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Karunakaran MM, Subramanian H, Jin Y, Mohammed F, Kimmel B, Juraske C, Starick L, Nöhren A, Länder N, Willcox CR, Singh R, Schamel WW, Nikolaev VO, Kunzmann V, Wiemer AJ, Willcox BE, Herrmann T. A distinct topology of BTN3A IgV and B30.2 domains controlled by juxtamembrane regions favors optimal human γδ T cell phosphoantigen sensing. Nat Commun 2023; 14:7617. [PMID: 37993425 PMCID: PMC10665462 DOI: 10.1038/s41467-023-41938-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/21/2023] [Indexed: 11/24/2023] Open
Abstract
Butyrophilin (BTN)-3A and BTN2A1 molecules control the activation of human Vγ9Vδ2 T cells during T cell receptor (TCR)-mediated sensing of phosphoantigens (PAg) derived from microbes and tumors. However, the molecular rules governing PAg sensing remain largely unknown. Here, we establish three mechanistic principles of PAg-mediated γδ T cell activation. First, in humans, following PAg binding to the intracellular BTN3A1-B30.2 domain, Vγ9Vδ2 TCR triggering involves the extracellular V-domain of BTN3A2/BTN3A3. Moreover, the localization of both protein domains on different chains of the BTN3A homo-or heteromers is essential for efficient PAg-mediated activation. Second, the formation of BTN3A homo-or heteromers, which differ in intracellular trafficking and conformation, is controlled by molecular interactions between the juxtamembrane regions of the BTN3A chains. Finally, the ability of PAg not simply to bind BTN3A-B30.2, but to promote its subsequent interaction with the BTN2A1-B30.2 domain, is essential for T-cell activation. Defining these determinants of cooperation and the division of labor in BTN proteins improves our understanding of PAg sensing and elucidates a mode of action that may apply to other BTN family members.
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Affiliation(s)
| | - Hariharan Subramanian
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Yiming Jin
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
| | - Fiyaz Mohammed
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, UK
| | - Brigitte Kimmel
- University Hospital Wuerzburg, Department of Internal Medicine II and Comprehensive Cancer Center (CCC) Mainfranken Wuerzburg, Wuerzburg, Germany
| | - Claudia Juraske
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Lisa Starick
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Anna Nöhren
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Nora Länder
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Carrie R Willcox
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, UK
| | - Rohit Singh
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
- Department of Pharmaceutical Sciences, School of Health Sciences & Technology, Dr. Vishwanath Karad, MIT World peace University, Pune, 411038, India
| | - Wolfgang W Schamel
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Viacheslav O Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Volker Kunzmann
- University Hospital Wuerzburg, Department of Internal Medicine II and Comprehensive Cancer Center (CCC) Mainfranken Wuerzburg, Wuerzburg, Germany
| | - Andrew J Wiemer
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Benjamin E Willcox
- Cancer Immunology and Immunotherapy Centre, Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, UK
| | - Thomas Herrmann
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany.
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Muñoz Sosa CJ, Issoglio FM, Carrizo ME. Crystal structure and mutational analysis of the human TRIM7 B30.2 domain provide insights into the molecular basis of its binding to glycogenin-1. J Biol Chem 2021; 296:100772. [PMID: 33989636 PMCID: PMC8203840 DOI: 10.1016/j.jbc.2021.100772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/30/2021] [Accepted: 05/09/2021] [Indexed: 01/01/2023] Open
Abstract
Tripartite motif (TRIM)7 is an E3 ubiquitin ligase that was first identified through its interaction with glycogenin-1 (GN1), the autoglucosyltransferase that initiates glycogen biosynthesis. A growing body of evidence indicates that TRIM7 plays an important role in cancer development, viral pathogenesis, and atherosclerosis and, thus, represents a potential therapeutic target. TRIM family proteins share a multidomain architecture with a conserved N-terminal TRIM and a variable C-terminal domain. Human TRIM7 contains the canonical TRIM motif and a B30.2 domain at the C terminus. To contribute to the understanding of the mechanism of action of TRIM7, we solved the X-ray crystal structure of its B30.2 domain (TRIM7B30.2) in two crystal forms at resolutions of 1.6 Å and 1.8 Å. TRIM7B30.2 exhibits the typical B30.2 domain fold, consisting of two antiparallel β-sheets of seven and six strands, arranged as a distorted β-sandwich. Furthermore, two long loops partially cover the concave face of the β-sandwich defined by the β-sheet of six strands, thus forming a positively charged cavity. We used sequence conservation and mutational analyses to provide evidence of a putative binding interface for GN1. These studies showed that Leu423, Ser499, and Cys501 of TRIM7B30.2 and the C-terminal 33 amino acids of GN1 are critical for this binding interaction. Molecular dynamics simulations also revealed that hydrogen bond and hydrophobic interactions play a major role in the stability of a modeled TRIM7B30.2-GN1 C-terminal peptide complex. These data provide useful information that could be used to target this interaction for the development of potential therapeutic agents.
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Affiliation(s)
- Christian J Muñoz Sosa
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) - CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Federico M Issoglio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) - CONICET and Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María E Carrizo
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) - CONICET and Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
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Diaz‐Granados A, Sterken MG, Overmars H, Ariaans R, Holterman M, Pokhare SS, Yuan Y, Pomp R, Finkers‐Tomczak A, Roosien J, Slootweg E, Elashry A, Grundler FM, Xiao F, Goverse A, Smant G. The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host. Mol Plant Pathol 2020; 21:66-82. [PMID: 31756029 PMCID: PMC6913204 DOI: 10.1111/mpp.12880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant-parasitic nematodes secrete effectors that manipulate plant cell morphology and physiology to achieve host invasion and establish permanent feeding sites. Effectors from the highly expanded SPRYSEC (SPRY domain with a signal peptide for secretion) family in potato cyst nematodes have been implicated in activation and suppression of plant immunity, but the mechanisms underlying these activities remain largely unexplored. To study the host mechanisms used by SPRYSEC effectors, we identified plant targets of GpRbp-1 from the potato cyst nematode Globodera pallida. Here, we show that GpRbp-1 interacts in yeast and in planta with a functional potato homologue of the Homology to E6-AP C-Terminus (HECT)-type ubiquitin E3 ligase UPL3, which is located in the nucleus. Potato lines lacking StUPL3 are not available, but the Arabidopsis mutant upl3-5 displaying a reduced UPL3 expression showed a consistently small but not significant decrease in susceptibility to cyst nematodes. We observed a major impact on the root transcriptome by the lower levels of AtUPL3 in the upl3-5 mutant, but surprisingly only in association with infections by cyst nematodes. To our knowledge, this is the first example that a HECT-type ubiquitin E3 ligase is targeted by a pathogen effector and that a member of this class of proteins specifically regulates gene expression under biotic stress conditions. Together, our data suggest that GpRbp-1 targets a specific component of the plant ubiquitination machinery to manipulate the stress response in host cells.
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Affiliation(s)
| | - Mark G. Sterken
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Hein Overmars
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Roel Ariaans
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Martijn Holterman
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Somnath S. Pokhare
- Department of Molecular PhytomedicineUniversity of BonnBonnGermany
- ICAR National Rice Research InstituteCuttack753006India
| | - Yulin Yuan
- Department of Plant SciencesUniversity of IdahoMoscowUSA
| | - Rikus Pomp
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Anna Finkers‐Tomczak
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
- KeyGene N.V.WageningenNetherlands
| | - Jan Roosien
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Erik Slootweg
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Abdenaser Elashry
- Department of Molecular PhytomedicineUniversity of BonnBonnGermany
- Strube Research GmbHHauptstrasse 138387SöllingenGermany
| | | | - Fangming Xiao
- Department of Plant SciencesUniversity of IdahoMoscowUSA
| | - Aska Goverse
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
| | - Geert Smant
- Laboratory of NematologyWageningen University and ResearchWageningenNetherlands
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Zhang D, Wei H, Xue H, Guo S, Wu B, Kuang Z. Backbone 1H, 13C, and 15N resonance assignments of the PRY-SPRY domain of RNF135. Biomol NMR Assign 2019; 13:299-304. [PMID: 31065957 DOI: 10.1007/s12104-019-09895-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
RING finger protein 135 (RNF135, also named Riplet or REUL) exerts multiple biological functions and its C-terminal PRY-SPRY/B30.2 domain is indispensable for most of these functions. RNF135 interacts with RIG-I (retinoic acid-inducible gene-I) via the PRY-SPRY domain and ubiquitinates RIG-I to promote innate anti-viral signaling, while mutations in the RNF135 gene can cause the Macrocephaly, macrosomia, facial dysmorphism (MMFD) syndrome, and RNF135 reportedly regulates the proliferation of glioblastoma cells as well as tongue cancer cells. Nevertheless, structure of full-length RNF135 or its PRY-SPRY domain has not been determined, and structural basis for molecular interactions involving RNF135 is largely unknown. Here we report the backbone 1H, 13C, and 15N chemical shift assignments of the PRY-SPRY domain of RNF135 and the secondary structure elements predicted based on chemical shifts, as well as the perturbations caused by the R286H mutation that is associated with MMFD syndrome. We found that the mutation did not alter the gross structure of the PRY-SPRY domain, so it may have impaired RNF135 function by affecting protein-protein interactions mediated by the domain.
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Affiliation(s)
- Danting Zhang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Huan Wei
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Shujun Guo
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Zhihe Kuang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China.
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5
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Luo Y, Li K, Yang J, Zhang D, Zhou Y, Kuang Z. Crystal structure of the SPRY domain of human SPSB2 in the apo state. Acta Crystallogr F Struct Biol Commun 2019; 75:412-418. [PMID: 31204687 PMCID: PMC6572098 DOI: 10.1107/s2053230x1900623x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/02/2019] [Indexed: 11/10/2022] Open
Abstract
The SPRY domain-containing SOCS box protein 2 (SPSB2) is one of four mammalian SPSB proteins that are characterized by a C-terminal SOCS box and a central SPRY/B30.2 domain. SPSB2 interacts with inducible nitric oxide synthase (iNOS) via the SPRY domain and polyubiquitinates iNOS, resulting in its proteasomal degradation. Inhibitors that can disrupt SPSB2-iNOS interaction and augment NO production may serve as novel anti-infective and anticancer agents. The previously determined murine SPSB2 structure may not reflect the true apo conformation of the iNOS-binding site. Here, the crystal structure of human SPSB2 SPRY domain in the apo state is reported at a resolution of 1.9 Å. Comparison of the apo and ligand-bound structures reveals that the iNOS-binding site is highly preformed and that major conformational changes do not occur upon ligand binding. Moreover, the C-terminal His6 tag of the recombinant protein binds to a shallow pocket adjacent to the iNOS-binding site on a crystallographically related SPSB2 molecule. These findings may help in structure-based and fragment-based SPSB2 inhibitor design in the future.
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Affiliation(s)
- Yanhong Luo
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Kefa Li
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Jinjin Yang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Danting Zhang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Yuying Zhou
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
| | - Zhihe Kuang
- Department of Cell Biology and Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, People’s Republic of China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, People’s Republic of China
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Choudhury NR, Heikel G, Trubitsyna M, Kubik P, Nowak JS, Webb S, Granneman S, Spanos C, Rappsilber J, Castello A, Michlewski G. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. BMC Biol 2017; 15:105. [PMID: 29117863 PMCID: PMC5678581 DOI: 10.1186/s12915-017-0444-9] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND TRIM25 is a novel RNA-binding protein and a member of the Tripartite Motif (TRIM) family of E3 ubiquitin ligases, which plays a pivotal role in the innate immune response. However, there is scarce knowledge about its RNA-related roles in cell biology. Furthermore, its RNA-binding domain has not been characterized. RESULTS Here, we reveal that the RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain, which we postulate to be a novel RNA-binding domain. Using CLIP-seq and SILAC-based co-immunoprecipitation assays, we uncover TRIM25's endogenous RNA targets and protein binding partners. We demonstrate that TRIM25 controls the levels of Zinc Finger Antiviral Protein (ZAP). Finally, we show that the RNA-binding activity of TRIM25 is important for its ubiquitin ligase activity towards itself (autoubiquitination) and its physiologically relevant target ZAP. CONCLUSIONS Our results suggest that many other proteins with the PRY/SPRY domain could have yet uncharacterized RNA-binding potential. Together, our data reveal new insights into the molecular roles and characteristics of RNA-binding E3 ubiquitin ligases and demonstrate that RNA could be an essential factor in their enzymatic activity.
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Affiliation(s)
- Nila Roy Choudhury
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Gregory Heikel
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Maryia Trubitsyna
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Roger Land Building, Edinburgh, EH9 3FF, UK
| | - Peter Kubik
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Jakub Stanislaw Nowak
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Sander Granneman
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, CH Waddington Building, Edinburgh, EH9 3BF, UK
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
- Department of Biotechnology, Technische Universität Berlin, 13353, Berlin, Germany
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Gracjan Michlewski
- Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK.
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