1
|
Timalsina B, Lee S, Kaang BK. Advances in the labelling and selective manipulation of synapses. Nat Rev Neurosci 2024:10.1038/s41583-024-00851-9. [PMID: 39174832 DOI: 10.1038/s41583-024-00851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Synapses are highly specialized neuronal structures that are essential for neurotransmission, and they are dynamically regulated throughout the lifetime. Although accumulating evidence indicates that these structures are crucial for information processing and storage in the brain, their precise roles beyond neurotransmission are yet to be fully appreciated. Genetically encoded fluorescent tools have deepened our understanding of synaptic structure and function, but developing an ideal methodology to selectively visualize, label and manipulate synapses remains challenging. Here, we provide an overview of currently available synapse labelling techniques and describe their extension to enable synapse manipulation. We categorize these approaches on the basis of their conceptual bases and target molecules, compare their advantages and limitations and propose potential modifications to improve their effectiveness. These methods have broad utility, particularly for investigating mechanisms of synaptic function and synaptopathy.
Collapse
Affiliation(s)
- Binod Timalsina
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Sangkyu Lee
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea
| | - Bong-Kiun Kaang
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, South Korea.
| |
Collapse
|
2
|
Ren H, Ou Q, Pu Q, Lou Y, Yang X, Han Y, Liu S. Comprehensive Review on Bimolecular Fluorescence Complementation and Its Application in Deciphering Protein-Protein Interactions in Cell Signaling Pathways. Biomolecules 2024; 14:859. [PMID: 39062573 PMCID: PMC11274695 DOI: 10.3390/biom14070859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Signaling pathways are responsible for transmitting information between cells and regulating cell growth, differentiation, and death. Proteins in cells form complexes by interacting with each other through specific structural domains, playing a crucial role in various biological functions and cell signaling pathways. Protein-protein interactions (PPIs) within cell signaling pathways are essential for signal transmission and regulation. The spatiotemporal features of PPIs in signaling pathways are crucial for comprehending the regulatory mechanisms of signal transduction. Bimolecular fluorescence complementation (BiFC) is one kind of imaging tool for the direct visualization of PPIs in living cells and has been widely utilized to uncover novel PPIs in various organisms. BiFC demonstrates significant potential for application in various areas of biological research, drug development, disease diagnosis and treatment, and other related fields. This review systematically summarizes and analyzes the technical advancement of BiFC and its utilization in elucidating PPIs within established cell signaling pathways, including TOR, PI3K/Akt, Wnt/β-catenin, NF-κB, and MAPK. Additionally, it explores the application of this technology in revealing PPIs within the plant hormone signaling pathways of ethylene, auxin, Gibberellin, and abscisic acid. Using BiFC in conjunction with CRISPR-Cas9, live-cell imaging, and ultra-high-resolution microscopy will enhance our comprehension of PPIs in cell signaling pathways.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Shiping Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China; (H.R.); (Q.O.); (Q.P.); (Y.L.); (X.Y.); (Y.H.)
| |
Collapse
|
3
|
Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024; 226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [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: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Membrane proteins play pivotal roles in a wide array of cellular processes and constitute approximately a quarter of the protein-coding genes across all organisms. Despite their ubiquity and biological significance, our understanding of these proteins remains notably less comprehensive compared to their soluble counterparts. This disparity in knowledge can be attributed, in part, to the inherent challenges associated with employing specialized techniques for the investigation of membrane protein insertion and topology. This review will center on a discussion of molecular biology methodologies and computational prediction tools designed to elucidate the insertion and topology of helical membrane proteins.
Collapse
Affiliation(s)
- Gerard Duart
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ricardo Graña-Montes
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Noelia Pastor-Cantizano
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain
| | - Ismael Mingarro
- Departament de Bioquímica i Biologia Molecular, Institut Universitari de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, E-46100 Burjassot, Spain.
| |
Collapse
|
4
|
Wu Y, Jensen N, Rossner MJ, Wehr MC. Exploiting Cell-Based Assays to Accelerate Drug Development for G Protein-Coupled Receptors. Int J Mol Sci 2024; 25:5474. [PMID: 38791511 PMCID: PMC11121687 DOI: 10.3390/ijms25105474] [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: 04/22/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are relevant targets for health and disease as they regulate various aspects of metabolism, proliferation, differentiation, and immune pathways. They are implicated in several disease areas, including cancer, diabetes, cardiovascular diseases, and mental disorders. It is worth noting that about a third of all marketed drugs target GPCRs, making them prime pharmacological targets for drug discovery. Numerous functional assays have been developed to assess GPCR activity and GPCR signaling in living cells. Here, we review the current literature of genetically encoded cell-based assays to measure GPCR activation and downstream signaling at different hierarchical levels of signaling, from the receptor to transcription, via transducers, effectors, and second messengers. Singleplex assay formats provide one data point per experimental condition. Typical examples are bioluminescence resonance energy transfer (BRET) assays and protease cleavage assays (e.g., Tango or split TEV). By contrast, multiplex assay formats allow for the parallel measurement of multiple receptors and pathways and typically use molecular barcodes as transcriptional reporters in barcoded assays. This enables the efficient identification of desired on-target and on-pathway effects as well as detrimental off-target and off-pathway effects. Multiplex assays are anticipated to accelerate drug discovery for GPCRs as they provide a comprehensive and broad identification of compound effects.
Collapse
Affiliation(s)
- Yuxin Wu
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| | - Niels Jensen
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Moritz J. Rossner
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C. Wehr
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstr. 6, 81669 Munich, Germany
| |
Collapse
|
5
|
Bae J, Kim J, Choi J, Lee H, Koh M. Split Proteins and Reassembly Modules for Biological Applications. Chembiochem 2024; 25:e202400123. [PMID: 38530024 DOI: 10.1002/cbic.202400123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Split systems, modular entities enabling controlled biological processes, have become instrumental in biological research. This review highlights their utility across applications like gene regulation, protein interaction identification, and biosensor development. Covering significant progress over the last decade, it revisits traditional split proteins such as GFP, luciferase, and inteins, and explores advancements in technologies like Cas proteins and base editors. We also examine reassembly modules and their applications in diverse fields, from gene regulation to therapeutic innovation. This review offers a comprehensive perspective on the recent evolution of split systems in biological research.
Collapse
Affiliation(s)
- Jieun Bae
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Jonghoon Kim
- Department of Chemistry and Integrative Institute of Basic Science, Soongsil University, Seoul, 06978, Republic of Korea
| | - Jongdoo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Hwiyeong Lee
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| | - Minseob Koh
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan, 46241, Republic of Korea
| |
Collapse
|
6
|
Anderson NT, Xie JS, Chacko AN, Liu VL, Fan KC, Mukherjee A. Rational Design of a Circularly Permuted Flavin-Based Fluorescent Protein. Chembiochem 2024; 25:e202300814. [PMID: 38356332 PMCID: PMC11065581 DOI: 10.1002/cbic.202300814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 02/16/2024]
Abstract
Flavin-based fluorescent proteins are oxygen-independent reporters that hold great promise for imaging anaerobic and hypoxic biological systems. In this study, we explored the feasibility of applying circular permutation, a valuable method for the creation of fluorescent sensors, to flavin-based fluorescent proteins. We used rational design and structural data to identify a suitable location for circular permutation in iLOV, a flavin-based reporter derived from A. thaliana. However, relocating the N- and C-termini to this position resulted in a significant reduction in fluorescence. This loss of fluorescence was reversible, however, by fusing dimerizing coiled coils at the new N- and C-termini to compensate for the increase in local chain entropy. Additionally, by inserting protease cleavage sites in circularly permuted iLOV, we developed two protease sensors and demonstrated their application in mammalian cells. In summary, our work establishes the first approach to engineer circularly permuted FbFPs optimized for high fluorescence and further showcases the utility of circularly permuted FbFPs to serve as a scaffold for sensor engineering.
Collapse
Affiliation(s)
| | - Jason S. Xie
- Department of Molecular, Cellular, and Developmental Biology
| | | | - Vannie L. Liu
- Department of Molecular, Cellular, and Developmental Biology
| | | | | |
Collapse
|
7
|
Ohara N, Kawakami N, Arai R, Adachi N, Ikeda A, Senda T, Miyamoto K. Fusion then fission: splitting and reassembly of an artificial fusion-protein nanocage. Chem Commun (Camb) 2024; 60:4605-4608. [PMID: 38586927 DOI: 10.1039/d4cc00115j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A split-protein system is a simple approach to introduce new termini which are useful as modification sites in protein engineering, but has been adapted mainly for monomeric proteins. Here we demonstrate the design of split subunits of the 60-mer artificial fusion-protein nanocage TIP60. The subunit fragments successfully reformed the cage structure in the same manner as prior to splitting. One of the newly introduced terminals at the interior surface can be modified using a tag peptide and green fluorescent protein. Therefore, the termini could serve as a versatile modification site for incorporating a wide variety of functional peptides and proteins.
Collapse
Affiliation(s)
- Naoya Ohara
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Norifumi Kawakami
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| | - Ryoichi Arai
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Ueda, Nagano 386-8567, Japan
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Akihito Ikeda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho, Tsukuba 305-0801, Japan
| | - Kenji Miyamoto
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan.
| |
Collapse
|
8
|
Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, Leonard JN. Building Synthetic Biosensors Using Red Blood Cell Proteins. ACS Synth Biol 2024; 13:1273-1289. [PMID: 38536408 DOI: 10.1021/acssynbio.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
As the use of engineered cell therapies expands from pioneering efforts in cancer immunotherapy to other applications, an attractive but less explored approach is the use of engineered red blood cells (RBCs). Compared to other cells, RBCs have a very long circulation time and reside in the blood compartment, so they could be ideally suited for applications as sentinel cells that enable in situ sensing and diagnostics. However, we largely lack tools for converting RBCs into biosensors. A unique challenge is that RBCs remodel their membranes during maturation, shedding many membrane components, suggesting that an RBC-specific approach may be needed. Toward addressing this need, here we develop a biosensing architecture built on RBC membrane proteins that are retained through erythropoiesis. This biosensor employs a mechanism in which extracellular ligand binding is transduced into intracellular reconstitution of a split output protein (including either a fluorophore or an enzyme). By comparatively evaluating a range of biosensor architectures, linker types, scaffold choices, and output signals, we identify biosensor designs and design features that confer substantial ligand-induced signal in vitro. Finally, we demonstrate that erythroid precursor cells engineered with our RBC-protein biosensors function in vivo. This study establishes a foundation for developing RBC-based biosensors that could ultimately address unmet needs including noninvasive monitoring of physiological signals for a range of diagnostic applications.
Collapse
Affiliation(s)
- Taylor B Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Taylor F Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Te Ling
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Kelly A Sarnese
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - John D Crispino
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, United States
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
| |
Collapse
|
9
|
Choi J, Chen W, Liao H, Li X, Shendure J. A molecular proximity sensor based on an engineered, dual-component guide RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.14.553235. [PMID: 37645782 PMCID: PMC10461971 DOI: 10.1101/2023.08.14.553235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
One of the goals of synthetic biology is to enable the design of arbitrary molecular circuits with programmable inputs and outputs. Such circuits bridge the properties of electronic and natural circuits, processing information in a predictable manner within living cells. Genome editing is a potentially powerful component of synthetic molecular circuits, whether for modulating the expression of a target gene or for stably recording information to genomic DNA. However, programming molecular events such as protein-protein interactions or induced proximity as triggers for genome editing remains challenging. Here we demonstrate a strategy termed "P3 editing", which links protein-protein proximity to the formation of a functional CRISPRCas9 dual-component guide RNA. By engineering the crRNA:tracrRNA interaction, we demonstrate that various known protein-protein interactions, as well as the chemically-induced dimerization of protein domains, can be used to activate prime editing or base editing in human cells. Additionally, we explore how P3 editing can incorporate outputs from ADAR-based RNA sensors, potentially allowing specific RNAs to induce specific genome edits within a larger circuit. Our strategy enhances the controllability of CRISPR-based genome editing, facilitating its use in synthetic molecular circuits deployed in living cells.
Collapse
Affiliation(s)
- Junhong Choi
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Hanna Liao
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Seattle Hub for Synthetic Biology, Seattle, WA 98195, USA
| |
Collapse
|
10
|
Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 PMCID: PMC11324865 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
Collapse
Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| |
Collapse
|
11
|
Takahashi K, Nishiyama T, Umezawa N, Inoue Y, Akiba I, Dewa T, Ikeda A, Mizuno T. Delivery of external proteins into the cytoplasm using protein capsules modified with IgG on the surface, created from the amphiphilic two helix-bundle protein OLE-ZIP. Chem Commun (Camb) 2024; 60:968-971. [PMID: 38165681 DOI: 10.1039/d3cc05347d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
This study explores a new method for delivering therapeutic proteins into specific cells using OLE-ZIP capsules that present IgG. OLE-ZIP capsules is a spherical caspules prepared from amphihilic dimetic coiled-coil peptide, OLE-ZIP. Upon presenting cetuximab, these capsules showed preferential uptake in A431 cells and increased cytotoxicity when loaded with RNase A.
Collapse
Affiliation(s)
- Kousuke Takahashi
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan.
| | - Taiki Nishiyama
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan.
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Yasumichi Inoue
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Isamu Akiba
- Faculty of Environmental Engineering, the University of Kitakyushu, 1-1 Hibikino, Wakamatsu, Kitakyushu, Fukuoka 808-0135, Japan
| | - Takehisa Dewa
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan.
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Atsushi Ikeda
- Applied Chemistry Program, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
| | - Toshihisa Mizuno
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan.
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya, Aichi 466-8555, Japan
| |
Collapse
|
12
|
Purkait D, Ilyas M, Atmakuri K. Protein-Protein Interactions: Bimolecular Fluorescence Complementation and Cytology Two Hybrid. Methods Mol Biol 2024; 2715:247-257. [PMID: 37930533 DOI: 10.1007/978-1-0716-3445-5_16] [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: 11/07/2023]
Abstract
Identifying protein-protein interactions between machine components of bacterial secretion systems and their cognate substrates is central to delineating how the machines operate to translocate their substrates. Further, establishing which among the machine components and their substrates interact with each other facilitates (i) advancement in our understanding of the architecture and assembly of the machines, (ii) understanding the substrates' translocation routes and mechanisms, and (iii) how the machines and the substrates talk to each other. Currently, though diverse biochemical methods exist in identifying direct and indirect protein-protein interactions, they primarily remain in vitro and can be quite labor intensive. They also may capture/exhibit false-positive interactions because of barrier breakdowns as part of methodology. Thus, adopting novel genetic approaches to help visualize the same in vivo can yield quick, advantageous, reliable, and informative protein-protein interactions data. Here, we describe the easily adoptable bimolecular fluorescence complementation and cytology-based two-hybrid assays to understand the bacterial secretions systems.
Collapse
Affiliation(s)
- Dyuti Purkait
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Mohd Ilyas
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Krishnamohan Atmakuri
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India.
| |
Collapse
|
13
|
Mehlhorn D, Wallmeroth N, Berendzen KW, Grefen C. 2 in 1 Vectors Improve in Planta BiFC and FRET Analysis. Methods Mol Biol 2024; 2772:149-168. [PMID: 38411812 DOI: 10.1007/978-1-0716-3710-4_11] [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: 02/28/2024]
Abstract
Protein-protein interactions (PPIs) play vital roles in all subcellular processes, and a number of tools have been developed for their detection and analysis. Each method has its unique set of benefits and drawbacks that need to be considered prior application. In fact, researchers are spoilt for choice when it comes to deciding which method to use for the initial detection of a PPI and which to corroborate the findings. With constant improvements in microscope development, the possibilities of techniques to study PPIs in vivo, and in real time, are continuously enhanced and expanded. Here, we describe three common approaches, their recent improvements incorporating a 2-in-1 cloning approach, and their application in plant cell biology: ratiometric bimolecular fluorescence complementation (rBiFC), FRET acceptor photobleaching (FRET-AB), and fluorescent lifetime imaging (FRET-FLIM), using Nicotiana benthamiana leaves and Arabidopsis thaliana cell culture protoplasts as transient expression systems.
Collapse
Affiliation(s)
- Dietmar Mehlhorn
- Molecular & Cellular Botany, Ruhr-University Bochum, Bochum, Germany
| | - Niklas Wallmeroth
- Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Kenneth W Berendzen
- Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | | |
Collapse
|
14
|
Ma X, Mandausch FJ, Wu Y, Sahoo VK, Ma W, Leoni G, Hostiuc M, Wintgens JP, Qiu J, Kannaiyan N, Rossner MJ, Wehr MC. Comprehensive split TEV based protein-protein interaction screening reveals TAOK2 as a key modulator of Hippo signalling to limit growth. Cell Signal 2024; 113:110917. [PMID: 37813295 DOI: 10.1016/j.cellsig.2023.110917] [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: 06/14/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
The conserved Hippo signalling pathway plays a crucial role in tumour formation by limiting tissue growth and proliferation. At the core of this pathway are tumour suppressor kinases STK3/4 and LATS1/2, which limit the activity of the oncogene YAP1, the primary downstream effector. Here, we employed a split TEV-based protein-protein interaction screen to assess the physical interactions among 28 key Hippo pathway components and potential upstream modulators. This screen led us to the discovery of TAOK2 as pivotal modulator of Hippo signalling, as it binds to the pathway's core kinases, STK3/4 and LATS1/2, and leads to their phosphorylation. Specifically, our findings revealed that TAOK2 binds to and phosphorylates LATS1, resulting in the reduction of YAP1 phosphorylation and subsequent transcription of oncogenes. Consequently, this decrease led to a decrease in cell proliferation and migration. Interestingly, a correlation was observed between reduced TAOK2 expression and decreased patient survival time in certain types of human cancers, including lung and kidney cancer as well as glioma. Moreover, in cellular models corresponding to these cancer types the downregulation of TAOK2 by CRISPR inhibition led to reduced phosphorylation of LATS1 and increased proliferation rates, supporting TAOK2's role as tumour suppressor gene. By contrast, overexpression of TAOK2 in these cellular models lead to increased phospho-LATS1 but reduced cell proliferation. As TAOK2 is a druggable kinase, targeting TAOK2 could serve as an attractive pharmacological approach to modulate cell growth and potentially offer strategies for combating cancer.
Collapse
Affiliation(s)
- Xiao Ma
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Fiona J Mandausch
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Yuxin Wu
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Vivek K Sahoo
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Wenbo Ma
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Giovanna Leoni
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany
| | - Madalina Hostiuc
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Jan P Wintgens
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Jiajun Qiu
- Department of Otolaryngology Head & Neck Surgery, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | | | - Moritz J Rossner
- Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany; Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, University Hospital, Ludwig Maximilian University of Munich, Nussbaumstr. 7, 80336 Munich, Germany
| | - Michael C Wehr
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstr. 7, 80336 Munich, Germany; Systasy Bioscience GmbH, Balanstr. 6, 81669, Munich, Germany.
| |
Collapse
|
15
|
Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
Collapse
Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
| |
Collapse
|
16
|
Dolberg TB, Gunnels TF, Ling T, Sarnese KA, Crispino JD, Leonard JN. Building synthetic biosensors using red blood cell proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.16.571988. [PMID: 38168174 PMCID: PMC10760168 DOI: 10.1101/2023.12.16.571988] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
As the use of engineered cell therapies expands from pioneering efforts in cancer immunotherapy to other applications, an attractive but less explored approach is the use of engineered red blood cells (RBCs). Compared to other cells, RBCs have a very long circulation time and reside in the blood compartment, so they could be ideally suited for applications as sentinel cells that enable in situ sensing and diagnostics. However, we largely lack tools for converting RBCs into biosensors. A unique challenge is that RBCs remodel their membranes during maturation, shedding many membrane components, suggesting that an RBC-specific approach may be needed. Towards addressing this need, here we develop a biosensing architecture built on RBC membrane proteins that are retained through erythropoiesis. This biosensor employs a mechanism in which extracellular ligand binding is transduced into intracellular reconstitution of a split output protein (including either a fluorophore or an enzyme). By comparatively evaluating a range of biosensor architectures, linker types, scaffold choices, and output signals, we identify biosensor designs and design features that confer substantial ligand-induced signal in vitro. Finally, we demonstrate that erythroid precursor cells engineered with our RBC protein biosensors function in vivo. This study establishes a foundation for developing RBC-based biosensors that could ultimately address unmet needs including non-invasive monitoring of physiological signals for a range of diagnostic applications.
Collapse
Affiliation(s)
- Taylor B. Dolberg
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Taylor F. Gunnels
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Te Ling
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Kelly A. Sarnese
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - John D. Crispino
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Joshua N. Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Interdisciplinary Biological Sciences Training Program, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, 60208, USA
| |
Collapse
|
17
|
Sarhadi TR, Panse JS, Nagotu S. Mind the gap: Methods to study membrane contact sites. Exp Cell Res 2023; 431:113756. [PMID: 37633408 DOI: 10.1016/j.yexcr.2023.113756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/28/2023]
Abstract
Organelles are dynamic entities whose functions are essential for the optimum functioning of cells. It is now known that the juxtaposition of organellar membranes is essential for the exchange of metabolites and their communication. These functional apposition sites are termed membrane contact sites. Dynamic membrane contact sites between various sub-cellular structures such as mitochondria, endoplasmic reticulum, peroxisomes, Golgi apparatus, lysosomes, lipid droplets, plasma membrane, endosomes, etc. have been reported in various model systems. The burgeoning area of research on membrane contact sites has witnessed several manuscripts in recent years that identified the contact sites and components involved. Several methods have been developed to identify, measure and analyze the membrane contact sites. In this manuscript, we aim to discuss important methods developed to date that are used to study membrane contact sites.
Collapse
Affiliation(s)
- Tanveera Rounaque Sarhadi
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Janhavee Shirish Panse
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
| |
Collapse
|
18
|
Shi Z, Gao X, Zhang W, Chen B, Wang M, Liao K, Wang Z, Ren L, Zhai Y, Qiu Y, Wang X, Lin Y. Novel Bimolecular Fluorescence Complementation (BiFC) Assay for Visualization of the Protein-Protein Interactions and Cellular Protein Complex Localizations. Mol Biotechnol 2023:10.1007/s12033-023-00860-6. [PMID: 37751129 DOI: 10.1007/s12033-023-00860-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 08/16/2023] [Indexed: 09/27/2023]
Abstract
Investigations of protein-protein interactions (PPIs) are of paramount importance for comprehending cellular processes within biological systems. The bimolecular fluorescence complementation (BiFC) assay presents a convenient methodology for visualizing PPIs within live cells. While a range of fluorescent proteins have been introduced into the BiFC system, there is a growing demand for new fluorescent proteins to accommodate the expanding requirements of researchers. This study describes the introduction of Tagged blue fluorescent protein 2 (TagBFP2) into the BiFC assay to verify the interaction between two proteins, with Enhanced yellow fluorescent protein (EYFP) employed as a positive control. Both fluorescent proteins demonstrated optimal performance in this study. Compared to EYFP, the BiFC system utilizing TagBFP2 yielded a higher signal-to-noise ratio, which facilitated differentiation of the signal of PPIs from noise and enabled employment of other fluorescent proteins within the BiFC assay. Notably, the utilization of a fluorescent secondary antibody in immunofluorescence applications or the tagging of an interest protein with a fluorescent protein occupied the green or yellow channel. Overall, the present article introduces a BiFC assay that is highly straightforward, reliable, and replicable, with the ability to be completed within 1 week. This method requires neither expensive instrumentation nor technical skills of a high order.
Collapse
Affiliation(s)
- Zhonggang Shi
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
- Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
| | - Xing Gao
- Department of Medical Oncology, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi, People's Republic of China
| | - Wenrui Zhang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
- Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
| | - Binghong Chen
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
| | - Mengying Wang
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
- Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
| | - Keman Liao
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
| | - Zhihan Wang
- Department of Neurosurgery, Shanghai Pudong Hospital, Fudan University, Shanghai, 201399, People's Republic of China
| | - Li Ren
- Department of Neurosurgery, Shanghai Pudong Hospital, Fudan University, Shanghai, 201399, People's Republic of China
| | - Yujia Zhai
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Yueyang Road 320, Shanghai, 200031, China
| | - Yongming Qiu
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China
| | - Xuhui Wang
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai JiaoTong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, People's Republic of China.
- Department of Neurosurgery, Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, People's Republic of China.
| | - Yingying Lin
- Brain Injury Center, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China.
- Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No. 160 Pujian Road, Pudong District, Shanghai, 200127, People's Republic of China.
| |
Collapse
|
19
|
Zhang N, Meng X, Jiang H, Ge H, Qian K, Zheng Y, Park Y, Wang J. Restoration of energy homeostasis under oxidative stress: Duo synergistic AMPK pathways regulating arginine kinases. PLoS Genet 2023; 19:e1010843. [PMID: 37535699 PMCID: PMC10427004 DOI: 10.1371/journal.pgen.1010843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 08/15/2023] [Accepted: 06/26/2023] [Indexed: 08/05/2023] Open
Abstract
Rapid depletion of cellular ATP can occur by oxidative stress induced by reactive oxygen species (ROS). Maintaining energy homeostasis requires the key molecular components AMP-activated protein kinase (AMPK) and arginine kinase (AK), an invertebrate orthologue of the mammalian creatine kinase (CK). Here, we deciphered two independent and synergistic pathways of AMPK acting on AK by using the beetle Tribolium castaneum as a model system. First, AMPK acts on transcriptional factor forkhead box O (FOXO) leading to phosphorylation and nuclear translocation of the FOXO. The phospho-FOXO directly promotes the expression of AK upon oxidative stress. Concomitantly, AMPK directly phosphorylates the AK to switch the direction of enzymatic catalysis for rapid production of ATP from the phosphoarginine-arginine pool. Further in vitro assays revealed that Sf9 cells expressing phospho-deficient AK mutants displayed the lower ATP/ADP ratio and cell viability under paraquat-induced oxidative stress conditions when compared with Sf9 cells expressing wild-type AKs. Additionally, the AMPK-FOXO-CK pathway is also involved in the restoration of ATP homeostasis under oxidative stress in mammalian HEK293 cells. Overall, we provide evidence that two distinct AMPK-AK pathways, transcriptional and post-translational regulations, are coherent responders to acute oxidative stresses and distinguished from classical AMPK-mediated long-term metabolic adaptations to energy challenge.
Collapse
Affiliation(s)
- Nan Zhang
- College of Plant Protection, Yangzhou University, Yangzhou, China
- Jiangsu Lixiahe Institute of Agricultural Sciences, Yangzhou, China
| | - Xiangkun Meng
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Heng Jiang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Huichen Ge
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Kun Qian
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yang Zheng
- College of Plant Protection, Yangzhou University, Yangzhou, China
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, Kansas, United States of America
| | - Jianjun Wang
- College of Plant Protection, Yangzhou University, Yangzhou, China
| |
Collapse
|
20
|
Chen G, Obal D. Detecting and measuring of GPCR signaling - comparison of human induced pluripotent stem cells and immortal cell lines. Front Endocrinol (Lausanne) 2023; 14:1179600. [PMID: 37293485 PMCID: PMC10244570 DOI: 10.3389/fendo.2023.1179600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 04/12/2023] [Indexed: 06/10/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are a large family of transmembrane proteins that play a major role in many physiological processes, and thus GPCR-targeted drug development has been widely promoted. Although research findings generated in immortal cell lines have contributed to the advancement of the GPCR field, the homogenous genetic backgrounds, and the overexpression of GPCRs in these cell lines make it difficult to correlate the results with clinical patients. Human induced pluripotent stem cells (hiPSCs) have the potential to overcome these limitations, because they contain patient specific genetic information and can differentiate into numerous cell types. To detect GPCRs in hiPSCs, highly selective labeling and sensitive imaging techniques are required. This review summarizes existing resonance energy transfer and protein complementation assay technologies, as well as existing and new labeling methods. The difficulties of extending existing detection methods to hiPSCs are discussed, as well as the potential of hiPSCs to expand GPCR research towards personalized medicine.
Collapse
Affiliation(s)
- Gaoxian Chen
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, United States
| | - Detlef Obal
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, United States
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, United States
| |
Collapse
|
21
|
Hiasa S, Fujimori T, Aiki S, Ueda H, Tsuboi T, Kitaguchi T. Development of green fluorescent protein-based cAMP indicators for covering a wide range of cAMP concentrations. RSC Adv 2023; 13:15514-15520. [PMID: 37223420 PMCID: PMC10201545 DOI: 10.1039/d3ra01390a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023] Open
Abstract
There is a wide range in the concentration of intracellular cyclic adenosine 3',5'-monophosphate (cAMP), which mediates specific effects as a second messenger in pathways affecting many physiological processes. Here, we developed green fluorescent cAMP indicators, named Green Falcan (Green fluorescent protein-based indicator visualizing cAMP dynamics) with various EC50 values (0.3, 1, 3, 10 μM) for covering the wide range of intracellular cAMP concentrations. The fluorescence intensity of Green Falcans increased in a cAMP dose-dependent manner, with a dynamic range of over 3-fold. Green Falcans showed a high specificity for cAMP over its structural analogues. When we expressed Green Falcans in HeLa cells, these indicators were applicable for visualization of cAMP dynamics in the low concentration range compared to the previously developed cAMP indicators, and visualized distinct kinetics of cAMP in various pathways with high spatiotemporal resolution in living cells. Furthermore, we demonstrated that Green Falcans are applicable to dual-color imaging with R-GECO, a red fluorescent Ca2+ indicator, in the cytoplasm and the nucleus. This study shows that Green Falcans open up a new avenue for understanding hierarchal and cooperative interactions with other molecules in various cAMP signaling pathways by multi-color imaging.
Collapse
Affiliation(s)
- Sohei Hiasa
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama-shi Kanagawa 226-8501 Japan
| | - Takeru Fujimori
- School of Life Science and Technology, Department of Life Science and Technology, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama-shi Kanagawa 226-8501 Japan
| | - Saki Aiki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo 3-8-1 Komaba, Meguro-ku Tokyo 153-8902 Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama-shi Kanagawa 226-8503 Japan
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo 3-8-1 Komaba, Meguro-ku Tokyo 153-8902 Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta-cho, Midori-ku Yokohama-shi Kanagawa 226-8503 Japan
| |
Collapse
|
22
|
Dai Y, Farag M, Lee D, Zeng X, Kim K, Son HI, Guo X, Su J, Peterson N, Mohammed J, Ney M, Shapiro DM, Pappu RV, Chilkoti A, You L. Programmable synthetic biomolecular condensates for cellular control. Nat Chem Biol 2023; 19:518-528. [PMID: 36747054 PMCID: PMC10786170 DOI: 10.1038/s41589-022-01252-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/21/2022] [Indexed: 02/08/2023]
Abstract
The formation of biomolecular condensates mediated by a coupling of associative and segregative phase transitions plays a critical role in controlling diverse cellular functions in nature. This has inspired the use of phase transitions to design synthetic systems. While design rules of phase transitions have been established for many synthetic intrinsically disordered proteins, most efforts have focused on investigating their phase behaviors in a test tube. Here, we present a rational engineering approach to program the formation and physical properties of synthetic condensates to achieve intended cellular functions. We demonstrate this approach through targeted plasmid sequestration and transcription regulation in bacteria and modulation of a protein circuit in mammalian cells. Our approach lays the foundation for engineering designer condensates for synthetic biology applications.
Collapse
Affiliation(s)
- Yifan Dai
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA
| | - Mina Farag
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Dongheon Lee
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Xiangze Zeng
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Kyeri Kim
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Hye-In Son
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Xiao Guo
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Jonathan Su
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Nikhil Peterson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Javid Mohammed
- Department of Immunology, Duke University, Durham, NC, USA
| | - Max Ney
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Daniel Mark Shapiro
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates (CBC), James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
| | - Lingchong You
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
- Duke Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
| |
Collapse
|
23
|
Nakatsu F, Tsukiji S. Chemo- and opto-genetic tools for dissecting the role of membrane contact sites in living cells: Recent advances and limitations. Curr Opin Chem Biol 2023; 73:102262. [PMID: 36731242 DOI: 10.1016/j.cbpa.2022.102262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 02/04/2023]
Abstract
Membrane contact sites (MCSs) are morphologically defined intracellular structures where cellular membranes are closely apposed. Recent progress has significantly advanced our understanding of MCSs with the use of new tools and techniques. Visualization of MCSs in living cells by split fluorescence proteins or FRET-based techniques tells us the dynamic property of MCSs. Manipulation of MCSs by chemically-induced dimerization (CID) or light-induced dimerization (LID) greatly contributes to our understanding of their functional aspects including inter-organelle lipid transport mediated by lipid transfer proteins (LTPs). Here we highlight recent advances in these tools and techniques as applied to MCSs, and we discuss their advantages and limitations.
Collapse
Affiliation(s)
- Fubito Nakatsu
- Department of Neurochemistry and Molecular Cell Biology, Niigata University School of Medicine and Graduate School of Medical/Dental Sciences, Niigata 951-8510, Japan.
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan; Department of Nanopharmaceutical Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
| |
Collapse
|
24
|
Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
Collapse
Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| |
Collapse
|
25
|
Bignon C, Longhi S. In Vivo Protein-Protein Binding Competition Assay Based on Split-GFP Reassembly: Proof of Concept. Biomolecules 2023; 13:biom13020354. [PMID: 36830723 PMCID: PMC9952896 DOI: 10.3390/biom13020354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
The split-green fluorescent protein (GFP) reassembly assay is a well-established approach to study protein-protein interactions (PPIs). In this assay, when two interacting proteins X and Y, respectively fused to residues 1-157 and to residues 158-237 of GFP, are co-expressed in E. coli, the two GFP halves are brought to sufficient proximity to reassociate and fold to recreate the functional GFP. At constant protein expression level, the intensity of fluorescence produced by the bacteria is proportional to the binding affinity of X to Y. We hypothesized that adding a third partner (Z) endowed with an affinity for either X or Y would lead to an in vivo competition assay. We report here the different steps of the set-up of this competition assay, and define the experimental conditions required to obtained reliable results. Results show that this competition assay is a potentially interesting tool for screening libraries of binding inhibitors, Z being either a protein or a chemical reagent.
Collapse
|
26
|
Recent Advances in the Study of Gas Vesicle Proteins and Application of Gas Vesicles in Biomedical Research. Life (Basel) 2022; 12:life12091455. [PMID: 36143491 PMCID: PMC9501494 DOI: 10.3390/life12091455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 12/01/2022] Open
Abstract
The formation of gas vesicles has been investigated in bacteria and haloarchaea for more than 50 years. These air-filled nanostructures allow cells to stay at a certain height optimal for growth in their watery environment. Several gvp genes are involved and have been studied in Halobacterium salinarum, cyanobacteria, Bacillus megaterium, and Serratia sp. ATCC39006 in more detail. GvpA and GvpC form the gas vesicle shell, and additional Gvp are required as minor structural proteins, chaperones, an ATP-hydrolyzing enzyme, or as gene regulators. We analyzed the Gvp proteins of Hbt. salinarum with respect to their protein–protein interactions, and developed a model for the formation of these nanostructures. Gas vesicles are also used in biomedical research. Since they scatter waves and produce ultrasound contrast, they could serve as novel contrast agent for ultrasound or magnetic resonance imaging. Additionally, gas vesicles were engineered as acoustic biosensors to determine enzyme activities in cells. These applications are based on modifications of the surface protein GvpC that alter the mechanical properties of the gas vesicles. In addition, gas vesicles have been decorated with GvpC proteins fused to peptides of bacterial or viral pathogens and are used as tools for vaccine development.
Collapse
|
27
|
Development of a red fluorescent protein-based cGMP indicator applicable for live-cell imaging. Commun Biol 2022; 5:833. [PMID: 36064581 PMCID: PMC9445041 DOI: 10.1038/s42003-022-03790-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/02/2022] [Indexed: 11/08/2022] Open
Abstract
Cyclic guanosine 3', 5'-monophosphate (cGMP) is a second messenger that regulates a variety of physiological processes. Here, we develop a red fluorescent protein-based cGMP indicator, "Red cGull". The fluorescence intensity of Red cGull increase more than sixfold in response to cGMP. The features of this indicator include an EC50 of 0.33 μM for cGMP, an excitation and emission peak at 567 nm and 591 nm, respectively. Live-cell imaging analysis reveal the utility of Red cGull for dual-colour imaging and its ability to be used in conjunction with optogenetics tools. Using enteroendocrine cell lines, Red cGull detects an increase in cGMP following the application of L-arginine. An increase in intracellular cGMP is found to be inhibited by Ca2+, and L-arginine-mediated hormone secretion is not potentiated. We propose that Red cGull will facilitate future research in cell signalling in relation to cGMP and its interplay with other signalling molecules.
Collapse
|
28
|
Rhys GG, Cross JA, Dawson WM, Thompson HF, Shanmugaratnam S, Savery NJ, Dodding MP, Höcker B, Woolfson DN. De novo designed peptides for cellular delivery and subcellular localisation. Nat Chem Biol 2022; 18:999-1004. [PMID: 35836017 DOI: 10.1038/s41589-022-01076-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/03/2022] [Indexed: 12/14/2022]
Abstract
Increasingly, it is possible to design peptide and protein assemblies de novo from first principles or computationally. This approach provides new routes to functional synthetic polypeptides, including designs to target and bind proteins of interest. Much of this work has been developed in vitro. Therefore, a challenge is to deliver de novo polypeptides efficiently to sites of action within cells. Here we describe the design, characterisation, intracellular delivery, and subcellular localisation of a de novo synthetic peptide system. This system comprises a dual-function basic peptide, programmed both for cell penetration and target binding, and a complementary acidic peptide that can be fused to proteins of interest and introduced into cells using synthetic DNA. The designs are characterised in vitro using biophysical methods and X-ray crystallography. The utility of the system for delivery into mammalian cells and subcellular targeting is demonstrated by marking organelles and actively engaging functional protein complexes.
Collapse
Affiliation(s)
- Guto G Rhys
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Jessica A Cross
- School of Chemistry, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | | | - Harry F Thompson
- School of Chemistry, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | | | - Nigel J Savery
- School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Mark P Dodding
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK. .,School of Biochemistry, University of Bristol, Bristol, UK. .,BrisSynBio, University of Bristol, Bristol, UK.
| |
Collapse
|
29
|
Graham TGW, Ferrie JJ, Dailey GM, Tjian R, Darzacq X. Detecting molecular interactions in live-cell single-molecule imaging with proximity-assisted photoactivation (PAPA). eLife 2022; 11:e76870. [PMID: 35976226 PMCID: PMC9531946 DOI: 10.7554/elife.76870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule imaging provides a powerful way to study biochemical processes in live cells, yet it remains challenging to track single molecules while simultaneously detecting their interactions. Here, we describe a novel property of rhodamine dyes, proximity-assisted photoactivation (PAPA), in which one fluorophore (the 'sender') can reactivate a second fluorophore (the 'receiver') from a dark state. PAPA requires proximity between the two fluorophores, yet it operates at a longer average intermolecular distance than Förster resonance energy transfer (FRET). We show that PAPA can be used in live cells both to detect protein-protein interactions and to highlight a subpopulation of labeled protein complexes in which two different labels are in proximity. In proof-of-concept experiments, PAPA detected the expected correlation between androgen receptor self-association and chromatin binding at the single-cell level. These results establish a new way in which a photophysical property of fluorophores can be harnessed to study molecular interactions in single-molecule imaging of live cells.
Collapse
Affiliation(s)
- Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - John Joseph Ferrie
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| |
Collapse
|
30
|
Neitz H, Paul NB, Häge FR, Lindner C, Graebner R, Kovermann M, Thomas F. Identification of novel functional mini-receptors by combinatorial screening of split-WW domains. Chem Sci 2022; 13:9079-9090. [PMID: 36091217 PMCID: PMC9365081 DOI: 10.1039/d2sc01078j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
β-Sheet motifs such as the WW domain are increasingly being explored as building blocks for synthetic biological applications. Since the sequence-structure relationships of β-sheet motifs are generally complex compared to the well-studied α-helical coiled coil (CC), other approaches such as combinatorial screening should be included to vary the function of the peptide. In this study, we present a combinatorial approach to identify novel functional mini-proteins based on the WW-domain scaffold, which takes advantage of the successful reconstitution of the fragmented WW domain of hPin1 (hPin1WW) by CC association. Fragmentation of hPin1WW was performed in both loop 1 (CC-hPin1WW-L1) and loop 2 (CC-hPin1WW-L2), and the respective fragments were linked to the strands of an antiparallel heterodimeric CC. Structural analysis by CD and NMR spectroscopy revealed structural reconstitution of the WW-domain scaffold only in CC-hPin1WW-L1, but not in CC-hPin1WW-L2. Furthermore, by using 1H-15N HSQC NMR, fluorescence and CD spectroscopy, we demonstrated that binding properties of fragmented hPin1WW in CC-hPin1WW-L1 were fully restored by CC association. To demonstrate the power of this approach as a combinatorial screening platform, we synthesized a four-by-six library of N- and C-terminal hPin1WW-CC peptide fragments that was screened for a WW domain that preferentially binds to ATP over cAMP, phophocholine, or IP6. Using this screening platform, we identified one WW domain, which specifically binds ATP, and a phosphorylcholine-specific WW-based mini-receptor, both having binding dissociation constants in the lower micromolar range.
Collapse
Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg Am Hubland Würzburg 97074 Germany
| | - Niels Benjamin Paul
- Institute of Organic and Biomolecular Chemistry, University of Göttingen Tammannstr. 2 Göttingen 37077 Germany
| | - Florian R Häge
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Roman Graebner
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz Universitätsstraße 10 Konstanz 78457 Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University Im Neuenheimer Feld 270 Heidelberg 69120 Germany
- Centre for Advanced Materials, Heidelberg University Im Neuenheimer Feld 225 Heidelberg 69120 Germany
| |
Collapse
|
31
|
Skeeters SS, Camp T, Fan H, Zhang K. The expanding role of split protein complementation in opsin-free optogenetics. Curr Opin Pharmacol 2022; 65:102236. [PMID: 35609383 PMCID: PMC9308681 DOI: 10.1016/j.coph.2022.102236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
A comprehensive understanding of signaling mechanisms helps interpret fundamental biological processes and restore cell behavior from pathological conditions. Signaling outcome depends not only on the activity of each signaling component but also on their dynamic interaction in time and space, which remains challenging to probe by biochemical and cell-based assays. Opsin-based optogenetics has transformed neural science research with its spatiotemporal modulation of the activity of excitable cells. Motivated by this advantage, opsin-free optogenetics extends the power of light to a larger spectrum of signaling molecules. This review summarizes commonly used opsin-free optogenetic strategies, presents a historical overview of split protein complementation, and highlights the adaptation of split protein recombination as optogenetic sensors and actuators.
Collapse
|
32
|
Tn
FLXopen
: Markerless Transposons for Functional Fluorescent Fusion Proteins and Protein Interaction Prediction. Microbiol Spectr 2022; 10:e0242821. [PMID: 35499319 PMCID: PMC9241775 DOI: 10.1128/spectrum.02428-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescence microscopy of cells expressing proteins translationally linked to a fluorophore can be a powerful tool to investigate protein localization dynamics in vivo. One major obstacle to reliably analyze biologically relevant localization is the construction of a fusion protein that is both fluorescent and functional. Here, we develop a strategy to construct fluorescent fusions at theoretically any location in the protein by using TnFLXopen random transposon mutagenesis to randomly insert a gene encoding a fluorescent protein. Moreover, insertions within a target gene are enriched by an inducible gene-trap strategy and selection by fluorescence activated cell sorting. Using this approach, we isolate a variety of fluorescent fusions to FtsZ that exhibit ring-like localization and a fusion to the flagellar stator protein that both is functional for supporting motility and localizes as fluorescent puncta. Finally, we further modify TnFLXopen to insert the coding sequence for the C-terminal half of mVenus for use in bimolecular fluorescence complementation (BiFC) and the in vivo detection of protein-protein interaction candidates. As proof-of-concept, the DivIVA polar scaffolding protein was fused to the N terminus of mVenus, the C terminus of mVenus was delivered by transposition, and a combination of fluorescence activated cell sorter (FACS) sorting and whole-genome sequencing identified the known self-interaction of DivIVA as well as other possible candidate interactors. We suggest that the FACS selection is a viable alternative to antibiotic selection in transposon mutagenesis that can generate new fluorescent tools for in vivo protein characterization. IMPORTANCE Transposon mutagenesis is a powerful tool for random mutagenesis, as insertion of a transposon and accompanying antibiotic resistance cassette often disrupt gene function. Here, we present a series of transposons with fluorescent protein genes which, when integrated in frame, may be selected with a fluorescence activated cell sorter (FACS). An open reading frame runs continuously through the transposon such that fluorescent protein fusions may be inserted theoretically anywhere in the primary sequence and potentially preserve function of the target protein. Finally, the transposons were further modified to randomly insert a partial fluorescent protein compatible with bimolecular fluorescence complementation (BiFC) to identify protein interaction candidates.
Collapse
|
33
|
Yang Z, Fok HKF, Luo J, Yang Y, Wang R, Huang X, Sun F. B 12-induced reassembly of split photoreceptor protein enables photoresponsive hydrogels with tunable mechanics. SCIENCE ADVANCES 2022; 8:eabm5482. [PMID: 35363531 PMCID: PMC10938628 DOI: 10.1126/sciadv.abm5482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Although the tools based on split proteins have found broad applications, ranging from controlled biological signaling to advanced molecular architectures, many of them suffer from drawbacks such as background reassembly, low thermodynamic stability, and static structural features. Here, we present a chemically inducible protein assembly method enabled by the dissection of the carboxyl-terminal domain of a B12-dependent photoreceptor, CarHC. The resulting segments reassemble efficiently upon addition of cobalamin (AdoB12, MeB12, or CNB12). Photolysis of the cofactors such as AdoB12 and MeB12 further leads to stable protein adducts harboring a bis-His-ligated B12. Split CarHC enables the creation of a series of protein hydrogels, of which the mechanics can be either photostrengthened or photoweakened, depending on the type of B12. These materials are also well suited for three dimensional cell culturing. Together, this new protein chemistry, featuring negligible background autoassembly, stable conjugation, and phototunability, has opened up opportunities for designing smart materials.
Collapse
Affiliation(s)
- Zhongguang Yang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Hong Kiu Francis Fok
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Jiren Luo
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Yang Yang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Ri Wang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Xinyu Huang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Fei Sun
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen 518036, China
- Biomedical Research Institute, Shenzhen Peking University–The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
- HKUST Shenzhen Research Institute, Shenzhen 518057, China
| |
Collapse
|
34
|
McLure RJ, Radford SE, Brockwell DJ. High-throughput directed evolution: a golden era for protein science. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
35
|
Zhou K, Litfin T, Solayman M, Zhao H, Zhou Y, Zhan J. High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing. Int J Biol Macromol 2022; 203:543-552. [PMID: 35120933 DOI: 10.1016/j.ijbiomac.2022.01.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Splitting a protein at a position may lead to self- or assisted-complementary fragments depending on whether two resulting fragments can reconstitute to maintain the native function spontaneously or require assistance from two interacting molecules. Assisted complementary fragments with high contrast are an important tool for probing biological interactions. However, only a small number of assisted-complementary split-variants have been identified due to manual, labour-intensive optimization of a candidate gene. Here, we introduce a technique for high-throughput split-protein profiling (HiTS) that allows fast identification of self- and assisted complementary positions by transposon mutagenesis, a rapamycin-regulated FRB-FKBP protein interaction pair, and deep sequencing. We test this technique by profiling three antibiotic-resistant genes (fosfomycin-resistant gene, fosA3, erythromycin-resistant gene, ermB, and chloramphenicol-resistant gene, catI). Self- and assisted complementary fragments discovered by the high-throughput technique were subsequently confirmed by low-throughput testing of individual split positions. Thus, the HiTS technique provides a quicker alternative for discovering the proteins with suitable self- and assisted-complementary split positions when combining with a readout such as fluorescence, bioluminescence, cell survival, gene transcription or genome editing.
Collapse
Affiliation(s)
- Kai Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
| | - Thomas Litfin
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Md Solayman
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia
| | - Huijun Zhao
- Centre for Clean Environment and Energy, Griffith University, Gold Coast Campus, Queensland 4222, Australia
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr Southport, QLD 4222, Australia; Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China.
| |
Collapse
|
36
|
Liu S, Li S, Krezel AM, Li W. Stabilization and structure determination of integral membrane proteins by termini restraining. Nat Protoc 2022; 17:540-565. [PMID: 35039670 DOI: 10.1038/s41596-021-00656-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Integral membrane proteins isolated from cellular environment often lose activity and native conformation required for functional analyses and structural studies. Even in their native state, they lack sufficient surfaces to form crystal contacts. Furthermore, most of them are too small for cryogenic electron microscopy detection and too big for solution NMR. To overcome these difficulties, we recently developed a strategy to stabilize the folded state of membrane proteins by restraining their two termini with a self-assembling protein coupler. The termini-restrained membrane proteins from distinct functional families retain their activities and show increased stability and yield. This strategy enables their structure determination at near-atomic resolution by facilitating the entire pipeline from crystallization, crystal identification, diffraction enhancement and phase determination, to electron density improvement. Furthermore, stabilization of membrane proteins enables their biochemical and biophysical characterization. Here we present the protocol of membrane protein engineering (2 weeks), quality assessment (1-2 weeks), protein production (1-6 weeks), crystallization (1-2 weeks), diffraction improvement (1-3 months) and crystallographic data analysis (1 week). This protocol is intended not only for structural biologists, but also for biochemists, biophysicists and pharmaceutical scientists whose research focuses on membrane proteins.
Collapse
Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrzej M Krezel
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
37
|
Poggio E, Brini M, Calì T. Get Closer to the World of Contact Sites: A Beginner's Guide to Proximity-Driven Fluorescent Probes. CONTACT (THOUSAND OAKS (VENTURA COUNTY, CALIF.)) 2022; 5:25152564221135748. [PMID: 37366505 PMCID: PMC10243574 DOI: 10.1177/25152564221135748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
To maintain cellular homeostasis and to coordinate the proper response to a specific stimulus, information must be integrated throughout the cell in a well-organized network, in which organelles are the crucial nodes and membrane contact sites are the main edges. Membrane contact sites are the cellular subdomains where two or more organelles come into close apposition and interact with each other. Even though many inter-organelle contacts have been identified, most of them are still not fully characterized, therefore their study is an appealing and expanding field of research. Thanks to significant technological progress, many tools are now available or are in rapid development, making it difficult to choose which one is the most suitable for answering a specific biological question. Here we distinguish two different experimental approaches for studying inter-organelle contact sites. The first one aims to morphologically characterize the sites of membrane contact and to identify the molecular players involved, relying mainly on the application of biochemical and electron microscopy (EM)-related methods. The second approach aims to understand the functional importance of a specific contact, focusing on spatio-temporal details. For this purpose, proximity-driven fluorescent probes are the experimental tools of choice, since they allow the monitoring and quantification of membrane contact sites and their dynamics in living cells under different cellular conditions or upon different stimuli. In this review, we focus on these tools with the purpose of highlighting their great versatility and how they can be applied in the study of membrane contacts. We will extensively describe all the different types of proximity-driven fluorescent tools, discussing their benefits and drawbacks, ultimately providing some suggestions to choose and apply the appropriate methods on a case-to-case basis and to obtain the best experimental outcomes.
Collapse
Affiliation(s)
- Elena Poggio
- Department of Biology (DiBio), University of
Padova, Padova, Italy
| | - Marisa Brini
- Department of Biology (DiBio), University of
Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
| | - Tito Calì
- Study Center for Neurodegeneration (CESNE),
University of Padova, Padova, Italy
- Department of Biomedical Sciences (DSB),
University of Padova, Padova, Italy
- Padova Neuroscience Center (PNC), University
of Padova, Padova, Italy
| |
Collapse
|
38
|
Yadala R, Ratnikava M, Lermontova I. Bimolecular Fluorescence Complementation to Test for Protein-Protein Interactions and to Uncover Regulatory Mechanisms During Gametogenesis. Methods Mol Biol 2022; 2484:107-120. [PMID: 35461448 DOI: 10.1007/978-1-0716-2253-7_9] [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: 06/14/2023]
Abstract
Bimolecular fluorescence complementation (BiFC) assay is one of the sensitive techniques that allows to investigate direct protein-protein interactions (PPI) in vivo and visualize the subcellular localization of interacting proteins. It is based on splitting of a fluorescent protein into two nonfluorescent parts accordingly fused to two putative interacting partners. If interaction between studied proteins is possible, nonfluorescent parts come to close proximity resulting in reconstitution of the functional fluorescent protein and giving fluorescence under certain wavelength. BiFC analysis implies transient or stable expression of the proteins of interest and can be used as a method to test or validate the direct PPI in various biological pathways, including the regulation of gametogenesis, which is the main focus of this book. In our protocol we give detailed information for beginners about three main steps of BiFC analysis of centromeric protein interactions. These steps include (1) generation of appropriate expression clones with the help of Gateway cloning technology, (2) infiltration of Nicotiana benthamiana plants by Agrobacteria containing generated constructs, and (3) microscopic analysis of plants under fluorescence microscope. Also, we discuss appropriate negative controls that can be used for evaluation as well as recommendable vector systems, possible artifacts and measures to avoid artifactual interactions for BiFC assay.
Collapse
Affiliation(s)
- Ramakrishna Yadala
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Maryia Ratnikava
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Inna Lermontova
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| |
Collapse
|
39
|
Xie S, Li H, Yao F, Huang J, Yang X, Chen X, Liu Q, Zhuang M, He S. PUPIL enables mapping and stamping of transient electrical connectivity in developing nervous systems. Cell Rep 2021; 37:109853. [PMID: 34686323 DOI: 10.1016/j.celrep.2021.109853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/25/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022] Open
Abstract
Currently, many genetic methods are available for mapping chemical connectivity, but analogous methods for electrical synapses are lacking. Here, we present pupylation-based interaction labeling (PUPIL), a genetically encoded system for noninvasively mapping and stamping transient electrical synapses in the mouse brain. Upon fusion of connexin 26 (CX26) with the ligase PafA, pupylation yields tag puncta following conjugation of its substrate, a biotin- or fluorescent-protein-tagged PupE, to the neighboring proteins of electrical synapses containing CX26-PafA. Tag puncta are validated to correlate well with functional electrical synapses in immature neurons. Furthermore, puncta are retained in mature neurons when electrical synapses mostly disappear-suggesting successful stamping. We use PUPIL to uncover spatial subcellular localizations of electrical synapses and approach their physiological functions during development. Thus, PUPIL is a powerful tool for probing electrical connectivity patterns in complex nervous systems and has great potential for transient receptors and ion channels as well.
Collapse
Affiliation(s)
- Shu Xie
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing, China
| | - Haixiang Li
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing, China
| | - Fenyong Yao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China
| | - Jiechang Huang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaomei Yang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China
| | - Xin Chen
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Liu
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China; Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhuang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China
| | - Shuijin He
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, Shanghai 201210, China.
| |
Collapse
|
40
|
Yang J, Ding S. Chimeric RNA-binding protein-based killing switch targeting hepatocellular carcinoma cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:683-695. [PMID: 34589286 PMCID: PMC8463442 DOI: 10.1016/j.omtn.2021.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Cancer cell-specific killing switches are synthetic circuits developed as an intelligent weapon to specifically eliminate malignant cells. RNA-delivered synthetic circuits provide safer means to control oncolytic functions, in which proteolysis-responding capsid-cNOT7 is developed to enable logic computation and modular design. Unfortunately, although circuits containing these capsid-cNOT7s exhibited good performance when introduced as replicons, in modified mRNA (modRNA) delivery, the performance was not quite as good. To improve this situation, alternative modules suitable for modRNA delivery need to be developed. An attractive option is RNA-binding protein (RBP)/riboswitches. In this study, RBPs were engineered by fusing with degron and cleavage sites. The compatibility of these chimeric RBPs with proteolysis-based sensing units were tested. Eight two-input logic gates and four three-input logic gates were implemented. After building this chimeric RBP-based system, we constructed a hepatocellular carcinoma (HCC) cell-specific killing circuit using two proteolysis-based sensing units, a two-input logic OR gate, and a leakproof apoptosis-inducing actuator, which distinguished HCC cells and induced apoptosis in a mixed IMR90-PLC/PRF/5 population.
Collapse
Affiliation(s)
- Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| |
Collapse
|
41
|
Dewey JA, Azizi SA, Lu V, Dickinson BC. A System for the Evolution of Protein-Protein Interaction Inducers. ACS Synth Biol 2021; 10:2096-2110. [PMID: 34319091 DOI: 10.1021/acssynbio.1c00276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecules that induce interactions between proteins, often referred to as "molecular glues", are increasingly recognized as important therapeutic modalities and as entry points for rewiring cellular signaling networks. Here, we report a new PACE-based method to rapidly select and evolve molecules that mediate interactions between otherwise noninteracting proteins: rapid evolution of protein-protein interaction glues (rePPI-G). By leveraging proximity-dependent split RNA polymerase-based biosensors, we developed E. coli-based detection and selection systems that drive gene expression outputs only when interactions between target proteins are induced. We then validated the system using engineered bivalent molecular glues, showing that rePPI-G robustly selects for molecules that induce the target interaction. Proof-of-concept evolutions demonstrated that rePPI-G reduces the "hook effect" of the engineered molecular glues, due at least in part to tuning the interaction affinities of each individual component of the bifunctional molecule. Altogether, this work validates rePPI-G as a continuous, phage-based evolutionary technology for optimizing molecular glues, providing a strategy for developing molecules that reprogram protein-protein interactions.
Collapse
Affiliation(s)
- Jeffrey A. Dewey
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Vivian Lu
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60615, United States
| |
Collapse
|
42
|
Methodological approaches for the analysis of transmembrane domain interactions: A systematic review. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183712. [PMID: 34331948 DOI: 10.1016/j.bbamem.2021.183712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/28/2021] [Accepted: 07/21/2021] [Indexed: 11/20/2022]
Abstract
The study of protein-protein interactions (PPI) has proven fundamental for the understanding of the most relevant cell processes. Any protein domain can participate in PPI, including transmembrane (TM) segments that can establish interactions with other TM domains (TMDs). However, the hydrophobic nature of TMDs and the environment they occupy complicates the study of intramembrane PPI, which demands the use of specific approaches and techniques. In this review, we will explore some of the strategies available to study intramembrane PPI in vitro, in vivo, and, in silico, focusing on those techniques that could be carried out in a standard molecular biology laboratory regarding its previous experience with membrane proteins.
Collapse
|
43
|
Wang S, Zhang F, Mei M, Wang T, Yun Y, Yang S, Zhang G, Yi L. A split protease-E. coli ClpXP system quantifies protein-protein interactions in Escherichia coli cells. Commun Biol 2021; 4:841. [PMID: 34230602 PMCID: PMC8260793 DOI: 10.1038/s42003-021-02374-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 06/10/2021] [Indexed: 12/04/2022] Open
Abstract
Characterizing protein–protein interactions (PPIs) is an effective method to help explore protein function. Here, through integrating a newly identified split human Rhinovirus 3 C (HRV 3 C) protease, super-folder GFP (sfGFP), and ClpXP-SsrA protein degradation machinery, we developed a fluorescence-assisted single-cell methodology (split protease-E. coli ClpXP (SPEC)) to explore protein–protein interactions for both eukaryotic and prokaryotic species in E. coli cells. We firstly identified a highly efficient split HRV 3 C protease with high re-assembly ability and then incorporated it into the SPEC method. The SPEC method could convert the cellular protein-protein interaction to quantitative fluorescence signals through a split HRV 3 C protease-mediated proteolytic reaction with high efficiency and broad temperature adaptability. Using SPEC method, we explored the interactions among effectors of representative type I-E and I-F CRISPR/Cas complexes, which combining with subsequent studies of Cas3 mutations conferred further understanding of the functions and structures of CRISPR/Cas complexes. Wang et al. developed a fluorescence-assisted single-cell methodology (split protease-E. coli ClpXP (SPEC)) to characterise protein-protein interactions for both eukaryotic and prokaryotic species in E. coli cells. Their method can quantify these interactions with high sensitivity, easy manipulation, and broad temperature adaptability
Collapse
Affiliation(s)
- Shengchen Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Faying Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Ting Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Hubei, China.
| |
Collapse
|
44
|
Blaszczak E, Lazarewicz N, Sudevan A, Wysocki R, Rabut G. Protein-fragment complementation assays for large-scale analysis of protein-protein interactions. Biochem Soc Trans 2021; 49:1337-1348. [PMID: 34156434 PMCID: PMC8286835 DOI: 10.1042/bst20201058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
Protein-protein interactions (PPIs) orchestrate nearly all biological processes. They are also considered attractive drug targets for treating many human diseases, including cancers and neurodegenerative disorders. Protein-fragment complementation assays (PCAs) provide a direct and straightforward way to study PPIs in living cells or multicellular organisms. Importantly, PCAs can be used to detect the interaction of proteins expressed at endogenous levels in their native cellular environment. In this review, we present the principle of PCAs and discuss some of their advantages and limitations. We describe their application in large-scale experiments to investigate PPI networks and to screen or profile PPI targeting compounds.
Collapse
Affiliation(s)
- Ewa Blaszczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
- Univ Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes) – UMR 6290, F-35000 Rennes, France
| | - Aswani Sudevan
- Univ Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes) – UMR 6290, F-35000 Rennes, France
| | - Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Gwenaël Rabut
- Univ Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes) – UMR 6290, F-35000 Rennes, France
| |
Collapse
|
45
|
Mita M, Sugawara I, Harada K, Ito M, Takizawa M, Ishida K, Ueda H, Kitaguchi T, Tsuboi T. Development of red genetically encoded biosensor for visualization of intracellular glucose dynamics. Cell Chem Biol 2021; 29:98-108.e4. [PMID: 34197723 DOI: 10.1016/j.chembiol.2021.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/19/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022]
Abstract
Glucose is the main source of energy for organisms, and it is important to understand the spatiotemporal dynamics of intracellular glucose. Single fluorescent protein-based glucose indicators, named "Red Glifons" have been developed that apply to live-cell and dual-color imaging. These indicators exhibited more than 3-fold increase in fluorescence intensity in the presence of 10 mM glucose. The two Red Glifons developed have different half-maximal effective concentration (EC50) values for glucose (300 μM and 3,000 μM) and are able to monitor a wide range of glucose dynamics. Red Glifon combined with green indicators allowing visualization of the interplay between glucose and ATP, lactate, or pyruvate. Glucose influx in the pharyngeal muscle of Caenorhabditis elegans, enteroendocrine cells, and human iPS cell-derived cardiac myocytes was observed using the Red Glifons. Thus these red glucose indicators serve as a multi-color imaging toolkit for investigating complex interactions in energy metabolism.
Collapse
Affiliation(s)
- Marie Mita
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Izumi Sugawara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Kazuki Harada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Motoki Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Mai Takizawa
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Kentaro Ishida
- Myoridge Co. Ltd., 46-29 Yoshidashimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.
| |
Collapse
|
46
|
Development of a Single Fluorescent Protein-Based Green Glucose Indicator by Semirational Molecular Design and Molecular Evolution. Methods Mol Biol 2021. [PMID: 34050465 DOI: 10.1007/978-1-0716-1258-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Advances in live-cell imaging have been accelerated by the development of various fluorescent indicators. However, indicators that are suitable for multicolor imaging remain a challenge to develop. Herein, we have developed a single fluorescent protein (FP)-based indicator using a semirational molecular design and a molecular evolution approach. We first inserted a ligand-binding domain into the vicinity of an FP chromophore to convert the conformational change induced by ligand binding into a change in fluorescence intensity. We then optimized the linker regions between the FP and the ligand-binding domain to greatly expand the dynamic range (F/F0) of the indicator. Our design and optimization methods are highly versatile and can be used to develop any single FP-based indicators, which will further advance the utility of live-cell imaging.
Collapse
|
47
|
Winkler J, Mylle E, De Meyer A, Pavie B, Merchie J, Grones P, Van Damme D. Visualizing protein-protein interactions in plants by rapamycin-dependent delocalization. THE PLANT CELL 2021; 33:1101-1117. [PMID: 33793859 PMCID: PMC7612334 DOI: 10.1093/plcell/koab004] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/15/2020] [Indexed: 05/19/2023]
Abstract
Identifying protein-protein interactions (PPIs) is crucial for understanding biological processes. Many PPI tools are available, yet only some function within the context of a plant cell. Narrowing down even further, only a few tools allow complex multi-protein interactions to be visualized. Here, we present a conditional in vivo PPI tool for plant research that meets these criteria. Knocksideways in plants (KSP) is based on the ability of rapamycin to alter the localization of a bait protein and its interactors via the heterodimerization of FKBP and FRB domains. KSP is inherently free from many limitations of other PPI systems. This in vivo tool does not require spatial proximity of the bait and prey fluorophores and it is compatible with a broad range of fluorophores. KSP is also a conditional tool and therefore the visualization of the proteins in the absence of rapamycin acts as an internal control. We used KSP to confirm previously identified interactions in Nicotiana benthamiana leaf epidermal cells. Furthermore, the scripts that we generated allow the interactions to be quantified at high throughput. Finally, we demonstrate that KSP can easily be used to visualize complex multi-protein interactions. KSP is therefore a versatile tool with unique characteristics and applications that complements other plant PPI methods.
Collapse
Affiliation(s)
- Joanna Winkler
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Evelien Mylle
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Andreas De Meyer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | | | - Julie Merchie
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Peter Grones
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Daniёl Van Damme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| |
Collapse
|
48
|
Yang J, Ding S. Engineering L7Ae for RNA-Only Delivery Kill Switch Targeting CMS2 Type Colorectal Cancer Cells. ACS Synth Biol 2021; 10:1095-1105. [PMID: 33939419 DOI: 10.1021/acssynbio.0c00612] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The lack of specific-targeting therapy to precisely identify and kill malignant cells while sparing others is a great challenge in colorectal cancer (CRC) treatment. In the era of molecular classification of tumors, CRC has been grouped into four Consensus Molecular Subtypes. Accounting for 37% of all types, the CMS2 group (canonical type) shows distinguishing features: WNT and MYC signaling activation. In this study, we designed an RNA-only delivery kill switch to specifically eliminate CMS2 type CRC cells. The sensing and logic processing functions are integrated by the newly engineered L7Ae, which can not only detect the stability of β-catenin protein and the presence of cytoplasm located Myc/Myc-nick, but also do logic computation. The circuit specifically eliminated HCT-116 cells while sparing other kinds of cells, showing a proof-of-principle approach to precisely target CMS2 type CRC.
Collapse
Affiliation(s)
- Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China
- Beijing Key Laboratory for Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China
- Beijing Key Laboratory for Helicobacter pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| |
Collapse
|
49
|
Wolf P, Gavins G, Beck‐Sickinger AG, Seitz O. Strategies for Site-Specific Labeling of Receptor Proteins on the Surfaces of Living Cells by Using Genetically Encoded Peptide Tags. Chembiochem 2021; 22:1717-1732. [PMID: 33428317 PMCID: PMC8248378 DOI: 10.1002/cbic.202000797] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/08/2021] [Indexed: 12/14/2022]
Abstract
Fluorescence microscopy imaging enables receptor proteins to be investigated within their biological context. A key challenge is to site-specifically incorporate reporter moieties into proteins without interfering with biological functions or cellular networks. Small peptide tags offer the opportunity to combine inducible labeling with small tag sizes that avoid receptor perturbation. Herein, we review the current state of live-cell labeling of peptide-tagged cell-surface proteins. Considering their importance as targets in medicinal chemistry, we focus on membrane receptors such as G protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). We discuss peptide tags that i) are subject to enzyme-mediated modification reactions, ii) guide the complementation of reporter proteins, iii) form coiled-coil complexes, and iv) interact with metal complexes. Given our own contributions in the field, we place emphasis on peptide-templated labeling chemistry.
Collapse
Affiliation(s)
- Philipp Wolf
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Georgina Gavins
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| | - Annette G. Beck‐Sickinger
- Faculty of Life SciencesInstitute of BiochemistryLeipzig UniversityBrüderstrasse 3404103LeipzigGermany
| | - Oliver Seitz
- Faculty of Mathematics and Natural SciencesDepartment of ChemistryHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
| |
Collapse
|
50
|
Don EK, Maschirow A, Radford RAW, Scherer NM, Vidal-Itriago A, Hogan A, Maurel C, Formella I, Stoddart JJ, Hall TE, Lee A, Shi B, Cole NJ, Laird AS, Badrock AP, Chung RS, Morsch M. In vivo Validation of Bimolecular Fluorescence Complementation (BiFC) to Investigate Aggregate Formation in Amyotrophic Lateral Sclerosis (ALS). Mol Neurobiol 2021; 58:2061-2074. [PMID: 33415684 PMCID: PMC8018926 DOI: 10.1007/s12035-020-02238-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/25/2020] [Indexed: 10/28/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a form of motor neuron disease (MND) that is characterized by the progressive loss of motor neurons within the spinal cord, brainstem, and motor cortex. Although ALS clinically manifests as a heterogeneous disease, with varying disease onset and survival, a unifying feature is the presence of ubiquitinated cytoplasmic protein inclusion aggregates containing TDP-43. However, the precise mechanisms linking protein inclusions and aggregation to neuronal loss are currently poorly understood. Bimolecular fluorescence complementation (BiFC) takes advantage of the association of fluorophore fragments (non-fluorescent on their own) that are attached to an aggregation-prone protein of interest. Interaction of the proteins of interest allows for the fluorescent reporter protein to fold into its native state and emit a fluorescent signal. Here, we combined the power of BiFC with the advantages of the zebrafish system to validate, optimize, and visualize the formation of ALS-linked aggregates in real time in a vertebrate model. We further provide in vivo validation of the selectivity of this technique and demonstrate reduced spontaneous self-assembly of the non-fluorescent fragments in vivo by introducing a fluorophore mutation. Additionally, we report preliminary findings on the dynamic aggregation of the ALS-linked hallmark proteins Fus and TDP-43 in their corresponding nuclear and cytoplasmic compartments using BiFC. Overall, our data demonstrates the suitability of this BiFC approach to study and characterize ALS-linked aggregate formation in vivo. Importantly, the same principle can be applied in the context of other neurodegenerative diseases and has therefore critical implications to advance our understanding of pathologies that underlie aberrant protein aggregation.
Collapse
Affiliation(s)
- Emily K Don
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Alina Maschirow
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Rowan A W Radford
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Natalie M Scherer
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Andrés Vidal-Itriago
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Alison Hogan
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Cindy Maurel
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Isabel Formella
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jack J Stoddart
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Thomas E Hall
- Institute for Molecular Bioscience, The University of Queensland, QLD, St Lucia, 4072, Australia
| | - Albert Lee
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Bingyang Shi
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Nicholas J Cole
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Angela S Laird
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Andrew P Badrock
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, Sydney, NSW, 2109, Australia.
| |
Collapse
|