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Putyrski M, Vakhrusheva O, Bonn F, Guntur S, Vorobyov A, Brandts C, Dikic I, Ernst A. Disrupting the LC3 Interaction Region (LIR) Binding of Selective Autophagy Receptors Sensitizes AML Cell Lines to Cytarabine. Front Cell Dev Biol 2020; 8:208. [PMID: 32296703 PMCID: PMC7137635 DOI: 10.3389/fcell.2020.00208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
Short linear motifs (SLiMs) located in disordered regions of multidomain proteins are important for the organization of protein-protein interaction networks. By dynamic association with their binding partners, SLiMs enable assembly of multiprotein complexes, pivotal for the regulation of various aspects of cell biology in higher organisms. Despite their importance, there is a paucity of molecular tools to study SLiMs of endogenous proteins in live cells. LC3 interacting regions (LIRs), being quintessential for orchestrating diverse stages of autophagy, are a prominent example of SLiMs and mediate binding to the ubiquitin-like LC3/GABARAP family of proteins. The role of LIRs ranges from the posttranslational processing of their binding partners at early stages of autophagy to the binding of selective autophagy receptors (SARs) to the autophagosome. In order to generate tools to study LIRs in cells, we engineered high affinity binders of LIR motifs of three archetypical SARs: OPTN, p62, and NDP52. In an array of in vitro and cellular assays, the engineered binders were shown to have greatly improved affinity and specificity when compared with the endogenous LC3/GABARAP family of proteins, thus providing a unique possibility for modulating LIR interactions in living systems. We exploited these novel tools to study the impact of LIR inhibition on the fitness and the responsiveness to cytarabine treatment of THP-1 cells - a model for studying acute myeloid leukemia (AML). Our results demonstrate that inhibition of LIR of a single autophagy receptor is insufficient to sensitize the cells to cytarabine, while simultaneous inhibition of three LIR motifs in three distinct SARs reduces the IC50 of the chemotherapeutic.
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Affiliation(s)
- Mateusz Putyrski
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Olesya Vakhrusheva
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Suchithra Guntur
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Andrew Vorobyov
- Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Christian Brandts
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany.,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany.,University Cancer Center Frankfurt, Goethe-University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Andreas Ernst
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
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Wang S, Ding M, Xue B, Hou Y, Sun Y. Live Cell Visualization of Multiple Protein-Protein Interactions with BiFC Rainbow. ACS Chem Biol 2018; 13:1180-1188. [PMID: 29283249 DOI: 10.1021/acschembio.7b00931] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As one of the most powerful tools to visualize PPIs in living cells, bimolecular fluorescence complementation (BiFC) has gained great advancement during recent years, including deep tissue imaging with far-red or near-infrared fluorescent proteins or super-resolution imaging with photochromic fluorescent proteins. However, little progress has been made toward simultaneous detection and visualization of multiple PPIs in the same cell, mainly due to the spectral crosstalk. In this report, we developed novel BiFC assays based on large-Stokes-shift fluorescent proteins (LSS-FPs) to detect and visualize multiple PPIs in living cells. With the large excitation/emission spectral separation, LSS-FPs can be imaged together with normal Stokes shift fluorescent proteins to realize multicolor BiFC imaging using a simple illumination scheme. We also further demonstrated BiFC rainbow combining newly developed BiFC assays with previously established mCerulean/mVenus-based BiFC assays to achieve detection and visualization of four PPI pairs in the same cell. Additionally, we prove that with the complete spectral separation of mT-Sapphire and CyOFP1, LSS-FP-based BiFC assays can be readily combined with intensity-based FRET measurement to detect ternary protein complex formation with minimal spectral crosstalk. Thus, our newly developed LSS-FP-based BiFC assays not only expand the fluorescent protein toolbox available for BiFC but also facilitate the detection and visualization of multiple protein complex interactions in living cells.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Miao Ding
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingping Hou
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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Stolz A, Putyrski M, Kutle I, Huber J, Wang C, Major V, Sidhu SS, Youle RJ, Rogov VV, Dötsch V, Ernst A, Dikic I. Fluorescence-based ATG8 sensors monitor localization and function of LC3/GABARAP proteins. EMBO J 2016; 36:549-564. [PMID: 28028054 DOI: 10.15252/embj.201695063] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/23/2016] [Accepted: 11/27/2016] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a cellular surveillance pathway that balances metabolic and energy resources and transports specific cargos, including damaged mitochondria, other broken organelles, or pathogens for degradation to the lysosome. Central components of autophagosomal biogenesis are six members of the LC3 and GABARAP family of ubiquitin-like proteins (mATG8s). We used phage display to isolate peptides that possess bona fide LIR (LC3-interacting region) properties and are selective for individual mATG8 isoforms. Sensitivity of the developed sensors was optimized by multiplication, charge distribution, and fusion with a membrane recruitment (FYVE) or an oligomerization (PB1) domain. We demonstrate the use of the engineered peptides as intracellular sensors that recognize specifically GABARAP, GABL1, GABL2, and LC3C, as well as a bispecific sensor for LC3A and LC3B. By using an LC3C-specific sensor, we were able to monitor recruitment of endogenous LC3C to Salmonella during xenophagy, as well as to mitochondria during mitophagy. The sensors are general tools to monitor the fate of mATG8s and will be valuable in decoding the biological functions of the individual LC3/GABARAPs.
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Affiliation(s)
- Alexandra Stolz
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
| | - Mateusz Putyrski
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - Ivana Kutle
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Jessica Huber
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Chunxin Wang
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Viktória Major
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Richard J Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, Germany
| | - Andreas Ernst
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II Goethe University, Frankfurt am Main, Germany .,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
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Govor IV, Tatarets AL, Obukhova OM, Terpetschnig EA, Gellerman G, Patsenker LD. Tracing the conformational changes in BSA using FRET with environmentally-sensitive squaraine probes. Methods Appl Fluoresc 2016; 4:024007. [DOI: 10.1088/2050-6120/4/2/024007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Goedhart J, van Unen J, Adjobo-Hermans MJW, Gadella TWJ. Signaling efficiency of Gαq through its effectors p63RhoGEF and GEFT depends on their subcellular location. Sci Rep 2014; 3:2284. [PMID: 23884432 PMCID: PMC3722567 DOI: 10.1038/srep02284] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/10/2013] [Indexed: 02/02/2023] Open
Abstract
The p63RhoGEF and GEFT proteins are encoded by the same gene and both members of the Dbl family of guanine nucleotide exchange factors. These proteins can be activated by the heterotrimeric G-protein subunit Gαq. We show that p63RhoGEF is located at the plasma membrane, whereas GEFT is confined to the cytoplasm. Live-cell imaging studies yielded quantitative information on diffusion coefficients, association rates and encounter times of GEFT and p63RhoGEF. Calcium signaling was examined as a measure of the signal transmission, revealing more efficient signaling through the membrane-associated p63RhoGEF. A rapamycin dependent recruitment system was used to dynamically alter the subcellular location and concentration of GEFT, showing efficient signaling through GEFT only upon membrane recruitment. Together, our results show efficient signal transmission through membrane located effectors, and highlight a role for increased concentration rather than increased encounter times due to membrane localization in the Gαq mediated pathways to p63RhoGEF and PLCβ.
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Affiliation(s)
- Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, P.O. Box 94215, NL-1090 GE Amsterdam, The Netherlands.
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Bojarski P, Kulak L, Walczewska-Szewc K, Synak A, Marzullo VM, Luini A, D'Auria S. Long-distance FRET analysis: a Monte Carlo simulation study. J Phys Chem B 2011; 115:10120-5. [PMID: 21780798 DOI: 10.1021/jp202152m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A new method for extending the utilizable range of Förster resonance energy transfer (FRET) is proposed and tested by the Monte Carlo technique. The obtained results indicate that the efficiency of FRET can be significantly enhanced at a given distance if the energy transfer takes place toward multiple acceptors that are closely located on a macromolecule instead of a single acceptor molecule as it is currently used in FRET analysis. On the other hand, reasonable FRET efficiency can be obtained at significantly longer distances than in the case of a single acceptor. Randomly distributed and parallel orientated acceptor transition moments with respect to the transition moment of the donor molecule have been analyzed as two extreme cases. As expected, a parallel orientation of donor and acceptor transition moments results in a more efficient excitation energy transfer. This finding could be used to directly reveal the assembly/deassembly of large protein complexes in a cell by fluorescence microscopy.
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Affiliation(s)
- Piotr Bojarski
- Molecular Spectroscopy Division, Institute of Experimental Physics, University of Gdańsk, Wita Stwosza 57, 80-952 Gdańsk, Poland.
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Piljić A, de Diego I, Wilmanns M, Schultz C. Rapid development of genetically encoded FRET reporters. ACS Chem Biol 2011; 6:685-91. [PMID: 21506563 DOI: 10.1021/cb100402n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To meet the demand on genetically encoded reporter molecules for live cell imaging, we introduce a new facile combined cloning and FRET reporter analysis strategy. The versatile and fully orthogonal cloning approach involves a set of up to 36 vectors featuring a variety of fluorescent protein FRET pairs and different length linkers. The construct set was successfully applied to two calmodulin-binding proteins, the death-associated protein kinase 1 (DAPK1) and calcium/calmodulin-dependent protein kinase II α (Camk2a). Clone analysis and reporter validation was performed by printing plasmid DNA arrays and subsequent semiautomated microscopy of reversely transfected cells. Characterization of the best performing DAPK1 and Camk2a reporters revealed significant differences in translating calcium signals into kinase responses despite the close functional and structural similarity.
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Affiliation(s)
- Alen Piljić
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Iñaki de Diego
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology & Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Lee KB, Hwang JM, Choi IS, Rho J, Choi JS, Kim GH, Kim SI, Kim S, Lee ZW. Direct Monitoring of the Inhibition of Protein-Protein Interactions in Cells by Translocation of PKCδ Fusion Proteins. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005333] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Lee KB, Hwang JM, Choi IS, Rho J, Choi JS, Kim GH, Kim SI, Kim S, Lee ZW. Direct Monitoring of the Inhibition of Protein-Protein Interactions in Cells by Translocation of PKCδ Fusion Proteins. Angew Chem Int Ed Engl 2011; 50:1314-7. [DOI: 10.1002/anie.201005333] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Indexed: 11/09/2022]
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Time-resolved luminescence resonance energy transfer imaging of protein-protein interactions in living cells. Proc Natl Acad Sci U S A 2010; 107:13582-7. [PMID: 20643966 DOI: 10.1073/pnas.1002025107] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Förster resonance energy transfer (FRET) with fluorescent proteins permits high spatial resolution imaging of protein-protein interactions in living cells. However, substantial non-FRET fluorescence background can obscure small FRET signals, making many potential interactions unobservable by conventional FRET techniques. Here we demonstrate time-resolved microscopy of luminescence resonance energy transfer (LRET) for live-cell imaging of protein-protein interactions. A luminescent terbium complex, TMP-Lumi4, was introduced into cultured cells using two methods: (i) osmotic lysis of pinocytic vesicles; and (ii) reversible membrane permeabilization with streptolysin O. Upon intracellular delivery, the complex was observed to bind specifically and stably to transgenically expressed Escherichia coli dihydrofolate reductase (eDHFR) fusion proteins. LRET between the eDHFR-bound terbium complex and green fluorescent protein (GFP) was detected as long-lifetime, sensitized GFP emission. Background signals from cellular autofluorescence and directly excited GFP fluorescence were effectively eliminated by imposing a time delay (10 micros) between excitation and detection. Background elimination made it possible to detect interactions between the first PDZ domain of ZO-1 (fused to eDHFR) and the C-terminal YV motif of claudin-1 (fused to GFP) in single microscope images at subsecond time scales. We observed a highly significant (P<10(-6)), six-fold difference between the mean, donor-normalized LRET signal from cells expressing interacting fusion proteins and from control cells expressing noninteracting mutants. The results show that time-resolved LRET microscopy with a selectively targeted, luminescent terbium protein label affords improved speed and sensitivity over conventional FRET methods for a variety of live-cell imaging and screening applications.
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11
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Schultz C. Fluorescent revelations. ACTA ACUST UNITED AC 2009; 16:107-11. [PMID: 19246000 DOI: 10.1016/j.chembiol.2009.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2009] [Revised: 02/03/2009] [Accepted: 02/04/2009] [Indexed: 12/22/2022]
Abstract
A fluorescent protein from jellyfish changed the way life science research is performed today. Its discovery, the first expression in an animal, the determination of its structure, the details of the mechanism behind the fluorescence, and diversification of the fluorescent properties has made green fluorescent protein a unique tool in the biological sciences, and the scientists that made key contributions to these developments were awarded the 2008 Nobel Prize in Chemistry.
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Affiliation(s)
- Carsten Schultz
- European Molecular Biology Laboratory, Cell Biology and Biophysical Instrumentation Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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