1
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Lee HN, Lee SE, Inn KS, Seong J. Optical sensing and control of T cell signaling pathways. Front Physiol 2024; 14:1321996. [PMID: 38269062 PMCID: PMC10806162 DOI: 10.3389/fphys.2023.1321996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
T cells regulate adaptive immune responses through complex signaling pathways mediated by T cell receptor (TCR). The functional domains of the TCR are combined with specific antibodies for the development of chimeric antigen receptor (CAR) T cell therapy. In this review, we first overview current understanding on the T cell signaling pathways as well as traditional methods that have been widely used for the T cell study. These methods, however, are still limited to investigating dynamic molecular events with spatiotemporal resolutions. Therefore, genetically encoded biosensors and optogenetic tools have been developed to study dynamic T cell signaling pathways in live cells. We review these cutting-edge technologies that revealed dynamic and complex molecular mechanisms at each stage of T cell signaling pathways. They have been primarily applied to the study of dynamic molecular events in TCR signaling, and they will further aid in understanding the mechanisms of CAR activation and function. Therefore, genetically encoded biosensors and optogenetic tools offer powerful tools for enhancing our understanding of signaling mechanisms in T cells and CAR-T cells.
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Affiliation(s)
- Hae Nim Lee
- Brain Science Institute, Korea Institute of Science and Technoloy, Seoul, Republic of Korea
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Eun Lee
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Soo Inn
- Department of Converging Science and Technology, Kyung Hee University, Seoul, Republic of Korea
| | - Jihye Seong
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Wide River Institute of Immunology, Seoul National University, Hongcheon, Republic of Korea
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2
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Chen X, Leśniewska B, Boikine R, Yun N, Mody TA, Vaddepalli P, Schneitz K. Arabidopsis MCTP family member QUIRKY regulates the formation of the STRUBBELIG receptor kinase complex. PLANT PHYSIOLOGY 2023; 193:2538-2554. [PMID: 37668394 DOI: 10.1093/plphys/kiad489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/05/2023] [Accepted: 07/16/2023] [Indexed: 09/06/2023]
Abstract
Intercellular communication plays a central role in organogenesis. Tissue morphogenesis in Arabidopsis (Arabidopsis thaliana) requires signaling mediated by a cell surface complex containing the atypical receptor kinase STRUBBELIG (SUB) and the multiple C2 domains and transmembrane region protein QUIRKY (QKY). QKY is required to stabilize SUB at the plasma membrane. However, it is unclear what the in vivo architecture of the QKY/SUB signaling complex is, how it is controlled, and how it relates to the maintenance of SUB at the cell surface. We addressed these questions using a combination of genetics, yeast 2-hybrid assays, and Förster resonance energy transfer (FRET)/fluorescence lifetime imaging microscopy (FLIM) in epidermal cells of seedling roots. We found that QKY promotes the formation of SUB homooligomers in vivo. Homooligomerization of SUB appeared to involve its extracellular domain. We also showed that QKY and SUB physically interact and form a complex at the cell surface in vivo. In addition, the data showed that the N-terminal C2A-B region of QKY interacts with the intracellular domain of SUB. They further revealed that this interaction is essential to maintain SUB levels at the cell surface. Finally, we provided evidence that QKY forms homomultimers in vivo in a SUB-independent manner. We suggest a model in which the physical interaction of QKY with SUB mediates the oligomerization of SUB and attenuates its internalization, thereby maintaining sufficiently high levels of SUB at the cell surface required for the control of tissue morphogenesis.
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Affiliation(s)
- Xia Chen
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Barbara Leśniewska
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Rodion Boikine
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Nicole Yun
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Tejasvinee Atul Mody
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Prasad Vaddepalli
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
| | - Kay Schneitz
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising 85354, Germany
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3
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Mathur D, Díaz SA, Hildebrandt N, Pensack RD, Yurke B, Biaggne A, Li L, Melinger JS, Ancona MG, Knowlton WB, Medintz IL. Pursuing excitonic energy transfer with programmable DNA-based optical breadboards. Chem Soc Rev 2023; 52:7848-7948. [PMID: 37872857 PMCID: PMC10642627 DOI: 10.1039/d0cs00936a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 10/25/2023]
Abstract
DNA nanotechnology has now enabled the self-assembly of almost any prescribed 3-dimensional nanoscale structure in large numbers and with high fidelity. These structures are also amenable to site-specific modification with a variety of small molecules ranging from drugs to reporter dyes. Beyond obvious application in biotechnology, such DNA structures are being pursued as programmable nanoscale optical breadboards where multiple different/identical fluorophores can be positioned with sub-nanometer resolution in a manner designed to allow them to engage in multistep excitonic energy-transfer (ET) via Förster resonance energy transfer (FRET) or other related processes. Not only is the ability to create such complex optical structures unique, more importantly, the ability to rapidly redesign and prototype almost all structural and optical analogues in a massively parallel format allows for deep insight into the underlying photophysical processes. Dynamic DNA structures further provide the unparalleled capability to reconfigure a DNA scaffold on the fly in situ and thus switch between ET pathways within a given assembly, actively change its properties, and even repeatedly toggle between two states such as on/off. Here, we review progress in developing these composite materials for potential applications that include artificial light harvesting, smart sensors, nanoactuators, optical barcoding, bioprobes, cryptography, computing, charge conversion, and theranostics to even new forms of optical data storage. Along with an introduction into the DNA scaffolding itself, the diverse fluorophores utilized in these structures, their incorporation chemistry, and the photophysical processes they are designed to exploit, we highlight the evolution of DNA architectures implemented in the pursuit of increased transfer efficiency and the key lessons about ET learned from each iteration. We also focus on recent and growing efforts to exploit DNA as a scaffold for assembling molecular dye aggregates that host delocalized excitons as a test bed for creating excitonic circuits and accessing other quantum-like optical phenomena. We conclude with an outlook on what is still required to transition these materials from a research pursuit to application specific prototypes and beyond.
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Affiliation(s)
- Divita Mathur
- Department of Chemistry, Case Western Reserve University, Cleveland OH 44106, USA
| | - Sebastián A Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
| | - Niko Hildebrandt
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
- Department of Engineering Physics, McMaster University, Hamilton, L8S 4L7, Canada
| | - Ryan D Pensack
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Bernard Yurke
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Austin Biaggne
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Lan Li
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
- Center for Advanced Energy Studies, Idaho Falls, ID 83401, USA
| | - Joseph S Melinger
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
| | - Mario G Ancona
- Electronics Science and Technology Division, Code 6800, U.S. Naval Research Laboratory, Washington, DC 20375, USA
- Department of Electrical and Computer Engineering, Florida State University, Tallahassee, FL 32310, USA
| | - William B Knowlton
- Micron School of Materials Science & Engineering, Boise State University, Boise, ID 83725, USA.
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, USA.
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4
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Babu Manoharan G, Guzmán C, Najumudeen AK, Abankwa D. Detection of Ras nanoclustering-dependent homo-FRET using fluorescence anisotropy measurements. Eur J Cell Biol 2023; 102:151314. [PMID: 37058825 DOI: 10.1016/j.ejcb.2023.151314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023] Open
Abstract
The small GTPase Ras is frequently mutated in cancer and a driver of tumorigenesis. The recent years have shown great progress in drug-targeting Ras and understanding how it operates on the plasma membrane. We now know that Ras is non-randomly organized into proteo-lipid complexes on the membrane, called nanoclusters. Nanoclusters contain only a few Ras proteins and are necessary for the recruitment of downstream effectors, such as Raf. If tagged with fluorescent proteins, the dense packing of Ras in nanoclusters can be analyzed by Förster/ fluorescence resonance energy transfer (FRET). Loss of FRET can therefore report on decreased nanoclustering and any process upstream of it, such as Ras lipid modifications and correct trafficking. Thus, cellular FRET screens employing Ras-derived fluorescence biosensors are potentially powerful tools to discover chemical or genetic modulators of functional Ras membrane organization. Here we implement fluorescence anisotropy-based homo-FRET measurements of Ras-derived constructs labelled with only one fluorescent protein on a confocal microscope and a fluorescence plate reader. We show that homo-FRET of both H-Ras- and K-Ras-derived constructs can sensitively report on Ras-lipidation and -trafficking inhibitors, as well as on genetic perturbations of proteins regulating membrane anchorage. By exploiting the switch I/II-binding Ras-dimerizing compound BI-2852, this assay is also suitable to report on the engagement of the K-Ras switch II pocket by small molecules such as AMG 510. Given that homo-FRET only requires one fluorescent protein tagged Ras construct, this approach has significant advantages to create Ras-nanoclustering FRET-biosensor reporter cell lines, as compared to the more common hetero-FRET approaches.
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Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camilo Guzmán
- Euro-BioImaging ERIC, Statutory Seat, Turku, Finland
| | - Arafath Kaja Najumudeen
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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5
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Skakun VV, Digris A, Nolles A, Borst JW, Visser A. Revealing heterogeneity in correlation times of EGFP encapsulated in complex coacervate core micelles by analysis of fluorescence anisotropies. Methods Appl Fluoresc 2022; 10. [PMID: 35952674 DOI: 10.1088/2050-6120/ac8911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/11/2022] [Indexed: 11/11/2022]
Abstract
Encapsulation of enhanced green fluorescent protein (EGFP) in complex coacervate core micelles (C3Ms) can be established by mixing EGFP with diblock polymers at equal charge ratio. It has previously been shown that this encapsulation system is highly dynamic, implying existence of different populations; GFP free in solution or complexed with polymers (small complexes) and EGFP encapsulated in C3Ms. We performed time resolved fluorescence anisotropy experiments to determine the relative populations of EGFP encapsulated in C3Ms using three different fluorescence anisotropy decay analysis methods. First, Maximum Entropy Method (MEM) data analysis was employed for five different EGFP concentrations in C3Ms that were mixed with dark fluorescent proteins (10, 20, 30, 40 and 50% EGFP, respectively). In all cases, correlation-time distributions between 0.1 and 100 ns (on a logarithmic timescale) are clearly visible showing bimodal distribution. The distribution between 0.1 and 2.0 ns is due to homo-FRET between EGFP molecules packed in micelles and the distribution between 8 and 30 ns coincides with the correlation-time distribution of free EGFP in solution. The fraction of homo-FRET distribution linearly increases with increase of relative micellar EGFP concentrations. These MEM results were corroborated by two different analysis methods: global population analysis of all five fluorescence anisotropy decays arising from EGFP in micelles together with the one of free EGFP (direct analysis of anisotropies) and global associative population analysis of anisotropies by fitting parallel and perpendicular fluorescence decay components. In contrast to global analyses approaches, the MEM method directly reveals distributions of correlation times without any prior information about the sample. However, global associative analysis of anisotropies by fitting parallel and perpendicular fluorescence decay components is the only method that allows to estimate accurately fractions of free fluorophores in solution and encapsulated fluorophores.
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Affiliation(s)
- Victor V Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, Nezavisimisty Ave., 4, Minsk, 220030, BELARUS
| | - Anatoli Digris
- Department of Systems Analysis and Computer Simulation, Belarusian State University, Nezavisimisty Ave., 4, Minsk, 220030, BELARUS
| | - Antsje Nolles
- Wageningen University & Research, Stippeneng 4, Wageningen, Gelderland, 6700 HB, NETHERLANDS
| | - Jan Willem Borst
- Laboratory of Biochemistry, Microspectroscopy Research Facility , Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Gelderland, 6700 HB, NETHERLANDS
| | - Antonie Visser
- Wageningen University & Research, Stippeneng 4, Wageningen, Gelderland, 6700 HB, NETHERLANDS
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6
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Weidtkamp-Peters S, Rehwald S, Stahl Y. Homo-FRET Imaging to Study Protein-Protein Interaction and Complex Formation in Plants. Methods Mol Biol 2022; 2379:197-208. [PMID: 35188664 DOI: 10.1007/978-1-0716-1791-5_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein-protein interactions in living plant cells can be measured by changes in fluorescence anisotropy due to homo-FRET (Förster Resonance Energy Transfer). Here, the energy transfer between identical fluorophores, e.g., enhanced green fluorescent protein (EGFP) fused to a protein of interest, serves as a read-out for protein interaction and clustering. By applying homo-FRET imaging, not only dimeric complexes, but also bigger homomeric complex formation can be followed in vivo at high spatial and temporal resolution. Therefore, this method provides a powerful tool to investigate changes in complex formation over time in their natural environment with high precision at a subcellular level. Here, we describe the necessary theoretical background and how homo-FRET imaging is practically carried out. We also discuss potential pitfalls and points of consideration.
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Affiliation(s)
| | | | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany.
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7
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Chaudhary A, Schneitz K. Using Steady-State Fluorescence Anisotropy to Study Protein Clustering. Methods Mol Biol 2022; 2457:253-260. [PMID: 35349145 DOI: 10.1007/978-1-0716-2132-5_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: 06/14/2023]
Abstract
Signaling pathways rely on the precise control of protein-protein interactions. Therefore, it is essential to be able to investigate such interactions with spatiotemporal resolution and in live cells. Here we describe a microscope-based fluorescence spectrometry technique to investigate homotypic interactions between GFP-labeled fusion proteins in a rapid and reproducible fashion using fluorescence anisotropy. This method is of great value for the study of protein complexes in live tissue with subcellular resolution.
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Affiliation(s)
- Ajeet Chaudhary
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Kay Schneitz
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.
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8
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Díaz-García C, Renart ML, Poveda JA, Giudici AM, González-Ros JM, Prieto M, Coutinho A. Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements. Int J Mol Sci 2021; 22:ijms222111954. [PMID: 34769384 PMCID: PMC8584343 DOI: 10.3390/ijms222111954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/16/2022] Open
Abstract
The allosteric coupling between activation and inactivation processes is a common feature observed in K+ channels. Particularly, in the prokaryotic KcsA channel the K+ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pKa of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.
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Affiliation(s)
- Clara Díaz-García
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Maria Lourdes Renart
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
- Correspondence: (M.L.R.); (A.C.)
| | - José Antonio Poveda
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Ana Marcela Giudici
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - José M. González-Ros
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche, Universidad Miguel Hernández, 03202 Elche, Spain; (J.A.P.); (A.M.G.); (J.M.G.-R.)
| | - Manuel Prieto
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- iBB, Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal; (C.D.-G.); (M.P.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: (M.L.R.); (A.C.)
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9
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Mahbub S, Saha S, Ramakrishna G, Furgal JC. Beads on a Chain Fluorescent Oligomeric Materials: Interactions of Conjugated Organic Cross-Linkers with Silsesquioxane Cages. J Phys Chem B 2021; 125:11457-11472. [PMID: 34641684 DOI: 10.1021/acs.jpcb.1c05282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organic electronic materials have advantages over inorganics in terms of versatility, cost, and processability. Recent advancements in organic materials for light-emitting diodes (OLED), field effect transistors (OFET), and photovoltaics have engendered extensive innovation potential on this field. In this research, we focus on synthesizing SQ (silsesquioxane) based oligomers cross-linked by dibromo-aromatic linkers and explore how the cross-linker influences their photophysical properties. Bis-trialkoxy silyl (linker) model compounds were synthesized to compare noncage photophysical properties with the oligomers. Several techniques such as UV/vis, fluorescence, FTIR, and thermal gravimetric analysis (TGA) have been used to characterize the systems. Time-resolved fluorescence and femtosecond transient absorption spectroscopy were used to understand the excited state dynamics of these materials. Studies were carried out to understand the differences between monomers and oligomers and potential energy transfer and charge transfer between the cages and cross-linking chromophores. Transient absorption showed lower energy absorption from the excited states, suggesting short-range communication between moieties. Single photon counting studies have shown distinct lifetime differences between most linkers and cages display possible excitation energy transfer through these materials. Transient absorption anisotropy measurements have shown signatures for excitation energy transfer between linker chromophores for oligomeric compounds. The silsesquioxane (SQ) backbone of the oligomers gives substantial thermal stability as well as solution processability, giving better flexibility for achieving energy transfer between linking chromophores.
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Affiliation(s)
- Shahrea Mahbub
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Sukanya Saha
- Department of Chemistry and Biochemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
| | - Guda Ramakrishna
- Department of Chemistry and Biochemistry, Western Michigan University, Kalamazoo, Michigan 49008, United States
| | - Joseph C Furgal
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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10
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Chaudhary A, Chen X, Leśniewska B, Boikine R, Gao J, Wolf S, Schneitz K. Cell wall damage attenuates root hair patterning and tissue morphogenesis mediated by the receptor kinase STRUBBELIG. Development 2021; 148:270854. [PMID: 34251020 DOI: 10.1242/dev.199425] [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] [Received: 01/12/2021] [Accepted: 06/14/2021] [Indexed: 01/15/2023]
Abstract
Cell wall remodeling is essential for the control of growth and development as well as the regulation of stress responses. However, the underlying cell wall monitoring mechanisms remain poorly understood. Regulation of root hair fate and flower development in Arabidopsis thaliana requires signaling mediated by the atypical receptor kinase STRUBBELIG (SUB). Furthermore, SUB is involved in cell wall integrity signaling and regulates the cellular response to reduced levels of cellulose, a central component of the cell wall. Here, we show that continuous exposure to sub-lethal doses of the cellulose biosynthesis inhibitor isoxaben results in altered root hair patterning and floral morphogenesis. Genetically impairing cellulose biosynthesis also results in root hair patterning defects. We further show that isoxaben exerts its developmental effects through the attenuation of SUB signaling. Our evidence indicates that downregulation of SUB is a multi-step process and involves changes in SUB complex architecture at the plasma membrane, enhanced removal of SUB from the cell surface, and downregulation of SUB transcript levels. The results provide molecular insight into how the cell wall regulates cell fate and tissue morphogenesis.
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Affiliation(s)
- Ajeet Chaudhary
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Xia Chen
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Barbara Leśniewska
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rodion Boikine
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Jin Gao
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Sebastian Wolf
- Cell wall signaling group, Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Kay Schneitz
- Plant Developmental Biology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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11
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Modulation and dynamics of cell membrane heterogeneities. Chem Phys Lipids 2020; 233:105006. [PMID: 33144069 DOI: 10.1016/j.chemphyslip.2020.105006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 01/02/2023]
Abstract
Numerous studies provide evidence that the lipid bilayer of the plasma membrane contains lateral nanodomains, and that these are functionally important regulators of transmembrane cell signaling. Depending on their chemical composition and the biophysical mechanism bringing the lipids together, multiple types of nanodomains exist in the inner and the outer leaflet of the plasma membrane bilayer. In intact cells, these domains are smaller than the optical resolution limit of light microscopy and also highly dynamic. Recently, advanced fluorescence methods have provided data to characterize many biophysical and thermodynamic aspects of these nanodomains. In this review, we summarize the physicochemical determinants of nanodomain formation, stability and extent. Then, we detail how these nanodomains play a structural role by anchoring nucleation sites for the membrane cytoskeleton on the lipid bilayer. Further, we review the existing literature on mechanisms that modulate the nanodomain size and stability, both acute and chronic events. We conclude that regulation of the nanodomains distribution in the lipid bilayer of the plasma membrane is important for modulation of transmembrane signaling. However, only very few modulators of nanodomain stability and size have been quantified in cells, suggesting interesting directions for future studies.
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12
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Kashida H, Kawai H, Azuma H, Araki Y, Wada T, Asanuma H. Quantitative Analyses of Förster Resonance Energy Transfer between Identical Pyrene Chromophores (Homo‐FRET) In DNA Scaffolds. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Hiromu Kashida
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hayato Kawai
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Hidenori Azuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials Tohoku University 2-1-1, Katahira, Aoba-ku Sendai 980-8577 Japan
| | - Hiroyuki Asanuma
- Department of Biomolecular Engineering Graduate School of Engineering Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
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Heckmeier PJ, Agam G, Teese MG, Hoyer M, Stehle R, Lamb DC, Langosch D. Determining the Stoichiometry of Small Protein Oligomers Using Steady-State Fluorescence Anisotropy. Biophys J 2020; 119:99-114. [PMID: 32553128 DOI: 10.1016/j.bpj.2020.05.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 11/19/2022] Open
Abstract
A large fraction of soluble and membrane-bound proteins exists as non-covalent dimers, trimers, and higher-order oligomers. The experimental determination of the oligomeric state or stoichiometry of proteins remains a nontrivial challenge. In one approach, the protein of interest is genetically fused to green fluorescent protein (GFP). If a fusion protein assembles into a non-covalent oligomeric complex, exciting their GFP moiety with polarized fluorescent light elicits homotypic Förster resonance energy transfer (homo-FRET), in which the emitted radiation is partially depolarized. Fluorescence depolarization is associated with a decrease in fluorescence anisotropy that can be exploited to calculate the oligomeric state. In a classical approach, several parameters obtained through time-resolved and steady-state anisotropy measurements are required for determining the stoichiometry of the oligomers. Here, we examined novel approaches in which time-resolved measurements of reference proteins provide the parameters that can be used to interpret the less expensive steady-state anisotropy data of candidates. In one approach, we find that using average homo-FRET rates (kFRET), average fluorescence lifetimes (τ), and average anisotropies of those fluorophores that are indirectly excited by homo-FRET (rET) do not compromise the accuracy of calculated stoichiometries. In the other approach, fractional photobleaching of reference oligomers provides a novel parameter a whose dependence on stoichiometry allows one to quantitatively interpret the increase of fluorescence anisotropy seen after photobleaching the candidates. These methods can at least reliably distinguish monomers from dimers and trimers.
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Affiliation(s)
- Philipp J Heckmeier
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Ganesh Agam
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Mark G Teese
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany
| | - Maria Hoyer
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM), Chair Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, Garching, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany.
| | - Dieter Langosch
- Center for Integrated Protein Science Munich (CIPSM), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Freising, Germany.
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14
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Camacho R, Täuber D, Scheblykin IG. Fluorescence Anisotropy Reloaded-Emerging Polarization Microscopy Methods for Assessing Chromophores' Organization and Excitation Energy Transfer in Single Molecules, Particles, Films, and Beyond. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1805671. [PMID: 30721532 DOI: 10.1002/adma.201805671] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/12/2018] [Indexed: 06/09/2023]
Abstract
Fluorescence polarization is widely used to assess the orientation/rotation of molecules, and the excitation energy transfer between closely located chromophores. Emerging since the 1990s, single molecule fluorescence spectroscopy and imaging stimulate the application of light polarization for studying molecular organization and energy transfer beyond ensemble averaging. Here, traditional fluorescence polarization and linear dichroism methods used for bulk samples are compared with techniques specially developed for, or inspired by, single molecule fluorescence spectroscopy. Techniques for assessing energy transfer in anisotropic samples, where the traditional fluorescence anisotropy framework is not readily applicable, are discussed in depth. It is shown that the concept of a polarization portrait and the single funnel approximation can lay the foundation for alternative energy transfer metrics. Examples ranging from fundamental studies of photoactive materials (conjugated polymers, light-harvesting aggregates, and perovskite semiconductors) to Förster resonant energy transfer (FRET)-based biomedical imaging are presented. Furthermore, novel uses of light polarization for super-resolution optical imaging are mentioned as well as strategies for avoiding artifacts in polarization microscopy.
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Affiliation(s)
- Rafael Camacho
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, B-3001, Leuven, Belgium
| | - Daniela Täuber
- Chemical Physics and NanoLund, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
- Biopolarisation, Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, D-07745, Jena, Germany
- Institute of Solid State Physics, FSU Jena, Helmholtzweg 3, D-07743, Jena, Germany
| | - Ivan G Scheblykin
- Chemical Physics and NanoLund, Lund University, P.O. Box 124, SE-22100, Lund, Sweden
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15
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Berleth M, Berleth N, Minges A, Hänsch S, Burkart RC, Stork B, Stahl Y, Weidtkamp-Peters S, Simon R, Groth G. Molecular Analysis of Protein-Protein Interactions in the Ethylene Pathway in the Different Ethylene Receptor Subfamilies. FRONTIERS IN PLANT SCIENCE 2019; 10:726. [PMID: 31231408 PMCID: PMC6566107 DOI: 10.3389/fpls.2019.00726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/16/2019] [Indexed: 05/06/2023]
Abstract
Signal perception and transmission of the plant hormone ethylene are mediated by a family of receptor histidine kinases located at the Golgi-ER network. Similar to bacterial and other plant receptor kinases, these receptors work as dimers or higher molecular weight oligomers at the membrane. Sequence analysis and functional studies of different isoforms suggest that the ethylene receptor family is classified into two subfamilies. In Arabidopsis, the type-I subfamily has two members (ETR1 and ERS1) and the type-II subfamily has three members (ETR2, ERS2, and EIN4). Whereas subfamily-I of the Arabidopsis receptors and their interactions with downstream elements in the ethylene pathway has been extensively studied in the past; related information on subfamily-II is sparse. In order to dissect the role of type-II receptors in the ethylene pathway and to decode processes associated with this receptor subfamily on a quantitative molecular level, we have applied biochemical and spectroscopic studies on purified recombinant receptors and downstream elements of the ethylene pathway. To this end, we have expressed purified ETR2 as a prototype of the type-II subfamily, ETR1 for the type-I subfamily and downstream ethylene pathway proteins CTR1 and EIN2. Functional folding of the purified receptors was demonstrated by CD spectroscopy and autokinase assays. Quantitative analysis of protein-protein interactions (PPIs) by microscale thermophoresis (MST) revealed that ETR2 has similar affinities for CTR1 and EIN2 as previously reported for the subfamily-I prototype ETR1 suggesting similar roles in PPI-mediated signal transfer for both subfamilies. We also used in planta fluorescence studies on transiently expressed proteins in Nicotiana benthamiana leaf cells to analyze homo- and heteromer formation of receptors. These studies show that type-II receptors as well as the type-I receptors form homo- and heteromeric complexes at these conditions. Notably, type-II receptor homomers and type-II:type-I heteromers are more stable than type-I homomers as indicated by their lower dissociation constants obtained in microscale thermophoresis studies. The enhanced stability of type-II complexes emphasizes the important role of type-II receptors in the ethylene pathway.
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Affiliation(s)
- Mareike Berleth
- Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Niklas Berleth
- Institute of Molecular Medicine I, Heinrich Heine University, Düsseldorf, Germany
| | - Alexander Minges
- Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf, Germany
| | - Sebastian Hänsch
- Center for Advanced Imaging, Heinrich Heine University, Düsseldorf, Germany
| | | | - Björn Stork
- Institute of Molecular Medicine I, Heinrich Heine University, Düsseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | | | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | - Georg Groth
- Institute of Biochemical Plant Physiology, Heinrich Heine University, Düsseldorf, Germany
- *Correspondence: Georg Groth, ;
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16
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Kashida H, Kawai H, Maruyama R, Kokubo Y, Araki Y, Wada T, Asanuma H. Quantitative evaluation of energy migration between identical chromophores enabled by breaking symmetry. Commun Chem 2018. [DOI: 10.1038/s42004-018-0093-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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17
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Snell NE, Rao VP, Seckinger KM, Liang J, Leser J, Mancini AE, Rizzo MA. Homotransfer of FRET Reporters for Live Cell Imaging. BIOSENSORS-BASEL 2018; 8:bios8040089. [PMID: 30314323 PMCID: PMC6316388 DOI: 10.3390/bios8040089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/01/2023]
Abstract
Förster resonance energy transfer (FRET) between fluorophores of the same species was recognized in the early to mid-1900s, well before modern heterotransfer applications. Recently, homotransfer FRET principles have re-emerged in biosensors that incorporate genetically encoded fluorescent proteins. Homotransfer offers distinct advantages over the standard heterotransfer FRET method, some of which are related to the use of fluorescence polarization microscopy to quantify FRET between two fluorophores of identical color. These include enhanced signal-to-noise, greater compatibility with other optical sensors and modulators, and new design strategies based upon the clustering or dimerization of singly-labeled sensors. Here, we discuss the theoretical basis for measuring homotransfer using polarization microscopy, procedures for data collection and processing, and we review the existing genetically-encoded homotransfer biosensors.
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Affiliation(s)
- Nicole E Snell
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Vishnu P Rao
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Kendra M Seckinger
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Junyi Liang
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Jenna Leser
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - Allison E Mancini
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
| | - M A Rizzo
- Department of Physiology, University of Maryland School of Medicine, 660 W Redwood St/HH525B, Baltimore, MD 21201, USA.
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18
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Camacho R, Täuber D, Hansen C, Shi J, Bousset L, Melki R, Li JY, Scheblykin IG. 2D polarization imaging as a low-cost fluorescence method to detect α-synuclein aggregation ex vivo in models of Parkinson's disease. Commun Biol 2018; 1:157. [PMID: 30302401 PMCID: PMC6168587 DOI: 10.1038/s42003-018-0156-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 08/28/2018] [Indexed: 12/15/2022] Open
Abstract
A hallmark of Parkinson's disease is the formation of large protein-rich aggregates in neurons, where α-synuclein is the most abundant protein. A standard approach to visualize aggregation is to fluorescently label the proteins of interest. Then, highly fluorescent regions are assumed to contain aggregated proteins. However, fluorescence brightness alone cannot discriminate micrometer-sized regions with high expression of non-aggregated proteins from regions where the proteins are aggregated on the molecular scale. Here, we demonstrate that 2-dimensional polarization imaging can discriminate between preformed non-aggregated and aggregated forms of α-synuclein, and detect increased aggregation in brain tissues of transgenic mice. This imaging method assesses homo-FRET between labels by measuring fluorescence polarization in excitation and emission simultaneously, which translates into higher contrast than fluorescence anisotropy imaging. Exploring earlier aggregation states of α-synuclein using such technically simple imaging method could lead to crucial improvements in our understanding of α-synuclein-mediated pathology in Parkinson's Disease.
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Affiliation(s)
- Rafael Camacho
- Chemical Physics and NanoLund, Lund University, P.O. Box 124,, 22100, Lund, Sweden
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Daniela Täuber
- Chemical Physics and NanoLund, Lund University, P.O. Box 124,, 22100, Lund, Sweden
- Biopolarisation, Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745, Jena, Germany
- Institute of Solid State Physics, FSU Jena, Helmholtzweg 3, 07743, Jena, Germany
| | - Christian Hansen
- Neural Plasticity and Repair Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, BMC A10, 22184, Lund, Sweden
- Molecular Neurobiology, Department of Experimental Medical Science, BMC B11, 221 84, Lund, Sweden
| | - Juanzi Shi
- Chemical Physics and NanoLund, Lund University, P.O. Box 124,, 22100, Lund, Sweden
| | - Luc Bousset
- Institut Fancois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, 18 Route du Panorama, 92265, Fontenay-Aux-Roses cedex, France
| | - Ronald Melki
- Institut Fancois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, 18 Route du Panorama, 92265, Fontenay-Aux-Roses cedex, France
| | - Jia-Yi Li
- Neural Plasticity and Repair Unit, Wallenberg Neuroscience Center, Department of Experimental Medical Science, Lund University, BMC A10, 22184, Lund, Sweden.
- Institute of Health Sciences, China Medical University, 110122, Shenyang, People's Republic of China.
| | - Ivan G Scheblykin
- Chemical Physics and NanoLund, Lund University, P.O. Box 124,, 22100, Lund, Sweden.
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19
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Teunissen AJP, Pérez-Medina C, Meijerink A, Mulder WJM. Investigating supramolecular systems using Förster resonance energy transfer. Chem Soc Rev 2018; 47:7027-7044. [PMID: 30091770 PMCID: PMC6441672 DOI: 10.1039/c8cs00278a] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Supramolecular systems have applications in areas as diverse as materials science, biochemistry, analytical chemistry, and nanomedicine. However, analyzing such systems can be challenging due to the wide range of time scales, binding strengths, distances, and concentrations at which non-covalent phenomena take place. Due to their versatility and sensitivity, Förster resonance energy transfer (FRET)-based techniques are excellently suited to meet such challenges. Here, we detail the ways in which FRET has been used to study non-covalent interactions in both synthetic and biological supramolecular systems. Among other topics, we examine methods to measure molecular forces, determine protein conformations, monitor assembly kinetics, and visualize in vivo drug release from nanoparticles. Furthermore, we highlight multiplex FRET techniques, discuss the field's limitations, and provide a perspective on new developments.
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Affiliation(s)
- Abraham J. P. Teunissen
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Carlos Pérez-Medina
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Andries Meijerink
- Department of Chemistry, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Willem J. M. Mulder
- Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Laboratory of Chemical biology, Department of Biomedical Engineering and Institute for Complex Molecular systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, The Netherlands
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20
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Ross BL, Tenner B, Markwardt ML, Zviman A, Shi G, Kerr JP, Snell NE, McFarland JJ, Mauban JR, Ward CW, Rizzo MA, Zhang J. Single-color, ratiometric biosensors for detecting signaling activities in live cells. eLife 2018; 7:e35458. [PMID: 29968564 PMCID: PMC6037473 DOI: 10.7554/elife.35458] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/16/2018] [Indexed: 11/22/2022] Open
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of signal transduction by enabling the real-time tracking of signaling activities in live cells. Investigating the interaction between signaling networks has become increasingly important to understanding complex cellular phenomena, necessitating an update of the biosensor toolkit to allow monitoring and perturbing multiple activities simultaneously in the same cell. We therefore developed a new class of fluorescent biosensors based on homo-FRET, deemed FLuorescence Anisotropy REporters (FLAREs), which combine the multiplexing ability of single-color sensors with a quantitative, ratiometric readout. Using an array of color variants, we were able to demonstrate multiplexed imaging of three activity reporters simultaneously in the same cell. We further demonstrate the compatibility of FLAREs for use with optogenetic tools as well as intravital two-photon imaging.
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Affiliation(s)
- Brian L Ross
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Department of Biomedical EngineeringJohns Hopkins UniversityBaltimoreUnited States
| | - Brian Tenner
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Program in Molecular BiophysicsJohns Hopkins University School of MedicineBaltimoreUnited States
| | - Michele L Markwardt
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Adam Zviman
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Guoli Shi
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Jaclyn P Kerr
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Nicole E Snell
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | | | - Joseph R Mauban
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Christopher W Ward
- Department of OrthopaedicsUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Megan A Rizzo
- Department of PhysiologyUniversity of Maryland BaltimoreBaltimoreUnited States
| | - Jin Zhang
- Department of PharmacologyUniversity of California, San DiegoSan DiegoUnited States
- Program in Molecular BiophysicsJohns Hopkins University School of MedicineBaltimoreUnited States
- Department of Pharmacology and Molecular SciencesJohns Hopkins University School of MedicineBaltimoreUnited States
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21
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Grossmann G, Krebs M, Maizel A, Stahl Y, Vermeer JEM, Ott T. Green light for quantitative live-cell imaging in plants. J Cell Sci 2018; 131:jcs.209270. [PMID: 29361538 DOI: 10.1242/jcs.209270] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Plants exhibit an intriguing morphological and physiological plasticity that enables them to thrive in a wide range of environments. To understand the cell biological basis of this unparalleled competence, a number of methodologies have been adapted or developed over the last decades that allow minimal or non-invasive live-cell imaging in the context of tissues. Combined with the ease to generate transgenic reporter lines in specific genetic backgrounds or accessions, we are witnessing a blooming in plant cell biology. However, the imaging of plant cells entails a number of specific challenges, such as high levels of autofluorescence, light scattering that is caused by cell walls and their sensitivity to environmental conditions. Quantitative live-cell imaging in plants therefore requires adapting or developing imaging techniques, as well as mounting and incubation systems, such as micro-fluidics. Here, we discuss some of these obstacles, and review a number of selected state-of-the-art techniques, such as two-photon imaging, light sheet microscopy and variable angle epifluorescence microscopy that allow high performance and minimal invasive live-cell imaging in plants.
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Affiliation(s)
- Guido Grossmann
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.,Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany
| | - Melanie Krebs
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Alexis Maizel
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Joop E M Vermeer
- Laboratory for Cell Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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22
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Akamatsu K, Shikazono N, Saito T. New method for estimating clustering of DNA lesions induced by physical/chemical mutagens using fluorescence anisotropy. Anal Biochem 2017; 536:78-89. [PMID: 28827125 DOI: 10.1016/j.ab.2017.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/02/2017] [Accepted: 08/11/2017] [Indexed: 12/31/2022]
Abstract
We have developed a new method for estimating the localization of DNA damage such as apurinic/apyrimidinic sites (APs) on DNA using fluorescence anisotropy. This method is aimed at characterizing clustered DNA damage produced by DNA-damaging agents such as ionizing radiation and genotoxic chemicals. A fluorescent probe with an aminooxy group (AlexaFluor488) was used to label APs. We prepared a pUC19 plasmid with APs by heating under acidic conditions as a model for damaged DNA, and subsequently labeled the APs. We found that the observed fluorescence anisotropy (robs) decreases as averaged AP density (λAP: number of APs per base pair) increases due to homo-FRET, and that the APs were randomly distributed. We applied this method to three DNA-damaging agents, 60Co γ-rays, methyl methanesulfonate (MMS), and neocarzinostatin (NCS). We found that robs-λAP relationships differed significantly between MMS and NCS. At low AP density (λAP < 0.001), the APs induced by MMS seemed to not be closely distributed, whereas those induced by NCS were remarkably clustered. In contrast, the AP clustering induced by 60Co γ-rays was similar to, but potentially more likely to occur than, random distribution. This simple method can be used to estimate mutagenicity of ionizing radiation and genotoxic chemicals.
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Affiliation(s)
- Ken Akamatsu
- Radiation DNA Damage Research Group, Kansai Photon Science Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
| | - Naoya Shikazono
- Radiation DNA Damage Research Group, Kansai Photon Science Institute, National Institutes for Quantum and Radiological Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Takeshi Saito
- Radiation Biochemistry and Biological Function, Research Reactor Institute, Kyoto University, Kumatori, Sennan, Osaka 590-0494, Japan
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23
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Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered. Sci Rep 2017; 7:5460. [PMID: 28710349 PMCID: PMC5511215 DOI: 10.1038/s41598-017-05539-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/30/2017] [Indexed: 11/30/2022] Open
Abstract
It is a fundamental question in cell biology and biophysics whether sphingomyelin (SM)- and cholesterol (Chol)- driven nanodomains exist in living cells and in model membranes. Biophysical studies on model membranes revealed SM and Chol driven micrometer-sized liquid-ordered domains. Although the existence of such microdomains has not been proven for the plasma membrane, such lipid mixtures have been often used as a model system for ‘rafts’. On the other hand, recent super resolution and single molecule results indicate that the plasma membrane might organize into nanocompartments. However, due to the limited resolution of those techniques their unambiguous characterization is still missing. In this work, a novel combination of Förster resonance energy transfer and Monte Carlo simulations (MC-FRET) identifies directly 10 nm large nanodomains in liquid-disordered model membranes composed of lipid mixtures containing SM and Chol. Combining MC-FRET with solid-state wide-line and high resolution magic angle spinning NMR as well as with fluorescence correlation spectroscopy we demonstrate that these nanodomains containing hundreds of lipid molecules are fluid and disordered. In terms of their size, fluidity, order and lifetime these nanodomains may represent a relevant model system for cellular membranes and are closely related to nanocompartments suggested to exist in cellular membranes.
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24
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Tenner B, Mehta S, Zhang J. Optical sensors to gain mechanistic insights into signaling assemblies. Curr Opin Struct Biol 2016; 41:203-210. [PMID: 27611602 PMCID: PMC5423777 DOI: 10.1016/j.sbi.2016.07.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/29/2016] [Indexed: 11/17/2022]
Abstract
Protein complexes play a major role in transducing information from outside the cell into instructions for growth and survival, and understanding how these complexes relay and shape intracellular signals has been a central question in signaling biology. Fluorescent proteins have proven paramount in opening windows for researchers to peer into the architecture and inner workings of signaling assemblies within the living cell and in real-time. In this review, we will provide readers with a current perspective on the development and use of genetically encoded optical probes to dissect the function of signaling complexes.
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Affiliation(s)
- Brian Tenner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, United States; Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, United States.
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25
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de Bruin G, Xin BT, Florea BI, Overkleeft HS. Proteasome Subunit Selective Activity-Based Probes Report on Proteasome Core Particle Composition in a Native Polyacrylamide Gel Electrophoresis Fluorescence-Resonance Energy Transfer Assay. J Am Chem Soc 2016; 138:9874-80. [PMID: 27428761 DOI: 10.1021/jacs.6b04207] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most mammalian tissues contain a single proteasome species: constitutive proteasomes. Tissues able to express, next to the constitutive proteasome catalytic activities (β1c, β2c, β5c), the three homologous activities, β1i, β2i and β5i, may contain numerous distinct proteasome particles: immunoproteasomes (composed of β1i, β2i and β5i) and mixed proteasomes containing a mix of these activities. This work describes the development of new subunit-selective activity-based probes and their use in an activity-based protein profiling assay that allows the detection of various proteasome particles. Tissue extracts are treated with subunit-specific probes bearing distinct fluorophores and subunit-specific inhibitors. The samples are resolved by native polyacrylamide gel electrophoresis, after which fluorescence-resonance energy transfer (FRET) reports on the nature of proteasomes present.
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Affiliation(s)
- Gerjan de Bruin
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bo-Tao Xin
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Bogdan I Florea
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Herman S Overkleeft
- Gorlaeus Laboratories, Leiden Institute of Chemistry , Einsteinweg 55, 2333 CC Leiden, The Netherlands
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26
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Amaro M, Šachl R, Jurkiewicz P, Coutinho A, Prieto M, Hof M. Time-resolved fluorescence in lipid bilayers: selected applications and advantages over steady state. Biophys J 2016; 107:2751-2760. [PMID: 25517142 DOI: 10.1016/j.bpj.2014.10.058] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/23/2014] [Accepted: 10/29/2014] [Indexed: 01/23/2023] Open
Abstract
Fluorescence methods are versatile tools for obtaining dynamic and topological information about biomembranes because the molecular interactions taking place in lipid membranes frequently occur on the same timescale as fluorescence emission. The fluorescence intensity decay, in particular, is a powerful reporter of the molecular environment of a fluorophore. The fluorescence lifetime can be sensitive to the local polarity, hydration, viscosity, and/or presence of fluorescence quenchers/energy acceptors within several nanometers of the vicinity of a fluorophore. Illustrative examples of how time-resolved fluorescence measurements can provide more valuable and detailed information about a system than the time-integrated (steady-state) approach will be presented in this review: 1), determination of membrane polarity and mobility using time-dependent spectral shifts; 2), identification of submicroscopic domains by fluorescence lifetime imaging microscopy; 3), elucidation of membrane leakage mechanisms from dye self-quenching assays; and 4), evaluation of nanodomain sizes by time-resolved Förster resonance energy transfer measurements.
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Affiliation(s)
- Mariana Amaro
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Radek Šachl
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Piotr Jurkiewicz
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic
| | - Ana Coutinho
- Centre for Molecular Chemistry and Physics and Instituto de Nanociência e Nanotecnologia, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Departamento Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Manuel Prieto
- Centre for Molecular Chemistry and Physics and Instituto de Nanociência e Nanotecnologia, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Martin Hof
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Prague, Czech Republic.
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Abstract
The local structure and composition of the outer membrane of an animal cell are important factors in the control of many membrane processes and mechanisms. These include signaling, sorting, and exo- and endocytic processes that are occurring all the time in a living cell. Paradoxically, not only are the local structure and composition of the membrane matters of much debate and discussion, the mechanisms that govern its genesis remain highly controversial. Here, we discuss a swathe of new technological advances that may be applied to understand the local structure and composition of the membrane of a living cell from the molecular scale to the scale of the whole membrane.
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Affiliation(s)
- Thomas S van Zanten
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
| | - Satyajit Mayor
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
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28
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Chavan TS, Muratcioglu S, Marszalek R, Jang H, Keskin O, Gursoy A, Nussinov R, Gaponenko V. Plasma membrane regulates Ras signaling networks. CELLULAR LOGISTICS 2015; 5:e1136374. [PMID: 27054048 PMCID: PMC4820813 DOI: 10.1080/21592799.2015.1136374] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/31/2022]
Abstract
Ras GTPases activate more than 20 signaling pathways, regulating such essential cellular functions as proliferation, survival, and migration. How Ras proteins control their signaling diversity is still a mystery. Several pieces of evidence suggest that the plasma membrane plays a critical role. Among these are: (1) selective recruitment of Ras and its effectors to particular localities allowing access to Ras regulators and effectors; (2) specific membrane-induced conformational changes promoting Ras functional diversity; and (3) oligomerization of membrane-anchored Ras to recruit and activate Raf. Taken together, the membrane does not only attract and retain Ras but also is a key regulator of Ras signaling. This can already be gleaned from the large variability in the sequences of Ras membrane targeting domains, suggesting that localization, environment and orientation are important factors in optimizing the function of Ras isoforms.
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Affiliation(s)
- Tanmay Sanjeev Chavan
- Department of Medicinal Chemistry; University of Illinois at Chicago; Chicago, IL USA
| | - Serena Muratcioglu
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Richard Marszalek
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago; Chicago, IL USA
| | - Hyunbum Jang
- Cancer and Inflammation Program; Basic Science Program; Leidos Biomedical Research, Inc.; Frederick National Laboratory for Cancer Research; National Cancer Institute at Frederick; Frederick, MD USA
| | - Ozlem Keskin
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics; Koc University; Istanbul, Turkey
| | - Ruth Nussinov
- Cancer and Inflammation Program; Basic Science Program; Leidos Biomedical Research, Inc.; Frederick National Laboratory for Cancer Research; National Cancer Institute at Frederick; Frederick, MD USA
- Sackler Institute of Molecular Medicine; Department of Human Genetics and Molecular Medicine; Sackler School of Medicine; Tel Aviv University; Tel Aviv, Israel
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics; University of Illinois at Chicago; Chicago, IL USA
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29
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Kreder R, Pyrshev KA, Darwich Z, Kucherak OA, Mély Y, Klymchenko AS. Solvatochromic Nile Red probes with FRET quencher reveal lipid order heterogeneity in living and apoptotic cells. ACS Chem Biol 2015; 10:1435-42. [PMID: 25710589 DOI: 10.1021/cb500922m] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Detecting and imaging lipid microdomains (rafts) in cell membranes remain a challenge despite intensive research in the field. Two types of fluorescent probes are used for this purpose: one specifically labels a given phase (liquid ordered, Lo, or liquid disordered, Ld), while the other, being environment-sensitive (solvatochromic), stains the two phases in different emission colors. Here, we combined the two approaches by designing a phase-sensitive probe of the Ld phase and a quencher of the Ld phase. The former is an analogue of the recently developed Nile Red-based probe NR12S, bearing a bulky hydrophobic chain (bNR10S), while the latter is based on Black Hole Quencher-2 designed as bNR10S (bQ10S). Fluorescence spectroscopy of large unilamellar vesicles and microscopy of giant vesicles showed that the bNR10S probe can partition specifically into the Ld phase, while bQ10S can specifically quench the NR12S probe in the Ld phase so that only its fraction in the Lo phase remains fluorescent. Thus, the toolkit of two probes with quencher can specifically target Ld and Lo phases and identify their lipid order from the emission color. Application of this toolkit in living cells (HeLa, CHO, and 293T cell lines) revealed heterogeneity in the cell plasma membranes, observed as distinct probe environments close to the Lo and Ld phases of model membranes. In HeLa cells undergoing apoptosis, our toolkit showed the formation of separate domains of the Ld-like phase in the form of blebs. The developed tools open new possibilities in lipid raft research.
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Affiliation(s)
- Rémy Kreder
- Laboratoire de Biophotonique
et Pharmacologie, UMR 7213
CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route
du Rhin, 67401 Illkirch, France
| | - Kyrylo A. Pyrshev
- Laboratoire de Biophotonique
et Pharmacologie, UMR 7213
CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route
du Rhin, 67401 Illkirch, France
- Laboratory
of Nanobiotechnologies, Department of Molecular Immunology, Palladin Institute of Biochemistry of the NASU, Kiev 01601, Ukraine
| | - Zeinab Darwich
- Laboratoire de Biophotonique
et Pharmacologie, UMR 7213
CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route
du Rhin, 67401 Illkirch, France
| | - Oleksandr A. Kucherak
- Laboratoire de Biophotonique
et Pharmacologie, UMR 7213
CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route
du Rhin, 67401 Illkirch, France
| | - Yves Mély
- Laboratoire de Biophotonique
et Pharmacologie, UMR 7213
CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route
du Rhin, 67401 Illkirch, France
| | - Andrey S. Klymchenko
- Laboratoire de Biophotonique
et Pharmacologie, UMR 7213
CNRS, Faculté de Pharmacie, Université de Strasbourg, 74, Route
du Rhin, 67401 Illkirch, France
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Radbruch H, Bremer D, Mothes R, Günther R, Rinnenthal JL, Pohlan J, Ulbricht C, Hauser AE, Niesner R. Intravital FRET: Probing Cellular and Tissue Function in Vivo. Int J Mol Sci 2015; 16:11713-27. [PMID: 26006244 PMCID: PMC4463726 DOI: 10.3390/ijms160511713] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/13/2015] [Indexed: 12/02/2022] Open
Abstract
The development of intravital Förster Resonance Energy Transfer (FRET) is required to probe cellular and tissue function in the natural context: the living organism. Only in this way can biomedicine truly comprehend pathogenesis and develop effective therapeutic strategies. Here we demonstrate and discuss the advantages and pitfalls of two strategies to quantify FRET in vivo-ratiometrically and time-resolved by fluorescence lifetime imaging-and show their concrete application in the context of neuroinflammation in adult mice.
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Affiliation(s)
- Helena Radbruch
- Neuropathology, Charité-University of Medicine, Berlin 10117, Germany.
| | - Daniel Bremer
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | - Ronja Mothes
- Neuropathology, Charité-University of Medicine, Berlin 10117, Germany.
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | - Robert Günther
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | | | - Julian Pohlan
- Neuropathology, Charité-University of Medicine, Berlin 10117, Germany.
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
| | - Carolin Ulbricht
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
- Immundynamics and Intravital Microscopy, Charité-University of Medicine, Berlin 10117, Germany.
| | - Anja E Hauser
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
- Immundynamics and Intravital Microscopy, Charité-University of Medicine, Berlin 10117, Germany.
| | - Raluca Niesner
- Germany German Rheumatism Research Center, Berlin 10117, Germany.
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31
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Melo AM, Fedorov A, Prieto M, Coutinho A. Exploring homo-FRET to quantify the oligomer stoichiometry of membrane-bound proteins involved in a cooperative partition equilibrium. Phys Chem Chem Phys 2015; 16:18105-17. [PMID: 24722583 DOI: 10.1039/c4cp00060a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The establishment of protein-protein interactions between membrane-bound proteins is associated with several biological functions and dysfunctions. Here, an analytical framework that uses energy homo transfer to directly probe quantitatively the oligomerization state of membrane-bound proteins engaged in a three-state cooperative partition is presented. Briefly, this model assumes that monomeric protein molecules partition into the bilayer surface and reversibly assemble into oligomers with k subunits. A general equation relating the overall steady-state fluorescence anisotropy of the sample to its fractional labeling was derived by considering explicitly that the anisotropy of mixed oligomers containing i-labeled monomers is inversely proportional to the number of labeled subunits per oligomer (Runnels and Scarlata limit). This method was very robust in describing the electrostatic interaction of Alexa Fluor 488 fluorescently labeled lysozyme (Lz-A488) with phosphatidylserine-containing membranes. The pronounced decrease detected in the fluorescence anisotropy of Lz-A488 always correlated with the system reaching a high membrane surface density of the protein (at a low lipid-to-protein (L/P) molar ratio). The occurrence of energy homo transfer-induced fluorescence depolarization was further confirmed by measuring the anisotropy decays of Lz-A488 under these conditions. A global analysis of the steady-state anisotropy data obtained under a wide range of experimental conditions (variable anionic lipid content of the liposomes, L/P molar ratios and protein fractional labeling) confirmed that membrane-bound Lz-A488 assembled into oligomeric complexes, possibly with a stoichiometry of k = 6 ± 1. This study illustrates that even in the presence of a coupled partition-oligomerization equilibrium, steady-state anisotropy measurements provide a simple and reliable tool to monitor the self-assembly of membrane-bound proteins.
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Affiliation(s)
- Ana M Melo
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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32
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33
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Fernandes F, Coutinho A, Prieto M, Loura LMS. Electrostatically driven lipid-protein interaction: Answers from FRET. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1837-48. [PMID: 25769805 DOI: 10.1016/j.bbamem.2015.02.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/23/2015] [Indexed: 12/13/2022]
Abstract
Electrostatics govern the association of a large number of proteins with cellular membranes. In some cases, these proteins present specialized lipid-binding modules or membrane targeting domains while in other cases association is achieved through nonspecific interaction of unstructured clusters of basic residues with negatively charged lipids. Given its spatial resolution in the nanometer range, Förster resonance energy transfer (FRET) is a powerful tool to give insight into protein-lipid interactions and provide molecular level information which is difficult to retrieve with other spectroscopic techniques. In this review we present and discuss the basic formalisms of both hetero- and homo-FRET pertinent to the most commonly encountered problems in lipid-protein interaction studies and highlight some examples of implementations of different FRET methodologies to characterize lipid/protein systems in which electrostatic interactions play a crucial role. This article is part of a Special Issue entitled: Lipid-protein interactions.
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Affiliation(s)
- Fábio Fernandes
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Ana Coutinho
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal; Dep. Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Manuel Prieto
- Centro de Química-Física Molecular and Institute of Nanoscience and Nanotechnology, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Luís M S Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal; Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal.
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34
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Gomez GA, McLachlan RW, Wu SK, Caldwell BJ, Moussa E, Verma S, Bastiani M, Priya R, Parton RG, Gaus K, Sap J, Yap AS. An RPTPα/Src family kinase/Rap1 signaling module recruits myosin IIB to support contractile tension at apical E-cadherin junctions. Mol Biol Cell 2015; 26:1249-62. [PMID: 25631816 PMCID: PMC4454173 DOI: 10.1091/mbc.e14-07-1223] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cell-cell adhesion couples the contractile cortices of epithelial cells together, generating tension to support a range of morphogenetic processes. E-cadherin adhesion plays an active role in generating junctional tension by promoting actin assembly and cortical signaling pathways that regulate myosin II. Multiple myosin II paralogues accumulate at mammalian epithelial cell-cell junctions. Earlier, we found that myosin IIA responds to Rho-ROCK signaling to support junctional tension in MCF-7 cells. Although myosin IIB is also found at the zonula adherens (ZA) in these cells, its role in junctional contractility and its mode of regulation are less well understood. We now demonstrate that myosin IIB contributes to tension at the epithelial ZA. Further, we identify a receptor type-protein tyrosine phosphatase alpha-Src family kinase-Rap1 pathway as responsible for recruiting myosin IIB to the ZA and supporting contractile tension. Overall these findings reinforce the concept that orthogonal E-cadherin-based signaling pathways recruit distinct myosin II paralogues to generate the contractile apparatus at apical epithelial junctions.
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Affiliation(s)
- Guillermo A Gomez
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Robert W McLachlan
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Selwin K Wu
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Benjamin J Caldwell
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Elliott Moussa
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Suzie Verma
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Michele Bastiani
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Rashmi Priya
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Robert G Parton
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | - Katharina Gaus
- UNSW Australia, ARC Centre of Excellence in Advanced Molecular Imaging and Australian Centre for Nanomedicine, Sydney 2052, Australia
| | - Jan Sap
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS Bâtiment Lamarck, F-75205 Paris Cedex 13, France
| | - Alpha S Yap
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
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35
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Ma L, Yang F, Zheng J. Application of fluorescence resonance energy transfer in protein studies. J Mol Struct 2014; 1077:87-100. [PMID: 25368432 DOI: 10.1016/j.molstruc.2013.12.071] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Since the physical process of fluorescence resonance energy transfer (FRET) was elucidated more than six decades ago, this peculiar fluorescence phenomenon has turned into a powerful tool for biomedical research due to its compatibility in scale with biological molecules as well as rapid developments in novel fluorophores and optical detection techniques. A wide variety of FRET approaches have been devised, each with its own advantages and drawbacks. Especially in the last decade or so, we are witnessing a flourish of FRET applications in biological investigations, many of which exemplify clever experimental design and rigorous analysis. Here we review the current stage of FRET methods development with the main focus on its applications in protein studies in biological systems, by summarizing the basic components of FRET techniques, most established quantification methods, as well as potential pitfalls, illustrated by example applications.
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Affiliation(s)
- Linlin Ma
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA ; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Fan Yang
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
| | - Jie Zheng
- Department of Physiology and Membrane Biology, University of California School of Medicine, Davis, CA 95616, USA
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36
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Devauges V, Matthews DR, Aluko J, Nedbal J, Levitt JA, Poland SP, Coban O, Weitsman G, Monypenny J, Ng T, Ameer-Beg SM. Steady-state acceptor fluorescence anisotropy imaging under evanescent excitation for visualisation of FRET at the plasma membrane. PLoS One 2014; 9:e110695. [PMID: 25360776 PMCID: PMC4215982 DOI: 10.1371/journal.pone.0110695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/15/2014] [Indexed: 11/22/2022] Open
Abstract
We present a novel imaging system combining total internal reflection fluorescence (TIRF) microscopy with measurement of steady-state acceptor fluorescence anisotropy in order to perform live cell Förster Resonance Energy Transfer (FRET) imaging at the plasma membrane. We compare directly the imaging performance of fluorescence anisotropy resolved TIRF with epifluorescence illumination. The use of high numerical aperture objective for TIRF required correction for induced depolarization factors. This arrangement enabled visualisation of conformational changes of a Raichu-Cdc42 FRET biosensor by measurement of intramolecular FRET between eGFP and mRFP1. Higher activity of the probe was found at the cell plasma membrane compared to intracellularly. Imaging fluorescence anisotropy in TIRF allowed clear differentiation of the Raichu-Cdc42 biosensor from negative control mutants. Finally, inhibition of Cdc42 was imaged dynamically in live cells, where we show temporal changes of the activity of the Raichu-Cdc42 biosensor.
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Affiliation(s)
- Viviane Devauges
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Daniel R. Matthews
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Justin Aluko
- Department of Physics, King's College London, London, United Kingdom
| | - Jakub Nedbal
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - James A. Levitt
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Simon P. Poland
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Oana Coban
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Gregory Weitsman
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - James Monypenny
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Tony Ng
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Simon M. Ameer-Beg
- Richard Dimbleby Cancer Research Laboratory, Division of Cancer Studies and Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom
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37
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Gholami Z, Hanley Q. Controlled assembly of SNAP-PNA-fluorophore systems on DNA templates to produce fluorescence resonance energy transfer. Bioconjug Chem 2014; 25:1820-8. [PMID: 25191824 DOI: 10.1021/bc500319p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The SNAP protein is a widely used self-labeling tag that can be used for tracking protein localization and trafficking in living systems. A model system providing controlled alignment of SNAP-tag units can provide a new way to study clustering of fusion proteins. In this work, fluorescent SNAP-PNA conjugates were controllably assembled on DNA frameworks, forming dimers, trimers, and tetramers. Modification of peptide nucleic acid (PNA) with the O(6)-benzyl guanine (BG) group allowed the generation of site-selective covalent links between PNA and the SNAP protein. The modified BG-PNAs were labeled with fluorescent Atto dyes and subsequently chemo-selectively conjugated to SNAP protein. Efficient assembly into dimer and oligomer forms was verified via size exclusion chromatography (SEC), electrophoresis (SDS-PAGE), and fluorescence spectroscopy. DNA-directed assembly of homo- and heterodimers of SNAP-PNA constructs induced homo- and hetero-FRET, respectively. Longer DNA scaffolds controllably aligned similar fluorescent SNAP-PNA constructs into higher oligomers exhibiting homo-FRET. The combined SEC and homo-FRET studies indicated the 1:1 and saturated assemblies of SNAP-PNA-fluorophore:DNA formed preferentially in this system. This suggested a kinetic/stoichiometric model of assembly rather than binomially distributed products. These BG-PNA-fluorophore building blocks allow facile introduction of fluorophores and/or assembly directing moieties onto any protein containing SNAP. Template-directed assembly of PNA-modified SNAP proteins may be used to investigate clustering behavior both with and without fluorescent labels, which may find use in the study of assembly processes in cells.
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Affiliation(s)
- Zahra Gholami
- School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
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38
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When one plus one does not equal two: fluorescence anisotropy in aggregates and multiply labeled proteins. Biophys J 2014; 106:1457-66. [PMID: 24703307 DOI: 10.1016/j.bpj.2014.02.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/13/2014] [Accepted: 02/25/2014] [Indexed: 12/11/2022] Open
Abstract
The behavior of fluorescence anisotropy and polarization in systems with multiple dyes is well known. Homo-FRET and its consequent energy migration cause the fluorescence anisotropy to decrease as the number of like fluorophores within energy transfer distance increases. This behavior is well understood when all subunits within a cluster are saturated with fluorophores. However, incomplete labeling as might occur from a mixture of endogenous and labeled monomer units, incomplete saturation of binding sites, or photobleaching produces stochastic mixtures. Models in widespread and longstanding use that describe these mixtures apply an assumption of equal fluorescence efficiency for all sites first stated by Weber and Daniel in 1966. The assumption states that fluorophores have the same brightness when free in solution as they do in close proximity to each other in a cluster. The assumption simplifies descriptions of anisotropy trends as the fractional labeling of the cluster changes. However, fluorophores in close proximity often exhibit nonadditivity due to such things as self-quenching behavior or exciplex formation. Therefore, the anisotropy of stochastic mixtures of fluorophore clusters of a particular size will depend on the behavior of those fluorophores in clusters. We present analytical expressions for fractionally labeled clusters exhibiting a range of behaviors, and experimental results from two systems: an assembled tetrameric cluster of fluorescent proteins and stochastically labeled bovine serum albumin containing up to 24 fluorophores. The experimental results indicate that clustered species do not follow the assumption of equal fluorescence efficiency in the systems studied with clustered fluorophores showing reduced fluorescence intensity. Application of the assumption of equal fluorescence efficiency will underpredict anisotropy and consequently underestimate cluster size in these two cases. The theoretical results indicate that careful selection of the fractional labeling in strongly quenched systems will enhance opportunities to determine cluster sizes, making accessible larger clusters than are currently considered possible.
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Koskinen M, Hotulainen P. Measuring F-actin properties in dendritic spines. Front Neuroanat 2014; 8:74. [PMID: 25140131 PMCID: PMC4122166 DOI: 10.3389/fnana.2014.00074] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/16/2014] [Indexed: 12/28/2022] Open
Abstract
During the last decade, numerous studies have demonstrated that the actin cytoskeleton plays a pivotal role in the control of dendritic spine shape. Synaptic stimulation rapidly changes the actin dynamics and many actin regulators have been shown to play roles in neuron functionality. Accordingly, defects in the regulation of the actin cytoskeleton in neurons have been implicated in memory disorders. Due to the small size of spines, it is difficult to detect changes in the actin structures in dendritic spines by conventional light microscopy imaging. Instead, to know how tightly actin filaments are bundled together, and how fast the filaments turnover, we need to use advanced microscopy techniques, such as fluorescence recovery after photobleaching (FRAP), photoactivatable green fluorescent protein (PAGFP) fluorescence decay and fluorescence anisotropy. Fluorescence anisotropy, which measures the Förster resonance energy transfer (FRET) between two GFP fluorophores, has been proposed as a method to measure the level of actin polymerization. Here, we propose a novel idea that fluorescence anisotropy could be more suitable to study the level of actin filament bundling instead of actin polymerization. We validate the method in U2OS cell line where the actin structures can be clearly distinguished and apply to analyze how actin filament organization in dendritic spines changes during neuronal maturation. In addition to fluorescence anisotropy validation, we take a critical look at the properties and limitations of FRAP and PAGFP fluorescence decay methods and offer our proposals for the analysis methods for these approaches. These three methods complement each other, each providing additional information about actin dynamics and organization in dendritic spines.
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Affiliation(s)
- Mikko Koskinen
- Neuroscience Center, University of Helsinki Helsinki, Finland
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40
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Lei C, Huang Y, Nie Z, Hu J, Li L, Lu G, Han Y, Yao S. A Supercharged Fluorescent Protein as a Versatile Probe for Homogeneous DNA Detection and Methylation Analysis. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403615] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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41
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Lei C, Huang Y, Nie Z, Hu J, Li L, Lu G, Han Y, Yao S. A Supercharged Fluorescent Protein as a Versatile Probe for Homogeneous DNA Detection and Methylation Analysis. Angew Chem Int Ed Engl 2014; 53:8358-62. [DOI: 10.1002/anie.201403615] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Indexed: 01/19/2023]
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42
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Brooks AJ, Dai W, O'Mara ML, Abankwa D, Chhabra Y, Pelekanos RA, Gardon O, Tunny KA, Blucher KM, Morton CJ, Parker MW, Sierecki E, Gambin Y, Gomez GA, Alexandrov K, Wilson IA, Doxastakis M, Mark AE, Waters MJ. Mechanism of activation of protein kinase JAK2 by the growth hormone receptor. Science 2014; 344:1249783. [PMID: 24833397 DOI: 10.1126/science.1249783] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Signaling from JAK (Janus kinase) protein kinases to STAT (signal transducers and activators of transcription) transcription factors is key to many aspects of biology and medicine, yet the mechanism by which cytokine receptors initiate signaling is enigmatic. We present a complete mechanistic model for activation of receptor-bound JAK2, based on an archetypal cytokine receptor, the growth hormone receptor. For this, we used fluorescence resonance energy transfer to monitor positioning of the JAK2 binding motif in the receptor dimer, substitution of the receptor extracellular domains with Jun zippers to control the position of its transmembrane (TM) helices, atomistic modeling of TM helix movements, and docking of the crystal structures of the JAK2 kinase and its inhibitory pseudokinase domain with an opposing kinase-pseudokinase domain pair. Activation of the receptor dimer induced a separation of its JAK2 binding motifs, driven by a ligand-induced transition from a parallel TM helix pair to a left-handed crossover arrangement. This separation leads to removal of the pseudokinase domain from the kinase domain of the partner JAK2 and pairing of the two kinase domains, facilitating trans-activation. This model may well generalize to other class I cytokine receptors.
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Affiliation(s)
- Andrew J Brooks
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia.
| | - Wei Dai
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA
| | - Megan L O'Mara
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia
| | - Daniel Abankwa
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Yash Chhabra
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Rebecca A Pelekanos
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Olivier Gardon
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Kathryn A Tunny
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Kristopher M Blucher
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Craig J Morton
- Biota Structural Biology Laboratory and Australian Cancer Research Foundation (ACRF) Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Michael W Parker
- Biota Structural Biology Laboratory and Australian Cancer Research Foundation (ACRF) Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia. Department of Biochemistry and Molecular Biology and Bio21 Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Emma Sierecki
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Yann Gambin
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Guillermo A Gomez
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Kirill Alexandrov
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia
| | - Ian A Wilson
- Scripps Research Institute, La Jolla, CA 92037, USA
| | - Manolis Doxastakis
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77004, USA
| | - Alan E Mark
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia. The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia
| | - Michael J Waters
- The University of Queensland, Institute for Molecular Bioscience (IMB), St Lucia, Queensland 4072, Australia.
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43
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Valley CC, Lidke KA, Lidke DS. The spatiotemporal organization of ErbB receptors: insights from microscopy. Cold Spring Harb Perspect Biol 2014; 6:cshperspect.a020735. [PMID: 24370847 DOI: 10.1101/cshperspect.a020735] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Signal transduction is regulated by protein-protein interactions. In the case of the ErbB family of receptor tyrosine kinases (RTKs), the precise nature of these interactions remains a topic of debate. In this review, we describe state-of-the-art imaging techniques that are providing new details into receptor dynamics, clustering, and interactions. We present the general principles of these techniques, their limitations, and the unique observations they provide about ErbB spatiotemporal organization.
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Affiliation(s)
- Christopher C Valley
- Department of Pathology and the Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico 87131
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Abstract
Fluorescence can be characterized by its intensity, position, wavelength, lifetime, and polarization. The more of these features are acquired in a single measurement, the more can be learned about the sample, i.e., the microenvironment of the fluorescence probe. Polarization-resolved fluorescence lifetime imaging-time-resolved fluorescence anisotropy imaging, TR-FAIM-allows mapping of viscosity or binding or of homo-FRET which can indicate dimerization or generally oligomerization.
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Affiliation(s)
- Klaus Suhling
- Department of Physics, King's College London, London, UK
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Hu H, Liu S, Li D, Wang M, Moats R, Shan H, Conti PS, Li Z. The synthesis of lanthanide-doped GdVO4ultrathin nanosheets with great optical and paramagnetic properties for FRET biodetection and in vivo MR imaging. J Mater Chem B 2014; 2:3998-4007. [DOI: 10.1039/c4tb00144c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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46
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Crosby KC, Postma M, Hink MA, Zeelenberg CHC, Adjobo-Hermans MJW, Gadella TWJ. Quantitative analysis of self-association and mobility of annexin A4 at the plasma membrane. Biophys J 2013; 104:1875-85. [PMID: 23663830 DOI: 10.1016/j.bpj.2013.02.057] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/19/2013] [Accepted: 02/27/2013] [Indexed: 11/19/2022] Open
Abstract
Annexins, found in most eukaryotic species, are cytosolic proteins that are able to bind negatively-charged phospholipids in a calcium-dependent manner. Annexin A4 (AnxA4) has been implicated in diverse cellular processes, including the regulation of exocytosis and ion-transport; however, its precise mechanistic role is not fully understood. AnxA4 has been shown to aggregate on lipid layers upon Ca(2+) binding in vitro, a characteristic that may be critical for its function. We have utilized advanced fluorescence microscopy to discern details on the mobility and self-assembly of AnxA4 after Ca(2+) influx at the plasma membrane in living cells. Total internal reflection microscopy in combination with Förster resonance energy transfer reveals that there is a delay between initial plasma membrane binding and the beginning of self-assembly and this process continues after the cytoplasmic pool has completely relocated. Number-and-brightness analysis suggests that the predominant membrane bound mobile form of the protein is trimeric. There also exists a pool of AnxA4 that forms highly immobile aggregates at the membrane. Fluorescence recovery after photobleaching suggests that the relative proportion of these two forms varies and is correlated with membrane morphology.
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Affiliation(s)
- Kevin C Crosby
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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Heukers R, Vermeulen JF, Fereidouni F, Bader AN, Voortman J, Roovers RC, Gerritsen HC, van Bergen En Henegouwen PMP. Endocytosis of EGFR requires its kinase activity and N-terminal transmembrane dimerization motif. J Cell Sci 2013; 126:4900-12. [PMID: 23943881 DOI: 10.1242/jcs.128611] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
EGFR signaling is attenuated by endocytosis and degradation of receptor-ligand complexes in lysosomes. Endocytosis of EGFR is known to be regulated by multiple post-translational modifications. The observation that prevention of these modifications does not block endocytosis completely, suggests the involvement of other mechanism(s). Recently, receptor clustering has been suggested to induce internalization of multiple types of membrane receptors. However, the mechanism of clustering-induced internalization remains unknown. We have used biparatopic antibody fragments from llama (VHHs) to induce EGFR clustering without stimulating tyrosine kinase activity. Using this approach, we have found an essential role for the N-terminal GG4-like dimerization motif in the transmembrane domain (TMD) for clustering-induced internalization. Moreover, conventional EGF-induced receptor internalization depends exclusively on this TMD dimerization and kinase activity. Mutations in this dimerization motif eventually lead to reduced EGFR degradation and sustained signaling. We propose a novel role for the TMD dimerization motif in the negative-feedback control of EGFR. The widely conserved nature of GG4-like dimerization motifs in transmembrane proteins suggests a general role for these motifs in clustering-induced internalization.
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Affiliation(s)
- Raimond Heukers
- Cell Biology, Department of Biology, Science Faculty, Utrecht University, 3584 CH Utrecht, The Netherlands
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Lozano MM, Liu Z, Sunnick E, Janshoff A, Kumar K, Boxer SG. Colocalization of the ganglioside G(M1) and cholesterol detected by secondary ion mass spectrometry. J Am Chem Soc 2013; 135:5620-30. [PMID: 23514537 PMCID: PMC3639293 DOI: 10.1021/ja310831m] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The characterization of the lateral organization of components in biological membranes and the evolution of this arrangement in response to external triggers remain a major challenge. The concept of lipid rafts is widely invoked; however, direct evidence of the existence of these ephemeral entities remains elusive. We report here the use of secondary ion mass spectrometry (SIMS) to image the cholesterol-dependent cohesive phase separation of the ganglioside GM1 into nano- and microscale assemblies in a canonical lipid raft composition of lipids. This assembly of domains was interrogated in a model membrane system composed of palmitoyl sphingomyelin (PSM), cholesterol, and an unsaturated lipid (dioleoylphosphatidylcholine, DOPC). Orthogonal isotopic labeling of every lipid bilayer component and monofluorination of GM1 allowed generation of molecule specific images using a NanoSIMS. Simultaneous detection of six different ion species in SIMS, including secondary electrons, was used to generate ion ratio images whose signal intensity values could be correlated to composition through the use of calibration curves from standard samples. Images of this system provide the first direct, molecule specific, visual evidence for the colocalization of cholesterol and GM1 in supported lipid bilayers and further indicate the presence of three compositionally distinct phases: (1) the interdomain region; (2) micrometer-scale domains (d > 3 μm); (3) nanometer-scale domains (d = 100 nm to 1 μm) localized within the micrometer-scale domains and the interdomain region. PSM-rich, nanometer-scale domains prefer to partition within the more ordered, cholesterol-rich/DOPC-poor/GM1-rich micrometer-scale phase, while GM1-rich, nanometer-scale domains prefer to partition within the surrounding, disordered, cholesterol-poor/PSM-rich/DOPC-rich interdomain phase.
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Affiliation(s)
- Mónica M. Lozano
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
| | - Zhao Liu
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155-5813
| | - Eva Sunnick
- Institute of Physical Chemistry, University of Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Andreas Janshoff
- Institute of Physical Chemistry, University of Göttingen, Tammannstr. 6, 37077 Göttingen, Germany
| | - Krishna Kumar
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155-5813
- Cancer Center, Tufts Medical Center, Boston, Massachusetts 02110
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5080
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49
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A novel homogeneous immunoassay for anthrax detection based on the AlphaLISA method: detection of B. anthracis spores and protective antigen (PA) in complex samples. Anal Bioanal Chem 2013; 405:3965-72. [DOI: 10.1007/s00216-013-6752-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 12/17/2012] [Accepted: 01/16/2013] [Indexed: 02/07/2023]
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50
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Moderation of Arabidopsis root stemness by CLAVATA1 and ARABIDOPSIS CRINKLY4 receptor kinase complexes. Curr Biol 2013; 23:362-71. [PMID: 23394827 DOI: 10.1016/j.cub.2013.01.045] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 12/21/2012] [Accepted: 01/15/2013] [Indexed: 11/20/2022]
Abstract
BACKGROUND The root system of higher plants originates from the activity of a root meristem, which comprises a group of highly specialized and long-lasting stem cells. Their maintenance and number is controlled by the quiescent center (QC) cells and by feedback signaling from differentiated cells. Root meristems may have evolved from structurally distinct shoot meristems; however, no common player acting in stemness control has been found so far. RESULTS We show that CLAVATA1 (CLV1), a key receptor kinase in shoot stemness maintenance, performs a similar but distinct role in root meristems. We report that CLV1 is signaling, activated by the peptide ligand CLAVATA3/EMBRYO SURROUNDING REGION40 (CLE40), together with the receptor kinase ARABIDOPSIS CRINKLY4 (ACR4) to restrict root stemness. Both CLV1 and ACR4 overlap in their expression domains in the distal root meristem and localize to the plasma membrane (PM) and plasmodesmata (PDs), where ACR4 preferentially accumulates. Using multiparameter fluorescence image spectroscopy (MFIS), we show that CLV1 and ACR4 can form homo- and heteromeric complexes that differ in their composition depending on their subcellular localization. CONCLUSIONS We hypothesize that these homo- and heteromeric complexes may differentially regulate distal root meristem maintenance. We conclude that essential components of the ancestral shoot stemness regulatory system also act in the root and that the specific interaction of CLV1 with ACR4 serves to moderate and control stemness homeostasis in the root meristem. The structural differences between these two meristem types may have necessitated this recruitment of ACR4 for signaling by CLV1.
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