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Tiwari A, Verma N, Shukla H, Mishra S, Kennedy K, Chatterjee T, Kuldeep J, Parwez S, Siddiqi MI, Ralph SA, Mishra S, Habib S. DNA N-glycosylases Ogg1 and EndoIII as components of base excision repair in Plasmodium falciparum organelles. Int J Parasitol 2024:S0020-7519(24)00137-1. [PMID: 38964640 DOI: 10.1016/j.ijpara.2024.06.005] [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: 03/13/2024] [Revised: 05/31/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The integrity of genomes of the two crucial organelles of the malaria parasite - an apicoplast and mitochondrion in each cell - must be maintained by DNA repair mediated by proteins targeted to these compartments. We explored the localisation and function of Plasmodium falciparum base excision repair (BER) DNA N-glycosylase homologs PfEndoIII and PfOgg1. These N-glycosylases would putatively recognise DNA lesions prior to the action of apurinic/apyrimidinic (AP)-endonucleases. Both Ape1 and Apn1 endonucleases have earlier been shown to function solely in the parasite mitochondrion. Immunofluorescence localisation showed that PfEndoIII was exclusively mitochondrial. PfOgg1 was not seen clearly in mitochondria when expressed as a PfOgg1leader-GFP fusion, although chromatin immunoprecipitation assays showed that it could interact with both mitochondrial and apicoplast DNA. Recombinant PfEndoIII functioned as a DNA N-glycosylase as well as an AP-lyase on thymine glycol (Tg) lesions. We further studied the importance of Ogg1 in the malaria life cycle using reverse genetic approaches in Plasmodium berghei. Targeted disruption of PbOgg1 resulted in loss of 8-oxo-G specific DNA glycosylase/lyase activity. PbOgg1 knockout did not affect blood, mosquito or liver stage development but caused reduced blood stage infection after inoculation of sporozoites in mice. A significant reduction in erythrocyte infectivity by PbOgg1 knockout hepatic merozoites was also observed, thus showing that PbOgg1 ensures smooth transition from liver to blood stage infection. Our results strengthen the view that the Plasmodium mitochondrial genome is an important site for DNA repair by the BER pathway.
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Affiliation(s)
- Anupama Tiwari
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Neetu Verma
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Himadri Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Shivani Mishra
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Kit Kennedy
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010 Australia
| | - Tribeni Chatterjee
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Jitendra Kuldeep
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Shahid Parwez
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - M I Siddiqi
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Stuart A Ralph
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, 3010 Australia
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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Chatterjee T, Tiwari A, Gupta R, Shukla H, Varshney A, Mishra S, Habib S. A Plasmodium apicoplast-targeted unique exonuclease/FEN exhibits interspecies functional differences attributable to an insertion that alters DNA-binding. Nucleic Acids Res 2024:gkae512. [PMID: 38888125 DOI: 10.1093/nar/gkae512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024] Open
Abstract
The human malaria parasite Plasmodium falciparum genome is among the most A + T rich, with low complexity regions (LCRs) inserted in coding sequences including those for proteins targeted to its essential relict plastid (apicoplast). Replication of the apicoplast genome (plDNA), mediated by the atypical multifunctional DNA polymerase PfPrex, would require additional enzymatic functions for lagging strand processing. We identified an apicoplast-targeted, [4Fe-4S]-containing, FEN/Exo (PfExo) with a long LCR insertion and detected its interaction with PfPrex. Distinct from other known exonucleases across organisms, PfExo recognized a wide substrate range; it hydrolyzed 5'-flaps, processed dsDNA as a 5'-3' exonuclease, and was a bipolar nuclease on ssDNA and RNA-DNA hybrids. Comparison with the rodent P. berghei ortholog PbExo, which lacked the insertion and [4Fe-4S], revealed interspecies functional differences. The insertion-deleted PfExoΔins behaved like PbExo with a limited substrate repertoire because of compromised DNA binding. Introduction of the PfExo insertion into PbExo led to gain of activities that the latter initially lacked. Knockout of PbExo indicated essentiality of the enzyme for survival. Our results demonstrate the presence of a novel apicoplast exonuclease with a functional LCR that diversifies substrate recognition, and identify it as the candidate flap-endonuclease and RNaseH required for plDNA replication and maintenance.
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Affiliation(s)
- Tribeni Chatterjee
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Anupama Tiwari
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ritika Gupta
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Himadri Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Aastha Varshney
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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3
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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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4
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Charneau S, de Oliveira LS, Zenonos Z, Hopp CS, Bastos IMD, Loew D, Lombard B, Pandolfo Silveira A, de Carvalho Nardeli Basílio Lobo G, Bao SN, Grellier P, Rayner JC. APEX2-based proximity proteomic analysis identifies candidate interactors for Plasmodium falciparum knob-associated histidine-rich protein in infected erythrocytes. Sci Rep 2024; 14:11242. [PMID: 38755230 PMCID: PMC11099048 DOI: 10.1038/s41598-024-61295-w] [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: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 05/18/2024] Open
Abstract
The interaction of Plasmodium falciparum-infected red blood cells (iRBCs) with the vascular endothelium plays a crucial role in malaria pathology and disease. KAHRP is an exported P. falciparum protein involved in iRBC remodelling, which is essential for the formation of protrusions or "knobs" on the iRBC surface. These knobs and the proteins that are concentrated within them allow the parasites to escape the immune response and host spleen clearance by mediating cytoadherence of the iRBC to the endothelial wall, but this also slows down blood circulation, leading in some cases to severe cerebral and placental complications. In this work, we have applied genetic and biochemical tools to identify proteins that interact with P. falciparum KAHRP using enhanced ascorbate peroxidase 2 (APEX2) proximity-dependent biotinylation and label-free shotgun proteomics. A total of 30 potential KAHRP-interacting candidates were identified, based on the assigned fragmented biotinylated ions. Several identified proteins have been previously reported to be part of the Maurer's clefts and knobs, where KAHRP resides. This study may contribute to a broader understanding of P. falciparum protein trafficking and knob architecture and shows for the first time the feasibility of using APEX2-proximity labelling in iRBCs.
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Affiliation(s)
- Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil.
| | - Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Zenon Zenonos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Biologics Engineering, Oncology R&D, AstraZenecaGranta Park, Cambridge, UK
| | - Christine S Hopp
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Izabela M D Bastos
- Laboratory of Host Pathogen Interaction, Department of Cell Biology, Institute of Biology, University of Brasília, Brasília, 70910-900, Brazil
| | - Damarys Loew
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Bérangère Lombard
- Institut Curie, Centre de Recherche, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ariane Pandolfo Silveira
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | | | - Sônia Nair Bao
- Laboratory of Microscopy and Microanalysis, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, 70910-900, Brazil
| | - Philippe Grellier
- UMR 7245 MCAM Molecules of Communication and Adaptation of Microorganisms, Muséum National d'Histoire Naturelle, CNRS, 75231, Paris Cedex 05, France
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
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5
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Mamudu CO, Tebamifor ME, Sule MO, Dokunmu TM, Ogunlana OO, Iheagwam FN. Apicoplast-Resident Processes: Exploiting the Chink in the Armour of Plasmodium falciparum Parasites. Adv Pharmacol Pharm Sci 2024; 2024:9940468. [PMID: 38765186 PMCID: PMC11101256 DOI: 10.1155/2024/9940468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/25/2024] [Accepted: 04/20/2024] [Indexed: 05/21/2024] Open
Abstract
The discovery of a relict plastid, also known as an apicoplast (apicomplexan plastid), that houses housekeeping processes and metabolic pathways critical to Plasmodium parasites' survival has prompted increased research on identifying potent inhibitors that can impinge on apicoplast-localised processes. The apicoplast is absent in humans, yet it is proposed to originate from the eukaryote's secondary endosymbiosis of a primary symbiont. This symbiotic relationship provides a favourable microenvironment for metabolic processes such as haem biosynthesis, Fe-S cluster synthesis, isoprenoid biosynthesis, fatty acid synthesis, and housekeeping processes such as DNA replication, transcription, and translation, distinct from analogous mammalian processes. Recent advancements in comprehending the biology of the apicoplast reveal it as a vulnerable organelle for malaria parasites, offering numerous potential targets for effective antimalarial therapies. We provide an overview of the metabolic processes occurring in the apicoplast and discuss the organelle as a viable antimalarial target in light of current advances in drug discovery. We further highlighted the relevance of these metabolic processes to Plasmodium falciparum during the different stages of the lifecycle.
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Affiliation(s)
- Collins Ojonugwa Mamudu
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
| | - Mercy Eyitomi Tebamifor
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
| | - Mary Ohunene Sule
- Confluence University of Science and Technology, Osara, Kogi, Nigeria
| | - Titilope Modupe Dokunmu
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
| | - Olubanke Olujoke Ogunlana
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
- Covenant University Public Health and Wellbeing Research Cluster, Covenant University, Ota, Nigeria
| | - Franklyn Nonso Iheagwam
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant University Public Health and Wellbeing Research Cluster, Covenant University, Ota, Nigeria
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K. Raval P, MacLeod AI, Gould SB. A molecular atlas of plastid and mitochondrial proteins reveals organellar remodeling during plant evolutionary transitions from algae to angiosperms. PLoS Biol 2024; 22:e3002608. [PMID: 38713727 PMCID: PMC11135702 DOI: 10.1371/journal.pbio.3002608] [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: 09/18/2023] [Revised: 05/29/2024] [Accepted: 03/28/2024] [Indexed: 05/09/2024] Open
Abstract
Algae and plants carry 2 organelles of endosymbiotic origin that have been co-evolving in their host cells for more than a billion years. The biology of plastids and mitochondria can differ significantly across major lineages and organelle changes likely accompanied the adaptation to new ecological niches such as the terrestrial habitat. Based on organelle proteome data and the genomes of 168 phototrophic (Archaeplastida) versus a broad range of 518 non-phototrophic eukaryotes, we screened for changes in plastid and mitochondrial biology across 1 billion years of evolution. Taking into account 331,571 protein families (or orthogroups), we identify 31,625 protein families that are unique to primary plastid-bearing eukaryotes. The 1,906 and 825 protein families are predicted to operate in plastids and mitochondria, respectively. Tracing the evolutionary history of these protein families through evolutionary time uncovers the significant remodeling the organelles experienced from algae to land plants. The analyses of gained orthogroups identifies molecular changes of organelle biology that connect to the diversification of major lineages and facilitated major transitions from chlorophytes en route to the global greening and origin of angiosperms.
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Affiliation(s)
- Parth K. Raval
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexander I. MacLeod
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
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7
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Kalamuddin M, Shakri AR, Wang C, Min H, Li X, Cui L, Miao J. MYST regulates DNA repair and forms a NuA4-like complex in the malaria parasite Plasmodium falciparum. mSphere 2024; 9:e0014024. [PMID: 38564734 PMCID: PMC11036802 DOI: 10.1128/msphere.00140-24] [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: 02/21/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Histone lysine acetyltransferase MYST-associated NuA4 complex is conserved from yeast to humans and plays key roles in cell cycle regulation, gene transcription, and DNA replication/repair. Here, we identified a Plasmodium falciparum MYST-associated complex, PfNuA4, which contains 11 of the 13 conserved NuA4 subunits. Reciprocal pulldowns using PfEAF2, a shared component between the NuA4 and SWR1 complexes, not only confirmed the PfNuA4 complex but also identified the PfSWR1 complex, a histone remodeling complex, although their identities are low compared to the homologs in yeast or humans. Notably, both H2A.Z/H2B.Z were associated with the PfSWR1 complex, indicating that this complex is involved in the deposition of H2A.Z/H2B.Z, the variant histone pair that is enriched in the activated promoters. Overexpression of PfMYST resulted in earlier expression of genes involved in cell cycle regulation, DNA replication, and merozoite invasion, and upregulation of the genes related to antigenic variation and DNA repair. Consistently, PfMYST overexpression led to high basal phosphorylated PfH2A (γ-PfH2A), the mark of DNA double-strand breaks, and conferred protection against genotoxic agent methyl methanesulfonate (MMS), X-rays, and artemisinin, the first-line antimalarial drug. In contrast, the knockdown of PfMYST caused a delayed parasite recovery upon MMS treatment. MMS induced the gradual disappearance of PfMYST in the cytoplasm and concomitant accumulation of PfMYST in the nucleus, suggesting cytoplasm-nucleus shuttling of PfMYST. Meanwhile, PfMYST colocalized with the γ-PfH2A, indicating PfMYST was recruited to the DNA damage sites. Collectively, PfMYST plays critical roles in cell cycle regulation, gene transcription, and DNA replication/DNA repair in this low-branching parasitic protist.IMPORTANCEUnderstanding gene regulation and DNA repair in malaria parasites is critical for identifying targets for antimalarials. This study found PfNuA4, a PfMYST-associated, histone modifier complex, and PfSWR1, a chromatin remodeling complex in malaria parasite Plasmodium falciparum. These complexes are divergent due to the low identities compared to their homologs from yeast and humans. Furthermore, overexpression of PfMYST resulted in substantial transcriptomic changes, indicating that PfMYST is involved in regulating the cell cycle, antigenic variation, and DNA replication/repair. Consistently, PfMYST was found to protect against DNA damage caused by the genotoxic agent methyl methanesulfonate, X-rays, and artemisinin, the first-line antimalarial drug. Additionally, DNA damage led to the relocation of cytoplasmic PfMYST to the nucleus and colocalization of PfMYST with γ-PfH2A, the mark of DNA damage. In summary, this study demonstrated that the PfMYST complex has critical functions in regulating cell cycle, antigenic variation, and DNA replication/DNA repair in P. falciparum.
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Affiliation(s)
- Mohammad Kalamuddin
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Ahmad Rushdi Shakri
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Hui Min
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Xiaolian Li
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
| | - Liwang Cui
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jun Miao
- Department of Internal Medicine, University of South Florida, Morsani College of Medicine, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
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8
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Dong H, Yang J, He K, Zheng WB, Lai DH, Liu J, Ding HY, Wu RB, Brown KM, Hide G, Lun ZR, Zhu XQ, Long S. The Toxoplasma monocarboxylate transporters are involved in the metabolism within the apicoplast and are linked to parasite survival. eLife 2024; 12:RP88866. [PMID: 38502570 PMCID: PMC10950331 DOI: 10.7554/elife.88866] [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] [Indexed: 03/21/2024] Open
Abstract
The apicoplast is a four-membrane plastid found in the apicomplexans, which harbors biosynthesis and organelle housekeeping activities in the matrix. However, the mechanism driving the flux of metabolites, in and out, remains unknown. Here, we used TurboID and genome engineering to identify apicoplast transporters in Toxoplasma gondii. Among the many novel transporters, we show that one pair of apicomplexan monocarboxylate transporters (AMTs) appears to have evolved from a putative host cell that engulfed a red alga. Protein depletion showed that AMT1 and AMT2 are critical for parasite growth. Metabolite analyses supported the notion that AMT1 and AMT2 are associated with biosynthesis of isoprenoids and fatty acids. However, stronger phenotypic defects were observed for AMT2, including in the inability to establish T. gondii parasite virulence in mice. This study clarifies, significantly, the mystery of apicoplast transporter composition and reveals the importance of the pair of AMTs in maintaining the apicoplast activity in apicomplexans.
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Affiliation(s)
- Hui Dong
- National Key Laboratory of Veterinary Public Health Safety, and College of Veterinary Medicine, China Agricultural University, Beijing, China
- National Animal Protozoa Laboratory and School of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jiong Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kai He
- National Key Laboratory of Veterinary Public Health Safety, and College of Veterinary Medicine, China Agricultural University, Beijing, China
- National Animal Protozoa Laboratory and School of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wen-Bin Zheng
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - De-Hua Lai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Jing Liu
- National Key Laboratory of Veterinary Public Health Safety, and College of Veterinary Medicine, China Agricultural University, Beijing, China
- National Animal Protozoa Laboratory and School of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hui-Yong Ding
- National Key Laboratory of Veterinary Public Health Safety, and College of Veterinary Medicine, China Agricultural University, Beijing, China
- National Animal Protozoa Laboratory and School of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rui-Bin Wu
- National Key Laboratory of Veterinary Public Health Safety, and College of Veterinary Medicine, China Agricultural University, Beijing, China
- National Animal Protozoa Laboratory and School of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Kevin M Brown
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, United States
| | - Geoff Hide
- Biomedical Research and Innovation Centre and Environmental Research and Innovation Centre, School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
| | - Zhao-Rong Lun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Shaojun Long
- National Key Laboratory of Veterinary Public Health Safety, and College of Veterinary Medicine, China Agricultural University, Beijing, China
- National Animal Protozoa Laboratory and School of Veterinary Medicine, China Agricultural University, Beijing, China
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9
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Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CK, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase PhoD as a determinant of antiparasitic resistance. Proc Natl Acad Sci U S A 2024; 121:e2312987121. [PMID: 38377214 PMCID: PMC10907312 DOI: 10.1073/pnas.2312987121] [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: 08/07/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024] Open
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites and the lack of specific drugs necessitate the discovery of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of Babesia spp. (B. bovis and B. divergens). We identified a potent antibabesial, MMV019266, from the Malaria Box, and selected for resistance in two species of Babesia. After sequencing of multiple independently derived lines in the two species, we identified mutations in a membrane-bound metallodependent phosphatase (phoD). In both species, the mutations were found in the phoD-like phosphatase domain. Using reverse genetics, we validated that mutations in bdphoD confer resistance to MMV019266 in B. divergens. We have also demonstrated that BdPhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of BdPhoD alter the sensitivity to MMV019266 in the parasite. Overexpression of BdPhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting BdPhoD is a pro-susceptibility factor. Together, we have generated a robust pipeline for identification of resistance loci and identified BdPhoD as a resistance mechanism in Babesia species.
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Affiliation(s)
- Caroline D. Keroack
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Brendan Elsworth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Jacob A. Tennessen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Aditya S. Paul
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Renee Hua
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Luz Ramirez-Ramirez
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Sida Ye
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Cristina K. Moreira
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
| | - Marvin J. Meyers
- Department of Chemistry, Saint Louis University, St. Louis, MO63103
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts, Boston, MA02125
- Center for Personalized Cancer Therapy, University of Massachusetts, Boston, MA02125
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA02115
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10
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Crispim M, Verdaguer IB, Hernández A, Kronenberger T, Fenollar À, Yamaguchi LF, Alberione MP, Ramirez M, de Oliveira SS, Katzin AM, Izquierdo L. Beyond the MEP Pathway: A novel kinase required for prenol utilization by malaria parasites. PLoS Pathog 2024; 20:e1011557. [PMID: 38277417 PMCID: PMC10849223 DOI: 10.1371/journal.ppat.1011557] [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: 07/18/2023] [Revised: 02/07/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
A proposed treatment for malaria is a combination of fosmidomycin and clindamycin. Both compounds inhibit the methylerythritol 4-phosphate (MEP) pathway, the parasitic source of farnesyl and geranylgeranyl pyrophosphate (FPP and GGPP, respectively). Both FPP and GGPP are crucial for the biosynthesis of several essential metabolites such as ubiquinone and dolichol, as well as for protein prenylation. Dietary prenols, such as farnesol (FOH) and geranylgeraniol (GGOH), can rescue parasites from MEP inhibitors, suggesting the existence of a missing pathway for prenol salvage via phosphorylation. In this study, we identified a gene in the genome of P. falciparum, encoding a transmembrane prenol kinase (PolK) involved in the salvage of FOH and GGOH. The enzyme was expressed in Saccharomyces cerevisiae, and its FOH/GGOH kinase activities were experimentally validated. Furthermore, conditional knockout parasites (Δ-PolK) were created to investigate the biological importance of the FOH/GGOH salvage pathway. Δ-PolK parasites were viable but displayed increased susceptibility to fosmidomycin. Their sensitivity to MEP inhibitors could not be rescued by adding prenols. Additionally, Δ-PolK parasites lost their capability to utilize prenols for protein prenylation. Experiments using culture medium supplemented with whole/delipidated human plasma in transgenic parasites revealed that human plasma has components that can diminish the effectiveness of fosmidomycin. Mass spectrometry tests indicated that both bovine supplements used in culture and human plasma contain GGOH. These findings suggest that the FOH/GGOH salvage pathway might offer an alternate source of isoprenoids for malaria parasites when de novo biosynthesis is inhibited. This study also identifies a novel kind of enzyme related to isoprenoid metabolism.
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Affiliation(s)
- Marcell Crispim
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ignasi Bofill Verdaguer
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Agustín Hernández
- Center for Biological and Health Sciences, Integrated Unit for Research in Biodiversity (BIOTROP-CCBS), Federal University of São Carlos, São Carlos, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen, Germany
| | - Àngel Fenollar
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - María Pía Alberione
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Miriam Ramirez
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | - Alejandro Miguel Katzin
- Department of Parasitology, Institute of Biomedical Sciences of the University of São Paulo, São Paulo, Brazil
| | - Luis Izquierdo
- Barcelona Institute for Global Health (ISGlobal), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
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11
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Schmidt S, Wichers-Misterek JS, Behrens HM, Birnbaum J, Henshall IG, Dröge J, Jonscher E, Flemming S, Castro-Peña C, Mesén-Ramírez P, Spielmann T. The Kelch13 compartment contains highly divergent vesicle trafficking proteins in malaria parasites. PLoS Pathog 2023; 19:e1011814. [PMID: 38039338 PMCID: PMC10718435 DOI: 10.1371/journal.ppat.1011814] [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: 07/27/2023] [Revised: 12/13/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023] Open
Abstract
Single amino acid changes in the parasite protein Kelch13 (K13) result in reduced susceptibility of P. falciparum parasites to artemisinin and its derivatives (ART). Recent work indicated that K13 and other proteins co-localising with K13 (K13 compartment proteins) are involved in the endocytic uptake of host cell cytosol (HCCU) and that a reduction in HCCU results in reduced susceptibility to ART. HCCU is critical for parasite survival but is poorly understood, with the K13 compartment proteins among the few proteins so far functionally linked to this process. Here we further defined the composition of the K13 compartment by analysing more hits from a previous BioID, showing that MyoF and MCA2 as well as Kelch13 interaction candidate (KIC) 11 and 12 are found at this site. Functional analyses, tests for ART susceptibility as well as comparisons of structural similarities using AlphaFold2 predictions of these and previously identified proteins showed that vesicle trafficking and endocytosis domains were frequent in proteins involved in resistance or endocytosis (or both), comprising one group of K13 compartment proteins. While this strengthened the link of the K13 compartment to endocytosis, many proteins of this group showed unusual domain combinations and large parasite-specific regions, indicating a high level of taxon-specific adaptation of this process. Another group of K13 compartment proteins did not influence endocytosis or ART susceptibility and lacked detectable vesicle trafficking domains. We here identified the first protein of this group that is important for asexual blood stage development and showed that it likely is involved in invasion. Overall, this work identified novel proteins functioning in endocytosis and at the K13 compartment. Together with comparisons of structural predictions it provides a repertoire of functional domains at the K13 compartment that indicate a high level of adaption of endocytosis in malaria parasites.
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Affiliation(s)
- Sabine Schmidt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Jakob Birnbaum
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | - Jana Dröge
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Ernst Jonscher
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sven Flemming
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | | | | | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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12
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Siau A, Ang JW, Sheriff O, Hoo R, Loh HP, Tay D, Huang X, Yam XY, Lai SK, Meng W, Julca I, Kwan SS, Mutwil M, Preiser PR. Comparative spatial proteomics of Plasmodium-infected erythrocytes. Cell Rep 2023; 42:113419. [PMID: 37952150 DOI: 10.1016/j.celrep.2023.113419] [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: 02/15/2022] [Revised: 07/14/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023] Open
Abstract
Plasmodium parasites contribute to one of the highest global infectious disease burdens. To achieve this success, the parasite has evolved a range of specialized subcellular compartments to extensively remodel the host cell for its survival. The information to fully understand these compartments is likely hidden in the so far poorly characterized Plasmodium species spatial proteome. To address this question, we determined the steady-state subcellular location of more than 12,000 parasite proteins across five different species by extensive subcellular fractionation of erythrocytes infected by Plasmodium falciparum, Plasmodium knowlesi, Plasmodium yoelii, Plasmodium berghei, and Plasmodium chabaudi. This comparison of the pan-species spatial proteomes and their expression patterns indicates increasing species-specific proteins associated with the more external compartments, supporting host adaptations and post-transcriptional regulation. The spatial proteome offers comprehensive insight into the different human, simian, and rodent Plasmodium species, establishing a powerful resource for understanding species-specific host adaptation processes in the parasite.
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Affiliation(s)
- Anthony Siau
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Jing Wen Ang
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Omar Sheriff
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Regina Hoo
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Han Ping Loh
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Donald Tay
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Ximei Huang
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Xue Yan Yam
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Soak Kuan Lai
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Wei Meng
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Irene Julca
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Sze Siu Kwan
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Marek Mutwil
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore
| | - Peter R Preiser
- Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore.
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13
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Pietsch E, Ramaprasad A, Bielfeld S, Wohlfarter Y, Maco B, Niedermüller K, Wilcke L, Kloehn J, Keller MA, Soldati-Favre D, Blackman MJ, Gilberger TW, Burda PC. A patatin-like phospholipase is important for mitochondrial function in malaria parasites. mBio 2023; 14:e0171823. [PMID: 37882543 PMCID: PMC10746288 DOI: 10.1128/mbio.01718-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 10/27/2023] Open
Abstract
Plasmodium parasites rely on a functional electron transport chain (ETC) within their mitochondrion for proliferation, and compounds targeting mitochondrial functions are validated antimalarials. Here, we localize Plasmodium falciparum patatin-like phospholipase 2 (PfPNPLA2, PF3D7_1358000) to the mitochondrion and reveal that disruption of the PfPNPLA2 gene impairs asexual replication. PfPNPLA2-null parasites are hypersensitive to proguanil and inhibitors of the mitochondrial ETC, including atovaquone. In addition, PfPNPLA2-deficient parasites show reduced mitochondrial respiration and reduced mitochondrial membrane potential, indicating that disruption of PfPNPLA2 leads to a defect in the parasite ETC. Lipidomic analysis of the mitochondrial phospholipid cardiolipin (CL) reveals that loss of PfPNPLA2 is associated with a moderate shift toward shorter-chained and more saturated CL species, implying a contribution of PfPNPLA2 to CL remodeling. PfPNPLA2-deficient parasites display profound defects in gametocytogenesis, underlining the importance of a functional mitochondrial ETC during both the asexual and sexual development of the parasite. IMPORTANCE For their proliferation within red blood cells, malaria parasites depend on a functional electron transport chain (ETC) within their mitochondrion, which is the target of several antimalarial drugs. Here, we have used gene disruption to identify a patatin-like phospholipase, PfPNPLA2, as important for parasite replication and mitochondrial function in Plasmodium falciparum. Parasites lacking PfPNPLA2 show defects in their ETC and become hypersensitive to mitochondrion-targeting drugs. Furthermore, PfPNPLA2-deficient parasites show differences in the composition of their cardiolipins, a unique class of phospholipids with key roles in mitochondrial functions. Finally, we demonstrate that parasites devoid of PfPNPLA2 have a defect in gametocyte maturation, underlining the importance of a functional ETC for parasite transmission to the mosquito vector.
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Affiliation(s)
- Emma Pietsch
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Abhinay Ramaprasad
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Sabrina Bielfeld
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Yvonne Wohlfarter
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Bohumil Maco
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Korbinian Niedermüller
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Louisa Wilcke
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Markus A. Keller
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Michael J. Blackman
- Malaria Biochemistry Laboratory, The Francis Crick Institute, London, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Tim-Wolf Gilberger
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Paul-Christian Burda
- Centre for Structural Systems Biology, Hamburg, Germany
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
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14
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Lucky AB, Wang C, Shakri AR, Kalamuddin M, Chim-Ong A, Li X, Miao J. Plasmodium falciparum GCN5 plays a key role in regulating artemisinin resistance-related stress responses. Antimicrob Agents Chemother 2023; 67:e0057723. [PMID: 37702516 PMCID: PMC10583690 DOI: 10.1128/aac.00577-23] [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: 05/05/2023] [Accepted: 07/24/2023] [Indexed: 09/14/2023] Open
Abstract
Plasmodium falciparum causes the most severe malaria and is exposed to various environmental and physiological stresses in the human host. Given that GCN5 plays a critical role in regulating stress responses in model organisms, we aimed to elucidate PfGCN5's function in stress responses in P. falciparum. The protein level of PfGCN5 was substantially induced under three stress conditions [heat shock, low glucose starvation, and dihydroartemisinin, the active metabolite of artemisinin (ART)]. With a TetR-DOZI conditional knockdown (KD) system, we successfully down-regulated PfGCN5 to ~50% and found that KD parasites became more sensitive to all three stress conditions. Transcriptomic analysis via RNA-seq identified ~1,000 up- and down-regulated genes in the wild-type (WT) and KD parasites under these stress conditions. Importantly, DHA induced transcriptional alteration of many genes involved in many aspects of stress responses, which were heavily shared among the altered genes under heat shock and low glucose conditions, including ART-resistance-related genes such as K13 and coronin. Based on the expression pattern between WT and KD parasites under three stress conditions, ~300-400 genes were identified to be involved in PfGCN5-dependent, general, and stress-condition-specific responses with high levels of overlaps among three stress conditions. Notably, using ring-stage survival assay, we found that KD or inhibition of PfGCN5 could sensitize the ART-resistant parasites to the DHA treatment. All these indicate that PfGCN5 is pivotal in regulating general and ART-resistance-related stress responses in malaria parasites, implicating PfGCN5 as a potential target for malaria intervention.
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Affiliation(s)
- Amuza Byaruhanga Lucky
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Ahmad Rushdi Shakri
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Mohammad Kalamuddin
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Anongruk Chim-Ong
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Xiaolian Li
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Jun Miao
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
- Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA
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15
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Devi SB, Kumar S. Designing a multi-epitope chimeric protein from different potential targets: A potential vaccine candidate against Plasmodium. Mol Biochem Parasitol 2023; 255:111560. [PMID: 37084957 DOI: 10.1016/j.molbiopara.2023.111560] [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: 07/13/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Malaria is an infectious disease that has been a continuous threat to mankind since the time immemorial. Owing to the complex multi-staged life cycle of the plasmodium parasite, an effective malaria vaccine which is fully protective against the parasite infection is urgently needed to deal with the challenges. In the present study, essential parasite proteins were identified and a chimeric protein with multivalent epitopes was generated. The designed chimeric protein consists of best potential B and T cell epitopes from five different essential parasite proteins. Physiochemical studies of the chimeric protein showed that the modeled vaccine construct was thermo-stable, hydrophilic and antigenic in nature. And the binding of the vaccine construct with Toll-like receptor-4 (TLR-4) as revealed by the molecular docking suggests the possible interaction and role of the vaccine construct in activating the innate immune response. The constructed vaccine being a chimeric protein containing epitopes from different potential candidates could target different stages or pathways of the parasite. Moreover, the approach used in this study is time and cost effective, and can be applied in the discoveries of new potential vaccine targets for other pathogens.
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Affiliation(s)
- Sanasam Bijara Devi
- Department of Life science & Bioinformatics, Assam University, Silchar 788011 India.
| | - Sanjeev Kumar
- Department of Life science & Bioinformatics, Assam University, Silchar 788011 India
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16
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Machado M, Klaus S, Klaschka D, Guizetti J, Ganter M. Plasmodium falciparum CRK4 links early mitotic events to the onset of S-phase during schizogony. mBio 2023; 14:e0077923. [PMID: 37345936 PMCID: PMC10470535 DOI: 10.1128/mbio.00779-23] [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: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
Plasmodium falciparum proliferates through schizogony in the clinically relevant blood stage of infection. During schizogony, consecutive rounds of DNA replication and nuclear division give rise to multinucleated stages before cellularization occurs. Although these nuclei reside in a shared cytoplasm, DNA replication and nuclear division occur asynchronously. Here, by mapping the proteomic context of the S-phase-promoting kinase PfCRK4, we show that it has a dual role for nuclear-cycle progression: PfCRK4 orchestrates not only DNA replication, but in parallel also the rearrangement of intranuclear microtubules from hemispindles into early mitotic spindles. Live-cell imaging of a reporter parasite showed that these microtubule rearrangements coincide with the onset of DNA replication. Together, our data render PfCRK4 a key factor for nuclear-cycle progression, linking entry into S-phase with the initiation of mitotic events. In part, such links may compensate for the absence of canonical cell cycle checkpoints in P. falciparum. IMPORTANCE The human malaria parasite Plasmodium falciparum proliferates in erythrocytes through schizogony, forming multinucleated stages before cellularization occurs. In marked contrast to the pattern of proliferation seen in most model organisms, P. falciparum nuclei multiply asynchronously despite residing in a shared cytoplasm. This divergent mode of replication is, thus, a good target for therapeutic interventions. To exploit this potential, we investigated a key regulator of the parasite's unusual cell cycle, the kinase PfCRK4 and found that this kinase regulated not only DNA replication but also in parallel the rearrangement of nuclear microtubules into early mitotic spindles. Since canonical cell cycle checkpoints have not been described in P. falciparum parasites, linking entry into S-phase and the initiation of mitotic events via a kinase, may be an alternative means to exert control, which is typically achieved by checkpoints.
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Affiliation(s)
- Marta Machado
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Severina Klaus
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Darius Klaschka
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Julien Guizetti
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus Ganter
- Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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17
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Fierro MA, Hussain T, Campin LJ, Beck JR. Knock-sideways by inducible ER retrieval enables a unique approach for studying Plasmodium-secreted proteins. Proc Natl Acad Sci U S A 2023; 120:e2308676120. [PMID: 37552754 PMCID: PMC10433460 DOI: 10.1073/pnas.2308676120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 06/26/2023] [Indexed: 08/10/2023] Open
Abstract
Malaria parasites uniquely depend on protein secretion for their obligate intracellular lifestyle but approaches for dissecting Plasmodium-secreted protein functions are limited. We report knockER, a unique DiCre-mediated knock-sideways approach to sequester secreted proteins in the ER by inducible fusion with a KDEL ER-retrieval sequence. We show conditional ER sequestration of diverse proteins is not generally toxic, enabling loss-of-function studies. We employed knockER in multiple Plasmodium species to interrogate the trafficking, topology, and function of an assortment of proteins that traverse the secretory pathway to diverse compartments including the apicoplast (ClpB1), rhoptries (RON6), dense granules, and parasitophorous vacuole (EXP2, PTEX150, HSP101). Taking advantage of the unique ability to redistribute secreted proteins from their terminal destination to the ER, we reveal that vacuolar levels of the PTEX translocon component HSP101 but not PTEX150 are maintained in excess of what is required to sustain effector protein export into the erythrocyte. Intriguingly, vacuole depletion of HSP101 hypersensitized parasites to a destabilization tag that inhibits HSP101-PTEX complex formation but not to translational knockdown of the entire HSP101 pool, illustrating how redistribution of a target protein by knockER can be used to query function in a compartment-specific manner. Collectively, our results establish knockER as a unique tool for dissecting secreted protein function with subcompartmental resolution that should be widely amenable to genetically tractable eukaryotes.
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Affiliation(s)
- Manuel A. Fierro
- Department of Biomedical Sciences, Iowa State University, Ames, IA50011
| | - Tahir Hussain
- Department of Biomedical Sciences, Iowa State University, Ames, IA50011
| | - Liam J. Campin
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
| | - Josh R. Beck
- Department of Biomedical Sciences, Iowa State University, Ames, IA50011
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA50011
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18
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Keroack CD, Elsworth B, Tennessen JA, Paul AS, Hua R, Ramirez-Ramirez L, Ye S, Moreira CM, Meyers MJ, Zarringhalam K, Duraisingh MT. Comparative chemical genomics in Babesia species identifies the alkaline phosphatase phoD as a novel determinant of resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544849. [PMID: 37398106 PMCID: PMC10312741 DOI: 10.1101/2023.06.13.544849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Babesiosis is an emerging zoonosis and widely distributed veterinary infection caused by 100+ species of Babesia parasites. The diversity of Babesia parasites, coupled with the lack of potent inhibitors necessitates the discovery of novel conserved druggable targets for the generation of broadly effective antibabesials. Here, we describe a comparative chemogenomics (CCG) pipeline for the identification of novel and conserved targets. CCG relies on parallel in vitro evolution of resistance in independent populations of evolutionarily-related Babesia spp. ( B. bovis and B. divergens ). We identified a potent antibabesial inhibitor from the Malaria Box, MMV019266. We were able to select for resistance to this compound in two species of Babesia, achieving 10-fold or greater resistance after ten weeks of intermittent selection. After sequencing of multiple independently derived lines in the two species, we identified mutations in a single conserved gene in both species: a membrane-bound metallodependent phosphatase (putatively named PhoD). In both species, the mutations were found in the phoD-like phosphatase domain, proximal to the predicted ligand binding site. Using reverse genetics, we validated that mutations in PhoD confer resistance to MMV019266. We have also demonstrated that PhoD localizes to the endomembrane system and partially with the apicoplast. Finally, conditional knockdown and constitutive overexpression of PhoD alter the sensitivity to MMV019266 in the parasite: overexpression of PhoD results in increased sensitivity to the compound, while knockdown increases resistance, suggesting PhoD is a resistance mechanism. Together, we have generated a robust pipeline for identification of resistance loci, and identified PhoD as a novel determinant of resistance in Babesia species. Highlights Use of two species for in vitro evolution identifies a high confidence locus associated with resistance Resistance mutation in phoD was validated using reverse genetics in B. divergens Perturbation of phoD using function genetics results in changes in the level of resistance to MMV019266Epitope tagging reveals localization to the ER/apicoplast, a conserved localization with a similar protein in diatoms Together, phoD is a novel resistance determinant in multiple Babesia spp .
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Lucky AB, Wang C, Shakri AR, Kalamuddin M, Chim-Ong A, Li X, Miao J. Plasmodium falciparum GCN5 plays a key role in regulating artemisinin resistance-related stress responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523703. [PMID: 36711954 PMCID: PMC9882135 DOI: 10.1101/2023.01.11.523703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Plasmodium falciparum causes the most severe malaria and is exposed to various environmental and physiological stresses in the human host. Given that GCN5 plays a critical role in regulating stress responses in model organisms, we aimed to elucidate PfGCN5's function in stress responses in P. falciparum . The protein level of PfGCN5 was substantially induced under three stress conditions (heat shock, low glucose starvation, and dihydroartemisinin, the active metabolite of artemisinin (ART)). With a TetR-DOZI conditional knockdown (KD) system, we successfully down-regulated PfGCN5 to ∼50% and found that KD parasites became more sensitive to all three stress conditions. Transcriptomic analysis via RNA-seq identified ∼1,000 up-and down-regulated genes in the wildtype (WT) and KD parasites under these stress conditions. Importantly, DHA induced transcriptional alteration of many genes involved in many aspects of stress responses, which were heavily shared among the altered genes under heat shock and low glucose conditions, including ART-resistance-related genes such as K13 and coronin . Based on the expression pattern between WT and KD parasites under three stress conditions, ∼300-400 genes were identified to be involved in PfGCN5-dependent, general and stress-condition-specific responses with high levels of overlaps among three stress conditions. Notably, using ring-stage survival assay (RSA), we found that KD or inhibition of PfGCN5 could sensitize the ART-resistant parasites to the DHA treatment. All these indicate that PfGCN5 is pivotal in regulating general and ART-resistance-related stress responses in malaria parasites, implicating PfGCN5 as a potential target for malaria intervention. IMPORTANCE Malaria leads to about half a million deaths annually and these casualties were majorly caused by the infection of Plasmodium falciparum . This parasite strives to survive by defending against a variety of stress conditions, such as malaria cyclical fever (heat shock), starvation due to low blood sugar (glucose) levels (hypoglycemia), and drug treatment. Previous studies have revealed that P. falciparum has developed unique stress responses to different stresses including ART treatment, and ART-resistant parasites harbor elevated stress responses. In this study, we provide critical evidence on the role of PfGCN5, a histone modifier, and a chromatin coactivator, in regulating general and stress-specific responses in malaria parasites, indicating that PfGCN5 can be used as a potential target for anti-malaria intervention.
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20
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Christian R, Labbancz J, Usadel B, Dhingra A. Understanding protein import in diverse non-green plastids. Front Genet 2023; 14:969931. [PMID: 37007964 PMCID: PMC10063809 DOI: 10.3389/fgene.2023.969931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
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Affiliation(s)
- Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - June Labbancz
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Amit Dhingra,
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21
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Mathur V, Salomaki ED, Wakeman KC, Na I, Kwong WK, Kolisko M, Keeling PJ. Reconstruction of Plastid Proteomes of Apicomplexans and Close Relatives Reveals the Major Evolutionary Outcomes of Cryptic Plastids. Mol Biol Evol 2023; 40:6969433. [PMID: 36610734 PMCID: PMC9847631 DOI: 10.1093/molbev/msad002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 12/13/2022] [Indexed: 01/09/2023] Open
Abstract
Apicomplexans and related lineages comprise many obligate symbionts of animals; some of which cause notorious diseases such as malaria. They evolved from photosynthetic ancestors and transitioned into a symbiotic lifestyle several times, giving rise to species with diverse non-photosynthetic plastids. Here, we sought to reconstruct the evolution of the cryptic plastids in the apicomplexans, chrompodellids, and squirmids (ACS clade) by generating five new single-cell transcriptomes from understudied gregarine lineages, constructing a robust phylogenomic tree incorporating all ACS clade sequencing datasets available, and using these to examine in detail, the evolutionary distribution of all 162 proteins recently shown to be in the apicoplast by spatial proteomics in Toxoplasma. This expanded homology-based reconstruction of plastid proteins found in the ACS clade confirms earlier work showing convergence in the overall metabolic pathways retained once photosynthesis is lost, but also reveals differences in the degrees of plastid reduction in specific lineages. We show that the loss of the plastid genome is common and unexpectedly find many lineage- and species-specific plastid proteins, suggesting the presence of evolutionary innovations and neofunctionalizations that may confer new functional and metabolic capabilities that are yet to be discovered in these enigmatic organelles.
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Affiliation(s)
| | - Eric D Salomaki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
| | - Ina Na
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Waldan K Kwong
- Present address: Instituto Gulbenkian de Ciência (IGC) Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
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22
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Selection of an Aptamer against the Enzyme 1-deoxy-D-xylulose-5-phosphate Reductoisomerase from Plasmodium falciparum. Pharmaceutics 2022; 14:pharmaceutics14112515. [PMID: 36432706 PMCID: PMC9695703 DOI: 10.3390/pharmaceutics14112515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
The methyl erythritol phosphate (MEP) pathway of isoprenoid biosynthesis is essential for malaria parasites and also for several human pathogenic bacteria, thus representing an interesting target for future antimalarials and antibiotics and for diagnostic strategies. We have developed a DNA aptamer (D10) against Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), the second enzyme of this metabolic route. D10 binds in vitro to recombinant DXR from P. falciparum and Escherichia coli, showing at 10 µM a ca. 50% inhibition of the bacterial enzyme. In silico docking analysis indicates that D10 associates with DXR in solvent-exposed regions outside the active center pocket. According to fluorescence confocal microscopy data, this aptamer specifically targets in P. falciparum in vitro cultures the apicoplast organelle where the MEP pathway is localized and is, therefore, a highly specific marker of red blood cells parasitized by Plasmodium vs. naïve erythrocytes. D10 is also selective for the detection of MEP+ bacteria (e.g., E. coli and Pseudomonas aeruginosa) vs. those lacking DXR (e.g., Enterococcus faecalis). Based on these results, we discuss the potential of DNA aptamers in the development of ligands that can outcompete the performance of the well-established antibody technology for future therapeutic and diagnostic approaches.
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23
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Nieto NS, Parrott EE, Nelson SW. Ribonucleotide Misincorporation and Reverse Transcriptase Activities of Plasmodium falciparum Apicoplast DNA Polymerase. Biochemistry 2022; 61:2742-2750. [DOI: 10.1021/acs.biochem.2c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicholas S. Nieto
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
| | - Eric E. Parrott
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
| | - Scott W. Nelson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa50011, United States
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24
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TurboID Identification of Evolutionarily Divergent Components of the Nuclear Pore Complex in the Malaria Model Plasmodium berghei. mBio 2022; 13:e0181522. [PMID: 36040030 PMCID: PMC9601220 DOI: 10.1128/mbio.01815-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Twenty years since the publication of the Plasmodium falciparum and P. berghei genomes one-third of their protein-coding genes still lack functional annotation. In the absence of sequence and structural homology, protein-protein interactions can facilitate functional prediction of such orphan genes by mapping protein complexes in their natural cellular environment. The Plasmodium nuclear pore complex (NPC) is a case in point: it remains poorly defined; its constituents lack conservation with the 30+ proteins described in the NPC of many opisthokonts, a clade of eukaryotes that includes fungi and animals, but not Plasmodium. Here, we developed a labeling methodology based on TurboID fusion proteins, which allows visualization of the P. berghei NPC and facilitates the identification of its components. Following affinity purification and mass spectrometry, we identified 4 known nucleoporins (Nups) (138, 205, 221, and the bait 313), and verify interaction with the putative phenylalanine-glycine (FG) Nup637; we assigned 5 proteins lacking annotation (and therefore meaningful homology with proteins outside the genus) to the NPC, which is confirmed by green fluorescent protein (GFP) tagging. Based on gene deletion attempts, all new Nups — Nup176, 269, 335, 390, and 434 — are essential to parasite survival. They lack primary sequence homology with proteins outside the Plasmodium genus; albeit 2 incorporate short domains with structural homology to human Nup155 and yeast Nup157, and the condensin SMC (Structural Maintenance Of Chromosomes 4). The protocols developed here showcase the power of proximity labeling for elucidating protein complex composition and annotation of taxonomically restricted genes in Plasmodium. It opens the door to exploring the function of the Plasmodium NPC and understanding its evolutionary position.
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25
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Na Z, Dai X, Zheng SJ, Bryant CJ, Loh KH, Su H, Luo Y, Buhagiar AF, Cao X, Baserga SJ, Chen S, Slavoff SA. Mapping subcellular localizations of unannotated microproteins and alternative proteins with MicroID. Mol Cell 2022; 82:2900-2911.e7. [PMID: 35905735 PMCID: PMC9662605 DOI: 10.1016/j.molcel.2022.06.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/08/2022] [Accepted: 06/29/2022] [Indexed: 11/15/2022]
Abstract
Proteogenomic identification of translated small open reading frames has revealed thousands of previously unannotated, largely uncharacterized microproteins, or polypeptides of less than 100 amino acids, and alternative proteins (alt-proteins) that are co-encoded with canonical proteins and are often larger. The subcellular localizations of microproteins and alt-proteins are generally unknown but can have significant implications for their functions. Proximity biotinylation is an attractive approach to define the protein composition of subcellular compartments in cells and in animals. Here, we developed a high-throughput technology to map unannotated microproteins and alt-proteins to subcellular localizations by proximity biotinylation with TurboID (MicroID). More than 150 microproteins and alt-proteins are associated with subnuclear organelles. One alt-protein, alt-LAMA3, localizes to the nucleolus and functions in pre-rRNA transcription. We applied MicroID in a mouse model, validating expression of a conserved nuclear microprotein, and establishing MicroID for discovery of microproteins and alt-proteins in vivo.
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Affiliation(s)
- Zhenkun Na
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Xiaoyun Dai
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Shu-Jian Zheng
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Ken H Loh
- Laboratory of Molecular Genetics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Haomiao Su
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Yang Luo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Amber F Buhagiar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA
| | - Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Systems Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06529, USA.
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26
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Qian P, Wang X, Zhong CQ, Wang J, Cai M, Nguitragool W, Li J, Cui H, Yuan J. Inner membrane complex proteomics reveals a palmitoylation regulation critical for intraerythrocytic development of malaria parasite. eLife 2022; 11:77447. [PMID: 35775739 PMCID: PMC9293000 DOI: 10.7554/elife.77447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/24/2022] [Indexed: 11/21/2022] Open
Abstract
Malaria is caused by infection of the erythrocytes by the parasites Plasmodium. Inside the erythrocytes, the parasites multiply via schizogony, an unconventional cell division mode. The inner membrane complex (IMC), an organelle located beneath the parasite plasma membrane, serving as the platform for protein anchorage, is essential for schizogony. So far, the complete repertoire of IMC proteins and their localization determinants remain unclear. Here we used biotin ligase (TurboID)-based proximity labeling to compile the proteome of the schizont IMC of the rodent malaria parasite Plasmodium yoelii. In total, 300 TurboID-interacting proteins were identified. 18 of 21 selected candidates were confirmed to localize in the IMC, indicating good reliability. In light of the existing palmitome of Plasmodium falciparum, 83 proteins of the P. yoelii IMC proteome are potentially palmitoylated. We further identified DHHC2 as the major resident palmitoyl-acyl-transferase of the IMC. Depletion of DHHC2 led to defective schizont segmentation and growth arrest both in vitro and in vivo. DHHC2 was found to palmitoylate two critical IMC proteins CDPK1 and GAP45 for their IMC localization. In summary, this study reports an inventory of new IMC proteins and demonstrates a central role of DHHC2 in governing the IMC localization of proteins during the schizont development.
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Affiliation(s)
- Pengge Qian
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Xu Wang
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Chuan-Qi Zhong
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Jiaxu Wang
- Xiamen Center for Disease Control and Prevention, Xiamen, China
| | - Mengya Cai
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Mahidol University, Bangkok, Thailand
| | - Jian Li
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Huiting Cui
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Jing Yuan
- Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
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27
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Wunderlich J. Updated List of Transport Proteins in Plasmodium falciparum. Front Cell Infect Microbiol 2022; 12:926541. [PMID: 35811673 PMCID: PMC9263188 DOI: 10.3389/fcimb.2022.926541] [Citation(s) in RCA: 4] [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: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Malaria remains a leading cause of death and disease in many tropical and subtropical regions of the world. Due to the alarming spread of resistance to almost all available antimalarial drugs, novel therapeutic strategies are urgently needed. As the intracellular human malaria parasite Plasmodium falciparum depends entirely on the host to meet its nutrient requirements and the majority of its transmembrane transporters are essential and lack human orthologs, these have often been suggested as potential targets of novel antimalarial drugs. However, membrane proteins are less amenable to proteomic tools compared to soluble parasite proteins, and have thus not been characterised as well. While it had been proposed that P. falciparum had a lower number of transporters (2.5% of its predicted proteome) in comparison to most reference genomes, manual curation of information from various sources led to the identification of 197 known and putative transporter genes, representing almost 4% of all parasite genes, a proportion that is comparable to well-studied metazoan species. This transporter list presented here was compiled by collating data from several databases along with extensive literature searches, and includes parasite-encoded membrane-resident/associated channels, carriers, and pumps that are located within the parasite or exported to the host cell. It provides updated information on the substrates, subcellular localisation, class, predicted essentiality, and the presence or absence of human orthologs of P. falciparum transporters to quickly identify essential proteins without human orthologs for further functional characterisation and potential exploitation as novel drug targets.
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Affiliation(s)
- Juliane Wunderlich
- Max Planck Institute for Infection Biology, Berlin, Germany
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
- Centre for Structural Systems Biology, Hamburg, Germany
- *Correspondence: Juliane Wunderlich,
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28
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Kobakhidze G, Sethi A, Valimehr S, Ralph SA, Rouiller I. The AAA+ ATPase p97 as a novel parasite and tuberculosis drug target. Trends Parasitol 2022; 38:572-590. [DOI: 10.1016/j.pt.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
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29
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Okada M, Rajaram K, Swift RP, Mixon A, Maschek JA, Prigge ST, Sigala PA. Critical role for isoprenoids in apicoplast biogenesis by malaria parasites. eLife 2022; 11:73208. [PMID: 35257658 PMCID: PMC8959605 DOI: 10.7554/elife.73208] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/04/2022] [Indexed: 11/13/2022] Open
Abstract
Isopentenyl pyrophosphate (IPP) is an essential metabolic output of the apicoplast organelle in Plasmodium falciparum malaria parasites and is required for prenylation-dependent vesicular trafficking and other cellular processes. We have elucidated a critical and previously uncharacterized role for IPP in apicoplast biogenesis. Inhibiting IPP synthesis blocks apicoplast elongation and inheritance by daughter merozoites, and apicoplast biogenesis is rescued by exogenous IPP and polyprenols. Knockout of the only known isoprenoid-dependent apicoplast pathway, tRNA prenylation by MiaA, has no effect on blood-stage parasites and thus cannot explain apicoplast reliance on IPP. However, we have localized an annotated polyprenyl synthase (PPS) to the apicoplast. PPS knockdown is lethal to parasites, rescued by IPP and long- (C50) but not short-chain (≤C20) prenyl alcohols, and blocks apicoplast biogenesis, thus explaining apicoplast dependence on isoprenoid synthesis. We hypothesize that PPS synthesizes long-chain polyprenols critical for apicoplast membrane fluidity and biogenesis. This work critically expands the paradigm for isoprenoid utilization in malaria parasites and identifies a novel essential branch of apicoplast metabolism suitable for therapeutic targeting.
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Affiliation(s)
- Megan Okada
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Amanda Mixon
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - John Alan Maschek
- Metabolomics Core, University of Utah, Salt Lake City, United States
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Paul A Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
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30
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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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van Esveld SL, Meerstein‐Kessel L, Boshoven C, Baaij JF, Barylyuk K, Coolen JPM, van Strien J, Duim RAJ, Dutilh BE, Garza DR, Letterie M, Proellochs NI, de Ridder MN, Venkatasubramanian PB, de Vries LE, Waller RF, Kooij TWA, Huynen MA. A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. mSphere 2021; 6:e0061421. [PMID: 34494883 PMCID: PMC8550323 DOI: 10.1128/msphere.00614-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by antimalarial drugs. Most mitochondrial proteins are imported into this organelle, and our picture of the Plasmodium mitochondrial proteome remains incomplete. Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, coevolutionary relationships, and amino acid sequences, each with different coverage and reliability. To obtain a comprehensive, prioritized list of Plasmodium falciparum mitochondrial proteins, we rigorously analyzed and integrated eight data sets using Bayesian statistics into a predictive score per protein for mitochondrial localization. At a corrected false discovery rate of 25%, we identified 445 proteins with a sensitivity of 87% and a specificity of 97%. They include proteins that have not been identified as mitochondrial in other eukaryotes but have characterized homologs in bacteria that are involved in metabolism or translation. Mitochondrial localization of seven Plasmodium berghei orthologs was confirmed by epitope labeling and colocalization with a mitochondrial marker protein. One of these belongs to a newly identified apicomplexan mitochondrial protein family that in P. falciparum has four members. With the experimentally validated mitochondrial proteins and the complete ranked P. falciparum proteome, which we have named PlasmoMitoCarta, we present a resource to study unique proteins of Plasmodium mitochondria. IMPORTANCE The unique biology and medical relevance of the mitochondrion of the malaria parasite Plasmodium falciparum have made it the subject of many studies. However, we actually do not have a comprehensive assessment of which proteins reside in this organelle. Many omics data are available that are predictive of mitochondrial localization, such as proteomics data and expression data. Individual data sets are, however, rarely complete and can provide conflicting evidence. We integrated a wide variety of available omics data in a manner that exploits the relative strengths of the data sets. Our analysis gave a predictive score for the mitochondrial localization to each nuclear encoded P. falciparum protein and identified 445 likely mitochondrial proteins. We experimentally validated the mitochondrial localization of seven of the new mitochondrial proteins, confirming the quality of the complete list. These include proteins that have not been observed mitochondria before, adding unique mitochondrial functions to P. falciparum.
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Affiliation(s)
- Selma L. van Esveld
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Lisette Meerstein‐Kessel
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Cas Boshoven
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Jochem F. Baaij
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Konstantin Barylyuk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Joeri van Strien
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ronald A. J. Duim
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Bas E. Dutilh
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Daniel R. Garza
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marijn Letterie
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Nicholas I. Proellochs
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Michelle N. de Ridder
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | | | - Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
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32
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Kimmel J, Kehrer J, Frischknecht F, Spielmann T. Proximity-dependent biotinylation approaches to study apicomplexan biology. Mol Microbiol 2021; 117:553-568. [PMID: 34587292 DOI: 10.1111/mmi.14815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
In the last 10 years, proximity-dependent biotinylation (PDB) techniques greatly expanded the ability to study protein environments in the living cell that range from specific protein complexes to entire compartments. This is achieved by using enzymes such as BirA* and APEX that are fused to proteins of interest and biotinylate proteins in their proximity. PDB techniques are now also increasingly used in apicomplexan parasites. In this review, we first give an overview of the main PDB approaches and how they compare with other techniques that address similar questions. PDB is particularly valuable to detect weak or transient protein associations under physiological conditions and to study cellular structures that are difficult to purify or have a poorly understood protein composition. We also highlight new developments such as novel smaller or faster-acting enzyme variants and conditional PDB approaches, providing improvements in both temporal and spatial resolution which may offer broader application possibilities useful in apicomplexan research. In the second part, we review work using PDB techniques in apicomplexan parasites and how this expanded our knowledge about these medically important parasites.
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Affiliation(s)
- Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Kehrer
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany.,German Center for Infectious Disease Research, DZIF, Heidelberg, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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Kloehn J, Lacour CE, Soldati-Favre D. The metabolic pathways and transporters of the plastid organelle in Apicomplexa. Curr Opin Microbiol 2021; 63:250-258. [PMID: 34455306 DOI: 10.1016/j.mib.2021.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/19/2021] [Accepted: 07/24/2021] [Indexed: 11/26/2022]
Abstract
The apicoplast is the relict of a plastid organelle found in several disease-causing apicomplexan parasites such as Plasmodium spp. and Toxoplasma gondii. In these organisms, the organelle has lost its photosynthetic capability but harbours several fitness-conferring or essential metabolic pathways. Although maintaining the apicoplast and fuelling the metabolic pathways within requires the challenging constant import and export of numerous metabolites across its four membranes, only few apicoplast transporters have been identified to date, most of which are orphan transporters. Here we review the roles of metabolic pathways within the apicoplast and what is currently known about the few identified apicoplast metabolite transporters. We discuss what metabolites must get in and out of the apicoplast, the many transporters that are yet to be discovered, and what role these might play in parasite metabolism and as putative drug targets.
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Affiliation(s)
- Joachim Kloehn
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.
| | - Clément Em Lacour
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland.
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34
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de Oliveira LS, Alborghetti MR, Carneiro RG, Bastos IMD, Amino R, Grellier P, Charneau S. Calcium in the Backstage of Malaria Parasite Biology. Front Cell Infect Microbiol 2021; 11:708834. [PMID: 34395314 PMCID: PMC8355824 DOI: 10.3389/fcimb.2021.708834] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/14/2021] [Indexed: 12/26/2022] Open
Abstract
The calcium ion (Ca2+) is a ubiquitous second messenger involved in key biological processes in prokaryotes and eukaryotes. In Plasmodium species, Ca2+ signaling plays a central role in the parasite life cycle. It has been associated with parasite development, fertilization, locomotion, and host cell infection. Despite the lack of a canonical inositol-1,4,5-triphosphate receptor gene in the Plasmodium genome, pharmacological evidence indicates that inositol-1,4,5-triphosphate triggers Ca2+ mobilization from the endoplasmic reticulum. Other structures such as acidocalcisomes, food vacuole and mitochondria are proposed to act as supplementary intracellular Ca2+ reservoirs. Several Ca2+-binding proteins (CaBPs) trigger downstream signaling. Other proteins with no EF-hand motifs, but apparently involved with CaBPs, are depicted as playing an important role in the erythrocyte invasion and egress. It is also proposed that a cross-talk among kinases, which are not members of the family of Ca2+-dependent protein kinases, such as protein kinases G, A and B, play additional roles mediated indirectly by Ca2+ regulation. This statement may be extended for proteins directly related to invasion or egress, such as SUB1, ERC, IMC1I, IMC1g, GAP45 and EBA175. In this review, we update our understanding of aspects of Ca2+-mediated signaling correlated to the developmental stages of the malaria parasite life cycle.
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Affiliation(s)
- Lucas Silva de Oliveira
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
- UMR 7245 MCAM, Molécules de Communication et Adaptation des Micro-organismes, Muséum National d’Histoire Naturelle, CNRS, Équipe Parasites et Protistes Libres, Paris, France
| | - Marcos Rodrigo Alborghetti
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Renata Garcia Carneiro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Izabela Marques Dourado Bastos
- Laboratory of Host-Pathogen Interaction, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Rogerio Amino
- Unité Infection et Immunité Paludéennes, Institut Pasteur, Paris, France
| | - Philippe Grellier
- UMR 7245 MCAM, Molécules de Communication et Adaptation des Micro-organismes, Muséum National d’Histoire Naturelle, CNRS, Équipe Parasites et Protistes Libres, Paris, France
| | - Sébastien Charneau
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
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35
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Sakamoto H, Kita K, Matsuzaki M. A Novel 2A-peptide-containing Plasmid to Generate Stable Perkinsus marinus Cells Expressing Organelle-targeted Genes. J Eukaryot Microbiol 2021; 68:e12861. [PMID: 34051022 DOI: 10.1111/jeu.12861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genetic manipulation techniques for marine protists are not well-established, despite immense efforts. However, Perkinsus marinus is an exception and can be developed as a genetically tractable model organism for related protists. Here, we designed a new plasmid for P. marinus that allows two proteins from a single mRNA to be differently localized using a self-cleaving 2A peptide. This enabled us to establish a stable transfectant expressing a mitochondrially targeted fluorescent protein. The system can be applied to any protein in theory and would make a powerful tool for investigating unique organelles in P. marinus and related dinoflagellates.
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Affiliation(s)
- Hirokazu Sakamoto
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Host-Defense Biochemistry, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Motomichi Matsuzaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
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36
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Wichers JS, Wunderlich J, Heincke D, Pazicky S, Strauss J, Schmitt M, Kimmel J, Wilcke L, Scharf S, von Thien H, Burda PC, Spielmann T, Löw C, Filarsky M, Bachmann A, Gilberger TW. Identification of novel inner membrane complex and apical annuli proteins of the malaria parasite Plasmodium falciparum. Cell Microbiol 2021; 23:e13341. [PMID: 33830607 DOI: 10.1111/cmi.13341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/29/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023]
Abstract
The inner membrane complex (IMC) is a defining feature of apicomplexan parasites, which confers stability and shape to the cell, functions as a scaffolding compartment during the formation of daughter cells and plays an important role in motility and invasion during different life cycle stages of these single-celled organisms. To explore the IMC proteome of the malaria parasite Plasmodium falciparum we applied a proximity-dependent biotin identification (BioID)-based proteomics approach, using the established IMC marker protein Photosensitized INA-Labelled protein 1 (PhIL1) as bait in asexual blood-stage parasites. Subsequent mass spectrometry-based peptide identification revealed enrichment of 12 known IMC proteins and several uncharacterized candidate proteins. We validated nine of these previously uncharacterized proteins by endogenous GFP-tagging. Six of these represent new IMC proteins, while three proteins have a distinct apical localization that most likely represents structures described as apical annuli in Toxoplasma gondii. Additionally, various Kelch13 interacting candidates were identified, suggesting an association of the Kelch13 compartment and the IMC in schizont and merozoite stages. This work extends the number of validated IMC proteins in the malaria parasite and reveals for the first time the existence of apical annuli proteins in P. falciparum. Additionally, it provides evidence for a spatial association between the Kelch13 compartment and the IMC in late blood-stage parasites.
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Affiliation(s)
- Jan Stephan Wichers
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
| | - Juliane Wunderlich
- Centre for Structural Systems Biology, Hamburg, Germany.,European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Dorothee Heincke
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
| | - Samuel Pazicky
- Centre for Structural Systems Biology, Hamburg, Germany.,European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Jan Strauss
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
| | - Marius Schmitt
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jessica Kimmel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Louisa Wilcke
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
| | - Sarah Scharf
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Heidrun von Thien
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
| | - Paul-Christian Burda
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
| | - Tobias Spielmann
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology, Hamburg, Germany.,European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Michael Filarsky
- Centre for Structural Systems Biology, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
| | - Anna Bachmann
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany.,German Centre for Infection Research (DZIF), partner site Hamburg-Borstel-Lübeck-Riems, Braunschweig, Germany
| | - Tim W Gilberger
- Centre for Structural Systems Biology, Hamburg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.,University of Hamburg, Hamburg, Germany
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37
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YbeY, éminence grise of ribosome biogenesis. Biochem Soc Trans 2021; 49:727-745. [PMID: 33929506 DOI: 10.1042/bst20200669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/30/2022]
Abstract
YbeY is an ultraconserved small protein belonging to the unique heritage shared by most existing bacteria and eukaryotic organelles of bacterial origin, mitochondria and chloroplasts. Studied in more than a dozen of evolutionarily distant species, YbeY is invariably critical for cellular physiology. However, the exact mechanisms by which it exerts such penetrating influence are not completely understood. In this review, we attempt a transversal analysis of the current knowledge about YbeY, based on genetic, structural, and biochemical data from a wide variety of models. We propose that YbeY, in association with the ribosomal protein uS11 and the assembly GTPase Era, plays a critical role in the biogenesis of the small ribosomal subunit, and more specifically its platform region, in diverse genetic systems of bacterial type.
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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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39
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Van Vlierberghe M, Philippe H, Baurain D. Broadly sampled orthologous groups of eukaryotic proteins for the phylogenetic study of plastid-bearing lineages. BMC Res Notes 2021; 14:143. [PMID: 33865444 PMCID: PMC8052839 DOI: 10.1186/s13104-021-05553-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/02/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Identifying orthology relationships among sequences is essential to understand evolution, diversity of life and ancestry among organisms. To build alignments of orthologous sequences, phylogenomic pipelines often start with all-vs-all similarity searches, followed by a clustering step. For the protein clusters (orthogroups) to be as accurate as possible, proteomes of good quality are needed. Here, our objective is to assemble a data set especially suited for the phylogenomic study of algae and formerly photosynthetic eukaryotes, which implies the proper integration of organellar data, to enable distinguishing between several copies of one gene (paralogs), taking into account their cellular compartment, if necessary. DATA DESCRIPTION We submitted 73 top-quality and taxonomically diverse proteomes to OrthoFinder. We obtained 47,266 orthogroups and identified 11,775 orthogroups with at least two algae. Whenever possible, sequences were functionally annotated with eggNOG and tagged after their genomic and target compartment(s). Then we aligned and computed phylogenetic trees for the orthogroups with IQ-TREE. Finally, these trees were further processed by identifying and pruning the subtrees exclusively composed of plastid-bearing organisms to yield a set of 31,784 clans suitable for studying photosynthetic organism genome evolution.
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Affiliation(s)
- Mick Van Vlierberghe
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Hervé Philippe
- Station D'Ecologie Théorique Et Expérimentale de Moulis, UMR CNRS 5321, Moulis, France.,Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Québec, Canada
| | - Denis Baurain
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium.
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Zapatero-Belinchón FJ, Carriquí-Madroñal B, Gerold G. Proximity labeling approaches to study protein complexes during virus infection. Adv Virus Res 2021; 109:63-104. [PMID: 33934830 DOI: 10.1016/bs.aivir.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular compartmentalization of proteins and protein complex formation allow cells to tightly control biological processes. Therefore, understanding the subcellular localization and interactions of a specific protein is crucial to uncover its biological function. The advent of proximity labeling (PL) has reshaped cellular proteomics in infection biology. PL utilizes a genetically modified enzyme that generates a "labeling cloud" by covalently labeling proteins in close proximity to the enzyme. Fusion of a PL enzyme to a specific antibody or a "bait" protein of interest in combination with affinity enrichment mass spectrometry (AE-MS) enables the isolation and identification of the cellular proximity proteome, or proxisome. This powerful methodology has been paramount for the mapping of membrane or membraneless organelles as well as for the understanding of hard-to-purify protein complexes, such as those of transmembrane proteins. Unsurprisingly, more and more infection biology research groups have recognized the potential of PL for the identification of host-pathogen interactions. In this chapter, we introduce the enzymes commonly used for PL labeling as well as recent promising advancements and summarize the major achievements in organelle mapping and nucleic acid PL. Moreover, we comprehensively describe the research on host-pathogen interactions using PL, giving special attention to studies in the field of virology.
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Affiliation(s)
- Francisco José Zapatero-Belinchón
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| | - Belén Carriquí-Madroñal
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gisa Gerold
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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41
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Zhou M, Varol A, Efferth T. Multi-omics approaches to improve malaria therapy. Pharmacol Res 2021; 167:105570. [PMID: 33766628 DOI: 10.1016/j.phrs.2021.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023]
Abstract
Malaria contributes to the most widespread infectious diseases worldwide. Even though current drugs are commercially available, the ever-increasing drug resistance problem by malaria parasites poses new challenges in malaria therapy. Hence, searching for efficient therapeutic strategies is of high priority in malaria control. In recent years, multi-omics technologies have been extensively applied to provide a more holistic view of functional principles and dynamics of biological mechanisms. We briefly review multi-omics technologies and focus on recent malaria progress conducted with the help of various omics methods. Then, we present up-to-date advances for multi-omics approaches in malaria. Next, we describe resistance phenomena to established antimalarial drugs and underlying mechanisms. Finally, we provide insight into novel multi-omics approaches, new drugs and vaccine developments and analyze current gaps in multi-omics research. Although multi-omics approaches have been successfully used in malaria studies, they are still limited. Many gaps need to be filled to bridge the gap between basic research and treatment of malaria patients. Multi-omics approaches will foster a better understanding of the molecular mechanisms of Plasmodium that are essential for the development of novel drugs and vaccines to fight this disastrous disease.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ayşegül Varol
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany.
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42
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Biddau M, Santha Kumar TR, Henrich P, Laine LM, Blackburn GJ, Chokkathukalam A, Li T, Lee Sim K, King L, Hoffman SL, Barrett MP, Coombs GH, McFadden GI, Fidock DA, Müller S, Sheiner L. Plasmodium falciparum LipB mutants display altered redox and carbon metabolism in asexual stages and cannot complete sporogony in Anopheles mosquitoes. Int J Parasitol 2021; 51:441-453. [PMID: 33713652 PMCID: PMC8126644 DOI: 10.1016/j.ijpara.2020.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 11/06/2022]
Abstract
Apicoplast LipB deletion leads to changed antioxidant expression that precedes and coincides with accelerated differentiation. 3D7 Plasmodium exhibits changes in glycolysis and tricarboxylic acid cycle activity after deletion of apicoplast LipB. When LipB is deleted from NF54 Plasmodium, the resulting parasites cannot complete their development in mosquitoes.
Malaria is still one of the most important global infectious diseases. Emergence of drug resistance and a shortage of new efficient antimalarials continue to hamper a malaria eradication agenda. Malaria parasites are highly sensitive to changes in the redox environment. Understanding the mechanisms regulating parasite redox could contribute to the design of new drugs. Malaria parasites have a complex network of redox regulatory systems housed in their cytosol, in their mitochondrion and in their plastid (apicoplast). While the roles of enzymes of the thioredoxin and glutathione pathways in parasite survival have been explored, the antioxidant role of α-lipoic acid (LA) produced in the apicoplast has not been tested. To take a first step in teasing a putative role of LA in redox regulation, we analysed a mutant Plasmodium falciparum (3D7 strain) lacking the apicoplast lipoic acid protein ligase B (lipB) known to be depleted of LA. Our results showed a change in expression of redox regulators in the apicoplast and the cytosol. We further detected a change in parasite central carbon metabolism, with lipB deletion resulting in changes to glycolysis and tricarboxylic acid cycle activity. Further, in another Plasmodium cell line (NF54), deletion of lipB impacted development in the mosquito, preventing the detection of infectious sporozoite stages. While it is not clear at this point if the observed phenotypes are linked, these findings flag LA biosynthesis as an important subject for further study in the context of redox regulation in asexual stages, and point to LipB as a potential target for the development of new transmission drugs.
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Affiliation(s)
- Marco Biddau
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom; Department of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.
| | - T R Santha Kumar
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Philipp Henrich
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Larissa M Laine
- Department of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Gavin J Blackburn
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | - Tao Li
- Sanaria Inc., Rockville, MD 20850, USA
| | | | - Lewis King
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
| | | | - Michael P Barrett
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom; Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Graham H Coombs
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | | | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sylke Müller
- Department of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom; Department of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.
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Martins-Duarte ÉS, Sheiner L, Reiff SB, de Souza W, Striepen B. Replication and partitioning of the apicoplast genome of Toxoplasma gondii is linked to the cell cycle and requires DNA polymerase and gyrase. Int J Parasitol 2021; 51:493-504. [PMID: 33581138 PMCID: PMC8113025 DOI: 10.1016/j.ijpara.2020.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/30/2020] [Accepted: 11/08/2020] [Indexed: 10/26/2022]
Abstract
Apicomplexans are the causative agents of numerous important infectious diseases including malaria and toxoplasmosis. Most of them harbour a chloroplast-like organelle called the apicoplast that is essential for the parasites' metabolism and survival. While most apicoplast proteins are nuclear encoded, the organelle also maintains its own genome, a 35 kb circle. In this study we used Toxoplasma gondii to identify and characterise essential proteins involved in apicoplast genome replication and to understand how apicoplast genome segregation unfolds over time. We demonstrated that the DNA replication enzymes Prex, DNA gyrase and DNA single stranded binding protein localise to the apicoplast. We show in knockdown experiments that apicoplast DNA Gyrase A and B, and Prex are required for apicoplast genome replication and growth of the parasite. Analysis of apicoplast genome replication by structured illumination microscopy in T. gondii tachyzoites showed that apicoplast nucleoid division and segregation initiate at the beginning of S phase and conclude during mitosis. Thus, the replication and division of the apicoplast nucleoid is highly coordinated with nuclear genome replication and mitosis. Our observations highlight essential components of apicoplast genome maintenance and shed light on the timing of this process in the context of the overall parasite cell cycle.
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Affiliation(s)
- Érica S Martins-Duarte
- Laboratório de Quimioterapia de Protozoários Egler Chiari, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil.
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, 120 University Place Glasgow, United Kingdom
| | - Sarah B Reiff
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Wanderley de Souza
- Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil; Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA, USA; Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA. USA
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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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Dousti M, Manzano-Román R, Rashidi S, Barzegar G, Ahmadpour NB, Mohammadi A, Hatam G. A proteomic glimpse into the effect of antimalarial drugs on Plasmodium falciparum proteome towards highlighting possible therapeutic targets. Pathog Dis 2021; 79:ftaa071. [PMID: 33202000 DOI: 10.1093/femspd/ftaa071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
There is no effective vaccine against malaria; therefore, chemotherapy is to date the only choice to fight against this infectious disease. However, there is growing evidences of drug-resistance mechanisms in malaria treatments. Therefore, the identification of new drug targets is an urgent need for the clinical management of the disease. Proteomic approaches offer the chance of determining the effects of antimalarial drugs on the proteome of Plasmodium parasites. Accordingly, we reviewed the effects of antimalarial drugs on the Plasmodium falciparum proteome pointing out the relevance of several proteins as possible drug targets in malaria treatment. In addition, some of the P. falciparum stage-specific altered proteins and parasite-host interactions might play important roles in pathogenicity, survival, invasion and metabolic pathways and thus serve as potential sources of drug targets. In this review, we have identified several proteins, including thioredoxin reductase, helicases, peptidyl-prolyl cis-trans isomerase, endoplasmic reticulum-resident calcium-binding protein, choline/ethanolamine phosphotransferase, purine nucleoside phosphorylase, apical membrane antigen 1, glutamate dehydrogenase, hypoxanthine guanine phosphoribosyl transferase, heat shock protein 70x, knob-associated histidine-rich protein and erythrocyte membrane protein 1, as promising antimalarial drugs targets. Overall, proteomic approaches are able to partially facilitate finding possible drug targets. However, the integration of other 'omics' and specific pharmaceutical techniques with proteomics may increase the therapeutic properties of the critical proteins identified in the P. falciparum proteome.
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Affiliation(s)
- Majid Dousti
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Sajad Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Barzegar
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Alireza Mohammadi
- Department of Disease Control, Komijan Treatment and Health Network, Arak University of Medical Science, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Jonsdottir TK, Gabriela M, Gilson PR. The Role of Malaria Parasite Heat Shock Proteins in Protein Trafficking and Remodelling of Red Blood Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1340:141-167. [PMID: 34569024 DOI: 10.1007/978-3-030-78397-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The genus Plasmodium comprises intracellular eukaryotic parasites that infect many vertebrate groups and cause deadly malaria disease in humans. The parasites employ a suite of heat shock proteins to help traffic other proteins to different compartments within their own cells and that of the host cells they parasitise. This review will cover the role of these chaperones in protein export and host cell modification in the asexual blood stage of the human parasite P. falciparum which is the most deadly and well-studied parasite species. We will examine the role chaperones play in the import of proteins into the secretory pathway from where they are escorted to the vacuole space surrounding the intraerythrocytic parasite. Here, other heat shock proteins unfold protein cargoes and extrude them into the red blood cell (RBC) cytosol from where additional chaperones of parasite and possibly host origin refold the cargo proteins and guide them to their final functional destinations within their RBC host cells. The secretory pathway also serves as a launch pad for proteins targeted to the non-photosynthetic apicoplast organelle of endosymbiotic origin, and the role of heat shock proteins in trafficking proteins here will be reviewed. Finally, the function of chaperones in protein trafficking into the mitochondrion, the remaining organelle of endosymbiotic origin, will be discussed.
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Affiliation(s)
- Thorey K Jonsdottir
- Burnet Institute, Melbourne, VIC, Australia.,Department of Microbiology and Immunology, University of Melbourne, Parkville, VIC, Australia
| | - Mikha Gabriela
- Burnet Institute, Melbourne, VIC, Australia.,School of Medicine, Deakin University, Waurn Ponds, VIC, Australia
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CaaX-Like Protease of Cyanobacterial Origin Is Required for Complex Plastid Biogenesis in Malaria Parasites. mBio 2020; 11:mBio.01492-20. [PMID: 33024034 PMCID: PMC7542359 DOI: 10.1128/mbio.01492-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Plasmodium parasites, which cause malaria, and related apicomplexans are important human and veterinary pathogens. These parasites represent a highly divergent and understudied branch of eukaryotes, and as such often defy the expectations set by model organisms. One striking example of unique apicomplexan biology is the apicoplast, an essential but nonphotosynthetic plastid derived from an unusual secondary (eukaryote-eukaryote) endosymbiosis. Endosymbioses are a major driver of cellular innovation, and apicoplast biogenesis pathways represent a hot spot for molecular evolution. We previously conducted an unbiased screen for apicoplast biogenesis genes in P. falciparum to uncover these essential and innovative pathways. Here, we validate a novel gene candidate from our screen and show that its role in apicoplast biogenesis does not match its functional annotation predicted by model eukaryotes. Our findings suggest that an uncharacterized chloroplast maintenance pathway has been reused for complex plastid biogenesis in this divergent branch of pathogens. Plasmodium parasites and related apicomplexans contain an essential “complex plastid” organelle of secondary endosymbiotic origin, the apicoplast. Biogenesis of this complex plastid poses a unique challenge requiring evolution of new cellular machinery. We previously conducted a mutagenesis screen for essential apicoplast biogenesis genes to discover organellar pathways with evolutionary and biomedical significance. Here we validate and characterize a gene candidate from our screen, Pf3D7_0913500. Using a conditional knockdown strain, we show that Pf3D7_0913500 depletion causes growth inhibition that is rescued by the sole essential product of the apicoplast, isopentenyl pyrophosphate (IPP), and results in apicoplast loss. Because Pf3D7_0913500 had no previous functional annotation, we name it apicoplast-minus IPP-rescued 4 (AMR4). AMR4 has an annotated CaaX protease and bacteriocin processing (CPBP) domain, which in eukaryotes typically indicates a role in CaaX postprenylation processing. Indeed, AMR4 is the only putative CaaX-like protease in Plasmodium parasites which are known to require protein prenylation, and we confirm that the conserved catalytic residue of AMR4 (E352) is required for its apicoplast function. However, we unexpectedly find that AMR4 does not act in a CaaX postprenylation processing pathway in Plasmodium falciparum. Instead, we find that AMR4 is imported into the apicoplast and is derived from a cyanobacterial CPBP gene which was retained through both primary and secondary endosymbiosis. Our findings suggest that AMR4 is not a true CaaX protease, but instead it performs a conserved, uncharacterized chloroplast function that has been retained for complex plastid biogenesis.
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48
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Swift RP, Rajaram K, Keutcha C, Liu HB, Kwan B, Dziedzic A, Jedlicka AE, Prigge ST. The NTP generating activity of pyruvate kinase II is critical for apicoplast maintenance in Plasmodium falciparum. eLife 2020; 9:e50807. [PMID: 32815516 PMCID: PMC7556864 DOI: 10.7554/elife.50807] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/20/2020] [Indexed: 12/20/2022] Open
Abstract
The apicoplast of Plasmodium falciparum parasites is believed to rely on the import of three-carbon phosphate compounds for use in organelle anabolic pathways, in addition to the generation of energy and reducing power within the organelle. We generated a series of genetic deletions in an apicoplast metabolic bypass line to determine which genes involved in apicoplast carbon metabolism are required for blood-stage parasite survival and organelle maintenance. We found that pyruvate kinase II (PyrKII) is essential for organelle maintenance, but that production of pyruvate by PyrKII is not responsible for this phenomenon. Enzymatic characterization of PyrKII revealed activity against all NDPs and dNDPs tested, suggesting that it may be capable of generating a broad range of nucleotide triphosphates. Conditional mislocalization of PyrKII resulted in decreased transcript levels within the apicoplast that preceded organelle disruption, suggesting that PyrKII is required for organelle maintenance due to its role in nucleotide triphosphate generation.
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Affiliation(s)
- Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Cyrianne Keutcha
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Hans B Liu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Bobby Kwan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Anne E Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
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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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50
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Guo Q, Li D, Zhai Y, Gu Z. CCPRD: A Novel Analytical Framework for the Comprehensive Proteomic Reference Database Construction of NonModel Organisms. ACS OMEGA 2020; 5:15370-15384. [PMID: 32637811 PMCID: PMC7331046 DOI: 10.1021/acsomega.0c01278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Protein reference databases are a critical part of producing efficient proteomic analyses. However, the method for constructing clean, efficient, and comprehensive protein reference databases of nonmodel organisms is lacking. Existing methods either do not have contamination control procedures, or these methods rely on a three-frame and/or six-frame translation that sharply increases the search space and the need for computational resources. Herein, we propose a framework for constructing a customized comprehensive proteomic reference database (CCPRD) from draft genomes and deep sequencing transcriptomes. Its effectiveness is demonstrated by incorporating the proteomes of nematocysts from endoparasitic cnidarian: myxozoans. By applying customized contamination removal procedures, contaminations in omic data were successfully identified and removed. This is an effective method that does not result in overdecontamination. This can be shown by comparing the CCPRD MS results with an artificially contaminated database and another database with removed contaminations in genomes and transcriptomes added back. CCPRD outperformed traditional frame-based methods by identifying 35.2-50.7% more peptides and 35.8-43.8% more proteins, with a maximum of 84.6% in size reduction. A BUSCO analysis showed that the CCPRD maintained a relatively high level of completeness compared to traditional methods. These results confirm the superiority of the CCPRD over existing methods in peptide and protein identification numbers, database size, and completeness. By providing a general framework for generating the reference database, the CCPRD, which does not need a high-quality genome, can potentially be applied to nonmodel organisms and significantly contribute to proteomic research.
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Affiliation(s)
- Qingxiang Guo
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Dan Li
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Yanhua Zhai
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Zemao Gu
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
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