1
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Atakpa-Adaji P, Ivanova A, Kujawa K, Taylor CW. KRAP regulates mitochondrial Ca2+ uptake by licensing IP3 receptor activity and stabilizing ER-mitochondrial junctions. J Cell Sci 2024; 137:jcs261728. [PMID: 38786982 PMCID: PMC11234384 DOI: 10.1242/jcs.261728] [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: 10/16/2023] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
Inositol 1,4,5-trisphosphate (IP3) receptors (IP3Rs) are high-conductance channels that allow the regulated redistribution of Ca2+ from the endoplasmic reticulum (ER) to the cytosol and, at specialized membrane contact sites (MCSs), to other organelles. Only a subset of IP3Rs release Ca2+ to the cytosol in response to IP3. These 'licensed' IP3Rs are associated with Kras-induced actin-interacting protein (KRAP, also known as ITPRID2) beneath the plasma membrane. It is unclear whether KRAP regulates IP3Rs at MCSs. We show, using simultaneous measurements of Ca2+ concentration in the cytosol and mitochondrial matrix, that KRAP also licenses IP3Rs to release Ca2+ to mitochondria. Loss of KRAP abolishes cytosolic and mitochondrial Ca2+ signals evoked by stimulation of IP3Rs via endogenous receptors. KRAP is located at ER-mitochondrial membrane contact sites (ERMCSs) populated by IP3R clusters. Using a proximity ligation assay between IP3R and voltage-dependent anion channel 1 (VDAC1), we show that loss of KRAP reduces the number of ERMCSs. We conclude that KRAP regulates Ca2+ transfer from IP3Rs to mitochondria by both licensing IP3R activity and stabilizing ERMCSs.
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Affiliation(s)
- Peace Atakpa-Adaji
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Adelina Ivanova
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Karolina Kujawa
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Colin W. Taylor
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
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2
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Chaisupa P, Wright RC. State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering. SLAS Technol 2024; 29:100113. [PMID: 37918525 DOI: 10.1016/j.slast.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States; Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, United States.
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3
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Gui T, Fleming C, Manzato C, Bourgeois B, Sirati N, Heuer J, Papadionysiou I, Montfort DIV, Gijzen MV, Smits LMM, Burgering BMT, Madl T, Schuijers J. Targeted perturbation of signaling-driven condensates. Mol Cell 2023; 83:4141-4157.e11. [PMID: 37977121 DOI: 10.1016/j.molcel.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
Biomolecular condensates have emerged as a major organizational principle in the cell. However, the formation, maintenance, and dissolution of condensates are still poorly understood. Transcriptional machinery partitions into biomolecular condensates at key cell identity genes to activate these. Here, we report a specific perturbation of WNT-activated β-catenin condensates that disrupts oncogenic signaling. We use a live-cell condensate imaging method in human cancer cells to discover FOXO and TCF-derived peptides that specifically inhibit β-catenin condensate formation on DNA, perturb nuclear β-catenin condensates in cells, and inhibit β-catenin-driven transcriptional activation and colorectal cancer cell growth. We show that these peptides compete with homotypic intermolecular interactions that normally drive condensate formation. Using this framework, we derive short peptides that specifically perturb condensates and transcriptional activation of YAP and TAZ in the Hippo pathway. We propose a "monomer saturation" model in which short interacting peptides can be used to specifically inhibit condensate-associated transcription in disease.
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Affiliation(s)
- Tianshu Gui
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Cassio Fleming
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Caterina Manzato
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria
| | - Nafiseh Sirati
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Jasper Heuer
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Ioanna Papadionysiou
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Daniel I van Montfort
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Merel van Gijzen
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Lydia M M Smits
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Boudewijn M T Burgering
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Jurian Schuijers
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Oncode Institute, 3721 AL Utrecht, the Netherlands.
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4
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Frecot DI, Froehlich T, Rothbauer U. 30 years of nanobodies - an ongoing success story of small binders in biological research. J Cell Sci 2023; 136:jcs261395. [PMID: 37937477 DOI: 10.1242/jcs.261395] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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5
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Sekar V, Mármol-Sánchez E, Kalogeropoulos P, Stanicek L, Sagredo EA, Widmark A, Doukoumopoulos E, Bonath F, Biryukova I, Friedländer MR. Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE. Nat Biotechnol 2023:10.1038/s41587-023-01951-0. [PMID: 37735263 DOI: 10.1038/s41587-023-01951-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
MicroRNAs (miRNAs) exert their gene regulatory effects on numerous biological processes based on their selection of target transcripts. Current experimental methods available to identify miRNA targets are laborious and require millions of cells. Here we have overcome these limitations by fusing the miRNA effector protein Argonaute2 to the RNA editing domain of ADAR2, allowing the detection of miRNA targets transcriptome-wide in single cells. miRNAs guide the fusion protein to their natural target transcripts, causing them to undergo A>I editing, which can be detected by sensitive single-cell RNA sequencing. We show that agoTRIBE identifies functional miRNA targets, which are supported by evolutionary sequence conservation. In one application of the method we study microRNA interactions in single cells and identify substantial differential targeting across the cell cycle. AgoTRIBE also provides transcriptome-wide measurements of RNA abundance and allows the deconvolution of miRNA targeting in complex tissues at the single-cell level.
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Affiliation(s)
- Vaishnovi Sekar
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Laura Stanicek
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eduardo A Sagredo
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Albin Widmark
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | | | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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6
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Tsuruta A, Kanetani D, Shiiba Y, Inoki T, Yoshida Y, Matsunaga N, Koyanagi S, Ohdo S. Modulation of cell physiology by bispecific nanobodies enabling changes in the intracellular localization of organelle proteins. Biochem Pharmacol 2023; 215:115708. [PMID: 37506923 DOI: 10.1016/j.bcp.2023.115708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/08/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
Proteins localize to their respective organelles in cells. This localization is changed by activation or repression in response to signal transduction. Therefore, the appropriate intracellular localization of proteins is important for their functions to be exerted. However, difficulties are associated with controlling the localization of endogenous proteins. In the present study, we developed a conceptually new method of controlling the intracellular localization of endogenous proteins using bispecific nanobodies (BiNbs). BiNbs recognize proteins expressed in the inner membrane, cytoskeleton, nucleus, and peroxisomes, but not in mitochondria or endoplasmic reticulum. BiNbs designed to recognize β-CATENIN and the intrinsic cytosolic protein VIMENTIN (3 × Flag β-CAT-VIM BiNbs) decreased the β-CATENIN-mediated transactivation of target genes by preventing its nuclear localization. Furthermore, 3 × Flag β-CAT-VIM BiNbs suppressed the proliferation and invasion of the VIMENTIN-expressing breast cancer cell line MDA-MB-231, but not MDA-MB-468, in which the expression of VIMENTIN was defective. The present results revealed that changes in the intracellular localization of specific proteins by BiNbs modulated the physiology and functions of cells. The development of BiNbs to recognize proteins specifically expressed in target cells may be a useful approach for eliciting cell-selective effects.
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Affiliation(s)
- Akito Tsuruta
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daiki Kanetani
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuki Shiiba
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takuto Inoki
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuya Yoshida
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Matsunaga
- Department of Clinical Pharmacokinetics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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7
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Chen YL, Xie XX, Zheng P, Zhu C, Ma H, Khalid Z, Xie YJ, Dang YZ, Ye Y, Sheng N, Zhong N, Lei WH, Zhang C, Zhang LJ, Jin T, Cao MJ. Selection, identification and crystal structure of shark-derived single-domain antibodies against a green fluorescent protein. Int J Biol Macromol 2023; 247:125852. [PMID: 37460076 DOI: 10.1016/j.ijbiomac.2023.125852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/05/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023]
Abstract
Shark variable domain of new antigen receptors (VNARs) are the smallest naturally occurring binding domains with properties of low complexity, small size, cytoplasmic expression, and ease of engineering. Green fluorescent protein (GFP) molecules have been analyzed in conventional microscopy, but their spectral characteristics preclude their use in techniques offering substantially higher resolution. Besides, the GFP molecules can be quenched in acidic environment, which makes it necessary to develop anti-GFP antibody to solve these problems. In view of the diverse applications of GFP and unique physicochemical features of VNAR, the present study aims to generate VNARs against GFP. Here, we identified 36 VNARs targeting eCGP123, an extremely stable GFP, by phage display from three immunized sharks. These VNARs bound to eCGP123 with affinity constant KD values ranging from 6.76 to 605 nM. Among them, two lead VNARs named aGFP-14 and aGFP-15 with nanomolar eCGP123-binding affinity were selected for in-depth characterization. aGFP-14 and aGFP-15 recognized similar epitopes on eCGP123. X-ray crystallography studies clarified the mechanism by which aGFP14 interacts with eCGP123. aGFP-14 also showed cross-reaction with EGFP, with KD values of 47.2 nM. Finally, immunostaining analyses demonstrated that aGFP-14 was able to bind effectively to the EGFP expressed in both cultured cells and mouse brain tissues, and can be used as a fluorescence amplifier for EGFP. Our research demonstrates a feasible idea for the screening and production of shark-derived VNARs. The two high-affinity VNARs developed in the study contribute to the diversity of GFP sdAbs and may enhance the applications of GFP.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Peiyi Zheng
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Chenchen Zhu
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Huan Ma
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Zunera Khalid
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Yang-Jie Xie
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yi-Zhao Dang
- Fisheries College, Jimei University, Xiamen 361021, China
| | - Yaxin Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Nengyin Sheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Wen-Hui Lei
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | | | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China.
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China.
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8
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Danielsson BE, George Abraham B, Mäntylä E, Cabe JI, Mayer CR, Rekonen A, Ek F, Conway DE, Ihalainen TO. Nuclear lamina strain states revealed by intermolecular force biosensor. Nat Commun 2023; 14:3867. [PMID: 37391402 PMCID: PMC10313699 DOI: 10.1038/s41467-023-39563-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Nuclear lamins have been considered an important structural element of the nucleus. The nuclear lamina is thought both to shield DNA from excessive mechanical forces and to transmit mechanical forces onto the DNA. However, to date there is not yet a technical approach to directly measure mechanical forces on nuclear lamins at the protein level. To overcome this limitation, we developed a nanobody-based intermolecular tension FRET biosensor capable of measuring the mechanical strain of lamin filaments. Using this sensor, we were able to show that the nuclear lamina is subjected to significant force. These forces are dependent on nuclear volume, actomyosin contractility, functional LINC complex, chromatin condensation state, cell cycle, and EMT. Interestingly, large forces were also present on nucleoplasmic lamins, indicating that these lamins may also have an important mechanical role in the nucleus. Overall, we demonstrate that the nanobody-based approach allows construction of biosensors for complex protein structures for mechanobiology studies.
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Affiliation(s)
- Brooke E Danielsson
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Bobin George Abraham
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Elina Mäntylä
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jolene I Cabe
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Carl R Mayer
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Anna Rekonen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Frans Ek
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Daniel E Conway
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio, USA.
- The Ohio State University and Arthur G. James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA.
| | - Teemu O Ihalainen
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland.
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9
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Hammarén MM, Luukinen H, Sillanpää A, Remans K, Lapouge K, Custódio T, Löw C, Myllymäki H, Montonen T, Seeger M, Robertson J, Nyman TA, Savijoki K, Parikka M. In vitro and ex vivo proteomics of Mycobacterium marinum biofilms and the development of biofilm-binding synthetic nanobodies. mSystems 2023:e0107322. [PMID: 37184670 DOI: 10.1128/msystems.01073-22] [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: 05/16/2023] Open
Abstract
The antibiotic-tolerant biofilms present in tuberculous granulomas add an additional layer of complexity when treating mycobacterial infections, including tuberculosis (TB). For a more efficient treatment of TB, the biofilm forms of mycobacteria warrant specific attention. Here, we used Mycobacterium marinum (Mmr) as a biofilm-forming model to identify the abundant proteins covering the biofilm surface. We used biotinylation/streptavidin-based proteomics on the proteins exposed at the Mmr biofilm matrices in vitro to identify 448 proteins and ex vivo proteomics to detect 91 Mmr proteins from the mycobacterial granulomas isolated from adult zebrafish. In vitro and ex vivo proteomics data are available via ProteomeXchange with identifier PXD033425 and PXD039416, respectively. Data comparisons pinpointed the molecular chaperone GroEL2 as the most abundant Mmr protein within the in vitro and ex vivo proteomes, while its paralog, GroEL1, with a known role in biofilm formation, was detected with slightly lower intensity values. To validate the surface exposure of these targets, we created in-house synthetic nanobodies (sybodies) against the two chaperones and identified sybodies that bind the mycobacterial biofilms in vitro and those present in ex vivo granulomas. Taken together, the present study reports a proof-of-concept showing that surface proteomics in vitro and ex vivo proteomics combined are a valuable strategy to identify surface-exposed proteins on the mycobacterial biofilm. Biofilm-surface-binding nanobodies could be eventually used as homing agents to deliver biofilm-targeting treatments to the sites of persistent biofilm infection.
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Affiliation(s)
- Milka Marjut Hammarén
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hanna Luukinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alina Sillanpää
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tânia Custódio
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Henna Myllymäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Toni Montonen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markus Seeger
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Joseph Robertson
- Department of Immunology, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Tuula A Nyman
- Department of Immunology, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Kirsi Savijoki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mataleena Parikka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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10
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Cohen HA, Zomot E, Nataniel T, Militsin R, Palty R. The SOAR of STIM1 interacts with plasma membrane lipids to form ER-PM contact sites. Cell Rep 2023; 42:112238. [PMID: 36906853 DOI: 10.1016/j.celrep.2023.112238] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/15/2023] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Depletion of Ca2+ from the endoplasmic reticulum (ER) causes the ER Ca2+ sensor STIM1 to form membrane contact sites (MCSs) with the plasma membrane (PM). At the ER-PM MCS, STIM1 binds to Orai channels to induce cellular Ca2+ entry. The prevailing view of this sequential process is that STIM1 interacts with the PM and with Orai1 using two separate modules: a C-terminal polybasic domain (PBD) for the interaction with PM phosphoinositides and the STIM-Orai activation region (SOAR) for the interaction with Orai channels. Here, using electron and fluorescence microscopy and protein-lipid interaction assays, we show that oligomerization of the SOAR promotes direct interaction with PM phosphoinositides to trap STIM1 at ER-PM MCSs. The interaction depends on a cluster of conserved lysine residues within the SOAR and is co-regulated by the STIM1 coil-coiled 1 and inactivation domains. Collectively, our findings uncover a molecular mechanism for formation and regulation of ER-PM MCSs by STIM1.
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Affiliation(s)
- Hadas Achildiev Cohen
- Department of Biochemistry, Technion Integrated Cancer Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Elia Zomot
- Department of Biochemistry, Technion Integrated Cancer Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Tomer Nataniel
- Department of Biochemistry, Technion Integrated Cancer Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Ruslana Militsin
- Department of Biochemistry, Technion Integrated Cancer Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel
| | - Raz Palty
- Department of Biochemistry, Technion Integrated Cancer Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel.
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11
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Chen YL, Xie XX, Zhong N, Sun LC, Lin D, Zhang LJ, Weng L, Jin T, Cao MJ. Research Progresses and Applications of Fluorescent Protein Antibodies: A Review Focusing on Nanobodies. Int J Mol Sci 2023; 24:4307. [PMID: 36901737 PMCID: PMC10002328 DOI: 10.3390/ijms24054307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Since the discovery of fluorescent proteins (FPs), their rich fluorescence spectra and photochemical properties have promoted widespread biological research applications. FPs can be classified into green fluorescent protein (GFP) and its derivates, red fluorescent protein (RFP) and its derivates, and near-infrared FPs. With the continuous development of FPs, antibodies targeting FPs have emerged. The antibody, a class of immunoglobulin, is the main component of humoral immunity that explicitly recognizes and binds antigens. Monoclonal antibody, originating from a single B cell, has been widely applied in immunoassay, in vitro diagnostics, and drug development. The nanobody is a new type of antibody entirely composed of the variable domain of a heavy-chain antibody. Compared with conventional antibodies, these small and stable nanobodies can be expressed and functional in living cells. In addition, they can easily access grooves, seams, or hidden antigenic epitopes on the surface of the target. This review provides an overview of various FPs, the research progress of their antibodies, particularly nanobodies, and advanced applications of nanobodies targeting FPs. This review will be helpful for further research on nanobodies targeting FPs, making FPs more valuable in biological research.
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Affiliation(s)
- Yu-Lei Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xin-Xin Xie
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ning Zhong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Le-Chang Sun
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Duanquan Lin
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ling-Jing Zhang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Ling Weng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Tengchuan Jin
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei 230007, China
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
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12
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Duan T, Rodriguez-Tirado F, Geyer PK. Immunohistochemical Analysis of Nuclear Lamina Structures in the Drosophila Ovary Using CRISPR-Tagged Genes. Methods Mol Biol 2023; 2626:109-134. [PMID: 36715902 DOI: 10.1007/978-1-0716-2970-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The Drosophila ovary represents an outstanding model for investigating tissue homeostasis. Females continuously produce oocytes throughout their lifetime. However, as females age, fecundity declines, in part, due to changes in ovarian niche function and germline stem cell (GSC) homeostasis. Understanding the dynamics of GSC maintenance will provide needed insights into how coordinated tissue homeostasis is lost during aging. Critical regulators of GSC maintenance are proteins that reside in the nuclear lamina (NL), including the NL proteins emerin and Barrier-to-Autointegration Factor (BAF). Continued investigation of how emerin, BAF, and other NL proteins contribute to GSC function depends upon the availability of antibodies for NL proteins, a limiting resource. In this chapter, we discuss strategies for using clustered regularly interspaced short palindromic repeats (CRISPR) genomic editing to produce endogenously tagged NL genes to circumvent this obstacle, using the generation of the gfp-baf allele as an example. We describe strategies for validation of tagged alleles. Finally, we outline methods for immunohistochemical analysis of resulting tagged-NL proteins.
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Affiliation(s)
- Tingting Duan
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Felipe Rodriguez-Tirado
- Department of Biochemistry and Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Pamela K Geyer
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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13
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Burgstaller S, Wagner TR, Bischof H, Bueckle S, Padamsey A, Frecot D, Kaiser PD, Skrabak D, Malli R, Lukowski R, Rothbauer U. Monitoring extracellular ion and metabolite dynamics with recombinant nanobody-fused biosensors. iScience 2022; 25:104907. [PMID: 36046190 PMCID: PMC9421384 DOI: 10.1016/j.isci.2022.104907] [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] [Received: 04/13/2022] [Revised: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Ion and analyte changes in the tumor microenvironment (TME) alter the metabolic activity of cancer cells, promote tumor cell growth, and impair anti-tumor immunity. Consequently, accurate determination and visualization of extracellular changes of analytes in real time is desired. In this study, we genetically combined FRET-based biosensors with nanobodies (Nbs) to specifically visualize and monitor extracellular changes in K+, pH, and glucose on cell surfaces. We demonstrated that these Nb-fused biosensors quantitatively visualized K+ alterations on cancer and non-cancer cell lines and primary neurons. By implementing a HER2-specific Nb, we generated functional K+ and pH sensors, which specifically stained HER2-positive breast cancer cells. Based on the successful development of several Nb-fused biosensor combinations, we anticipate that this approach can be readily extended to other biosensors and will open new opportunities for the study of extracellular analytes in advanced experimental settings. Generation of recombinant nanobody-fused FRET biosensors Nb-fused biosensors specifically bind targets on the outer surface of various cells Cellular bound Nb-biosensors visualize extracellular analyte changes in real time
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Affiliation(s)
- Sandra Burgstaller
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Helmut Bischof
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Sarah Bueckle
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Aman Padamsey
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Desiree Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - David Skrabak
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Roland Malli
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
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14
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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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15
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San Martín A, Arce-Molina R, Aburto C, Baeza-Lehnert F, Barros LF, Contreras-Baeza Y, Pinilla A, Ruminot I, Rauseo D, Sandoval PY. Visualizing physiological parameters in cells and tissues using genetically encoded indicators for metabolites. Free Radic Biol Med 2022; 182:34-58. [PMID: 35183660 DOI: 10.1016/j.freeradbiomed.2022.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
The study of metabolism is undergoing a renaissance. Since the year 2002, over 50 genetically-encoded fluorescent indicators (GEFIs) have been introduced, capable of monitoring metabolites with high spatial/temporal resolution using fluorescence microscopy. Indicators are fusion proteins that change their fluorescence upon binding a specific metabolite. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides. They permit monitoring relative levels, concentrations, and fluxes in living systems. At a minimum they report relative levels and, in some cases, absolute concentrations may be obtained by performing ad hoc calibration protocols. Proper data collection, processing, and interpretation are critical to take full advantage of these new tools. This review offers a survey of the metabolic indicators that have been validated in mammalian systems. Minimally invasive, these indicators have been instrumental for the purposes of confirmation, rebuttal and discovery. We envision that this powerful technology will foster metabolic physiology.
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Affiliation(s)
- A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile.
| | - R Arce-Molina
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - C Aburto
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | | | - L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Y Contreras-Baeza
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - A Pinilla
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - D Rauseo
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile
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16
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Barakat S, Berksöz M, Zahedimaram P, Piepoli S, Erman B. Nanobodies as molecular imaging probes. Free Radic Biol Med 2022; 182:260-275. [PMID: 35240292 DOI: 10.1016/j.freeradbiomed.2022.02.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 12/12/2022]
Abstract
Camelidae derived single-domain antibodies (sdAbs), commonly known as nanobodies (Nbs), are the smallest antibody fragments with full antigen-binding capacity. Owing to their desirable properties such as small size, high specificity, strong affinity, excellent stability, and modularity, nanobodies are on their way to overtake conventional antibodies in terms of popularity. To date, a broad range of nanobodies have been generated against different molecular targets with applications spanning basic research, diagnostics, and therapeutics. In the field of molecular imaging, nanobody-based probes have emerged as a powerful tool. Radioactive or fluorescently labeled nanobodies are now used to detect and track many targets in different biological systems using imaging techniques. In this review, we provide an overview of the use of nanobodies as molecular probes. Additionally, we discuss current techniques for the generation, conjugation, and intracellular delivery of nanobodies.
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Affiliation(s)
- Sarah Barakat
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Melike Berksöz
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Pegah Zahedimaram
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Tuzla, Istanbul, Turkey.
| | - Sofia Piepoli
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
| | - Batu Erman
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Bogazici University, 34342, Bebek, Istanbul, Turkey.
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17
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Abstract
The Wnt pathway is central to a host of developmental and disease-related processes. The remarkable conservation of this intercellular signaling cascade throughout metazoan lineages indicates that it coevolved with multicellularity to regulate the generation and spatial arrangement of distinct cell types. By regulating cell fate specification, mitotic activity, and cell polarity, Wnt signaling orchestrates development and tissue homeostasis, and its dysregulation is implicated in developmental defects, cancer, and degenerative disorders. We review advances in our understanding of this key pathway, from Wnt protein production and secretion to relay of the signal in the cytoplasm of the receiving cell. We discuss the evolutionary history of this pathway as well as endogenous and synthetic modulators of its activity. Finally, we highlight remaining gaps in our knowledge of Wnt signal transduction and avenues for future research. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ellen Youngsoo Rim
- Howard Hughes Medical Institute, Department of Developmental Biology, and Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, California, USA;
| | - Hans Clevers
- Hubrecht Institute and Oncode Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, The Netherlands
| | - Roel Nusse
- Howard Hughes Medical Institute, Department of Developmental Biology, and Institute for Stem Cell Biology and Regenerative Medicine, School of Medicine, Stanford University, Stanford, California, USA;
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18
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Park J, Demirer GS, Cheung LS. Toolboxes for plant systems biology research. Curr Opin Biotechnol 2022; 75:102692. [PMID: 35144172 DOI: 10.1016/j.copbio.2022.102692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
The terms 'systems' and 'synthetic biology' are often used together, with most scientists striding between the two fields rather than adhering to a single side. Often too, scientists want to understand a system to inform the design of gene circuits that could endow it with new functions. However, this does not need to be the progression of research, as synthetic constructs can help improve our understanding of a system. Here, we review synthetic biology tool kits with the potential to overcome pleiotropic effects, compensatory mechanisms, and redundancy in plants. Combined with -omics techniques, these tools could reveal novel insights on plant growth and development, an aim that has gained renewed urgency given the impact of climate change on crop productivity.
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Affiliation(s)
- Jihyun Park
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gozde S Demirer
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA; Department of Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lily S Cheung
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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19
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Ziegler MJ, Yserentant K, Dunsing V, Middel V, Gralak AJ, Pakari K, Bargstedt J, Kern C, Petrich A, Chiantia S, Strähle U, Herten DP, Wombacher R. Mandipropamid as a chemical inducer of proximity for in vivo applications. Nat Chem Biol 2022; 18:64-69. [PMID: 34934192 PMCID: PMC8709788 DOI: 10.1038/s41589-021-00922-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
Direct control of protein interactions by chemically induced protein proximity holds great potential for both cell and synthetic biology as well as therapeutic applications. Low toxicity, orthogonality and excellent cell permeability are important criteria for chemical inducers of proximity (CIPs), in particular for in vivo applications. Here, we present the use of the agrochemical mandipropamid (Mandi) as a highly efficient CIP in cell culture systems and living organisms. Mandi specifically induces complex formation between a sixfold mutant of the plant hormone receptor pyrabactin resistance 1 (PYR1) and abscisic acid insensitive (ABI). It is orthogonal to other plant hormone-based CIPs and rapamycin-based CIP systems. We demonstrate the applicability of the Mandi system for rapid and efficient protein translocation in mammalian cells and zebrafish embryos, protein network shuttling and manipulation of endogenous proteins.
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Affiliation(s)
- Michael J Ziegler
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Klaus Yserentant
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Institute of Cardiovascular Sciences & School of Chemistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Valentin Dunsing
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Volker Middel
- Institute of Biological and Chemical Systems (IBCS)-Biological Information Processing (BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Antoni J Gralak
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Kaisa Pakari
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Jörn Bargstedt
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Christoph Kern
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Annett Petrich
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Salvatore Chiantia
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Uwe Strähle
- Institute of Biological and Chemical Systems (IBCS)-Biological Information Processing (BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Dirk-Peter Herten
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Institute of Cardiovascular Sciences & School of Chemistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
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20
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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21
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Wagner TR, Rothbauer U. Nanobodies - Little helpers unravelling intracellular signaling. Free Radic Biol Med 2021; 176:46-61. [PMID: 34536541 DOI: 10.1016/j.freeradbiomed.2021.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022]
Abstract
The identification of diagnostic and therapeutic targets requires a comprehensive understanding of cellular processes, for which advanced technologies in biomedical research are needed. The emergence of nanobodies (Nbs) derived from antibody fragments of camelid heavy chain-only antibodies as intracellular research tools offers new possibilities to study and modulate target antigens in living cells. Here we summarize this rapidly changing field, beginning with a brief introduction of Nbs, followed by an overview of how target-specific Nbs can be generated, and introduce the selection of intrabodies as research tools. Intrabodies, by definition, are intracellular functional Nbs that target ectopic or endogenous intracellular antigens within living cells. Such binders can be applied in various formats, e.g. as chromobodies for live cell microscopy or as biosensors to decipher complex intracellular signaling pathways. In addition, protein knockouts can be achieved by target-specific Nbs, while modulating Nbs have the potential as future therapeutics. The development of fine-tunable and switchable Nb-based systems that simultaneously provide spatial and temporal control has recently taken the application of these binders to the next level.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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22
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Wang Z, Li L, Hu R, Zhong P, Zhang Y, Cheng S, Jiang H, Liu R, Ding Y. Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry. Protein Sci 2021; 30:2298-2309. [PMID: 34562299 PMCID: PMC8521304 DOI: 10.1002/pro.4194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023]
Abstract
Red fluorescent proteins (RFPs) are powerful tools used in molecular biology research. Although RFP can be easily monitored in vivo, manipulation of RFP by suitable nanobodies binding to different epitopes of RFP is still desired. Thus, it is crucial to obtain structural information on how the different nanobodies interact with RFP. Here, we determined the crystal structures of the LaM2-mCherry and LaM4-mCherry complexes at 1.4 and 1.9 Å resolution. Our results showed that LaM2 binds to the side of the mCherry β-barrel, while LaM4 binds to the bottom of the β-barrel. The distinct binding sites of LaM2 and LaM4 were further verified by isothermal titration calorimetry, fluorescence-based size exclusion chromatography, and dynamic light scattering assays. Mutation of the residues at the LaM2 or LaM4 binding interface to mCherry significantly decreased the binding affinity of the nanobody to mCherry. Our results also showed that LaM2 and LaM4 can bind to mCherry simultaneously, which is crucial for recruiting multiple operation elements to the RFP. The binding of LaM2 or LaM4 did not significantly change the chromophore environment of mCherry, which is important for fluorescence quantification assays, while several GFP nanobodies significantly altered the fluorescence. Our results provide atomic resolution interaction information on the binding of nanobodies LaM2 and LaM4 with mCherry, which is important for developing detection and manipulation methods for RFP-based biotechnology.
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Affiliation(s)
- Ziying Wang
- School of Life SciencesFudan UniversityShanghaiChina
| | - Long Li
- Department of MacromoleculesFudan UniversityShanghaiChina
| | - Rongting Hu
- Department of MacromoleculesFudan UniversityShanghaiChina
| | - Peiyu Zhong
- School of Life SciencesFudan UniversityShanghaiChina
| | - Yiran Zhang
- School of Life SciencesFudan UniversityShanghaiChina
| | - Shihao Cheng
- School of Life SciencesFudan UniversityShanghaiChina
| | - He Jiang
- School of Life SciencesFudan UniversityShanghaiChina
| | - Rui Liu
- School of Life SciencesFudan UniversityShanghaiChina
| | - Yu Ding
- School of Life SciencesFudan UniversityShanghaiChina
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23
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Deng DJ, Xia QC, Jia GS, Suo F, Chen JL, Sun L, Wang JQ, Wang SM, Du LL, Wang Y, Jin QW. Perturbation of kinetochore function using GFP-binding protein in fission yeast. G3 GENES|GENOMES|GENETICS 2021; 11:6353032. [PMID: 34849791 PMCID: PMC8527488 DOI: 10.1093/g3journal/jkab290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/10/2021] [Indexed: 11/12/2022]
Abstract
Abstract
Using genetic mutations to study protein functions in vivo is a central paradigm of modern biology. Single-domain camelid antibodies generated against GFP have been engineered as nanobodies or GFP-binding proteins (GBPs) that can bind GFP as well as some GFP variants with high affinity and selectivity. In this study, we have used GBP-mCherry fusion protein as a tool to perturb the natural functions of a few kinetochore proteins in the fission yeast Schizosaccharomyces pombe. We found that cells simultaneously expressing GBP-mCherry and the GFP-tagged inner kinetochore protein Cnp1 are sensitive to high temperature and microtubule drug thiabendazole (TBZ). In addition, kinetochore-targeted GBP-mCherry by a few major kinetochore proteins with GFP tags causes defects in faithful chromosome segregation. Thus, this setting compromises the functions of kinetochores and renders cells to behave like conditional mutants. Our study highlights the potential of using GBP as a general tool to perturb the function of some GFP-tagged proteins in vivo with the objective of understanding their functional relevance to certain physiological processes, not only in yeasts, but also potentially in other model systems.
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Affiliation(s)
- Da-Jie Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qian-Cheng Xia
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jia-Li Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Li Sun
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jin-Qing Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shuang-Min Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yamei Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Quan-Wen Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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24
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Vigano MA, Ell CM, Kustermann MMM, Aguilar G, Matsuda S, Zhao N, Stasevich TJ, Affolter M, Pyrowolakis G. Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster. Development 2021; 148:dev191700. [PMID: 33593816 PMCID: PMC7990863 DOI: 10.1242/dev.191700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 02/09/2021] [Indexed: 01/01/2023]
Abstract
Cellular development and function rely on highly dynamic molecular interactions among proteins distributed in all cell compartments. Analysis of these interactions has been one of the main topics in cellular and developmental research, and has been mostly achieved by the manipulation of proteins of interest (POIs) at the genetic level. Although genetic strategies have significantly contributed to our current understanding, targeting specific interactions of POIs in a time- and space-controlled manner or analysing the role of POIs in dynamic cellular processes, such as cell migration or cell division, would benefit from more-direct approaches. The recent development of specific protein binders, which can be expressed and function intracellularly, along with advancement in synthetic biology, have contributed to the creation of a new toolbox for direct protein manipulations. Here, we have selected a number of short-tag epitopes for which protein binders from different scaffolds have been generated and showed that single copies of these tags allowed efficient POI binding and manipulation in living cells. Using Drosophila, we also find that single short tags can be used for POI manipulation in vivo.
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Affiliation(s)
- M Alessandra Vigano
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Clara-Maria Ell
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Manuela M M Kustermann
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Gustavo Aguilar
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Shinya Matsuda
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - George Pyrowolakis
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
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25
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Wagner TR, Rothbauer U. Nanobodies Right in the Middle: Intrabodies as Toolbox to Visualize and Modulate Antigens in the Living Cell. Biomolecules 2020; 10:biom10121701. [PMID: 33371447 PMCID: PMC7767433 DOI: 10.3390/biom10121701] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/01/2023] Open
Abstract
In biomedical research, there is an ongoing demand for new technologies to elucidate disease mechanisms and develop novel therapeutics. This requires comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, post-translational modifications and dynamic interactions of cellular components. Traceable intracellular binding molecules provide new opportunities for real-time cellular diagnostics. Most prominently, intrabodies derived from antibody fragments of heavy-chain only antibodies of camelids (nanobodies) have emerged as highly versatile and attractive probes to study and manipulate antigens within the context of living cells. In this review, we provide an overview on the selection, delivery and usage of intrabodies to visualize and monitor cellular antigens in living cells and organisms. Additionally, we summarize recent advances in the development of intrabodies as cellular biosensors and their application to manipulate disease-related cellular processes. Finally, we highlight switchable intrabodies, which open entirely new possibilities for real-time cell-based diagnostics including live-cell imaging, target validation and generation of precisely controllable binding reagents for future therapeutic applications.
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Affiliation(s)
- Teresa R. Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
- Correspondence: ; Tel.: +49-7121-5153-0415; Fax: +49-7121-5153-0816
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26
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Nanobodies as Versatile Tool for Multiscale Imaging Modalities. Biomolecules 2020; 10:biom10121695. [PMID: 33353213 PMCID: PMC7767244 DOI: 10.3390/biom10121695] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Molecular imaging is constantly growing in different areas of preclinical biomedical research. Several imaging methods have been developed and are continuously updated for both in vivo and in vitro applications, in order to increase the information about the structure, localization and function of molecules involved in physiology and disease. Along with these progresses, there is a continuous need for improving labeling strategies. In the last decades, the single domain antigen-binding fragments nanobodies (Nbs) emerged as important molecular imaging probes. Indeed, their small size (~15 kDa), high stability, affinity and modularity represent desirable features for imaging applications, providing higher tissue penetration, rapid targeting, increased spatial resolution and fast clearance. Accordingly, several Nb-based probes have been generated and applied to a variety of imaging modalities, ranging from in vivo and in vitro preclinical imaging to super-resolution microscopy. In this review, we will provide an overview of the state-of-the-art regarding the use of Nbs in several imaging modalities, underlining their extreme versatility and their enormous potential in targeting molecules and cells of interest in both preclinical and clinical studies.
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27
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Soetens E, Ballegeer M, Saelens X. An Inside Job: Applications of Intracellular Single Domain Antibodies. Biomolecules 2020; 10:biom10121663. [PMID: 33322697 PMCID: PMC7764588 DOI: 10.3390/biom10121663] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Sera of camelid species contain a special kind of antibody that consists only of heavy chains. The variable antigen binding domain of these heavy chain antibodies can be expressed as a separate entity, called a single domain antibody that is characterized by its small size, high solubility and oftentimes exceptional stability. Because of this, most single domain antibodies fold correctly when expressed in the reducing environment of the cytoplasm, and thereby retain their antigen binding specificity. Single domain antibodies can thus be used to target a broad range of intracellular proteins. Such intracellular single domain antibodies are also known as intrabodies, and have proven to be highly useful tools for basic research by allowing visualization, disruption and even targeted degradation of intracellular proteins. Furthermore, intrabodies can be used to uncover prospective new therapeutic targets and have the potential to be applied in therapeutic settings in the future. In this review we provide a brief overview of recent advances in the field of intracellular single domain antibodies, focusing on their use as research tools and potential therapeutic applications. Special attention is given to the available methods that allow delivery of single domain antibodies into cells.
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Affiliation(s)
- Eline Soetens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Marlies Ballegeer
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, B-9052 Ghent, Belgium; (E.S.); (M.B.)
- Department of Biochemistry and Microbiology, Ghent University, B-9000 Ghent, Belgium
- Correspondence:
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28
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de Beer MA, Giepmans BNG. Nanobody-Based Probes for Subcellular Protein Identification and Visualization. Front Cell Neurosci 2020; 14:573278. [PMID: 33240044 PMCID: PMC7667270 DOI: 10.3389/fncel.2020.573278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.
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Affiliation(s)
- Marit A de Beer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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29
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Wilkes J, Scott-Tucker A, Wright M, Crabbe T, Scrutton NS. Exploiting Single Domain Antibodies as Regulatory Parts to Modulate Monoterpenoid Production in E. coli. ACS Synth Biol 2020; 9:2828-2839. [PMID: 32927940 DOI: 10.1021/acssynbio.0c00375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic biology and metabolic engineering offer potentially green and attractive routes to the production of high value compounds. The provision of high-quality parts and pathways is crucial in enabling the biosynthesis of chemicals using synthetic biology. While a number of regulatory parts that provide control at the transcriptional and translational level have been developed, relatively few exist at the protein level. Single domain antibodies (sdAb) such as camelid heavy chain variable fragments (VHH) possess binding characteristics which could be exploited for their development and use as novel parts for regulating metabolic pathways at the protein level in microbial cell factories. Here, a platform for the use of VHH as tools in Escherichia coli is developed and subsequently used to modulate linalool production in E. coli. The coproduction of a Design of Experiments (DoE) optimized pBbE8k His6-VHHCyDisCo system alongside a heterologous linalool production pathway facilitated the identification of anti-bLinS VHH that functioned as modulators of bLinS. This resulted in altered product profiles and significant variation in the titers of linalool, geraniol, nerolidol, and indole obtained. The ability to alter the production levels of high value terpenoids, such as linalool, in a tunable manner at the protein level could represent a significant step forward for the development of improved microbial cell factories. This study serves as a proof of principle indicating that VHH can be used to modulate enzyme activity in engineered pathways within E. coli. Given their almost limitless binding potential, we posit that single domain antibodies could emerge as powerful regulatory parts in synthetic biology applications.
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Affiliation(s)
- Jonathan Wilkes
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | | | - Mike Wright
- UCB Pharma Ltd., Slough, SL1 3WE, United Kingdom
| | - Tom Crabbe
- UCB Pharma Ltd., Slough, SL1 3WE, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, United Kingdom
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30
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Zhang C, Ötjengerdes RM, Roewe J, Mejias R, Marschall ALJ. Applying Antibodies Inside Cells: Principles and Recent Advances in Neurobiology, Virology and Oncology. BioDrugs 2020; 34:435-462. [PMID: 32301049 PMCID: PMC7391400 DOI: 10.1007/s40259-020-00419-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To interfere with cell function, many scientists rely on methods that target DNA or RNA due to the ease with which they can be applied. Proteins are usually the final executors of function but are targeted only indirectly by these methods. Recent advances in targeted degradation of proteins based on proteolysis-targeting chimaeras (PROTACs), ubiquibodies, deGradFP (degrade Green Fluorescent Protein) and other approaches have demonstrated the potential of interfering directly at the protein level for research and therapy. Proteins can be targeted directly and very specifically by antibodies, but using antibodies inside cells has so far been considered to be challenging. However, it is possible to deliver antibodies or other proteins into the cytosol using standard laboratory equipment. Physical methods such as electroporation have been demonstrated to be efficient and validated thoroughly over time. The expression of intracellular antibodies (intrabodies) inside cells is another way to interfere with intracellular targets at the protein level. Methodological strategies to target the inside of cells with antibodies, including delivered antibodies and expressed antibodies, as well as applications in the research areas of neurobiology, viral infections and oncology, are reviewed here. Antibodies have already been used to interfere with a wide range of intracellular targets. Disease-related targets included proteins associated with neurodegenerative diseases such as Parkinson's disease (α-synuclein), Alzheimer's disease (amyloid-β) or Huntington's disease (mutant huntingtin [mHtt]). The applications of intrabodies in the context of viral infections include targeting proteins associated with HIV (e.g. HIV1-TAT, Rev, Vif, gp41, gp120, gp160) and different oncoviruses such as human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV) and Epstein-Barr virus, and they have been used to interfere with various targets related to different processes in cancer, including oncogenic pathways, proliferation, cell cycle, apoptosis, metastasis, angiogenesis or neo-antigens (e.g. p53, human epidermal growth factor receptor-2 [HER2], signal transducer and activator of transcription 3 [STAT3], RAS-related RHO-GTPase B (RHOB), cortactin, vascular endothelial growth factor receptor 2 [VEGFR2], Ras, Bcr-Abl). Interfering at the protein level allows questions to be addressed that may remain unanswered using alternative methods. This review addresses why direct targeting of proteins allows unique insights, what is currently feasible in vitro, and how this relates to potential therapeutic applications.
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Affiliation(s)
- Congcong Zhang
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rina M Ötjengerdes
- Hannover Medical School (MHH), Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Julian Roewe
- German Cancer Consortium (DKTK) Clinical Cooperation Unit (CCU) Neuroimmunology and Brain TumorImmunology (D170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rebeca Mejias
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea L J Marschall
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Brunswick, Germany.
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31
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Ibrahim AFM, Shen L, Tatham MH, Dickerson D, Prescott AR, Abidi N, Xirodimas DP, Hay RT. Antibody RING-Mediated Destruction of Endogenous Proteins. Mol Cell 2020; 79:155-166.e9. [PMID: 32454028 PMCID: PMC7332993 DOI: 10.1016/j.molcel.2020.04.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/20/2020] [Accepted: 04/27/2020] [Indexed: 01/05/2023]
Abstract
To understand gene function, the encoding DNA or mRNA transcript can be manipulated and the consequences observed. However, these approaches do not have a direct effect on the protein product of the gene, which is either permanently abrogated or depleted at a rate defined by the half-life of the protein. We therefore developed a single-component system that could induce the rapid degradation of the specific endogenous protein itself. A construct combining the RING domain of ubiquitin E3 ligase RNF4 with a protein-specific camelid nanobody mediates target destruction by the ubiquitin proteasome system, a process we describe as antibody RING-mediated destruction (ARMeD). The technique is highly specific because we observed no off-target protein destruction. Furthermore, bacterially produced nanobody-RING fusion proteins electroporated into cells induce degradation of target within minutes. With increasing availability of protein-specific nanobodies, this method will allow rapid and specific degradation of a wide range of endogenous proteins.
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Affiliation(s)
- Adel F M Ibrahim
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Linnan Shen
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - David Dickerson
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alan R Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Naima Abidi
- Cell Biology Research Centre of Montpellier, CNRS, UMR 5237, Montpellier, France
| | - Dimitris P Xirodimas
- Cell Biology Research Centre of Montpellier, CNRS, UMR 5237, Montpellier, France
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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32
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Rossini M, Pizzo P, Filadi R. Better to keep in touch: investigating inter‐organelle cross‐talk. FEBS J 2020; 288:740-755. [DOI: 10.1111/febs.15451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/28/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Michela Rossini
- Department of Biomedical Sciences University of Padua Padua Italy
| | - Paola Pizzo
- Department of Biomedical Sciences University of Padua Padua Italy
- Neuroscience Institute National Research Council (CNR) Padua Italy
| | - Riccardo Filadi
- Department of Biomedical Sciences University of Padua Padua Italy
- Neuroscience Institute National Research Council (CNR) Padua Italy
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33
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Küey C, Larocque G, Clarke NI, Royle SJ. Unintended perturbation of protein function using GFP nanobodies in human cells. J Cell Sci 2019; 132:jcs234955. [PMID: 31601614 PMCID: PMC6857592 DOI: 10.1242/jcs.234955] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Tagging a protein of interest with GFP using genome editing is a popular approach to study protein function in cell and developmental biology. To avoid re-engineering cell lines or organisms in order to introduce additional tags, functionalized nanobodies that bind GFP can be used to extend the functionality of the GFP tag. We developed functionalized nanobodies, which we termed 'dongles', that could add, for example, an FKBP tag to a GFP-tagged protein of interest, enabling knocksideways experiments in GFP knock-in cell lines. The power of knocksideways is that it allows investigators to rapidly switch the protein from an active to an inactive state. We show that dongles allow for effective knocksideways of GFP-tagged proteins in genome-edited human cells. However, we discovered that nanobody binding to dynamin-2-GFP caused inhibition of dynamin function prior to knocksideways. The function of GFP-tagged tumor protein D54 (TPD54, also known as TPD52L2) in anterograde traffic was also perturbed by dongles. While these issues potentially limit the application of dongles, we discuss strategies for their deployment as cell biological tools.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Cansu Küey
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Gabrielle Larocque
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Nicholas I Clarke
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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34
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Weiss RA, Verrips CT. Nanobodies that Neutralize HIV. Vaccines (Basel) 2019; 7:vaccines7030077. [PMID: 31370301 PMCID: PMC6789485 DOI: 10.3390/vaccines7030077] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 11/16/2022] Open
Abstract
Nanobodies or VHH (variable domains of heavy-chain only antibodies) are derived from camelid species such as llamas and camels. Nanobodies isolated and selected through phage display can neutralize a broad range of human immunodeficiency virus type 1 (HIV-1) strains. Nanobodies fit into canyons on the HIV envelope that may not be accessible to IgG (immunoglobulin G) containing both heavy and light chains, and they tend to have long CDR3 (complementarity-determining region 3) loops that further enhance recognition of otherwise cryptic epitopes. Nanobodies are readily expressed at high levels in bacteria and yeast, as well as by viral vectors, and they form relatively stable, heat-resistant molecules. Nanobodies can be linked to human Fc chains to gain immune effector functions. Bivalent and trivalent nanobodies recognizing the same or distinct epitopes on the envelope glycoproteins, gp120 and gp41, greatly increase the potency of HIV-1 neutralization. Nanobodies have potential applications for HIV-1 diagnostics, vaccine design, microbicides, immunoprophylaxis, and immunotherapy.
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Affiliation(s)
- Robin A Weiss
- Division of Infection & Immunity, University College London, 90 Gower Street, London WC1E 6BT, UK.
| | - C Theo Verrips
- QVQ Holding bv, Padualaan 8, 3584 CL Utrecht, The Netherlands.
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