101
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Shlosman I, Fivenson EM, Gilman MSA, Sisley TA, Walker S, Bernhardt TG, Kruse AC, Loparo JJ. Allosteric activation of cell wall synthesis during bacterial growth. Nat Commun 2023; 14:3439. [PMID: 37301887 PMCID: PMC10257715 DOI: 10.1038/s41467-023-39037-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
The peptidoglycan (PG) cell wall protects bacteria against osmotic lysis and determines cell shape, making this structure a key antibiotic target. Peptidoglycan is a polymer of glycan chains connected by peptide crosslinks, and its synthesis requires precise spatiotemporal coordination between glycan polymerization and crosslinking. However, the molecular mechanism by which these reactions are initiated and coupled is unclear. Here we use single-molecule FRET and cryo-EM to show that an essential PG synthase (RodA-PBP2) responsible for bacterial elongation undergoes dynamic exchange between closed and open states. Structural opening couples the activation of polymerization and crosslinking and is essential in vivo. Given the high conservation of this family of synthases, the opening motion that we uncovered likely represents a conserved regulatory mechanism that controls the activation of PG synthesis during other cellular processes, including cell division.
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Affiliation(s)
- Irina Shlosman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Morgan S A Gilman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Tyler A Sisley
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Suzanne Walker
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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102
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Mergiya TF, Gundersen JET, Kanhema T, Brighter G, Ishizuka Y, Bramham CR. Detection of Arc/Arg3.1 oligomers in rat brain: constitutive and synaptic activity-evoked dimer expression in vivo. Front Mol Neurosci 2023; 16:1142361. [PMID: 37363319 PMCID: PMC10289200 DOI: 10.3389/fnmol.2023.1142361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
The immediate early gene product activity-regulated cytoskeleton-associated protein (Arc or Arg3.1) is a major regulator of long-term synaptic plasticity with critical roles in postnatal cortical development and memory formation. However, the molecular basis of Arc function is undefined. Arc is a hub protein with interaction partners in the postsynaptic neuronal compartment and nucleus. Previous in vitro biochemical and biophysical analysis of purified recombinant Arc showed formation of low-order oligomers and larger particles including retrovirus-like capsids. Here, we provide evidence for naturally occurring Arc oligomers in the mammalian brain. Using in situ protein crosslinking to trap weak Arc-Arc interactions, we identified in various preparations a prominent Arc immunoreactive band on SDS-PAGE of molecular mass corresponding to a dimer. While putative trimers, tetramers and heavier Arc species were detected, they were of lower abundance. Stimulus-evoked induction of Arc expression and dimer formation was first demonstrated in SH-SY5Y neuroblastoma cells treated with the muscarinic cholinergic agonist, carbachol, and in primary cortical neuronal cultures treated with brain-derived neurotrophic factor (BDNF). In the dentate gyrus (DG) of adult anesthetized rats, induction of long-term potentiation (LTP) by high-frequency stimulation (HFS) of medial perforant synapses or by brief intrahippocampal infusion of BDNF led to a massive increase in Arc dimer expression. Arc immunoprecipitation of crosslinked DG tissue showed enhanced dimer expression during 4 h of LTP maintenance. Mass spectrometric proteomic analysis of immunoprecipitated, gel-excised bands corroborated detection of Arc dimer. Furthermore, Arc dimer was constitutively expressed in naïve cortical, hippocampal and DG tissue, with the lowest levels in the DG. Taken together the results implicate Arc dimer as the predominant low-oligomeric form in mammalian brain, exhibiting regional differences in its constitutive expression and enhanced synaptic activity-evoked expression in LTP.
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Affiliation(s)
- Tadiwos F. Mergiya
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, Bergen, Norway
| | - Jens Edvard Trygstad Gundersen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, Bergen, Norway
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, Bergen, Norway
| | - Grant Brighter
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Yuta Ishizuka
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Clive R. Bramham
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Mohn Research Center for the Brain, University of Bergen, Bergen, Norway
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103
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Rahman MS, Han MJ, Kim SW, Kang SM, Kim BR, Kim H, Lee CJ, Noh JE, Kim H, Lee JO, Jang SK. Structure-Guided Development of Bivalent Aptamers Blocking SARS-CoV-2 Infection. Molecules 2023; 28:4645. [PMID: 37375202 DOI: 10.3390/molecules28124645] [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: 05/22/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused devastation to human society through its high virulence, infectivity, and genomic mutations, which reduced the efficacy of vaccines. Here, we report the development of aptamers that effectively interfere with SARS-CoV-2 infection by targeting its spike protein, which plays a pivotal role in host cell entry of the virus through interaction with the viral receptor angiotensin-converting enzyme 2 (ACE2). To develop highly effective aptamers and to understand their mechanism in inhibiting viral infection, we determined the three-dimensional (3D) structures of aptamer/receptor-binding domain (RBD) complexes using cryogenic electron microscopy (cryo-EM). Moreover, we developed bivalent aptamers targeting two distinct regions of the RBD in the spike protein that directly interact with ACE2. One aptamer interferes with the binding of ACE2 by blocking the ACE2-binding site in RBD, and the other aptamer allosterically inhibits ACE2 by binding to a distinct face of RBD. Using the 3D structures of aptamer-RBD complexes, we minimized and optimized these aptamers. By combining the optimized aptamers, we developed a bivalent aptamer that showed a stronger inhibitory effect on virus infection than the component aptamers. This study confirms that the structure-based aptamer-design approach has a high potential in developing antiviral drugs against SARS-CoV-2 and other viruses.
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Affiliation(s)
- Md Shafiqur Rahman
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Min Jung Han
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Sang Won Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Seong Mu Kang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Bo Ri Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Heesun Kim
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Chang Jun Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Jung Eun Noh
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Hanseong Kim
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
| | - Sung Key Jang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang-si 37673, Republic of Korea
- Division of Integrative Bioscience & Biotechnology, POSTECH Biotech Center, Pohang University of Science and Technology, Nam-gu, Pohang-si 37673, Republic of Korea
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104
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Gullberg RC, Frydman J. Novel Mode of nanoLuciferase Packaging in SARS-CoV-2 Virions and VLPs Provides Versatile Reporters for Virus Production. Viruses 2023; 15:1335. [PMID: 37376634 DOI: 10.3390/v15061335] [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: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
SARS-CoV-2 is a positive-strand RNA virus in the Coronaviridae family that is responsible for morbidity and mortality worldwide. To better understand the molecular pathways leading to SARS-CoV-2 virus assembly, we examined a virus-like particle (VLP) system co-expressing all structural proteins together with an mRNA reporter encoding nanoLuciferase (herein nLuc). Surprisingly, the 19 kDa nLuc protein itself was encapsidated into VLPs, providing a better reporter than nLuc mRNA itself. Strikingly, infecting nLuc-expressing cells with the SARS-CoV-2, NL63 or OC43 coronaviruses yielded virions containing packaged nLuc that served to report viral production. In contrast, infection with the flaviviruses, dengue or Zika, did not lead to nLuc packaging and secretion. A panel of reporter protein variants revealed that the packaging is size-limited and requires cytoplasmic expression, indicating that the large virion of coronaviruses can encaspidate a small cytoplasmic reporter protein. Our findings open the way for powerful new approaches to measure coronavirus particle production, egress and viral entry mechanisms.
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Affiliation(s)
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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105
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Zhang Y, Zhao L, Wang Q, Zhang Z, Ren X, Yang X, Zeng S, Lv L, Zhao L, Su S, Chen X, Fu B. A novel epitope tag from rabies virus has versatile in vitro applications. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12546-9. [PMID: 37166480 DOI: 10.1007/s00253-023-12546-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Fusion tag technology is an important tool for rapid separation, purification, and characterization of proteins. Combined with monoclonal antibodies, tag epitope systems can be rapidly adapted to many assay systems. A monoclonal antibody that reacts with the matrix protein of the rabies virus CVS-11 strain was reported. The epitope (termed M) targeted by this antibody contains only six amino acids. We examine whether this specific sequence epitope can be applied as a protein tag. We show ectopic expression of M-tagged proteins has little impact on cell viability or major signaling pathways. The M tag system can be used for western blotting, immunoprecipitation, immunofluorescence staining, and flow cytometry assays. The results indicate the specificity, sensitivity, and versatility of this novel epitope tag system are comparable to the widely used FLAG tag system, providing researchers with an additional tool for molecular analysis. KEY POINTS: • A short peptide (Pro Pro Tyr Asp Asp Asp) can be applied as a new tag. • The new epitope-tagging fusion system has no effect on the main cellular signaling pathway. • The epitope-tagging fusion system can be widely used for western blotting, immunoprecipitation, immunofluorescence, flow cytometry, etc.
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Affiliation(s)
- Yuelan Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Lin Zhao
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Qinyang Wang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Zhuyou Zhang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xiaoyan Ren
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Xue Yang
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Shaowei Zeng
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Linyue Lv
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural Universitygrid, 35155.37, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoqi Chen
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Bishi Fu
- Department of Rheumatology and Immunology, State Key Laboratory of Virology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Pulmonary and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China.
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106
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Zhou J, Ge Q, Wang D, Guo Q, Tao Y. Engineering a modular double-transmembrane synthetic receptor system for customizing cellular programs. Cell Rep 2023; 42:112385. [PMID: 37043348 DOI: 10.1016/j.celrep.2023.112385] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/21/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
Implementation of designer receptors in engineered cells confers them to sense a particular physiological or disease state and respond with user-defined programs. To expand the therapeutic application scope of engineered cells, synthetic receptors realized through different strategies are in great demand. Here, we develop a synthetic receptor system that exerts dual control by incorporating two transmembrane helices for the signal chain. Together with a sensor-actuator device with minimal background signals and a positive loop circuit, this receptor system can sensitively respond to extracellular protein signals. We demonstrate that this synthetic receptor system can be readily adapted to respond to various inputs, such as interleukin-1 (IL-1), programmed death ligand 1 (PD-L1), and HER2, and release customized outputs, including fluorescence signals and the therapeutic molecule IL-2. The robust signaling ability and generality of this receptor system promise it to be a useful tool in the field of cell engineering for fundamental research and translational applications.
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Affiliation(s)
- Jingru Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiangqiang Ge
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Dandan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China
| | - Qiong Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
| | - Yuyong Tao
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Center for Cross-disciplinary Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, P.R. China.
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107
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Kiss L, Rhinesmith T, Luptak J, Dickson CF, Weidenhausen J, Smyly S, Yang JC, Maslen SL, Sinning I, Neuhaus D, Clift D, James LC. Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates. Nat Commun 2023; 14:2160. [PMID: 37061529 PMCID: PMC10105713 DOI: 10.1038/s41467-023-37504-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: 06/29/2022] [Accepted: 03/20/2023] [Indexed: 04/17/2023] Open
Abstract
TRIM proteins are the largest family of E3 ligases in mammals. They include the intracellular antibody receptor TRIM21, which is responsible for mediating targeted protein degradation during Trim-Away. Despite their importance, the ubiquitination mechanism of TRIM ligases has remained elusive. Here we show that while Trim-Away activation results in ubiquitination of both ligase and substrate, ligase ubiquitination is not required for substrate degradation. N-terminal TRIM21 RING ubiquitination by the E2 Ube2W can be inhibited by N-terminal acetylation, but this doesn't prevent substrate ubiquitination nor degradation. Instead, uncoupling ligase and substrate degradation prevents ligase recycling and extends functional persistence in cells. Further, Trim-Away degrades substrates irrespective of whether they contain lysines or are N-terminally acetylated, which may explain the ability of TRIM21 to counteract fast-evolving pathogens and degrade diverse substrates.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Tyler Rhinesmith
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jakub Luptak
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Claire F Dickson
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging School of Medical Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Jonas Weidenhausen
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
- EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Shannon Smyly
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Irmgard Sinning
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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108
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Westlund E, Bergenstråle A, Pokhrel A, Chan H, Skoglund U, Daley DO, Söderström B. Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring in Escherichia coli. Curr Genet 2023; 69:153-163. [PMID: 37022498 PMCID: PMC10163087 DOI: 10.1007/s00294-023-01266-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/07/2023]
Abstract
Understanding where proteins are localized in a bacterial cell is essential for understanding their function and regulation. This is particularly important for proteins that are involved in cell division, which localize at the division septum and assemble into highly regulated complexes. Current knowledge of these complexes has been greatly facilitated by super-resolution imaging using fluorescent protein fusions. Herein, we demonstrate with FtsZ that single-molecule PALM images can be obtained in-vivo using a genetically fused nanotag (ALFA), and a corresponding nanobody fused to mEos3.2. The methodology presented is applicable to other bacterial proteins.
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Affiliation(s)
- Emma Westlund
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Axel Bergenstråle
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Alaska Pokhrel
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Helena Chan
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Ulf Skoglund
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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109
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Ishii S, Chino H, Ode KL, Kurikawa Y, Ueda HR, Matsuura A, Mizushima N, Itakura E. CCPG1 recognizes endoplasmic reticulum luminal proteins for selective ER-phagy. Mol Biol Cell 2023; 34:ar29. [PMID: 36735498 PMCID: PMC10092646 DOI: 10.1091/mbc.e22-09-0432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The endoplasmic reticulum (ER) is a major cell compartment where protein synthesis, folding, and posttranslational modifications occur with assistance from a wide variety of chaperones and enzymes. Quality control systems selectively eliminate abnormal proteins that accumulate inside the ER due to cellular stresses. ER-phagy, that is, selective autophagy of the ER, is a mechanism that maintains or reestablishes cellular and ER-specific homeostasis through removal of abnormal proteins. However, how ER luminal proteins are recognized by the ER-phagy machinery remains unclear. Here, we applied the aggregation-prone protein, six-repeated islet amyloid polypeptide (6xIAPP), as a model ER-phagy substrate and found that cell cycle progression 1 (CCPG1), which is an ER-phagy receptor, efficiently mediates its degradation via ER-phagy. We also identified prolyl 3-hydroxylase family member 4 (P3H4) as an endogenous cargo of CCPG1-dependent ER-phagy. The ER luminal region of CCPG1 contains several highly conserved regions that we refer to as cargo-interacting regions (CIRs); these interact directly with specific luminal cargos for ER-phagy. Notably, 6xIAPP and P3H4 interact directly with different CIRs. These findings indicate that CCPG1 is a bispecific ER-phagy receptor for ER luminal proteins and the autophagosomal membrane that contributes to the efficient removal of aberrant ER-resident proteins through ER-phagy.
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Affiliation(s)
- Shunsuke Ishii
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Chiba 263-8522, Japan
| | - Haruka Chino
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka 565-0871, Japan
| | - Akira Matsuura
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Tokyo 113-0033, Japan
| | - Eisuke Itakura
- Department of Biology, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
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110
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Saal KA, Shaib AH, Mougios N, Crzan D, Opazo F, Rizzoli SO. Heat denaturation enables multicolor X10-STED microscopy. Sci Rep 2023; 13:5366. [PMID: 37005431 PMCID: PMC10067834 DOI: 10.1038/s41598-023-32524-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Expansion microscopy (ExM) improves imaging quality by physically enlarging the biological specimens. In principle, combining a large expansion factor with optical super-resolution should provide extremely high imaging precision. However, large expansion factors imply that the expanded specimens are dim and are therefore poorly suited for optical super-resolution. To solve this problem, we present a protocol that ensures the expansion of the samples up to 10-fold, in a single expansion step, through high-temperature homogenization (X10ht). The resulting gels exhibit a higher fluorescence intensity than gels homogenized using enzymatic digestion (based on proteinase K). This enables the sample analysis by multicolor stimulated emission depletion (STED) microscopy, for a final resolution of 6-8 nm in neuronal cell cultures or isolated vesicles. X10ht also enables the expansion of 100-200 µm thick brain samples, up to 6-fold. The better epitope preservation also enables the use of nanobodies as labeling probes and the implementation of post-expansion signal amplification. We conclude that X10ht is a promising tool for nanoscale resolution in biological samples.
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Affiliation(s)
- Kim Ann Saal
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Ali H Shaib
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nikolaos Mougios
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany
| | - Dagmar Crzan
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- NanoTag Biotechnologies GmbH, Rudolf Wissell Str. 28a, 37079, Göttingen, Germany
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany
| | - Silvio O Rizzoli
- Department of Sensory- and Neurophysiology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Sieboldt-Str. 3a, 37075, Göttingen, Germany.
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111
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Chernov KG, Manoilov KY, Oliinyk OS, Shcherbakova DM, Verkhusha VV. Photodegradable by Yellow-Orange Light degFusionRed Optogenetic Module with Autocatalytically Formed Chromophore. Int J Mol Sci 2023; 24:6526. [PMID: 37047499 PMCID: PMC10095432 DOI: 10.3390/ijms24076526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Optogenetic systems driven by yellow-orange light are required for the simultaneous regulation of several cellular processes. We have engineered the red fluorescent protein FusionRed into a 26 kDa monomeric optogenetic module, called degFusionRed. Unlike other fluorescent protein-based optogenetic domains, which exhibit light-induced self-inactivation by generating reactive oxygen species, degFusionRed undergoes proteasomal degradation upon illumination with 567 nm light. Similarly to the parent protein, degFusionRed has minimal absorbance at 450 nm and above 650 nm, making it spectrally compatible with blue and near-infrared-light-controlled optogenetic tools. The autocatalytically formed chromophore provides degFusionRed with an additional advantage over most optogenetic tools that require the binding of the exogenous chromophores, the amount of which varies in different cells. The degFusionRed efficiently performed in the engineered light-controlled transcription factor and in the targeted photodegradation of the protein of interest, demonstrating its versatility as the optogenetic module of choice for spectral multiplexed interrogation of various cellular processes.
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Affiliation(s)
| | - Kyrylo Yu. Manoilov
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olena S. Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Daria M. Shcherbakova
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Vladislav V. Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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112
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Tomihari A, Kiyota M, Matsuura A, Itakura E. Alpha 2-macroglobulin acts as a clearance factor in the lysosomal degradation of extracellular misfolded proteins. Sci Rep 2023; 13:4680. [PMID: 36977730 PMCID: PMC10050189 DOI: 10.1038/s41598-023-31104-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Proteostasis regulates protein folding and degradation; its maintenance is essential for resistance to stress and aging. The loss of proteostasis is associated with many age-related diseases. Within the cell, molecular chaperones facilitate the refolding of misfolded proteins into their bioactive forms, thus preventing undesirable interactions and aggregation. Although the mechanisms of intracellular protein degradation pathways for intracellular misfolded proteins have been extensively studied, the protein degradation pathway for extracellular proteins remain poorly understood. In this study, we identified several misfolded proteins that are substrates for alpha 2-macroglobulin (α2M), an extracellular chaperone. We also established a lysosomal internalization assay for α2M, which revealed that α2M mediates the lysosomal degradation of extracellular misfolded proteins. Comparative analyses of α2M and clusterin, another extracellular chaperone, indicated that α2M preferentially targets aggregation-prone proteins. Thus, we present the degradation pathway of α2M, which interacts with aggregation-prone proteins for lysosomal degradation via selective internalization.
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Affiliation(s)
- Ayaka Tomihari
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Inage-Ku, Chiba, 263-8522, Japan
| | - Mako Kiyota
- Department of Biology, Graduate School of Science and Engineering, Chiba University, Inage-Ku, Chiba, 263-8522, Japan
| | - Akira Matsuura
- Department of Biology, Graduate School of Science, Chiba University, Inage-Ku, Chiba, 263-8522, Japan
| | - Eisuke Itakura
- Department of Biology, Graduate School of Science, Chiba University, Inage-Ku, Chiba, 263-8522, Japan.
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113
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Tsirigotaki A, Dansercoer A, Verschueren KHG, Marković I, Pollmann C, Hafer M, Felix J, Birck C, Van Putte W, Catteeuw D, Tavernier J, Fernando Bazan J, Piehler J, Savvides SN, Verstraete K. Mechanism of receptor assembly via the pleiotropic adipokine Leptin. Nat Struct Mol Biol 2023; 30:551-563. [PMID: 36959263 DOI: 10.1038/s41594-023-00941-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/06/2023] [Indexed: 03/25/2023]
Abstract
The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and mechanism of Leptin-mediated LEP-R assemblies has remained unclear. Intriguingly, the signaling-competent isoform of LEP-R is only lowly abundant amid several inactive short LEP-R isoforms contributing to a mechanistic conundrum. Here we show by X-ray crystallography and cryo-EM that, in contrast to long-standing paradigms, Leptin induces type I cytokine receptor assemblies featuring 3:3 stoichiometry and demonstrate such Leptin-induced trimerization of LEP-R on living cells via single-molecule microscopy. In mediating these assemblies, Leptin undergoes drastic restructuring that activates its site III for binding to the Ig domain of an adjacent LEP-R. These interactions are abolished by mutations linked to obesity. Collectively, our study provides the structural and mechanistic framework for how evolutionarily conserved Leptin:LEP-R assemblies with 3:3 stoichiometry can engage distinct LEP-R isoforms to achieve signaling.
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Affiliation(s)
- Alexandra Tsirigotaki
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ann Dansercoer
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Koen H G Verschueren
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Iva Marković
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Christoph Pollmann
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Maximillian Hafer
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Jan Felix
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Catherine Birck
- Integrated Structural Biology Platform, Centre for Integrative Biology (CBI), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U1258, University of Strasbourg, Illkirch, France
| | | | - Dominiek Catteeuw
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Orionis Biosciences, Ghent, Belgium
| | - J Fernando Bazan
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- ħ Bioconsulting llc, Stillwater, MN, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Kenneth Verstraete
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
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114
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Immunosensor for realtime monitoring of the expression of recombinant proteins during bioprocess. Anal Biochem 2023; 665:115069. [PMID: 36716945 DOI: 10.1016/j.ab.2023.115069] [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: 12/10/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Recombinant protein expression and purification are crucial in modern life sciences research. A fluorescent immunosensor termed Quenchbody (Q-body) was developed for real-time monitoring of FLAG-fused protein expression. Detection results showed that the limit of detection of the 3 × FLAG peptide detected by the TAMRA-labeled anti-FLAG Q-body was as low as 3.1 nM, with a half-maximal effective concentration of 21.4 nM. Furthermore, the anti-FLAG Q-body was used for detecting different proteins fused with a FLAG-tag at the N- or C-terminal. Subsequently, the constructed Q-body was used to monitor the real-time fermentation process of single-strand DNA-binding protein in Escherichia coli. Unlike previously reported Q-bodies that widely used Fab or scFv, the present study used a full-length anti-FLAG IgG for the first time. Owing to its excellent detection speed and sensitivity, the FLAG Q-body immunosensor has the potential to quantify and monitor target recombinant proteins in multiple biological processes in real-time.
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115
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Eklund AS, Jungmann R. Optimized Coiled-Coil Interactions for Multiplexed Peptide-PAINT. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206347. [PMID: 36642829 DOI: 10.1002/smll.202206347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Super-resolution microscopy has revolutionized how researchers characterize samples in the life sciences in the last decades. Amongst methods employing single-molecule localization microscopy, DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) is a relatively easy-to-implement method that uses the programmable and repetitive binding of dye-labeled DNA imager strands to their respective docking strands. Recently developed Peptide-PAINT replaces the interaction of oligonucleotides by short coiled-coil peptide sequences leading to an improved labeling scheme by reducing linkage errors to target proteins. However, only one coiled-coil pair is currently available for Peptide-PAINT, preventing multiplexed imaging. In this study, the initial Peptide-PAINT E/K coil is improved by modifying its length for optimized binding kinetics leading to improved localization precisions. Additionally, an orthogonal P3/P4 coil pair is introduced, enabling 2-plex Peptide-PAINT imaging and benchmarking its performance and orthogonality using single-molecule and DNA origami assays. Finally, the P3/P4 peptide pair is used to image the human epidermal growth factor receptors 2 (ErbB2/Her2) in 2D and 3D at the single receptor level using genetically encoded peptide tags.
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Affiliation(s)
- Alexandra S Eklund
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Planegg, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Planegg, Germany
- Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
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116
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Zuo H, Wang X, Liu W, Chen Z, Liu R, Yang H, Xia C, Xie J, Sun T, Ning B. Nanobody-based magnetic chemiluminescence immunoassay for one-pot detection of ochratoxin A. Talanta 2023; 258:124388. [PMID: 36921368 DOI: 10.1016/j.talanta.2023.124388] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/03/2023] [Accepted: 02/18/2023] [Indexed: 03/16/2023]
Abstract
Ochratoxin A (OTA) contamination seriously threatens food safety and human health and requires sensitive and rapid tools for monitoring. In this study, a convenient enzyme-linked immunosorbent assay based on Avi-labeled nanobody Nb-2G/streptavidin-alkaline phosphatase and magnetic beads (MBS-ELISA) was established for the sensitive detection of OTA, which could be used for one-pot detection without immobilization. After optimization, the 50% inhibitory concentration (IC50) and the lowest limit of detection value of the MBS-ELISA was 1.17 ng/mL and 0.07 ng/mL and the linear range was 248.8 pg/mL-5.28 ng/mL, respectively, which accords with state criteria for food safety. The developed one-step MBS-ELISA was almost 20-times more sensitive than the classic BA-ELISA and could generate results within 15 min, which was significantly less than the classic BA-ELISA at approximately 3 h. The MBS-ELISA indicated good recovery (86.4-114.3%) in spiked sorghum, buckwheat, and mung bean. Thus, MBS-ELISA represents a very promising strategy for the simple, rapid, and accurate detection of OTA and other toxic and hazardous contaminants.
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Affiliation(s)
- Hu Zuo
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xinyang Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wentao Liu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zongfen Chen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Ruonan Liu
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Han Yang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Chunyan Xia
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Jinli Xie
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Tieqiang Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
| | - Baoan Ning
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, China.
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117
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Vullhorst D, Bloom MS, Akella N, Buonanno A. ER-PM Junctions on GABAergic Interneurons Are Organized by Neuregulin 2/VAP Interactions and Regulated by NMDA Receptors. Int J Mol Sci 2023; 24:2908. [PMID: 36769244 PMCID: PMC9917868 DOI: 10.3390/ijms24032908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Neuregulins (NRGs) signal via ErbB receptors to regulate neural development, excitability, synaptic and network activity, and behaviors relevant to psychiatric disorders. Bidirectional signaling between NRG2/ErbB4 and NMDA receptors is thought to homeostatically regulate GABAergic interneurons in response to increased excitatory neurotransmission or elevated extracellular glutamate levels. Unprocessed proNRG2 forms discrete clusters on cell bodies and proximal dendrites that colocalize with the potassium channel Kv2.1 at specialized endoplasmic reticulum-plasma membrane (ER-PM) junctions, and NMDA receptor activation triggers rapid dissociation from ER-PM junctions and ectodomain shedding by ADAM10. Here, we elucidate the mechanistic basis of proNRG2 clustering at ER-PM junctions and its regulation by NMDA receptors. Importantly, we demonstrate that proNRG2 promotes the formation of ER-PM junctions by directly binding the ER-resident membrane tether VAP, like Kv2.1. The proNRG2 intracellular domain harbors two non-canonical, low-affinity sites that cooperatively mediate VAP binding. One of these is a cryptic and phosphorylation-dependent VAP binding motif that is dephosphorylated following NMDA receptor activation, thus revealing how excitatory neurotransmission promotes the dissociation of proNRG2 from ER-PM junctions. Therefore, proNRG2 and Kv2.1 can independently function as VAP-dependent organizers of neuronal ER-PM junctions. Based on these and prior studies, we propose that proNRG2 and Kv2.1 serve as co-regulated downstream effectors of NMDA receptors to homeostatically regulate GABAergic interneurons.
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Affiliation(s)
- Detlef Vullhorst
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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118
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Single-molecule visualization of mRNA circularization during translation. Exp Mol Med 2023; 55:283-289. [PMID: 36720916 PMCID: PMC9981743 DOI: 10.1038/s12276-023-00933-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/04/2022] [Accepted: 12/04/2022] [Indexed: 02/02/2023] Open
Abstract
Translation is mediated by precisely orchestrated sequential interactions among translation initiation components, mRNA, and ribosomes. Biochemical, structural, and genetic techniques have revealed the fundamental mechanism that determines what occurs and when, where and in what order. Most mRNAs are circularized via the eIF4E-eIF4G-PABP interaction, which stabilizes mRNAs and enhances translation by recycling ribosomes. However, studies using single-molecule fluorescence imaging have allowed for the visualization of complex data that opposes the traditional "functional circularization" theory. Here, we briefly introduce single-molecule techniques applied to studies on mRNA circularization and describe the results of in vitro and live-cell imaging. Finally, we discuss relevant insights and questions gained from single-molecule research related to translation.
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119
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Zhao C, MacKinnon R. Structural and functional analyses of a GPCR-inhibited ion channel TRPM3. Neuron 2023; 111:81-91.e7. [PMID: 36283409 DOI: 10.1016/j.neuron.2022.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022]
Abstract
G-protein coupled receptors (GPCRs) govern the physiological response to stimuli by modulating the activity of downstream effectors, including ion channels. TRPM3 is an ion channel inhibited by GPCRs through direct interaction with G protein (Gβγ) released upon their activation. This GPCR-TRPM3 signaling pathway contributes to the analgesic effect of morphine. Here, we characterized Gβγ inhibition of TRPM3 using electrophysiology and single particle cryo-electron microscopy (cryo-EM). From electrophysiology, we obtained a half inhibition constant (IC50) of ∼240 nM. Using cryo-EM, we determined structures of mouse TRPM3 expressed in human cells with and without Gβγ and with and without PIP2, a lipid required for TRPM3 activity, at resolutions of 2.7-4.7 Å. Gβγ-TRPM3 interfaces vary depending on PIP2 occupancy; however, in all cases, Gβγ appears loosely attached to TRPM3. The IC50 in electrophysiology experiments raises the possibility that additional unknown factors may stabilize the TRPM3-Gβγ complex.
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Affiliation(s)
- Chen Zhao
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, the Rockefeller University, New York, NY 10065, United States
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, the Rockefeller University, New York, NY 10065, United States.
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120
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Facile repurposing of peptide-MHC-restricted antibodies for cancer immunotherapy. Nat Biotechnol 2023:10.1038/s41587-022-01567-w. [PMID: 36593402 DOI: 10.1038/s41587-022-01567-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Monoclonal antibodies (Abs) that recognize major histocompatability complex (MHC)-presented tumor antigens in a manner similar to T cell receptors (TCRs) have great potential as cancer immunotherapeutics. However, isolation of 'TCR-mimic' (TCRm) Abs is laborious because Abs have not evolved the structurally nuanced peptide-MHC restriction of αβ-TCRs. Here, we present a strategy for rapid isolation of highly peptide-specific and 'MHC-restricted' Abs by re-engineering preselected Abs that engage peptide-MHC in a manner structurally similar to that of conventional αβ-TCRs. We created structure-based libraries focused on the peptide-interacting residues of TCRm Ab complementarity-determining region (CDR) loops, and rapidly generated MHC-restricted Abs to both mouse and human tumor antigens that specifically killed target cells when formatted as IgG, bispecific T cell engager (BiTE) and chimeric antigen receptor-T (CAR-T). Crystallographic analysis of one selected pMHC-restricted Ab revealed highly peptide-specific recognition, validating the engineering strategy. This approach can yield tumor antigen-specific antibodies in several weeks, potentially enabling rapid clinical translation.
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121
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D'Ercole C, de Marco A. Isolation of Adhirons Specific for Plant Protoplast Membrane Biomarkers Is Simplified by Phagemid Design. Methods Mol Biol 2023; 2681:33-45. [PMID: 37405641 DOI: 10.1007/978-1-0716-3279-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Phage display is an effective method to retrieve binders specific for a target epitope from a large clone library. Nevertheless, the panning process allows for the accumulation of some contaminant clones into the selected phage pool and, consequently, each clone requires individual screening to verify its actual specificity. This step is time-consuming, independently on the chosen method, and relies on the availability of reliable reagents. Since phages display a single binder responsible for the antigen recognition but their coat is formed by several repeats of the same proteins, the targeting of coat epitopes is often exploited to amplify the signal. Commercial anti-M13 antibodies are commonly labeled with peroxidase or FITC but customized antibodies might be necessary for specific applications. Here, we report a protocol describing the selection of anti-protoplast Adhirons that relies on the availability of nanobodies fused to a fluorescent protein to use during flow cytometry screening. Specifically, when preparing our Adhiron synthetic library, we designed a new phagemid that allows the expression of the clones fused to three tags. These can interact with a large variety of commercial and home-made reagents, selected according to the needs of the downstream characterization process. In the described case, we combined the ALFA-tagged Adhirons with an anti-ALFAtag nanobody fused with the fluorescent protein mRuby3.
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Affiliation(s)
- Claudia D'Ercole
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Nova Gorica, Slovenia
| | - Ario de Marco
- Laboratory of Environmental and Life Sciences, University of Nova Gorica, Rožna Dolina, Nova Gorica, Slovenia.
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122
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Grahn AK, Allen GL, Kay BK. Efficient Cloning of Inserts for Phage Display by Golden Gate Assembly. Methods Mol Biol 2023; 2702:191-203. [PMID: 37679620 DOI: 10.1007/978-1-0716-3381-6_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] [Indexed: 09/09/2023]
Abstract
Phage display enables the discovery of high-affinity binders. In phage display, one commonly uses traditional cloning methods to insert DNA into the coding region of one of the five capsid proteins. Here we describe the use of a new vector with kanamycin resistance and BsaI sites for the utilization of Golden Gate cloning into the N-terminus of mature protein III. We also describe the successful pentavalent display of six different inserts: the AviD-tag, the Z-domain of protein A, the Myc-tag, the ALFA nanobody, the BC2 nanobody, and the Flag-tag.
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Rudd-Schmidt JA, Laine RF, Noori T, Brennan AJ, Voskoboinik I. ALFA-PRF: a novel approach to detect murine perforin release from CTLs into the immune synapse. Front Immunol 2022; 13:931820. [PMID: 36618385 PMCID: PMC9813862 DOI: 10.3389/fimmu.2022.931820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
When killing through the granule exocytosis pathway, cytotoxic lymphocytes release key effector molecules into the immune synapse, perforin and granzymes, to initiate target cell killing. The pore-forming perforin is essential for the function of cytotoxic lymphocytes, as its pores disrupt the target cell membrane and allow diffusion of pro-apoptotic serine proteases, granzyme, into the target cell, where they initiate various cell death cascades. Unlike human perforin, the detection of its murine counterpart in a live cell system has been problematic due its relatively low expression level and the lack of sensitive antibodies. The lack of a suitable methodology to visualise murine perforin secretion into the synapse hinders the study of the cytotoxic lymphocyte secretory machinery in murine models of human disease. Here, we describe a novel recombinant technology, whereby a short ALFA-tag sequence has been fused with the amino-terminus of a mature murine perforin, and this allowed its detection by the highly specific FluoTag®-X2 anti-ALFA nanobodies using both Total Internal Reflection Fluorescence (TIRF) microscopy of an artificial synapse, and confocal microscopy of the physiological immune synapse with a target cell. This methodology can have broad application in the field of cytotoxic lymphocyte biology and for the many models of human disease.
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Affiliation(s)
- Jesse A. Rudd-Schmidt
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,*Correspondence: Ilia Voskoboinik, ; Jesse A. Rudd-Schmidt,
| | - Romain F. Laine
- Medical Research Council (MRC)-Laboratory for Molecular Cell Biology, University College London, London, United Kingdom,The Francis Crick Institute, London, United Kingdom,MicrographiaBio, Translation & Innovation Hub, London, United Kingdom
| | - Tahereh Noori
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Amelia J. Brennan
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Ilia Voskoboinik
- Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia,*Correspondence: Ilia Voskoboinik, ; Jesse A. Rudd-Schmidt,
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124
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Application of ALFA-Tagging in the Nematode Model Organisms Caenorhabditis elegans and Pristionchus pacificus. Cells 2022; 11:cells11233875. [PMID: 36497133 PMCID: PMC9740511 DOI: 10.3390/cells11233875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The detection, manipulation and purification of proteins is key in modern life sciences studies. To achieve this goal, a plethora of epitope tags have been employed in model organisms from bacteria to humans. Recently, the introduction of the rationally designed ALFA-tag resulted in a highly versatile tool with a very broad spectrum of potential applications. ALFA-tagged proteins can be detected by nanobodies, the single-domain antibodies of camelids, allowing for super-resolution microscopy and immunoprecipitation in biochemical applications. Here, we introduce ALFA-tagging into the two nematode model organisms Caenorhabditis elegans and Pristionchus pacificus. We show that the introduction of the DNA sequence, corresponding to the 13 amino acid sequence of the ALFA-tag, can easily be accommodated by CRISPR engineering. We provide examples of high-resolution protein expression in both nematodes. Finally, we use the GW182 ortholog Ppa-ain-1 to show successful pulldowns in P. pacificus. Thus, the ALFA-tag represents a novel epitope tag for nematode research with a broad spectrum of applications.
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125
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Gibbons M, Hong JM, Foster M, Chavarha M, Shao S, Ching L, Church VA, Schiff L, Ahadi S, Berndl M, Jess P, Pawlosky A. Million spot binding array platform for exploring and optimizing multiple simultaneous detection events. STAR Protoc 2022; 3:101829. [DOI: 10.1016/j.xpro.2022.101829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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126
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Lim CS, Jang YH, Lee GY, Han GM, Jeong HJ, Kim JW, Lee JO. TLR3 forms a highly organized cluster when bound to a poly(I:C) RNA ligand. Nat Commun 2022; 13:6876. [PMID: 36371424 PMCID: PMC9653405 DOI: 10.1038/s41467-022-34602-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 10/25/2022] [Indexed: 11/15/2022] Open
Abstract
Toll-like Receptor 3 (TLR3) initiates a potent anti-viral immune response by binding to double-stranded RNA ligands. Previous crystallographic studies showed that TLR3 forms a homodimer when bound to a 46-base pair RNA ligand. However, this short RNA fails to initiate a robust immune response. To obtain structural insights into the length dependency of TLR3 ligands, we determine the cryo-electron microscopy structure of full-length TLR3 in a complex with a synthetic RNA ligand with an average length of ~400 base pairs. In the structure, the dimeric TLR3 units are clustered along the double-stranded RNA helix in a highly organized and cooperative fashion with a uniform inter-dimer spacing of 103 angstroms. The intracellular and transmembrane domains are dispensable for the clustering because their deletion does not interfere with the cluster formation. Our structural observation suggests that ligand-induced clustering of TLR3 dimers triggers the ordered assembly of intracellular signaling adaptors and initiates a robust innate immune response.
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Affiliation(s)
- Chan Seok Lim
- Department of Life Sciences and POSTECH, Pohang, 37673 Korea
| | - Yoon Ha Jang
- Department of Life Sciences and POSTECH, Pohang, 37673 Korea
| | - Ga Young Lee
- Department of Life Sciences and POSTECH, Pohang, 37673 Korea
| | - Gu Min Han
- Department of Life Sciences and POSTECH, Pohang, 37673 Korea
| | - Hye Jin Jeong
- grid.49100.3c0000 0001 0742 4007Institute of Membrane Proteins, POSTECH, Pohang, 37673 Korea
| | - Ji Won Kim
- Department of Life Sciences and POSTECH, Pohang, 37673 Korea ,grid.49100.3c0000 0001 0742 4007Institute of Membrane Proteins, POSTECH, Pohang, 37673 Korea
| | - Jie-Oh Lee
- Department of Life Sciences and POSTECH, Pohang, 37673 Korea ,grid.49100.3c0000 0001 0742 4007Institute of Membrane Proteins, POSTECH, Pohang, 37673 Korea
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127
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Bloemeke N, Meighen‐Berger K, Hitzenberger M, Bach NC, Parr M, Coelho JPL, Frishman D, Zacharias M, Sieber SA, Feige MJ. Intramembrane client recognition potentiates the chaperone functions of calnexin. EMBO J 2022; 41:e110959. [PMID: 36314723 PMCID: PMC9753464 DOI: 10.15252/embj.2022110959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
One-third of the human proteome is comprised of membrane proteins, which are particularly vulnerable to misfolding and often require folding assistance by molecular chaperones. Calnexin (CNX), which engages client proteins via its sugar-binding lectin domain, is one of the most abundant ER chaperones, and plays an important role in membrane protein biogenesis. Based on mass spectrometric analyses, we here show that calnexin interacts with a large number of nonglycosylated membrane proteins, indicative of additional nonlectin binding modes. We find that calnexin preferentially bind misfolded membrane proteins and that it uses its single transmembrane domain (TMD) for client recognition. Combining experimental and computational approaches, we systematically dissect signatures for intramembrane client recognition by calnexin, and identify sequence motifs within the calnexin TMD region that mediate client binding. Building on this, we show that intramembrane client binding potentiates the chaperone functions of calnexin. Together, these data reveal a widespread role of calnexin client recognition in the lipid bilayer, which synergizes with its established lectin-based substrate binding. Molecular chaperones thus can combine different interaction modes to support the biogenesis of the diverse eukaryotic membrane proteome.
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Affiliation(s)
- Nicolas Bloemeke
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Kevin Meighen‐Berger
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Manuel Hitzenberger
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Nina C Bach
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Marina Parr
- Department of Bioinformatics, TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Joao PL Coelho
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Dmitrij Frishman
- Department of Bioinformatics, TUM School of Life SciencesTechnical University of MunichFreisingGermany
| | - Martin Zacharias
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Stephan A Sieber
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
| | - Matthias J Feige
- Department of Bioscience, Center for Functional Protein Assemblies (CPA), TUM School of Natural SciencesTechnical University of MunichGarchingGermany
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128
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Akhuli D, Dhar A, Viji AS, Bhojappa B, Palani S. ALIBY: ALFA Nanobody-Based Toolkit for Imaging and Biochemistry in Yeast. mSphere 2022; 7:e0033322. [PMID: 36190134 PMCID: PMC9599267 DOI: 10.1128/msphere.00333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Specialized epitope tags continue to be integral components of various biochemical and cell biological applications such as fluorescence microscopy, immunoblotting, immunoprecipitation, and protein purification. However, until recently, no single tag could offer this complete set of functionalities on its own. Here, we present a plasmid-based toolkit named ALIBY (ALFA toolkit for imaging and biochemistry in yeast) that provides a universal workflow to adopt the versatile ALFA tag/NbALFA system within the well-established model organism Saccharomyces cerevisiae. The kit comprises tagging plasmids for labeling a protein of interest with the ALFA tag and detection plasmids encoding fluorescent-protein-tagged NbALFA for live-cell imaging purposes. We demonstrate the suitability of ALIBY for visualizing the spatiotemporal localization of yeast proteins (i.e., the cytoskeleton, nucleus, centrosome, mitochondria, vacuole, endoplasmic reticulum, exocyst, and divisome) in live cells. Our approach has yielded an excellent signal-to-noise ratio without off-target effects or any effect on cell growth. In summary, our yeast-specific toolkit aims to simplify and further advance the live-cell imaging of differentially abundant yeast proteins while also being suitable for biochemical applications. IMPORTANCE In yeast research, conventional fluorescent protein tags and small epitope tags are widely used to study the spatiotemporal dynamics and activity of proteins. Although proven to be efficient, these tags lack the versatility for use across different cell biological and biochemical studies of a given protein of interest. Therefore, there is an urgent need for a unified platform for visualization and biochemical and functional analyses of proteins of interest in yeast. Here, we have engineered ALIBY, a plasmid-based toolkit that expands the benefits of the recently developed ALFA tag/NbALFA system to studies in the well-established model organism Saccharomyces cerevisiae. We demonstrate that ALIBY provides a simple and versatile strain construction workflow for long-duration live-cell imaging and biochemical applications in yeast.
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Affiliation(s)
- Dipayan Akhuli
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Anubhav Dhar
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Aileen Sara Viji
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Bindu Bhojappa
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Saravanan Palani
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
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129
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Zhang Q, Miyamoto A, Watanabe S, Arimori T, Sakai M, Tomisaki M, Kiuchi T, Takagi J, Watanabe N. Engineered fast-dissociating antibody fragments for multiplexed super-resolution microscopy. CELL REPORTS METHODS 2022; 2:100301. [PMID: 36313806 PMCID: PMC9606137 DOI: 10.1016/j.crmeth.2022.100301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/07/2022] [Accepted: 08/31/2022] [Indexed: 05/22/2023]
Abstract
Image reconstruction by integrating exchangeable single-molecule localization (IRIS) achieves multiplexed super-resolution imaging by high-density labeling with fast exchangeable fluorescent probes. However, previous methods to develop probes for individual targets required a great amount of time and effort. Here, we introduce a method for generating recombinant IRIS probes with a new mutagenesis strategy that can be widely applied to existing antibody sequences. Several conserved tyrosine residues at the base of complementarity-determining regions were identified as candidate sites for site-directed mutagenesis. With a high probability, mutations at candidate sites accelerated the off rate of recombinant antibody-based probes without compromising specific binding. We were able to develop IRIS probes from five monoclonal antibodies and three single-domain antibodies. We demonstrate multiplexed localization of endogenous proteins in primary neurons that visualizes small synaptic connections with high binding density. It is now practically feasible to generate fast-dissociating fluorescent probes for multitarget super-resolution imaging.
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Affiliation(s)
- Qianli Zhang
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Akitoshi Miyamoto
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Shin Watanabe
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Takao Arimori
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masanori Sakai
- Kyoto University Faculty of Engineering, Kyoto 606-8317, Japan
| | - Madoka Tomisaki
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
| | - Tai Kiuchi
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Naoki Watanabe
- Laboratory of Single-Molecule Cell Biology, Kyoto University Graduate School of Biostudies, Kyoto 606-8501, Japan
- Department of Pharmacology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
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130
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Guna A, Stevens TA, Inglis AJ, Replogle JM, Esantsi TK, Muthukumar G, Shaffer KCL, Wang ML, Pogson AN, Jones JJ, Lomenick B, Chou TF, Weissman JS, Voorhees RM. MTCH2 is a mitochondrial outer membrane protein insertase. Science 2022; 378:317-322. [PMID: 36264797 PMCID: PMC9674023 DOI: 10.1126/science.add1856] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the mitochondrial outer membrane, α-helical transmembrane proteins play critical roles in cytoplasmic-mitochondrial communication. Using genome-wide CRISPR screens, we identified MTCH2, and its paralog MTCH1, and showed that it is required for insertion of biophysically diverse tail-anchored (TA), signal-anchored, and multipass proteins, but not outer membrane β-barrel proteins. Purified MTCH2 was sufficient to mediate insertion into reconstituted proteoliposomes. Functional and mutational studies suggested that MTCH2 has evolved from a solute carrier transporter. MTCH2 uses membrane-embedded hydrophilic residues to function as a gatekeeper for the outer membrane, controlling mislocalization of TAs into the endoplasmic reticulum and modulating the sensitivity of leukemia cells to apoptosis. Our identification of MTCH2 as an insertase provided a mechanistic explanation for the diverse phenotypes and disease states associated with MTCH2 dysfunction. We showed that MTCH2 was both necessary and sufficient for insertion of diverse α-helical proteins into the mitochondrial outer membrane, and was the defining member of a family of insertases that have co-opted the SLC25 transporter fold.
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Affiliation(s)
- Alina Guna
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Taylor A Stevens
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Alison J Inglis
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Gayathri Muthukumar
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kelly C L Shaffer
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Maxine L Wang
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Angela N Pogson
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jeff J Jones
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Brett Lomenick
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 East California Avenue, Pasadena, CA 91125, USA
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131
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Cabalteja CC, Sachdev S, Cheloha RW. Rapid Covalent Labeling of Membrane Proteins on Living Cells Using a Nanobody-Epitope Tag Pair. Bioconjug Chem 2022; 33:1867-1875. [PMID: 36107739 PMCID: PMC10200341 DOI: 10.1021/acs.bioconjchem.2c00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic molecules that form a covalent bond upon binding to a targeted biomolecule (proximity-induced reactivity) are the subject of intense biomedical interest for the unique pharmacological properties imparted by irreversible binding. However, off-target covalent labeling and the lack of molecules with sufficient specificity limit more widespread applications. We describe the first example of a cross-linking platform that uses a synthetic peptide epitope and a single domain antibody (or nanobody) pair to form a covalent linkage rapidly and specifically. The rate of the cross-linking reaction between peptide and nanobody is faster than most other biocompatible cross-linking reactions, and it can be used to label live cells expressing receptor-nanobody fusions. The rapid kinetics of this system allowed us to probe the consequences on signaling for ligand cross-linking to the A2A-adenosine receptor. Our method may be generally useful to site-specifically link synthetic molecules to receptors on mammalian cell surfaces.
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Affiliation(s)
- Chino C. Cabalteja
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD USA 20894
| | - Shivani Sachdev
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD USA 20894
| | - Ross W. Cheloha
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD USA 20894
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132
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Pinto-Espinoza C, Guillou C, Rissiek B, Wilmes M, Javidi E, Schwarz N, Junge M, Haag F, Liaukouskaya N, Wanner N, Nicke A, Stortelers C, Tan YV, Adriouch S, Magnus T, Koch-Nolte F. Effective targeting of microglial P2X7 following intracerebroventricular delivery of nanobodies and nanobody-encoding AAVs. Front Pharmacol 2022; 13:1029236. [PMID: 36299894 PMCID: PMC9589454 DOI: 10.3389/fphar.2022.1029236] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/23/2022] [Indexed: 11/19/2022] Open
Abstract
The P2X7 ion channel is a key sensor for extracellular ATP and a key trigger of sterile inflammation. Intravenous injection of nanobodies that block P2X7 has shown to be beneficial in mouse models of systemic inflammation. P2X7 has also emerged as an attractive therapeutic target for inflammatory brain diseases. However, little is known about the ability of nanobodies to cross the BBB. Here we evaluated the ability of P2X7-specific nanobodies to reach and to block P2X7 on microglia following intravenous or intracerebral administration. For this study, we reformatted and sequence-optimized P2X7 nanobodies for higher stability and elevated isoelectric point. Following injection of nanobodies or nanobody-encoding adeno-associated viral vectors (AAV), we monitored the occupancy and blockade of microglial P2X7 in vivo using ex vivo flow cytometry. Our results show that P2X7 on microglia was within minutes completely occupied and blocked by intracerebroventricularly injected nanobodies, even at low doses. In contrast, very high doses were required to achieve similar effects when injected intravenously. The endogenous production of P2X7-antagonistic nanobodies following intracerebral or intramuscular injection of nanobody-encoding AAVs resulted in a long-term occupancy and blockade of P2X7 on microglia. Our results provide new insights into the conditions for the delivery of nanobodies to microglial P2X7 and point to AAV-mediated delivery of P2X7 nanobodies as a promising strategy for the treatment of sterile brain inflammation.
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Affiliation(s)
- Carolina Pinto-Espinoza
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charlotte Guillou
- Normandie Univ, UNIROUEN, INSERM U1234, Pathophysiology, Autoimmunity and Immunotherapy (PanTHER), Rouen, France
| | - Björn Rissiek
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Wilmes
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ehsan Javidi
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicole Schwarz
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- MSH- Medical School Hamburg- Dep. Anatomy, Hamburg, Germany
| | - Marten Junge
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Nicola Wanner
- Department of Nephrology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, Munich, Germany
| | | | - Yossan-Var Tan
- Normandie Univ, UNIROUEN, INSERM U1234, Pathophysiology, Autoimmunity and Immunotherapy (PanTHER), Rouen, France
| | - Sahil Adriouch
- Normandie Univ, UNIROUEN, INSERM U1234, Pathophysiology, Autoimmunity and Immunotherapy (PanTHER), Rouen, France
| | - Tim Magnus
- Department of Neurology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- *Correspondence: Friedrich Koch-Nolte,
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133
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Diisonitrile Lipopeptides Mediate Resistance to Copper Starvation in Pathogenic Mycobacteria. mBio 2022; 13:e0251322. [PMID: 36197089 PMCID: PMC9600254 DOI: 10.1128/mbio.02513-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial pathogens and their hosts engage in intense competition for critical nutrients during infection, including metals such as iron, copper, and zinc. Some metals are limited by the host, and some are deployed by the host as antimicrobials. To counter metal limitation, pathogens deploy high-affinity metal acquisition systems, best exemplified by siderophores to acquire iron. Although pathogen strategies to resist the toxic effects of high Cu have been elucidated, the role of Cu starvation and the existence of Cu acquisition systems are less well characterized. In this study, we examined the role of diisonitrile chalkophores of pathogenic mycobacteria, synthesized by the enzymes encoded by the virulence-associated nrp gene cluster, in metal acquisition. nrp gene cluster expression is strongly induced by starvation or chelation of Cu but not starvation of Zn or excess Cu. Mycobacterium tuberculosis and Mycobacterium marinum strains lacking the nrp-encoded nonribosomal peptide sythetase, the fadD10 adenylate-forming enzyme, or the uncharacterized upstream gene ppe1 are all sensitized to Cu, but not Zn, starvation. This low Cu sensitivity is rescued by genetic complementation or by provision of a synthetic diisonitrile chalkophore. These data demonstrate that diisonitrile lipopeptides in mycobacteria are chalkophores that facilitate survival under Cu-limiting conditions and suggest that Cu starvation is a relevant stress for M. tuberculosis in the host.
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134
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Frodyma DE, Troia TC, Rao C, Svoboda RA, Berg JA, Shinde DD, Thomas VC, Lewis RE, Fisher KW. PGC-1β and ERRα Promote Glutamine Metabolism and Colorectal Cancer Survival via Transcriptional Upregulation of PCK2. Cancers (Basel) 2022; 14:4879. [PMID: 36230802 PMCID: PMC9562873 DOI: 10.3390/cancers14194879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/29/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Previous studies have shown that Peroxisome Proliferator-Activated Receptor Gamma, Coactivator 1 Beta (PGC-1β) and Estrogen-Related Receptor Alpha (ERRα) are over-expressed in colorectal cancer and promote tumor survival. METHODS In this study, we use immunoprecipitation of epitope tagged endogenous PGC-1β and inducible PGC-1β mutants to show that amino acid motif LRELL on PGC-1β is responsible for the physical interaction with ERRα and promotes ERRα mRNA and protein expression. We use RNAsequencing to determine the genes regulated by both PGC-1β & ERRα and find that mitochondrial Phosphoenolpyruvate Carboxykinase 2 (PCK2) is the gene that decreased most significantly after depletion of both genes. RESULTS Depletion of PCK2 in colorectal cancer cells was sufficient to reduce anchorage-independent growth and inhibit glutamine utilization by the TCA cycle. Lastly, shRNA-mediated depletion of ERRα decreased anchorage-independent growth and glutamine metabolism, which could not be rescued by plasmid derived expression of PCK2. DISCUSSION These findings suggest that transcriptional control of PCK2 is one mechanism used by PGC-1β and ERRα to promote glutamine metabolism and colorectal cancer cell survival.
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Affiliation(s)
- Danielle E. Frodyma
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Thomas C. Troia
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Chaitra Rao
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Robert A. Svoboda
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jordan A. Berg
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Dhananjay D. Shinde
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vinai C. Thomas
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Robert E. Lewis
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kurt W. Fisher
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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135
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Lorentzen J, Pedersen DV, Gadeberg TAF, Andersen GR. Structure determination of an unstable macromolecular complex enabled by nanobody-peptide bridging. Protein Sci 2022; 31:e4432. [PMID: 36173177 PMCID: PMC9601772 DOI: 10.1002/pro.4432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/17/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022]
Abstract
Structure determination of macromolecular complexes is challenging if subunits can dissociate during crystallization or preparation of electron microscopy grids. We present an approach where a labile complex is stabilized by linking subunits though introduction of a peptide tag in one subunit that is recognized by a nanobody tethered to a second subunit. This allowed crystal structure determination at 3.9 Å resolution of the highly non‐globular 320 kDa proconvertase formed by complement components C3b, factor B, and properdin. Whereas the binding mode of properdin to C3b is preserved, an internal rearrangement occurs in the zymogen factor B von Willebrand domain type A domain compared to the proconvertase not bound to properdin. The structure emphasizes the role of two noncanonical loops in thrombospondin repeats 5 and 6 of properdin in augmenting the activity of the C3 convertase. We suggest that linking of subunits through peptide specific tethered nanobodies represents a simple alternative to approaches like affinity maturation and chemical cross‐linking for the stabilization of large macromolecular complexes. Besides applications for structural biology, nanobody bridging may become a new tool for biochemical analysis of unstable macromolecular complexes and in vitro selection of highly specific binders for such complexes. PDB Code(s): 7NOZ;
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Affiliation(s)
- Josefine Lorentzen
- Department of Molecular Biology and Genetics, Section for Protein ScienceAarhus UniversitetAarhusDenmark
| | | | - Trine Amalie Fogh Gadeberg
- Department of Molecular Biology and Genetics, Section for Protein ScienceAarhus UniversitetAarhusDenmark
| | - Gregers Rom Andersen
- Department of Molecular Biology and Genetics, Section for Protein ScienceAarhus UniversitetAarhusDenmark
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136
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Yoo TY, Mitchison T. Quantification of nuclear transport inhibition by SARS-CoV-2 ORF6 using a broadly applicable live-cell dose-response pipeline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.12.10.472151. [PMID: 34931191 PMCID: PMC8687474 DOI: 10.1101/2021.12.10.472151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
SARS coronavirus ORF6 inhibits the classical nuclear import pathway to antagonize host antiviral responses. Several models were proposed to explain its inhibitory function, but quantitative measurement is needed for model evaluation and refinement. We report a broadly applicable live-cell method for calibrated dose-response characterization of the nuclear transport alteration by a protein of interest. Using this method, we found that SARS-CoV-2 ORF6 is ~15 times more potent than SARS-CoV-1 ORF6 in inhibiting bidirectional nuclear transport, due to differences in the NUP98-binding C-terminal region that is required for the inhibition. The N-terminal region promotes membrane binding and was required for activity, but could be replaced by constructs which forced oligomerization in solution. Based on these data, we propose that the hydrophobic N-terminal region drives oligomerization of ORF6 to multivalently cross-link the FG domains of NUP98 at the nuclear pore complex, and this multivalent binding inhibits bidirectional transport.
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137
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Nanobody-based RFP-dependent Cre recombinase for selective anterograde tracing in RFP-expressing transgenic animals. Commun Biol 2022; 5:979. [PMID: 36114373 PMCID: PMC9481622 DOI: 10.1038/s42003-022-03944-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 09/05/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractTransgenic animals expressing fluorescent proteins are widely used to label specific cells and proteins. By using a split Cre recombinase fused with mCherry-binding nanobodies or designed ankyrin repeat proteins, we created Cre recombinase dependent on red fluorescent protein (RFP) (Cre-DOR). Functional binding units for monomeric RFPs are different from those for polymeric RFPs. We confirmed selective target RFP-dependent gene expression in the mouse cerebral cortex using stereotaxic injection of adeno-associated virus vectors. In estrogen receptor-beta (Esr2)-mRFP1 mice and gastrin-releasing peptide receptor (Grpr)-mRFP1 rats, we confirmed that Cre-DOR can be used for selective tracing of the neural projection from RFP-expressing specific neurons. Cellular localization of RFPs affects recombination efficiency of Cre-DOR, and light and chemical-induced nuclear translocation of an RFP-fused protein can modulate Cre-DOR efficiency. Our results provide a method for manipulating gene expression in specific cells expressing RFPs and expand the repertory of nanobody-based genetic tools.
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138
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Ishizuka Y, Mergiya TF, Baldinotti R, Xu J, Hallin EI, Markússon S, Kursula P, Bramham CR. Development and Validation of Arc Nanobodies: New Tools for Probing Arc Dynamics and Function. Neurochem Res 2022; 47:2656-2666. [PMID: 35307777 PMCID: PMC9463278 DOI: 10.1007/s11064-022-03573-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/06/2022]
Abstract
Activity-regulated cytoskeleton-associated (Arc) protein plays key roles in long-term synaptic plasticity, memory, and cognitive flexibility. However, an integral understanding of Arc mechanisms is lacking. Arc is proposed to function as an interaction hub in neuronal dendrites and the nucleus, yet Arc can also form retrovirus-like capsids with proposed roles in intercellular communication. Here, we sought to develop anti-Arc nanobodies (ArcNbs) as new tools for probing Arc dynamics and function. Six ArcNbs representing different clonal lines were selected from immunized alpaca. Immunoblotting with recombinant ArcNbs fused to a small ALFA-epitope tag demonstrated binding to recombinant Arc as well as endogenous Arc from rat cortical tissue. ALFA-tagged ArcNb also provided efficient immunoprecipitation of stimulus-induced Arc after carbachol-treatment of SH-SY5Y neuroblastoma cells and induction of long-term potentiation in the rat dentate gyrus in vivo. Epitope mapping showed that all Nbs recognize the Arc C-terminal region containing the retroviral Gag capsid homology domain, comprised of tandem N- and C-lobes. ArcNbs E5 and H11 selectively bound the N-lobe, which harbors a peptide ligand binding pocket specific to mammals. Four additional ArcNbs bound the region containing the C-lobe and C-terminal tail. For use as genetically encoded fluorescent intrabodies, we show that ArcNbs fused to mScarlet-I are uniformly expressed, without aggregation, in the cytoplasm and nucleus of HEK293FT cells. Finally, mScarlet-I-ArcNb H11 expressed as intrabody selectively bound the N-lobe and enabled co-immunoprecipitation of full-length intracellular Arc. ArcNbs are versatile tools for live-cell labeling and purification of Arc, and interrogation of Arc capsid domain specific functions.
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Affiliation(s)
- Yuta Ishizuka
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway.
- Department of Pathophysiology and Metabolism, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, 701-0192, Japan.
| | - Tadiwos F Mergiya
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
- Mohn Center for Research on the Brain, University of Bergen, Bergen, Norway
| | - Rodolfo Baldinotti
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
- Mohn Center for Research on the Brain, University of Bergen, Bergen, Norway
| | - Ju Xu
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
| | - Erik I Hallin
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
| | - Sigurbjörn Markússon
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, Jonas Lies 91, 5009, Bergen, Norway.
- Mohn Center for Research on the Brain, University of Bergen, Bergen, Norway.
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139
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Wilson SC, Caveney NA, Yen M, Pollmann C, Xiang X, Jude KM, Hafer M, Tsutsumi N, Piehler J, Garcia KC. Organizing structural principles of the IL-17 ligand-receptor axis. Nature 2022; 609:622-629. [PMID: 35863378 PMCID: PMC9477748 DOI: 10.1038/s41586-022-05116-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/15/2022] [Indexed: 12/01/2022]
Abstract
The IL-17 family of cytokines and receptors have central roles in host defence against infection and development of inflammatory diseases1. The compositions and structures of functional IL-17 family ligand-receptor signalling assemblies remain unclear. IL-17E (also known as IL-25) is a key regulator of type 2 immune responses and driver of inflammatory diseases, such as allergic asthma, and requires both IL-17 receptor A (IL-17RA) and IL-17RB to elicit functional responses2. Here we studied IL-25-IL-17RB binary and IL-25-IL-17RB-IL-17RA ternary complexes using a combination of cryo-electron microscopy, single-molecule imaging and cell-based signalling approaches. The IL-25-IL-17RB-IL-17RA ternary signalling assembly is a C2-symmetric complex in which the IL-25-IL-17RB homodimer is flanked by two 'wing-like' IL-17RA co-receptors through a 'tip-to-tip' geometry that is the key receptor-receptor interaction required for initiation of signal transduction. IL-25 interacts solely with IL-17RB to allosterically promote the formation of the IL-17RB-IL-17RA tip-to-tip interface. The resulting large separation between the receptors at the membrane-proximal level may reflect proximity constraints imposed by the intracellular domains for signalling. Cryo-electron microscopy structures of IL-17A-IL-17RA and IL-17A-IL-17RA-IL-17RC complexes reveal that this tip-to-tip architecture is a key organizing principle of the IL-17 receptor family. Furthermore, these studies reveal dual actions for IL-17RA sharing among IL-17 cytokine complexes, by either directly engaging IL-17 cytokines or alternatively functioning as a co-receptor.
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Affiliation(s)
- Steven C Wilson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathanael A Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michelle Yen
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christoph Pollmann
- Divison of Biophysics, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Xinyu Xiang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maximillian Hafer
- Divison of Biophysics, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jacob Piehler
- Divison of Biophysics, Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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140
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Fryer T, Rogers JD, Mellor C, Kohler TN, Minter R, Hollfelder F. Gigavalent Display of Proteins on Monodisperse Polyacrylamide Hydrogels as a Versatile Modular Platform for Functional Assays and Protein Engineering. ACS CENTRAL SCIENCE 2022; 8:1182-1195. [PMID: 36032770 PMCID: PMC9413441 DOI: 10.1021/acscentsci.2c00576] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The assembly of robust, modular biological components into complex functional systems is central to synthetic biology. Here, we apply modular "plug and play" design principles to a solid-phase protein display system that facilitates protein purification and functional assays. Specifically, we capture proteins on polyacrylamide hydrogel display beads (PHD beads) made in microfluidic droplet generators. These monodisperse PHD beads are decorated with predefined amounts of anchors, methacrylate-PEG-benzylguanine (BG) and methacrylate-PEG-chloroalkane (CA), that react covalently with SNAP-/Halo-tag fusion proteins, respectively, in a specific, orthogonal, and stable fashion. Anchors, and thus proteins, are distributed throughout the entire bead volume, allowing attachment of ∼109 protein molecules per bead (⌀ 20 μm) -a higher density than achievable with commercial surface-modified beads. We showcase a diverse array of protein modules that enable the secondary capture of proteins, either noncovalently (IgG and SUMO-tag) or covalently (SpyCatcher, SpyTag, SnpCatcher, and SnpTag), in mono- and multivalent display formats. Solid-phase protein binding and enzymatic assays are carried out, and incorporating the photocleavable protein PhoCl enables the controlled release of modules via visible-light irradiation for functional assays in solution. We utilize photocleavage for valency engineering of an anti-TRAIL-R1 scFv, enhancing its apoptosis-inducing potency ∼50-fold through pentamerization.
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Affiliation(s)
- Thomas Fryer
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
- Antibody
Discovery and Protein Engineering, R&D, AstraZeneca, Milstein
Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Joel David Rogers
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
- Antibody
Discovery and Protein Engineering, R&D, AstraZeneca, Milstein
Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Christopher Mellor
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Timo N. Kohler
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Ralph Minter
- Antibody
Discovery and Protein Engineering, R&D, AstraZeneca, Milstein
Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Florian Hollfelder
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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141
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Connelly GG, Kirkland OO, Bohannon S, Lim DC, Wilson RM, Richards EJ, Tay DM, Jee H, Hellinger RD, Hoang NK, Hao L, Chhabra A, Martin-Alonso C, Tan EK, Koehler AN, Yaffe MB, London WB, Lee PY, Krammer F, Bohannon RC, Bhatia SN, Sikes HD, Li H. Direct capture of neutralized RBD enables rapid point-of-care assessment of SARS-CoV-2 neutralizing antibody titer. CELL REPORTS METHODS 2022; 2:100273. [PMID: 35942328 PMCID: PMC9350670 DOI: 10.1016/j.crmeth.2022.100273] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/13/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
Abstract
Neutralizing antibody (NAb) titer is a key biomarker of protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but point-of-care methods for assessing NAb titer are not widely available. Here, we present a lateral flow assay that captures SARS-CoV-2 receptor-binding domain (RBD) that has been neutralized from binding angiotensin-converting enzyme 2 (ACE2). Quantification of neutralized RBD in this assay correlates with NAb titer from vaccinated and convalescent patients. This methodology demonstrated superior performance in assessing NAb titer compared with either measurement of total anti-spike immunoglobulin G titer or quantification of the absolute reduction in binding between ACE2 and RBD. Our testing platform has the potential for mass deployment to aid in determining at population scale the degree of protective immunity individuals may have following SARS-CoV-2 vaccination or infection and can enable simple at-home assessment of NAb titer.
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Affiliation(s)
- Guinevere G. Connelly
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Orville O. Kirkland
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Daniel C. Lim
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert M. Wilson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward J. Richards
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Dragonfly Therapeutics, Waltham, MA 02451, USA
| | - Dousabel M. Tay
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hyuk Jee
- Division of Rheumatology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Riley D. Hellinger
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ngoc K. Hoang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liang Hao
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arnav Chhabra
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Satellite Bio, Cambridge, MA 02139, USA
| | - Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward K.W. Tan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Angela N. Koehler
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael B. Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wendy B. London
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Pui Y. Lee
- Division of Rheumatology, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Florian Krammer
- Department of Microbiology, and Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Sangeeta N. Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
- Institute for Medical Engineering and Science, and Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Wyss Institute at Harvard, Boston, MA 02115, USA
| | - Hadley D. Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hojun Li
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
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142
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Cabalteja CC, Sachdev S, Cheloha RW. Characterization of a Nanobody-Epitope Tag Interaction and Its Application for Receptor Engineering. ACS Chem Biol 2022; 17:2296-2303. [PMID: 35930411 PMCID: PMC10200313 DOI: 10.1021/acschembio.2c00407] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Peptide epitope tags offer a valuable means for detection and manipulation of protein targets for which high quality detection reagents are not available. Most commonly used epitope tags are bound by conventional, full-size antibodies (Abs). The complex architecture of Abs complicates their application in protein engineering and intracellular applications. To address these shortcomings, single domain antibodies (nanobodies, Nbs) that recognize short peptide epitopes have become increasingly prized. Here, we characterize the interaction between a Nb (Nb6E) and a 14-mer peptide epitope. We identify residues in the peptide epitope essential for high affinity binding. Using this information in combination with computational modeling we propose a mode of interaction between Nb6E and this epitope. We apply this nanobody-epitope pair to augment the potency of a ligand at an engineered adenosine A2A receptor. This characterization of the nanobody-epitope pair opens the door to diverse applications including mechanistic studies of the G protein-coupled receptor function.
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Affiliation(s)
- Chino C. Cabalteja
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
| | - Shivani Sachdev
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
| | - Ross W. Cheloha
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes, Digestive, and Kidney Diseases; National Institutes of Health. Bethesda, MD 20892, USA
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143
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Keller L, Tardy C, Ligat L, Le Pennec S, Bery N, Koraïchi F, Chinestra P, David M, Gence R, Favre G, Cabantous S, Olichon A. Tripartite split-GFP assay to identify selective intracellular nanobody that suppresses GTPase RHOA subfamily downstream signaling. Front Immunol 2022; 13:980539. [PMID: 36059552 PMCID: PMC9433928 DOI: 10.3389/fimmu.2022.980539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/29/2022] [Indexed: 11/24/2022] Open
Abstract
Strategies based on intracellular expression of artificial binding domains present several advantages over manipulating nucleic acid expression or the use of small molecule inhibitors. Intracellularly-functional nanobodies can be considered as promising macrodrugs to study key signaling pathways by interfering with protein-protein interactions. With the aim of studying the RAS-related small GTPase RHOA family, we previously isolated, from a synthetic phage display library, nanobodies selective towards the GTP-bound conformation of RHOA subfamily proteins that lack selectivity between the highly conserved RHOA-like and RAC subfamilies of GTPases. To identify RHOA/ROCK pathway inhibitory intracellular nanobodies, we implemented a stringent, subtractive phage display selection towards RHOA-GTP followed by a phenotypic screen based on F-actin fiber loss. Intracellular interaction and intracellular selectivity between RHOA and RAC1 proteins was demonstrated by adapting the sensitive intracellular protein-protein interaction reporter based on the tripartite split-GFP method. This strategy led us to identify a functional intracellular nanobody, hereafter named RH28, that does not cross-react with the close RAC subfamily and blocks/disrupts the RHOA/ROCK signaling pathway in several cell lines without further engineering or functionalization. We confirmed these results by showing, using SPR assays, the high specificity of the RH28 nanobody towards the GTP-bound conformation of RHOA subfamily GTPases. In the metastatic melanoma cell line WM266-4, RH28 expression triggered an elongated cellular phenotype associated with a loss of cellular contraction properties, demonstrating the efficient intracellular blocking of RHOA/B/C proteins downstream interactions without the need of manipulating endogenous gene expression. This work paves the way for future therapeutic strategies based on protein-protein interaction disruption with intracellular antibodies.
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Affiliation(s)
- Laura Keller
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
| | - Claudine Tardy
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Laetitia Ligat
- Le Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, Plateau de Protéomique, Toulouse, France
| | - Soazig Le Pennec
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Nicolas Bery
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Faten Koraïchi
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Patrick Chinestra
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Mélissa David
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Rémi Gence
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Gilles Favre
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
| | - Stéphanie Cabantous
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
- *Correspondence: Stéphanie Cabantous, ; Aurélien Olichon,
| | - Aurélien Olichon
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1188 Diabète athérothrombose Réunion Océan Indien (DéTROI), Université de La Réunion, Saint Denis de La Réunion, France
- *Correspondence: Stéphanie Cabantous, ; Aurélien Olichon,
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Kusakari K, Machida T, Ishida Y, Omori T, Suzuki T, Sekimata M, Wada I, Fujita T, Sekine H. The complex formation of MASP-3 with pattern recognition molecules of the lectin complement pathway retains MASP-3 in the circulation. Front Immunol 2022; 13:907023. [PMID: 36052069 PMCID: PMC9425028 DOI: 10.3389/fimmu.2022.907023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/27/2022] [Indexed: 12/02/2022] Open
Abstract
The complement system plays an important role in host defense and is activated via three different activation pathways. We have previously reported that mannose-binding lectin-associated serine protease (MASP)-3, unlike its splicing variant MASP-1, circulates in an active form and is essential for the activation of the alternative pathway (AP) via the activation of complement factor D (FD). On the other hand, like MASP-1 and MASP-2 of the lectin pathway (LP), MASP-3 forms a complex with the pattern recognition molecules (PRMs) of the LP (LP-PRMs). Both MASP-1 and MASP-2 can be activated efficiently when the LP-PRMs complexed with them bind to their ligands. On the other hand, it remains unclear how MASP-3 is activated, or whether complex formation of MASP-3 with LP-PRMs is involved in activation of MASP-3 or its efficiency in the circulation. To address these issues, we generated wild-type (WT) and four mutant recombinant mouse MASP-3 proteins fused with PA (human podoplanin dodecapeptide)-tag (rmMASP-3-PAs), the latter of which have single amino acid substitution for alanine in the CUB1 or CUB2 domain responsible for binding to LP-PRMs. The mutant rmMASP-3-PAs showed significantly reduced in-vivo complex formation with LP-PRMs when compared with WT rmMASP-3-PA. In the in-vivo kinetic analysis of MASP-3 activation, both WT and mutant rmMASP-3-PAs were cleaved into the active forms as early as 30 minutes in the circulation of mice, and no significant difference in the efficiency of MASP-3 cleavage was observed throughout an observation period of 48 hours after intravenous administration. All sera collected 3 hours after administration of each rmMASP-3-PA showed full restoration of the active FD and AP activity in MASP-3-deficient mouse sera at the same levels as WT mouse sera. Unexpectedly, all mutant rmMASP-3-PAs showed faster clearance from the circulation than the WT rmMASP-3-PA. To our knowledge, the current study is the first to show in-vivo kinetics of MASP-3 demonstrating rapid activation and clearance in the circulation. In conclusion, our results demonstrated that the complex formation of MASP-3 with LP-PRMs is not required for in-vivo activation of MASP-3 or its efficiency, but may contribute to the long-term retention of MASP-3 in the circulation.
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Affiliation(s)
- Kohei Kusakari
- Department of Immunology, Fukushima Medical University, Fukushima, Japan
| | - Takeshi Machida
- Department of Immunology, Fukushima Medical University, Fukushima, Japan
- *Correspondence: Takeshi Machida,
| | - Yumi Ishida
- Department of Immunology, Fukushima Medical University, Fukushima, Japan
| | - Tomoko Omori
- Department of Immunology, Fukushima Medical University, Fukushima, Japan
| | - Toshiyuki Suzuki
- Radioisotope Research Center, Fukushima Medical University, Fukushima, Japan
| | - Masayuki Sekimata
- Radioisotope Research Center, Fukushima Medical University, Fukushima, Japan
| | - Ikuo Wada
- Department of Cell Science, Institute of Biomedical Sciences, Fukushima Medical University, Fukushima, Japan
| | - Teizo Fujita
- Fukushima Prefectural General Hygiene Institute, Fukushima, Japan
| | - Hideharu Sekine
- Department of Immunology, Fukushima Medical University, Fukushima, Japan
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145
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Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. Proc Natl Acad Sci U S A 2022; 119:e2207200119. [PMID: 35858375 PMCID: PMC9388094 DOI: 10.1073/pnas.2207200119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αβ-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4β engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources.
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146
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Ren J, Xiong H, Huang C, Ji F, Jia L. An engineered peptide tag-specific nanobody for immunoaffinity chromatography application enabling efficient product recovery at mild conditions. J Chromatogr A 2022; 1676:463274. [DOI: 10.1016/j.chroma.2022.463274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
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147
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Cordell P, Carrington G, Curd A, Parker F, Tomlinson D, Peckham M. Affimers and nanobodies as molecular probes and their applications in imaging. J Cell Sci 2022; 135:276020. [PMID: 35848463 PMCID: PMC9450889 DOI: 10.1242/jcs.259168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibodies are the most widely used, traditional tool for labelling molecules in cells. In the past five to ten years, many new labelling tools have been developed with significant advantages over the traditional antibody. Here, we focus on nanobodies and the non-antibody binding scaffold proteins called Affimers. We explain how they are generated, selected and produced, and we describe how their small size, high binding affinity and specificity provides them with many advantages compared to antibodies. Of particular importance, their small size enables them to better penetrate dense cytoskeletal regions within cells, as well as tissues, providing them with specific advantage for super-resolution imaging, as they place the fluorophore with a few nanometres of the target protein being imaged. We expect these novel tools to be of broad interest to many cell biologists and anticipate them becoming the tools of choice for super-resolution imaging.
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148
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Oliinyk OS, Baloban M, Clark CL, Carey E, Pletnev S, Nimmerjahn A, Verkhusha VV. Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies. Nat Methods 2022; 19:740-750. [PMID: 35606446 DOI: 10.1038/s41592-022-01467-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/24/2022] [Indexed: 12/16/2022]
Abstract
Small near-infrared (NIR) fluorescent proteins (FPs) are much needed as protein tags for imaging applications. We developed a 17 kDa NIR FP, called miRFP670nano3, which brightly fluoresces in mammalian cells and enables deep-brain imaging. By exploring miRFP670nano3 as an internal tag, we engineered 32 kDa NIR fluorescent nanobodies, termed NIR-Fbs, whose stability and fluorescence strongly depend on the presence of specific intracellular antigens. NIR-Fbs allowed background-free visualization of endogenous proteins, detection of viral antigens, labeling of cells expressing target molecules and identification of double-positive cell populations with bispecific NIR-Fbs against two antigens. Applying NIR-Fbs as destabilizing fusion partners, we developed molecular tools for directed degradation of targeted proteins, controllable protein expression and modulation of enzymatic activities. Altogether, NIR-Fbs enable the detection and manipulation of a variety of cellular processes based on the intracellular protein profile.
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Affiliation(s)
- Olena S Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikhail Baloban
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Charles L Clark
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Erin Carey
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Vladislav V Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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149
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Live imaging of Yersinia translocon formation and immune recognition in host cells. PLoS Pathog 2022; 18:e1010251. [PMID: 35604950 PMCID: PMC9173619 DOI: 10.1371/journal.ppat.1010251] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/07/2022] [Accepted: 04/21/2022] [Indexed: 11/19/2022] Open
Abstract
Yersinia enterocolitica employs a type three secretion system (T3SS) to translocate immunosuppressive effector proteins into host cells. To this end, the T3SS assembles a translocon/pore complex composed of the translocator proteins YopB and YopD in host cell membranes serving as an entry port for the effectors. The translocon is formed in a Yersinia-containing pre-phagosomal compartment that is connected to the extracellular space. As the phagosome matures, the translocon and the membrane damage it causes are recognized by the cell-autonomous immune system. We infected cells in the presence of fluorophore-labeled ALFA-tag-binding nanobodies with a Y. enterocolitica strain expressing YopD labeled with an ALFA-tag. Thereby we could record the integration of YopD into translocons and its intracellular fate in living host cells. YopD was integrated into translocons around 2 min after uptake of the bacteria into a phosphatidylinositol-4,5-bisphosphate enriched pre-phagosomal compartment and remained there for 27 min on average. Damaging of the phagosomal membrane as visualized with recruitment of GFP-tagged galectin-3 occurred in the mean around 14 min after translocon formation. Shortly after recruitment of galectin-3, guanylate-binding protein 1 (GBP-1) was recruited to phagosomes, which was accompanied by a decrease in the signal intensity of translocons, suggesting their degradation or disassembly. In sum, we were able for the first time to film the spatiotemporal dynamics of Yersinia T3SS translocon formation and degradation and its sensing by components of the cell-autonomous immune system.
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150
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Moliner-Morro A, McInerney GM, Hanke L. Nanobodies in the limelight: Multifunctional tools in the fight against viruses. J Gen Virol 2022; 103. [PMID: 35579613 DOI: 10.1099/jgv.0.001731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibodies are natural antivirals generated by the vertebrate immune system in response to viral infection or vaccination. Unsurprisingly, they are also key molecules in the virologist's molecular toolbox. With new developments in methods for protein engineering, protein functionalization and application, smaller antibody-derived fragments are moving in focus. Among these, camelid-derived nanobodies play a prominent role. Nanobodies can replace full-sized antibodies in most applications and enable new possible applications for which conventional antibodies are challenging to use. Here we review the versatile nature of nanobodies, discuss their promise as antiviral therapeutics, for diagnostics, and their suitability as research tools to uncover novel aspects of viral infection and disease.
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Affiliation(s)
- Ainhoa Moliner-Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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