1
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Furlanetto V, Kalyani DC, Kostelac A, Puc J, Haltrich D, Hällberg BM, Divne C. Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius. J Mol Biol 2024; 436:168547. [PMID: 38508304 DOI: 10.1016/j.jmb.2024.168547] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/22/2024]
Abstract
Plant C-glycosylated aromatic polyketides are important for plant and animal health. These are specialized metabolites that perform functions both within the plant, and in interaction with soil or intestinal microbes. Despite the importance of these plant compounds, there is still limited knowledge of how they are metabolized. The Gram-positive aerobic soil bacterium Deinococcus aerius strain TR0125 and other Deinococcus species thrive in a wide range of harsh environments. In this work, we identified a C-glycoside deglycosylation gene cluster in the genome of D. aerius. The cluster includes three genes coding for a GMC-type oxidoreductase (DaCGO1) that oxidizes the glucosyl C3 position in aromatic C-glucosyl compounds, which in turn provides the substrate for the C-glycoside deglycosidase (DaCGD; composed of α+β subunits) that cleaves the glucosyl-aglycone C-C bond. Our results from size-exclusion chromatography, single particle cryo-electron microscopy and X-ray crystallography show that DaCGD is an α2β2 heterotetramer, which represents a novel oligomeric state among bacterial CGDs. Importantly, the high-resolution X-ray structure of DaCGD provides valuable insights into the activation of the catalytic hydroxide ion by Lys261. DaCGO1 is specific for the 6-C-glucosyl flavones isovitexin, isoorientin and the 2-C-glucosyl xanthonoid mangiferin, and the subsequent C-C-bond cleavage by DaCGD generated apigenin, luteolin and norathyriol, respectively. Of the substrates tested, isovitexin was the preferred substrate (DaCGO1, Km 0.047 mM, kcat 51 min-1; DaCGO1/DaCGD, Km 0.083 mM, kcat 0.42 min-1).
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Affiliation(s)
- Valentina Furlanetto
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, CBH, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Dayanand C Kalyani
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, CBH, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden
| | - Anja Kostelac
- Laboratory of Food Biotechnology, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria; Doctoral Programme BioToP-Biomolecular Technology of Proteins, BOKU-University of Natural Resources and Life Sciences, 1180 Vienna, Austria
| | - Jolanta Puc
- Laboratory of Food Biotechnology, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Dietmar Haltrich
- Laboratory of Food Biotechnology, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Christina Divne
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, CBH, KTH Royal Institute of Technology, 100 44 Stockholm, Sweden.
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2
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Sahin C, Motso A, Gu X, Feyrer H, Lama D, Arndt T, Rising A, Gese GV, Hällberg BM, Marklund EG, Schafer NP, Petzold K, Teilum K, Wolynes PG, Landreh M. Mass Spectrometry of RNA-Binding Proteins during Liquid-Liquid Phase Separation Reveals Distinct Assembly Mechanisms and Droplet Architectures. J Am Chem Soc 2023; 145:10659-10668. [PMID: 37145883 DOI: 10.1021/jacs.3c00932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) of heterogeneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through a combination of protein engineering, native ion mobility mass spectrometry, and molecular dynamics simulations. We used an LLPS-compatible spider silk domain and pH changes to control the self-assembly of the hnRNPs FUS, TDP-43, and hCPEB3, which are implicated in neurodegeneration, cancer, and memory storage. By releasing the proteins inside the mass spectrometer from their native assemblies, we could monitor conformational changes associated with liquid-liquid phase separation. We find that FUS monomers undergo an unfolded-to-globular transition, whereas TDP-43 oligomerizes into partially disordered dimers and trimers. hCPEB3, on the other hand, remains fully disordered with a preference for fibrillar aggregation over LLPS. The divergent assembly mechanisms revealed by ion mobility mass spectrometry of soluble protein species that exist under LLPS conditions suggest structurally distinct complexes inside liquid droplets that may impact RNA processing and translation depending on biological context.
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Affiliation(s)
- Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Aikaterini Motso
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Xinyu Gu
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Hannes Feyrer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
| | - Tina Arndt
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
| | - Anna Rising
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Box 7011, S-750 07 Uppsala, Sweden
| | - Genis Valentin Gese
- Department of Cell and Molecular Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 171 65 Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 171 65 Stockholm, Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 24 Uppsala, Sweden
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet - Biomedicum, Solnavägen 9, 17165 Solna, Sweden
- Department of Cell- and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden
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3
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Saluri M, Leppert A, Gese GV, Sahin C, Lama D, Kaldmäe M, Chen G, Elofsson A, Allison TM, Arsenian-Henriksson M, Johansson J, Lane DP, Hällberg BM, Landreh M. A "grappling hook" interaction connects self-assembly and chaperone activity of Nucleophosmin 1. PNAS Nexus 2023; 2:pgac303. [PMID: 36743470 PMCID: PMC9896144 DOI: 10.1093/pnasnexus/pgac303] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
How the self-assembly of partially disordered proteins generates functional compartments in the cytoplasm and particularly in the nucleus is poorly understood. Nucleophosmin 1 (NPM1) is an abundant nucleolar protein that forms large oligomers and undergoes liquid-liquid phase separation by binding RNA or ribosomal proteins. It provides the scaffold for ribosome assembly but also prevents protein aggregation as part of the cellular stress response. Here, we use aggregation assays and native mass spectrometry (MS) to examine the relationship between the self-assembly and chaperone activity of NPM1. We find that oligomerization of full-length NPM1 modulates its ability to retard amyloid formation in vitro. Machine learning-based structure prediction and cryo-electron microscopy reveal fuzzy interactions between the acidic disordered region and the C-terminal nucleotide-binding domain, which cross-link NPM1 pentamers into partially disordered oligomers. The addition of basic peptides results in a tighter association within the oligomers, reducing their capacity to prevent amyloid formation. Together, our findings show that NPM1 uses a "grappling hook" mechanism to form a network-like structure that traps aggregation-prone proteins. Nucleolar proteins and RNAs simultaneously modulate the association strength and chaperone activity, suggesting a mechanism by which nucleolar composition regulates the chaperone activity of NPM1.
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Affiliation(s)
- Mihkel Saluri
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | | | | | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden,Structural Biology and NMR laboratory and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, 2200 Copenhagen, Denmark
| | - Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | - Margit Kaldmäe
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | - Gefei Chen
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 57 Huddinge,, Sweden
| | - Arne Elofsson
- Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University, 114 19 Stockholm, Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre, School of Physical and Chemical Sciences, University of Canterbury, Upper Riccarton, Christchurch 8041, New Zealand
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
| | - Jan Johansson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 57 Huddinge,, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet – Biomedicum, Solnavägen 9, 171 65 Solna, Stockholm, Sweden
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4
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Zhu X, Xie X, Das H, Tan BG, Shi Y, Al-Behadili A, Peter B, Motori E, Valenzuela S, Posse V, Gustafsson CM, Hällberg BM, Falkenberg M. Non-coding 7S RNA inhibits transcription via mitochondrial RNA polymerase dimerization. Cell 2022; 185:2309-2323.e24. [PMID: 35662414 DOI: 10.1016/j.cell.2022.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/05/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022]
Abstract
The mitochondrial genome encodes 13 components of the oxidative phosphorylation system, and altered mitochondrial transcription drives various human pathologies. A polyadenylated, non-coding RNA molecule known as 7S RNA is transcribed from a region immediately downstream of the light strand promoter in mammalian cells, and its levels change rapidly in response to physiological conditions. Here, we report that 7S RNA has a regulatory function, as it controls levels of mitochondrial transcription both in vitro and in cultured human cells. Using cryo-EM, we show that POLRMT dimerization is induced by interactions with 7S RNA. The resulting POLRMT dimer interface sequesters domains necessary for promoter recognition and unwinding, thereby preventing transcription initiation. We propose that the non-coding 7S RNA molecule is a component of a negative feedback loop that regulates mitochondrial transcription in mammalian cells.
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Affiliation(s)
- Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Benedict G Tan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Elisa Motori
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany; Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, 50674 Cologne, Germany
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden.
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5
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022; 13:155. [PMID: 35013189 PMCID: PMC8748511 DOI: 10.1038/s41467-021-27610-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [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: 04/20/2021] [Accepted: 11/30/2021] [Indexed: 01/04/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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6
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Hanke L, Das H, Sheward DJ, Perez Vidakovics L, Urgard E, Moliner-Morro A, Kim C, Karl V, Pankow A, Smith NL, Porebski B, Fernandez-Capetillo O, Sezgin E, Pedersen GK, Coquet JM, Hällberg BM, Murrell B, McInerney GM. A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo. Nat Commun 2022. [PMID: 35013189 DOI: 10.1101/2021.03.20.436243v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Antibodies binding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike have therapeutic promise, but emerging variants show the potential for virus escape. This emphasizes the need for therapeutic molecules with distinct and novel neutralization mechanisms. Here we describe the isolation of a nanobody that interacts simultaneously with two RBDs from different spike trimers of SARS-CoV-2, rapidly inducing the formation of spike trimer-dimers leading to the loss of their ability to attach to the host cell receptor, ACE2. We show that this nanobody potently neutralizes SARS-CoV-2, including the beta and delta variants, and cross-neutralizes SARS-CoV. Furthermore, we demonstrate the therapeutic potential of the nanobody against SARS-CoV-2 and the beta variant in a human ACE2 transgenic mouse model. This naturally elicited bispecific monomeric nanobody establishes an uncommon strategy for potent inactivation of viral antigens and represents a promising antiviral against emerging SARS-CoV-2 variants.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bartlomiej Porebski
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oscar Fernandez-Capetillo
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel K Pedersen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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7
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Cipullo M, Gesé GV, Khawaja A, Hällberg BM, Rorbach J. Structural basis for late maturation steps of the human mitoribosomal large subunit. Nat Commun 2021; 12:3673. [PMID: 34135318 PMCID: PMC8209036 DOI: 10.1038/s41467-021-23617-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 03/02/2021] [Accepted: 05/07/2021] [Indexed: 01/29/2023] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) synthesize a critical set of proteins essential for oxidative phosphorylation. Therefore, mitoribosomal function is vital to the cellular energy supply. Mitoribosome biogenesis follows distinct molecular pathways that remain poorly understood. Here, we determine the cryo-EM structures of mitoribosomes isolated from human cell lines with either depleted or overexpressed mitoribosome assembly factor GTPBP5, allowing us to capture consecutive steps during mitoribosomal large subunit (mt-LSU) biogenesis. Our structures provide essential insights into the last steps of 16S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, which require the coordinated action of nine assembly factors. We show that mammalian-specific MTERF4 contributes to the folding of 16S rRNA, allowing 16 S rRNA methylation by MRM2, while GTPBP5 and NSUN4 promote fine-tuning rRNA rearrangements leading to PTC formation. Moreover, our data reveal an unexpected involvement of the elongation factor mtEF-Tu in mt-LSU assembly, where mtEF-Tu interacts with GTPBP5, similar to its interaction with tRNA during translational elongation.
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Affiliation(s)
- Miriam Cipullo
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solna, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Genís Valentín Gesé
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden
| | - Anas Khawaja
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solna, Sweden
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden.
- Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Hamburg, Germany.
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institutet, Solna, Sweden.
- Max Planck Institute Biology of Ageing-Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden.
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8
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Koenig PA, Das H, Liu H, Kümmerer BM, Gohr FN, Jenster LM, Schiffelers LDJ, Tesfamariam YM, Uchima M, Wuerth JD, Gatterdam K, Ruetalo N, Christensen MH, Fandrey CI, Normann S, Tödtmann JMP, Pritzl S, Hanke L, Boos J, Yuan M, Zhu X, Schmid-Burgk JL, Kato H, Schindler M, Wilson IA, Geyer M, Ludwig KU, Hällberg BM, Wu NC, Schmidt FI. Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. Science 2021; 371:eabe6230. [PMID: 33436526 PMCID: PMC7932109 DOI: 10.1126/science.abe6230] [Citation(s) in RCA: 244] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022]
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread, with devastating consequences. For passive immunization efforts, nanobodies have size and cost advantages over conventional antibodies. In this study, we generated four neutralizing nanobodies that target the receptor binding domain of the SARS-CoV-2 spike protein. We used x-ray crystallography and cryo-electron microscopy to define two distinct binding epitopes. On the basis of these structures, we engineered multivalent nanobodies with more than 100 times the neutralizing activity of monovalent nanobodies. Biparatopic nanobody fusions suppressed the emergence of escape mutants. Several nanobody constructs neutralized through receptor binding competition, whereas other monovalent and biparatopic nanobodies triggered aberrant activation of the spike fusion machinery. These premature conformational changes in the spike protein forestalled productive fusion and rendered the virions noninfectious.
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MESH Headings
- Amino Acid Substitution
- Angiotensin-Converting Enzyme 2/metabolism
- Animals
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antibody Affinity
- Antigens, Viral/immunology
- Binding Sites, Antibody
- COVID-19/immunology
- COVID-19/virology
- Cell Line
- Cryoelectron Microscopy
- Epitopes
- Humans
- Membrane Fusion
- Mutation
- Protein Binding
- Protein Conformation
- Protein Domains
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/metabolism
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Virus Replication
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Affiliation(s)
- Paul-Albert Koenig
- Core Facility Nanobodies, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beate M Kümmerer
- Institute of Virology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
- German Centre for Infection Research (DZIF), partner site Bonn-Cologne, 53127 Bonn, Germany
| | - Florian N Gohr
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Lea-Marie Jenster
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Lisa D J Schiffelers
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Yonas M Tesfamariam
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Miki Uchima
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Jennifer D Wuerth
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Karl Gatterdam
- Institute of Structural Biology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology, Section Molecular Virology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Maria H Christensen
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Caroline I Fandrey
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Sabine Normann
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Jan M P Tödtmann
- Core Facility Nanobodies, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Steffen Pritzl
- Core Facility Nanobodies, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Jannik Boos
- Institute of Human Genetics, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L Schmid-Burgk
- Institute for Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology, Section Molecular Virology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthias Geyer
- Institute of Structural Biology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
- Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Florian I Schmidt
- Core Facility Nanobodies, Medical Faculty, University of Bonn, 53127 Bonn, Germany.
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
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9
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Wu PS, Enervald E, Joelsson A, Palmberg C, Rutishauser D, Hällberg BM, Ström L. Post-translational Regulation of DNA Polymerase η, a Connection to Damage-Induced Cohesion in Saccharomyces cerevisiae. Genetics 2020; 216:1009-1022. [PMID: 33033113 PMCID: PMC7768261 DOI: 10.1534/genetics.120.303494] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Double-strand breaks that are induced postreplication trigger establishment of damage-induced cohesion in Saccharomyces cerevisiae, locally at the break site and genome-wide on undamaged chromosomes. The translesion synthesis polymerase, polymerase η, is required for generation of damage-induced cohesion genome-wide. However, its precise role and regulation in this process is unclear. Here, we investigated the possibility that the cyclin-dependent kinase Cdc28 and the acetyltransferase Eco1 modulate polymerase η activity. Through in vitro phosphorylation and structure modeling, we showed that polymerase η is an attractive substrate for Cdc28 Mutation of the putative Cdc28-phosphorylation site Ser14 to Ala not only affected polymerase η protein level, but also prevented generation of damage-induced cohesion in vivo We also demonstrated that Eco1 acetylated polymerase η in vitro Certain nonacetylatable polymerase η mutants showed reduced protein level, deficient nuclear accumulation, and increased ultraviolet irradiation sensitivity. In addition, we found that both Eco1 and subunits of the cohesin network are required for cell survival after ultraviolet irradiation. Our findings support functionally important Cdc28-mediated phosphorylation, as well as post-translational modifications of multiple lysine residues that modulate polymerase η activity, and provide new insights into understanding the regulation of polymerase η for damage-induced cohesion.
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Affiliation(s)
- Pei-Shang Wu
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Elin Enervald
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Angelica Joelsson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Carina Palmberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Dorothea Rutishauser
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm SE-171 77, Sweden
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10
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Custódio TF, Das H, Sheward DJ, Hanke L, Pazicky S, Pieprzyk J, Sorgenfrei M, Schroer MA, Gruzinov AY, Jeffries CM, Graewert MA, Svergun DI, Dobrev N, Remans K, Seeger MA, McInerney GM, Murrell B, Hällberg BM, Löw C. Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2. Nat Commun 2020; 11:5588. [PMID: 33149112 PMCID: PMC7642358 DOI: 10.1038/s41467-020-19204-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [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: 06/16/2020] [Accepted: 10/01/2020] [Indexed: 12/26/2022] Open
Abstract
The coronavirus SARS-CoV-2 is the cause of the ongoing COVID-19 pandemic. Therapeutic neutralizing antibodies constitute a key short-to-medium term approach to tackle COVID-19. However, traditional antibody production is hampered by long development times and costly production. Here, we report the rapid isolation and characterization of nanobodies from a synthetic library, known as sybodies (Sb), that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Several binders with low nanomolar affinities and efficient neutralization activity were identified of which Sb23 displayed high affinity and neutralized pseudovirus with an IC50 of 0.6 µg/ml. A cryo-EM structure of the spike bound to Sb23 showed that Sb23 binds competitively in the ACE2 binding site. Furthermore, the cryo-EM reconstruction revealed an unusual conformation of the spike where two RBDs are in the 'up' ACE2-binding conformation. The combined approach represents an alternative, fast workflow to select binders with neutralizing activity against newly emerging viruses.
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Affiliation(s)
- Tânia F Custódio
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Hrishikesh Das
- Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Samuel Pazicky
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Joanna Pieprzyk
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Martin A Schroer
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Andrey Yu Gruzinov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Melissa A Graewert
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607, Hamburg, Germany
| | - Nikolay Dobrev
- European Molecular Biology Laboratory (EMBL) Heidelberg, Protein Expression and Purification Core Facility, 69117, Heidelberg, Germany
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL) Heidelberg, Protein Expression and Purification Core Facility, 69117, Heidelberg, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
| | - B Martin Hällberg
- Centre for Structural Systems Biology (CSSB) and Karolinska Institutet VR-RÅC, Notkestrasse 85, D-22607, Hamburg, Germany.
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177, Stockholm, Sweden.
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany.
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11
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Hanke L, Vidakovics Perez L, Sheward DJ, Das H, Schulte T, Moliner-Morro A, Corcoran M, Achour A, Karlsson Hedestam GB, Hällberg BM, Murrell B, McInerney GM. An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nat Commun 2020; 11:4420. [PMID: 32887876 DOI: 10.1101/2020.06.02.130161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/08/2020] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Angiotensin-Converting Enzyme Inhibitors/pharmacology
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Camelids, New World/immunology
- Chlorocebus aethiops
- Coronavirus Infections/drug therapy
- Coronavirus Infections/virology
- Cryoelectron Microscopy
- Epitopes/immunology
- Epitopes/metabolism
- HEK293 Cells
- Humans
- Male
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/virology
- Protein Binding
- SARS-CoV-2
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/isolation & purification
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/antagonists & inhibitors
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vero Cells
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Vidakovics Perez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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12
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Hanke L, Vidakovics Perez L, Sheward DJ, Das H, Schulte T, Moliner-Morro A, Corcoran M, Achour A, Karlsson Hedestam GB, Hällberg BM, Murrell B, McInerney GM. An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction. Nat Commun 2020; 11:4420. [PMID: 32887876 PMCID: PMC7473855 DOI: 10.1038/s41467-020-18174-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/08/2020] [Indexed: 11/26/2022] Open
Abstract
SARS-CoV-2 enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here, we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. Ty1 binds the RBD with high affinity, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 Å resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the 'up' and 'down' conformations, sterically hindering RBD-ACE2 binding. While fusion to an Fc domain renders Ty1 extremely potent, Ty1 neutralizes SARS-CoV-2 spike pseudovirus as a 12.8 kDa nanobody, which can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.
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MESH Headings
- Amino Acid Sequence
- Angiotensin-Converting Enzyme 2
- Angiotensin-Converting Enzyme Inhibitors/pharmacology
- Animals
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/pharmacology
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Betacoronavirus/drug effects
- Betacoronavirus/immunology
- Betacoronavirus/metabolism
- Binding Sites
- COVID-19
- Camelids, New World/immunology
- Chlorocebus aethiops
- Coronavirus Infections/drug therapy
- Coronavirus Infections/virology
- Cryoelectron Microscopy
- Epitopes/immunology
- Epitopes/metabolism
- HEK293 Cells
- Humans
- Male
- Models, Molecular
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/virology
- Protein Binding
- SARS-CoV-2
- Single-Domain Antibodies/immunology
- Single-Domain Antibodies/isolation & purification
- Single-Domain Antibodies/pharmacology
- Spike Glycoprotein, Coronavirus/antagonists & inhibitors
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vero Cells
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Vidakovics Perez
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Virology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hrishikesh Das
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | | | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
- Karolinska Institutet VR-RÅC, Centre for Structural Systems Biology, Notkestraße 85, 22607, Hamburg, Germany.
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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13
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Reinhard L, Sridhara S, Hällberg BM. The MRPP1/MRPP2 complex is a tRNA-maturation platform in human mitochondria. Nucleic Acids Res 2017; 45:12469-12480. [PMID: 29040705 PMCID: PMC5716156 DOI: 10.1093/nar/gkx902] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/25/2017] [Indexed: 11/22/2022] Open
Abstract
Mitochondrial polycistronic transcripts are extensively processed to give rise to functional mRNAs, rRNAs and tRNAs; starting with the release of tRNA elements through 5′-processing by RNase P (MRPP1/2/3-complex) and 3′-processing by RNase Z (ELAC2). Here, we show using in vitro experiments that MRPP1/2 is not only a component of the mitochondrial RNase P but that it retains the tRNA product from the 5′-processing step and significantly enhances the efficiency of ELAC2-catalyzed 3′-processing for 17 of the 22 tRNAs encoded in the human mitochondrial genome. Furthermore, MRPP1/2 retains the tRNA product after ELAC2 processing and presents the nascent tRNA to the mitochondrial CCA-adding enzyme. Thus, in addition to being an essential component of the RNase P reaction, MRPP1/2 serves as a processing platform for several down-stream tRNA maturation steps in human mitochondria. These findings are of fundamental importance for our molecular understanding of disease-related mutations in MRPP1/2, ELAC2 and mitochondrial tRNA genes.
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Affiliation(s)
- Linda Reinhard
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.,Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology (CSSB), DESY-Campus, 22607 Hamburg, Germany
| | - Sagar Sridhara
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.,Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology (CSSB), DESY-Campus, 22607 Hamburg, Germany
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden.,Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology (CSSB), DESY-Campus, 22607 Hamburg, Germany.,European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany
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14
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Abstract
TGF-β signaling regulates cellular processes such as proliferation, differentiation and apoptosis through activation of SMAD transcription factors that are in turn modulated by members of the Ski-SnoN family. In this process, Ski has been shown to negatively modulate TGF-β signaling by disrupting active R-SMAD/Co-SMAD heteromers. Here, we show that the related regulator SnoN forms a stable complex with the R-SMAD (SMAD3) and the Co-SMAD (SMAD4). To rationalize this stabilization at the molecular level, we determined the crystal structure of a complex between the SAND domain of SnoN and the MH2-domain of SMAD4. This structure shows a binding mode that is compatible with simultaneous coordination of R-SMADs. Our results show that SnoN, and SMAD heteromers can form a joint structural core for the binding of other transcription modulators. The results are of fundamental importance for our understanding of the molecular mechanisms behind the modulation of TGF-β signaling.
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Affiliation(s)
- Karin Walldén
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Tomas Nyman
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, 22603 Hamburg, Germany.,European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany
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15
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Lapkouski M, Hällberg BM. Structure of mitochondrial poly(A) RNA polymerase reveals the structural basis for dimerization, ATP selectivity and the SPAX4 disease phenotype. Nucleic Acids Res 2015; 43:9065-75. [PMID: 26319014 PMCID: PMC4605311 DOI: 10.1093/nar/gkv861] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/14/2015] [Indexed: 01/23/2023] Open
Abstract
Polyadenylation, performed by poly(A) polymerases (PAPs), is a ubiquitous post-transcriptional modification that plays key roles in multiple aspects of RNA metabolism. Although cytoplasmic and nuclear PAPs have been studied extensively, the mechanism by which mitochondrial PAP (mtPAP) selects adenosine triphosphate over other nucleotides is unknown. Furthermore, mtPAP is unique because it acts as a dimer. However, mtPAP's dimerization requirement remains enigmatic. Here, we show the structural basis for mtPAP's nucleotide selectivity, dimerization and catalysis. Our structures reveal an intricate dimerization interface that features an RNA-recognition module formed through strand complementation. Further, we propose the structural basis for the N478D mutation that drastically reduces the length of poly(A) tails on mitochondrial mRNAs in patients with spastic ataxia 4 (SPAX4), a severe and progressive neurodegenerative disease.
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Affiliation(s)
- Mikalai Lapkouski
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, 22607 Hamburg, Germany
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, 22607 Hamburg, Germany European Molecular Biology Laboratory, Hamburg Unit, 22607 Hamburg, Germany
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16
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Tan TC, Kracher D, Gandini R, Sygmund C, Kittl R, Haltrich D, Hällberg BM, Ludwig R, Divne C. Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation. Nat Commun 2015; 6:7542. [PMID: 26151670 PMCID: PMC4507011 DOI: 10.1038/ncomms8542] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/19/2015] [Indexed: 02/06/2023] Open
Abstract
A new paradigm for cellulose depolymerization by fungi focuses on an oxidative mechanism involving cellobiose dehydrogenases (CDH) and copper-dependent lytic polysaccharide monooxygenases (LPMO); however, mechanistic studies have been hampered by the lack of structural information regarding CDH. CDH contains a haem-binding cytochrome (CYT) connected via a flexible linker to a flavin-dependent dehydrogenase (DH). Electrons are generated from cellobiose oxidation catalysed by DH and shuttled via CYT to LPMO. Here we present structural analyses that provide a comprehensive picture of CDH conformers, which govern the electron transfer between redox centres. Using structure-based site-directed mutagenesis, rapid kinetics analysis and molecular docking, we demonstrate that flavin-to-haem interdomain electron transfer (IET) is enabled by a haem propionate group and that rapid IET requires a closed CDH state in which the propionate is tightly enfolded by DH. Following haem reduction, CYT reduces LPMO to initiate oxygen activation at the copper centre and subsequent cellulose depolymerization.
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Affiliation(s)
- Tien-Chye Tan
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Daniel Kracher
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Rosaria Gandini
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
| | - Christoph Sygmund
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Roman Kittl
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Dietmar Haltrich
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - B. Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm S-17177, Sweden
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg 22603, Germany; and Centre for Structural Systems Biology (CSSB), DESY-Campus, Hamburg 22603, Germany
| | - Roland Ludwig
- Food Biotechnology Laboratory, Department of Food Science and Technology, Vienna Institute of Biotechnology (VIBT), BOKU—University of Natural Resources and Life Sciences, Muthgasse 18, Vienna A-1190, Austria
| | - Christina Divne
- School of Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, Stockholm S-10691, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelelaboratoriet, Scheeles väg 2, Stockholm S-17177, Sweden
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Reinhard L, Sridhara S, Hällberg BM. Structure of the nuclease subunit of human mitochondrial RNase P. Nucleic Acids Res 2015; 43:5664-72. [PMID: 25953853 PMCID: PMC4477676 DOI: 10.1093/nar/gkv481] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 04/30/2015] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial RNA polymerase produces long polycistronic precursors that contain the mRNAs, rRNAs and tRNAs needed for mitochondrial translation. Mitochondrial RNase P (mt-RNase P) initiates the maturation of the precursors by cleaving at the 5' ends of the tRNAs. Human mt-RNase P is only active as a tripartite complex (mitochondrial RNase P proteins 1-3; MRPP1-3), whereas plant and trypanosomal RNase Ps (PRORPs)-albeit homologous to MRPP3-are active as single proteins. The reason for this discrepancy has so far remained obscure. Here, we present the crystal structure of human MRPP3, which features a remarkably distorted and hence non-productive active site that we propose will switch to a fully productive state only upon association with MRPP1, MRPP2 and pre-tRNA substrate. We suggest a mechanism in which MRPP1 and MRPP2 both deliver the pre-tRNA substrate and activate MRPP3 through an induced-fit process.
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Affiliation(s)
- Linda Reinhard
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, 22607 Hamburg, Germany
| | - Sagar Sridhara
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, 22607 Hamburg, Germany
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, 22607 Hamburg, Germany European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany
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18
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Posse V, Shahzad S, Falkenberg M, Hällberg BM, Gustafsson CM. TEFM is a potent stimulator of mitochondrial transcription elongation in vitro. Nucleic Acids Res 2015; 43:2615-24. [PMID: 25690892 PMCID: PMC4357710 DOI: 10.1093/nar/gkv105] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
A single-subunit RNA polymerase, POLRMT, transcribes the mitochondrial genome in human cells. Recently, a factor termed as the mitochondrial transcription elongation factor, TEFM, was shown to stimulate transcription elongation in vivo, but its effect in vitro was relatively modest. In the current work, we have isolated active TEFM in recombinant form and used a reconstituted in vitro transcription system to characterize its activities. We show that TEFM strongly promotes POLRMT processivity as it dramatically stimulates the formation of longer transcripts. TEFM also abolishes premature transcription termination at conserved sequence block II, an event that has been linked to primer formation during initiation of mtDNA synthesis. We show that POLRMT pauses at a wide range of sites in a given DNA sequence. In the absence of TEFM, this leads to termination; however, the presence of TEFM abolishes this effect and aids POLRMT in continuation of transcription. Further, we show that TEFM substantially increases the POLRMT affinity to an elongation-like DNA:RNA template. In combination with previously published in vivo observations, our data establish TEFM as an essential component of the mitochondrial transcription machinery.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Saba Shahzad
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany European Molecular Biology Laboratory, Hamburg Unit, D-22603 Hamburg, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
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Abstract
Understanding regulation of mitochondrial DNA (mtDNA) expression is of considerable interest given that mitochondrial dysfunction is important in human pathology and aging. Similar to the situation in bacteria, there is no compartmentalization between transcription and translation in mitochondria; hence, both processes are likely to have a direct molecular crosstalk. Accumulating evidence suggests that there are important mechanisms for regulation of mammalian mtDNA expression at the posttranscriptional level. Regulation of mRNA maturation, mRNA stability, translational coordination, ribosomal biogenesis, and translation itself all form the basis for controlling oxidative phosphorylation capacity. Consequently, a wide variety of inherited human mitochondrial diseases are caused by mutations of nuclear genes regulating various aspects of mitochondrial translation. Furthermore, mutations of mtDNA, associated with human disease and aging, often affect tRNA genes critical for mitochondrial translation. Recent advances in molecular understanding of mitochondrial translation regulation will most likely provide novel avenues for modulating mitochondrial function for treating human disease.
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Affiliation(s)
- B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY Campus, 22603 Hamburg, Germany; European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 509 31 Cologne, Germany; Department of Laboratory Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden.
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20
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Posse V, Hoberg E, Dierckx A, Shahzad S, Koolmeister C, Larsson NG, Wilhelmsson LM, Hällberg BM, Gustafsson CM. The amino terminal extension of mammalian mitochondrial RNA polymerase ensures promoter specific transcription initiation. Nucleic Acids Res 2014; 42:3638-47. [PMID: 24445803 PMCID: PMC3973307 DOI: 10.1093/nar/gkt1397] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mammalian mitochondrial transcription is executed by a single subunit mitochondrial RNA polymerase (Polrmt) and its two accessory factors, mitochondrial transcription factors A and B2 (Tfam and Tfb2m). Polrmt is structurally related to single-subunit phage RNA polymerases, but it also contains a unique N-terminal extension (NTE) of unknown function. We here demonstrate that the NTE functions together with Tfam to ensure promoter-specific transcription. When the NTE is deleted, Polrmt can initiate transcription in the absence of Tfam, both from promoters and non-specific DNA sequences. Additionally, when in presence of Tfam and a mitochondrial promoter, the NTE-deleted mutant has an even higher transcription activity than wild-type polymerase, indicating that the NTE functions as an inhibitory domain. Our studies lead to a model according to which Tfam specifically recruits wild-type Polrmt to promoter sequences, relieving the inhibitory effect of the NTE, as a first step in transcription initiation. In the second step, Tfb2m is recruited into the complex and transcription is initiated.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg, Sweden, Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden, Department of Cell and Molecular Biology, Karolinska Institutet, S-171 77 Stockholm, Sweden, Department of Laboratory Medicine, Karolinska Institutet, SE-17177 Stockholm, Sweden, Max Planck Institute for Biology of Ageing, Gleueler Str. 50 a D-50931 Cologne, Germany, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany and European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany
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21
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Campanacci V, Lartigue A, Hällberg BM, Jones TA, Giudici-Orticoni MT, Tegoni M, Cambillau C. Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding. Proc Natl Acad Sci U S A 2003; 100:5069-74. [PMID: 12697900 PMCID: PMC154299 DOI: 10.1073/pnas.0836654100] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2002] [Indexed: 11/18/2022] Open
Abstract
Chemosensory proteins (CSPs) have been proposed to transport hydrophobic chemicals from air to olfactory or taste receptors. They have been isolated from several sensory organs of a wide range of insect species. The x-ray structure of CSPMbraA6, a 112-aa antennal protein from the moth Mamestra brassicae (Mbra), was shown to exhibit a novel type of alpha-helical fold. We have performed a structural and binding study of CSPMbraA6 to get some insights into its possible molecular function. Tryptophan fluorescence quenching demonstrates the ability of CSPMbraA6 to bind several types of semio-chemicals or surrogate ligands with microM K(d). Its crystal structure in complex with one of these compounds, 12-bromo-dodecanol, reveals extensive conformational changes on binding, resulting in the formation of a large cavity filled by three ligand molecules. Furthermore, binding cooperativity was demonstrated for some ligands, suggesting a stepwise binding. The peculiar rearrangement of CSPMbraA6 conformation and the cooperativity phenomenon might trigger the recognition of chemicals by receptors and induce subsequent signal transduction.
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Affiliation(s)
- Valerie Campanacci
- Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Centre National de la Recherche Scientifique and Universités d'Aix-Marseille I & II, 31 Chemin J. Aiguier, 13402 Marseille Cedex 20, France
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