1
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Loya-Lopez SI, Allen HN, Duran P, Calderon-Rivera A, Gomez K, Kumar U, Shields R, Zeng R, Dwivedi A, Saurabh S, Korczeniewska OA, Khanna R. Intranasal CRMP2-Ubc9 inhibitor regulates Na V 1.7 to alleviate trigeminal neuropathic pain. Pain 2024; 165:573-588. [PMID: 37751532 PMCID: PMC10922202 DOI: 10.1097/j.pain.0000000000003053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/25/2023] [Indexed: 09/28/2023]
Abstract
ABSTRACT Dysregulation of voltage-gated sodium Na V 1.7 channels in sensory neurons contributes to chronic pain conditions, including trigeminal neuropathic pain. We previously reported that chronic pain results in part from increased SUMOylation of collapsin response mediator protein 2 (CRMP2), leading to an increased CRMP2/Na V 1.7 interaction and increased functional activity of Na V 1.7. Targeting this feed-forward regulation, we developed compound 194 , which inhibits CRMP2 SUMOylation mediated by the SUMO-conjugating enzyme Ubc9. We further demonstrated that 194 effectively reduces the functional activity of Na V 1.7 channels in dorsal root ganglia neurons and alleviated inflammatory and neuropathic pain. Here, we used a comprehensive array of approaches, encompassing biochemical, pharmacological, genetic, electrophysiological, and behavioral analyses, to assess the functional implications of Na V 1.7 regulation by CRMP2 in trigeminal ganglia (TG) neurons. We confirmed the expression of Scn9a , Dpysl2 , and UBE2I within TG neurons. Furthermore, we found an interaction between CRMP2 and Na V 1.7, with CRMP2 being SUMOylated in these sensory ganglia. Disrupting CRMP2 SUMOylation with compound 194 uncoupled the CRMP2/Na V 1.7 interaction, impeded Na V 1.7 diffusion on the plasma membrane, and subsequently diminished Na V 1.7 activity. Compound 194 also led to a reduction in TG neuron excitability. Finally, when intranasally administered to rats with chronic constriction injury of the infraorbital nerve, 194 significantly decreased nociceptive behaviors. Collectively, our findings underscore the critical role of CRMP2 in regulating Na V 1.7 within TG neurons, emphasizing the importance of this indirect modulation in trigeminal neuropathic pain.
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Affiliation(s)
- Santiago I. Loya-Lopez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Heather N. Allen
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Paz Duran
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Aida Calderon-Rivera
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Kimberly Gomez
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
| | - Upasana Kumar
- Center for Orofacial Pain and Temporomandibular Disorders, Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ 07101, United States of America
| | - Rory Shields
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ 07101, United States of America
| | - Rui Zeng
- Department of Chemistry, College of Arts and Sciences, New York University, 100 Washington Square East, New York, NY 10003, United States of America
| | - Akshat Dwivedi
- Department of Chemistry, College of Arts and Sciences, New York University, 100 Washington Square East, New York, NY 10003, United States of America
| | - Saumya Saurabh
- Department of Chemistry, College of Arts and Sciences, New York University, 100 Washington Square East, New York, NY 10003, United States of America
| | - Olga A. Korczeniewska
- Center for Orofacial Pain and Temporomandibular Disorders, Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ 07101, United States of America
- Rutgers School of Graduate Studies, Newark Health Science Campus, Newark, NJ 07101, United States of America
| | - Rajesh Khanna
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, New York, United States of America
- NYU Pain Research Center, 433 First Avenue, New York, NY 10010, United States of America
- Department of Neuroscience and Physiology and Neuroscience Institute, School of Medicine, New York University, New York, NY, 10010, USA
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2
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Loya-Lopez SI, Allen HN, Duran P, Calderon-Rivera A, Gomez K, Kumar U, Shields R, Zeng R, Dwivedi A, Saurabh S, Korczeniewska OA, Khanna R. Intranasal CRMP2-Ubc9 Inhibitor Regulates Na V 1.7 to Alleviate Trigeminal Neuropathic Pain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.16.549195. [PMID: 37502910 PMCID: PMC10370107 DOI: 10.1101/2023.07.16.549195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Dysregulation of voltage-gated sodium Na V 1.7 channels in sensory neurons contributes to chronic pain conditions, including trigeminal neuropathic pain. We previously reported that chronic pain results in part from increased SUMOylation of collapsin response mediator protein 2 (CRMP2), leading to an increased CRMP2/Na V 1.7 interaction and increased functional activity of Na V 1.7. Targeting this feed-forward regulation, we developed compound 194 , which inhibits CRMP2 SUMOylation mediated by the SUMO-conjugating enzyme Ubc9. We further demonstrated that 194 effectively reduces the functional activity of Na V 1.7 channels in dorsal root ganglia neurons and alleviated inflammatory and neuropathic pain. Here, we employed a comprehensive array of investigative approaches, encompassing biochemical, pharmacological, genetic, electrophysiological, and behavioral analyses, to assess the functional implications of Na V 1.7 regulation by CRMP2 in trigeminal ganglia (TG) neurons. We confirmed the expression of Scn9a , Dpysl2 , and UBE2I within TG neurons. Furthermore, we found an interaction between CRMP2 and Na V 1.7, with CRMP2 being SUMOylated in these sensory ganglia. Disrupting CRMP2 SUMOylation with compound 194 uncoupled the CRMP2/Na V 1.7 interaction, impeded Na V 1.7 diffusion on the plasma membrane, and subsequently diminished Na V 1.7 activity. Compound 194 also led to a reduction in TG neuron excitability. Finally, when intranasally administered to rats with chronic constriction injury of the infraorbital nerve (CCI-ION), 194 significantly decreased nociceptive behaviors. Collectively, our findings underscore the critical role of CRMP2 in regulating Na V 1.7 within TG neurons, emphasizing the importance of this indirect modulation in trigeminal neuropathic pain.
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3
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Deng Z, Li L, Jia H, Li NF, He J, Li MD, Phillips DL, Li Y. Insights into the Photodynamics of Fluorescence Emission and Singlet Oxygen Generation of Fluorogen Activating Protein-Malachite Green Systems. Chemistry 2023; 29:e202203684. [PMID: 36453719 DOI: 10.1002/chem.202203684] [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: 11/25/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022]
Abstract
The self-assembled fluorogen activating protein (FAP)-malachite green (MG) complex is a well-established protein-ligand system, which can realize binding-caused fluorescence turn-on of MG and singlet oxygen (1 O2 ) generation by MG iodination. To clarify the mechanism of fluorescence activation and 1 O2 generation, the photodynamics of different halogen-substituted MG derivatives and their corresponding FAP-MG complexes were studied by femtosecond transient absorption spectroscopy and theoretical computations. The results show that the rotation of MG is restricted by FAP binding, which prevents a rapid internal conversion to allow a longer lifetime for the excited MG to undergo fluorescence emission and intersystem crossing. Moreover, these FAP-MG complexes exhibit notably varied fluorescence quantum yields (ΦFL ) and 1 O2 yields. The study on the decay pathways indicates that such an anti-heavy atom effect predominately stems from the lifetimes of the excited-state species. The photodynamic mechanism study here will lead to more advanced FAP-MG systems with high spatiotemporal resolution.
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Affiliation(s)
- Ziqi Deng
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Lan Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Han Jia
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Nga-Fong Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jiaxing He
- Department of Chemistry and Key Laboratory for Preparation and, Application of Ordered Structure Materials of Guangdong Providence, Shantou University, Shantou, 515063, Guangdong, China
| | - Ming-De Li
- Department of Chemistry and Key Laboratory for Preparation and, Application of Ordered Structure Materials of Guangdong Providence, Shantou University, Shantou, 515063, Guangdong, China
| | - David Lee Phillips
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ying Li
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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4
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Kompa J, Bruins J, Glogger M, Wilhelm J, Frei MS, Tarnawski M, D’Este E, Heilemann M, Hiblot J, Johnsson K. Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy. J Am Chem Soc 2023; 145:3075-3083. [PMID: 36716211 PMCID: PMC9912333 DOI: 10.1021/jacs.2c11969] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors. In stimulated emission depletion (STED) microscopy, probe exchange of xHTLs allows imaging with reduced photobleaching as compared to covalent HaloTag labeling. Transient binding of fluorogenic xHTLs to HaloTag fusion proteins enables points accumulation for imaging in nanoscale topography (PAINT) and MINFLUX microscopy. We furthermore introduce pairs of xHTLs and HaloTag mutants for dual-color PAINT and STED microscopy. xHTLs thus open up new possibilities in imaging across microscopy platforms for a widely used labeling approach.
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Affiliation(s)
- Julian Kompa
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Jorick Bruins
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Marius Glogger
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue
Str. 7, Frankfurt 60438, Germany
| | - Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Michelle S. Frei
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany,Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Elisa D’Este
- Optical
Microscopy Facility, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue
Str. 7, Frankfurt 60438, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany,
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany,Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland,
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5
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He J, Zhou Y, Liu Y, Guo R, Jiang J, Bruchez MP. Fluorogen-Activating-Protein-Loaded Tantalum Oxide Nanoshells for in Vivo On-Demand Fluorescence/Photoacoustic Imaging. ACS APPLIED BIO MATERIALS 2022; 5:1057-1063. [PMID: 35191667 DOI: 10.1021/acsabm.1c01113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optical imaging of targeted compartments within living animals has been widely adopted in many research areas. In particular, various fluorescence-based probes and emerged photoacoustic molecules that enable sensitive and specific imaging through tissue have greatly advanced clinically relevant studies. However, delivery and signal penetration have placed requirements on the performance of conventional optical probes. Here, we use hallow tantalum oxide (TaOx) nanoparticles to enclose fluorogen-activating protein (FAP) for the in vivo fluorescence and photoacoustic imaging of cancer cells. We found that the TaOx shell can provide a natural cover for the enclosed fluorogen/FAP complexes, protecting them from photobleaching and common biodegradation. Moreover, we have developed a near-infrared excitable tetrafluorinated photoacoustic fluorogen for the specific and persistent photoacoustic imaging of tumors. We believe that this enclosing and delivery strategy of optical biomolecules will be an attractive alternative for bioimaging.
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Affiliation(s)
- Jianjun He
- College of Biology, Hunan University, Changsha 410082, China
| | - Yancen Zhou
- College of Biology, Hunan University, Changsha 410082, China
| | - Yinxia Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Rui Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Department of Biological Sciences, Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15217, United States
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6
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Saurabh S, Chong TN, Bayas C, Dahlberg PD, Cartwright HN, Moerner WE, Shapiro L. ATP-responsive biomolecular condensates tune bacterial kinase signaling. SCIENCE ADVANCES 2022; 8:eabm6570. [PMID: 35171683 PMCID: PMC8849385 DOI: 10.1126/sciadv.abm6570] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Biomolecular condensates formed via liquid-liquid phase separation enable spatial and temporal organization of enzyme activity. Phase separation in many eukaryotic condensates has been shown to be responsive to intracellular adenosine triphosphate (ATP) levels, although the consequences of these mechanisms for enzymes sequestered within the condensates are unknown. Here, we show that ATP depletion promotes phase separation in bacterial condensates composed of intrinsically disordered proteins. Enhanced phase separation promotes the sequestration and activity of a client kinase enabling robust signaling and maintenance of viability under the stress posed by nutrient scarcity. We propose that a diverse repertoire of condensates can serve as control knobs to tune enzyme sequestration and reactivity in response to the metabolic state of bacterial cells.
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Affiliation(s)
- Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Corresponding author. (S.S.); (L.S.)
| | - Trisha N. Chong
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Camille Bayas
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Corresponding author. (S.S.); (L.S.)
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7
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Whinn KS, Kaur G, Lewis JS, Schauer GD, Mueller SH, Jergic S, Maynard H, Gan ZY, Naganbabu M, Bruchez MP, O'Donnell ME, Dixon NE, van Oijen AM, Ghodke H. Nuclease dead Cas9 is a programmable roadblock for DNA replication. Sci Rep 2019; 9:13292. [PMID: 31527759 PMCID: PMC6746809 DOI: 10.1038/s41598-019-49837-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/31/2019] [Indexed: 01/19/2023] Open
Abstract
Limited experimental tools are available to study the consequences of collisions between DNA-bound molecular machines. Here, we repurpose a catalytically inactivated Cas9 (dCas9) construct as a generic, novel, targetable protein-DNA roadblock for studying mechanisms underlying enzymatic activities on DNA substrates in vitro. We illustrate the broad utility of this tool by demonstrating replication fork arrest by the specifically bound dCas9-guideRNA complex to arrest viral, bacterial and eukaryotic replication forks in vitro.
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Affiliation(s)
- Kelsey S Whinn
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Gurleen Kaur
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Jacob S Lewis
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Grant D Schauer
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, 10065, USA
| | - Stefan H Mueller
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Slobodan Jergic
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Hamish Maynard
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Zhong Yan Gan
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Matharishwan Naganbabu
- Department of Chemistry and Molecular Biosensors and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry and Molecular Biosensors and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania, 15213, USA
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller University, New York, NY, 10065, USA
| | - Nicholas E Dixon
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia
| | - Antoine M van Oijen
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
| | - Harshad Ghodke
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, Wollongong, New South Wales, 2522, Australia.
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
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8
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Ayele TM, Knutson SD, Ellipilli S, Hwang H, Heemstra JM. Fluorogenic Photoaffinity Labeling of Proteins in Living Cells. Bioconjug Chem 2019; 30:1309-1313. [PMID: 30978287 DOI: 10.1021/acs.bioconjchem.9b00203] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genetically encoded fluorescent proteins or small-molecule probes that recognize specific protein binding partners can be used to label proteins to study their localization and function with fluorescence microscopy. However, these approaches are limited in signal-to-background resolution and the ability to temporally control labeling. Herein, we describe a covalent protein labeling technique using a fluorogenic malachite green probe functionalized with a photoreactive cross-linker. This enables a controlled covalent attachment to a genetically encodable fluorogen activating protein (FAP) with low background signal. We demonstrate covalent labeling of a protein in vitro as well as in live mammalian cells. This method is straightforward, displays high labeling specificity, and results in improved signal-to-background ratios in photoaffinity labeling of target proteins. Additionally, this probe provides temporal control over reactivity, enabling future applications in real-time monitoring of cellular events.
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Affiliation(s)
- Tewoderos M Ayele
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Steve D Knutson
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Satheesh Ellipilli
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Hyun Hwang
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Jennifer M Heemstra
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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9
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Pimenta FM, Chiappetta G, Le Saux T, Vinh J, Jullien L, Gautier A. Chromophore Renewal and Fluorogen-Binding Tags: A Match Made to Last. Sci Rep 2017; 7:12316. [PMID: 28951577 PMCID: PMC5615068 DOI: 10.1038/s41598-017-12400-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/08/2017] [Indexed: 01/20/2023] Open
Abstract
Fluorogen-binding tags, which activate the fluorescence of a specific chromophore (so-called fluorogen) upon reversible binding, have recently been proposed as a way of reducing photobleaching via fluorogen renewal. However, no generic methodology has been proposed to systematically analyze the photodamage of the fluorogen and the protein tag. Using Y-FAST (Yellow Fluorescence-activating and Absorption-Shifting Tag) as a case study we propose here a generic experimental and theoretical approach to assess how fluorogen renewal reduces the apparent photobleaching rate of a fluorogen-binding tag. Y-FAST has its apparent photobleaching rate greatly reduced by fluorogen renewal and its photostability is mainly limited by oxidation of specific residues in the protein scaffold by reactive oxygen species generated by the bound fluorogen. This study sets the groundwork for the optimization of fluorogenic systems, helping guide rational improvements to their photostability.
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Affiliation(s)
- Frederico M Pimenta
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France
| | - Giovanni Chiappetta
- ESPCI Biological Mass Spectrometry and Proteomics USR 3149 CNRS/ESPCI-PSL, Paris, France
| | - Thomas Le Saux
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France
| | - Joëlle Vinh
- ESPCI Biological Mass Spectrometry and Proteomics USR 3149 CNRS/ESPCI-PSL, Paris, France
| | - Ludovic Jullien
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France.
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France.
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10
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Bozhanova NG, Baranov MS, Klementieva NV, Sarkisyan KS, Gavrikov AS, Yampolsky IV, Zagaynova EV, Lukyanov SA, Lukyanov KA, Mishin AS. Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem Sci 2017; 8:7138-7142. [PMID: 29147545 PMCID: PMC5676496 DOI: 10.1039/c7sc01628j] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/01/2017] [Indexed: 11/21/2022] Open
Abstract
A novel method of protein labeling uses the highly dynamic reversible association of a cell-permeable fluorogenic dye and lipocalin Blc mutants.
We present protein-PAINT – the implementation of the general principles of PAINT (Point Accumulation for Imaging in Nanoscale Topography) for live-cell protein labeling. Our method employs the specific binding of cell-permeable fluorogenic dyes to genetically encoded protein tags. We engineered three mutants of the bacterial lipocalin Blc that possess different affinities to a fluorogenic dye and exhibit a strong increase in fluorescence intensity upon binding. This allows for rapid labeling and washout of intracellular targets on a time scale from seconds to a few minutes. We demonstrate an order of magnitude higher photostability of the fluorescence signal in comparison with spectrally similar fluorescent proteins. Protein-PAINT ensures prolonged super-resolution fluorescence microscopy of living cells in both single molecule detection and stimulated emission depletion regimes.
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Affiliation(s)
- Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | | | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Centre for Genomic Regulation (CRG) , The Barcelona Institute for Science and Technology , Dr Aiguader 88 , 08003 Barcelona , Spain
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Pirogov Russian National Research Medical University , Moscow , Russia
| | | | - Sergey A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia.,Pirogov Russian National Research Medical University , Moscow , Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
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11
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Saurabh S, Perez AM, Comerci CJ, Shapiro L, Moerner WE. Super-Resolution Microscopy and Single-Protein Tracking in Live Bacteria Using a Genetically Encoded, Photostable Fluoromodule. ACTA ACUST UNITED AC 2017. [PMID: 28627757 DOI: 10.1002/cpcb.21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Visualization of dynamic protein structures in live cells is crucial for understanding the mechanisms governing biological processes. Fluorescence microscopy is a sensitive tool for this purpose. In order to image proteins in live bacteria using fluorescence microscopy, one typically genetically fuses the protein of interest to a photostable fluorescent tag. Several labeling schemes are available to accomplish this. Particularly, hybrid tags that combine a fluorescent or fluorogenic dye with a genetically encoded protein (such as enzymatic labels) have been used successfully in multiple cell types. However, their use in bacteria has been limited due to challenges imposed by a complex bacterial cell wall. Here, we describe the use of a genetically encoded photostable fluoromodule that can be targeted to cytosolic and membrane proteins in the Gram negative bacterium Caulobacter crescentus. Additionally, we summarize methods to use this fluoromodule for single protein imaging and super-resolution microscopy using stimulated emission depletion. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Stanford University, Stanford, California
| | - Adam M Perez
- Department of Developmental Biology, Beckman Center for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, California.,Department of Biology, Stanford University, Stanford, California
| | - Colin J Comerci
- Biophysics Program, Stanford University, Stanford, California
| | - Lucy Shapiro
- Department of Developmental Biology, Beckman Center for Molecular and Genetic Medicine, Stanford University School of Medicine, Stanford, California
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California
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12
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Gallo E, Jarvik JW. Breaking the color barrier - a multi-selective antibody reporter offers innovative strategies of fluorescence detection. J Cell Sci 2017; 130:2644-2653. [PMID: 28615413 DOI: 10.1242/jcs.202952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 06/08/2017] [Indexed: 01/14/2023] Open
Abstract
A novel bi-partite fluorescence platform exploits the high affinity and selectivity of antibody scaffolds to capture and activate small-molecule fluorogens. In this report, we investigated the property of multi-selectivity activation by a single antibody against diverse cyanine family fluorogens. Our fluorescence screen identified three cell-impermeant fluorogens, each with unique emission spectra (blue, green and red) and nanomolar affinities. Most importantly, as a protein fusion tag to G-protein-coupled receptors, the antibody biosensor retained full activity - displaying bright fluorogen signals with minimal background on live cells. Because fluorogen-activating antibodies interact with their target ligands via non-covalent interactions, we were able to perform advanced multi-color detection strategies on live cells, previously difficult or impossible with conventional reporters. We found that by fine-tuning the concentrations of the different color fluorogen molecules in solution, a user may interchange the fluorescence signal (onset versus offset), execute real-time signal exchange via fluorogen competition, measure multi-channel fluorescence via co-labeling, and assess real-time cell surface receptor traffic via pulse-chase experiments. Thus, here we inform of an innovative reporter technology based on tri-color signal that allows user-defined fluorescence tuning in live-cell applications.
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Affiliation(s)
- Eugenio Gallo
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jonathan W Jarvik
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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13
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Saurabh S, Perez AM, Comerci CJ, Shapiro L, Moerner WE. Super-resolution Imaging of Live Bacteria Cells Using a Genetically Directed, Highly Photostable Fluoromodule. J Am Chem Soc 2016; 138:10398-401. [PMID: 27479076 DOI: 10.1021/jacs.6b05943] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The rapid development in fluorescence microscopy and imaging techniques has greatly benefited our understanding of the mechanisms governing cellular processes at the molecular level. In particular, super-resolution microscopy methods overcome the diffraction limit to observe nanoscale cellular structures with unprecedented detail, and single-molecule tracking provides precise dynamic information about the motions of labeled proteins and oligonucleotides. Enhanced photostability of fluorescent labels (i.e., maximum emitted photons before photobleaching) is a critical requirement for achieving the ultimate spatio-temporal resolution with either method. While super-resolution imaging has greatly benefited from highly photostable fluorophores, a shortage of photostable fluorescent labels for bacteria has limited its use in these small but relevant organisms. In this study, we report the use of a highly photostable fluoromodule, dL5, to genetically label proteins in the Gram-negative bacterium Caulobacter crescentus, enabling long-time-scale protein tracking and super-resolution microscopy. dL5 imaging relies on the activation of the fluorogen Malachite Green (MG) and can be used to label proteins sparsely, enabling single-protein detection in live bacteria without initial bleaching steps. dL5-MG complexes emit 2-fold more photons before photobleaching compared to organic dyes such as Cy5 and Alexa 647 in vitro, and 5-fold more photons compared to eYFP in vivo. We imaged fusions of dL5 to three different proteins in live Caulobacter cells using stimulated emission depletion microscopy, yielding a 4-fold resolution enhancement compared to diffraction-limited imaging. Importantly, dL5 fusions to an intermediate filament protein CreS are significantly less perturbative compared to traditional fluorescent protein fusions. To the best of our knowledge, this is the first demonstration of the use of fluorogen activating proteins for super-resolution imaging in live bacterial cells.
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Affiliation(s)
- Saumya Saurabh
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Adam M Perez
- Department of Developmental Biology, Stanford University School of Medicine , Stanford, California 94305, United States.,Department of Biology, Stanford University , Stanford, California 94305, United States
| | - Colin J Comerci
- Biophysics Program, Stanford University , Stanford, California 94305, United States
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine , Stanford, California 94305, United States
| | - W E Moerner
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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14
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Naganbabu M, Perkins LA, Wang Y, Kurish J, Schmidt BF, Bruchez MP. Multiexcitation Fluorogenic Labeling of Surface, Intracellular, and Total Protein Pools in Living Cells. Bioconjug Chem 2016; 27:1525-31. [PMID: 27159569 PMCID: PMC4911959 DOI: 10.1021/acs.bioconjchem.6b00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
Malachite
green (MG) is a fluorogenic dye that shows fluorescence enhancement
upon binding to its engineered cognate protein, a fluorogen activating
protein (FAP). Energy transfer donors such as cyanine and rhodamine
dyes have been conjugated with MG to modify the spectral properties
of the fluorescent complexes, where the donor dyes transfer energy
through Förster resonance energy transfer to the MG complex
resulting in binding-conditional fluorescence emission in the far-red
region. In this article, we use a violet-excitable dye as a donor
to sensitize the far-red emission of the MG-FAP complex. Two blue
emitting fluorescent coumarin dyes were coupled to MG and evaluated
for energy transfer to the MG-FAP complex via its secondary excitation
band. 6,8-Difluoro-7-hydroxycoumarin-3-carboxylic acid (Pacific blue,
PB) showed the most efficient energy transfer and maximum brightness
in the far-red region upon violet (405 nm) excitation. These blue-red
(BluR) tandem dyes are spectrally varied from other tandem dyes and
are able to produce fluorescence images of the MG-FAP complex with
a large Stokes shift (>250 nm). These dyes are cell-permeable and
are used to label intracellular proteins. Used together with a cell-impermeable
hexa-Cy3-MG (HCM) dye that labels extracellular proteins, we are able
to visualize extracellular, intracellular, and total pools of cellular
protein using one fluorogenic tag that combines with distinct dyes
to effect different spectral characteristics.
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Affiliation(s)
- Matharishwan Naganbabu
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Lydia A Perkins
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Yi Wang
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Jeffery Kurish
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Brigitte F Schmidt
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
| | - Marcel P Bruchez
- Department of Chemistry, ‡Department of Biological Sciences, and §Molecular Biosensors and Imaging Center, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh 15213, Pennsylvania, United States
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15
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Backlund MP, Arbabi A, Petrov PN, Arbabi E, Saurabh S, Faraon A, Moerner WE. Removing Orientation-Induced Localization Biases in Single-Molecule Microscopy Using a Broadband Metasurface Mask. NATURE PHOTONICS 2016; 10:459-462. [PMID: 27574529 PMCID: PMC5001689 DOI: 10.1038/nphoton.2016.93] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 04/11/2016] [Indexed: 05/21/2023]
Abstract
Nanoscale localization of single molecules is a crucial function in several advanced microscopy techniques, including single-molecule tracking and wide-field super-resolution imaging 1. To date, a central consideration of such techniques is how to optimize the precision of molecular localization. However, as these methods continue to push toward the nanometre size scale, an increasingly important concern is the localization accuracy. In particular, single fluorescent molecules emit with an anisotropic radiation pattern of an oscillating electric dipole, which can cause significant localization biases using common estimators 2-5. Here we present the theory and experimental demonstration of a solution to this problem based on azimuthal filtering in the Fourier plane of the microscope. We do so using a high efficiency dielectric metasurface polarization/phase device composed of nanoposts with sub-wavelength spacing 6. The method is demonstrated both on fluorophores embedded in a polymer matrix, and in dL5 protein complexes that bind Malachite green 7, 8.
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Affiliation(s)
- Mikael P. Backlund
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
| | - Amir Arbabi
- T. J. Watson Laboratory of Applied Physics, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125
| | - Petar N. Petrov
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
| | - Ehsan Arbabi
- T. J. Watson Laboratory of Applied Physics, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125
| | - Saumya Saurabh
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
| | - Andrei Faraon
- T. J. Watson Laboratory of Applied Physics, California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125
- A.F. for questions regarding the metasurface mask. Contact:
| | - W. E. Moerner
- Department of Chemistry, Stanford University, 375 North-South Mall, Stanford, CA 94305
- Correspondence should be directed to W.E.M. for questions regarding the experiment, Contact:
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