1
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Thiele PJ, Mela-Lopez R, Blandin SA, Klug D. Let it glow: genetically encoded fluorescent reporters in Plasmodium. Malar J 2024; 23:114. [PMID: 38643106 PMCID: PMC11032601 DOI: 10.1186/s12936-024-04936-9] [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: 01/10/2024] [Accepted: 04/06/2024] [Indexed: 04/22/2024] Open
Abstract
The use of fluorescent proteins (FPs) in Plasmodium parasites has been key to understand the biology of this obligate intracellular protozoon. FPs like the green fluorescent protein (GFP) enabled to explore protein localization, promoter activity as well as dynamic processes like protein export and endocytosis. Furthermore, FP biosensors have provided detailed information on physiological parameters at the subcellular level, and fluorescent reporter lines greatly extended the malariology toolbox. Still, in order to achieve optimal results, it is crucial to know exactly the properties of the FP of choice and the genetic scenario in which it will be used. This review highlights advantages and disadvantages of available landing sites and promoters that have been successfully applied for the ectopic expression of FPs in Plasmodium berghei and Plasmodium falciparum. Furthermore, the properties of newly developed FPs beyond DsRed and EGFP, in the visualization of cells and cellular structures as well as in the sensing of small molecules are discussed.
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Affiliation(s)
- Pia J Thiele
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Raquel Mela-Lopez
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Stéphanie A Blandin
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France
| | - Dennis Klug
- Inserm, CNRS, Université de Strasbourg, UPR9022/U1257, Mosquito Immune Responses (MIR), IBMC, F-67000, Strasbourg, France.
- Institute of Physiology and Pathophysiology, Department of Molecular Cell Physiology, Philipps University Marburg, 35037, Marburg, Germany.
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2
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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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3
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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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4
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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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5
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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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6
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The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite. Nat Commun 2021; 12:4563. [PMID: 34315897 PMCID: PMC8316339 DOI: 10.1038/s41467-021-24814-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 07/09/2021] [Indexed: 01/02/2023] Open
Abstract
The emergence and spread of Plasmodium falciparum parasites resistant to front-line antimalarial artemisinin-combination therapies (ACT) threatens to erase the considerable gains against the disease of the last decade. Here, we develop a large-scale phenotypic screening pipeline and use it to carry out a large-scale forward-genetic phenotype screen in P. falciparum to identify genes allowing parasites to survive febrile temperatures. Screening identifies more than 200 P. falciparum mutants with differential responses to increased temperature. These mutants are more likely to be sensitive to artemisinin derivatives as well as to heightened oxidative stress. Major processes critical for P. falciparum tolerance to febrile temperatures and artemisinin include highly essential, conserved pathways associated with protein-folding, heat shock and proteasome-mediated degradation, and unexpectedly, isoprenoid biosynthesis, which originated from the ancestral genome of the parasite’s algal endosymbiont-derived plastid, the apicoplast. Apicoplast-targeted genes in general are upregulated in response to heat shock, as are other Plasmodium genes with orthologs in plant and algal genomes. Plasmodium falciparum parasites appear to exploit their innate febrile-response mechanisms to mediate resistance to artemisinin. Both responses depend on endosymbiont-derived genes in the parasite’s genome, suggesting a link to the evolutionary origins of Plasmodium parasites in free-living ancestors. Repeating fever is a hallmark of malaria. Here, a large-scale forward genetic screen in malaria-causing Plasmodium falciparum identifies genes associated with parasite tolerance to host fever, including apicoplast targeted isoprenoid biosynthesis—sharing features with artemisinin resistance.
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7
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Davis MM, Lamichhane R, Bruce BD. Elucidating Protein Translocon Dynamics with Single-Molecule Precision. Trends Cell Biol 2021; 31:569-583. [PMID: 33865650 DOI: 10.1016/j.tcb.2021.03.009] [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: 11/11/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/28/2023]
Abstract
Translocons are protein assemblies that facilitate the targeting and transport of proteins into and across biological membranes. Our understanding of these systems has been advanced using genetics, biochemistry, and structural biology. Despite these classic advances, until recently we have still largely lacked a detailed understanding of how translocons recognize and facilitate protein translocation. With the advent and improvements of cryogenic electron microscopy (cryo-EM) single-particle analysis and single-molecule fluorescence microscopy, the details of how translocons function are finally emerging. Here, we introduce these methods and evaluate their importance in understanding translocon structure, function, and dynamics.
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Affiliation(s)
- Madeline M Davis
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Rajan Lamichhane
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Department of Microbiology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Graduate Program in Genome Science and Technology, University of Tennessee at Knoxville, Knoxville, TN 37996, USA; Chemical and Biomolecular Engineering, University of Tennessee at Knoxville, Knoxville, TN 37996, USA.
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8
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Oberstaller J, Otto TD, Rayner JC, Adams JH. Essential Genes of the Parasitic Apicomplexa. Trends Parasitol 2021; 37:304-316. [PMID: 33419671 DOI: 10.1016/j.pt.2020.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
Genome-scale mutagenesis screens for genes essential for apicomplexan parasite survival have been completed in three species: Plasmodium falciparum, the major human malaria parasite, Plasmodium berghei, a model rodent malaria parasite, and the more distantly related Toxoplasma gondii, the causative agent of toxoplasmosis. These three species share 2606 single-copy orthologs, 1500 of which have essentiality data in all three screens. In this review, we explore the overlap between these datasets to define the core essential genes of the phylum Apicomplexa. We further discuss the implications of these groundbreaking studies for understanding apicomplexan parasite biology, and we identify promising areas of focus for developing new pan-apicomplexan parasite interventions.
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Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Centre of Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge, Cambridgeshire, CB2 0XY, UK
| | - John H Adams
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
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9
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Okada M, Guo P, Nalder SA, Sigala PA. Doxycycline has distinct apicoplast-specific mechanisms of antimalarial activity. eLife 2020; 9:60246. [PMID: 33135634 PMCID: PMC7669263 DOI: 10.7554/elife.60246] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/01/2020] [Indexed: 12/02/2022] Open
Abstract
Doxycycline (DOX) is a key antimalarial drug thought to kill Plasmodium parasites by blocking protein translation in the essential apicoplast organelle. Clinical use is primarily limited to prophylaxis due to delayed second-cycle parasite death at 1–3 µM serum concentrations. DOX concentrations > 5 µM kill parasites with first-cycle activity but are thought to involve off-target mechanisms outside the apicoplast. We report that 10 µM DOX blocks apicoplast biogenesis in the first cycle and is rescued by isopentenyl pyrophosphate, an essential apicoplast product, confirming an apicoplast-specific mechanism. Exogenous iron rescues parasites and apicoplast biogenesis from first- but not second-cycle effects of 10 µM DOX, revealing that first-cycle activity involves a metal-dependent mechanism distinct from the delayed-death mechanism. These results critically expand the paradigm for understanding the fundamental antiparasitic mechanisms of DOX and suggest repurposing DOX as a faster acting antimalarial at higher dosing whose multiple mechanisms would be expected to limit parasite resistance.
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Affiliation(s)
- Megan Okada
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Ping Guo
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Shai-Anne Nalder
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Paul A Sigala
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
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10
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Swift RP, Rajaram K, Liu HB, Dziedzic A, Jedlicka AE, Roberts AD, Matthews KA, Jhun H, Bumpus NN, Tewari SG, Wallqvist A, Prigge ST. A mevalonate bypass system facilitates elucidation of plastid biology in malaria parasites. PLoS Pathog 2020; 16:e1008316. [PMID: 32059044 PMCID: PMC7046295 DOI: 10.1371/journal.ppat.1008316] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/27/2020] [Accepted: 01/10/2020] [Indexed: 12/03/2022] Open
Abstract
Malaria parasites rely on a plastid organelle for survival during the blood stages of infection. However, the entire organelle is dispensable as long as the isoprenoid precursor, isopentenyl pyrophosphate (IPP), is supplemented in the culture medium. We engineered parasites to produce isoprenoid precursors from a mevalonate-dependent pathway, creating a parasite line that replicates normally after the loss of the apicoplast organelle. We show that carbon-labeled mevalonate is specifically incorporated into isoprenoid products, opening new avenues for researching this essential class of metabolites in malaria parasites. We also show that essential apicoplast proteins, such as the enzyme target of the drug fosmidomycin, can be deleted in this mevalonate bypass parasite line, providing a new method to determine the roles of other important apicoplast-resident proteins. Several antibacterial drugs kill malaria parasites by targeting basic processes, such as transcription, in the organelle. We used metabolomic and transcriptomic methods to characterize parasite metabolism after azithromycin treatment triggered loss of the apicoplast and found that parasite metabolism and the production of apicoplast proteins is largely unaltered. These results provide insight into the effects of apicoplast-disrupting drugs, several of which have been used to treat malaria infections in humans. Overall, the mevalonate bypass system provides a way to probe essential aspects of apicoplast biology and study the effects of drugs that target apicoplast processes. Malaria parasites rely on an organelle called the apicoplast for growth and survival. Antimalarial drugs such as azithromycin inhibit basic processes in the apicoplast and result in the disruption of the organelle. Surprisingly, addition of a single metabolite, isopentenyl pyrophosphate (IPP), allows the parasites to survive in culture after disruption of the apicoplast. Unfortunately, using IPP to study this phenomenon has several limitations: IPP is prohibitively expensive, has to be used at high concentrations, and has a half-life less than 5 hours. To address these problems, we engineered parasites to express four enzymes from an alternative pathway capable of producing IPP in the parasites. We validated this new system and used it to metabolically label essential metabolites, to delete an essential apicoplast protein, and to characterize the state of apicoplast-disrupted parasites. A key finding from these studies comes from transcriptomic and metabolomic analysis of parasites treated with the drug azithromycin. We found that apicoplast disruption results in few changes in parasite metabolism. In particular, the expression of hundreds of nuclear-encoded apicoplast proteins are not affected by disruption of the apicoplast organelle, making it likely that apicoplast metabolic pathways and processes are still functional in apicoplast-disrupted parasites.
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Affiliation(s)
- Russell P. Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Hans B. Liu
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Anne E. Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Aleah D. Roberts
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Krista A. Matthews
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Hugo Jhun
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Namandje N. Bumpus
- Department of Medicine (Division of Clinical Pharmacology), Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shivendra G. Tewari
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, Maryland, United States of America
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, Maryland, United States of America
| | - Sean T. Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
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11
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Kennedy K, Crisafulli EM, Ralph SA. Delayed Death by Plastid Inhibition in Apicomplexan Parasites. Trends Parasitol 2019; 35:747-759. [PMID: 31427248 DOI: 10.1016/j.pt.2019.07.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/11/2023]
Abstract
The discovery of a plastid in apicomplexan parasites was hoped to be a watershed moment in the treatment of parasitic diseases as it revealed drug targets that are implicitly divergent from host molecular processes. Indeed, this organelle, known as the apicoplast, has since been a productive therapeutic target for pharmaceutical interventions against infections by Plasmodium, Toxoplasma, Babesia, and Theileria. However, some inhibitors of the apicoplast are restricted in their treatment utility because of their slow-kill kinetics, and this characteristic is called the delayed death effect. Here we review the recent genetic and pharmacological experiments that interrogate the causes of delayed death and explore the foundation of this phenomenon in Plasmodium and Toxoplasma parasites.
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Affiliation(s)
- Kit Kennedy
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Emily M Crisafulli
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, 3010, Australia.
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12
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Zhang Y, Song G, Lal NK, Nagalakshmi U, Li Y, Zheng W, Huang PJ, Branon TC, Ting AY, Walley JW, Dinesh-Kumar SP. TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity. Nat Commun 2019; 10:3252. [PMID: 31324801 PMCID: PMC6642208 DOI: 10.1038/s41467-019-11202-z] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/01/2019] [Indexed: 11/25/2022] Open
Abstract
Nucleotide-binding leucine-rich repeat (NLR) immune receptors play a critical role in defence against pathogens in plants and animals. However, we know very little about NLR-interacting proteins and the mechanisms that regulate NLR levels. Here, we used proximity labeling (PL) to identify the proteome proximal to N, which is an NLR that confers resistance to Tobacco mosaic virus (TMV). Evaluation of different PL methods indicated that TurboID-based PL provides more efficient levels of biotinylation than BioID and BioID2 in plants. TurboID-based PL of N followed by quantitative proteomic analysis and genetic screening revealed multiple regulators of N-mediated immunity. Interestingly, a putative E3 ubiquitin ligase, UBR7, directly interacts with the TIR domain of N. UBR7 downregulation leads to an increased amount of N protein and enhanced TMV resistance. TMV-p50 effector disrupts the N-UBR7 interaction and relieves negative regulation of N. These findings demonstrate the utility of TurboID-based PL in plants and the N-interacting proteins we identified enhance our understanding of the mechanisms underlying NLR regulation.
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Affiliation(s)
- Yongliang Zhang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA.
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Neeraj K Lal
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Yuanyuan Li
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Wenjie Zheng
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Pin-Jui Huang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Tess C Branon
- Departments of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alice Y Ting
- Departments of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA.
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