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Olasz B, Smithers L, Evans GL, Anandan A, Murcha MW, Vrielink A. Structural analysis of the SAM domain of the Arabidopsis mitochondrial tRNA import receptor. J Biol Chem 2024; 300:107258. [PMID: 38582448 PMCID: PMC11063897 DOI: 10.1016/j.jbc.2024.107258] [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: 10/24/2023] [Revised: 03/10/2024] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
Mitochondria are membrane-bound organelles of endosymbiotic origin with limited protein-coding capacity. The import of nuclear-encoded proteins and nucleic acids is required and essential for maintaining organelle mass, number, and activity. As plant mitochondria do not encode all the necessary tRNA types required, the import of cytosolic tRNA is vital for organelle maintenance. Recently, two mitochondrial outer membrane proteins, named Tric1 and Tric2, for tRNA import component, were shown to be involved in the import of cytosolic tRNA. Tric1/2 binds tRNAalavia conserved residues in the C-terminal Sterile Alpha Motif (SAM) domain. Here we report the X-ray crystal structure of the Tric1 SAM domain. We identified the ability of the SAM domain to form a helical superstructure with six monomers per helical turn and key amino acid residues responsible for its formation. We determined that the oligomerization of the Tric1 SAM domain may play a role in protein function whereby mutation of Gly241 introducing a larger side chain at this position disrupted the oligomer and resulted in the loss of RNA binding capability. Furthermore, complementation of Arabidopsis thaliana Tric1/2 knockout lines with a mutated Tric1 failed to restore the defective plant phenotype. AlphaFold2 structure prediction of both the SAM domain and Tric1 support a cyclic pentameric or hexameric structure. In the case of a hexameric structure, a pore of sufficient dimensions to transfer tRNA across the mitochondrial membrane is observed. Our results highlight the importance of oligomerization of Tric1 for protein function.
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Affiliation(s)
- Bence Olasz
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Luke Smithers
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Genevieve L Evans
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Anandhi Anandan
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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2
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Allen JR, Wilkinson EG, Strader LC. Creativity comes from interactions: modules of protein interactions in plants. FEBS J 2022; 289:1492-1514. [PMID: 33774929 PMCID: PMC8476656 DOI: 10.1111/febs.15847] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023]
Abstract
Protein interactions are the foundation of cell biology. For robust signal transduction to occur, proteins interact selectively and modulate their behavior to direct specific biological outcomes. Frequently, modular protein interaction domains are central to these processes. Some of these domains bind proteins bearing post-translational modifications, such as phosphorylation, whereas other domains recognize and bind to specific amino acid motifs. Other modules act as diverse protein interaction scaffolds or can be multifunctional, forming head-to-head homodimers and binding specific peptide sequences or membrane phospholipids. Additionally, the so-called head-to-tail oligomerization domains (SAM, DIX, and PB1) can form extended polymers to regulate diverse aspects of biology. Although the mechanism and structures of these domains are diverse, they are united by their modularity. Together, these domains are versatile and facilitate the evolution of complex protein interaction networks. In this review, we will highlight the role of select modular protein interaction domains in various aspects of plant biology.
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Affiliation(s)
- Jeffrey R. Allen
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Edward G. Wilkinson
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
| | - Lucia C. Strader
- Department of Biology, Washington University in St. Louis, MO, USA,Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, MO, USA,Center for Engineering Mechanobiology (CEMB), Washington University in St. Louis, MO, USA,Department of Biology, Duke University, Durham, NC, USA
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3
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The miR-378c-Samd1 circuit promotes phenotypic modulation of vascular smooth muscle cells and foam cells formation in atherosclerosis lesions. Sci Rep 2021; 11:10548. [PMID: 34006929 PMCID: PMC8131603 DOI: 10.1038/s41598-021-89981-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs have emerged as key regulators in vascular diseases and are involved in the formation of atherosclerotic lesions. However, the atherosclerotic-specific MicroRNAs and their functional roles in atherosclerosis are unclear. Here, we report that miR-378c protects against atherosclerosis by directly targeting Sterile Alpha Motif Domain Containing 1 (Samd1), a predicted transcriptional repressor. miR-378c was strikingly reduced in atherosclerotic plaques and blood of acute coronary syndrome (ACS) patients relative to healthy controls. Suppression of miR-378c promoted vascular smooth muscle cells (VSMCs) phenotypic transition during atherosclerosis. We also reported for the first time that Samd1 prolonged immobilization of LDL on the VSMCs, thus facilitated LDL oxidation and subsequently foam cell formation. Further, we found that Samd1 contains predicted DNA binding domain and directly binds to DNA regions as a transcriptional repressor. Together, we uncovered a novel mechanism whereby miR-378c-Samd1 circuit participates in two key elements of atherosclerosis, VSMCs phenotypic transition and LDL oxidation. Our results provided a better understanding of atherosclerosis pathophysiology and potential therapeutic management by targeting miR-378c-Samd1 circuit.
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Rodríguez Gama A, Miller T, Halfmann R. Mechanics of a molecular mousetrap-nucleation-limited innate immune signaling. Biophys J 2021; 120:1150-1160. [PMID: 33460595 PMCID: PMC8059202 DOI: 10.1016/j.bpj.2021.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/17/2022] Open
Abstract
Innate immune responses, such as cell death and inflammatory signaling, are typically switch-like in nature. They also involve "prion-like" self-templating polymerization of one or more signaling proteins into massive macromolecular assemblies known as signalosomes. Despite the wealth of atomic-resolution structural information on signalosomes, how the constituent polymers nucleate and whether the switch-like nature of that event at the molecular scale relates to the digital nature of innate immune signaling at the cellular scale remains unknown. In this perspective, we review current knowledge of innate immune signalosome assembly, with an emphasis on structural constraints that allow the proteins to accumulate in inactive soluble forms poised for abrupt polymerization. We propose that structurally encoded nucleation barriers to protein polymerization kinetically regulate the corresponding pathways, which allows for extremely sensitive, rapid, and decisive signaling upon pathogen detection. We discuss how nucleation barriers satisfy the rigorous on-demand functions of the innate immune system but also predispose the system to precocious activation that may contribute to progressive age-associated inflammation.
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Affiliation(s)
| | - Tayla Miller
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, Missouri; Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas.
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5
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Sporny M, Guez-Haddad J, Lebendiker M, Ulisse V, Volf A, Mim C, Isupov MN, Opatowsky Y. Structural Evidence for an Octameric Ring Arrangement of SARM1. J Mol Biol 2019; 431:3591-3605. [PMID: 31278906 DOI: 10.1016/j.jmb.2019.06.030] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/16/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022]
Abstract
SARM1 induces axonal degeneration in response to various insults and is therefore considered an attractive drug target for the treatment of neuro-degenerative diseases as well as for brain and spinal cord injuries. SARM1 activity depends on the integrity of the protein's SAM domains, as well as on the enzymatic conversion of NAD+ to ADPR (ADP Ribose) products by the SARM1's TIR domain. Therefore, inhibition of either SAM or TIR functions may constitute an effective therapeutic strategy. However, there is currently no SARM1-directed therapeutic approach available because of an insufficient structural and mechanistic understanding of this protein. In this study, we found that SARM1 assembles into an octameric ring. This arrangement was not described before in other SAM proteins, but is reminiscent of the apoptosome and inflammasome-well-known apoptotic ring-like oligomers. We show that both SARM1 and the isolated tandem SAM1-2 domains form octamers in solution, and electron microscopy analysis reveals an octameric ring of SARM1. We determined the crystal structure of SAM1-2 and found that it also forms a closed octameric ring in the crystal lattice. The SAM1-2 ring interactions are mediated by complementing "lock and key" hydrophobic grooves and inserts and electrostatic charges between the neighboring protomers. We have mutated several interacting SAM1-2 interfaces and measured how these mutations affect SARM1 apoptotic activity in cultured cells, and in this way identified critical oligomerization sites that facilitate cell death. These results highlight the importance of oligomerization for SARM1 function and reveal critical epitopes for future targeted drug development.
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Affiliation(s)
- Michael Sporny
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Julia Guez-Haddad
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Mario Lebendiker
- Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Israel
| | - Valeria Ulisse
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Allison Volf
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Carsten Mim
- Department of Biomedical Engineering and Health Solutions, Royal Technical Institute (KTH), Stockholm, Sweden; Department of Nutrition and Biosciences, Karolinska Institute, Huddinge, Sweden
| | | | - Yarden Opatowsky
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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6
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Kukuk L, Dingley AJ, Granzin J, Nagel-Steger L, Thiagarajan-Rosenkranz P, Ciupka D, Hänel K, Batra-Safferling R, Pacheco V, Stoldt M, Pfeffer K, Beer-Hammer S, Willbold D, Koenig BW. Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association. Sci Rep 2019; 9:54. [PMID: 30631134 PMCID: PMC6328559 DOI: 10.1038/s41598-018-37185-3] [Citation(s) in RCA: 10] [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: 04/30/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022] Open
Abstract
Sterile alpha motif (SAM) domains are protein interaction modules that are involved in a diverse range of biological functions such as transcriptional and translational regulation, cellular signalling, and regulation of developmental processes. SH3 domain-containing protein expressed in lymphocytes 1 (SLy1) is involved in immune regulation and contains a SAM domain of unknown function. In this report, the structure of the SLy1 SAM domain was solved and revealed that this SAM domain forms a symmetric homodimer through a novel interface. The interface consists primarily of the two long C-terminal helices, α5 and α5', of the domains packing against each other. The dimerization is characterized by a dissociation constant in the lower micromolar range. A SLy1 SAM domain construct with an extended N-terminus containing five additional amino acids of the SLy1 sequence further increases the stability of the homodimer, making the SLy1 SAM dimer two orders of magnitude more stable than previously studied SAM homodimers, suggesting that the SLy1 SAM dimerization is of functional significance. The SLy1 SAM homodimer contains an exposed mid-loop surface on each monomer, which may provide a scaffold for mediating interactions with other SAM domain-containing proteins via a typical mid-loop-end-helix interface.
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Affiliation(s)
- Laura Kukuk
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Andrew J Dingley
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Joachim Granzin
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Pallavi Thiagarajan-Rosenkranz
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Ciupka
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Karen Hänel
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Renu Batra-Safferling
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Victor Pacheco
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Makromolekulare Chemie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Straße 31, 79104, Freiburg, Germany
| | - Matthias Stoldt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Sandra Beer-Hammer
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, und Interfakultäres Zentrum für Pharmakogenomik und Arzneimittelforschung (ICePhA), Eberhard-Karls-Universität Tübingen, Wilhelmstraße 56, 72074, Tübingen, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Bernd W Koenig
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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7
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Mariotti L, Templeton CM, Ranes M, Paracuellos P, Cronin N, Beuron F, Morris E, Guettler S. Tankyrase Requires SAM Domain-Dependent Polymerization to Support Wnt-β-Catenin Signaling. Mol Cell 2016; 63:498-513. [PMID: 27494558 PMCID: PMC4980433 DOI: 10.1016/j.molcel.2016.06.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 05/13/2016] [Accepted: 06/13/2016] [Indexed: 01/14/2023]
Abstract
The poly(ADP-ribose) polymerase (PARP) Tankyrase (TNKS and TNKS2) is paramount to Wnt-β-catenin signaling and a promising therapeutic target in Wnt-dependent cancers. The pool of active β-catenin is normally limited by destruction complexes, whose assembly depends on the polymeric master scaffolding protein AXIN. Tankyrase, which poly(ADP-ribosyl)ates and thereby destabilizes AXIN, also can polymerize, but the relevance of these polymers has remained unclear. We report crystal structures of the polymerizing TNKS and TNKS2 sterile alpha motif (SAM) domains, revealing versatile head-to-tail interactions. Biochemical studies informed by these structures demonstrate that polymerization is required for Tankyrase to drive β-catenin-dependent transcription. We show that the polymeric state supports PARP activity and allows Tankyrase to effectively access destruction complexes through enabling avidity-dependent AXIN binding. This study provides an example for regulated signal transduction in non-membrane-enclosed compartments (signalosomes), and it points to novel potential strategies to inhibit Tankyrase function in oncogenic Wnt signaling.
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Affiliation(s)
- Laura Mariotti
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Catherine M Templeton
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Michael Ranes
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Patricia Paracuellos
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Nora Cronin
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Edward Morris
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK
| | - Sebastian Guettler
- Division of Structural Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK; Division of Cancer Biology, The Institute of Cancer Research (ICR), London SW7 3RP, UK.
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8
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DaRosa PA, Ovchinnikov S, Xu W, Klevit RE. Structural insights into SAM domain-mediated tankyrase oligomerization. Protein Sci 2016; 25:1744-52. [PMID: 27328430 DOI: 10.1002/pro.2968] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/16/2016] [Indexed: 12/28/2022]
Abstract
Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP-ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain-mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head-to-tail polymer that facilitates TNKS self-association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM-TNKS2 SAM) hetero-oligomeric structures mediated by their SAM domains. Though wild-type tankyrase proteins have very low solubility, model-based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP-ribosyl)ation (PARylation) and PARylation-dependent ubiquitylation.
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Affiliation(s)
- Paul A DaRosa
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195.,Department of Biological Structure, University of Washington, Seattle, Washington, 98195
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington, 98195
| | - Wenqing Xu
- Department of Biological Structure, University of Washington, Seattle, Washington, 98195
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington, 98195
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