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Liang J, Smith AW. The Oligomeric State of Vasorin in the Plasma Membrane Measured Non-Invasively by Quantitative Fluorescence Fluctuation Spectroscopy. Int J Mol Sci 2024; 25:4115. [PMID: 38612924 PMCID: PMC11012933 DOI: 10.3390/ijms25074115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Vasorin (VASN), a transmembrane protein heavily expressed in endothelial cells, has garnered recent interest due to its key role in vascular development and pathology. The oligomeric state of VASN is a crucial piece of knowledge given that receptor clustering is a frequent regulatory mechanism in downstream signaling activation and amplification. However, documentation of VASN oligomerization is currently absent. In this brief report, we describe the measurement of VASN oligomerization in its native membranous environment, leveraging a class of fluorescence fluctuation spectroscopy. Our investigation revealed that the majority of VASN resides in a monomeric state, while a minority of VASN forms homodimers in the cellular membrane. This result raises the intriguing possibility that ligand-independent clustering of VASN may play a role in transforming growth factor signaling.
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Affiliation(s)
- Junyi Liang
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Adam W. Smith
- Department of Chemistry, University of Akron, Akron, OH 44325, USA
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
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2
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Hedde PN, Barylko B, Binns DD, Jameson DM, Albanesi JP. Differential Mobility and Self-Association of Arc/Arg3.1 in the Cytoplasm and Nucleus of Living Cells. ACS Chem Neurosci 2022; 13:876-882. [PMID: 35319179 DOI: 10.1021/acschemneuro.1c00744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Arc, also known as Arg3.1, is an activity-dependent immediate-early gene product that plays essential roles in memory consolidation. A pool of Arc is located in the postsynaptic cytoplasm, where it promotes AMPA receptor endocytosis and cytoskeletal remodeling. However, Arc is also found in the nucleus, with a major portion being associated with promyelocytic leukemia nuclear bodies (PML-NBs). Nuclear Arc has been implicated in epigenetic control of gene transcription associated with learning and memory. In this study, we use a battery of fluorescence nanoimaging approaches to characterize the behavior of Arc ectopically expressed in heterologous cells. Our results indicate that in the cytoplasm, Arc exists predominantly as monomers and dimers associated with slowly diffusing particles. In contrast, nuclear Arc is almost exclusively monomeric and displays a higher diffusivity than cytoplasmic Arc. We further show that Arc moves freely and rapidly between PML-NBs and the nucleoplasm and that its movement within PML-NBs is relatively unobstructed.
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Affiliation(s)
- Per Niklas Hedde
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, 651 Ilalo Street, BSB 222, University of Hawaii, Honolulu, Hawaii 96813, United States
| | - Barbara Barylko
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, Texas 75390, United States
| | - Derk D. Binns
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, Texas 75390, United States
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, 651 Ilalo Street, BSB 222, University of Hawaii, Honolulu, Hawaii 96813, United States
| | - Joseph P. Albanesi
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park, Dallas, Texas 75390, United States
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3
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Killeen TD, Rahman S, Badu DN, Biener G, Stoneman MR, Raicu V. Fluorescence Intensity Fluctuation Analysis of Protein Oligomerization in Cell Membranes. Curr Protoc 2022; 2:e384. [PMID: 35312215 DOI: 10.1002/cpz1.384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fluorescence fluctuation spectroscopy (FFS) encompasses a bevy of techniques that involve analyzing fluorescence intensity fluctuations occurring due to fluorescently labeled molecules diffusing in and out of a microscope's focal region. Statistical analysis of these fluctuations may reveal the oligomerization (i.e., association) state of said molecules. We have recently developed a new FFS-based method, termed Two-Dimensional Fluorescence Intensity Fluctuation (2D FIF) spectrometry, which provides quantitative information on the size and stability of protein oligomers as a function of receptor concentration. This article describes protocols for employing FIF spectrometry to quantify the oligomerization of a membrane protein of interest, with specific instructions regarding cell preparation, image acquisition, and analysis of images given in detail. Application of the FIF Spectrometry Suite, a software package designed for applying FIF analysis on fluorescence images, is emphasized in the protocol. Also discussed in detail is the identification, removal, and/or analysis of inhomogeneous regions of the membrane that appear as bright spots. The 2D FIF approach is particularly suited to assess the effects of agonists and antagonists on the oligomeric size of membrane receptors of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of live cells expressing protein constructs Basic Protocol 2: Image acquisition and noise correction Basic Protocol 3: Drawing and segmenting regions of interest Basic Protocol 4: Calculating the molecular brightness and concentration of individual image segments Basic Protocol 5: Combining data subsets using a manual procedure (Optional) Alternate Protocol 1: Combining data subsets using the advanced FIF spectrometry suite (Optional; alternative to Basic Protocol 5) Basic Protocol 6: Performing meta-analysis of brightness spectrograms Alternate Protocol 2: Performing meta-analysis of brightness spectrograms (alternative to Basic Protocol 6) Basic Protocol 7: Spot extraction and analysis using a manual procedure or by writing a program (Optional) Alternate Protocol 3: Automated spot extraction and analysis (Optional; alternative to Protocol 7) Support Protocol: Monomeric brightness determination.
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Affiliation(s)
- Tom D Killeen
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Sadia Rahman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Dammar N Badu
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Gabriel Biener
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Michael R Stoneman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Valerică Raicu
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin.,Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
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4
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Tassin TC, Barylko B, Hedde PN, Chen Y, Binns DD, James NG, Mueller JD, Jameson DM, Taussig R, Albanesi JP. Gain-of-Function Properties of a Dynamin 2 Mutant Implicated in Charcot-Marie-Tooth Disease. Front Cell Neurosci 2021; 15:745940. [PMID: 34744632 PMCID: PMC8563704 DOI: 10.3389/fncel.2021.745940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/29/2021] [Indexed: 11/29/2022] Open
Abstract
Mutations in the gene encoding dynamin 2 (DNM2), a GTPase that catalyzes membrane constriction and fission, are associated with two autosomal-dominant motor disorders, Charcot-Marie-Tooth disease (CMT) and centronuclear myopathy (CNM), which affect nerve and muscle, respectively. Many of these mutations affect the pleckstrin homology domain of DNM2, yet there is almost no overlap between the sets of mutations that cause CMT or CNM. A subset of CMT-linked mutations inhibit the interaction of DNM2 with phosphatidylinositol (4,5) bisphosphate, which is essential for DNM2 function in endocytosis. In contrast, CNM-linked mutations inhibit intramolecular interactions that normally suppress dynamin self-assembly and GTPase activation. Hence, CNM-linked DNM2 mutants form abnormally stable polymers and express enhanced assembly-dependent GTPase activation. These distinct effects of CMT and CNM mutations are consistent with current findings that DNM2-dependent CMT and CNM are loss-of-function and gain-of-function diseases, respectively. In this study, we present evidence that at least one CMT-causing DNM2 mutant (ΔDEE; lacking residues 555DEE557) forms polymers that, like the CNM mutants, are resistant to disassembly and display enhanced GTPase activation. We further show that the ΔDEE mutant undergoes 2-3-fold higher levels of tyrosine phosphorylation than wild-type DNM2. These results suggest that molecular mechanisms underlying the absence of pathogenic overlap between DNM2-dependent CMT and CNM should be re-examined.
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Affiliation(s)
- Tara C. Tassin
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Barbara Barylko
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Per Niklas Hedde
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA, United States
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - Derk D. Binns
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Nicholas G. James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Joachim D. Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, United States
| | - David M. Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Ronald Taussig
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
| | - Joseph P. Albanesi
- Department of Pharmacology, U.T. Southwestern Medical Center, Dallas, TX, United States
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Abstract
The miniSPIM is a miniaturized light-sheet microscope that enables imaging with optical sectioning on mobile camera devices such as smartphones and single-board computers. Applications of the miniSPIM include biosensing, field research, and education where maximum portability and robustness, low power consumption, and low cost are key. Here, it is shown how all of the components of a simple light-sheet microscope can be integrated within a footprint smaller than the average smartphone. Example applications include the quantification of the motion of microparticles and bacteria in fluids, the characterization of solvent polarity based on spectral shifts of the lipid probe Nile Red, and three-dimensional (3D) and time-lapse autofluorescence imaging of a live zebrafish embryo.
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Affiliation(s)
- Per Niklas Hedde
- Beckman Laser Institute, University of California Irvine, Irvine, California 92612, United States
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697, United States
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, California 92697, United States
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6
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Nederveen-Schippers LM, Pathak P, Keizer-Gunnink I, Westphal AH, van Haastert PJM, Borst JW, Kortholt A, Skakun V. Combined FCS and PCH Analysis to Quantify Protein Dimerization in Living Cells. Int J Mol Sci 2021; 22:ijms22147300. [PMID: 34298920 PMCID: PMC8307594 DOI: 10.3390/ijms22147300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/29/2022] Open
Abstract
Protein dimerization plays a crucial role in the regulation of numerous biological processes. However, detecting protein dimers in a cellular environment is still a challenge. Here we present a methodology to measure the extent of dimerization of GFP-tagged proteins in living cells, using a combination of fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis of single-color fluorescence fluctuation data. We named this analysis method brightness and diffusion global analysis (BDGA) and adapted it for biological purposes. Using cell lysates containing different ratios of GFP and tandem-dimer GFP (diGFP), we show that the average brightness per particle is proportional to the fraction of dimer present. We further adapted this methodology for its application in living cells, and we were able to distinguish GFP, diGFP, as well as ligand-induced dimerization of FKBP12 (FK506 binding protein 12)-GFP. While other analysis methods have only sporadically been used to study dimerization in living cells and may be prone to errors, this paper provides a robust approach for the investigation of any cytosolic protein using single-color fluorescence fluctuation spectroscopy.
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Affiliation(s)
- Laura M. Nederveen-Schippers
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Pragya Pathak
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Ineke Keizer-Gunnink
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Adrie H. Westphal
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Peter J. M. van Haastert
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
| | - Jan Willem Borst
- Laboratory of Biochemistry, Wageningen University & Research, 6708 WE Wageningen, The Netherlands; (A.H.W.); (J.W.B.)
| | - Arjan Kortholt
- Department of Cell Biochemistry, University of Groningen, 9747 AG Groningen, The Netherlands; (L.M.N.-S.); (P.P.); (I.K.-G.); (P.J.M.v.H.)
- Correspondence: (A.K.); (V.S.)
| | - Victor Skakun
- Department of Systems Analysis and Computer Simulation, Belarusian State University, 220030 Minsk, Belarus
- Correspondence: (A.K.); (V.S.)
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7
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de Man SMA, Zwanenburg G, van der Wal T, Hink MA, van Amerongen R. Quantitative live-cell imaging and computational modeling shed new light on endogenous WNT/CTNNB1 signaling dynamics. eLife 2021; 10:e66440. [PMID: 34190040 PMCID: PMC8341982 DOI: 10.7554/elife.66440] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/29/2021] [Indexed: 12/16/2022] Open
Abstract
WNT/CTNNB1 signaling regulates tissue development and homeostasis in all multicellular animals, but the underlying molecular mechanism remains incompletely understood. Specifically, quantitative insight into endogenous protein behavior is missing. Here, we combine CRISPR/Cas9-mediated genome editing and quantitative live-cell microscopy to measure the dynamics, diffusion characteristics and absolute concentrations of fluorescently tagged, endogenous CTNNB1 in human cells under both physiological and oncogenic conditions. State-of-the-art imaging reveals that a substantial fraction of CTNNB1 resides in slow-diffusing cytoplasmic complexes, irrespective of the activation status of the pathway. This cytoplasmic CTNNB1 complex undergoes a major reduction in size when WNT/CTNNB1 is (hyper)activated. Based on our biophysical measurements, we build a computational model of WNT/CTNNB1 signaling. Our integrated experimental and computational approach reveals that WNT pathway activation regulates the dynamic distribution of free and complexed CTNNB1 across different subcellular compartments through three regulatory nodes: the destruction complex, nucleocytoplasmic shuttling, and nuclear retention.
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Affiliation(s)
- Saskia MA de Man
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Gooitzen Zwanenburg
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Tanne van der Wal
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Mark A Hink
- Molecular Cytology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
- van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
| | - Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of AmsterdamAmsterdamNetherlands
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8
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Bock A, Annibale P, Konrad C, Hannawacker A, Anton SE, Maiellaro I, Zabel U, Sivaramakrishnan S, Falcke M, Lohse MJ. Optical Mapping of cAMP Signaling at the Nanometer Scale. Cell 2020; 182:1519-1530.e17. [PMID: 32846156 DOI: 10.1016/j.cell.2020.07.035] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/30/2020] [Accepted: 07/23/2020] [Indexed: 10/23/2022]
Abstract
Cells relay a plethora of extracellular signals to specific cellular responses by using only a few second messengers, such as cAMP. To explain signaling specificity, cAMP-degrading phosphodiesterases (PDEs) have been suggested to confine cAMP to distinct cellular compartments. However, measured rates of fast cAMP diffusion and slow PDE activity render cAMP compartmentalization essentially impossible. Using fluorescence spectroscopy, we show that, contrary to earlier data, cAMP at physiological concentrations is predominantly bound to cAMP binding sites and, thus, immobile. Binding and unbinding results in largely reduced cAMP dynamics, which we term "buffered diffusion." With a large fraction of cAMP being buffered, PDEs can create nanometer-size domains of low cAMP concentrations. Using FRET-cAMP nanorulers, we directly map cAMP gradients at the nanoscale around PDE molecules and the areas of resulting downstream activation of cAMP-dependent protein kinase (PKA). Our study reveals that spatiotemporal cAMP signaling is under precise control of nanometer-size domains shaped by PDEs that gate activation of downstream effectors.
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Affiliation(s)
- Andreas Bock
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany.
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Charlotte Konrad
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Annette Hannawacker
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Selma E Anton
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Isabella Maiellaro
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Martin Falcke
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Department of Physics, Humboldt University, Newtonstr. 15, 12489 Berlin, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany; Institute for Chemistry and Biochemistry, Free University, Takustr. 3, 14195 Berlin, Germany; ISAR Bioscience Institute, 82152 Munich/Planegg, Germany.
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9
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Sanstrum BJ, Goo BMSS, Holden DZY, Delgado DD, Nguyen TPN, Lee KD, James NG. Fluctuation Imaging of LRRK2 Reveals that the G2019S Mutation Alters Spatial and Membrane Dynamics. Molecules 2020; 25:E2561. [PMID: 32486414 DOI: 10.3390/molecules25112561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/20/2020] [Accepted: 05/22/2020] [Indexed: 12/29/2022] Open
Abstract
Mutations within the Leucine-Rich Repeat Kinase 2 (LRRK2) gene are the most common genetic cause of autosomal and sporadic Parkinson’s disease (PD). LRRK2 is a large multidomain kinase that has reported interactions with several membrane proteins, including Rab and Endophilin, and has recently been proposed to function as a regulator of vesicular trafficking. It is unclear whether or how the spatiotemporal organization of the protein is altered due to LRRK2 activity. Therefore, we utilized fluctuation-based microscopy along with FLIM/FRET to examine the cellular properties and membrane recruitment of WT LRRK2-GFP (WT) and the PD mutant G2019S LRRK2-GFP (G2019S). We show that both variants can be separated into two distinct populations within the cytosol; a freely diffusing population associated with monomer/dimer species and a slower, likely vesicle-bound population. G2019S shows a significantly higher propensity to self-associate in both the cytosol and membrane regions when compared to WT. G2019S expression also resulted in increased hetero-interactions with Endophilin A1 (EndoA1), reduced cellular vesicles, and altered clathrin puncta dynamics associated with the plasma membrane. This finding was associated with a reduction in transferrin endocytosis in cells expressing G2019S, which indicates disruption of endocytic protein recruitment near the plasma membrane. Overall, this study uncovered multiple dynamic alterations to the LRRK2 protein as a result of the G2019S mutation—all of which could lead to neurodegeneration associated with PD.
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10
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Hedde PN, Staaf E, Singh SB, Johansson S, Gratton E. Pair Correlation Analysis Maps the Dynamic Two-Dimensional Organization of Natural Killer Cell Receptors at the Synapse. ACS Nano 2019; 13:14274-14282. [PMID: 31747251 PMCID: PMC8427743 DOI: 10.1021/acsnano.9b07486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In living systems, the contact between cells is the basis of recognition, differentiation, and orchestration of an immune response. Obstacles and barriers to biomolecular motion, especially for receptors at cellular synapses, critically control these functions by creating an anisotropic environment. Whereas conventional fluorescence fluctuation methods, such as fluorescence correlation spectroscopy or fluorescence recovery after photobleaching, can only measure the isotropic diffusion of molecules, the two-dimensional pair correlation function (2D-pCF) approach probes the anisotropic paths at different spatial locations within an image, allowing the creation of high-resolution maps that can visualize and quantify how molecules move in a living cell. In this work, we show how the 2D-pCF method maps the environment in cellular synapses as perceived by natural killer (NK) cell receptors. In cultured human HLA null 721.221 cells, 2D-pCF reveals the motion of inhibitory receptor HLA-Cw4-YFP coexpressed with KIR3DL1 to be highly directional around specific loci, while these restrictions were absent in the case of HLA-B51-YFP coexpressed with KIR2DL1. Further, in freshly isolated educated (H-2Dd) and uneducated (MHC-/-) primary murine NK cells, the 2D-pCF method shows significant differences in the paths taken by activating receptor NKp46 and inhibitory receptor Ly49A in educated compared to uneducated cells. Altogether, we demonstrate that the 2D-pCF method is very powerful in informing about the spatial organization of motion in cells. Our data support the hypothesis that flexibility in the spatial arrangement of membrane receptors, that is, the absence of barriers, is crucial for NK cell function.
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Affiliation(s)
- Per Niklas Hedde
- Laboratory
for Fluorescence Dynamics, University of
California Irvine, Irvine, California 92697, United States
- Department
of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii 96813, United States
- E-mail:
| | - Elina Staaf
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sunitha Bagawath Singh
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sofia Johansson
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Enrico Gratton
- Laboratory
for Fluorescence Dynamics, University of
California Irvine, Irvine, California 92697, United States
- E-mail: (lead contact)
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11
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Briddon SJ, Kilpatrick LE, Hill SJ. Studying GPCR Pharmacology in Membrane Microdomains: Fluorescence Correlation Spectroscopy Comes of Age. Trends Pharmacol Sci 2017; 39:158-174. [PMID: 29277246 DOI: 10.1016/j.tips.2017.11.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are organised within the cell membrane into highly ordered macromolecular complexes along with other receptors and signalling proteins. Understanding how heterogeneity in these complexes affects the pharmacology and functional response of these receptors is crucial for developing new and more selective ligands. Fluorescence correlation spectroscopy (FCS) and related techniques such as photon counting histogram (PCH) analysis and image-based FCS can be used to interrogate the properties of GPCRs in these membrane microdomains, as well as their interaction with fluorescent ligands. FCS analyses fluorescence fluctuations within a small-defined excitation volume to yield information about their movement, concentration and molecular brightness (aggregation). These techniques can be used on live cells with single-molecule sensitivity and high spatial resolution. Once the preserve of specialist equipment, FCS techniques can now be applied using standard confocal microscopes. This review describes how FCS and related techniques have revealed novel insights into GPCR biology.
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Affiliation(s)
- Stephen J Briddon
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK
| | - Laura E Kilpatrick
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK.
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12
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Hedde PN, Gratton E. Selective plane illumination microscopy with a light sheet of uniform thickness formed by an electrically tunable lens. Microsc Res Tech 2016; 81:924-928. [PMID: 27338568 DOI: 10.1002/jemt.22707] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/02/2016] [Accepted: 06/02/2016] [Indexed: 11/11/2022]
Abstract
Light sheet microscopy is a powerful technique for rapid, three-dimensional fluorescence imaging of large specimen such as drosophila and zebrafish embryos. Yet, beam divergence results in a loss of axial resolution at the periphery of the light sheet. Here, we demonstrate how an electrically tunable lens can be utilized to maintain the minimal, diffraction-limited thickness of the light sheet over a wide field of view (>600 µm) at high frame rates (40 fps). This mode of operation is necessary for the application of fluorescence fluctuation spectroscopy in images. Microsc. Res. Tech. 81:924-928, 2018. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Per Niklas Hedde
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California, USA
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13
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Wu B, Buxbaum AR, Katz ZB, Yoon YJ, Singer RH. Quantifying Protein-mRNA Interactions in Single Live Cells. Cell 2015; 162:211-20. [PMID: 26140598 DOI: 10.1016/j.cell.2015.05.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/04/2015] [Accepted: 05/19/2015] [Indexed: 11/17/2022]
Abstract
Specific binding proteins are crucial for the correct spatiotemporal expression of mRNA. To understand this process, a method is required to characterize RNA-protein interactions in single living cells with subcellular resolution. We combined endogenous single RNA and protein detection with two-photon fluorescence fluctuation analysis to measure the average number of proteins bound to mRNA at specific locations within live cells. We applied this to quantify the known binding of zipcode binding protein 1 (ZBP1) and ribosomes to β-actin mRNA within subcellular compartments of primary fibroblasts and neurons. ZBP1-mRNA binding did not occur in nuclei, contrary to previous conclusions. ZBP1 interaction with β-actin mRNA was enhanced perinuclearly in neurons compared to fibroblasts. Cytoplasmic ZBP1 and ribosome binding to the mRNA were anti-correlated depending on their location in the cell. These measurements support a mechanism whereby ZBP1 inhibits translation of localizing mRNA until its release from the mRNA peripherally, allowing ribosome binding.
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Affiliation(s)
- Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Zachary B Katz
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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14
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Youker RT, Teng H. Measuring protein dynamics in live cells: protocols and practical considerations for fluorescence fluctuation microscopy. J Biomed Opt 2014; 19:90801. [PMID: 25260867 PMCID: PMC4183152 DOI: 10.1117/1.jbo.19.9.090801] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 08/12/2014] [Accepted: 07/31/2014] [Indexed: 06/03/2023]
Abstract
Quantitative analysis of protein complex stoichiometries and mobilities are critical for elucidating the mechanisms that regulate cellular pathways. Fluorescence fluctuation spectroscopy (FFS) techniques can measure protein dynamics, such as diffusion coefficients and formation of complexes, with extraordinary precision and sensitivity. Complete calibration and characterization of the microscope instrument is necessary in order to avoid artifacts during data acquisition and to capitalize on the full capabilities of FFS techniques. We provide an overview of the theory behind FFS techniques, discuss calibration procedures, provide protocols, and give practical considerations for performing FFS experiments. One important parameter recovered from FFS measurements is the relative molecular brightness that can correlate with oligomerization. Three methods for measuring molecular brightness (fluorescence correlation spectroscopy, photon-counting histogram, and number and brightness analysis) recover similar values when measuring samples under ideal conditions in vitro. However, examples are given illustrating that these different methods used for calculating molecular brightness of fluorescent molecules in cells are not always equivalent. Methods relying on spot measurements are more prone to bleaching and movement artifacts that can lead to underestimation of brightness values. We advocate for the use of multiple FFS techniques to study molecular brightnesses to overcome and compliment limitations of individual techniques.
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Affiliation(s)
- Robert T. Youker
- University of Pittsburgh School of
Medicine, Renal-Electrolyte Division, Pittsburgh, Pennsylvania
15261, United States
- Western Carolina University,
Department of Biology, Cullowhee, North Carolina 28723, United
States
| | - Haibing Teng
- Carnegie Mellon University,
Molecular Biosensor and Imaging Center (MBIC), Pittsburgh, Pennsylvania 15213,
United States
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15
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Li J, Chen Y, Li M, Carpenter MA, McDougle RM, Luengas EM, Macdonald PJ, Harris RS, Mueller JD. APOBEC3 multimerization correlates with HIV-1 packaging and restriction activity in living cells. J Mol Biol 2014; 426:1296-307. [PMID: 24361275 PMCID: PMC3977201 DOI: 10.1016/j.jmb.2013.12.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/10/2013] [Accepted: 12/10/2013] [Indexed: 12/30/2022]
Abstract
APOBEC3G belongs to a family of DNA cytosine deaminases that are involved in the restriction of a broad number of retroviruses including human immunodeficiency virus type 1 (HIV-1). Prior studies have identified two distinct mechanistic steps in Vif-deficient HIV-1 restriction: packaging into virions and deaminating viral cDNA. APOBEC3A, for example, although highly active, is not packaged and is therefore not restrictive. APOBEC3G, on the other hand, although having weaker enzymatic activity, is packaged into virions and is strongly restrictive. Although a number of studies have described the propensity for APOBEC3 oligomerization, its relevance to HIV-1 restriction remains unclear. Here, we address this problem by examining APOBEC3 oligomerization in living cells using molecular brightness analysis. We find that APOBEC3G forms high-order multimers as a function of protein concentration. In contrast, APOBEC3A, APOBEC3C and APOBEC2 are monomers at all tested concentrations. Among other members of the APOBEC3 family, we show that the multimerization propensities of APOBEC3B, APOBEC3D, APOBEC3F and APOBEC3H (haplotype II) bear more resemblance to APOBEC3G than to APOBEC3A/3C/2. Prior studies have shown that all of these multimerizing APOBEC3 proteins, but not the monomeric family members, have the capacity to package into HIV-1 particles and restrict viral infectivity. This correlation between oligomerization and restriction is further evidenced by two different APOBEC3G mutants, which are each compromised for multimerization, packaging and HIV-1 restriction. Overall, our results imply that multimerization of APOBEC3 proteins may be related to the packaging mechanism and ultimately to virus restriction.
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Affiliation(s)
- Jinhui Li
- School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA
| | - Ming Li
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Michael A Carpenter
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Rebecca M McDougle
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Elizabeth M Luengas
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Patrick J Macdonald
- Department of Biomedical Engineering, University of Minnesota, 312 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Reuben S Harris
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Joachim D Mueller
- School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biomedical Engineering, University of Minnesota, 312 Church Street Southeast, Minneapolis, MN 55455, USA.
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James NG, Digman MA, Ross JA, Barylko B, Wang L, Li J, Chen Y, Mueller JD, Gratton E, Albanesi JP, Jameson DM. A mutation associated with centronuclear myopathy enhances the size and stability of dynamin 2 complexes in cells. Biochim Biophys Acta Gen Subj 2013; 1840:315-21. [PMID: 24016602 DOI: 10.1016/j.bbagen.2013.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 08/31/2013] [Accepted: 09/03/2013] [Indexed: 12/17/2022]
Abstract
BACKGROUND Dynamin 2 (Dyn2) is a ~100kDa GTPase that assembles around the necks of nascent endocytic and Golgi vesicles and catalyzes membrane scission. Mutations in Dyn2 that cause centronuclear myopathy (CNM) have been shown to stabilize Dyn2 polymers against GTP-dependent disassembly in vitro. Precisely timed regulation of assembly and disassembly is believed to be critical for Dyn2 function in membrane vesiculation, and the CNM mutations interfere with this regulation by shifting the equilibrium toward the assembled state. METHODS In this study we use two fluorescence fluctuation spectroscopy (FFS) approaches to show that a CNM mutant form of Dyn2 also has a greater propensity to self-assemble in the cytosol and on the plasma membrane of living cells. RESULTS Results obtained using brightness analysis indicate that unassembled wild-type Dyn2 is predominantly tetrameric in the cytosol, although different oligomeric species are observed, depending on the concentration of expressed protein. In contrast, an R369W mutant identified in CNM patients forms higher-order oligomers at concentrations above 1μM. Investigation of Dyn2-R369W by Total Internal Reflection Fluorescence (TIRF) FFS reveals that this mutant forms larger and more stable clathrin-containing structures on the plasma membrane than wild-type Dyn2. CONCLUSIONS AND GENERAL SIGNIFICANCE These observations may explain defects in membrane trafficking reported in CNM patient cells and in heterologous systems expressing CNM-associated Dyn2 mutants.
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Affiliation(s)
- Nicholas G James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, Biosciences 222, Honolulu, HI 96813, USA
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Abstract
Single-cell studies of gene regulation suggest that transcription dynamics play a fundamental role in determining expression heterogeneity within a population. In addition, the three-dimensional organization of the nucleus seems to both reflect and influence expression patterns in the cell. Therefore, to gain a holistic understanding of transcriptional regulation, it is necessary to develop methods for studying transcription of single genes in living cells with high spatial and temporal resolution. In this chapter, we describe a recently developed approach for visualizing and quantifying pre-mRNA synthesis at a single active gene in the nucleus. The approach is based on the high-affinity interaction between MS2/PP7 bacteriophage coat proteins and RNA hairpins which are transcribed by the gene of interest. The MS2/PP7 coat protein is fused to a fluorescent protein and binds the nascent mRNA, allowing for detection of single transcription events in the fluorescence microscope. By time-lapse fluorescence imaging and quantitative image analysis, one can generate a time trace of fluorescence intensity at the site of transcription. By temporal autocorrelation analysis, one can determine enzymatic activities of RNAP such as initiation rate and elongation rate. In this protocol, we summarize the experimental concept, design, and execution for real-time observation of transcription in living cells.
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Affiliation(s)
- Matthew L. Ferguson
- Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD 20892
| | - Daniel R. Larson
- Center for Cancer Research, National Cancer Institute, National Institutes of Health Bethesda, MD 20892
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Macháň R, Hof M. Recent developments in fluorescence correlation spectroscopy for diffusion measurements in planar lipid membranes. Int J Mol Sci 2010; 11:427-457. [PMID: 20386647 PMCID: PMC2852847 DOI: 10.3390/ijms11020427] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/11/2010] [Accepted: 01/15/2010] [Indexed: 12/11/2022] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule technique used mainly for determination of mobility and local concentration of molecules. This review describes the specific problems of FCS in planar systems and reviews the state of the art experimental approaches such as 2-focus, Z-scan or scanning FCS, which overcome most of the artefacts and limitations of standard FCS. We focus on diffusion measurements of lipids and proteins in planar lipid membranes and review the contributions of FCS to elucidating membrane dynamics and the factors influencing it, such as membrane composition, ionic strength, presence of membrane proteins or frictional coupling with solid support.
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Affiliation(s)
- Radek Macháň
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i., Dolejškova 2155/3, 182 23 Prague, Czech Republic; E-Mail:
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of ASCR, v.v.i., Dolejškova 2155/3, 182 23 Prague, Czech Republic; E-Mail:
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