1
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Chen Y, Wang J, Zheng C, Liu Z. Cryo-Electron Microscopy in the Study of Antiviral Innate Immunity. Methods Mol Biol 2025; 2854:177-188. [PMID: 39192129 DOI: 10.1007/978-1-0716-4108-8_18] [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] [Indexed: 08/29/2024]
Abstract
Cryo-electron microscopy is a powerful methodology in structural biology and has been broadly used in high-resolution structure determination for challenging samples, which are not readily available for traditional techniques. In particular, the strength of super macro-complexes and the lack of a need for crystals for cryo-EM make this technique feasible for the structural study of complexes involved in antiviral innate immunity. This chapter presents detailed information and experimental procedures of Cryo-EM for determining the structures of the complexes using STING as an example. The procedures included a sample quality check, high-resolution data acquisition, and image processing for Cryo-EM 3D structure determination.
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Affiliation(s)
- Yan Chen
- School of Medicine, Shaoguan University, Shaoguan, Guangdong, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Jingyu Wang
- Distinct HealthCare Medical Center, Changsha Section, Shenzhen, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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2
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Parves MR, Solares MJ, Dearnaley WJ, Kelly DF. Elucidating structural variability in p53 conformers using combinatorial refinement strategies and molecular dynamics. Cancer Biol Ther 2024; 25:2290732. [PMID: 38073067 PMCID: PMC10732606 DOI: 10.1080/15384047.2023.2290732] [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: 09/12/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Low molecular weight proteins and protein assemblies can now be investigated using cryo-electron microscopy (EM) as a complement to traditional structural biology techniques. It is important, however, to not lose sight of the dynamic information inherent in macromolecules that give rise to their exquisite functionality. As computational methods continue to advance the field of biomedical imaging, so must strategies to resolve the minute details of disease-related entities. Here, we employed combinatorial modeling approaches to assess flexible properties among low molecular weight proteins (~100 kDa or less). Through a blend of rigid body refinement and simulated annealing, we determined new hidden conformations for wild type p53 monomer and dimer forms. Structures for both states converged to yield new conformers, each revealing good stereochemistry and dynamic information about the protein. Based on these insights, we identified fluid parts of p53 that complement the stable central core of the protein responsible for engaging DNA. Molecular dynamics simulations corroborated the modeling results and helped pinpoint the more flexible residues in wild type p53. Overall, the new computational methods may be used to shed light on other small protein features in a vast ensemble of structural data that cannot be easily delineated by other algorithms.
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Affiliation(s)
- Md Rimon Parves
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Biochemistry, Microbiology, and Molecular Biology Graduate Program, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Maria J. Solares
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
- Molecular, Cellular, and Integrative Biosciences Graduate Program, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - William J. Dearnaley
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
| | - Deborah F. Kelly
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
- Center for Structural Oncology, Pennsylvania State University, University Park, PA, USA
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3
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Pichkur EB, Vorovitch MF, Ivanova AL, Protopopova EV, Loktev VB, Osolodkin DI, Ishmukhametov AA, Samygina VR. The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution. Emerg Microbes Infect 2024; 13:2313849. [PMID: 38465849 DOI: 10.1080/22221751.2024.2313849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
Abstract
Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE cases are registered annually despite the availability of effective formaldehyde-inactivated full-virion vaccines due to insufficient vaccination coverage, as well as sporadic cases of vaccine breakthrough. The development of improved vaccines would benefit from the atomic resolution structure of the antigen. Here we report the refined single-particle cryo-electron microscopy (cryo-EM) structure of the inactivated mature TBEV vaccine strain Sofjin-Chumakov (Far-Eastern subtype) at a resolution of 3.0 Å. The increase of the resolution with respect to the previously published structures of TBEV strains Hypr and Kuutsalo-14 (European subtype) was reached due to improvement of the virus sample quality achieved by the optimized preparation methods. All the surface epitopes of TBEV were structurally conserved in the inactivated virions. ELISA studies with monoclonal antibodies supported the hypothesis of TBEV protein shell cross-linking upon inactivation with formaldehyde.
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Affiliation(s)
| | - Mikhail F Vorovitch
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Alla L Ivanova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
| | - Elena V Protopopova
- State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russian Federation
| | - Valery B Loktev
- State Research Center of Virology and Biotechnology "Vector", Novosibirsk, Russian Federation
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russian Federation
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4
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Moiseenko A, Zhang Y, Vorovitch MF, Ivanova AL, Liu Z, Osolodkin DI, Egorov AM, Ishmukhametov AA, Sokolova OS. Structural diversity of tick-borne encephalitis virus particles in the inactivated vaccine based on strain Sofjin. Emerg Microbes Infect 2024; 13:2290833. [PMID: 38073510 DOI: 10.1080/22221751.2023.2290833] [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: 10/16/2023] [Accepted: 11/29/2023] [Indexed: 03/12/2024]
Abstract
The main approach to preventing tick-borne encephalitis (TBE) is vaccination. Formaldehyde-inactivated TBE vaccines have a proven record of safety and efficiency but have never been characterized structurally with atomic resolution. We report a cryoelectron microscopy (cryo-EM) structure of the formaldehyde-inactivated TBE virus (TBEV) of Sofjin-Chumakov strain representing the Far-Eastern subtype. A 3.8 Å resolution reconstruction reveals the structural integrity of the envelope E proteins, specifically the E protein ectodomains. The comparative study shows a high structural similarity to the previously published structures of the TBEV European subtype strains Hypr and Kuutsalo-14. A fraction of inactivated virions exhibits asymmetric features including the deformations of the membrane profile. We propose that the heterogeneity is caused by inactivation and perform a local variability analysis on the small parts of the envelope protein shell to reveal membrane curvature features possibly induced by the inactivation. The results of this study will have implications for the design of novel vaccines against diseases caused by flaviviruses.
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Affiliation(s)
- Andrey Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yichen Zhang
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
| | - Mikhail F Vorovitch
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alla L Ivanova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
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5
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Sun H, Xia L, Li J, Zhang Y, Zhang G, Huang P, Wang X, Cui Y, Fang T, Fan P, Zhou Q, Chi X, Yu C. A novel bispecific antibody targeting two overlapping epitopes in RBD improves neutralizing potency and breadth against SARS-CoV-2. Emerg Microbes Infect 2024; 13:2373307. [PMID: 38953857 PMCID: PMC11249148 DOI: 10.1080/22221751.2024.2373307] [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: 03/11/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
SARS-CoV-2 has been evolving into a large number of variants, including the highly pathogenic Delta variant, and the currently prevalent Omicron subvariants with extensive evasion capability, which raises an urgent need to develop new broad-spectrum neutralizing antibodies. Herein, we engineer two IgG-(scFv)2 form bispecific antibodies with overlapping epitopes (bsAb1) or non-overlapping epitopes (bsAb2). Both bsAbs are significantly superior to the parental monoclonal antibodies in terms of their antigen-binding and virus-neutralizing activities against all tested circulating SARS-CoV-2 variants including currently dominant JN.1. The bsAb1 can efficiently neutralize all variants insensitive to parental monoclonal antibodies or the cocktail with IC50 lower than 20 ng/mL, even slightly better than bsAb2. Furthermore, the cryo-EM structures of bsAb1 in complex with the Omicron spike protein revealed that bsAb1 with overlapping epitopes effectively locked the S protein, which accounts for its conserved neutralization against Omicron variants. The bispecific antibody strategy engineered from overlapping epitopes provides a novel solution for dealing with viral immune evasion.
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Affiliation(s)
- Hancong Sun
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Lingyun Xia
- Center for Infectious Disease Research, Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Jianhua Li
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Yuanyuan Zhang
- Center for Infectious Disease Research, Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Guanying Zhang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Ping Huang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Xingxing Wang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Key Laboratory of Public Health Detection and Etiological Research of Zhejiang Province, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Yue Cui
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Ting Fang
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Pengfei Fan
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Qiang Zhou
- Center for Infectious Disease Research, Research Center for Industries of the Future, Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Institute of Biology, Westlake Institute for Advanced Study, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Xiangyang Chi
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
| | - Changming Yu
- Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, People’s Republic of China
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6
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Sangwung P, Ho JD, Siddall T, Lin J, Tomas A, Jones B, Sloop KW. Class B1 GPCRs: insights into multireceptor pharmacology for the treatment of metabolic disease. Am J Physiol Endocrinol Metab 2024; 327:E600-E615. [PMID: 38984948 DOI: 10.1152/ajpendo.00371.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 06/14/2024] [Accepted: 07/01/2024] [Indexed: 07/11/2024]
Abstract
The secretin-like, class B1 subfamily of seven transmembrane-spanning G protein-coupled receptors (GPCRs) consists of 15 members that coordinate important physiological processes. These receptors bind peptide ligands and use a distinct mechanism of activation that is driven by evolutionarily conserved structural features. For the class B1 receptors, the C-terminus of the cognate ligand is initially recognized by the receptor via an N-terminal extracellular domain that forms a hydrophobic ligand-binding groove. This binding enables the N-terminus of the ligand to engage deep into a large volume, open transmembrane pocket of the receptor. Importantly, the phylogenetic basis of this ligand-receptor activation mechanism has provided opportunities to engineer analogs of several class B1 ligands for therapeutic use. Among the most accepted of these are drugs targeting the glucagon-like peptide-1 (GLP-1) receptor for the treatment of type 2 diabetes and obesity. Recently, multifunctional agonists possessing activity at the GLP-1 receptor and the glucose-dependent insulinotropic polypeptide (GIP) receptor, such as tirzepatide, and others that also contain glucagon receptor activity, have been developed. In this article, we review members of the class B1 GPCR family with focus on receptors for GLP-1, GIP, and glucagon, including their signal transduction and receptor trafficking characteristics. The metabolic importance of these receptors is also highlighted, along with the benefit of polypharmacologic ligands. Furthermore, key structural features and comparative analyses of high-resolution cryogenic electron microscopy structures for these receptors in active-state complexes with either native ligands or multifunctional agonists are provided, supporting the pharmacological basis of such therapeutic agents.
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Affiliation(s)
- Panjamaporn Sangwung
- Molecular Pharmacology, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States
| | - Joseph D Ho
- Department of Structural Biology, Lilly Biotechnology Center, San Diego, California, United States
| | - Tessa Siddall
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Jerry Lin
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Ben Jones
- Section of Investigative Medicine, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Kyle W Sloop
- Diabetes, Obesity and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States
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7
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Souza Amado de Carvalho R, Rasel MSI, Khandelwal NK, Tomasiak TM. Cryo-EM reveals a phosphorylated R-domain envelops the NBD1 catalytic domain in an ABC transporter. Life Sci Alliance 2024; 7:e202402779. [PMID: 39209537 PMCID: PMC11361370 DOI: 10.26508/lsa.202402779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Many ATP-binding cassette transporters are regulated by phosphorylation on long and disordered loops which presents a challenge to visualize with structural methods. We have trapped an activated state of the regulatory domain (R-domain) of yeast cadmium factor 1 (Ycf1) by enzymatically enriching the phosphorylated state. A 3.23 Å cryo-EM structure reveals an R-domain structure with four phosphorylated residues and the position for the entire R-domain. The structure reveals key R-domain interactions including a bridging interaction between NBD1 and NBD2 and an interaction with the R-insertion, another regulatory region. We scanned these interactions by systematically replacing segments along the entire R-domain with scrambled combinations of alanine, glycine, and glutamine and probing function under cellular conditions that require the Ycf1 function. We find a close match with these interactions and interacting regions on our R-domain structure that points to the importance of most well-structured segments for function. We propose a model where the R-domain stabilizes a transport-competent state upon phosphorylation by enveloping NBD1 entirely.
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Affiliation(s)
| | - Md Shamiul Islam Rasel
- https://ror.org/03m2x1q45 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Nitesh K Khandelwal
- https://ror.org/03m2x1q45 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Thomas M Tomasiak
- https://ror.org/03m2x1q45 Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
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8
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Mark E, Ramos PC, Kayser F, Höckendorff J, Dohmen RJ, Wendler P. Structural roles of Ump1 and β-subunit propeptides in proteasome biogenesis. Life Sci Alliance 2024; 7:e202402865. [PMID: 39260885 PMCID: PMC11391049 DOI: 10.26508/lsa.202402865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024] Open
Abstract
The yeast pre1-1(β4-S142F) mutant accumulates late 20S proteasome core particle precursor complexes (late-PCs). We report a 2.1 Å cryo-EM structure of this intermediate with full-length Ump1 trapped inside, and Pba1-Pba2 attached to the α-ring surfaces. The structure discloses intimate interactions of Ump1 with β2- and β5-propeptides, which together fill most of the antechambers between the α- and β-rings. The β5-propeptide is unprocessed and separates Ump1 from β6 and β7. The β2-propeptide is disconnected from the subunit by autocatalytic processing and localizes between Ump1 and β3. A comparison of different proteasome maturation states reveals that maturation goes along with global conformational changes in the rings, initiated by structuring of the proteolytic sites and their autocatalytic activation. In the pre1-1 strain, β2 is activated first enabling processing of β1-, β6-, and β7-propeptides. Subsequent maturation of β5 and β1 precedes degradation of Ump1, tightening of the complex, and finally release of Pba1-Pba2.
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Affiliation(s)
- Eric Mark
- https://ror.org/03bnmw459 Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany
| | - Paula C Ramos
- https://ror.org/00rcxh774 Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Fleur Kayser
- https://ror.org/03bnmw459 Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany
| | - Jörg Höckendorff
- https://ror.org/00rcxh774 Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - R Jürgen Dohmen
- https://ror.org/00rcxh774 Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Petra Wendler
- https://ror.org/03bnmw459 Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany
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9
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Sehgal E, Wohlenberg C, Soukup EM, Viscardi MJ, Serrão VHB, Arribere JA. High-resolution reconstruction of a C. elegans ribosome sheds light on evolutionary dynamics and tissue specificity. RNA (NEW YORK, N.Y.) 2024; 30:1513-1528. [PMID: 39209556 DOI: 10.1261/rna.080103.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Caenorhabditis elegans is an important model organism for human health and disease, with foundational contributions to the understanding of gene expression and tissue patterning in animals. An invaluable tool in modern gene expression research is the presence of a high-resolution ribosome structure, though no such structure exists for C. elegans Here, we present a high-resolution single-particle cryogenic electron microscopy (cryo-EM) reconstruction and molecular model of a C. elegans ribosome, revealing a significantly streamlined animal ribosome. Many facets of ribosome structure are conserved in C. elegans, including overall ribosomal architecture and the mechanism of cycloheximide, whereas other facets, such as expansion segments and eL28, are rapidly evolving. We identify uL5 and uL23 as two instances of tissue-specific ribosomal protein paralog expression conserved in Caenorhabditis, suggesting that C. elegans ribosomes vary across tissues. The C. elegans ribosome structure will provide a basis for future structural, biochemical, and genetic studies of translation in this important animal system.
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Affiliation(s)
- Enisha Sehgal
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Chloe Wohlenberg
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Evan M Soukup
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Marcus J Viscardi
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Vitor Hugo Balasco Serrão
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
- Biomolecular Cryoelectron Microscopy Facility, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Joshua A Arribere
- Department of MCD Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
- RNA Center, University of California at Santa Cruz, Santa Cruz, California 95064, USA
- Genomics Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA
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10
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Guo CJ, Zhang Z, Lu JL, Zhong J, Wu YF, Guo SY, Liu JL. Structural Basis of Bifunctional CTP/dCTP Synthase. J Mol Biol 2024; 436:168750. [PMID: 39173734 DOI: 10.1016/j.jmb.2024.168750] [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: 04/29/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 08/24/2024]
Abstract
The final step in the de novo synthesis of cytidine 5'-triphosphate (CTP) is catalyzed by CTP synthase (CTPS), which can form cytoophidia in all three domains of life. Recently, we have discovered that CTPS binds to ribonucleotides (NTPs) to form filaments, and have successfully resolved the structures of Drosophila melanogaster CTPS bound with NTPs. Previous biochemical studies have shown that CTPS can bind to deoxyribonucleotides (dNTPs) to produce 2'-deoxycytidine-5'-triphosphate (dCTP). However, the structural basis of CTPS binding to dNTPs is still unclear. In this study, we find that Drosophila CTPS can also form filaments with dNTPs. Using cryo-electron microscopy, we are able to resolve the structure of Drosophila melanogaster CTPS bound to dNTPs with a resolution of up to 2.7 Å. By combining these structural findings with biochemical analysis, we compare the binding and reaction characteristics of NTPs and dNTPs with CTPS. Our results indicate that the same enzyme can act bifunctionally as CTP/dCTP synthase in vitro, and provide a structural basis for these activities.
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Affiliation(s)
- Chen-Jun Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zherong Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Jia-Li Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiale Zhong
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu-Fen Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shu-Ying Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom.
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11
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Wang T, Li Z, Xu K, Huang W, Huang G, Zhang QC, Yan N. CryoSeek: A strategy for bioentity discovery using cryoelectron microscopy. Proc Natl Acad Sci U S A 2024; 121:e2417046121. [PMID: 39382995 DOI: 10.1073/pnas.2417046121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Accepted: 09/10/2024] [Indexed: 10/11/2024] Open
Abstract
Structural biology is experiencing a paradigm shift from targeted structural determination to structure-guided discovery of previously uncharacterized bioentities. We employed cryoelectron microscopy (cryo-EM) to analyze filtered water samples collected from the Tsinghua Lotus Pond. Here, we report the structural determination and characterization of two highly similar helical fibrils, named TLP-1a and TLP-1b, each approximately 8 nm in diameter with a 15-Å wide tunnel. These fibrils are assembled from a similar protein protomer, whose structure was conveniently automodeled in CryoNet. The protomer structure does not match any available experimental structures, but shares the same fold as many predicted structures of unknown functions. The amino-terminal β strand of protomer n + 4 inserts into a cleft in protomer n to complete an immunoglobulin (Ig)-like domain. This packing mechanism, known as donor-strand exchange (DSE), has been observed in several bacterial pilus assemblies, wherein the donor is protomer n + 1. Despite distinct shape and thickness, this reminiscence suggests that TLP-1a/b fibrils may represent uncharacterized bacterial pili. Our study demonstrates an emerging paradigm in structural biology, where high-resolution structural determination precedes and drives the identification and characterization of completely unknown objects.
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Affiliation(s)
- Tongtong Wang
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhangqiang Li
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kui Xu
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenze Huang
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaoxingyu Huang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang, China
| | - Qiangfeng Cliff Zhang
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Nieng Yan
- Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation, Shenzhen 518107, Guangdong, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong, China
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12
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Jeong J, Park J, Young Mo G, Shin J, Cho Y. Structural Basis for the Recognition of GPRC5D by Talquetamab, a Bispecific Antibody for Multiple Myeloma. J Mol Biol 2024; 436:168748. [PMID: 39181182 DOI: 10.1016/j.jmb.2024.168748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
Multiple myeloma (MM) is a complex hematological malignancy characterized by abnormal antibody production from plasma cells. Despite advances in the treatment, many patients experience disease relapse or become refractory to treatment. G-protein-coupled receptor class C group 5 member D (GPRC5D), an orphan GPCR predominantly expressed in MM cells, is emerging as a promising target for MM immunotherapy. Talquetamab, a Food and Drug Administration-approved T-cell-directing bispecific antibody developed for treatment of MM, targets GPRC5D. Here, we elucidate the structure of GPRC5D complexed with the Fab fragment of talquetamab, using cryo-electron microscopy, providing the basis for recognition of GPRC5D by the bispecific antibody. GPRC5D forms a symmetric homodimer with the interface between transmembrane helix (TM) 4 of one protomer and TM4/5 of the other protomer. A single talquetamab Fab interacts with the GPRC5D dimer with its orientation toward the dimer interface. All six complementarity-determining regions of talquetamab engage with extracellular loops and TM3/5/7. In particular, the side-chain of an arginine residue from the antibody penetrates into a shallow pocket on the extracellular surface of GPRC5D. The structure offers insights for optimizing antibody design against GPRC5D for relapsed or refractory MM therapy.
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Affiliation(s)
- Jihong Jeong
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Junhyeon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Geun Young Mo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Jinwoo Shin
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea
| | - Yunje Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbook 37673, South Korea; Institute of Convergence Science, Yonsei University, Seoul 166-20, South Korea.
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13
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Larsen ST, Dannersø JK, Nielsen CJF, Poulsen LR, Palmgren M, Nissen P. Conserved N-terminal Regulation of the ACA8 Calcium Pump with Two Calmodulin Binding Sites. J Mol Biol 2024; 436:168747. [PMID: 39168442 DOI: 10.1016/j.jmb.2024.168747] [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: 12/05/2023] [Revised: 07/30/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Abstract
The autoinhibited plasma membrane calcium ATPase ACA8 from A. thaliana has an N-terminal autoinhibitory domain. Binding of calcium-loaded calmodulin at two sites located at residues 42-62 and 74-96 relieves autoinhibition of ACA8 activity. Through activity studies and a yeast complementation assay we investigated wild-type (WT) and N-terminally truncated ACA8 constructs (Δ20, Δ30, Δ35, Δ37, Δ40, Δ74 and Δ100) to explore the role of conserved motifs in the N-terminal segment preceding the calmodulin binding sites. Furthermore, we purified WT, Δ20- and Δ100-ACA8, tested activity in vitro and performed structural studies of purified Δ20-ACA8 stabilized in a lipid nanodisc to explore the mechanism of autoinhibition. We show that an N-terminal segment between residues 20 and 35 including conserved Phe32, upstream of the calmodulin binding sites, is important for autoinhibition and the activation by calmodulin. Cryo-EM structure determination at 3.3 Å resolution of a beryllium fluoride inhibited E2 form, and at low resolution for an E1 state combined with AlphaFold prediction provide a model for autoinhibition, consistent with the mutational studies.
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Affiliation(s)
- Sigrid Thirup Larsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus, Denmark
| | - Josephine Karlsen Dannersø
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus, Denmark
| | - Christine Juul Fælled Nielsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus, Denmark
| | - Lisbeth Rosager Poulsen
- Department of Plant and Environmental Sciences, Copenhagen University, Thorvaldsensvej 40, DK-1871, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, Copenhagen University, Thorvaldsensvej 40, DK-1871, Denmark
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Aarhus, Denmark.
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14
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Wang M, Gao Y, Shen C, Yang W, Peng Q, Cheng J, Shen HM, Yang Y, Gao GF, Shi Y. A human monoclonal antibody targeting the monomeric N6 neuraminidase confers protection against avian H5N6 influenza virus infection. Nat Commun 2024; 15:8871. [PMID: 39402031 DOI: 10.1038/s41467-024-53301-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 10/09/2024] [Indexed: 10/17/2024] Open
Abstract
The influenza neuraminidase (NA) is a potential target for the development of a next-generation influenza vaccine, but its antigenicity is not well understood. Here, we isolate an anti-N6 human monoclonal antibody, named 18_14D, from an H5N6 avian influenza virus (AIV) infected patient. The antibody weakly inhibits enzymatic activity but confers protection in female mice, mainly via ADCC function. The cryo-EM structure shows that 18_14D binds to a unique epitope on the lateral surface of the N6 tetramer, preventing the formation of tightly closed NA tetramers. These findings contribute to the molecular understanding of protective immune responses to NA of AIVs in humans and open an avenue for the rational design of NA-based vaccines.
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Affiliation(s)
- Min Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China
| | - Yuan Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Chenguang Shen
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Southern Medical University, Guangzhou, China
| | - Wei Yang
- Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Jinlong Cheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Han-Ming Shen
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China.
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
- Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
- Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China.
- Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
- Health Science Center, Ningbo University, Ningbo, China.
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15
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Ko YH, Lokareddy RK, Doll SG, Yeggoni DP, Girdhar A, Mawn I, Klim JR, Rizvi NF, Meyers R, Gillilan RE, Guo L, Cingolani G. Single Acetylation-mimetic Mutation in TDP-43 Nuclear Localization Signal Disrupts Importin α1/β Signaling. J Mol Biol 2024; 436:168751. [PMID: 39181183 PMCID: PMC11443512 DOI: 10.1016/j.jmb.2024.168751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/19/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Cytoplasmic aggregation of the TAR-DNA binding protein of 43 kDa (TDP-43) is the hallmark of sporadic amyotrophic lateral sclerosis (ALS). Most ALS patients with TDP-43 aggregates in neurons and glia do not have mutations in the TDP-43 gene but contain aberrantly post-translationally modified TDP-43. Here, we found that a single acetylation-mimetic mutation (K82Q) near the TDP-43 minor Nuclear Localization Signal (NLS) box, which mimics a post-translational modification identified in an ALS patient, can lead to TDP-43 mislocalization to the cytoplasm and irreversible aggregation. We demonstrate that the acetylation mimetic disrupts binding to importins, halting nuclear import and preventing importin α1/β anti-aggregation activity. We propose that perturbations near the NLS are an additional mechanism by which a cellular insult other than a genetically inherited mutation leads to TDP-43 aggregation and loss of function. Our findings are relevant to deciphering the molecular etiology of sporadic ALS.
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Affiliation(s)
- Ying-Hui Ko
- Dept. of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Ravi K Lokareddy
- Dept. of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA
| | - Steven G Doll
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; Dept. of Neurology, Johns Hopkins University School of Medicine, 1800 Orleans St Baltimore, Baltimore, MD 21287, USA
| | - Daniel P Yeggoni
- Dept. of Cell Biology, UConn Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Amandeep Girdhar
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Ian Mawn
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | | | | | | | - Richard E Gillilan
- Macromolecular Diffraction Facility, Cornell High Energy Synchrotron Source (MacCHESS), Cornell University, 161 Synchrotron Drive, Ithaca, NY 14853, USA
| | - Lin Guo
- Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.
| | - Gino Cingolani
- Dept. of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, 1825 University Blvd, Birmingham, AL 35294, USA.
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16
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Liu R, Sun J, Li LF, Cheng Y, Li M, Fu L, Li S, Peng G, Wang Y, Liu S, Qu X, Ran J, Li X, Pang E, Qiu HJ, Wang Y, Qi J, Wang H, Gao GF. Structural basis for difunctional mechanism of m-AMSA against African swine fever virus pP1192R. Nucleic Acids Res 2024; 52:11301-11316. [PMID: 39166497 PMCID: PMC11472052 DOI: 10.1093/nar/gkae703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/24/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024] Open
Abstract
The African swine fever virus (ASFV) type II topoisomerase (Topo II), pP1192R, is the only known Topo II expressed by mammalian viruses and is essential for ASFV replication in the host cytoplasm. Herein, we report the structures of pP1192R in various enzymatic stages using both X-ray crystallography and single-particle cryo-electron microscopy. Our data structurally define the pP1192R-modulated DNA topology changes. By presenting the A2+-like metal ion at the pre-cleavage site, the pP1192R-DNA-m-AMSA complex structure provides support for the classical two-metal mechanism in Topo II-mediated DNA cleavage and a better explanation for nucleophile formation. The unique inhibitor selectivity of pP1192R and the difunctional mechanism of pP1192R inhibition by m-AMSA highlight the specificity of viral Topo II in the poison binding site. Altogether, this study provides the information applicable to the development of a pP1192R-targeting anti-ASFV strategy.
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Affiliation(s)
- Ruili Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450046, China
- Beijing Life Science Academy, Beijing 102200, China
| | - Junqing Sun
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, Shanxi Province 030801, China
| | - Lian-Feng Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Yingxian Cheng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan Province 450046, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meilin Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Lifeng Fu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Su Li
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Guorui Peng
- China/WOAH Reference Laboratory for Classical Swine Fever, China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Yanjin Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Sheng Liu
- SUSTech Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiao Qu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaqi Ran
- Department of Biological Sciences, School of life Science, Liaoning University, Shenyang, Liaoning Province 110030, China
| | - Xiaomei Li
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, Shanxi Province 030032, China
| | - Erqi Pang
- Shanxi Academy of Advanced Research and Innovation, Taiyuan, Shanxi Province 030032, China
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High-Containment Facilities for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin Province 150069, China
| | - Yanli Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Han Wang
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100091, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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17
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Saju A, Chen PP, Weng TH, Tsai SY, Tanaka A, Tseng YT, Chang CC, Wang CH, Shimamoto Y, Hsia KC. HURP binding to the vinca domain of β-tubulin accounts for cancer drug resistance. Nat Commun 2024; 15:8844. [PMID: 39397030 PMCID: PMC11471760 DOI: 10.1038/s41467-024-53139-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 09/30/2024] [Indexed: 10/15/2024] Open
Abstract
Vinca alkaloids, a class of tubulin-binding agent, are widely used in treating cancer, yet the emerging resistance compromises their efficacy. Hepatoma up-regulated protein (HURP), a microtubule-associated protein displaying heightened expression across various cancer types, reduces cancer cells' sensitivity to vinca-alkaloid drugs upon overexpression. However, the molecular basis behind this drug resistance remains unknown. Here we discover a tubulin-binding domain within HURP, and establish its role in regulating microtubule growth. Cryo-EM analysis reveals interactions between HURP's tubulin-binding domain and the vinca domain on β-tubulin -- the site targeted by vinca alkaloid drugs. Importantly, HURP competes directly with vinorelbine, a vinca alkaloid-based chemotherapeutic agent, countering microtubule growth defects caused by vinorelbine both in vitro and in vivo. Our findings elucidate a mechanism driving drug resistance in HURP-overexpressing cancer cells and emphasize HURP tubulin-binding domain's role in mitotic spindle assembly. This underscores its potential as a therapeutic target to improve cancer treatment.
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Affiliation(s)
- Athira Saju
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program and National Defense Medical Center, Taipei, Taiwan
| | - Po-Pang Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Institute of Biochemistry and Molecular biology, College of Life Sciences, National Yang-Ming Chiao-Tung University, Hsinchu, Taiwan
| | - Tzu-Han Weng
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Su-Yi Tsai
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Akihiro Tanaka
- Department of Chromosome Science, National Institute of Genetics, Shizuoka, Japan
| | - Yu-Ting Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Chia Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yuta Shimamoto
- Department of Chromosome Science, National Institute of Genetics, Shizuoka, Japan
| | - Kuo-Chiang Hsia
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
- Molecular and Cell Biology, Taiwan International Graduate Program and National Defense Medical Center, Taipei, Taiwan.
- Institute of Biochemistry and Molecular biology, College of Life Sciences, National Yang-Ming Chiao-Tung University, Hsinchu, Taiwan.
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18
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Liao F, Yu G, Zhang C, Liu Z, Li X, He Q, Yin H, Liu X, Li Z, Zhang H. Structural basis for the concerted antiphage activity in the SIR2-HerA system. Nucleic Acids Res 2024; 52:11336-11348. [PMID: 39217465 PMCID: PMC11472057 DOI: 10.1093/nar/gkae750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 08/07/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Recently, a novel two-gene bacterial defense system against phages, encoding a SIR2 NADase and a HerA ATPase/helicase, has been identified. However, the molecular mechanism of the bacterial SIR2-HerA immune system remains unclear. Here, we determine the cryo-EM structures of SIR2, HerA and their complex from Paenibacillus sp. 453MF in different functional states. The SIR2 proteins oligomerize into a dodecameric ring-shaped structure consisting of two layers of interlocked hexamers, in which each subunit exhibits an auto-inhibited conformation. Distinct from the canonical AAA+ proteins, HerA hexamer alone in this antiphage system adopts a split spiral arrangement, which is stabilized by a unique C-terminal extension. SIR2 and HerA proteins assemble into a ∼1.1 MDa torch-shaped complex to fight against phage infection. Importantly, disruption of the interactions between SIR2 and HerA largely abolishes the antiphage activity. Interestingly, binding alters the oligomer state of SIR2, switching from a dodecamer to a tetradecamer state. The formation of the SIR2-HerA binary complex activates NADase and nuclease activities in SIR2 and ATPase and helicase activities in HerA. Together, our study not only provides a structural basis for the functional communications between SIR2 and HerA proteins, but also unravels a novel concerted antiviral mechanism through NAD+ degradation, ATP hydrolysis, and DNA cleavage.
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Affiliation(s)
- Fumeng Liao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Guimei Yu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhikun Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xuzichao Li
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Qiuqiu He
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hang Yin
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Heng Zhang
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, International Joint Laboratory of Ocular Diseases (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Cellular Homeostasis and Disease, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
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19
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Dong X, Sheng K, Gebert LR, Aiyer S, MacRae I, Lyumkis D, Williamson J. Assembly of the bacterial ribosome with circularly permuted rRNA. Nucleic Acids Res 2024; 52:11254-11265. [PMID: 39036963 PMCID: PMC11472049 DOI: 10.1093/nar/gkae636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024] Open
Abstract
Co-transcriptional assembly is an integral feature of the formation of RNA-protein complexes that mediate translation. For ribosome synthesis, prior studies have indicated that the strict order of transcription of rRNA domains may not be obligatory during bacterial ribosome biogenesis, since a series of circularly permuted rRNAs are viable. In this work, we report the structural insights into assembly of the bacterial ribosome large subunit (LSU) based on cryo-EM density maps of intermediates that accumulate during in vitro ribosome synthesis using a set of circularly permuted (CiPer) rRNAs. The observed ensemble of 23 resolved ribosome large subunit intermediates reveals conserved assembly routes with an underlying hierarchy among cooperative assembly blocks. There are intricate interdependencies for the formation of key structural rRNA helices revealed from the circular permutation of rRNA. While the order of domain synthesis is not obligatory, the order of domain association does appear to proceed with a particular order, likely due to the strong evolutionary pressure on efficient ribosome synthesis. This work reinforces the robustness of the known assembly hierarchy of the bacterial large ribosomal subunit and offers a coherent view of how efficient assembly of CiPer rRNAs can be understood in that context.
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MESH Headings
- RNA, Ribosomal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- Cryoelectron Microscopy
- Nucleic Acid Conformation
- Ribosome Subunits, Large, Bacterial/metabolism
- Ribosome Subunits, Large, Bacterial/chemistry
- Ribosome Subunits, Large, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- Models, Molecular
- Ribosomes/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
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Affiliation(s)
- Xiyu Dong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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20
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Zhou F, Zhang Y, Zhu Y, Zhou Q, Shi Y, Hu Q. Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase. SCIENCE ADVANCES 2024; 10:eado4880. [PMID: 39383219 PMCID: PMC11463273 DOI: 10.1126/sciadv.ado4880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 09/04/2024] [Indexed: 10/11/2024]
Abstract
Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic organization of ACCs is largely unknown. Here, we determined the cryo-electron microscopy (EM) structure of human ACC1 in its inactive state, which forms a unique filament structure and is in complex with acetyl-CoA. We also determined the cryo-EM structure of human ACC1 activated by dephosphorylation and citrate treatment, at a resolution of 2.55 Å. Notably, the covalently linked biotin binds to a site that is distant from the acetyl-CoA binding site when acetyl-CoA is absent, suggesting a potential coordination between biotin binding and acetyl-CoA binding. These findings provide insights into the structural dynamics and regulatory mechanisms of human ACCs.
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Affiliation(s)
- Fayang Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
| | - Yuanyuan Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yuyao Zhu
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
| | - Qiang Zhou
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yigong Shi
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Qi Hu
- School of Life Sciences, Westlake University, Hangzhou 310024, China
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310058, China
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21
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Anso I, Zouhir S, Sana TG, Krasteva PV. Structural basis for synthase activation and cellulose modification in the E. coli Type II Bcs secretion system. Nat Commun 2024; 15:8799. [PMID: 39394223 PMCID: PMC11470070 DOI: 10.1038/s41467-024-53113-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 09/24/2024] [Indexed: 10/13/2024] Open
Abstract
Bacterial cellulosic polymers constitute a prevalent class of biofilm matrix exopolysaccharides that are synthesized by several types of bacterial cellulose secretion (Bcs) systems, which include conserved cyclic diguanylate (c-di-GMP)-dependent cellulose synthase modules together with diverse accessory subunits. In E. coli, the biogenesis of phosphoethanolamine (pEtN)-modified cellulose relies on the BcsRQABEFG macrocomplex, encompassing inner-membrane and cytosolic subunits, and an outer membrane porin, BcsC. Here, we use cryogenic electron microscopy to shed light on the molecular mechanisms of BcsA-dependent recruitment and stabilization of a trimeric BcsG pEtN-transferase for polymer modification, and a dimeric BcsF-dependent recruitment of an otherwise cytosolic BcsE2R2Q2 regulatory complex. We further demonstrate that BcsE, a secondary c-di-GMP sensor, can remain dinucleotide-bound and retain the essential-for-secretion BcsRQ partners onto the synthase even in the absence of direct c-di-GMP-synthase complexation, likely lowering the threshold for c-di-GMP-dependent synthase activation. Such activation-by-proxy mechanism could allow Bcs secretion system activity even in the absence of substantial intracellular c-di-GMP increase, and is reminiscent of other widespread synthase-dependent polysaccharide secretion systems where dinucleotide sensing and/or synthase stabilization are carried out by key co-polymerase subunits.
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Affiliation(s)
- Itxaso Anso
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600, Pessac, France
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac, F-33600, France
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
| | - Samira Zouhir
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600, Pessac, France
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac, F-33600, France
- Laboratoire de Biologie et Pharmacologie Appliquée (LBPA), CNRS UMR8113, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Thibault Géry Sana
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600, Pessac, France
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac, F-33600, France
| | - Petya Violinova Krasteva
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600, Pessac, France.
- Structural Biology of Biofilms Group, European Institute of Chemistry and Biology (IECB), 2 Rue Robert Escarpit, Pessac, F-33600, France.
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22
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Ai H, Tong Z, Deng Z, Shi Q, Tao S, Sun G, Liang J, Sun M, Wu X, Zheng Q, Liang L, Yin H, Li JB, Gao S, Tian C, Liu L, Pan M. Mechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168. Nat Chem Biol 2024:10.1038/s41589-024-01750-x. [PMID: 39394267 DOI: 10.1038/s41589-024-01750-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 09/14/2024] [Indexed: 10/13/2024]
Abstract
The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent K13 and K15 (K13/15) sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to site-specifically ubiquitinate H2A K13/15 has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c~Ub (ubiquitin) in complex with nucleosomes. Here we developed chemical strategies and determined the cryo-electron microscopy structures of the RNF168-UbcH5c~Ub-nucleosome complex captured in transient H2A K13/15 monoubiquitination and adjacent dual monoubiquitination reactions, providing a 'helix-anchoring' mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the 'compass-binding' mode of dimeric E3 ligases. Our work not only provides structural snapshots of H2A K13/15 site-specific monoubiquitination and adjacent dual monoubiquitination but also offers a near-atomic-resolution structural framework for understanding pathogenic amino acid substitutions and physiological modifications of RNF168.
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Affiliation(s)
- Huasong Ai
- Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zebin Tong
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zhiheng Deng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qiang Shi
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Shixian Tao
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Gaoge Sun
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiawei Liang
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Maoshen Sun
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xiangwei Wu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qingyun Zheng
- Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lujun Liang
- Center for Bioanalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, China
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Shuai Gao
- Department of Urology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Changlin Tian
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Lei Liu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China.
| | - Man Pan
- Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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23
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Wang P, Christianson BM, Ugurlar D, Mao R, Zhang Y, Liu ZK, Zhang YY, Gardner AM, Gao J, Zhang YZ, Liu LN. Architectures of photosynthetic RC-LH1 supercomplexes from Rhodobacter blasticus. SCIENCE ADVANCES 2024; 10:eadp6678. [PMID: 39383221 PMCID: PMC11463270 DOI: 10.1126/sciadv.adp6678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 09/06/2024] [Indexed: 10/11/2024]
Abstract
The reaction center-light-harvesting complex 1 (RC-LH1) plays an essential role in the primary reactions of bacterial photosynthesis. Here, we present high-resolution structures of native monomeric and dimeric RC-LH1 supercomplexes from Rhodobacter (Rba.) blasticus using cryo-electron microscopy. The RC-LH1 monomer is composed of an RC encircled by an open LH1 ring comprising 15 αβ heterodimers and a PufX transmembrane polypeptide. In the RC-LH1 dimer, two crossing PufX polypeptides mediate dimerization. Unlike Rhodabacter sphaeroides counterpart, Rba. blasticus RC-LH1 dimer has a less bent conformation, lacks the PufY subunit near the LH1 opening, and includes two extra LH1 αβ subunits, forming a more enclosed S-shaped LH1 ring. Spectroscopic assays reveal that these unique structural features are accompanied by changes in the kinetics of quinone/quinol trafficking between RC-LH1 and cytochrome bc1. Our findings reveal the assembly principles and structural variability of photosynthetic RC-LH1 supercomplexes, highlighting diverse strategies used by phototrophic bacteria to optimize light-harvesting and electron transfer in competitive environments.
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Affiliation(s)
- Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bern M. Christianson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Deniz Ugurlar
- Thermo Fisher Scientific, Life Sciences EMEA, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Ruichao Mao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yi Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ze-Kun Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ying-Yue Zhang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - Adrian M. Gardner
- Department of Chemistry, Stephenson Institute of Renewable Energy, and Early Career Laser Laboratory, University of Liverpool, L69 7ZF Liverpool, UK
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lu-Ning Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, L69 7ZB Liverpool, United Kingdom
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24
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Wang Y, Wang C, Guan Z, Cao J, Xu J, Wang S, Cui Y, Wang Q, Chen Y, Yin Y, Zhang D, Liu H, Sun M, Jin S, Tao P, Zou T. DNA methylation activates retron Ec86 filaments for antiphage defense. Cell Rep 2024; 43:114857. [PMID: 39395169 DOI: 10.1016/j.celrep.2024.114857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/08/2024] [Accepted: 09/25/2024] [Indexed: 10/14/2024] Open
Abstract
Retrons are a class of multigene antiphage defense systems typically consisting of a retron reverse transcriptase, a non-coding RNA, and a cognate effector. Although triggers for several retron systems have been discovered recently, the complete mechanism by which these systems detect invading phages and mediate defense remains unclear. Here, we focus on the retron Ec86 defense system, elucidating its modes of activation and mechanisms of action. We identified a phage-encoded DNA cytosine methyltransferase (Dcm) as a trigger of the Ec86 system and demonstrated that Ec86 is activated upon multicopy single-stranded DNA (msDNA) methylation. We further elucidated the structure of a tripartite retron Ec86-effector filament assembly that is primed for activation by Dcm and capable of hydrolyzing nicotinamide adenine dinucleotide (NAD+). These findings provide insights into the retron Ec86 defense mechanism and underscore an emerging theme of antiphage defense through supramolecular complex assemblies.
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Affiliation(s)
- Yanjing Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chen Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Cao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia Xu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangshuang Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongqing Cui
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yibei Chen
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongqi Yin
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Sun
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Pan Tao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
| | - Tingting Zou
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.
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25
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Crowe C, Nakasone MA, Chandler S, Craigon C, Sathe G, Tatham MH, Makukhin N, Hay RT, Ciulli A. Mechanism of degrader-targeted protein ubiquitinability. SCIENCE ADVANCES 2024; 10:eado6492. [PMID: 39392888 PMCID: PMC11468923 DOI: 10.1126/sciadv.ado6492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 09/09/2024] [Indexed: 10/13/2024]
Abstract
Small-molecule degraders of disease-driving proteins offer a clinically proven modality with enhanced therapeutic efficacy and potential to tackle previously undrugged targets. Stable and long-lived degrader-mediated ternary complexes drive fast and profound target degradation; however, the mechanisms by which they affect target ubiquitination remain elusive. Here, we show cryo-EM structures of the VHL Cullin 2 RING E3 ligase with the degrader MZ1 directing target protein Brd4BD2 toward UBE2R1-ubiquitin, and Lys456 at optimal positioning for nucleophilic attack. In vitro ubiquitination and mass spectrometry illuminate a patch of favorably ubiquitinable lysines on one face of Brd4BD2, with cellular degradation and ubiquitinomics confirming the importance of Lys456 and nearby Lys368/Lys445, identifying the "ubiquitination zone." Our results demonstrate the proficiency of MZ1 in positioning the substrate for catalysis, the favorability of Brd4BD2 for ubiquitination by UBE2R1, and the flexibility of CRL2 for capturing suboptimal lysines. We propose a model for ubiquitinability of degrader-recruited targets, providing a mechanistic blueprint for further rational drug design.
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Affiliation(s)
- Charlotte Crowe
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Mark A. Nakasone
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Sarah Chandler
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Conner Craigon
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Gajanan Sathe
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Michael H. Tatham
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Ronald T. Hay
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
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26
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Kuhm T, Taisne C, de Agrela Pinto C, Gross L, Giannopoulou EA, Huber ST, Pardon E, Steyaert J, Tans SJ, Jakobi AJ. Structural basis of antimicrobial membrane coat assembly by human GBP1. Nat Struct Mol Biol 2024:10.1038/s41594-024-01400-9. [PMID: 39394410 DOI: 10.1038/s41594-024-01400-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 09/05/2024] [Indexed: 10/13/2024]
Abstract
Guanylate-binding proteins (GBPs) are interferon-inducible guanosine triphosphate hydrolases (GTPases) mediating host defense against intracellular pathogens. Their antimicrobial activity hinges on their ability to self-associate and coat pathogen-associated compartments or cytosolic bacteria. Coat formation depends on GTPase activity but how nucleotide binding and hydrolysis prime coat formation remains unclear. Here, we report the cryo-electron microscopy structure of the full-length human GBP1 dimer in its guanine nucleotide-bound state and describe the molecular ultrastructure of the GBP1 coat on liposomes and bacterial lipopolysaccharide membranes. Conformational changes of the middle and GTPase effector domains expose the isoprenylated C terminus for membrane association. The α-helical middle domains form a parallel, crossover arrangement essential for coat formation and position the extended effector domain for intercalation into the lipopolysaccharide layer of gram-negative membranes. Nucleotide binding and hydrolysis create oligomeric scaffolds with contractile abilities that promote membrane extrusion and fragmentation. Our data offer a structural and mechanistic framework for understanding GBP1 effector functions in intracellular immunity.
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Affiliation(s)
- Tanja Kuhm
- Department of Bionanoscience, Kavli Insitute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Clémence Taisne
- Department of Bionanoscience, Kavli Insitute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cecilia de Agrela Pinto
- Department of Bionanoscience, Kavli Insitute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Evdokia A Giannopoulou
- Department of Bionanoscience, Kavli Insitute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Stefan T Huber
- Department of Bionanoscience, Kavli Insitute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Els Pardon
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sander J Tans
- Department of Bionanoscience, Kavli Insitute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- AMOLF, Amsterdam, The Netherlands
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Insitute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
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27
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Fernández I, Bontems F, Brun D, Coquin Y, Goverde CA, Correia BE, Gessain A, Buseyne F, Rey FA, Backovic M. Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses. SCIENCE ADVANCES 2024; 10:eado7035. [PMID: 39392890 PMCID: PMC11468914 DOI: 10.1126/sciadv.ado7035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 09/06/2024] [Indexed: 10/13/2024]
Abstract
Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures of retroviral Envs are those from human and simian immunodeficiency viruses from the subfamily of orthoretroviruses, which are only distantly related to the FVs. We report the cryo-electron microscopy structures of the FV Env ectodomain in the pre- and post-fusion states, which unexpectedly demonstrate structural similarity with the fusion protein (F) of paramyxo- and pneumoviruses, implying an evolutionary link between the viral fusogens. We describe the structural features that are unique to the FV Env and propose a mechanistic model for its conformational change, highlighting how the interplay of its structural elements could drive membrane fusion and viral entry. The structural knowledge on the FV Env now provides a framework for functional investigations, which can benefit the design of FV Env variants with improved features for use as gene therapy vectors.
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Affiliation(s)
- Ignacio Fernández
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France
| | - François Bontems
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris Saclay, 91190 Gif-sur-Yvette, France
| | - Delphine Brun
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France
| | - Youna Coquin
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Casper A. Goverde
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Bruno E. Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Florence Buseyne
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité d’Epidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Felix A. Rey
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France
| | - Marija Backovic
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité de Virologie Structurale, 75015 Paris, France
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28
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Long Y, Zhu Z, Zhou Z, Yang C, Chao Y, Wang Y, Zhou Q, Wang MW, Qu Q. Structural insights into human zinc transporter ZnT1 mediated Zn 2+ efflux. EMBO Rep 2024:10.1038/s44319-024-00287-3. [PMID: 39390258 DOI: 10.1038/s44319-024-00287-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 09/06/2024] [Accepted: 09/18/2024] [Indexed: 10/12/2024] Open
Abstract
Zinc transporter 1 (ZnT1), the principal carrier of cytosolic zinc to the extracellular milieu, is important for cellular zinc homeostasis and resistance to zinc toxicity. Despite recent advancements in the structural characterization of various zinc transporters, the mechanism by which ZnTs-mediated Zn2+ translocation is coupled with H+ or Ca2+ remains unclear. To visualize the transport dynamics, we determined the cryo-electron microscopy (cryo-EM) structures of human ZnT1 at different functional states. ZnT1 dimerizes via extensive interactions between the cytosolic (CTD), the transmembrane (TMD), and the unique cysteine-rich extracellular (ECD) domains. At pH 7.5, both protomers adopt an outward-facing (OF) conformation, with Zn2+ ions coordinated at the TMD binding site by distinct compositions. At pH 6.0, ZnT1 complexed with Zn2+ exhibits various conformations [OF/OF, OF/IF (inward-facing), and IF/IF]. These conformational snapshots, together with biochemical investigation and molecular dynamic simulations, shed light on the mechanism underlying the proton-dependence of ZnT1 transport.
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Affiliation(s)
- Yonghui Long
- Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Zhini Zhu
- Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Zixuan Zhou
- Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Chuanhui Yang
- Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Yulin Chao
- Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Yuwei Wang
- Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Ming-Wei Wang
- Research Center for Deepsea Bioresources, 572025, Sanya, Hainan, China
- School of Pharmacy, Hainan Medical University, 570228, Haikou, China
| | - Qianhui Qu
- Shanghai Stomatological Hospital, School of Stomatology, Institutes of Biomedical Sciences, Fudan University, 200032, Shanghai, China.
- Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Department of Systems Biology for Medicine, Fudan University, 200032, Shanghai, China.
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29
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Tammaro C, Plavec Z, Myllymäki L, Mitchell C, Consalvi S, Biava M, Ciogli A, Domanska A, Leppilampi V, Buckner C, Manetto S, Sciò P, Coluccia A, Laajala M, Dondio GM, Bigogno C, Marjomäki V, Butcher SJ, Poce G. SAR Analysis of Novel Coxsackie virus A9 Capsid Binders. J Med Chem 2024; 67:17144-17161. [PMID: 39292620 DOI: 10.1021/acs.jmedchem.4c00701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
Abstract
Enterovirus infections are common in humans, yet there are no approved antiviral treatments. In this study we concentrated on inhibition of one of the Enterovirus B (EV-B), namely Coxsackievirus A9 (CVA9), using a combination of medicinal chemistry, virus inhibition assays, structure determination from cryogenic electron microscopy and molecular modeling, to determine the structure activity relationships for a promising class of novel N-phenylbenzylamines. Of the new 29 compounds synthesized, 10 had half maximal effective concentration (EC50) values between 0.64-10.46 μM, and of these, 7 had 50% cytotoxicity concentration (CC50) values higher than 200 μM. In addition, this new series of compounds showed promising physicochemical properties and act through capsid stabilization, preventing capsid expansion and subsequent release of the genome.
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Affiliation(s)
- Chiara Tammaro
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Zlatka Plavec
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, & Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Laura Myllymäki
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40500 Jyväskylä, Finland
| | - Cristopher Mitchell
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, & Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Sara Consalvi
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Mariangela Biava
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessia Ciogli
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Aušra Domanska
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, & Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Valtteri Leppilampi
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, & Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Cienna Buckner
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, & Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Simone Manetto
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Pietro Sciò
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Mira Laajala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40500 Jyväskylä, Finland
| | | | | | - Varpu Marjomäki
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, 40500 Jyväskylä, Finland
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, & Helsinki Institute of Life Sciences-Institute of Biotechnology, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Giovanna Poce
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, 00185 Rome, Italy
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30
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Tong M, Xu J, Li W, Jiang K, Yang Y, Chen Z, Jiao X, Meng X, Wang M, Hong J, Long H, Liu SJ, Lim B, Gao X. A highly conserved SusCD transporter determines the import and species-specific antagonism of Bacteroides ubiquitin homologues. Nat Commun 2024; 15:8794. [PMID: 39389974 PMCID: PMC11467351 DOI: 10.1038/s41467-024-53149-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
Efficient interbacterial competitions and diverse defensive strategies employed by various bacteria play a crucial role in acquiring a hold within a dense microbial community. The gut symbiont Bacteroides fragilis secretes an antimicrobial ubiquitin homologue (BfUbb) that targets an essential periplasmic PPIase to drive intraspecies bacterial competition. However, the mechanisms by which BfUbb enters the periplasm and its potential for interspecies antagonism remain poorly understood. Here, we employ transposon mutagenesis and identify a highly conserved TonB-dependent transporter SusCD (designated as ButCD) in B. fragilis as the BfUbb transporter. As a putative protein-related nutrient utilization system, ButCD is widely distributed across diverse Bacteroides species with varying sequence similarity, resulting in distinct import efficiency of Bacteroides ubiquitin homologues (BUbb) and thereby determining the species-specific toxicity of BUbb. Cryo-EM structural and functional investigations of the BfUbb-ButCD complex uncover distinctive structural features of ButC that are crucial for its targeting by BfUbb. Animal studies further demonstrate the specific and efficient elimination of enterotoxigenic B. fragilis (ETBF) in the murine gut by BfUbb, suggesting its potential as a therapeutic against ETBF-associated inflammatory bowel disease and colorectal cancer. Our findings provide a comprehensive elucidation of the species-specific toxicity exhibited by BUbb and explore its potential applications.
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Affiliation(s)
- Ming Tong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jinghua Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Weixun Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Kun Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yan Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhe Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xuyao Jiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Mingyu Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jie Hong
- NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai Cancer Institute, Shanghai, 200001, China
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bentley Lim
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Xiang Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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31
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Yu J, Kumar A, Zhang X, Martin C, Van Holsbeeck K, Raia P, Koehl A, Laeremans T, Steyaert J, Manglik A, Ballet S, Boland A, Stoeber M. Structural basis of μ-opioid receptor targeting by a nanobody antagonist. Nat Commun 2024; 15:8687. [PMID: 39384768 PMCID: PMC11464722 DOI: 10.1038/s41467-024-52947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 09/24/2024] [Indexed: 10/11/2024] Open
Abstract
The μ-opioid receptor (μOR), a prototypical G protein-coupled receptor (GPCR), is the target of opioid analgesics such as morphine and fentanyl. Due to the severe side effects of current opioid drugs, there is considerable interest in developing novel modulators of μOR function. Most GPCR ligands today are small molecules, however biologics, including antibodies and nanobodies, represent alternative therapeutics with clear advantages such as affinity and target selectivity. Here, we describe the nanobody NbE, which selectively binds to the μOR and acts as an antagonist. We functionally characterize NbE as an extracellular and genetically encoded μOR ligand and uncover the molecular basis for μOR antagonism by determining the cryo-EM structure of the NbE-μOR complex. NbE displays a unique ligand binding mode and achieves μOR selectivity by interactions with the orthosteric pocket and extracellular receptor loops. Based on a β-hairpin loop formed by NbE that deeply protrudes into the μOR, we design linear and cyclic peptide analogs that recapitulate NbE's antagonism. The work illustrates the potential of nanobodies to uniquely engage with GPCRs and describes lower molecular weight μOR ligands that can serve as a basis for therapeutic developments.
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MESH Headings
- Receptors, Opioid, mu/metabolism
- Receptors, Opioid, mu/chemistry
- Receptors, Opioid, mu/antagonists & inhibitors
- Single-Domain Antibodies/chemistry
- Single-Domain Antibodies/metabolism
- Single-Domain Antibodies/pharmacology
- Humans
- Cryoelectron Microscopy
- Ligands
- HEK293 Cells
- Animals
- Protein Binding
- Binding Sites
- Models, Molecular
- Analgesics, Opioid/pharmacology
- Analgesics, Opioid/chemistry
- Analgesics, Opioid/metabolism
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/metabolism
- Peptides, Cyclic/pharmacology
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Affiliation(s)
- Jun Yu
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Amit Kumar
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Xuefeng Zhang
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Charlotte Martin
- Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kevin Van Holsbeeck
- Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Pierre Raia
- Department of Plant Sciences, University of Geneva, Geneva, Switzerland
| | - Antoine Koehl
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, USA
| | | | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Steven Ballet
- Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Andreas Boland
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
| | - Miriam Stoeber
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland.
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32
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Becker AE, Kochanowski P, Wu PK, Wątor E, Chen W, Guchhait K, Biela AP, Grudnik P, Park JI. ERK1/2 interaction with DHPS regulates eIF5A deoxyhypusination independently of ERK kinase activity. Cell Rep 2024; 43:114831. [PMID: 39392755 DOI: 10.1016/j.celrep.2024.114831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 08/20/2024] [Accepted: 09/19/2024] [Indexed: 10/13/2024] Open
Abstract
This study explores a non-kinase effect of extracellular regulated kinases 1/2 (ERK1/2) on the interaction between deoxyhypusine synthase (DHPS) and its substrate, eukaryotic translation initiation factor 5A (eIF5A). We report that Raf/MEK/ERK activation decreases the DHPS-ERK1/2 interaction while increasing DHPS-eIF5A association in cells. We determined the cryoelectron microscopy (cryo-EM) structure of the DHPS-ERK2 complex at 3.5 Å to show that ERK2 hinders substrate entrance to the DHPS active site, subsequently inhibiting deoxyhypusination in vitro. In cells, impairing the ERK2 activation loop, but not the catalytic site, prolongs the DHPS-ERK2 interaction irrespective of Raf/MEK signaling. The ERK2 Ser-Pro-Ser motif, but not the common docking or F-site recognition sites, also regulates this complex. These data suggest that ERK1/2 dynamically regulate the DHPS-eIF5A interaction in response to Raf/MEK activity, regardless of its kinase function. In contrast, ERK1/2 kinase activity is necessary to regulate the expression of DHPS and eIF5A. These findings highlight an ERK1/2-mediated dual kinase-dependent and -independent regulation of deoxyhypusination.
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Affiliation(s)
- Andrew E Becker
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Paweł Kochanowski
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Pui-Kei Wu
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Elżbieta Wątor
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Wenjing Chen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Koushik Guchhait
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Artur P Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Przemysław Grudnik
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Jong-In Park
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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33
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Shaib AH, Chouaib AA, Chowdhury R, Altendorf J, Mihaylov D, Zhang C, Krah D, Imani V, Spencer RKW, Georgiev SV, Mougios N, Monga M, Reshetniak S, Mimoso T, Chen H, Fatehbasharzad P, Crzan D, Saal KA, Alawieh MM, Alawar N, Eilts J, Kang J, Soleimani A, Müller M, Pape C, Alvarez L, Trenkwalder C, Mollenhauer B, Outeiro TF, Köster S, Preobraschenski J, Becherer U, Moser T, Boyden ES, Aricescu AR, Sauer M, Opazo F, Rizzoli SO. One-step nanoscale expansion microscopy reveals individual protein shapes. Nat Biotechnol 2024:10.1038/s41587-024-02431-9. [PMID: 39385007 DOI: 10.1038/s41587-024-02431-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 09/13/2024] [Indexed: 10/11/2024]
Abstract
The attainable resolution of fluorescence microscopy has reached the subnanometer range, but this technique still fails to image the morphology of single proteins or small molecular complexes. Here, we expand the specimens at least tenfold, label them with conventional fluorophores and image them with conventional light microscopes, acquiring videos in which we analyze fluorescence fluctuations. One-step nanoscale expansion (ONE) microscopy enables the visualization of the shapes of individual membrane and soluble proteins, achieving around 1-nm resolution. We show that conformational changes are readily observable, such as those undergone by the ~17-kDa protein calmodulin upon Ca2+ binding. ONE is also applied to clinical samples, analyzing the morphology of protein aggregates in cerebrospinal fluid from persons with Parkinson disease, potentially aiding disease diagnosis. This technology bridges the gap between high-resolution structural biology techniques and light microscopy, providing new avenues for discoveries in biology and medicine.
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Affiliation(s)
- Ali H Shaib
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany.
| | - Abed Alrahman Chouaib
- Department of Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Rajdeep Chowdhury
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Department of Chemistry, GITAM School of Science, GITAM, Hyderabad, India
| | - Jonas Altendorf
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Chi Zhang
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Donatus Krah
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Vanessa Imani
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Russell K W Spencer
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany
| | - Svilen Veselinov Georgiev
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Nikolaos Mougios
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Mehar Monga
- Biochemistry of Membrane Dynamics Group, Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany
| | - Sofiia Reshetniak
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Tiago Mimoso
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Han Chen
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Parisa Fatehbasharzad
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Dagmar Crzan
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Kim-Ann Saal
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Mohamad Mahdi Alawieh
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
| | - Nadia Alawar
- Department of Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Janna Eilts
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Jinyoung Kang
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alireza Soleimani
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany
| | - Marcus Müller
- Institute for Theoretical Physics, Georg-August University, Göttingen, Germany
| | - Constantin Pape
- Institute of Computer Science, Georg-August University Göttingen, Göttingen, Germany
| | | | - Claudia Trenkwalder
- Department of Neurosurgery, University Medical Center, Göttingen, Germany
- Paracelsus-Elena-Klinik, Kassel, Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurology, University Medical Center, Göttingen, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Julia Preobraschenski
- Biochemistry of Membrane Dynamics Group, Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Ute Becherer
- Department of Cellular Neurophysiology, Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Tobias Moser
- Biochemistry of Membrane Dynamics Group, Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
- Auditory Neuroscience and Synaptic Nanophysiology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Edward S Boyden
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Markus Sauer
- Department of Biotechnology and Biophysics, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Felipe Opazo
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- NanoTag Biotechnologies GmbH, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology, University Medical Center Göttingen, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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34
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Liu Y, Zhao X, Shi J, Wang Y, Liu H, Hu YF, Hu B, Shuai H, Yuen TTT, Chai Y, Liu F, Gong HR, Li J, Wang X, Jiang S, Zhang X, Zhang Y, Li X, Wang L, Hartnoll M, Zhu T, Hou Y, Huang X, Yoon C, Wang Y, He Y, Zhou M, Du L, Zhang X, Chan WM, Chen LL, Cai JP, Yuan S, Zhou J, Huang JD, Yuen KY, To KKW, Chan JFW, Zhang BZ, Sun L, Wang P, Chu H. Lineage-specific pathogenicity, immune evasion, and virological features of SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3. Nat Commun 2024; 15:8728. [PMID: 39379369 PMCID: PMC11461813 DOI: 10.1038/s41467-024-53033-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024] Open
Abstract
SARS-CoV-2 JN.1 with an additional L455S mutation on spike when compared with its parental variant BA.2.86 has outcompeted all earlier variants to become the dominant circulating variant. Recent studies investigated the immune resistance of SARS-CoV-2 JN.1 but additional factors are speculated to contribute to its global dominance, which remain elusive until today. Here, we find that SARS-CoV-2 JN.1 has a higher infectivity than BA.2.86 in differentiated primary human nasal epithelial cells (hNECs). Mechanistically, we demonstrate that the gained infectivity of SARS-CoV-2 JN.1 over BA.2.86 associates with increased entry efficiency conferred by L455S and better spike cleavage in hNECs. Structurally, S455 altered the mode of binding of JN.1 spike protein to ACE2 when compared to BA.2.86 spike at ACE2H34, and modified the internal structure of JN.1 spike protein by increasing the number of hydrogen bonds with neighboring residues. These findings indicate that a single mutation (L455S) enhances virus entry in hNECs and increases immune evasiveness, which contribute to the robust transmissibility of SARS-CoV-2 JN.1. We further evaluate the in vitro and in vivo virological characteristics between SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3, and identify key lineage-specific features of the two Omicron sublineages that contribute to our understanding on Omicron antigenicity, transmissibility, and pathogenicity.
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Affiliation(s)
- Yuanchen Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiaoyu Zhao
- Shanghai Sci-Tech Inno Center for Infection & Immunity, National Medical Center for Infectious Diseases, Huashan Hospital, Institute of Infection and Health, Fudan University, Shanghai, China
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jialu Shi
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yajie Wang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Huan Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Ye-Fan Hu
- BayVax Biotech Limited, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong, China
| | - Bingjie Hu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Huiping Shuai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Terrence Tsz-Tai Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yue Chai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Feifei Liu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Hua-Rui Gong
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jiayan Li
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Xun Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Shujun Jiang
- Department of Infectious Diseases, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiang Zhang
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yanliang Zhang
- Department of Infectious Diseases, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Xiangnan Li
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Lei Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Madeline Hartnoll
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Tianrenzheng Zhu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yuxin Hou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Xiner Huang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Chaemin Yoon
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yang Wang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Yixin He
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Minmin Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lianzhao Du
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xiaojuan Zhang
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Lin-Lei Chen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
| | - Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Materials Innovation Institute for Life Sciences and Energy (MILES), HKU-SIRI, Shenzhen, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou, Hainan Province, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
- Academician Workstation of Hainan Province, Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Haikou, Hainan Province, China.
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.
- Guangzhou Laboratory, Guangzhou, Guangdong Province, China.
| | - Bao-Zhong Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Lei Sun
- Shanghai Fifth People's Hospital, Shanghai Institute of Infectious Disease and Biosecurity, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Pengfei Wang
- Shanghai Pudong Hospital, Fudan University Pudong Medical Center, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
- Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.
- Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, China.
- Materials Innovation Institute for Life Sciences and Energy (MILES), HKU-SIRI, Shenzhen, China.
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Xin Y, Xian R, Yang Y, Cong J, Rao Z, Li X, Chen Y. Structural and functional insights into the T-even type bacteriophage topoisomerase II. Nat Commun 2024; 15:8719. [PMID: 39379365 PMCID: PMC11461880 DOI: 10.1038/s41467-024-53037-3] [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: 04/23/2024] [Accepted: 09/26/2024] [Indexed: 10/10/2024] Open
Abstract
T-even type bacteriophages are virulent phages commonly used as model organisms, playing a crucial role in understanding various biological processes. One such process involves the regulation of DNA topology during phage replication upon host infection, governed by type IIA DNA topoisomerases. In spite of various studies on prokaryotic and eukaryotic counterparts, viral topoisomerase II remains insufficiently understood, especially the unique domain composition of T4 phage. In this study, we determine the cryo-EM structures of topoisomerase II from T4 and T6 phages, including full-length structures of both apo and DNA-binding states which have never been determined before. Together with other conformational states, these structures provide an explicit blueprint of mechanisms of phage topoisomerase II. Particularly, the asymmetric dimeric interactions observed in cryo-EM structures of T6 phage topoisomerase II ATPase domain and central domain bound with DNA shed light on the asynchronous ATP usage and asynchronous cleavage of the G-segment DNA, respectively. The elucidation of phage topoisomerase II's structures and functions not only enhances our understanding of mechanisms and evolutionary parallels with prokaryotic and eukaryotic homologs but also highlights its potential as a model for developing type IIA topoisomerase inhibitors.
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Affiliation(s)
- Yuhui Xin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runqi Xian
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunge Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingyuan Cong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zihe Rao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China.
| | - Xuemei Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Yutao Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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36
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Scharffenberger SC, Wan YH, Homad LJ, Kher G, Haynes AM, Poudel B, Sinha IR, Aldridge N, Pai A, Bibby M, Chhan CB, Davis AR, Moodie Z, Palacio MB, Escolano A, McElrath MJ, Boonyaratanakornkit J, Pancera M, McGuire AT. Targeting RSV-neutralizing B cell receptors with anti-idiotypic antibodies. Cell Rep 2024; 43:114811. [PMID: 39383036 DOI: 10.1016/j.celrep.2024.114811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/23/2024] [Accepted: 09/16/2024] [Indexed: 10/11/2024] Open
Abstract
Respiratory syncytial virus (RSV) causes lower respiratory tract infections with significant morbidity and mortality at the extremes of age. Vaccines based on the viral fusion protein are approved for adults over 60, but infant protection relies on passive immunity via antibody transfer or maternal vaccination. An infant vaccine that rapidly elicits protective antibodies would fulfill a critical unmet need. Antibodies arising from the VH3-21/VL1-40 gene pairing can neutralize RSV without the need for affinity maturation, making them attractive to target through vaccination. Here, we develop an anti-idiotypic monoclonal antibody (ai-mAb) immunogen that is specific for unmutated VH3-21/VL1-40 B cell receptors (BCRs). The ai-mAb efficiently engages B cells with bona fide target BCRs and does not activate off-target non-neutralizing B cells, unlike recombinant pre-fusion (preF) protein used in current RSV vaccines. These results establish proof of concept for using an ai-mAb-derived vaccine to target B cells hardwired to produce RSV-neutralizing antibodies.
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Affiliation(s)
- Samuel C Scharffenberger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Yu-Hsin Wan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Leah J Homad
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Gargi Kher
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Austin M Haynes
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Bibhav Poudel
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Irika R Sinha
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Nicholas Aldridge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ayana Pai
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Madeleine Bibby
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Crystal B Chhan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Amelia R Davis
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Maria Belen Palacio
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - Amelia Escolano
- Vaccine and Immunotherapy Center, Wistar Institute, Philadelphia, PA 19104, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jim Boonyaratanakornkit
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA.
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37
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Wang S, Siddique R, Hall MC, Rice PA, Chang L. Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition. Cell 2024:S0092-8674(24)01071-7. [PMID: 39383864 DOI: 10.1016/j.cell.2024.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/01/2024] [Accepted: 09/13/2024] [Indexed: 10/11/2024]
Abstract
Tn7-like transposons are characterized by their ability to insert specifically into host chromosomes. Recognition of the attachment (att) site by TnsD recruits the TnsABC proteins to form the transpososome and facilitate transposition. Although this pathway is well established, atomic-level structural insights of this process remain largely elusive. Here, we present the cryo-electron microscopy (cryo-EM) structures of the TnsC-TnsD-att DNA complex and the TnsABCD transpososome from the Tn7-like transposon in Peltigera membranacea cyanobiont 210A, a type I-B CRISPR-associated transposon. Our structures reveal a striking bending of the att DNA, featured by the intercalation of an arginine side chain of TnsD into a CC/GG dinucleotide step. The TnsABCD transpososome structure reveals TnsA-TnsB interactions and demonstrates that TnsC not only recruits TnsAB but also directly participates in the transpososome assembly. These findings provide mechanistic insights into targeted DNA insertion by Tn7-like transposons, with implications for improving the precision and efficiency of their genome-editing applications.
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Affiliation(s)
- Shukun Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Romana Siddique
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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38
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Kim S, Ko S, Kim M, Jang Y, Hyun J. Cryo-EM structure of orf virus scaffolding protein orfv075. Biochem Biophys Res Commun 2024; 728:150334. [PMID: 38968773 DOI: 10.1016/j.bbrc.2024.150334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
Capsid-like poxvirus scaffold proteins self-assemble into semi-regular lattice that govern the formation of spherical immature virus particles. The scaffolding is a critical step in virus morphogenesis as exemplified by the drug rifampicin that impairs the recruitment of scaffold onto the viral membrane in vaccinia virus (VACV). Here we report cryo-electron microscopy structure of scaffolding protein Orfv075 of orf virus (ORFV) that causes smallpox-like diseases in sheep, goats and occasionally humans via zoonotic infection. We demonstrate that the regions that are involved in intertrimeric interactions for scaffold assembly are largely conserved in comparison to its VACV orthologue protein D13 whose intermediate assembly structures have been previously characterized. By contrast, less conserved regions are located away from these interfaces, indicating both viruses share similar assembly mechanisms. We also show that the phenylalanine-rich binding site of rifampicin in D13 is conserved in Orfv075, and molecular docking simulation confirms similar binding modes. Our study provides structural basis of scaffolding protein as a target for anti-poxvirus treatment across wide range of poxvirus genera.
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Affiliation(s)
- Seungmi Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sumin Ko
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minjae Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yeontae Jang
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyung Hyun
- School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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39
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Sun D, Storek KM, Tegunov D, Yang Y, Arthur CP, Johnson M, Quinn JG, Liu W, Han G, Girgis HS, Alexander MK, Murchison AK, Shriver S, Tam C, Ijiri H, Inaba H, Sano T, Yanagida H, Nishikawa J, Heise CE, Fairbrother WJ, Tan MW, Skelton N, Sandoval W, Sellers BD, Ciferri C, Smith PA, Reid PC, Cunningham CN, Rutherford ST, Payandeh J. The discovery and structural basis of two distinct state-dependent inhibitors of BamA. Nat Commun 2024; 15:8718. [PMID: 39379361 PMCID: PMC11461620 DOI: 10.1038/s41467-024-52512-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/09/2024] [Indexed: 10/10/2024] Open
Abstract
BamA is the central component of the essential β-barrel assembly machine (BAM), a conserved multi-subunit complex that dynamically inserts and folds β-barrel proteins into the outer membrane of Gram-negative bacteria. Despite recent advances in our mechanistic and structural understanding of BamA, there are few potent and selective tool molecules that can bind to and modulate BamA activity. Here, we explored in vitro selection methods and different BamA/BAM protein formulations to discover peptide macrocycles that kill Escherichia coli by targeting extreme conformational states of BamA. Our studies show that Peptide Targeting BamA-1 (PTB1) targets an extracellular divalent cation-dependent binding site and locks BamA into a closed lateral gate conformation. By contrast, PTB2 targets a luminal binding site and traps BamA into an open lateral gate conformation. Our results will inform future antibiotic discovery efforts targeting BamA and provide a template to prospectively discover modulators of other dynamic integral membrane proteins.
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Affiliation(s)
- Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Kelly M Storek
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Dimitry Tegunov
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Ying Yang
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Christopher P Arthur
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Altos Labs, Redwood City, CA, USA
| | - Matthew Johnson
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - John G Quinn
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
| | - Weijing Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Guanghui Han
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
- PTM Bio, Alameda, CA, USA
| | - Hany S Girgis
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Mary Kate Alexander
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Austin K Murchison
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Stephanie Shriver
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | - Christine Tam
- Department of BioMolecular Resources, Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | | | - Christopher E Heise
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, USA
- Septerna, South San Francisco, CA, USA
| | - Wayne J Fairbrother
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Nicholas Skelton
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin D Sellers
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Vilya, South San Francisco, CA, USA
| | - Claudio Ciferri
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Peter A Smith
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
- Revagenix, San Mateo, CA, USA
| | | | - Christian N Cunningham
- Department of Peptide Therapeutics, Genentech Inc., South San Francisco, CA, USA.
- PeptiDream, Kawasaki, Japan.
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
- Exelixis, Alameda, CA, USA.
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40
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Gemin O, Gluc M, Rosa H, Purdy M, Niemann M, Peskova Y, Mattei S, Jomaa A. Ribosomes hibernate on mitochondria during cellular stress. Nat Commun 2024; 15:8666. [PMID: 39379376 PMCID: PMC11461667 DOI: 10.1038/s41467-024-52911-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 09/23/2024] [Indexed: 10/10/2024] Open
Abstract
Cell survival under nutrient-deprived conditions relies on cells' ability to adapt their organelles and rewire their metabolic pathways. In yeast, glucose depletion induces a stress response mediated by mitochondrial fragmentation and sequestration of cytosolic ribosomes on mitochondria. This cellular adaptation promotes survival under harsh environmental conditions; however, the underlying mechanism of this response remains unknown. Here, we demonstrate that upon glucose depletion protein synthesis is halted. Cryo-electron microscopy structure of the ribosomes show that they are devoid of both tRNA and mRNA, and a subset of the particles depicted a conformational change in rRNA H69 that could prevent tRNA binding. Our in situ structural analyses reveal that the hibernating ribosomes tether to fragmented mitochondria and establish eukaryotic-specific, higher-order storage structures by assembling into oligomeric arrays on the mitochondrial surface. Notably, we show that hibernating ribosomes exclusively bind to the outer mitochondrial membrane via the small ribosomal subunit during cellular stress. We identify the ribosomal protein Cpc2/RACK1 as the molecule mediating ribosomal tethering to mitochondria. This study unveils the molecular mechanism connecting mitochondrial stress with the shutdown of protein synthesis and broadens our understanding of cellular responses to nutrient scarcity and cell quiescence.
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Affiliation(s)
- Olivier Gemin
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | - Maciej Gluc
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA
| | - Higor Rosa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | - Michael Purdy
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA
| | - Moritz Niemann
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | - Yelena Peskova
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA
| | - Simone Mattei
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, Heidelberg, Germany.
- European Molecular Biology Laboratory, Imaging Centre, Meyerhofstraße 1, Heidelberg, Germany.
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics and Center for Cell and Membrane Physiology, School of Medicine, University of Virginia, Charlottesville, USA.
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, USA.
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41
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Junglas B, Kartte D, Kutzner M, Hellmann N, Ritter I, Schneider D, Sachse C. Structural basis for Vipp1 membrane binding: from loose coats and carpets to ring and rod assemblies. Nat Struct Mol Biol 2024:10.1038/s41594-024-01399-z. [PMID: 39379528 DOI: 10.1038/s41594-024-01399-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 09/05/2024] [Indexed: 10/10/2024]
Abstract
Vesicle-inducing protein in plastids 1 (Vipp1) is critical for thylakoid membrane biogenesis and maintenance. Although Vipp1 has recently been identified as a member of the endosomal sorting complexes required for transport III superfamily, it is still unknown how Vipp1 remodels membranes. Here, we present cryo-electron microscopy structures of Synechocystis Vipp1 interacting with membranes: seven structures of helical and stacked-ring assemblies at 5-7-Å resolution engulfing membranes and three carpet structures covering lipid vesicles at ~20-Å resolution using subtomogram averaging. By analyzing ten structures of N-terminally truncated Vipp1, we show that helix α0 is essential for membrane tubulation and forms the membrane-anchoring domain of Vipp1. Lastly, using a conformation-restrained Vipp1 mutant, we reduced the structural plasticity of Vipp1 and determined two structures of Vipp1 at 3.0-Å resolution, resolving the molecular details of membrane-anchoring and intersubunit contacts of helix α0. Our data reveal membrane curvature-dependent structural transitions from carpets to rings and rods, some of which are capable of inducing and/or stabilizing high local membrane curvature triggering membrane fusion.
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Affiliation(s)
- Benedikt Junglas
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - David Kartte
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Mirka Kutzner
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nadja Hellmann
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ilona Ritter
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Dirk Schneider
- Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons, ER-C-3/Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany.
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42
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Hayes BK, Harper M, Venugopal H, Lewis JM, Wright A, Lee HC, Steele JR, Steer DL, Schittenhelm RB, Boyce JD, McGowan S. Structure of a Rhs effector clade domain provides mechanistic insights into type VI secretion system toxin delivery. Nat Commun 2024; 15:8709. [PMID: 39379370 PMCID: PMC11461821 DOI: 10.1038/s41467-024-52950-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 09/26/2024] [Indexed: 10/10/2024] Open
Abstract
The type VI secretion system (T6SS) is a molecular machine utilised by many Gram-negative bacteria to deliver antibacterial toxins into adjacent cells. Here we present the structure of Tse15, a T6SS Rhs effector from the nosocomial pathogen Acinetobacter baumannii. Tse15 forms a triple layered β-cocoon Rhs domain with an N-terminal α-helical clade domain and an unfolded C-terminal toxin domain inside the Rhs cage. Tse15 is cleaved into three domains, through independent auto-cleavage events involving aspartyl protease activity for toxin self-cleavage and a nucleophilic glutamic acid for N-terminal clade cleavage. Proteomic analyses identified that significantly more peptides from the N-terminal clade and toxin domains were secreted than from the Rhs cage, suggesting toxin delivery often occurs without the cage. We propose the clade domain acts as an internal chaperone to mediate toxin tethering to the T6SS machinery. Conservation of the clade domain in other Gram-negative bacteria suggests this may be a common mechanism for delivery.
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Affiliation(s)
- Brooke K Hayes
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Marina Harper
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Jessica M Lewis
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Amy Wright
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia
| | - Han-Chung Lee
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Joel R Steele
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - David L Steer
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - John D Boyce
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia.
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia.
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia.
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia.
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43
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Chi P, Ou G, Liu S, Ma Q, Lu Y, Li J, Li J, Qi Q, Han Z, Zhang Z, Liu Q, Guo L, Chen J, Wang X, Huang W, Li L, Deng D. Cryo-EM structure of the human subcortical maternal complex and the associated discovery of infertility-associated variants. Nat Struct Mol Biol 2024:10.1038/s41594-024-01396-2. [PMID: 39379527 DOI: 10.1038/s41594-024-01396-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 08/28/2024] [Indexed: 10/10/2024]
Abstract
The functionally conserved subcortical maternal complex (SCMC) is essential for early embryonic development in mammals. Reproductive disorders caused by pathogenic variants in NLRP5, TLE6 and OOEP, three core components of the SCMC, have attracted much attention over the past several years. Evaluating the pathogenicity of a missense variant in the SCMC is limited by the lack of information on its structure, although we recently solved the structure of the mouse SCMC and proposed that reproductive disorders caused by pathogenic variants are related to the destabilization of the SCMC core complex. Here we report the cryogenic electron microscopy structure of the human SCMC and uncover that the pyrin domain of NLRP5 is essential for the stability of SCMC. By combining prediction of SCMC stability and in vitro reconstitution, we provide a method for identifying deleterious variants, and we successfully identify a new pathogenic variant of TLE6 (p.A396T). Thus, on the basis of the structure of the human SCMC, we offer a strategy for the diagnosis of reproductive disorders and the discovery of new infertility-associated variants.
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Affiliation(s)
- Pengliang Chi
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Guojin Ou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- Clinical Laboratory, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Sibei Liu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qianhong Ma
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yuechao Lu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jinhong Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jialu Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- NHC key Laboratory of Chronobiology, Sichuan University, Chengdu, China
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Qianqian Qi
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- Clinical Laboratory, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Zhuo Han
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- NHC key Laboratory of Chronobiology, Sichuan University, Chengdu, China
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Zihan Zhang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- NHC key Laboratory of Chronobiology, Sichuan University, Chengdu, China
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Qingting Liu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Li Guo
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jing Chen
- Laboratory of Pediatric Surgery, Department of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiang Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wei Huang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Dong Deng
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
- NHC key Laboratory of Chronobiology, Sichuan University, Chengdu, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China.
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44
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Biester A, Grahame DA, Drennan CL. Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy. Proc Natl Acad Sci U S A 2024; 121:e2410995121. [PMID: 39361653 DOI: 10.1073/pnas.2410995121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 08/27/2024] [Indexed: 10/05/2024] Open
Abstract
Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH3+). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO2) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO2, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from Methanosarcina thermophila (MetCODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our MetCODH/ACS structure with our MetCODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization.
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Affiliation(s)
- Alison Biester
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David A Grahame
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
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45
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Wenger ES, Schultz K, Marmorstein R, Christianson DW. Engineering substrate channeling in a bifunctional terpene synthase. Proc Natl Acad Sci U S A 2024; 121:e2408064121. [PMID: 39365814 DOI: 10.1073/pnas.2408064121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 08/26/2024] [Indexed: 10/06/2024] Open
Abstract
Fusicoccadiene synthase from Phomopsis amygdala (PaFS) is a bifunctional terpene synthase. It contains a prenyltransferase (PT) domain that generates geranylgeranyl diphosphate (GGPP) from dimethylallyl diphosphate and three equivalents of isopentenyl diphosphate, and a cyclase domain that converts GGPP into fusicoccadiene, a precursor of the diterpene glycoside Fusicoccin A. The two catalytic domains are connected by a flexible 69-residue linker. The PT domain mediates oligomerization to form predominantly octamers, with cyclase domains randomly splayed out around the PT core. Surprisingly, despite the random positioning of cyclase domains, substrate channeling is operative in catalysis since most of the GGPP generated by the PT remains on the enzyme for cyclization. Here, we demonstrate that covalent linkage of the PT and cyclase domains is not required for GGPP channeling, although covalent linkage may improve channeling efficiency. Moreover, GGPP competition experiments with other diterpene cyclases indicate that the PaFS PT and cyclase domains are preferential partners regardless of whether they are covalently linked or not. The cryoelectron microscopy structure of the 600-kD "linkerless" construct, in which the 69-residue linker is spliced out and replaced with the tripeptide PTQ, reveals that cyclase pairs associate with all four sides of the PT octamer and exhibit fascinating quaternary structural flexibility. These results suggest that optimal substrate channeling is achieved when a cyclase domain associates with the side of the PT octamer, regardless of whether the two domains are covalently linked and regardless of whether this interaction is transient or locked in place.
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Affiliation(s)
- Eliott S Wenger
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Kollin Schultz
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ronen Marmorstein
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
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46
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Yajima H, Anraku Y, Kaku Y, Kimura KT, Plianchaisuk A, Okumura K, Nakada-Nakura Y, Atarashi Y, Hemmi T, Kuroda D, Takahashi Y, Kita S, Sasaki J, Sumita H, Ito J, Maenaka K, Sato K, Hashiguchi T. Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1. Nat Commun 2024; 15:8574. [PMID: 39375326 PMCID: PMC11458767 DOI: 10.1038/s41467-024-52808-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 09/18/2024] [Indexed: 10/09/2024] Open
Abstract
Since 2019, SARS-CoV-2 has undergone mutations, resulting in pandemic and epidemic waves. The SARS-CoV-2 spike protein, crucial for cellular entry, binds to the ACE2 receptor exclusively when its receptor-binding domain (RBD) adopts the up-conformation. However, whether ACE2 also interacts with the RBD in the down-conformation to facilitate the conformational shift to RBD-up remains unclear. Herein, we present the structures of the BA.2.86 and the JN.1 spike proteins bound to ACE2. Notably, we successfully observed the ACE2-bound down-RBD, indicating an intermediate structure before the RBD-up conformation. The wider and mobile angle of RBDs in the up-state provides space for ACE2 to interact with the down-RBD, facilitating the transition to the RBD-up state. The K356T, but not N354-linked glycan, contributes to both of infectivity and neutralizing-antibody evasion in BA.2.86. These structural insights the spike-protein dynamics would help understand the mechanisms underlying SARS-CoV-2 infection and its neutralization.
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Affiliation(s)
- Hisano Yajima
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yuki Anraku
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yu Kaku
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kanako Terakado Kimura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kaho Okumura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Liberal Arts, Sophia University, Tokyo, Japan
| | - Yoshiko Nakada-Nakura
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yusuke Atarashi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases; Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Takuya Hemmi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Daisuke Kuroda
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases; Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Yoshimasa Takahashi
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases; Shinjuku-ku, Tokyo, 162-8640, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Shunsuke Kita
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Hiromi Sumita
- Research Administration Office, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- Division of Pathogen Structure, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan
- Kyushu University, Fukuoka, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan.
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan.
- CREST, Japan Science and Technology Agency, Kawaguchi, Japan.
- Kyoto University Immunomonitoring Center, Kyoto University, Kyoto, Japan.
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47
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Crespillo-Casado A, Pothukuchi P, Naydenova K, Yip MCJ, Young JM, Boulanger J, Dharamdasani V, Harper C, Hammoudi PM, Otten EG, Boyle K, Gogoi M, Malik HS, Randow F. Recognition of phylogenetically diverse pathogens through enzymatically amplified recruitment of RNF213. EMBO Rep 2024:10.1038/s44319-024-00280-w. [PMID: 39375464 DOI: 10.1038/s44319-024-00280-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 09/19/2024] [Accepted: 09/20/2024] [Indexed: 10/09/2024] Open
Abstract
Innate immunity senses microbial ligands known as pathogen-associated molecular patterns (PAMPs). Except for nucleic acids, PAMPs are exceedingly taxa-specific, thus enabling pattern recognition receptors to detect cognate pathogens while ignoring others. How the E3 ubiquitin ligase RNF213 can respond to phylogenetically distant pathogens, including Gram-negative Salmonella, Gram-positive Listeria, and eukaryotic Toxoplasma, remains unknown. Here we report that the evolutionary history of RNF213 is indicative of repeated adaptation to diverse pathogen target structures, especially in and around its newly identified CBM20 carbohydrate-binding domain, which we have resolved by cryo-EM. We find that RNF213 forms coats on phylogenetically distant pathogens. ATP hydrolysis by RNF213's dynein-like domain is essential for coat formation on all three pathogens studied as is RZ finger-mediated E3 ligase activity for bacteria. Coat formation is not diffusion-limited but instead relies on rate-limiting initiation events and subsequent cooperative incorporation of further RNF213 molecules. We conclude that RNF213 responds to evolutionarily distant pathogens through enzymatically amplified cooperative recruitment.
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Affiliation(s)
- Ana Crespillo-Casado
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Prathyush Pothukuchi
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Matthew C J Yip
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Vimisha Dharamdasani
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ceara Harper
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Pierre-Mehdi Hammoudi
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Elsje G Otten
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Keith Boyle
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Mayuri Gogoi
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Felix Randow
- MRC Laboratory of Molecular Biology, Division of Protein and Nucleic Acid Chemistry, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- University of Cambridge, Department of Medicine, Addenbrooke's Hospital, Cambridge, CB2 2QQ, UK.
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48
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Yang G, Wang D, Liu B. Structure of the Nipah virus polymerase phosphoprotein complex. Nat Commun 2024; 15:8673. [PMID: 39375338 PMCID: PMC11458586 DOI: 10.1038/s41467-024-52701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 09/19/2024] [Indexed: 10/09/2024] Open
Abstract
The Nipah virus (NiV), a member of the Paramyxoviridae family, is notorious for its high fatality rate in humans. The RNA polymerase machinery of NiV, comprising the large protein L and the phosphoprotein P, is essential for viral replication. This study presents the 2.9-Å cryo-electron microscopy structure of the NiV L-P complex, shedding light on its assembly and functionality. The structure not only demonstrates the molecular details of the conserved N-terminal domain, RNA-dependent RNA polymerase (RdRp), and GDP polyribonucleotidyltransferase of the L protein, but also the intact central oligomerization domain and the C-terminal X domain of the P protein. The P protein interacts extensively with the L protein, forming an antiparallel β-sheet among the P protomers and with the fingers subdomain of RdRp. The flexible linker domain of one P promoter extends its contact with the fingers subdomain to reach near the nascent RNA exit, highlighting the distinct characteristic of the NiV L-P interface. This distinctive tetrameric organization of the P protein and its interaction with the L protein provide crucial molecular insights into the replication and transcription mechanisms of NiV polymerase, ultimately contributing to the development of effective treatments and preventive measures against this Paramyxoviridae family deadly pathogen.
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Affiliation(s)
- Ge Yang
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Dong Wang
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Bin Liu
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.
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49
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Chen YS, Garcia-Castañeda M, Charalambous M, Rossi D, Sorrentino V, Van Petegem F. Cryo-EM investigation of ryanodine receptor type 3. Nat Commun 2024; 15:8630. [PMID: 39366997 PMCID: PMC11452665 DOI: 10.1038/s41467-024-52998-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 09/27/2024] [Indexed: 10/06/2024] Open
Abstract
Ryanodine Receptor isoform 3 (RyR3) is a large ion channel found in the endoplasmic reticulum membrane of many different cell types. Within the hippocampal region of the brain, it is found in dendritic spines and regulates synaptic plasticity. It controls myogenic tone in arteries and is upregulated in skeletal muscle in early development. RyR3 has a unique functional profile with a very high sensitivity to activating ligands, enabling high gain in Ca2+-induced Ca2+ release. Here we solve high-resolution cryo-EM structures of RyR3 in non-activating and activating conditions, revealing structural transitions that occur during channel opening. Addition of activating ligands yields only open channels, indicating an intrinsically high open probability under these conditions. RyR3 has reduced binding affinity to the auxiliary protein FKBP12.6 due to several sequence variations in the binding interface. We map disease-associated sequence variants and binding sites for known pharmacological agents. The N-terminal region contains ligand binding sites for a putative chloride anion and ATP, both of which are targeted by sequence variants linked to epileptic encephalopathy.
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Affiliation(s)
- Yu Seby Chen
- Department of Biochemistry and Molecular Biology, the Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Maricela Garcia-Castañeda
- Department of Biochemistry and Molecular Biology, the Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Maria Charalambous
- Department of Biochemistry and Molecular Biology, the Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniela Rossi
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Vincenzo Sorrentino
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, the Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada.
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50
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Adair BD, Field CO, Alonso JL, Xiong JP, Deng SX, Ahn HS, Mashin E, Clish CB, van Agthoven J, Yeager M, Guo Y, Tess DA, Landry DW, Poncz M, Arnaout MA. Platelet integrin αIIbβ3 plays a key role in a venous thrombogenesis mouse model. Nat Commun 2024; 15:8612. [PMID: 39366965 PMCID: PMC11452527 DOI: 10.1038/s41467-024-52869-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 09/21/2024] [Indexed: 10/06/2024] Open
Abstract
Venous thrombosis (VT) is a common vascular disease associated with reduced survival and a high recurrence rate. VT is initiated by the accumulation of platelets and neutrophils at sites of endothelial cell activation. A role for platelet αIIbβ3 in VT is not established, a task complicated by the increased bleeding risk caused by partial agonists such as tirofiban. Here, we show that m-tirofiban, a modified version of tirofiban, does not agonize αIIbβ3 based on lack of neoepitope expression and the cryo-EM structure of m-tirofiban/full-length αIIbβ3 complex. m-tirofiban abolishes agonist-induced platelet aggregation while preserving clot retraction ex vivo and, unlike tirofiban, it suppresses venous thrombogenesis in a mouse model without increasing bleeding. These findings establish a key role for αIIbβ3 in VT initiation and suggest that m-tirofiban and compounds with a similar structurally-defined mechanism of action merit consideration as potential thromboprophylaxis agents in patients at high risk for VT and hemorrhage.
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Affiliation(s)
- Brian D Adair
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Leukocyte Biology and Inflammation Laboratory, Massachusetts General Hospital, Boston, MA, USA
- Structural Biology Program, Massachusetts General Hospital, Boston, MA, USA
| | - Conroy O Field
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - José L Alonso
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Leukocyte Biology and Inflammation Laboratory, Massachusetts General Hospital, Boston, MA, USA
| | - Jian-Ping Xiong
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Leukocyte Biology and Inflammation Laboratory, Massachusetts General Hospital, Boston, MA, USA
- Structural Biology Program, Massachusetts General Hospital, Boston, MA, USA
| | - Shi-Xian Deng
- Department of Medicine, New York-Presbyterian Hospital-Columbia and Cornell, New York, NY, USA
| | - Hyun Sook Ahn
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | - Johannes van Agthoven
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Leukocyte Biology and Inflammation Laboratory, Massachusetts General Hospital, Boston, MA, USA
- Structural Biology Program, Massachusetts General Hospital, Boston, MA, USA
| | - Mark Yeager
- The Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, FL, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, VCU School of Pharmacy, Richmond, VA, USA
| | - David A Tess
- Department of Pharmacokinetics, Dynamics, and Metabolism, Pfizer Inc, Cambridge, MA, USA
| | - Donald W Landry
- Department of Medicine, New York-Presbyterian Hospital-Columbia and Cornell, New York, NY, USA
| | - Mortimer Poncz
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Amin Arnaout
- Division of Nephrology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Leukocyte Biology and Inflammation Laboratory, Massachusetts General Hospital, Boston, MA, USA.
- Structural Biology Program, Massachusetts General Hospital, Boston, MA, USA.
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