital, Victoria, Australia
| | | | - Shannon Kenny
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nina Gnädig
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Judith Straimer
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, New York, United States of America; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, New York, United States of America
| | - Julie A Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria, Australia
| | - Arjen M Dondorp
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford, United Kingdom
| | - Simon Foote
- John Curtin School of Medical Research, the Australian National University, Canberra, Australian Capital Territory, Australia
| | - Nectarios Klonis
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leann Tilley
- Department of Biochemistry and Molecular Biology and ARC Centre of Excellence for Coherent X-ray Science, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
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417
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Wang Z, Shrestha S, Li X, Miao J, Yuan L, Cabrera M, Grube C, Yang Z, Cui L. Prevalence of K13-propeller polymorphisms in Plasmodium falciparum from China-Myanmar border in 2007-2012. Malar J 2015; 14:168. [PMID: 25927592 PMCID: PMC4404080 DOI: 10.1186/s12936-015-0672-9] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/16/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The recent emergence and spread of artemisinin resistance in the Greater Mekong Subregion poses a great threat to malaria control and elimination. A K13-propeller gene (K13), PF3D7_1343700, has been associated lately with artemisinin resistance both in vitro and in vivo. This study aimed to investigate the K13 polymorphisms in Plasmodium falciparum parasites from the China-Myanmar border area where artemisinin use has the longest history. METHODS A total of 180 archived P. falciparum isolates containing 191 parasite clones, mainly collected in 2007-2012 from the China-Myanmar area, were used to obtain the full-length K13 gene sequences. RESULTS Seventeen point mutations were identified in 46.1% (88/191) parasite clones, of which seven were new. The F446I mutation predominated in 27.2% of the parasite clones. The C580Y mutation that is correlated with artemisinin resistance was detected at a low frequency of 1.6%. Collectively, 43.1% of the parasite clones contained point mutations in the kelch domain of the K13 gene. Moreover, there was a trend of increase in the frequency of parasites carrying kelch domain mutations through the years of sample collection. In addition, a microsatellite variation in the N-terminus of the K13 protein was found to have reached a high frequency (69.1%). CONCLUSIONS This study documented the presence of mutations in the K13 gene in parasite populations from the China-Myanmar border. Mutations present in the kelch domain have become prevalent (>40%). A predominant mutation F446I and a prevalent microsatellite variation in the N-terminus were identified, but their importance in artemisinin resistance remains to be elucidated.
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Affiliation(s)
- Zenglei Wang
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Sony Shrestha
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Xiaolian Li
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Jun Miao
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Lili Yuan
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China.
| | - Mynthia Cabrera
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Caitlin Grube
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, Yunnan Province, 650500, China.
| | - Liwang Cui
- Department of Entomology, The Pennsylvania State University, University Park, PA, 16802, USA.
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418
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Rajendran SRCK, Yau YY, Pandey D, Kumar A. CRISPR-Cas9 Based Genome Engineering: Opportunities in Agri-Food-Nutrition and Healthcare. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:261-75. [PMID: 25871888 DOI: 10.1089/omi.2015.0023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recently developed strategies and techniques that make use of the vast amount of genetic information to perform targeted perturbations in the genome of living organisms are collectively referred to as genome engineering. The wide array of applications made possible by the use of this technology range from agriculture to healthcare. This, along with the applications involving basic biological research, has made it a very dynamic and active field of research. This review focuses on the CRISPR system from its discovery and role in bacterial adaptive immunity to the most recent developments, and its possible applications in agriculture and modern medicine.
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Affiliation(s)
- Subin Raj Cheri Kunnumal Rajendran
- 1 Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology , Pantnagar, U.S. Nagar, Uttarakhand, India
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419
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Dantzler KW, Ravel DB, Brancucci NM, Marti M. Ensuring transmission through dynamic host environments: host-pathogen interactions in Plasmodium sexual development. Curr Opin Microbiol 2015; 26:17-23. [PMID: 25867628 DOI: 10.1016/j.mib.2015.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/09/2015] [Indexed: 01/08/2023]
Abstract
A renewed global commitment to malaria elimination lends urgency to understanding the biology of Plasmodium transmission stages. Recent progress toward uncovering the mechanisms underlying Plasmodium falciparum sexual differentiation and maturation reveals potential targets for transmission-blocking drugs and vaccines. The identification of parasite factors that alter sexual differentiation, including extracellular vesicles and a master transcriptional regulator, suggest that parasites make epigenetically controlled developmental decisions based on environmental cues. New insights into sexual development, especially host cell remodeling and sequestration in the bone marrow, highlight open questions regarding parasite homing to the tissue, transmigration across the vascular endothelium, and maturation in the parenchyma. Novel molecular and translational tools will provide further opportunities to define host-parasite interactions and design effective transmission-blocking therapeutics.
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Affiliation(s)
- Kathleen W Dantzler
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Deepali B Ravel
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Nicolas Mb Brancucci
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthias Marti
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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420
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DNA repair mechanisms and their biological roles in the malaria parasite Plasmodium falciparum. Microbiol Mol Biol Rev 2015; 78:469-86. [PMID: 25184562 DOI: 10.1128/mmbr.00059-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Research into the complex genetic underpinnings of the malaria parasite Plasmodium falciparum is entering a new era with the arrival of site-specific genome engineering. Previously restricted only to model systems but now expanded to most laboratory organisms, and even to humans for experimental gene therapy studies, this technology allows researchers to rapidly generate previously unattainable genetic modifications. This technological advance is dependent on DNA double-strand break repair (DSBR), specifically homologous recombination in the case of Plasmodium. Our understanding of DSBR in malaria parasites, however, is based largely on assumptions and knowledge taken from other model systems, which do not always hold true in Plasmodium. Here we describe the causes of double-strand breaks, the mechanisms of DSBR, and the differences between model systems and P. falciparum. These mechanisms drive basic parasite functions, such as meiosis, antigen diversification, and copy number variation, and allow the parasite to continually evolve in the contexts of host immune pressure and drug selection. Finally, we discuss the new technologies that leverage DSBR mechanisms to accelerate genetic investigations into this global infectious pathogen.
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421
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Sibley CH. Observing in real time the evolution of artemisinin resistance in Plasmodium falciparum. BMC Med 2015; 13:67. [PMID: 25889405 PMCID: PMC4379603 DOI: 10.1186/s12916-015-0316-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/10/2015] [Indexed: 01/25/2023] Open
Abstract
Simple genetic changes that correlate with drug resistance are used routinely to identify resistant pathogens. These "molecular markers" have usually been defined long after the phenotype of resistance was noted. The molecular changes at the "end game" reflect a long and complex evolution of genetic changes, but once a solidly resistant set of changes assembles under drug selection, that genotype is likely to become fixed, and resistant pathogens will spread widely. Artemisinins are currently used worldwide to treat malaria caused by Plasmodium falciparum, but parasite response has diminished rapidly in the Mekong region of Southeast Asia. Should artemisinins lose potency completely and this effect spread worldwide, effective malaria treatment would be almost impossible. The full range of modern methods has been applied to define rapidly the genetic changes responsible. Changes associated with artemisinin resistance are complex and seem to be evolving rapidly, especially in Southeast Asia. This is a rare chance to observe the early stages in evolution of resistance, and to develop strategies to reverse or mitigate the trend and to protect these key medicines.
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Affiliation(s)
- Carol Hopkins Sibley
- Worldwide Antimalarial Resistance Network, Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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422
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Matz JM, Kooij TWA. Towards genome-wide experimental genetics in the in vivo malaria model parasite Plasmodium berghei. Pathog Glob Health 2015; 109:46-60. [PMID: 25789828 DOI: 10.1179/2047773215y.0000000006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Plasmodium berghei was identified as a parasite of thicket rats (Grammomys dolichurus) and Anopheles dureni mosquitoes in African highland forests. Successful adaptation to a range of rodent and mosquito species established P. berghei as a malaria model parasite. The introduction of stable transfection technology, permitted classical reverse genetics strategies and thus systematic functional profiling of the gene repertoire. In the past 10 years following the publication of the P. berghei genome sequence, many new tools for experimental genetics approaches have been developed and existing ones have been improved. The infection of mice is the principal limitation towards a genome-wide repository of mutant parasite lines. In the past few years, there have been some promising and most welcome developments that allow rapid selection and isolation of recombinant parasites while simultaneously minimising animal usage. Here, we provide an overview of all the currently available tools and methods.
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423
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Artemisinin-resistant Plasmodium falciparum parasites exhibit altered patterns of development in infected erythrocytes. Antimicrob Agents Chemother 2015; 59:3156-67. [PMID: 25779582 DOI: 10.1128/aac.00197-15] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/08/2015] [Indexed: 01/08/2023] Open
Abstract
Artemisinin derivatives are used in combination with other antimalarial drugs for treatment of multidrug-resistant malaria worldwide. Clinical resistance to artemisinin recently emerged in southeast Asia, yet in vitro phenotypes for discerning mechanism(s) of resistance remain elusive. Here, we describe novel phenotypic resistance traits expressed by artemisinin-resistant Plasmodium falciparum. The resistant parasites exhibit altered patterns of development that result in reduced exposure to drug at the most susceptible stage of development in erythrocytes (trophozoites) and increased exposure in the most resistant stage (rings). In addition, a novel in vitro delayed clearance assay (DCA) that assesses drug effects on asexual stages was found to correlate with parasite clearance half-life in vivo as well as with mutations in the Kelch domain gene associated with resistance (Pf3D7_1343700). Importantly, all of the resistance phenotypes were stable in cloned parasites for more than 2 years without drug pressure. The results demonstrate artemisinin-resistant P. falciparum has evolved a novel mechanism of phenotypic resistance to artemisinin drugs linked to abnormal cell cycle regulation. These results offer insights into a novel mechanism of drug resistance in P. falciparum and new tools for monitoring the spread of artemisinin resistance.
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424
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Nacer A, Claes A, Roberts A, Scheidig-Benatar C, Sakamoto H, Ghorbal M, Lopez-Rubio JJ, Mattei D. Discovery of a novel and conserved Plasmodium falciparum exported protein that is important for adhesion of PfEMP1 at the surface of infected erythrocytes. Cell Microbiol 2015; 17:1205-16. [PMID: 25703704 PMCID: PMC4654329 DOI: 10.1111/cmi.12430] [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: 01/15/2015] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/27/2022]
Abstract
Plasmodium falciparum virulence is linked to its ability to sequester in post-capillary venules in the human host. Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is the main variant surface antigen implicated in this process. Complete loss of parasite adhesion is linked to a large subtelomeric deletion on chromosome 9 in a number of laboratory strains such as D10 and T9-96. Similar to the cytoadherent reference line FCR3, D10 strain expresses PfEMP1 on the surface of parasitized erythrocytes, however without any detectable cytoadhesion. To investigate which of the deleted subtelomeric genes may be implicated in parasite adhesion, we selected 12 genes for D10 complementation studies that are predicted to code for proteins exported to the red blood cell. We identified a novel single copy gene (PF3D7_0936500) restricted to P. falciparum that restores adhesion to CD36, termed here virulence-associated protein 1 (Pfvap1). Protein knockdown and gene knockout experiments confirmed a role of PfVAP1 in the adhesion process in FCR3 parasites. PfVAP1 is co-exported with PfEMP1 into the host cell via vesicle-like structures called Maurer's clefts. This study identifies a novel highly conserved parasite molecule that contributes to parasite virulence possibly by assisting PfEMP1 to establish functional adhesion at the host cell surface.
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Affiliation(s)
- Adéla Nacer
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France.,CNRS ERL9195, 25, Rue du Dr. Roux, Paris, F-75015, France
| | - Aurélie Claes
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France.,CNRS ERL9195, 25, Rue du Dr. Roux, Paris, F-75015, France
| | - Amy Roberts
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France.,CNRS ERL9195, 25, Rue du Dr. Roux, Paris, F-75015, France
| | - Christine Scheidig-Benatar
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France.,CNRS ERL9195, 25, Rue du Dr. Roux, Paris, F-75015, France
| | - Hiroshi Sakamoto
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France.,CNRS ERL9195, 25, Rue du Dr. Roux, Paris, F-75015, France
| | - Mehdi Ghorbal
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France
| | - Jose-Juan Lopez-Rubio
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France
| | - Denise Mattei
- Biology of Parasite-Host Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, 25, Rue du Dr. Roux, Paris, F-75015, France.,INSERM U1201, 25, Rue du Dr. Roux, Paris, F-75015, France.,CNRS ERL9195, 25, Rue du Dr. Roux, Paris, F-75015, France
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425
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Taylor SM, Parobek CM, DeConti DK, Kayentao K, Coulibaly SO, Greenwood BM, Tagbor H, Williams J, Bojang K, Njie F, Desai M, Kariuki S, Gutman J, Mathanga DP, Mårtensson A, Ngasala B, Conrad MD, Rosenthal PJ, Tshefu AK, Moormann AM, Vulule JM, Doumbo OK, ter Kuile FO, Meshnick SR, Bailey JA, Juliano JJ. Absence of putative artemisinin resistance mutations among Plasmodium falciparum in Sub-Saharan Africa: a molecular epidemiologic study. J Infect Dis 2015; 211:680-8. [PMID: 25180240 PMCID: PMC4402372 DOI: 10.1093/infdis/jiu467] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/21/2014] [Indexed: 11/12/2022] Open
Abstract
Plasmodium falciparum parasites that are resistant to artemisinins have been detected in Southeast Asia. Resistance is associated with several polymorphisms in the parasite's K13-propeller gene. The molecular epidemiology of these artemisinin resistance genotypes in African parasite populations is unknown. We developed an assay to quantify rare polymorphisms in parasite populations that uses a pooled deep-sequencing approach to score allele frequencies, validated it by evaluating mixtures of laboratory parasite strains, and then used it to screen P. falciparum parasites from >1100 African infections collected since 2002 from 14 sites across sub-Saharan Africa. We found no mutations in African parasite populations that are associated with artemisinin resistance in Southeast Asian parasites. However, we observed 15 coding mutations, including 12 novel mutations, and limited allele sharing between parasite populations, consistent with a large reservoir of naturally occurring K13-propeller variation. Although polymorphisms associated with artemisinin resistance in P. falciparum in Southeast Asia are not prevalent in sub-Saharan Africa, numerous K13-propeller coding polymorphisms circulate in Africa. Although their distributions do not support a widespread selective sweep for an artemisinin-resistant phenotype, the impact of these mutations on artemisinin susceptibility is unknown and will require further characterization. Rapid, scalable molecular surveillance offers a useful adjunct in tracking and containing artemisinin resistance.
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Affiliation(s)
- Steve M. Taylor
- Division of Infectious Diseases, Department of Medicine
- Duke Global Health Institute, Duke University Medical Center, Durham
- Department of Epidemiology, Gillings School of Global Public Health
| | | | | | - Kassoum Kayentao
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Medicine, Pharmacy, and Odontostomatology, University of Science, Techniques, and Technologies of Bamako, Mali
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
| | | | - Brian M. Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Harry Tagbor
- Department of Community Health, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi
| | - John Williams
- Navrongo Health Research Centre, Ghana Health Service, Navrongo
| | - Kalifa Bojang
- Medical Research Council Laboratories, Banjul, Gambia
| | - Fanta Njie
- Medical Research Council Laboratories, Banjul, Gambia
| | - Meghna Desai
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
- CDC–Kenya
| | | | - Julie Gutman
- Malaria Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia
| | - Don P. Mathanga
- Malaria Alert Center, University of Malawi College of Medicine, Blantyre
- Department of Community Health, College of Medicine, Lilongwe, Malawi
| | - Andreas Mårtensson
- Malaria Research, Department of Medicine Solna
- Global Health, Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Billy Ngasala
- Department of Parasitology, Muhumbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | | | - Antoinette K. Tshefu
- Ecole de Sante Publique, Faculte de Medicine, University of Kinshasa, Democratic Republic of the Congo
| | | | | | - Ogobara K. Doumbo
- Department of Epidemiology of Parasitic Diseases, Malaria Research and Training Center, Faculty of Medicine, Pharmacy, and Odontostomatology, University of Science, Techniques, and Technologies of Bamako, Mali
| | - Feiko O. ter Kuile
- Department of Clinical Sciences, Liverpool School of Tropical Medicine
- Center for Global Health Research, KEMRI, Kisumu, Kenya
| | | | - Jeffrey A. Bailey
- Division of Transfusion Medicine
- Program in Bioinformatics and Integrative Biology, University of Massachusetts School of Medicine, Worcester
| | - Jonathan J. Juliano
- Curriculum in Genetics and Molecular Biology
- Divison of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill
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426
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Kwiatkowski D. Malaria genomics: tracking a diverse and evolving parasite population. Int Health 2015; 7:82-4. [PMID: 25733556 PMCID: PMC4379983 DOI: 10.1093/inthealth/ihv007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 01/21/2015] [Accepted: 01/21/2015] [Indexed: 11/14/2022] Open
Abstract
Malaria parasites are continually evolving to evade the immune system and human attempts to control the disease. To eliminate malaria from regions where it is deeply entrenched we need ways of monitoring what is going on in the parasite population, detecting problematic changes as soon as they arise, and executing a prompt and effective response based on a deep understanding of this natural evolutionary process. Powerful new tools to address this problem are emerging from the fast-growing field of genomic epidemiology, driven by new sequencing technologies and computational methods that allow parasite genome variation to be studied in much greater detail and in many more samples than was previously considered possible. These new tools will provide a deep understanding of what is going on in the parasite population, generating actionable knowledge for strategic planning of control interventions, for monitoring their effects and steering them for greatest impact, and for raising the alert if things start to go wrong.
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Affiliation(s)
- Dominic Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA and Oxford University, Henry Wellcome Building for Molecular Physiology, Old Road Campus, Headington, Oxford, OX3 7BN, UK
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427
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Gomes AR, Bushell E, Schwach F, Girling G, Anar B, Quail MA, Herd C, Pfander C, Modrzynska K, Rayner JC, Billker O. A genome-scale vector resource enables high-throughput reverse genetic screening in a malaria parasite. Cell Host Microbe 2015; 17:404-413. [PMID: 25732065 PMCID: PMC4362957 DOI: 10.1016/j.chom.2015.01.014] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/01/2014] [Accepted: 01/07/2015] [Indexed: 10/30/2022]
Abstract
The genome-wide identification of gene functions in malaria parasites is hampered by a lack of reverse genetic screening methods. We present a large-scale resource of barcoded vectors with long homology arms for effective modification of the Plasmodium berghei genome. Cotransfecting dozens of vectors into the haploid blood stages creates complex pools of barcoded mutants, whose competitive fitness can be measured during infection of a single mouse using barcode sequencing (barseq). To validate the utility of this resource, we rescreen the P. berghei kinome, using published kinome screens for comparison. We find that several protein kinases function redundantly in asexual blood stages and confirm the targetability of kinases cdpk1, gsk3, tkl3, and PBANKA_082960 by genotyping cloned mutants. Thus, parallel phenotyping of barcoded mutants unlocks the power of reverse genetic screening for a malaria parasite and will enable the systematic identification of genes essential for in vivo parasite growth and transmission.
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Affiliation(s)
- Ana Rita Gomes
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Ellen Bushell
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Frank Schwach
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Gareth Girling
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Burcu Anar
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Colin Herd
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | - Claudia Pfander
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK
| | | | - Julian C Rayner
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK.
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1SA, UK.
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428
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Tun KM, Imwong M, Lwin KM, Win AA, Hlaing TM, Hlaing T, Lin K, Kyaw MP, Plewes K, Faiz MA, Dhorda M, Cheah PY, Pukrittayakamee S, Ashley EA, Anderson TJC, Nair S, McDew-White M, Flegg JA, Grist EPM, Guerin P, Maude RJ, Smithuis F, Dondorp AM, Day NPJ, Nosten F, White NJ, Woodrow CJ. Spread of artemisinin-resistant Plasmodium falciparum in Myanmar: a cross-sectional survey of the K13 molecular marker. THE LANCET. INFECTIOUS DISEASES 2015; 15:415-21. [PMID: 25704894 PMCID: PMC4374103 DOI: 10.1016/s1473-3099(15)70032-0] [Citation(s) in RCA: 315] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
BACKGROUND Emergence of artemisinin resistance in southeast Asia poses a serious threat to the global control of Plasmodium falciparum malaria. Discovery of the K13 marker has transformed approaches to the monitoring of artemisinin resistance, allowing introduction of molecular surveillance in remote areas through analysis of DNA. We aimed to assess the spread of artemisinin-resistant P falciparum in Myanmar by determining the relative prevalence of P falciparum parasites carrying K13-propeller mutations. METHODS We did this cross-sectional survey at malaria treatment centres at 55 sites in ten administrative regions in Myanmar, and in relevant border regions in Thailand and Bangladesh, between January, 2013, and September, 2014. K13 sequences from P falciparum infections were obtained mainly by passive case detection. We entered data into two geostatistical models to produce predictive maps of the estimated prevalence of mutations of the K13 propeller region across Myanmar. FINDINGS Overall, 371 (39%) of 940 samples carried a K13-propeller mutation. We recorded 26 different mutations, including nine mutations not described previously in southeast Asia. In seven (70%) of the ten administrative regions of Myanmar, the combined K13-mutation prevalence was more than 20%. Geospatial mapping showed that the overall prevalence of K13 mutations exceeded 10% in much of the east and north of the country. In Homalin, Sagaing Region, 25 km from the Indian border, 21 (47%) of 45 parasite samples carried K13-propeller mutations. INTERPRETATION Artemisinin resistance extends across much of Myanmar. We recorded P falciparum parasites carrying K13-propeller mutations at high prevalence next to the northwestern border with India. Appropriate therapeutic regimens should be tested urgently and implemented comprehensively if spread of artemisinin resistance to other regions is to be avoided. FUNDING Wellcome Trust-Mahidol University-Oxford Tropical Medicine Research Programme and the Bill & Melinda Gates Foundation.
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Affiliation(s)
- Kyaw M Tun
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar; Defence Services Medical Research Centre, Naypyitaw, Myanmar
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Mahidol University, Bangkok, Thailand; Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
| | - Khin M Lwin
- Shoklo Malaria Research Unit, Mae Sot, Thailand
| | - Aye A Win
- Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Institute of Medicine 1, Yangon, Myanmar
| | - Tin M Hlaing
- Defence Services Medical Research Centre, Naypyitaw, Myanmar
| | - Thaung Hlaing
- Defence Services Medical Research Centre, Naypyitaw, Myanmar; Department of Health, Ministry of Health, Naypyitaw, Myanmar
| | - Khin Lin
- Department of Medical Research, Upper Myanmar, Myanmar
| | - Myat P Kyaw
- Department of Medical Research, Lower Myanmar, Myanmar
| | - Katherine Plewes
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Abul Faiz
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Dev Care Foundation, Dhaka, Bangladesh
| | - Mehul Dhorda
- WorldWide Antimalarial Resistance Network, Oxford, UK; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Phaik Yeong Cheah
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Elizabeth A Ashley
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tim J C Anderson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shalini Nair
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Marina McDew-White
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Jennifer A Flegg
- WorldWide Antimalarial Resistance Network, Oxford, UK; School of Mathematical Sciences, Monash University, Melbourne, Australia
| | | | | | - Richard J Maude
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frank Smithuis
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Medical Action Myanmar, Yangon, Myanmar
| | - Arjen M Dondorp
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas P J Day
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - François Nosten
- Shoklo Malaria Research Unit, Mae Sot, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas J White
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Charles J Woodrow
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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429
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Straimer J, Gnädig NF, Witkowski B, Amaratunga C, Duru V, Ramadani AP, Dacheux M, Khim N, Zhang L, Lam S, Gregory PD, Urnov FD, Mercereau-Puijalon O, Benoit-Vical F, Fairhurst RM, Ménard D, Fidock DA. Drug resistance. K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates. Science 2015; 347:428-31. [PMID: 25502314 PMCID: PMC4349400 DOI: 10.1126/science.1260867] [Citation(s) in RCA: 507] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The emergence of artemisinin resistance in Southeast Asia imperils efforts to reduce the global malaria burden. We genetically modified the Plasmodium falciparum K13 locus using zinc-finger nucleases and measured ring-stage survival rates after drug exposure in vitro; these rates correlate with parasite clearance half-lives in artemisinin-treated patients. With isolates from Cambodia, where resistance first emerged, survival rates decreased from 13 to 49% to 0.3 to 2.4% after the removal of K13 mutations. Conversely, survival rates in wild-type parasites increased from ≤0.6% to 2 to 29% after the insertion of K13 mutations. These mutations conferred elevated resistance to recent Cambodian isolates compared with that of reference lines, suggesting a contemporary contribution of additional genetic factors. Our data provide a conclusive rationale for worldwide K13-propeller sequencing to identify and eliminate artemisinin-resistant parasites.
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Affiliation(s)
- Judith Straimer
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Nina F Gnädig
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Chanaki Amaratunga
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Valentine Duru
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Arba Pramundita Ramadani
- Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination UPR8241, Toulouse, France. Université de Toulouse, UPS, Institut National Polytechnique de Toulouse, Toulouse, France
| | - Mélanie Dacheux
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Nimol Khim
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Lei Zhang
- Sangamo BioSciences, Richmond, CA, USA
| | | | | | | | | | - Françoise Benoit-Vical
- Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination UPR8241, Toulouse, France. Université de Toulouse, UPS, Institut National Polytechnique de Toulouse, Toulouse, France
| | - Rick M Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Didier Ménard
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA. Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA.
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430
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Conway DJ. Paths to a malaria vaccine illuminated by parasite genomics. Trends Genet 2015; 31:97-107. [PMID: 25620796 PMCID: PMC4359294 DOI: 10.1016/j.tig.2014.12.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 11/24/2022]
Abstract
Discovery of vaccine candidate antigens by parasite genome sequence analyses. Genetic crosses, linkage group selection, and functional studies on parasites. Characterizing developmental and epigenetic variation alongside allelic polymorphism. Selection by naturally acquired immune responses helps to focus vaccine design.
More human death and disease is caused by malaria parasites than by all other eukaryotic pathogens combined. As early as the sequencing of the first human genome, malaria parasite genomics was prioritized to fuel the discovery of vaccine candidate antigens. This stimulated increased research on malaria, generating new understanding of the cellular and molecular mechanisms of infection and immunity. This review of recent developments illustrates how new approaches in parasite genomics, and increasingly large amounts of data from population studies, are helping to identify antigens that are promising lead targets. Although these results have been encouraging, effective discovery and characterization need to be coupled with more innovation and funding to translate findings into newly designed vaccine products for clinical trials.
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Affiliation(s)
- David J Conway
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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431
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432
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Affiliation(s)
- MAKOTO HIRAI
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine
| | - TOSHIHIRO MITA
- Department of Molecular and Cellular Parasitology, Juntendo University Graduate School of Medicine
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433
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Abstract
Trypanosoma cruzi is a protozoan parasite of humans and animals, affecting 10 to 20 million people and innumerable animals, primarily in the Americas. Despite being the largest cause of infection-induced heart disease worldwide, even among the neglected tropical diseases (NTDs) T. cruzi is considered one of the least well understood and understudied. The genetic complexity of T. cruzi as well as the limited set of efficient techniques for genome engineering contribute significantly to the relative lack of progress in and understanding of this pathogen. Here, we adapted the CRISPR-Cas9 system for the genetic engineering of T. cruzi, demonstrating rapid and efficient knockout of multiple endogenous genes, including essential genes. We observed that in the absence of a template, repair of the Cas9-induced double-stranded breaks (DSBs) in T. cruzi occurs exclusively by microhomology-mediated end joining (MMEJ) with various-sized deletions. When a template for DNA repair is provided, DSB repair by homologous recombination is achieved at an efficiency several orders of magnitude higher than that in the absence of CRISPR-Cas9-induced DSBs. We also demonstrate the high multiplexing capacity of CRISPR-Cas9 in T. cruzi by knocking down expression of an enzyme gene family consisting of 65 members, resulting in a significant reduction of enzymatic product with no apparent off-target mutations. Lastly, we show that Cas9 can mediate disruption of its own coding sequence, rescuing a growth defect in stable Cas9-expressing parasites. These results establish a powerful new tool for the analysis of gene functions in T. cruzi, enabling the study of essential genes and their functions and analysis of the many large families of related genes that occupy a substantial portion of the T. cruzi genome. Trypanosoma cruzi, the causative agent of human Chagas disease, is the leading worldwide cause of infectious myocarditis. Diagnostics for the infection are relatively poor, treatment options are limited and of variable effectiveness, and suitable vaccines are nonexistent. The T. cruzi genome is replete with genes of unknown function and greatly expanded gene families with hundreds of members. The absence of facile genetic engineering tools, including RNA interference, for T. cruzi has prevented elucidation of gene and gene family function and the development of better infection prevention and control measures. In this study, we demonstrate that the CRISPR-Cas9 system is a versatile and powerful tool for genome manipulations in T. cruzi, bringing new opportunities for unraveling the functions of previously uncharacterized genes and how this human pathogen engages its large families of genes encoding surface proteins to interact with human and animal hosts.
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434
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Cheeseman IH, McDew-White M, Phyo AP, Sriprawat K, Nosten F, Anderson TJC. Pooled sequencing and rare variant association tests for identifying the determinants of emerging drug resistance in malaria parasites. Mol Biol Evol 2014; 32:1080-90. [PMID: 25534029 PMCID: PMC4379400 DOI: 10.1093/molbev/msu397] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We explored the potential of pooled sequencing to swiftly and economically identify selective sweeps due to emerging artemisinin (ART) resistance in a South-East Asian malaria parasite population. ART resistance is defined by slow parasite clearance from the blood of ART-treated patients and mutations in the kelch gene (chr. 13) have been strongly implicated to play a role. We constructed triplicate pools of 70 slow-clearing (resistant) and 70 fast-clearing (sensitive) infections collected from the Thai–Myanmar border and sequenced these to high (∼150-fold) read depth. Allele frequency estimates from pools showed almost perfect correlation (Lin’s concordance = 0.98) with allele frequencies at 93 single nucleotide polymorphisms measured directly from individual infections, giving us confidence in the accuracy of this approach. By mapping genome-wide divergence (FST) between pools of drug-resistant and drug-sensitive parasites, we identified two large (>150 kb) regions (on chrs. 13 and 14) and 17 smaller candidate genome regions. To identify individual genes within these genome regions, we resequenced an additional 38 parasite genomes (16 slow and 22 fast-clearing) and performed rare variant association tests. These confirmed kelch as a major molecular marker for ART resistance (P = 6.03 × 10−6). This two-tier approach is powerful because pooled sequencing rapidly narrows down genome regions of interest, while targeted rare variant association testing within these regions can pinpoint the genetic basis of resistance. We show that our approach is robust to recurrent mutation and the generation of soft selective sweeps, which are predicted to be common in pathogen populations with large effective population sizes, and may confound more traditional gene mapping approaches.
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Affiliation(s)
| | | | - Aung Pyae Phyo
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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435
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Caro F, Ahyong V, Betegon M, DeRisi JL. Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages. eLife 2014; 3. [PMID: 25493618 PMCID: PMC4371882 DOI: 10.7554/elife.04106] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 11/06/2014] [Indexed: 12/11/2022] Open
Abstract
The characterization of the transcriptome and proteome of Plasmodium
falciparum has been a tremendous resource for the understanding of the
molecular physiology of this parasite. However, the translational dynamics that link
steady-state mRNA with protein levels are not well understood. In this study, we
bridge this disconnect by measuring genome-wide translation using ribosome profiling,
through five stages of the P. falciparum blood phase developmental
cycle. Our findings show that transcription and translation are tightly coupled, with
overt translational control occurring for less than 10% of the transcriptome.
Translationally regulated genes are predominantly associated with merozoite egress
functions. We systematically define mRNA 5′ leader sequences, and 3′
UTRs, as well as antisense transcripts, along with ribosome occupancy for each, and
establish that accumulation of ribosomes on 5′ leaders is a common transcript
feature. This work represents the highest resolution and broadest portrait of gene
expression and translation to date for this medically important parasite. DOI:http://dx.doi.org/10.7554/eLife.04106.001 The genome of an organism includes all of the genes or information necessary to
build, maintain, and replicate that organism. However, cells with the same
genome—such as a skin cell and a liver cell from the same person—can
look and behave very differently depending on which of the genes in their genomes
they express, and to what extent. For a gene to be expressed, its DNA is ‘transcribed’ to make an RNA
molecule, which is then ‘translated’ to make a protein. Efforts to
measure the transcription and translation processes in diseased cells, or in the
microorganisms that cause infections, may lead to new treatments and preventative
medicines. Such work is currently ongoing in the global effort to treat and prevent
malaria. Malaria is both preventable and curable, yet over 600,000 people are estimated to die
from this disease each year. The disease is caused by a single-celled parasite called
Plasmodium. Mosquitoes carry the parasites in their salivary
glands, and when a mosquito bites a human, these parasites are injected into the
bloodstream with the mosquito's saliva. Plasmodium parasites then
travel to and infect the liver, before bursting out of this tissue into the
bloodstream. Here, the parasites infect red blood cells and undergo rounds of
replication during which the symptoms of the disease are manifested. It is also
during this bloodstream phase that parasites can develop into forms capable of
infecting another mosquito and continuing the transmission cycle. The genes, RNA molecules, and proteins of the Plasmodium falciparum
parasite—which causes the most serious cases of malaria in humans—have
been cataloged to better understand the biology of this parasite. However, the
processes that control how, and when, an RNA transcript is translated into a protein
are not well understood. Now Caro et al. have uncovered which RNA molecules are being translated, and by how
much, during Plasmodium development within the blood. The
transcription and translation of genes in this parasite were found to be tightly
linked processes; the expression of only a few genes was controlled more by the
translation process than by transcription. These translationally regulated genes were
found mainly to be those that encode proteins involved in the parasite's exit from
the red blood cells and spread throughout the bloodstream. Caro et al. discovered that genetic regulation of the malaria parasite resembles a
preset genetic program, rather than a system that responds to changes and external
signals. As such, these findings suggest that targeting such a genetic program within
Plasmodium and preventing its implementation could prove an
effective strategy to curb the spread of malaria. DOI:http://dx.doi.org/10.7554/eLife.04106.002
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Affiliation(s)
- Florence Caro
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Vida Ahyong
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Miguel Betegon
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Joseph L DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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436
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Genetic mapping reveals that sinefungin resistance in Toxoplasma gondii is controlled by a putative amino acid transporter locus that can be used as a negative selectable marker. EUKARYOTIC CELL 2014; 14:140-8. [PMID: 25480939 DOI: 10.1128/ec.00229-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Quantitative trait locus (QTL) mapping studies have been integral in identifying and understanding virulence mechanisms in the parasite Toxoplasma gondii. In this study, we interrogated a different phenotype by mapping sinefungin (SNF) resistance in the genetic cross between type 2 ME49-FUDR(r) and type 10 VAND-SNF(r). The genetic map of this cross was generated by whole-genome sequencing of the progeny and subsequent identification of single nucleotide polymorphisms (SNPs) inherited from the parents. Based on this high-density genetic map, we were able to pinpoint the sinefungin resistance phenotype to one significant locus on chromosome IX. Within this locus, a single nonsynonymous SNP (nsSNP) resulting in an early stop codon in the TGVAND_290860 gene was identified, occurring only in the sinefungin-resistant progeny. Using CRISPR/CAS9, we were able to confirm that targeted disruption of TGVAND_290860 renders parasites sinefungin resistant. Because disruption of the SNR1 gene confers resistance, we also show that it can be used as a negative selectable marker to insert either a positive drug selection cassette or a heterologous reporter. These data demonstrate the power of combining classical genetic mapping, whole-genome sequencing, and CRISPR-mediated gene disruption for combined forward and reverse genetic strategies in T. gondii.
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437
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Abstract
I knew nothing and had thought nothing about parasites until 1971. In fact, if you had asked me before then, I might have commented that parasites were rather disgusting. I had been at the Johns Hopkins School of Medicine for three years, and I was on the lookout for a new project. In 1971, I came across a paper in the Journal of Molecular Biology by Larry Simpson, a classmate of mine in graduate school. Larry's paper described a remarkable DNA structure known as kinetoplast DNA (kDNA), isolated from a parasite. kDNA, the mitochondrial genome of trypanosomatids, is a DNA network composed of several thousand interlocked DNA rings. Almost nothing was known about it. I was looking for a project on DNA replication, and I wanted it to be both challenging and important. I had no doubt that working with kDNA would be a challenge, as I would be exploring uncharted territory. I was also sure that the project would be important when I learned that parasites with kDNA threaten huge populations in underdeveloped tropical countries. Looking again at Larry's paper, I found the electron micrographs of the kDNA networks to be rather beautiful. I decided to take a chance on kDNA. Little did I know then that I would devote the next forty years of my life to studying kDNA replication.
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Affiliation(s)
- Paul T Englund
- From the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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438
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Torrentino-Madamet M, Fall B, Benoit N, Camara C, Amalvict R, Fall M, Dionne P, Ba Fall K, Nakoulima A, Diatta B, Diemé Y, Ménard D, Wade B, Pradines B. Limited polymorphisms in k13 gene in Plasmodium falciparum isolates from Dakar, Senegal in 2012-2013. Malar J 2014; 13:472. [PMID: 25471113 PMCID: PMC4289025 DOI: 10.1186/1475-2875-13-472] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 11/28/2014] [Indexed: 11/21/2022] Open
Abstract
Background The emergence of Plasmodium falciparum resistance to artemisinin and its derivatives, manifested as delayed parasite clearance following the treatment, has developed in Southeast Asia. The spread of resistance to artemisinin from Asia to Africa may be catastrophic for malaria control and elimination worldwide. Recently, mutations in the propeller domain of the Kelch 13 (k13) gene (PF3D71343700) were associated with in vitro resistance to artemisinin and with delayed clearance after artemisinin treatment in southern Asia. The aim of the study was to characterize the genetic variability of k13 and to evaluate the molecular resistance to artemisinin for the first time in Senegal. Methods Plasmodium falciparum isolates were collected from 138 malaria patients in Dakar and its districts during the rainy season of October 2012 to January 2013 at the Hôpital Principal de Dakar. The k13 gene was amplified using nested PCR and sequenced. Results A very limited variability within the k13 gene in Senegalese P. falciparum isolates was identified. No polymorphism was detected in the six k13-propeller blades. Only two mutations, T149S (6.3%) and K189T (42.2%), and one (N) or two (NN) asparagine insertion at the codon 142 (4.7 and 6.3%, respectively) were detected in the Plasmodium/Apicomplexa-specific domain. None of the polymorphisms associated with artemisinin resistance in Southeast Asia was detected in the 138 P. falciparum from Dakar. Discussion The present data do not suggest widespread artemisinin resistance in Dakar in 2012–2013. Notably, the C580Y, R539T or Y493H substitutions that were associated with in vitro resistance or delayed parasite clearance in Southeast Asia were not observed in Dakar, nor were any of the polymorphisms observed in parasites from Southeast Asia, nor the M476I mutation that was selected in vitro with artemisinin pressure in a African parasite line.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Bruno Pradines
- Aix Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Marseille, France.
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439
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Abstract
Across the globe, over 200 million annual malaria infections result in up to 660,000 deaths, 77% of which occur in children under the age of five years. Although prevention is important, malaria deaths are typically prevented by using antimalarial drugs that eliminate symptoms and clear parasites from the blood. Artemisinins are one of the few remaining compound classes that can be used to cure multidrug-resistant Plasmodium falciparum infections. Unfortunately, clinical trials from Southeast Asia are showing that artemisinin-based treatments are beginning to lose their effectiveness, adding renewed urgency to the search for the genetic determinants of parasite resistance to this important drug class. We review the genetic and genomic approaches that have led to an improved understanding of artemisinin resistance, including the identification of resistance-conferring mutations in the P. falciparum kelch13 gene.
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440
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Ay F, Bunnik EM, Varoquaux N, Vert JP, Noble WS, Le Roch KG. Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum. Bioessays 2014; 37:182-94. [PMID: 25394267 DOI: 10.1002/bies.201400145] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plasmodium falciparum is the most deadly human malarial parasite, responsible for an estimated 207 million cases of disease and 627,000 deaths in 2012. Recent studies reveal that the parasite actively regulates a large fraction of its genes throughout its replicative cycle inside human red blood cells and that epigenetics plays an important role in this precise gene regulation. Here, we discuss recent advances in our understanding of three aspects of epigenetic regulation in P. falciparum: changes in histone modifications, nucleosome occupancy and the three-dimensional genome structure. We compare these three aspects of the P. falciparum epigenome to those of other eukaryotes, and show that large-scale compartmentalization is particularly important in determining histone decomposition and gene regulation in P. falciparum. We conclude by presenting a gene regulation model for P. falciparum that combines the described epigenetic factors, and by discussing the implications of this model for the future of malaria research.
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Affiliation(s)
- Ferhat Ay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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441
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Webster WAJ, McFadden GI. From the genome to the phenome: tools to understand the basic biology of Plasmodium falciparum. J Eukaryot Microbiol 2014; 61:655-71. [PMID: 25227912 DOI: 10.1111/jeu.12176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022]
Abstract
Malaria plagues one out of every 30 humans and contributes to almost a million deaths, and the problem could worsen. Our current therapeutic options are compromised by emerging resistance by the parasite to our front line drugs. It is thus imperative to better understand the basic biology of the parasite and develop novel drugs to stem this disease. The most facile approach to analyse a gene's function is to remove it from the genome or inhibit its activity. Although genetic manipulation of the human malaria parasite Plasmodium falciparum is a relatively standard procedure, there is no optimal method to perturb genes essential to the intraerythrocytic development cycle--the part of the life cycle that produces the clinical manifestation of malaria. This is a severe impediment to progress because the phenotype we wish to study is exactly the one that is so elusive. In the absence of any utilitarian way to conditionally delete essential genes, we are prevented from investigating the parasite's most vulnerable points. This review aims to focus on the development of tools identifying essential genes of P. falciparum and our ability to elicit phenotypic mutation.
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Affiliation(s)
- Wesley A J Webster
- Centre for Regional and Rural Futures, School of Life and Environmental Sciences, Deakin University, Burwood, 3125, Victoria, Australia; Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Melbourne, 3010, Victoria, Australia
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442
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Lee MC, Fidock DA. CRISPR-mediated genome editing of Plasmodium falciparum malaria parasites. Genome Med 2014; 6:63. [PMID: 25473431 PMCID: PMC4254425 DOI: 10.1186/s13073-014-0063-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/12/2014] [Indexed: 01/05/2023] Open
Abstract
The development of the CRISPR-Cas system is revolutionizing genome editing in a variety of organisms. The system has now been used to manipulate the genome of Plasmodium falciparum, the most lethal malaria-causing species. The ability to generate gene deletions or nucleotide substitutions rapidly and economically promises to accelerate the analysis of novel drug targets and to help elucidate the function of specific genes or gene families, while complementing genome-wide association studies.
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Affiliation(s)
- Marcus Cs Lee
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032 USA
| | - David A Fidock
- Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY 10032 USA ; Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY 10032 USA
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