1
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Blackwell AM, Jami-Alahmadi Y, Nasamu AS, Kudo S, Senoo A, Slam C, Tsumoto K, Wohlschlegel JA, Caaveiro JMM, Goldberg DE, Sigala PA. Malaria parasites require a divergent heme oxygenase for apicoplast gene expression and biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596652. [PMID: 38853871 PMCID: PMC11160694 DOI: 10.1101/2024.05.30.596652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Malaria parasites have evolved unusual metabolic adaptations that specialize them for growth within heme-rich human erythrocytes. During blood-stage infection, Plasmodium falciparum parasites internalize and digest abundant host hemoglobin within the digestive vacuole. This massive catabolic process generates copious free heme, most of which is biomineralized into inert hemozoin. Parasites also express a divergent heme oxygenase (HO)-like protein (PfHO) that lacks key active-site residues and has lost canonical HO activity. The cellular role of this unusual protein that underpins its retention by parasites has been unknown. To unravel PfHO function, we first determined a 2.8 Å-resolution X-ray structure that revealed a highly α-helical fold indicative of distant HO homology. Localization studies unveiled PfHO targeting to the apicoplast organelle, where it is imported and undergoes N-terminal processing but retains most of the electropositive transit peptide. We observed that conditional knockdown of PfHO was lethal to parasites, which died from defective apicoplast biogenesis and impaired isoprenoid-precursor synthesis. Complementation and molecular-interaction studies revealed an essential role for the electropositive N-terminus of PfHO, which selectively associates with the apicoplast genome and enzymes involved in nucleic acid metabolism and gene expression. PfHO knockdown resulted in a specific deficiency in levels of apicoplast-encoded RNA but not DNA. These studies reveal an essential function for PfHO in apicoplast maintenance and suggest that Plasmodium repurposed the conserved HO scaffold from its canonical heme-degrading function in the ancestral chloroplast to fulfill a critical adaptive role in organelle gene expression.
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Affiliation(s)
| | | | - Armiyaw S. Nasamu
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
| | - Shota Kudo
- Department of Chemistry & Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Akinobu Senoo
- Department of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Celine Slam
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT
| | - Kouhei Tsumoto
- Department of Chemistry & Biotechnology, The University of Tokyo, Tokyo, Japan
- Department of Bioengineering, University of Tokyo, Tokyo, Japan
| | | | - Jose M. M. Caaveiro
- Department of Chemistry & Biotechnology, The University of Tokyo, Tokyo, Japan
| | - Daniel E. Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
| | - Paul A. Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
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2
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Wirjanata G, Lin J, Dziekan JM, El Sahili A, Chung Z, Tjia S, Binte Zulkifli NE, Boentoro J, Tham R, Jia LS, Go KD, Yu H, Partridge A, Olsen D, Prabhu N, Sobota RM, Nordlund P, Lescar J, Bozdech Z. Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development. Cell Chem Biol 2024; 31:743-759.e8. [PMID: 38593807 DOI: 10.1016/j.chembiol.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/02/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Identification of new druggable protein targets remains the key challenge in the current antimalarial development efforts. Here we used mass-spectrometry-based cellular thermal shift assay (MS-CETSA) to identify potential targets of several antimalarials and drug candidates. We found that falcilysin (FLN) is a common binding partner for several drug candidates such as MK-4815, MMV000848, and MMV665806 but also interacts with quinoline drugs such as chloroquine and mefloquine. Enzymatic assays showed that these compounds can inhibit FLN proteolytic activity. Their interaction with FLN was explored systematically by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with lowered FLN expression demonstrated statistically significant increases in susceptibility toward MK-4815, MMV000848, and several quinolines. Importantly, the hydrophobic pocket of FLN appears amenable to inhibition and the structures reported here can guide the development of novel drugs against malaria.
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Affiliation(s)
- Grennady Wirjanata
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Infectious Diseases Labs & Singapore Immunology Network, Agency for Science, Technology and Research, 138648 Singapore, Singapore
| | - Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore
| | - Zara Chung
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Roy Tham
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Lai Si Jia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - David Olsen
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 637551, Singapore.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore.
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3
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Rizvi Z, Reddy GS, Gorde SM, Pundir P, Das D, Sijwali PS. Plasmodium falciparum contains functional SCF and CRL4 ubiquitin E3 ligases, and CRL4 is critical for cell division and membrane integrity. PLoS Pathog 2024; 20:e1012045. [PMID: 38416790 PMCID: PMC10927090 DOI: 10.1371/journal.ppat.1012045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 03/11/2024] [Accepted: 02/13/2024] [Indexed: 03/01/2024] Open
Abstract
Protein ubiquitination is essential for cellular homeostasis and regulation of several processes, including cell division and genome integrity. Ubiquitin E3 ligases determine substrate specificity for ubiquitination, and Cullin-RING E3 ubiquitin ligases (CRLs) make the largest group among the ubiquitin E3 ligases. Although conserved and most studied in model eukaryotes, CRLs remain underappreciated in Plasmodium and related parasites. To investigate the CRLs of human malaria parasite Plasmodium falciparum, we generated parasites expressing tagged P. falciparum cullin-1 (PfCullin-1), cullin-2 (PfCullin-2), Rbx1 (PfRbx1) and Skp1 (PfSkp1). PfCullin-1 and PfCullin-2 were predominantly expressed in erythrocytic trophozoite and schizont stages, with nucleocytoplasmic localization and chromatin association, suggesting their roles in different cellular compartments and DNA-associated processes. Immunoprecipitation, in vitro protein-protein interaction, and ubiquitination assay confirmed the presence of a functional Skp1-Cullin-1-Fbox (PfSCF) complex, comprising of PfCullin-1, PfRbx1, PfSkp1, PfFBXO1, and calcyclin binding protein. Immunoprecipitation, sequence analysis, and ubiquitination assay indicated that PfCullin-2 forms a functional human CRL4-like complex (PfCRL4), consisting of PfRbx1, cleavage and polyadenylation specificity factor subunit_A and WD40 repeat proteins. PfCullin-2 knock-down at the protein level, which would hinder PfCRL4 assembly, significantly decreased asexual and sexual erythrocytic stage development. The protein levels of several pathways, including protein translation and folding, lipid biosynthesis and transport, DNA replication, and protein degradation were significantly altered upon PfCullin-2 depletion, which likely reflects association of PfCRL4 with multiple pathways. PfCullin-2-depleted schizonts had poorly delimited merozoites and internal membraned structures, suggesting a role of PfCRL4 in maintaining membrane integrity. PfCullin-2-depleted parasites had a significantly lower number of nuclei/parasite than the normal parasites, indicating a crucial role of PfCRL4 in cell division. We demonstrate the presence of functional CRLs in P. falciparum, with crucial roles for PfCRL4 in cell division and maintaining membrane integrity.
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Affiliation(s)
- Zeba Rizvi
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
| | - G. Srinivas Reddy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
| | - Somesh M. Gorde
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
| | - Priyanka Pundir
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
| | - Divya Das
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
| | - Puran Singh Sijwali
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad-500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, UP, India
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4
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Lu J, Tong Y, Dong R, Yang Y, Hu W, Zhang M, Liu Q, Zhao S, Adams JH, Qin L, Chen X. Large DNA fragment knock-in and sequential gene editing in Plasmodium falciparum: a preliminary study using suicide-rescue-based CRISPR/Cas9 system. Mol Cell Biochem 2024; 479:99-107. [PMID: 37004637 PMCID: PMC10066980 DOI: 10.1007/s11010-023-04711-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/15/2023] [Indexed: 04/04/2023]
Abstract
CRISPR/Cas9 technology applied to Plasmodium falciparum offers the potential to greatly improve gene editing, but such expectations including large DNA fragment knock-ins and sequential gene editing have remained unfulfilled. Here, we achieved a major advance in addressing this challenge, especially for creating large DNA fragment knock-ins and sequential editing, by modifying our suicide-rescue-based system that has already been demonstrated to be highly efficient for conventional gene editing. This improved approach was confirmed to mediate efficient knock-ins of DNA fragments up to 6.3 kb, to produce "marker-free" genetically engineered parasites and to show potential for sequential gene editing. This represents an important advancement in establishing platforms for large-scale genome editing, which might gain a better understanding of gene function for the most lethal cause of malaria and contribute to adjusting synthetic biology strategies to live parasite malaria vaccine development. Site-directed knock-in of large DNA fragments is highly efficient using suicide-rescue-based CRISPR/Cas9 system, and sequential gene insertion is feasible but further confirmation is still needed.
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Affiliation(s)
- Junnan Lu
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Ying Tong
- CAS Lamvac Biotech Co., Ltd., No. 3 Lanyue Road, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
| | - Rui Dong
- CAS Lamvac Biotech Co., Ltd., No. 3 Lanyue Road, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
| | - Yijun Yang
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Wen Hu
- CAS Lamvac Biotech Co., Ltd., No. 3 Lanyue Road, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
| | - Minghong Zhang
- CAS Lamvac Biotech Co., Ltd., No. 3 Lanyue Road, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
| | - Quan Liu
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
- University of Chinese Academy of Sciences, No.19 (A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Siting Zhao
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
| | - John H Adams
- CAS Lamvac Biotech Co., Ltd., No. 3 Lanyue Road, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, 3720 Spectrum Blvf Suite 404, Tampa, FL, 33612, USA
| | - Li Qin
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China.
- CAS Lamvac Biotech Co., Ltd., No. 3 Lanyue Road, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China.
| | - Xiaoping Chen
- Laboratory of Pathogen Biology, State Key Laboratory of Respiratory Disease, Center for Infection and Immunity, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China.
- CAS Lamvac Biotech Co., Ltd., No. 3 Lanyue Road, Guangzhou Science Park, Guangzhou, 510530, Guangdong Province, People's Republic of China.
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5
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Lima C, Verdaguer IB, Wunderlich G, Katzin AM, Crabb BS, Gilson PR, Azevedo MF. Conditional expression of NanoLuc luciferase through a multimodular system offers rapid detection of antimalarial drug activity. Exp Parasitol 2023; 254:108620. [PMID: 37716462 DOI: 10.1016/j.exppara.2023.108620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023]
Abstract
Conditional gene expression is a powerful tool to investigate putative vaccine and drug targets, especially in a haploid organism such as Plasmodium falciparum. Inducible systems based on regulation of either transcription, translation, protein or mRNA stability, among others, allow switching on an off the expression of any desired gene causing specific gain or loss of function phenotypes. However, those systems can be cumbersome involving the construction of large plasmids and generation of multiple transgenic parasite lines. In addition, the dynamic range of regulation achieved is not predictable for each individual gene and can be insufficient to generate detectable phenotypes when the genes of interest are silenced. Here, we combined up to three distinct inducible systems to regulate the expression of a single gene. Expression of the reporter NanoLuc luciferase was regulated over 40-fold, which correlates to the regulation achieved by each individual system multiplied by each other. We applied the conditionally expressed NanoLuc to evaluate the effect of fast-acting antimalarials such as chloroquine and artesunate as well as of slower-acting ones such as atovaquone. The conditionally expressed reporter allowed faster and more reliable detection of toxicity to the parasite, which correlated to the expected action of each compound. Bioluminescence achieved by the expression of this inducible highly sensitive reporter is therefore a promising tool to investigate the temporal effect of potential new antimalarials. This single plasmid combination system might also prove useful to achieve sufficient regulation of genes of interest to produce loss-of-function phenotypes.
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Affiliation(s)
- Caroline Lima
- Federal University of Sao Paulo, Santos, Sao Paulo, Brazil
| | - Ignasi B Verdaguer
- Departamento de Parasitologia, Instituto de Ciência Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374, São Paulo, SP, 05508-900, Brazil
| | - Gerhard Wunderlich
- Departamento de Parasitologia, Instituto de Ciência Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374, São Paulo, SP, 05508-900, Brazil
| | - Alejandro M Katzin
- Departamento de Parasitologia, Instituto de Ciência Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374, São Paulo, SP, 05508-900, Brazil
| | - Brendan S Crabb
- Burnet Institute, Melbourne, VIC, 3004, Australia; University of Melbourne, VIC, 3052, Australia; Monash University, Melbourne, VIC, 3004, Australia
| | - Paul R Gilson
- Burnet Institute, Melbourne, VIC, 3004, Australia; University of Melbourne, VIC, 3052, Australia
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6
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Viegas J. Profile of Daniel E. Goldberg. Proc Natl Acad Sci U S A 2023; 120:e2314435120. [PMID: 37722042 PMCID: PMC10523458 DOI: 10.1073/pnas.2314435120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023] Open
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7
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Mansour H, Cabezas-Cruz A, Peucelle V, Farce A, Salomé-Desnoulez S, Metatla I, Guerrera IC, Hollin T, Khalife J. Characterization of GEXP15 as a Potential Regulator of Protein Phosphatase 1 in Plasmodium falciparum. Int J Mol Sci 2023; 24:12647. [PMID: 37628837 PMCID: PMC10454571 DOI: 10.3390/ijms241612647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/29/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
The Protein Phosphatase type 1 catalytic subunit (PP1c) (PF3D7_1414400) operates in combination with various regulatory proteins to specifically direct and control its phosphatase activity. However, there is little information about this phosphatase and its regulators in the human malaria parasite, Plasmodium falciparum. To address this knowledge gap, we conducted a comprehensive investigation into the structural and functional characteristics of a conserved Plasmodium-specific regulator called Gametocyte EXported Protein 15, GEXP15 (PF3D7_1031600). Through in silico analysis, we identified three significant regions of interest in GEXP15: an N-terminal region housing a PP1-interacting RVxF motif, a conserved domain whose function is unknown, and a GYF-like domain that potentially facilitates specific protein-protein interactions. To further elucidate the role of GEXP15, we conducted in vitro interaction studies that demonstrated a direct interaction between GEXP15 and PP1 via the RVxF-binding motif. This interaction was found to enhance the phosphatase activity of PP1. Additionally, utilizing a transgenic GEXP15-tagged line and live microscopy, we observed high expression of GEXP15 in late asexual stages of the parasite, with localization predominantly in the nucleus. Immunoprecipitation assays followed by mass spectrometry analyses revealed the interaction of GEXP15 with ribosomal- and RNA-binding proteins. Furthermore, through pull-down analyses of recombinant functional domains of His-tagged GEXP15, we confirmed its binding to the ribosomal complex via the GYF domain. Collectively, our study sheds light on the PfGEXP15-PP1-ribosome interaction, which plays a crucial role in protein translation. These findings suggest that PfGEXP15 could serve as a potential target for the development of malaria drugs.
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Affiliation(s)
- Hala Mansour
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
| | - Alejandro Cabezas-Cruz
- ANSES, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700 Maisons-Alfort, France;
| | - Véronique Peucelle
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
| | - Amaury Farce
- Univ. Lille, Inserm, CHU Lille, U1286–Infinite–Institute for Translational Research in Inflammation, 59000 Lille, France;
| | - Sophie Salomé-Desnoulez
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41–UAR 2014–PLBS, 59000 Lille, France;
| | - Ines Metatla
- Proteomics Platform Necker, Université Paris Cité–Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015 Paris, France; (I.M.); (I.C.G.)
| | - Ida Chiara Guerrera
- Proteomics Platform Necker, Université Paris Cité–Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015 Paris, France; (I.M.); (I.C.G.)
| | - Thomas Hollin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA
| | - Jamal Khalife
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Center for Infection and Immunity of Lille, 59000 Lille, France; (H.M.); (V.P.)
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8
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Ghosh S, Kundu R, Chandana M, Das R, Anand A, Beura S, Bobde RC, Jain V, Prabhu SR, Behera PK, Mohanty AK, Chakrapani M, Satyamoorthy K, Suryawanshi AR, Dixit A, Padmanaban G, Nagaraj VA. Distinct evolution of type I glutamine synthetase in Plasmodium and its species-specific requirement. Nat Commun 2023; 14:4216. [PMID: 37452051 PMCID: PMC10349072 DOI: 10.1038/s41467-023-39670-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Malaria parasite lacks canonical pathways for amino acid biosynthesis and depends primarily on hemoglobin degradation and extracellular resources for amino acids. Interestingly, a putative gene for glutamine synthetase (GS) is retained despite glutamine being an abundant amino acid in human and mosquito hosts. Here we show Plasmodium GS has evolved as a unique type I enzyme with distinct structural and regulatory properties to adapt to the asexual niche. Methionine sulfoximine (MSO) and phosphinothricin (PPT) inhibit parasite GS activity. GS is localized to the parasite cytosol and abundantly expressed in all the life cycle stages. Parasite GS displays species-specific requirement in Plasmodium falciparum (Pf) having asparagine-rich proteome. Targeting PfGS affects asparagine levels and inhibits protein synthesis through eIF2α phosphorylation leading to parasite death. Exposure of artemisinin-resistant Pf parasites to MSO and PPT inhibits the emergence of viable parasites upon artemisinin treatment.
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Affiliation(s)
- Sourav Ghosh
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Rajib Kundu
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Manjunatha Chandana
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, Odisha, India
| | - Rahul Das
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Aditya Anand
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Subhashree Beura
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Ruchir Chandrakant Bobde
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Vishal Jain
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Sowmya Ramakant Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Akshaya Kumar Mohanty
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Ispat General Hospital, Sector 19, Rourkela, 769005, Odisha, India
| | - Mahabala Chakrapani
- Department of Medicine, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Anshuman Dixit
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Govindarajan Padmanaban
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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9
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Ito D, Kondo Y, Takashima E, Iriko H, Thongkukiatkul A, Torii M, Otsuki H. Roles of the RON3 C-terminal fragment in erythrocyte invasion and blood-stage parasite proliferation in Plasmodium falciparum. Front Cell Infect Microbiol 2023; 13:1197126. [PMID: 37457963 PMCID: PMC10340547 DOI: 10.3389/fcimb.2023.1197126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
Plasmodium species cause malaria, and in the instance of Plasmodium falciparum is responsible for a societal burden of over 600,000 deaths annually. The symptoms and pathology of malaria are due to intraerythocytic parasites. Erythrocyte invasion is mediated by the parasite merozoite stage, and is accompanied by the formation of a parasitophorous vacuolar membrane (PVM), within which the parasite develops. The merozoite apical rhoptry organelle contains various proteins that contribute to erythrocyte attachment and invasion. RON3, a rhoptry bulb membrane protein, undergoes protein processing and is discharged into the PVM during invasion. RON3-deficient parasites fail to develop beyond the intraerythrocytic ring stage, and protein export into erythrocytes by the Plasmodium translocon of exported proteins (PTEX) apparatus is abrogated, as well as glucose uptake into parasites. It is known that truncated N- and C-terminal RON3 fragments are present in rhoptries, but it is unclear which RON3 fragments contribute to protein export by PTEX and glucose uptake through the PVM. To investigate and distinguish the roles of the RON3 C-terminal fragment at distinct developmental stages, we used a C-terminus tag for conditional and post-translational control. We demonstrated that RON3 is essential for blood-stage parasite survival, and knockdown of RON3 C-terminal fragment expression from the early schizont stage induces a defect in erythrocyte invasion and the subsequent development of ring stage parasites. Protein processing of full-length RON3 was partially inhibited in the schizont stage, and the RON3 C-terminal fragment was abolished in subsequent ring-stage parasites compared to the RON3 N-terminal fragment. Protein export and glucose uptake were abrogated specifically in the late ring stage. Plasmodial surface anion channel (PSAC) activity was partially retained, facilitating small molecule traffic across the erythrocyte membrane. The knockdown of the RON3 C-terminal fragment after erythrocyte invasion did not alter parasite growth. These data suggest that the RON3 C-terminal fragment participates in erythrocyte invasion and serves an essential role in the progression of ring-stage parasite growth by the establishment of the nutrient-permeable channel in the PVM, accompanying the transport of ring-stage parasite protein from the plasma membrane to the PVM.
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Affiliation(s)
- Daisuke Ito
- Division of Medical Zoology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Yoko Kondo
- Division of Medical Zoology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Hideyuki Iriko
- Division of Global Infectious Diseases, Department of Public Health, Graduate School of Health Sciences, Kobe University, Kobe, Japan
| | | | - Motomi Torii
- Division of Molecular Parasitology, Proteo-Science Center, Ehime University, Toon, Japan
| | - Hitoshi Otsuki
- Division of Medical Zoology, Department of Microbiology and Immunology, Faculty of Medicine, Tottori University, Yonago, Japan
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10
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Genetic Sequence Variation in the Plasmodium falciparum Histidine-Rich Protein 2 Gene from Field Isolates in Tanzania: Impact on Malaria Rapid Diagnosis. Genes (Basel) 2022; 13:genes13091642. [PMID: 36140809 PMCID: PMC9498557 DOI: 10.3390/genes13091642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/26/2022] [Accepted: 09/09/2022] [Indexed: 12/04/2022] Open
Abstract
Malaria rapid diagnosis test (RDT) is crucial for managing the disease, and the effectiveness of detection depends on parameters such as sensitivity and specificity of the RDT. Several factors can affect the performance of RDT. In this study, we focused on the pfhrp2 sequence variation and its impact on RDTs targeted by antigens encoded by Plasmodium falciparum histidine-rich protein 2 (pfhrp2). Field samples collected during cross-sectional surveys in Tanzania were sequenced to investigate the pfhrp2 sequence diversity and evaluate the impact on HRP2-based RDT performance. We observed significant mean differences in amino acid repeats between current and previous studies. Several new amino acid repeats were found to occur at different frequencies, including types AAY, AHHAHHAAN, and AHHAA. Based on the abundance of types 2 and 7 amino acid repeats, the binary predictive model was able to predict RDT insensitivity by about 69% in the study area. About 85% of the major epitopes targeted by monoclonal antibodies (MAbs) in RDT were identified. Our study suggested that the extensive sequence variation in pfhrp2 can contribute to reduced RDT sensitivity. The correlation between the different combinations of amino acid repeats and the performance of RDT in different malaria transmission settings should be investigated further.
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11
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Polino AJ, Miller JJ, Bhakat S, Mukherjee S, Bobba S, Bowman GR, Goldberg DE. The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function. J Biol Chem 2022; 298:102355. [PMID: 35952758 PMCID: PMC9478907 DOI: 10.1016/j.jbc.2022.102355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/19/2022] Open
Abstract
Plasmepsin V (PM V) is a pepsin-like aspartic protease essential for growth of the malarial parasite Plasmodium falciparum. Previous work has shown PM V to be an endoplasmic reticulum-resident protease that processes parasite proteins destined for export into the host cell. Depletion or inhibition of the enzyme is lethal during asexual replication within red blood cells as well as during the formation of sexual stage gametocytes. The structure of the Plasmodium vivax PM V has been characterized by X-ray crystallography, revealing a canonical pepsin fold punctuated by structural features uncommon to secretory aspartic proteases; however, the function of this unique structure is unclear. Here, we used parasite genetics to probe these structural features by attempting to rescue lethal PM V depletion with various mutant enzymes. We found an unusual nepenthesin 1-type insert in the PM V gene to be essential for parasite growth and PM V activity. Mutagenesis of the nepenthesin insert suggests that both its amino acid sequence and one of the two disulfide bonds that undergird its structure are required for the insert's role in PM V function. Furthermore, molecular dynamics simulations paired with Markov state modeling suggest that mutations to the nepenthesin insert may allosterically affect PM V catalysis through multiple mechanisms. Taken together, these data provide further insights into the structure of the P. falciparum PM V protease.
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Affiliation(s)
- Alexander J Polino
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Justin J Miller
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Soumendranath Bhakat
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sumit Mukherjee
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Suhas Bobba
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.
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12
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Cárdenas P, Esherick LY, Chambonnier G, Dey S, Turlo CV, Nasamu AS, Niles JC. GeneTargeter: Automated In Silico Design for Genome Editing in the Malaria Parasite, Plasmodium falciparum. CRISPR J 2022; 5:155-164. [PMID: 35191751 PMCID: PMC8892962 DOI: 10.1089/crispr.2021.0069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Functional characterization of the multitude of poorly described proteins in the human malarial pathogen, Plasmodium falciparum, requires tools to enable genome-scale perturbation studies. Here, we present GeneTargeter (genetargeter.mit.edu), a software tool for automating the design of homology-directed repair donor vectors to achieve gene knockouts, conditional knockdowns, and epitope tagging of P. falciparum genes. We demonstrate GeneTargeter-facilitated genome-scale design of six different types of knockout and conditional knockdown constructs for the P. falciparum genome and validate the computational design process experimentally with successful donor vector assembly and transfection. The software's modular nature accommodates arbitrary destination vectors and allows customizable designs that extend the genome manipulation outcomes attainable in Plasmodium and other organisms.
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Affiliation(s)
- Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lisl Y. Esherick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gaël Chambonnier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher V. Turlo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Armiyaw Sebastian Nasamu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Address correspondence to: Jacquin C. Niles, MD, PhD, Department of Biological Engineering, Massachusetts Institute of Technology, Room 56-341, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA,
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13
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Briquet S, Gissot M, Silvie O. A toolbox for conditional control of gene expression in apicomplexan parasites. Mol Microbiol 2021; 117:618-631. [PMID: 34564906 PMCID: PMC9293482 DOI: 10.1111/mmi.14821] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 01/29/2023]
Abstract
Apicomplexan parasites encompass diverse pathogens for humans and animals, including the causative agents of malaria and toxoplasmosis, Plasmodium spp. and Toxoplasma gondii. Genetic manipulation of these parasites has become central to explore parasite biology, unravel gene function and identify new targets for therapeutic strategies. Tremendous progress has been achieved over the past years with the advent of next generation sequencing and powerful genome editing methods. In particular, various methods for conditional gene expression have been developed in both Plasmodium and Toxoplasma to knockout or knockdown essential genes, or for inducible expression of master developmental regulators or mutant versions of proteins. Conditional gene expression can be achieved at three distinct levels. At the DNA level, inducible site‐specific recombinases allow conditional genome editing. At the RNA level, regulation can be achieved during transcription, using stage‐specific or regulatable promoters, or post‐transcriptionally through alteration of mRNA stability or translation. At the protein level, several systems have been developed for inducible degradation or displacement of a protein of interest. In this review, we provide an overview of current systems for conditional control of gene expression in Plasmodium and Toxoplasma parasites, highlighting the advantages and limitations of each approach.
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Affiliation(s)
- Sylvie Briquet
- INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Paris, France
| | - Mathieu Gissot
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, CIIL, Univ. Lille, Lille, France
| | - Olivier Silvie
- INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Paris, France
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14
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Asad M, Yamaryo-Botté Y, Hossain ME, Thakur V, Jain S, Datta G, Botté CY, Mohmmed A. An essential vesicular-trafficking phospholipase mediates neutral lipid synthesis and contributes to hemozoin formation in Plasmodium falciparum. BMC Biol 2021; 19:159. [PMID: 34380472 PMCID: PMC8359613 DOI: 10.1186/s12915-021-01042-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background Plasmodium falciparum is the pathogen responsible for the most devastating form of human malaria. As it replicates asexually in the erythrocytes of its human host, the parasite feeds on haemoglobin uptaken from these cells. Heme, a toxic by-product of haemoglobin utilization by the parasite, is neutralized into inert hemozoin in the food vacuole of the parasite. Lipid homeostasis and phospholipid metabolism are crucial for this process, as well as for the parasite’s survival and propagation within the host. P. falciparum harbours a uniquely large family of phospholipases, which are suggested to play key roles in lipid metabolism and utilization. Results Here, we show that one of the parasite phospholipase (P. falciparum lysophospholipase, PfLPL1) plays an essential role in lipid homeostasis linked with the haemoglobin degradation and heme conversion pathway. Fluorescence tagging showed that the PfLPL1 in infected blood cells localizes to dynamic vesicular structures that traffic from the host-parasite interface at the parasite periphery, through the cytosol, to get incorporated into a large vesicular lipid rich body next to the food-vacuole. PfLPL1 is shown to harbour enzymatic activity to catabolize phospholipids, and its transient downregulation in the parasite caused a significant reduction of neutral lipids in the food vacuole-associated lipid bodies. This hindered the conversion of heme, originating from host haemoglobin, into the hemozoin, and disrupted the parasite development cycle and parasite growth. Detailed lipidomic analyses of inducible knock-down parasites deciphered the functional role of PfLPL1 in generation of neutral lipid through recycling of phospholipids. Further, exogenous fatty-acids were able to complement downregulation of PfLPL1 to rescue the parasite growth as well as restore hemozoin levels. Conclusions We found that the transient downregulation of PfLPL1 in the parasite disrupted lipid homeostasis and caused a reduction in neutral lipids essentially required for heme to hemozoin conversion. Our study suggests a crucial link between phospholipid catabolism and generation of neutral lipids (TAGs) with the host haemoglobin degradation pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01042-z.
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Affiliation(s)
- Mohd Asad
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Yoshiki Yamaryo-Botté
- ApicoLipid Team, Institute for Advanced Biosciences, CNRS UMR5309, Université Grenoble Alpes, INSERM U1209, Grenoble, France
| | - Mohammad E Hossain
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Vandana Thakur
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Shaifali Jain
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Gaurav Datta
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Cyrille Y Botté
- ApicoLipid Team, Institute for Advanced Biosciences, CNRS UMR5309, Université Grenoble Alpes, INSERM U1209, Grenoble, France
| | - Asif Mohmmed
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110 067, India.
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15
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Abstract
Malaria, caused by infection with Plasmodium parasites, remains a significant global health concern. For decades, genetic intractability and limited tools hindered our ability to study essential proteins and pathways in Plasmodium falciparum, the parasite associated with the most severe malaria cases. However, recent years have seen major leaps forward in the ability to genetically manipulate P. falciparum parasites and conditionally control protein expression/function. The conditional knockdown systems used in P. falciparum target all 3 components of the central dogma, allowing researchers to conditionally control gene expression, translation, and protein function. Here, we review some of the common knockdown systems that have been adapted or developed for use in P. falciparum. Much of the work done using conditional knockdown approaches has been performed in asexual, blood-stage parasites, but we also highlight their uses in other parts of the life cycle and discuss new ways of applying these systems outside of the intraerythrocytic stages. With the use of these tools, the field’s understanding of parasite biology is ever increasing, and promising new pathways for antimalarial drug development are being discovered.
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16
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Cobb DW, Kudyba HM, Villegas A, Hoopmann MR, Baptista RP, Bruton B, Krakowiak M, Moritz RL, Muralidharan V. A redox-active crosslinker reveals an essential and inhibitable oxidative folding network in the endoplasmic reticulum of malaria parasites. PLoS Pathog 2021; 17:e1009293. [PMID: 33534803 PMCID: PMC7886143 DOI: 10.1371/journal.ppat.1009293] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/16/2021] [Accepted: 01/07/2021] [Indexed: 12/18/2022] Open
Abstract
Malaria remains a major global health problem, creating a constant need for research to identify druggable weaknesses in P. falciparum biology. As important components of cellular redox biology, members of the Thioredoxin (Trx) superfamily of proteins have received interest as potential drug targets in Apicomplexans. However, the function and essentiality of endoplasmic reticulum (ER)-localized Trx-domain proteins within P. falciparum has not been investigated. We generated conditional mutants of the protein PfJ2—an ER chaperone and member of the Trx superfamily—and show that it is essential for asexual parasite survival. Using a crosslinker specific for redox-active cysteines, we identified PfJ2 substrates as PfPDI8 and PfPDI11, both members of the Trx superfamily as well, which suggests a redox-regulatory role for PfJ2. Knockdown of these PDIs in PfJ2 conditional mutants show that PfPDI11 may not be essential. However, PfPDI8 is required for asexual growth and our data suggest it may work in a complex with PfJ2 and other ER chaperones. Finally, we show that the redox interactions between these Trx-domain proteins in the parasite ER and their substrates are sensitive to small molecule inhibition. Together these data build a model for how Trx-domain proteins in the P. falciparum ER work together to assist protein folding and demonstrate the suitability of ER-localized Trx-domain proteins for antimalarial drug development. One of the leading and persistent causes of childhood mortality in the world is malaria, which is caused by parasites from the genus Plasmodium. Unfortunately, the parasite has developed resistance to all available drugs, making the discovery of new drug targets and potential small molecule inhibitors of essential parasite biology a top priority. A critical pathway required for many different biological processes in the parasite is oxidative folding which requires members of the Thioredoxin (Trx) superfamily of proteins. But we know almost nothing about the function and essentiality of Trx-domain proteins that localize to the endoplasmic reticulum, the origin of the secretory pathway, within P. falciparum. Here we show that a network of Trx-domain containing proteins function together and are essential for parasite survival within human red blood cells. Further, we identify a small molecule inhibitor of the redox activities of these Trx-domain containing proteins. This study demonstrates the suitability of this pathway for future antimalarial drug development.
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Affiliation(s)
- David W. Cobb
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Heather M. Kudyba
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Alejandra Villegas
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Michael R. Hoopmann
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Rodrigo P. Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Georgia, United States of America
| | - Baylee Bruton
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
| | - Michelle Krakowiak
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
| | - Robert L. Moritz
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Vasant Muralidharan
- Department of Cellular Biology, University of Georgia, Georgia, United States of America
- Center for Tropical and Emerging Global Diseases, University of Georgia, Georgia, United States of America
- * E-mail:
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17
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Liu C, Yang Z, Cai M, Shi Y, Cui H, Yuan J. Generation of Plasmodium yoelii malaria parasite for conditional degradation of proteins. Mol Biochem Parasitol 2020; 241:111346. [PMID: 33307135 DOI: 10.1016/j.molbiopara.2020.111346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 11/28/2022]
Abstract
The auxin-inducible degron (AID) system is a robust chemical-genetic method for manipulating endogenous protein level by conditional proteasomal degradation via a small molecule. So far, this system has not been adapted in the P. yoelii, an important and widely used Plasmodium rodent parasite model for malaria biology. Here, using the CRISPR/Cas9 genome editing method, we generated two marker-free transgenic P. yoelii parasite lines (eef1a-Tir1 and soap-Tir1) stably expressing the Oryza sativa gene tir1 under the promoters of eef1a and soap respectively. These two lines develop normally during the parasite life cycle. In these backgrounds, we used the CRISPR/Cas9 method to tag two genes (cdc50c and fbxo1) with the AID motif and interrogate the expression of these two proteins with auxin. The eef1a-Tir1 line allows efficient degradation of the AID-tagged endogenous protein in the asexual schizont and sexual gametocyte stages, while the soap-Tir1 line allows protein degradation in the ookinetes. These two lines will be a useful resource for studying the Plasmodium parasite biology based on the P. yoelii.
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Affiliation(s)
- Chuanyuan Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhenke Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Mengya Cai
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yang Shi
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Huiting Cui
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jing Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signal Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
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18
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Govindasamy K, Bhanot P. Overlapping and distinct roles of CDPK family members in the pre-erythrocytic stages of the rodent malaria parasite, Plasmodium berghei. PLoS Pathog 2020; 16:e1008131. [PMID: 32866196 PMCID: PMC7485973 DOI: 10.1371/journal.ppat.1008131] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 09/11/2020] [Accepted: 07/08/2020] [Indexed: 11/29/2022] Open
Abstract
Invasion of hepatocytes by Plasmodium sporozoites initiates the pre-erythrocytic step of a malaria infection. Subsequent development of the parasite within hepatocytes and exit from them is essential for starting the disease-causing erythrocytic cycle. Identification of signaling pathways that operate in pre-erythrocytic stages provides insight into a critical step of infection and potential targets for chemoprotection from malaria. We demonstrate that P. berghei homologs of Calcium Dependent Protein Kinase 1 (CDPK1), CDPK4 and CDPK5 play overlapping but distinct roles in sporozoite invasion and parasite egress from hepatocytes. All three kinases are expressed in sporozoites. All three are required for optimal motility of sporozoites and consequently their invasion of hepatocytes. Increased cGMP can compensate for the functional loss of CDPK1 and CDPK5 during sporozoite invasion but cannot overcome loss of CDPK4. CDPK1 and CDPK5 expression is downregulated after sporozoite invasion. CDPK5 reappears in a subset of late stage liver stages and is present in all merosomes. Chemical inhibition of CDPK4 and depletion of CDPK5 in liver stages implicate these kinases in the formation and/or release of merosomes from mature liver stages. Furthermore, depletion of CDPK5 in merosomes significantly delays initiation of the erythrocytic cycle without affecting infectivity of hepatic merozoites. These data suggest that CDPK5 may be required for the rupture of merosomes. Our work provides evidence that sporozoite invasion requires CDPK1 and CDPK5, and suggests that CDPK5 participates in the release of hepatic merozoites. The malaria-parasite Plasmodium begins its mammalian cycle by infecting hepatocytes in the liver. A single parasite differentiates into tens of thousands of hepatic merozoites which exit the host cell in vesicles called merosomes. Hepatic merozoites initiate the first round of erythrocytic infection that eventually causes disease. We show that optimal invasion of liver cells by Plasmodium requires the action of three closely-related parasite kinases, CDPK1, 4 and 5. Loss of any of the three enzymes in the parasite significantly reduces infection of liver cells. Furthermore, CDPK5 is likely required for release of hepatic merozoites from merosomes and therefore for initiation of the erythrocytic cycle. A better understanding of how these kinases function could lead to drugs that prevent malaria.
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Affiliation(s)
- Kavitha Govindasamy
- Rutgers New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Newark, New Jersey, United States of America
| | - Purnima Bhanot
- Rutgers New Jersey Medical School, Department of Microbiology, Biochemistry and Molecular Genetics, Newark, New Jersey, United States of America
- * E-mail:
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19
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Abstract
Cryptosporidium parvum and Cryptosporidium hominis are leading pathogens responsible for diarrheal disease (cryptosporidiosis) and deaths in infants and children below 5 years of age. There are no effective treatment options and no vaccine for cryptosporidiosis. Therefore, there is an urgent need to identify essential gene targets and uncover their biological function to accelerate the development of new and effective anticryptosporidial drugs. Current genetic tool allows targeted disruption of gene function but leads to parasite lethality if the gene is essential for survival. In this study, we have developed a genetic tool for conditional degradation of proteins in Cryptosporidium spp., thus allowing us to study the function of essential genes. Our conditional system expands the molecular toolbox for Cryptosporidium, and it will help us to understand the biology of this important human diarrheal pathogen for the development of new drugs and vaccines. Cryptosporidium spp., protozoan parasites, are a leading cause of global diarrhea-associated morbidity and mortality in young children and immunocompromised individuals. The limited efficacy of the only available drug and lack of vaccines make it challenging to treat and prevent cryptosporidiosis. Therefore, the identification of essential genes and understanding their biological functions are critical for the development of new therapies. Currently, there is no genetic tool available to investigate the function of essential genes in Cryptosporidium spp. Here, we describe the development of the first conditional system in Cryptosporidium parvum. Our system utilizes the Escherichia coli dihydrofolate reductase degradation domain (DDD) and the stabilizing compound trimethoprim (TMP) for conditional regulation of protein levels in the parasite. We tested our system on the calcium-dependent protein kinase-1 (CDPK1), a leading drug target in C. parvum. By direct knockout strategy, we establish that cdpk1 is refractory to gene deletion, indicating its essentiality for parasite survival. Using CRISPR/Cas9, we generated transgenic parasites expressing CDPK1 with an epitope tag, and localization studies indicate its expression during asexual parasite proliferation. We then genetically engineered C. parvum to express CDPK1 tagged with DDD. We demonstrate that TMP can regulate CDPK1 levels in this stable transgenic parasite line, thus revealing the critical role of this kinase in parasite proliferation. Further, these transgenic parasites show TMP-mediated regulation of CDPK1 levels in vitro and an increased sensitivity to kinase inhibitor upon conditional knockdown. Overall, this study reports the development of a powerful conditional system that can be used to study essential genes in Cryptosporidium.
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20
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Abstract
Malaria elimination efforts have been repeatedly hindered by the evolution and spread of multidrug-resistant strains of Plasmodium falciparum. The absence of a commercially available vaccine emphasizes the need for a better understanding of Plasmodium biology in order to further translational research. This has been partly facilitated by targeted gene deletion strategies for the functional analysis of parasite genes. However, genes that are essential for parasite replication in erythrocytes are refractory to such methods, and require conditional knockdown or knockout approaches to dissect their function. One such approach is the TetR-DOZI system that employs multiple synthetic aptamers in the untranslated regions of target genes to control their expression in a tetracycline-dependent manner. Maintaining modified parasites with intact aptamer copies has been challenging since these repeats can be lost by recombination. By interspacing the aptamers with unique sequences, we created a stable genetic system that remains effective at controlling target gene expression. One of the most powerful approaches to understanding gene function involves turning genes on and off at will and measuring the impact at the cellular or organismal level. This particularly applies to the cohort of essential genes where traditional gene knockouts are inviable. In Plasmodium falciparum, conditional control of gene expression has been achieved by using multicomponent systems in which individual modules interact with each other to regulate DNA recombination, transcription, or posttranscriptional processes. The recently devised TetR-DOZI aptamer system relies on the ligand-regulatable interaction of a protein module with synthetic RNA aptamers to control the translation of a target gene. This technique has been successfully employed to study essential genes in P. falciparum and involves the insertion of several aptamer copies into the 3′ untranslated regions (UTRs), which provide control over mRNA fate. However, aptamer repeats are prone to recombination and one or more copies can be lost from the system, resulting in a loss of control over target gene expression. We rectified this issue by redesigning the aptamer array to minimize recombination while preserving the control elements. As proof of concept, we compared the original and modified arrays for their ability to knock down the levels of a putative essential apicoplast protein (PF3D7_0815700) and demonstrated that the modified array is highly stable and efficient. This redesign will enhance the utility of a tool that is quickly becoming a favored strategy for genetic studies in P. falciparum. IMPORTANCE Malaria elimination efforts have been repeatedly hindered by the evolution and spread of multidrug-resistant strains of Plasmodium falciparum. The absence of a commercially available vaccine emphasizes the need for a better understanding of Plasmodium biology in order to further translational research. This has been partly facilitated by targeted gene deletion strategies for the functional analysis of parasite genes. However, genes that are essential for parasite replication in erythrocytes are refractory to such methods, and require conditional knockdown or knockout approaches to dissect their function. One such approach is the TetR-DOZI system that employs multiple synthetic aptamers in the untranslated regions of target genes to control their expression in a tetracycline-dependent manner. Maintaining modified parasites with intact aptamer copies has been challenging since these repeats can be lost by recombination. By interspacing the aptamers with unique sequences, we created a stable genetic system that remains effective at controlling target gene expression.
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21
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Garten M, Beck JR, Roth R, Tenkova-Heuser T, Heuser J, Istvan ES, Bleck CKE, Goldberg DE, Zimmerberg J. Contacting domains segregate a lipid transporter from a solute transporter in the malarial host-parasite interface. Nat Commun 2020; 11:3825. [PMID: 32732874 PMCID: PMC7393353 DOI: 10.1038/s41467-020-17506-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/30/2020] [Indexed: 12/18/2022] Open
Abstract
The malaria parasite interfaces with its host erythrocyte (RBC) using a unique organelle, the parasitophorous vacuole (PV). The mechanism(s) are obscure by which its limiting membrane, the parasitophorous vacuolar membrane (PVM), collaborates with the parasite plasma membrane (PPM) to support the transport of proteins, lipids, nutrients, and metabolites between the cytoplasm of the parasite and the cytoplasm of the RBC. Here, we demonstrate that the PV has structure characterized by micrometer-sized regions of especially close apposition between the PVM and the PPM. To determine if these contact sites are involved in any sort of transport, we localize the PVM nutrient-permeable and protein export channel EXP2, as well as the PPM lipid transporter PfNCR1. We find that EXP2 is excluded from, but PfNCR1 is included within these regions of close apposition. We conclude that the host-parasite interface is structured to segregate those transporters of hydrophilic and hydrophobic substrates.
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Affiliation(s)
- Matthias Garten
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Josh R Beck
- Department of Biomedical Sciences, Iowa State University, Ames, IA, 50011, USA
| | - Robyn Roth
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tatyana Tenkova-Heuser
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - John Heuser
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eva S Istvan
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher K E Bleck
- Electron Microscopy Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel E Goldberg
- Departments of Medicine and Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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22
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Plastid biogenesis in malaria parasites requires the interactions and catalytic activity of the Clp proteolytic system. Proc Natl Acad Sci U S A 2020; 117:13719-13729. [PMID: 32482878 DOI: 10.1073/pnas.1919501117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The human malaria parasite, Plasmodium falciparum, contains an essential plastid called the apicoplast. Most apicoplast proteins are encoded by the nuclear genome and it is unclear how the plastid proteome is regulated. Here, we study an apicoplast-localized caseinolytic-protease (Clp) system and how it regulates organelle proteostasis. Using null and conditional mutants, we demonstrate that the P. falciparum Clp protease (PfClpP) has robust enzymatic activity that is essential for apicoplast biogenesis. We developed a CRISPR/Cas9-based system to express catalytically dead PfClpP, which showed that PfClpP oligomerizes as a zymogen and is matured via transautocatalysis. The expression of both wild-type and mutant Clp chaperone (PfClpC) variants revealed a functional chaperone-protease interaction. Conditional mutants of the substrate-adaptor (PfClpS) demonstrated its essential function in plastid biogenesis. A combination of multiple affinity purification screens identified the Clp complex composition as well as putative Clp substrates. This comprehensive study reveals the molecular composition and interactions influencing the proteolytic function of the apicoplast Clp system and demonstrates its central role in the biogenesis of the plastid in malaria parasites.
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23
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Gupta A, Bokhari AAB, Pillai AD, Crater AK, Gezelle J, Saggu G, Nasamu AS, Ganesan SM, Niles JC, Desai SA. Complex nutrient channel phenotypes despite Mendelian inheritance in a Plasmodium falciparum genetic cross. PLoS Pathog 2020; 16:e1008363. [PMID: 32069335 PMCID: PMC7048409 DOI: 10.1371/journal.ppat.1008363] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 02/28/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022] Open
Abstract
Malaria parasites activate a broad-selectivity ion channel on their host erythrocyte membrane to obtain essential nutrients from the bloodstream. This conserved channel, known as the plasmodial surface anion channel (PSAC), has been linked to parasite clag3 genes in P. falciparum, but epigenetic switching between the two copies of this gene hinders clear understanding of how the encoded protein determines PSAC activity. Here, we used linkage analysis in a P. falciparum cross where one parent carries a single clag3 gene to overcome the effects of switching and confirm a primary role of the clag3 product with high confidence. Despite Mendelian inheritance, CLAG3 conditional knockdown revealed remarkably preserved nutrient and solute uptake. Even more surprisingly, transport remained sensitive to a CLAG3 isoform-specific inhibitor despite quantitative knockdown, indicating that low doses of the CLAG3 transgene are sufficient to confer block. We then produced a complete CLAG3 knockout line and found it exhibits an incomplete loss of transport activity, in contrast to rhoph2 and rhoph3, two PSAC-associated genes that cannot be disrupted because nutrient uptake is abolished in their absence. Although the CLAG3 knockout did not incur a fitness cost under standard nutrient-rich culture conditions, this parasite could not be propagated in a modified medium that more closely resembles human plasma. These studies implicate oligomerization of CLAG paralogs encoded by various chromosomes in channel formation. They also reveal that CLAG3 is dispensable under standard in vitro conditions but required for propagation under physiological conditions.
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Affiliation(s)
- Ankit Gupta
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Abdullah A. B. Bokhari
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ajay D. Pillai
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Anna K. Crater
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Jeanine Gezelle
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Gagandeep Saggu
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Armiyaw S. Nasamu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Suresh M. Ganesan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jacquin C. Niles
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sanjay A. Desai
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
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24
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Erath J, Djuranovic S, Djuranovic SP. Adaptation of Translational Machinery in Malaria Parasites to Accommodate Translation of Poly-Adenosine Stretches Throughout Its Life Cycle. Front Microbiol 2019; 10:2823. [PMID: 31866984 PMCID: PMC6908487 DOI: 10.3389/fmicb.2019.02823] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/21/2019] [Indexed: 11/13/2022] Open
Abstract
Malaria is caused by unicellular apicomplexan parasites of the genus Plasmodium, which includes the major human parasite Plasmodium falciparum. The complex cycle of the malaria parasite in both mosquito and human hosts has been studied extensively. There is tight control of gene expression in each developmental stage, and at every level of gene synthesis: from RNA transcription, to its subsequent translation, and finally post-translational modifications of the resulting protein. Whole-genome sequencing of P. falciparum has laid the foundation for significant biological advances by revealing surprising genomic information. The P. falciparum genome is extremely AT-rich (∼80%), with a substantial portion of genes encoding intragenic polyadenosine (polyA) tracks being expressed throughout the entire parasite life cycle. In most eukaryotes, intragenic polyA runs act as negative regulators of gene expression. Recent studies have shown that translation of mRNAs containing 12 or more consecutive adenosines results in ribosomal stalling and frameshifting; activating mRNA surveillance mechanisms. In contrast, P. falciparum translational machinery can efficiently and accurately translate polyA tracks without activating mRNA surveillance pathways. This unique feature of P. falciparum raises interesting questions: (1) How is P. falciparum able to efficiently and correctly translate polyA track transcripts, and (2) What are the specifics of the translational machinery and mRNA surveillance mechanisms that separate P. falciparum from other organisms? In this review, we analyze possible evolutionary shifts in P. falciparum protein synthesis machinery that allow efficient translation of an AU rich-transcriptome. We focus on physiological and structural differences of P. falciparum stage specific ribosomes, ribosome-associated proteins, and changes in mRNA surveillance mechanisms throughout the complete parasite life cycle, with an emphasis on the mosquito and liver stages.
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Affiliation(s)
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, United States
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25
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Ntountoumi C, Vlastaridis P, Mossialos D, Stathopoulos C, Iliopoulos I, Promponas V, Oliver SG, Amoutzias GD. Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved. Nucleic Acids Res 2019; 47:9998-10009. [PMID: 31504783 PMCID: PMC6821194 DOI: 10.1093/nar/gkz730] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/16/2019] [Accepted: 08/15/2019] [Indexed: 01/27/2023] Open
Abstract
We provide the first high-throughput analysis of the properties and functional role of Low Complexity Regions (LCRs) in more than 1500 prokaryotic and phage proteomes. We observe that, contrary to a widespread belief based on older and sparse data, LCRs actually have a significant, persistent and highly conserved presence and role in many and diverse prokaryotes. Their specific amino acid content is linked to proteins with certain molecular functions, such as the binding of RNA, DNA, metal-ions and polysaccharides. In addition, LCRs have been repeatedly identified in very ancient, and usually highly expressed proteins of the translation machinery. At last, based on the amino acid content enriched in certain categories, we have developed a neural network web server to identify LCRs and accurately predict whether they can bind nucleic acids, metal-ions or are involved in chaperone functions. An evaluation of the tool showed that it is highly accurate for eukaryotic proteins as well.
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Affiliation(s)
- Chrysa Ntountoumi
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500, Greece
| | - Panayotis Vlastaridis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500, Greece
| | - Dimitris Mossialos
- Microbial Biotechnology-Molecular Bacteriology-Virology Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500, Greece
| | | | | | - Vasilios Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, New Campus, University of Cyprus, PO Box 20537, CY-1678 Nicosia, Cyprus
| | - Stephen G Oliver
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, CB2 1GA, UK
| | - Grigoris D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, 41500, Greece
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26
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Karpiyevich M, Adjalley S, Mol M, Ascher DB, Mason B, van der Heden van Noort GJ, Laman H, Ovaa H, Lee MCS, Artavanis-Tsakonas K. Nedd8 hydrolysis by UCH proteases in Plasmodium parasites. PLoS Pathog 2019; 15:e1008086. [PMID: 31658303 PMCID: PMC6837540 DOI: 10.1371/journal.ppat.1008086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/07/2019] [Accepted: 09/16/2019] [Indexed: 11/19/2022] Open
Abstract
Plasmodium parasites are the causative agents of malaria, a disease with wide public health repercussions. Increasing drug resistance and the absence of a vaccine make finding new chemotherapeutic strategies imperative. Components of the ubiquitin and ubiquitin-like pathways have garnered increased attention as novel targets given their necessity to parasite survival. Understanding how these pathways are regulated in Plasmodium and identifying differences to the host is paramount to selectively interfering with parasites. Here, we focus on Nedd8 modification in Plasmodium falciparum, given its central role to cell division and DNA repair, processes critical to Plasmodium parasites given their unusual cell cycle and requirement for refined repair mechanisms. By applying a functional chemical approach, we show that deNeddylation is controlled by a different set of enzymes in the parasite versus the human host. We elucidate the molecular determinants of the unusual dual ubiquitin/Nedd8 recognition by the essential PfUCH37 enzyme and, through parasite transgenics and drug assays, determine that only its ubiquitin activity is critical to parasite survival. Our experiments reveal interesting evolutionary differences in how neddylation is controlled in higher versus lower eukaryotes, and highlight the Nedd8 pathway as worthy of further exploration for therapeutic targeting in antimalarial drug design. Ubiquitin and ubiquitin-like post-translational modifications are evolutionarily conserved and involved in fundamental cellular processes essential to all eukaryotes. As such, enzymatic components of these pathways present attractive targets for therapeutic intervention for both chronic and communicable diseases. Nedd8 modification of cullin ubiquitin E3 ligases is critical to the viability of eukaryotic organisms and mediates cell cycle progression and DNA damage repair. Given the complex lifecycle and unusual replication mechanisms of the malaria parasite, one would expect neddylation to be of central importance to its survival, yet little is known about this pathway in Plasmodium. Here we present our findings on how Nedd8 removal is controlled in Plasmodium falciparum and how this pathway differs to that of its human host.
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Affiliation(s)
- Maryia Karpiyevich
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Sophie Adjalley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Marco Mol
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - David B. Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Melbourne, Melbourne, Australia
| | - Bethany Mason
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Heike Laman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marcus C. S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Cambridge, United Kingdom
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27
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Zhang J, Chen L, Zhang J, Wang Y. Drug Inducible CRISPR/Cas Systems. Comput Struct Biotechnol J 2019; 17:1171-1177. [PMID: 31462973 PMCID: PMC6709367 DOI: 10.1016/j.csbj.2019.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 06/18/2019] [Accepted: 07/26/2019] [Indexed: 11/24/2022] Open
Abstract
Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems have been employed as a powerful versatile technology for programmable gene editing, transcriptional modulation, epigenetic modulation, and genome labeling, etc. Yet better control of their activity is important to accomplish greater precision and to reduce undesired outcomes such as off-target events. The use of small molecules to control CRISPR/Cas activity represents a promising direction. Here, we provide an updated review on multiple drug inducible CRISPR/Cas systems and discuss their distinct properties. We arbitrarily divided the emerging drug inducible CRISPR/Cas systems into two categories based on whether at transcription or protein level does chemical control occurs. The first category includes Tet-On/Off system and Cre-dependent system. The second category includes chemically induced proximity systems, intein splicing system, 4-Hydroxytamoxifen-Estrogen Receptor based nuclear localization systems, allosterically regulated Cas9 system, and destabilizing domain mediated protein degradation systems. Finally, the advantages and limitations of each system were summarized.
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Key Words
- 4-OHT, 4-Hydroxytamoxifen
- ABA, abscisic acid
- ADs, activation domains
- CIP, chemically induced proximity
- CRISPR, clustered, regularly interspaced, short palindromic repeats
- Cas, CRISPR-associated protein
- CrRNA, CRISPR RNA
- DD, destabilizing domain
- DHFR, dihydrofolate reductase
- ER, Estrogen Receptor
- FKBP, FK506-binding protein
- FRB, FKBP-rapamycin-binding domain
- GA, gibberellin
- HIT, Hybrid drug Inducible CRISPR/Cas9 Technologies
- Hsp90, heat shock protein 90
- LBD, ligand binding domain
- LSL, loxP-stop-loxP
- MST, multiplex single transcript
- NES, nuclear export sequence
- NLS, nuclear localization sequence
- Ptet, tetO-containing promoter
- Sa, Staphylococcus areus
- Sp, Streptococcus pyogenes
- TMP, trimethoprim
- TRE, tetracycline response element
- TRE3G, Tet-On 3G protein
- TetO, tet operator
- TetR, Tet repressor protein
- VPR, VP64-P65-Rta
- arC9, allosterically regulated Cas9
- dCas9, dead Cas9
- dCpf1, dead Cpf1
- dLbCpf1, Lachnospiraceae bacterium dCpf1
- dox, doxycycline
- iPSCs, induced pluripotent stem cells
- rtTA, reverse-tTA
- sgRNA, single guide RNA
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Affiliation(s)
- Jingfang Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Li Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ju Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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28
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Lok JB. CRISPR/Cas9 Mutagenesis and Expression of Dominant Mutant Transgenes as Functional Genomic Approaches in Parasitic Nematodes. Front Genet 2019; 10:656. [PMID: 31379923 PMCID: PMC6646703 DOI: 10.3389/fgene.2019.00656] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
DNA transformation of parasitic nematodes enables novel approaches to validating predictions from genomic and transcriptomic studies of these important pathogens. Notably, proof of principle for CRISPR/Cas9 mutagenesis has been achieved in Strongyloides spp., allowing identification of molecules essential to the functions of sensory neurons that mediate behaviors comprising host finding, invasion, and location of predilection sites by parasitic nematodes. Likewise, CRISPR/Cas9 knockout of the developmental regulatory transcription factor Ss-daf-16 has validated its function in regulating morphogenesis of infective third-stage larvae in Strongyloides stercoralis. While encouraging, these studies underscore challenges that remain in achieving straightforward validation of essential intervention targets in parasitic nematodes. Chief among these is the likelihood that knockout of multifunctional regulators like Ss-DAF-16 or its downstream mediator, the nuclear receptor Ss-DAF-12, will produce phenotypes so complex as to defy interpretation and will render affected worms incapable of infecting their hosts, thus preventing establishment of stable mutant lines. Approaches to overcoming these impediments could involve refinements to current CRISPR/Cas9 methods in Strongyloides including regulatable Cas9 expression from integrated transgenes and CRISPR/Cas9 editing to ablate specific functional motifs in regulatory molecules without complete knockout. Another approach would express transgenes encoding regulatory molecules of interest with mutations designed to similarly ablate or degrade specific functional motifs such as the ligand binding domain of Ss-DAF-12 while preserving core functions such as DNA binding. Such mutant transgenes would be expected to exert a dominant interfering effect on their endogenous counterparts. Published reports validate the utility of such dominant-negative approaches in Strongyloides.
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Affiliation(s)
- James B Lok
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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29
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Roberts AD, Nair SC, Guerra AJ, Prigge ST. Development of a conditional localization approach to control apicoplast protein trafficking in malaria parasites. Traffic 2019; 20:571-582. [PMID: 31094037 DOI: 10.1111/tra.12656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 01/24/2023]
Abstract
Secretory proteins are of particular importance to apicomplexan parasites and comprise over 15% of the genomes of the human pathogens that cause diseases like malaria, toxoplasmosis and babesiosis as well as other diseases of agricultural significance. Here, we developed an approach that allows us to control the trafficking destination of secretory proteins in the human malaria parasite Plasmodium falciparum. Based on the unique structural requirements of apicoplast transit peptides, we designed three conditional localization domains (CLD1, 2 and 3) that can be used to control protein trafficking via the addition of a cell permeant ligand. Studies comparing the trafficking dynamics of each CLD show that CLD2 has the most optimal trafficking efficiency. To validate this system, we tested whether CLD2 could conditionally localize a biotin ligase called holocarboxylase synthetase 1 (HCS1) without interfering with the function of the enzyme. In a parasite line expressing CLD2-HCS1, we were able to control protein biotinylation in the apicoplast in a ligand-dependent manner, demonstrating the full functionality of the CLD tool. We have developed and validated a novel molecular tool that may be used in future studies to help elucidate the function of secretory proteins in malaria parasites.
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Affiliation(s)
- Aleah D Roberts
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sethu C Nair
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Alfredo J Guerra
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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30
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Walker MP, Lindner SE. Ribozyme-mediated, multiplex CRISPR gene editing and CRISPR interference (CRISPRi) in rodent-infectious Plasmodium yoelii. J Biol Chem 2019; 294:9555-9566. [PMID: 31043479 PMCID: PMC6579477 DOI: 10.1074/jbc.ra118.007121] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/23/2019] [Indexed: 11/06/2022] Open
Abstract
Malaria remains a major global health issue, affecting millions and killing hundreds of thousands of people annually. Efforts to break the transmission cycle of the causal Plasmodium parasite, and to cure those that are afflicted, rely upon functional characterization of genes essential to the parasite's growth and development. These studies are often based upon manipulations of the parasite genome to disrupt or modify a gene of interest to understand its importance and function. However, these approaches can be limited by the availability of selectable markers and the time required to generate transgenic parasites. Moreover, there also is a risk of disrupting native gene regulatory elements with the introduction of exogenous sequences. To address these limitations, we have developed CRISPR-RGR, a Streptococcus pyogenes (Sp)Cas9-based gene editing system for Plasmodium that utilizes a ribozyme-guide-ribozyme (RGR) single guide RNA (sgRNA) expression strategy with RNA polymerase II promoters. Using rodent-infectious Plasmodium yoelii, we demonstrate that both gene disruptions and coding sequence insertions are efficiently generated, producing marker-free parasites with homology arms as short as 80-100 bp. Additionally, we find that the common practice of using one sgRNA can produce both unintended plasmid integration and desired locus replacement editing events, whereas the use of two sgRNAs results in only locus replacement editing. Lastly, we show that CRISPR-RGR can be used for CRISPR interference (CRISPRi) by binding catalytically dead SpCas9 (dSpCas9) to the region upstream of a gene of interest, resulting in a position-dependent, but strand-independent reduction in gene expression. This robust and flexible system facilitates efficient genetic characterizations of rodent-infectious Plasmodium species.
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Affiliation(s)
- Michael P Walker
- From the Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Scott E Lindner
- From the Department of Biochemistry and Molecular Biology, Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802
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31
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Kudyba HM, Cobb DW, Fierro MA, Florentin A, Ljolje D, Singh B, Lucchi NW, Muralidharan V. The endoplasmic reticulum chaperone PfGRP170 is essential for asexual development and is linked to stress response in malaria parasites. Cell Microbiol 2019; 21:e13042. [PMID: 31087747 PMCID: PMC6699899 DOI: 10.1111/cmi.13042] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 04/09/2019] [Accepted: 05/09/2019] [Indexed: 12/24/2022]
Abstract
The vast majority of malaria mortality is attributed to one parasite species: Plasmodium falciparum. Asexual replication of the parasite within the red blood cell is responsible for the pathology of the disease. In Plasmodium, the endoplasmic reticulum (ER) is a central hub for protein folding and trafficking as well as stress response pathways. In this study, we tested the role of an uncharacterised ER protein, PfGRP170, in regulating these key functions by generating conditional mutants. Our data show that PfGRP170 localises to the ER and is essential for asexual growth, specifically required for proper development of schizonts. PfGRP170 is essential for surviving heat shock, suggesting a critical role in cellular stress response. The data demonstrate that PfGRP170 interacts with the Plasmodium orthologue of the ER chaperone, BiP. Finally, we found that loss of PfGRP170 function leads to the activation of the Plasmodium eIF2α kinase, PK4, suggesting a specific role for this protein in this parasite stress response pathway.
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Affiliation(s)
- Heather M Kudyba
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia.,Department of Cellular Biology, University of Georgia, Athens, Georgia
| | - David W Cobb
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia.,Department of Cellular Biology, University of Georgia, Athens, Georgia
| | - Manuel A Fierro
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia.,Department of Cellular Biology, University of Georgia, Athens, Georgia
| | - Anat Florentin
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia
| | - Dragan Ljolje
- Malaria Branch and Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Balwan Singh
- Malaria Branch and Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Naomi W Lucchi
- Malaria Branch and Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Vasant Muralidharan
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia.,Department of Cellular Biology, University of Georgia, Athens, Georgia
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32
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Bryant JM, Baumgarten S, Glover L, Hutchinson S, Rachidi N. CRISPR in Parasitology: Not Exactly Cut and Dried! Trends Parasitol 2019; 35:409-422. [DOI: 10.1016/j.pt.2019.03.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022]
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Kempaiah Nagappa L, Satha P, Govindaraju T, Balaram H. Phosphoglycolate phosphatase is a metabolic proofreading enzyme essential for cellular function in Plasmodium berghei. J Biol Chem 2019; 294:4997-5007. [PMID: 30700551 PMCID: PMC6442027 DOI: 10.1074/jbc.ac118.007143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/28/2019] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum (Pf) 4-nitrophenylphosphatase has been shown previously to be involved in vitamin B1 metabolism. Here, conducting a BLASTp search, we found that 4-nitrophenylphosphatase from Pf has significant homology with phosphoglycolate phosphatase (PGP) from mouse, human, and yeast, prompting us to reinvestigate the biochemical properties of the Plasmodium enzyme. Because the recombinant PfPGP enzyme is insoluble, we performed an extended substrate screen and extensive biochemical characterization of the recombinantly expressed and purified homolog from Plasmodium berghei (Pb), leading to the identification of 2-phosphoglycolate and 2-phospho-L-lactate as the relevant physiological substrates of PbPGP. 2-Phosphoglycolate is generated during repair of damaged DNA ends, 2-phospho-L-lactate is a product of pyruvate kinase side reaction, and both potently inhibit two key glycolytic enzymes, triosephosphate isomerase and phosphofructokinase. Hence, PGP-mediated clearance of these toxic metabolites is vital for cell survival and functioning. Our results differ significantly from those in a previous study, wherein the PfPGP enzyme has been inferred to act on 2-phospho-D-lactate and not on the L isomer. Apart from resolving the substrate specificity conflict through direct in vitro enzyme assays, we conducted PGP gene knockout studies in P. berghei, confirming that this conserved metabolic proofreading enzyme is essential in Plasmodium In summary, our findings establish PbPGP as an essential enzyme for normal physiological function in P. berghei and suggest that drugs that specifically inhibit Plasmodium PGP may hold promise for use in anti-malarial therapies.
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Affiliation(s)
| | - Pardhasaradhi Satha
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
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34
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To kill a piroplasm: genetic technologies to advance drug discovery and target identification in Babesia. Int J Parasitol 2019; 49:153-163. [DOI: 10.1016/j.ijpara.2018.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 12/26/2022]
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35
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Boucher MJ, Yeh E. Disruption of Apicoplast Biogenesis by Chemical Stabilization of an Imported Protein Evades the Delayed-Death Phenotype in Malaria Parasites. mSphere 2019; 4:e00710-18. [PMID: 30674649 PMCID: PMC6344605 DOI: 10.1128/msphere.00710-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 11/20/2022] Open
Abstract
Malaria parasites (Plasmodium spp.) contain a nonphotosynthetic plastid organelle called the apicoplast, which houses essential metabolic pathways and is required throughout the parasite life cycle. The biogenesis pathways responsible for apicoplast growth, division, and inheritance are of key interest as potential drug targets. Unfortunately, several known apicoplast biogenesis inhibitors are of limited clinical utility because they cause a peculiar "delayed-death" phenotype in which parasites do not stop replicating until the second lytic cycle posttreatment. Identifying apicoplast biogenesis pathways that avoid the delayed-death phenomenon is a priority. Here, we generated parasites targeting a murine dihydrofolate reductase (mDHFR) domain, which can be conditionally stabilized with the compound WR99210, to the apicoplast. Surprisingly, chemical stabilization of this exogenous fusion protein disrupted parasite growth in an apicoplast-specific manner after a single lytic cycle. WR99210-treated parasites exhibited an apicoplast biogenesis defect beginning within the same lytic cycle as drug treatment, indicating that stabilized mDHFR perturbs a non-delayed-death biogenesis pathway. While the precise mechanism-of-action of the stabilized fusion is still unclear, we hypothesize that it inhibits apicoplast protein import by stalling within and blocking translocons in the apicoplast membranes.IMPORTANCE Malaria is a major cause of global childhood mortality. To sustain progress in disease control made in the last decade, new antimalarial therapies are needed to combat emerging drug resistance. Malaria parasites contain a relict chloroplast called the apicoplast, which harbors new targets for drug discovery. Unfortunately, some drugs targeting apicoplast pathways exhibit a delayed-death phenotype, which results in a slow onset-of-action that precludes their use as fast-acting, frontline therapies. Identification of druggable apicoplast biogenesis factors that will avoid the delayed-death phenotype is an important priority. Here, we find that chemical stabilization of an apicoplast-targeted mDHFR domain disrupts apicoplast biogenesis and inhibits parasite growth after a single lytic cycle, suggesting a non-delayed-death target. Our finding indicates that further interrogation of the mechanism-of-action of this exogenous fusion protein may reveal novel therapeutic avenues.
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Affiliation(s)
- Michael J Boucher
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Ellen Yeh
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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36
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Balabaskaran-Nina P, Desai SA. Diverse target gene modifications in Plasmodium falciparum using Bxb1 integrase and an intronic attB. Parasit Vectors 2018; 11:548. [PMID: 30333047 PMCID: PMC6192176 DOI: 10.1186/s13071-018-3129-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/01/2018] [Indexed: 12/26/2022] Open
Abstract
Genetic manipulation of the human malaria parasite Plasmodium falciparum is needed to explore pathogen biology and evaluate antimalarial targets. It is, however, aggravated by a low transfection efficiency, a paucity of selectable markers and a biased A/T-rich genome. While various enabling technologies have been introduced over the past two decades, facile and broad-range modification of essential genes remains challenging. We recently devised a new application of the Bxb1 integrase strategy to meet this need through an intronic attB sequence within the gene of interest. Although this attB is silent and without effect on intron splicing or protein translation and function, it allows efficient gene modification with minimal risk of unwanted changes at other genomic sites. We describe the range of applications for this new method as well as specific cases where it is preferred over CRISPR-Cas9 and other technologies. The advantages and limitations of various strategies for endogenous gene editing are also discussed.
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Affiliation(s)
- Praveen Balabaskaran-Nina
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.,Present Address: Department of Epidemiology and Public Health, Central University of Tamil Nadu, Thiruvarur, India
| | - Sanjay A Desai
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA.
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37
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Kudyba HM, Cobb DW, Florentin A, Krakowiak M, Muralidharan V. CRISPR/Cas9 Gene Editing to Make Conditional Mutants of Human Malaria Parasite P. falciparum. J Vis Exp 2018. [PMID: 30295650 DOI: 10.3791/57747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Malaria is a significant cause of morbidity and mortality worldwide. This disease, which primarily affects those living in tropical and subtropical regions, is caused by infection with Plasmodium parasites. The development of more effective drugs to combat malaria can be accelerated by improving our understanding of the biology of this complex parasite. Genetic manipulation of these parasites is key to understanding their biology; however, historically the genome of P. falciparum has been difficult to manipulate. Recently, CRISPR/Cas9 genome editing has been utilized in malaria parasites, allowing for easier protein tagging, generation of conditional protein knockdowns, and deletion of genes. CRISPR/Cas9 genome editing has proven to be a powerful tool for advancing the field of malaria research. Here, we describe a CRISPR/Cas9 method for generating glmS-based conditional knockdown mutants in P. falciparum. This method is highly adaptable to other types of genetic manipulations, including protein tagging and gene knockouts.
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Affiliation(s)
- Heather M Kudyba
- Department of Cellular Biology, University of Georgia; Center for Tropical and Emerging Global Diseases, University of Georgia
| | - David W Cobb
- Department of Cellular Biology, University of Georgia
| | - Anat Florentin
- Department of Cellular Biology, University of Georgia; Center for Tropical and Emerging Global Diseases, University of Georgia
| | | | - Vasant Muralidharan
- Department of Cellular Biology, University of Georgia; Center for Tropical and Emerging Global Diseases, University of Georgia;
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38
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Park S, Burke RE, Kareva T, Kholodilov N, Aimé P, Franke TF, Levy O, Greene LA. Context-dependent expression of a conditionally-inducible form of active Akt. PLoS One 2018; 13:e0197899. [PMID: 29920520 PMCID: PMC6007834 DOI: 10.1371/journal.pone.0197899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/10/2018] [Indexed: 12/20/2022] Open
Abstract
Akt kinases are key signaling components in proliferation-competent and post-mitotic cells. Here, we sought to create a conditionally-inducible form of active Akt for both in vitro and in vivo applications. We fused a ligand-responsive Destabilizing Domain (DD) derived from E. coli dihydrofolate reductase to a constitutively active mutant form of Akt1, Akt(E40K). Prior work indicated that such fusion proteins may be stabilized and induced by a ligand, the antibiotic Trimethoprim (TMP). We observed dose-dependent, reversible induction of both total and phosphorylated/active DD-Akt(E40K) by TMP across several cellular backgrounds in culture, including neurons. Phosphorylation of FoxO4, an Akt substrate, was significantly elevated after DD-Akt(E40K) induction, indicating the induced protein was functionally active. The induced Akt(E40K) protected cells from apoptosis evoked by serum deprivation and was neuroprotective in two cellular models of Parkinson's disease (6-OHDA and MPP+ exposure). There was no significant protection without induction. We also evaluated Akt(E40K) induction by TMP in mouse substantia nigra and striatum after neuronal delivery via an AAV1 adeno-associated viral vector. While there was significant induction in striatum, there was no apparent induction in substantia nigra. To explore the possible basis for this difference, we examined DD-Akt(E40K) induction in cultured ventral midbrain neurons. Both dopaminergic and non-dopaminergic neurons in the cultures showed DD-Akt(E40K) induction after TMP treatment. However, basal DD-Akt(E40K) expression was 3-fold higher for dopaminergic neurons, resulting in a significantly lower induction by TMP in this population. Such findings suggest that dopaminergic neurons may be relatively inefficient in protein degradation, a property that could relate to their lack of apparent DD-Akt(E40K) induction in vivo and to their selective vulnerability in Parkinson's disease. In summary, we generated an inducible, biologically active form of Akt. The degree of inducibility appears to reflect cellular context that will inform the most appropriate applications for this and related reagents.
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Affiliation(s)
- Soyeon Park
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Robert E Burke
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America.,Department of Neurology, Columbia University Medical Center, New York, New York, United States of America
| | - Tatyana Kareva
- Department of Neurology, Columbia University Medical Center, New York, New York, United States of America
| | - Nikolai Kholodilov
- Department of Neurology, Columbia University Medical Center, New York, New York, United States of America
| | - Pascaline Aimé
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Thomas F Franke
- Department of Neuroscience, Icahn School of Medicine at Mt Sinai, New York, New York, United States of America
| | - Oren Levy
- Department of Neurology, Columbia University Medical Center, New York, New York, United States of America
| | - Lloyd A Greene
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, United States of America
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39
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Kogenaru M, Isalan M. Drug-Inducible Control of Lethality Genes: A Low Background Destabilizing Domain Architecture Applied to the Gal4-UAS System in Drosophila. ACS Synth Biol 2018; 7:1496-1506. [PMID: 29733646 PMCID: PMC6008732 DOI: 10.1021/acssynbio.7b00302] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Indexed: 11/28/2022]
Abstract
Destabilizing domains (DDs) are genetic tags that conditionally control the level of abundance of proteins-of-interest (POI) with specific stabilizing small-molecule drugs, rapidly and reversibly, in a wide variety of organisms. The amount of the DD-tagged fusion protein directly impacts its molecular function. Hence, it is important that the background levels be tightly regulated in the absence of any drug. This is especially true for classes of proteins that function at extremely low levels, such as lethality genes involved in tissue development and certain transcriptional activator proteins. Here, we establish the uninduced background and induction levels for two widely used DDs (FKBP and DHFR) by developing an accurate quantification method. We show that both DDs exhibit functional background levels in the absence of a drug, but each to a different degree. To overcome this limitation, we systematically test a double architecture for these DDs (DD-POI-DD) that completely suppresses the protein's function in an uninduced state, while allowing tunable functional levels upon adding a drug. As an example, we generate a drug-stabilizable Gal4 transcriptional activator with extremely low background levels. We show that this functions in vivo in the widely used Gal4-UAS bipartite expression system in Drosophila melanogaster. By regulating a cell death gene, we demonstrate that only the low background double architecture enables tight regulation of the lethal phenotype in vivo. These improved tools will enable applications requiring exceptionally tight control of protein function in living cells and organisms.
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Affiliation(s)
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
- Imperial College Centre
for
Synthetic Biology, Imperial College London, London, SW7 2AZ, United Kingdom
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40
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Kushwaha AK, Apolis L, Ito D, Desai SA. Increased Ca ++ uptake by erythrocytes infected with malaria parasites: Evidence for exported proteins and novel inhibitors. Cell Microbiol 2018; 20:e12853. [PMID: 29726084 DOI: 10.1111/cmi.12853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 12/12/2022]
Abstract
Malaria parasites export many proteins into their host erythrocytes and increase membrane permeability to diverse solutes. Although most solutes use a broad-selectivity channel known as the plasmodial surface anion channel, increased Ca++ uptake is mediated by a distinct, poorly characterised mechanism that appears to be essential for the intracellular parasite. Here, we examined infected cell Ca++ uptake with a kinetic fluorescence assay and the virulent human pathogen, Plasmodium falciparum. Cell surface labelling with N-hydroxysulfosuccinimide esters revealed differing effects on transport into infected and uninfected cells, indicating that Ca++ uptake at the infected cell surface is mediated by new or altered proteins at the host membrane. Conditional knockdown of PTEX, a translocon for export of parasite proteins into the host cell, significantly reduced infected cell Ca++ permeability, suggesting involvement of parasite-encoded proteins trafficked to the host membrane. A high-throughput chemical screen identified the first Ca++ transport inhibitors active against Plasmodium-infected cells. These novel chemical scaffolds inhibit both uptake and parasite growth; improved in vitro potency at reduced free [Ca++ ] is consistent with parasite killing specifically via action on one or more Ca++ transporters. These inhibitors should provide mechanistic insights into malaria parasite Ca++ transport and may be starting points for new antimalarial drugs.
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Affiliation(s)
- Ambuj K Kushwaha
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Liana Apolis
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Daisuke Ito
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Sanjay A Desai
- The Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
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41
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Hallée S, Thériault C, Gagnon D, Kehrer J, Frischknecht F, Mair GR, Richard D. Identification of a Golgi apparatus protein complex important for the asexual erythrocytic cycle of the malaria parasite Plasmodium falciparum. Cell Microbiol 2018; 20:e12843. [PMID: 29579782 DOI: 10.1111/cmi.12843] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 12/01/2022]
Abstract
Compared with other eukaryotic cell types, malaria parasites appear to possess a more rudimentary Golgi apparatus being composed of dispersed, unstacked cis and trans-cisternae. Despite playing a central role in the secretory pathway of the parasite, few Plasmodium Golgi resident proteins have been characterised. We had previously identified a new Golgi resident protein of unknown function, which we had named Golgi Protein 1, and now show that it forms a complex with a previously uncharacterised transmembrane protein (Golgi Protein 2, GP2). The Golgi Protein complex localises to the cis-Golgi throughout the erythrocytic cycle and potentially also during the mosquito stages. Analysis of parasite strains where GP1 expression is conditionally repressed and/or the GP2 gene is inactivated reveals that though the Golgi protein complex is not essential at any stage of the parasite life cycle, it is important for optimal asexual development in the blood stages.
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Affiliation(s)
- Stéphanie Hallée
- Centre de recherche en infectiologie, CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Catherine Thériault
- Centre de recherche en infectiologie, CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Dominic Gagnon
- Centre de recherche en infectiologie, CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Jessica Kehrer
- Integrative Parasitology, Department of Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Department of Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Gunnar R Mair
- Integrative Parasitology, Department of Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Dave Richard
- Centre de recherche en infectiologie, CHU de Québec-Université Laval, Quebec City, Quebec, Canada
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42
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Davies HM, Nofal SD, McLaughlin EJ, Osborne AR. Repetitive sequences in malaria parasite proteins. FEMS Microbiol Rev 2018; 41:923-940. [PMID: 29077880 DOI: 10.1093/femsre/fux046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
Five species of parasite cause malaria in humans with the most severe disease caused by Plasmodium falciparum. Many of the proteins encoded in the P. falciparum genome are unusually enriched in repetitive low-complexity sequences containing a limited repertoire of amino acids. These repetitive sequences expand and contract dynamically and are among the most rapidly changing sequences in the genome. The simplest repetitive sequences consist of single amino acid repeats such as poly-asparagine tracts that are found in approximately 25% of P. falciparum proteins. More complex repeats of two or more amino acids are also common in diverse parasite protein families. There is no universal explanation for the occurrence of repetitive sequences and it is possible that many confer no function to the encoded protein and no selective advantage or disadvantage to the parasite. However, there are increasing numbers of examples where repetitive sequences are important for parasite protein function. We discuss the diverse roles of low-complexity repetitive sequences throughout the parasite life cycle, from mediating protein-protein interactions to enabling the parasite to evade the host immune system.
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Affiliation(s)
- Heledd M Davies
- The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Stephanie D Nofal
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Emilia J McLaughlin
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Andrew R Osborne
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, Malet Street, London, WC1E 7HX, United Kingdom
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43
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Jayaraman V, Suryavanshi A, Kalale P, Kunala J, Balaram H. Biochemical characterization and essentiality of Plasmodium fumarate hydratase. J Biol Chem 2018; 293:5878-5894. [PMID: 29449371 DOI: 10.1074/jbc.m117.816298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 02/07/2018] [Indexed: 12/30/2022] Open
Abstract
Plasmodium falciparum (Pf), the causative agent of malaria, has an iron-sulfur cluster-containing class I fumarate hydratase (FH) that catalyzes the interconversion of fumarate to malate, a well-known reaction in the tricarboxylic acid cycle. In humans, the same reaction is catalyzed by class II FH that has no sequence or structural homology with the class I enzyme from Plasmodium Fumarate is generated in large quantities in the parasite as a by-product of AMP synthesis and is converted to malate by FH and then used in the generation of the key metabolites oxaloacetate, aspartate, and pyruvate. Previous studies have identified the FH reaction as being essential to P. falciparum, but biochemical characterization of PfFH that may provide leads for the development of specific inhibitors is lacking. Here, we report on the kinetic characterization of purified recombinant PfFH, functional complementation of fh deficiency in Escherichia coli, and mitochondrial localization in the parasite. We found that the substrate analog mercaptosuccinic acid is a potent PfFH inhibitor, with a Ki value in the nanomolar range. The fh gene could not be knocked out in Plasmodium berghei when transfectants were introduced into BALB/c mice; however, fh knockout was successful when C57BL/6 mice were used as host, suggesting that the essentiality of the fh gene to the parasite was mouse strain-dependent.
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Affiliation(s)
- Vijay Jayaraman
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka 560064, India
| | - Arpitha Suryavanshi
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka 560064, India
| | - Pavithra Kalale
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka 560064, India
| | - Jyothirmai Kunala
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka 560064, India
| | - Hemalatha Balaram
- From the Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, Karnataka 560064, India
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44
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Abstract
Genome sequencing has greatly contributed to our understanding of parasitic protozoa. This is particularly the case for Cryptosporidium species (phylum Apicomplexa) which are difficult to propagate. Because of their polymorphic nature, simple sequence repeats have been used extensively as genotypic markers to differentiate between isolates, but no global analysis of amino acid repeats in Cryptosporidium genomes has been reported. Taking advantage of several newly sequenced Cryptosporidium genomes, a comparative analysis of single-amino-acid repeats (SAARs) in seven species was undertaken. This analysis revealed a striking difference between the SAAR profile of the gastric and intestinal species which infect mammals and one species which infects birds. In average, total SAAR length in gastric species is only 25% of the cumulative SAAR length in the genome of Cryptosporidium parvum, Cryptosporidium hominis and Cryptosporidium meleagridis, species infectious to humans. The SAAR profile in the avian parasite Cryptosporidium baileyi stands out due to the presence of long asparagine repeats. Cryptosporidium baileyi proteins with repeats ⩾20 residues are significantly enriched in regulatory functions. As postulated for the related apicomplexan species Plasmodium falciparum, these observations suggest that Cryptosporidium SAARs evolve in response to selective pressure. The putative selective mechanisms driving SAAR evolution in Cryptosporidium species are unknown.
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Florentin A, Cobb DW, Fishburn JD, Cipriano MJ, Kim PS, Fierro MA, Striepen B, Muralidharan V. PfClpC Is an Essential Clp Chaperone Required for Plastid Integrity and Clp Protease Stability in Plasmodium falciparum. Cell Rep 2017; 21:1746-1756. [PMID: 29141210 PMCID: PMC5726808 DOI: 10.1016/j.celrep.2017.10.081] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/17/2017] [Accepted: 10/21/2017] [Indexed: 01/11/2023] Open
Abstract
The deadly malaria parasite Plasmodium falciparum contains a nonphotosynthetic plastid, known as the apicoplast, that functions to produce essential metabolites, and drugs that target the apicoplast are clinically effective. Several prokaryotic caseinolytic protease (Clp) genes have been identified in the Plasmodium genome. Using phylogenetic analysis, we focused on the Clp members that may form a regulated proteolytic complex in the apicoplast. We genetically targeted members of this complex and generated conditional mutants of the apicoplast-localized PfClpC chaperone and PfClpP protease. Conditional inhibition of the PfClpC chaperone resulted in growth arrest and apicoplast loss and was rescued by addition of the essential apicoplast-derived metabolite IPP. Using a double-conditional mutant parasite line, we discovered that the chaperone activity is required to stabilize the mature protease, revealing functional interactions. These data demonstrate the essential function of PfClpC in maintaining apicoplast integrity and its role in regulating the proteolytic activity of the Clp complex.
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Affiliation(s)
- Anat Florentin
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - David W Cobb
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Jillian D Fishburn
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Michael J Cipriano
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Paul S Kim
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Manuel A Fierro
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Vasant Muralidharan
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA.
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Abstract
Basic science holds enormous power for revealing the biological mechanisms of disease and, in turn, paving the way toward new, effective interventions. Recognizing this power, the 2011 Research Agenda for Malaria Eradication included key priorities in fundamental research that, if attained, could help accelerate progress toward disease elimination and eradication. The Malaria Eradication Research Agenda (malERA) Consultative Panel on Basic Science and Enabling Technologies reviewed the progress, continuing challenges, and major opportunities for future research. The recommendations come from a literature of published and unpublished materials and the deliberations of the malERA Refresh Consultative Panel. These areas span multiple aspects of the Plasmodium life cycle in both the human host and the Anopheles vector and include critical, unanswered questions about parasite transmission, human infection in the liver, asexual-stage biology, and malaria persistence. We believe an integrated approach encompassing human immunology, parasitology, and entomology, and harnessing new and emerging biomedical technologies offers the best path toward addressing these questions and, ultimately, lowering the worldwide burden of malaria.
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Martins RM, Macpherson CR, Claes A, Scheidig-Benatar C, Sakamoto H, Yam XY, Preiser P, Goel S, Wahlgren M, Sismeiro O, Coppée JY, Scherf A. An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum. Sci Rep 2017; 7:14042. [PMID: 29070841 PMCID: PMC5656681 DOI: 10.1038/s41598-017-12578-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 06/09/2017] [Indexed: 02/02/2023] Open
Abstract
Variegated surface antigen expression is key to chronic infection and pathogenesis of the human malaria parasite Plasmodium falciparum. This protozoan parasite expresses distinct surface molecules that are encoded by clonally variant gene families such as var, rif and stevor. The molecular mechanisms governing activation of individual members remain ill-defined. To investigate the molecular events of the initial transcriptional activation process we focused on a member of the apicomplexan ApiAP2 transcription factor family predicted to bind to the 5′ upstream regions of the var gene family, AP2-exp (PF3D7_1466400). Viable AP2-exp mutant parasites rely on expressing no less than a short truncated protein including the N-terminal AP2 DNA-binding domain. RNA-seq analysis in mutant parasites revealed transcriptional changes in a subset of exported proteins encoded by clonally variant gene families. Upregulation of RIFINs and STEVORs was validated at the protein levels. In addition, morphological alterations were observed on the surface of the host cells infected by the mutants. This work points to a complex regulatory network of clonally variant gene families in which transcription of a subset of members is regulated by the same transcription factor. In addition, we highlight the importance of the non-DNA binding AP2 domain in functional gene regulation.
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Affiliation(s)
- Rafael M Martins
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, Unit U1201, Paris, 75015, France. .,CNRS 5290/IRD 224/University of Montpellier ("MiVEGEC"), Montpellier, France.
| | - Cameron R Macpherson
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Aurélie Claes
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Christine Scheidig-Benatar
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Hiroshi Sakamoto
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France.,CNRS, ERL 9195, Paris, 75015, France.,INSERM, Unit U1201, Paris, 75015, France
| | - Xue Yan Yam
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Peter Preiser
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Suchi Goel
- MTC, Nobels väg 16, KI Solna Campus Karolinska Institutet, Box 280, SE-171 77, Stockholm, Sweden.,Institute of Science Education and Research (IISER), Tirupati Rami Reddy Nagar, 517507, Mangalam, Tirupati Andhra Pradhesh, India
| | - Mats Wahlgren
- MTC, Nobels väg 16, KI Solna Campus Karolinska Institutet, Box 280, SE-171 77, Stockholm, Sweden
| | - Odile Sismeiro
- Plateforme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Jean-Yves Coppée
- Plateforme 2, Transcriptome et Epigenome, Institut Pasteur, Paris, 75015, France
| | - Artur Scherf
- Unité Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75015, France. .,CNRS, ERL 9195, Paris, 75015, France. .,INSERM, Unit U1201, Paris, 75015, France.
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The Exported Chaperone PfHsp70x Is Dispensable for the Plasmodium falciparum Intraerythrocytic Life Cycle. mSphere 2017; 2:mSphere00363-17. [PMID: 28959740 PMCID: PMC5615134 DOI: 10.1128/msphere.00363-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 09/07/2017] [Indexed: 11/24/2022] Open
Abstract
Half of the world’s population lives at risk for malaria. The intraerythrocytic life cycle of Plasmodium spp. is responsible for clinical manifestations of malaria; therefore, knowledge of the parasite’s ability to survive within the erythrocyte is needed to combat the deadliest agent of malaria, P. falciparum. An outstanding question in the field is how P. falciparum undertakes the essential process of trafficking its proteins within the host cell. In most organisms, chaperones such as Hsp70 are employed in protein trafficking. Of the Plasmodium species causing human disease, the chaperone PfHsp70x is unique to P. falciparum, and it is the only parasite protein of its kind exported to the host (S. Külzer et al., Cell Microbiol 14:1784–1795, 2012). This has placed PfHsp70x as an ideal target to inhibit protein trafficking and kill the parasite. However, we show that PfHsp70x is not required for export of parasite effectors and it is not essential for parasite survival inside the RBC. Export of parasite proteins into the host erythrocyte is essential for survival of Plasmodium falciparum during its asexual life cycle. While several studies described key factors within the parasite that are involved in protein export, the mechanisms employed to traffic exported proteins within the host cell are currently unknown. Members of the Hsp70 family of chaperones, together with their Hsp40 cochaperones, facilitate protein trafficking in other organisms, and are thus likely used by P. falciparum in the trafficking of its exported proteins. A large group of Hsp40 proteins is encoded by the parasite and exported to the host cell, but only one Hsp70, P. falciparum Hsp70x (PfHsp70x), is exported with them. PfHsp70x is absent in most Plasmodium species and is found only in P. falciparum and closely related species that infect apes. Herein, we have utilized clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 genome editing in P. falciparum to investigate the essentiality of PfHsp70x. We show that parasitic growth was unaffected by knockdown of PfHsp70x using both the dihydrofolate reductase (DHFR)-based destabilization domain and the glmS ribozyme system. Similarly, a complete gene knockout of PfHsp70x did not affect the ability of P. falciparum to proceed through its intraerythrocytic life cycle. The effect of PfHsp70x knockdown/knockout on the export of proteins to the host red blood cell (RBC), including the critical virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1), was tested, and we found that this process was unaffected. These data show that although PfHsp70x is the sole exported Hsp70, it is not essential for the asexual development of P. falciparum. IMPORTANCE Half of the world’s population lives at risk for malaria. The intraerythrocytic life cycle of Plasmodium spp. is responsible for clinical manifestations of malaria; therefore, knowledge of the parasite’s ability to survive within the erythrocyte is needed to combat the deadliest agent of malaria, P. falciparum. An outstanding question in the field is how P. falciparum undertakes the essential process of trafficking its proteins within the host cell. In most organisms, chaperones such as Hsp70 are employed in protein trafficking. Of the Plasmodium species causing human disease, the chaperone PfHsp70x is unique to P. falciparum, and it is the only parasite protein of its kind exported to the host (S. Külzer et al., Cell Microbiol 14:1784–1795, 2012). This has placed PfHsp70x as an ideal target to inhibit protein trafficking and kill the parasite. However, we show that PfHsp70x is not required for export of parasite effectors and it is not essential for parasite survival inside the RBC.
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49
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Inducible protein stabilization system in Leishmania mexicana. Mol Biochem Parasitol 2017; 214:62-64. [DOI: 10.1016/j.molbiopara.2017.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/21/2022]
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50
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Datta G, Hossain ME, Asad M, Rathore S, Mohmmed A. Plasmodium falciparum OTU-like cysteine protease (PfOTU) is essential for apicoplast homeostasis and associates with noncanonical role of Atg8. Cell Microbiol 2017; 19. [PMID: 28423214 DOI: 10.1111/cmi.12748] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/12/2017] [Accepted: 04/05/2017] [Indexed: 12/19/2022]
Abstract
The metabolic pathways associated with the mitochondrion and the apicoplast in Plasmodium, 2 parasite organelles of prokaryotic origin, are considered as suitable drug targets. In the present study, we have identified functional role of a novel ovarian tumour unit (OTU) domain-containing cysteine protease of Plasmodium falciparum (PfOTU). A C-terminal regulatable fluorescent affinity tag on native protein was utilised for its localization and functional characterization. Detailed studies showed vesicular localization of PfOTU and its association with the apicoplast. Degradation-tag mediated knockdown of PfOTU resulted in abnormal apicoplast development and blocked development of parasites beyond early-schizont stages in subsequent cell cycle; downregulation of PfOTU hindered apicoplast protein import. Further, the isoprenoid precursor-mediated parasite growth-rescue experiments confirmed that PfOTU knockdown specifically effect development of functional apicoplast. We also provide evidence for a possible biological function of PfOTU in membrane deconjugation of Atg8, which may be linked with the apicoplast protein import. Overall, our results show that the PfOTU is involved in apicoplast homeostasis and associates with the noncanonical function of Atg8 in maintenance of parasite apicoplast.
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Affiliation(s)
- Gaurav Datta
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohammad E Hossain
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mohd Asad
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Sumit Rathore
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Asif Mohmmed
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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