1
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Longfield SF, Gormal RS, Feller M, Parutto P, Reingruber J, Wallis TP, Joensuu M, Augustine GJ, Martínez-Mármol R, Holcman D, Meunier FA. Synapsin 2a tetramerisation selectively controls the presynaptic nanoscale organisation of reserve synaptic vesicles. Nat Commun 2024; 15:2217. [PMID: 38472171 PMCID: PMC10933366 DOI: 10.1038/s41467-024-46256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Neurotransmitter release relies on the regulated fusion of synaptic vesicles (SVs) that are tightly packed within the presynaptic bouton of neurons. The mechanism by which SVs are clustered at the presynapse, while preserving their ability to dynamically recycle to support neuronal communication, remains unknown. Synapsin 2a (Syn2a) tetramerization has been suggested as a potential clustering mechanism. Here, we used Dual-pulse sub-diffractional Tracking of Internalised Molecules (DsdTIM) to simultaneously track single SVs from the recycling and the reserve pools, in live hippocampal neurons. The reserve pool displays a lower presynaptic mobility compared to the recycling pool and is also present in the axons. Triple knockout of Synapsin 1-3 genes (SynTKO) increased the mobility of reserve pool SVs. Re-expression of wild-type Syn2a (Syn2aWT), but not the tetramerization-deficient mutant K337Q (Syn2aK337Q), fully rescued these effects. Single-particle tracking revealed that Syn2aK337QmEos3.1 exhibited altered activity-dependent presynaptic translocation and nanoclustering. Therefore, Syn2a tetramerization controls its own presynaptic nanoclustering and thereby contributes to the dynamic immobilisation of the SV reserve pool.
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Affiliation(s)
- Shanley F Longfield
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matis Feller
- Group of Data Modelling and Computational Biology, IBENS, Ecole Normale Superieure, 75005, Paris, France
| | - Pierre Parutto
- Group of Data Modelling and Computational Biology, IBENS, Ecole Normale Superieure, 75005, Paris, France
| | - Jürgen Reingruber
- Group of Data Modelling and Computational Biology, IBENS, Ecole Normale Superieure, 75005, Paris, France
| | - Tristan P Wallis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Ramón Martínez-Mármol
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David Holcman
- Group of Data Modelling and Computational Biology, IBENS, Ecole Normale Superieure, 75005, Paris, France
- Department of Applied Mathematics and Theoretical Physics (DAMPT) visitor, University of Cambridge, and Churchill College, CB30DS, Cambridge, UK
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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2
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Doerries TJ, Chechkin AV, Metzler R. Apparent anomalous diffusion and non-Gaussian distributions in a simple mobile-immobile transport model with Poissonian switching. J R Soc Interface 2022; 19:20220233. [PMID: 35857918 PMCID: PMC9257594 DOI: 10.1098/rsif.2022.0233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/15/2022] [Indexed: 09/01/2023] Open
Abstract
We analyse mobile-immobile transport of particles that switch between the mobile and immobile phases with finite rates. Despite this seemingly simple assumption of Poissonian switching, we unveil a rich transport dynamics including significant transient anomalous diffusion and non-Gaussian displacement distributions. Our discussion is based on experimental parameters for tau proteins in neuronal cells, but the results obtained here are expected to be of relevance for a broad class of processes in complex systems. Specifically, we obtain that, when the mean binding time is significantly longer than the mean mobile time, transient anomalous diffusion is observed at short and intermediate time scales, with a strong dependence on the fraction of initially mobile and immobile particles. We unveil a Laplace distribution of particle displacements at relevant intermediate time scales. For any initial fraction of mobile particles, the respective mean squared displacement (MSD) displays a plateau. Moreover, we demonstrate a short-time cubic time dependence of the MSD for immobile tracers when initially all particles are immobile.
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Affiliation(s)
- Timo J. Doerries
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
| | - Aleksei V. Chechkin
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology, Wyspianskiego 27, 50-370 Wrocław, Poland
- Akhiezer Institute for Theoretical Physics, National Science Center ‘Kharkiv Institute of Physics and Technology’, 61108 Kharkiv, Ukraine
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, 14476 Potsdam, Germany
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3
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Reshetniak S, Ußling JE, Perego E, Rammner B, Schikorski T, Fornasiero EF, Truckenbrodt S, Köster S, Rizzoli SO. A comparative analysis of the mobility of 45 proteins in the synaptic bouton. EMBO J 2020; 39:e104596. [PMID: 32627850 PMCID: PMC7429486 DOI: 10.15252/embj.2020104596] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/20/2020] [Accepted: 05/29/2020] [Indexed: 02/01/2023] Open
Abstract
Many proteins involved in synaptic transmission are well known, and their features, as their abundance or spatial distribution, have been analyzed in systematic studies. This has not been the case, however, for their mobility. To solve this, we analyzed the motion of 45 GFP‐tagged synaptic proteins expressed in cultured hippocampal neurons, using fluorescence recovery after photobleaching, particle tracking, and modeling. We compared synaptic vesicle proteins, endo‐ and exocytosis cofactors, cytoskeleton components, and trafficking proteins. We found that movement was influenced by the protein association with synaptic vesicles, especially for membrane proteins. Surprisingly, protein mobility also correlated significantly with parameters as the protein lifetimes, or the nucleotide composition of their mRNAs. We then analyzed protein movement thoroughly, taking into account the spatial characteristics of the system. This resulted in a first visualization of overall protein motion in the synapse, which should enable future modeling studies of synaptic physiology.
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Affiliation(s)
- Sofiia Reshetniak
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany.,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Jan-Eike Ußling
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany
| | - Eleonora Perego
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany
| | - Burkhard Rammner
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany
| | - Thomas Schikorski
- Department of Neuroscience, Universidad Central del Caribe, Bayamon, PR, USA
| | - Eugenio F Fornasiero
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany
| | - Sven Truckenbrodt
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany.,International Max Planck Research School for Molecular Biology, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Silvio O Rizzoli
- Institute for Neuro- and Sensory Physiology and Biostructural Imaging of Neurodegeneration (BIN) Center, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
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4
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Stolle MDN, Fradin C. Anomalous Diffusion in Inverted Variable-Lengthscale Fluorescence Correlation Spectroscopy. Biophys J 2019; 116:791-806. [PMID: 30782396 PMCID: PMC6400862 DOI: 10.1016/j.bpj.2019.01.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 12/12/2018] [Accepted: 01/14/2019] [Indexed: 11/24/2022] Open
Abstract
Using fluorescence correlation spectroscopy (FCS) to distinguish between different types of diffusion processes is often a perilous undertaking because the analysis of the resulting autocorrelation data is model dependant. Two recently introduced strategies, however, can help move toward a model-independent interpretation of FCS experiments: 1) the obtention of correlation data at different length scales and 2) their inversion to retrieve the mean-squared displacement associated with the process under study. We use computer simulations to examine the signature of several biologically relevant diffusion processes (simple diffusion, continuous-time random walk, caged diffusion, obstructed diffusion, two-state diffusion, and diffusing diffusivity) in variable-length-scale FCS. We show that, when used in concert, length-scale variation and data inversion permit us to identify non-Gaussian processes and, regardless of Gaussianity, to retrieve their mean-squared displacement over several orders of magnitude in time. This makes unbiased discrimination between different classes of diffusion models possible.
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Affiliation(s)
- Michael D N Stolle
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Cécile Fradin
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
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5
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Activity-Dependence of Synaptic Vesicle Dynamics. J Neurosci 2017; 37:10597-10610. [PMID: 28954868 DOI: 10.1523/jneurosci.0383-17.2017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 08/08/2017] [Accepted: 08/15/2017] [Indexed: 11/21/2022] Open
Abstract
The proper function of synapses relies on efficient recycling of synaptic vesicles. The small size of synaptic boutons has hampered efforts to define the dynamical states of vesicles during recycling. Moreover, whether vesicle motion during recycling is regulated by neural activity remains largely unknown. We combined nanoscale-resolution tracking of individual synaptic vesicles in cultured hippocampal neurons from rats of both sexes with advanced motion analyses to demonstrate that the majority of recently endocytosed vesicles undergo sequences of transient dynamical states including epochs of directed, diffusional, and stalled motion. We observed that vesicle motion is modulated in an activity-dependent manner, with dynamical changes apparent in ∼20% of observed boutons. Within this subpopulation of boutons, 35% of observed vesicles exhibited acceleration and 65% exhibited deceleration, accompanied by corresponding changes in directed motion. Individual vesicles observed in the remaining ∼80% of boutons did not exhibit apparent dynamical changes in response to stimulation. More quantitative transient motion analyses revealed that the overall reduction of vesicle mobility, and specifically of the directed motion component, is the predominant activity-evoked change across the entire bouton population. Activity-dependent modulation of vesicle mobility may represent an important mechanism controlling vesicle availability and neurotransmitter release.SIGNIFICANCE STATEMENT Mechanisms governing synaptic vesicle dynamics during recycling remain poorly understood. Using nanoscale resolution tracking of individual synaptic vesicles in hippocampal synapses and advanced motion analysis tools we demonstrate that synaptic vesicles undergo complex sets of dynamical states that include epochs of directed, diffusive, and stalled motion. Most importantly, our analyses revealed that vesicle motion is modulated in an activity-dependent manner apparent as the reduction in overall vesicle mobility in response to stimulation. These results define the vesicle dynamical states during recycling and reveal their activity-dependent modulation. Our study thus provides fundamental new insights into the principles governing synaptic function.
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6
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Fradin C. On the importance of protein diffusion in biological systems: The example of the Bicoid morphogen gradient. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1676-1686. [PMID: 28919007 DOI: 10.1016/j.bbapap.2017.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 08/16/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Morphogens are proteins that form concentration gradients in embryos and developing tissues, where they act as postal codes, providing cells with positional information and allowing them to behave accordingly. Bicoid was the first discovered morphogen, and remains one of the most studied. It regulates segmentation in flies, forming a striking exponential gradient along the anterior-posterior axis of early Drosophila embryos, and activating the transcription of multiple target genes in a concentration-dependent manner. In this review, the work done by us and by others to characterize the mobility of Bicoid in D. melanogaster embryos is presented. The central role played by the diffusion of Bicoid in both the establishment of the gradient and the activation of target genes is discussed, and placed in the context of the need for these processes to be all at once rapid, precise and robust. The Bicoid system, and morphogen gradients in general, remain amongst the most amazing examples of the coexistence, often observed in living systems, of small-scale disorder and large-scale spatial order. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Cécile Fradin
- Dept. of Physics and Astronomy, McMaster University, 1280 Main St W., Hamilton, ON L8S 4M1, Canada
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7
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Mir M, Reimer A, Haines JE, Li XY, Stadler M, Garcia H, Eisen MB, Darzacq X. Dense Bicoid hubs accentuate binding along the morphogen gradient. Genes Dev 2017; 31:1784-1794. [PMID: 28982761 PMCID: PMC5666676 DOI: 10.1101/gad.305078.117] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 09/06/2017] [Indexed: 11/24/2022]
Abstract
Morphogen gradients direct the spatial patterning of developing embryos; however, the mechanisms by which these gradients are interpreted remain elusive. Here we used lattice light-sheet microscopy to perform in vivo single-molecule imaging in early Drosophila melanogaster embryos of the transcription factor Bicoid that forms a gradient and initiates patterning along the anteroposterior axis. In contrast to canonical models, we observed that Bicoid binds to DNA with a rapid off rate throughout the embryo such that its average occupancy at target loci is on-rate-dependent. We further observed Bicoid forming transient "hubs" of locally high density that facilitate binding as factor levels drop, including in the posterior, where we observed Bicoid binding despite vanishingly low protein levels. We propose that localized modulation of transcription factor on rates via clustering provides a general mechanism to facilitate binding to low-affinity targets and that this may be a prevalent feature of other developmental transcription factors.
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Affiliation(s)
- Mustafa Mir
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, 94720, USA
| | - Armando Reimer
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, 94720, USA
| | - Jenna E Haines
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, 94720, USA
| | - Xiao-Yong Li
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California, 94720, USA
| | - Michael Stadler
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, 94720, USA
| | - Hernan Garcia
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, 94720, USA
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, California, 94720, USA
| | - Michael B Eisen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, 94720, USA
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California, 94720, USA
- Department of Integrative Biology, University of California at Berkeley, Berkeley, California, 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, 94720, USA
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8
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Robinson BJ, Stanisavljevic B, Silverman MA, Scalettar BA. Stochastic Subcellular Organization of Dense-Core Vesicles Revealed by Point Pattern Analysis. Biophys J 2017; 111:852-863. [PMID: 27558728 DOI: 10.1016/j.bpj.2016.07.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/20/2016] [Accepted: 07/05/2016] [Indexed: 12/20/2022] Open
Abstract
Dense-core vesicles (DCVs) are regulated secretory organelles found in many types of neurons. In neurons of the hippocampus, their cargo includes proteins that mediate several pivotal processes, including differentiation and synaptic plasticity. Motivated by interest in DCV distribution and its impact on cargo action, we have used fluorescence microscopy and statistical analysis to develop a quantitative model of the subcellular organization of DCVs in hippocampal neurons that are spontaneously active (their most prevalent state). We also have tested the functionally motivated hypothesis that these organelles are synaptically enriched. Variance-to-mean ratio, frequency distribution, and Moran's autocorrelation analyses reveal that DCV distribution along shafts, and within synapses, follows Poisson statistics, establishing that stochastically dictated organization sustains cargo function. Occupancy in boutons exceeds that at nearby extrasynaptic axonal sites by approximately threefold, revealing significant local presynaptic enrichment. Widespread stochastic organization is consistent with the emerging functional importance of synaptically and extrasynaptically localized DCVs. Presynaptic enrichment is consistent with the established importance of protecting presynaptic sites from depletion of DCV cargo. These results enhance understanding of the link between DCV organization and mechanisms of cargo action, and they reinforce the emerging theme that randomness is a prevalent aspect of synaptic organization and composition.
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Affiliation(s)
- Benjamin J Robinson
- Department of Physics, Lewis & Clark College, Portland, Oregon; Department of Mathematics, Lewis & Clark College, Portland, Oregon
| | - Bogdan Stanisavljevic
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael A Silverman
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Bethe A Scalettar
- Department of Physics, Lewis & Clark College, Portland, Oregon; Program in Biochemistry and Molecular Biology, Lewis & Clark College, Portland, Oregon.
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9
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Measuring synaptic vesicles using cellular electrochemistry and nanoscale molecular imaging. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0048] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Hansen AS, Pustova I, Cattoglio C, Tjian R, Darzacq X. CTCF and cohesin regulate chromatin loop stability with distinct dynamics. eLife 2017; 6:e25776. [PMID: 28467304 PMCID: PMC5446243 DOI: 10.7554/elife.25776] [Citation(s) in RCA: 362] [Impact Index Per Article: 51.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/30/2017] [Indexed: 12/13/2022] Open
Abstract
Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding domains into loop structures, which are widely thought to be stable. Combining genomic and biochemical approaches we show that CTCF and cohesin co-occupy the same sites and physically interact as a biochemically stable complex. However, using single-molecule imaging we find that CTCF binds chromatin much more dynamically than cohesin (~1-2 min vs. ~22 min residence time). Moreover, after unbinding, CTCF quickly rebinds another cognate site unlike cohesin for which the search process is long (~1 min vs. ~33 min). Thus, CTCF and cohesin form a rapidly exchanging 'dynamic complex' rather than a typical stable complex. Since CTCF and cohesin are required for loop domain formation, our results suggest that chromatin loops are dynamic and frequently break and reform throughout the cell cycle.
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Affiliation(s)
- Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Iryna Pustova
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, United States
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
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11
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Hołyst R, Poniewierski A, Zhang X. Analytical form of the autocorrelation function for the fluorescence correlation spectroscopy. SOFT MATTER 2017; 13:1267-1275. [PMID: 28106203 DOI: 10.1039/c6sm02643e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Fluorescence correlation spectroscopy (FCS) can provide information about diffusion coefficients and rate constants of chemical reactions in small systems of interacting molecules. However, the interpretation of FCS experiments depends crucially on the model of the autocorrelation function for the fluorescence intensity fluctuations. In this theoretical work, we consider a system of fluorescent molecules that diffuse and interact with massive particles, e.g. surfactant micelles. Using the general formalism of FCS, we derive a new analytical approximation of the autocorrelation function for systems in which both diffusion and a binary reaction occur. This approximation provides a smooth interpolation between the limit of fast reaction (much faster than diffusion), and the opposite limit of slow reaction. Our studies of noncovalent interactions of micelles with dyes by FCS provided an experimental case to which the approximate autocorrelation function was successfully applied [X. Zhang, A. Poniewierski, A. Jelińska, A. Zagożdżon, A. Wisniewska, S. Hou and R. Hołyst, Soft Matter, 2016, 12, 8186-8194].
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Affiliation(s)
- Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Andrzej Poniewierski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Xuzhu Zhang
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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12
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Joensuu M, Padmanabhan P, Durisic N, Bademosi ATD, Cooper-Williams E, Morrow IC, Harper CB, Jung W, Parton RG, Goodhill GJ, Papadopulos A, Meunier FA. Subdiffractional tracking of internalized molecules reveals heterogeneous motion states of synaptic vesicles. J Cell Biol 2016; 215:277-292. [PMID: 27810917 PMCID: PMC5080683 DOI: 10.1083/jcb.201604001] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/30/2016] [Indexed: 11/23/2022] Open
Abstract
Joensuu et al. describe a tool for subdiffractional tracking of internalized molecules. They reveal that synaptic vesicles exhibit stochastic switching between heterogeneous diffusive and transport states in live hippocampal nerve terminals. Our understanding of endocytic pathway dynamics is severely restricted by the diffraction limit of light microscopy. To address this, we implemented a novel technique based on the subdiffractional tracking of internalized molecules (sdTIM). This allowed us to image anti–green fluorescent protein Atto647N-tagged nanobodies trapped in synaptic vesicles (SVs) from live hippocampal nerve terminals expressing vesicle-associated membrane protein 2 (VAMP2)–pHluorin with 36-nm localization precision. Our results showed that, once internalized, VAMP2–pHluorin/Atto647N–tagged nanobodies exhibited a markedly lower mobility than on the plasma membrane, an effect that was reversed upon restimulation in presynapses but not in neighboring axons. Using Bayesian model selection applied to hidden Markov modeling, we found that SVs oscillated between diffusive states or a combination of diffusive and transport states with opposite directionality. Importantly, SVs exhibiting diffusive motion were relatively less likely to switch to the transport motion. These results highlight the potential of the sdTIM technique to provide new insights into the dynamics of endocytic pathways in a wide variety of cellular settings.
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Affiliation(s)
- Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Pranesh Padmanabhan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adekunle T D Bademosi
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Isabel C Morrow
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Callista B Harper
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - WooRam Jung
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.,Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andreas Papadopulos
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia .,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia .,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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13
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An Intermittent Model for Intracellular Motions of Gold Nanostars by k-Space Scattering Image Correlation. Biophys J 2016; 109:2246-58. [PMID: 26636936 DOI: 10.1016/j.bpj.2015.10.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/09/2015] [Accepted: 10/21/2015] [Indexed: 11/20/2022] Open
Abstract
Anisotropic metallic nanoparticles have been devised as powerful potential tools for in vivo imaging, photothermal therapy, and drug delivery thanks to plasmon-enhanced absorption and scattering cross sections, ease in synthesis and functionalization, and controlled cytotoxicity. The rational design of all these applications requires the characterization of the nanoparticles intracellular trafficking pathways. In this work, we exploit live-cell time-lapse confocal reflectance microscopy and image correlation in both direct and reciprocal space to investigate the intracellular transport of branched gold nanostars (GNSs). Different transport mechanisms, spanning from pure Brownian diffusion to (sub-)ballistic superdiffusion, are revealed by temporal and spatio-temporal image correlation spectroscopy on the tens-of-seconds timescale. According to these findings, combined with numerical simulations and with a Bayesian (hidden Markov model-based) analysis of single particle tracking data, we ascribe the superdiffusive, subballistic behavior characterizing the GNSs dynamics to a two-state switching between Brownian diffusion in the cytoplasm and molecular motor-mediated active transport. For the investigation of intermittent-type transport phenomena, we derive an analytical theoretical framework for Fourier-space image correlation spectroscopy (kICS). At first, we evaluate the influence of all the dynamic and kinetic parameters (the diffusion coefficient, the drift velocity, and the transition rates between the diffusive and the active transport regimes) on simulated kICS correlation functions. Then we outline a protocol for data analysis and employ it to derive whole-cell maps for each parameter underlying the GNSs intracellular dynamics. Capable of identifying even simpler transport phenomena, whether purely diffusive or ballistic, our intermittent kICS approach allows an exhaustive investigation of the dynamics of GNSs and biological macromolecules.
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14
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Rothman JS, Kocsis L, Herzog E, Nusser Z, Silver RA. Physical determinants of vesicle mobility and supply at a central synapse. eLife 2016; 5. [PMID: 27542193 PMCID: PMC5025287 DOI: 10.7554/elife.15133] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 08/14/2016] [Indexed: 12/22/2022] Open
Abstract
Encoding continuous sensory variables requires sustained synaptic signalling. At several sensory synapses, rapid vesicle supply is achieved via highly mobile vesicles and specialized ribbon structures, but how this is achieved at central synapses without ribbons is unclear. Here we examine vesicle mobility at excitatory cerebellar mossy fibre synapses which sustain transmission over a broad frequency bandwidth. Fluorescent recovery after photobleaching in slices from VGLUT1Venus knock-in mice reveal 75% of VGLUT1-containing vesicles have a high mobility, comparable to that at ribbon synapses. Experimentally constrained models establish hydrodynamic interactions and vesicle collisions are major determinants of vesicle mobility in crowded presynaptic terminals. Moreover, models incorporating 3D reconstructions of vesicle clouds near active zones (AZs) predict the measured releasable pool size and replenishment rate from the reserve pool. They also show that while vesicle reloading at AZs is not diffusion-limited at the onset of release, diffusion limits vesicle reloading during sustained high-frequency signalling. DOI:http://dx.doi.org/10.7554/eLife.15133.001
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Affiliation(s)
- Jason Seth Rothman
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Laszlo Kocsis
- Laboratory of Cellular Neurophysiology, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Etienne Herzog
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany.,Team Synapse in Cognition, Interdisciplinary Institute for Neuroscience, Université de Bordeaux, UMR 5297, F-33000, Bordeaux, France
| | - Zoltan Nusser
- Laboratory of Cellular Neurophysiology, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Robin Angus Silver
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
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15
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Banks DS, Tressler C, Peters RD, Höfling F, Fradin C. Characterizing anomalous diffusion in crowded polymer solutions and gels over five decades in time with variable-lengthscale fluorescence correlation spectroscopy. SOFT MATTER 2016; 12:4190-4203. [PMID: 27050290 DOI: 10.1039/c5sm01213a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The diffusion of macromolecules in cells and in complex fluids is often found to deviate from simple Fickian diffusion. One explanation offered for this behavior is that molecular crowding renders diffusion anomalous, where the mean-squared displacement of the particles scales as 〈r(2)〉∝t(α) with α < 1. Unfortunately, methods such as fluorescence correlation spectroscopy (FCS) or fluorescence recovery after photobleaching (FRAP) probe diffusion only over a narrow range of lengthscales and cannot directly test the dependence of the mean-squared displacement (MSD) on time. Here we show that variable-lengthscale FCS (VLS-FCS), where the volume of observation is varied over several orders of magnitude, combined with a numerical inversion procedure of the correlation data, allows retrieving the MSD for up to five decades in time, bridging the gap between diffusion experiments performed at different lengthscales. In addition, we show that VLS-FCS provides a way to assess whether the propagator associated with the diffusion is Gaussian or non-Gaussian. We used VLS-FCS to investigate two systems where anomalous diffusion had been previously reported. In the case of dense cross-linked agarose gels, the measured MSD confirmed that the diffusion of small beads was anomalous at short lengthscales, with a cross-over to simple diffusion around ≈1 μm, consistent with a caged diffusion process. On the other hand, for solutions crowded with marginally entangled dextran molecules, we uncovered an apparent discrepancy between the MSD, found to be linear, and the propagators at short lengthscales, found to be non-Gaussian. These contradicting features call to mind the "anomalous, yet Brownian" diffusion observed in several biological systems, and the recently proposed "diffusing diffusivity" model.
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Affiliation(s)
- Daniel S Banks
- Department of Physics and Astronomy, McMaster University, 1280 Main St. W, Hamilton, ON L8S 4M1, Canada.
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16
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A nanoscale resolution view on synaptic vesicle dynamics. Synapse 2014; 69:256-67. [DOI: 10.1002/syn.21795] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/20/2014] [Accepted: 11/27/2014] [Indexed: 12/31/2022]
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17
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Single-molecule dynamics of enhanceosome assembly in embryonic stem cells. Cell 2014; 156:1274-1285. [PMID: 24630727 PMCID: PMC4040518 DOI: 10.1016/j.cell.2014.01.062] [Citation(s) in RCA: 414] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/16/2013] [Accepted: 01/27/2014] [Indexed: 11/21/2022]
Abstract
Enhancer-binding pluripotency regulators (Sox2 and Oct4) play a seminal role in embryonic stem (ES) cell-specific gene regulation. Here, we combine in vivo and in vitro single-molecule imaging, transcription factor (TF) mutagenesis, and ChIP-exo mapping to determine how TFs dynamically search for and assemble on their cognate DNA target sites. We find that enhanceosome assembly is hierarchically ordered with kinetically favored Sox2 engaging the target DNA first, followed by assisted binding of Oct4. Sox2/Oct4 follow a trial-and-error sampling mechanism involving 84-97 events of 3D diffusion (3.3-3.7 s) interspersed with brief nonspecific collisions (0.75-0.9 s) before acquiring and dwelling at specific target DNA (12.0-14.6 s). Sox2 employs a 3D diffusion-dominated search mode facilitated by 1D sliding along open DNA to efficiently locate targets. Our findings also reveal fundamental aspects of gene and developmental regulation by fine-tuning TF dynamics and influence of the epigenome on target search parameters.
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18
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Piskorz TK, Ochab-Marcinek A. A Universal Model of Restricted Diffusion for Fluorescence Correlation Spectroscopy. J Phys Chem B 2014; 118:4906-12. [DOI: 10.1021/jp502467u] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Tomasz K. Piskorz
- Department
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Anna Ochab-Marcinek
- Institute
of Physical Chemistry, Polish Academy of Sciences, ul. Kasprzaka
44/52, 01-224 Warsaw, Poland
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19
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Abstract
Synaptic vesicle recycling is one of the best-studied cellular pathways. Many of the proteins involved are known, and their interactions are becoming increasingly clear. However, as for many other pathways, it is still difficult to understand synaptic vesicle recycling as a whole. While it is generally possible to point out how synaptic reactions take place, it is not always easy to understand what triggers or controls them. Also, it is often difficult to understand how the availability of the reaction partners is controlled: how the reaction partners manage to find each other in the right place, at the right time. I present here an overview of synaptic vesicle recycling, discussing the mechanisms that trigger different reactions, and those that ensure the availability of reaction partners. A central argument is that synaptic vesicles bind soluble cofactor proteins, with low affinity, and thus control their availability in the synapse, forming a buffer for cofactor proteins. The availability of cofactor proteins, in turn, regulates the different synaptic reactions. Similar mechanisms, in which one of the reaction partners buffers another, may apply to many other processes, from the biogenesis to the degradation of the synaptic vesicle.
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Affiliation(s)
- Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen European Neuroscience Institute, Göttingen, Germany
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20
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Staras K, Mikulincer D, Gitler D. Monitoring and quantifying dynamic physiological processes in live neurons using fluorescence recovery after photobleaching. J Neurochem 2013; 126:213-22. [PMID: 23496032 DOI: 10.1111/jnc.12240] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 12/27/2022]
Abstract
The direct visualization of subcellular dynamic processes is often hampered by limitations in the resolving power achievable with conventional microscopy techniques. Fluorescence recovery after photobleaching has emerged as a highly informative approach to address this challenge, permitting the quantitative measurement of the movement of small organelles and proteins in living functioning cells, and offering detailed insights into fundamental cellular phenomena of physiological importance. In recent years, its implementation has benefited from the increasing availability of confocal microscopy systems and of powerful labeling techniques based on genetically encoded fluorescent proteins or other chemical markers. In this review, we present fluorescence recovery after photobleaching and related techniques in the context of contemporary neurobiological research and discuss quantitative and semi-quantitative approaches to their interpretation.
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Affiliation(s)
- Kevin Staras
- School of Life Sciences, University of Sussex, Brighton, UK
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21
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Mazza D, Abernathy A, Golob N, Morisaki T, McNally JG. A benchmark for chromatin binding measurements in live cells. Nucleic Acids Res 2012; 40:e119. [PMID: 22844090 PMCID: PMC3424588 DOI: 10.1093/nar/gks701] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Live-cell measurement of protein binding to chromatin allows probing cellular biochemistry in physiological conditions, which are difficult to mimic in vitro. However, different studies have yielded widely discrepant predictions, and so it remains uncertain how to make the measurements accurately. To establish a benchmark we measured binding of the transcription factor p53 to chromatin by three approaches: fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and single-molecule tracking (SMT). Using new procedures to analyze the SMT data and to guide the FRAP and FCS analysis, we show how all three approaches yield similar estimates for both the fraction of p53 molecules bound to chromatin (only about 20%) and the residence time of these bound molecules (∼1.8 s). We also apply these procedures to mutants in p53 chromatin binding. Our results support the model that p53 locates specific sites by first binding at sequence-independent sites.
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Affiliation(s)
- Davide Mazza
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, 20892, Bethesda, MD, USA
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22
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Lee S, Jung KJ, Jung HS, Chang S. Dynamics of multiple trafficking behaviors of individual synaptic vesicles revealed by quantum-dot based presynaptic probe. PLoS One 2012; 7:e38045. [PMID: 22666444 PMCID: PMC3362565 DOI: 10.1371/journal.pone.0038045] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 05/02/2012] [Indexed: 11/26/2022] Open
Abstract
Although quantum dots (QDs) have provided invaluable information regarding the diffusive behaviors of postsynaptic receptors, their application in presynaptic terminals has been rather limited. In addition, the diffraction-limited nature of the presynaptic bouton has hampered detailed analyses of the behaviors of synaptic vesicles (SVs) at synapses. Here, we created a quantum-dot based presynaptic probe and characterized the dynamic behaviors of individual SVs. As previously reported, the SVs exhibited multiple exchanges between neighboring boutons. Actin disruption induced a dramatic decrease in the diffusive behaviors of SVs at synapses while microtubule disruption only reduced extrasynaptic mobility. Glycine-induced synaptic potentiation produced significant increases in synaptic and inter-boutonal trafficking of SVs, which were NMDA receptor- and actin-dependent while NMDA-induced synaptic depression decreased the mobility of the SVs at synapses. Together, our results show that sPH-AP-QD revealed previously unobserved trafficking properties of SVs around synapses, and the dynamic modulation of SV mobility could regulate presynaptic efficacy during synaptic activity.
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Affiliation(s)
- Suho Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Kyung Jin Jung
- Division of Electron Microscopic research, Korea Basic Science Institute, Daejeon, South Korea
| | - Hyun Suk Jung
- Division of Electron Microscopic research, Korea Basic Science Institute, Daejeon, South Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Neuroscience Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
- Biomembrane Plasticity Research Center, Seoul National University College of Medicine, Seoul, South Korea
- Bio-Max Institute, Seoul National University College of Medicine, Seoul, South Korea
- * E-mail:
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23
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High- and low-mobility stages in the synaptic vesicle cycle. Biophys J 2010; 99:675-84. [PMID: 20643088 DOI: 10.1016/j.bpj.2010.04.054] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 04/12/2010] [Accepted: 04/20/2010] [Indexed: 11/24/2022] Open
Abstract
Synaptic vesicles need to be mobile to reach their release sites during synaptic activity. We investigated vesicle mobility throughout the synaptic vesicle cycle using both conventional and subdiffraction-resolution stimulated emission depletion fluorescence microscopy. Vesicle tracking revealed that recently endocytosed synaptic vesicles are highly mobile for a substantial time period after endocytosis. They later undergo a maturation process and integrate into vesicle clusters where they exhibit little mobility. Despite the differences in mobility, both recently endocytosed and mature vesicles are exchanged between synapses. Electrical stimulation does not seem to affect the mobility of the two types of vesicles. After exocytosis, the vesicle material is mobile in the plasma membrane, although the movement appears to be somewhat limited. Increasing the proportion of fused vesicles (by stimulating exocytosis while simultaneously blocking endocytosis) leads to substantially higher mobility. We conclude that both high- and low-mobility states are characteristic of synaptic vesicle movement.
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24
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Denker A, Rizzoli SO. Synaptic vesicle pools: an update. Front Synaptic Neurosci 2010; 2:135. [PMID: 21423521 PMCID: PMC3059705 DOI: 10.3389/fnsyn.2010.00135] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2010] [Accepted: 08/02/2010] [Indexed: 12/04/2022] Open
Abstract
During the last few decades synaptic vesicles have been assigned to a variety of functional and morphological classes or “pools”. We have argued in the past (Rizzoli and Betz, 2005) that synaptic activity in several preparations is accounted for by the function of three vesicle pools: the readily releasable pool (docked at active zones and ready to go upon stimulation), the recycling pool (scattered throughout the nerve terminals and recycling upon moderate stimulation), and finally the reserve pool (occupying most of the vesicle clusters and only recycling upon strong stimulation). We discuss here the advancements in the vesicle pool field which took place in the ensuing years, focusing on the behavior of different pools under both strong stimulation and physiological activity. Several new findings have enhanced the three-pool model, with, for example, the disparity between recycling and reserve vesicles being underlined by the observation that the former are mobile, while the latter are “fixed”. Finally, a number of altogether new concepts have also evolved such as the current controversy on the identity of the spontaneously recycling vesicle pool.
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Affiliation(s)
- Annette Denker
- European Neuroscience Institute, DFG Center for Molecular Physiology of the Brain Göttingen, Germany
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25
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Spatial distribution and mobility of the Ran GTPase in live interphase cells. Biophys J 2010; 97:2164-78. [PMID: 19843449 DOI: 10.1016/j.bpj.2009.07.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 07/14/2009] [Accepted: 07/30/2009] [Indexed: 12/30/2022] Open
Abstract
The GTPase Ran is a key regulator of molecular transport through nuclear pore complex (NPC) channels. To analyze the role of Ran in its nuclear transport function, we used several quantitative fluorescence techniques to follow the distribution and dynamics of an enhanced yellow fluorescent protein (EYFP)-Ran in HeLa cells. The diffusion coefficient of the majority of EYFP-Ran molecules throughout the cells corresponded to an unbound state, revealing the remarkably dynamic Ran regulation. Although we observed no significant immobile Ran populations in cells, approximately 10% of the cytoplasmic EYFP-Ran and 30% of the nuclear EYFP-Ran exhibited low mobility indicative of molecular interactions. The high fraction of slow nuclear EYFP-Ran reflects the expected numerous interactions of nuclear RanGTP with nuclear transport receptors. However, it is not high enough to support retention mechanisms as the main cause for the observed nuclear accumulation of Ran. The highest cellular concentration of EYFP-Ran was detected at the nuclear envelope, corresponding to approximately 200 endogenous Ran molecules for each NPC, and exceeding the currently estimated NPC channel transport capacity. Together with the relatively long residence time of EYFP-Ran at the nuclear envelope (33 +/- 14 ms), these observations suggest that only a fraction of the Ran concentrated at NPCs transits through NPC channels.
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26
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Vámosi G, Damjanovich S, Szöllosi J, Vereb G. Measurement of molecular mobility with fluorescence correlation spectroscopy. ACTA ACUST UNITED AC 2009; Chapter 2:Unit2.15. [PMID: 19816923 DOI: 10.1002/0471142956.cy0215s50] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a fluctuation method established three decades ago, whose application to cellular systems became popular in the last decade. Fluctuations of fluorescence emission are observed from a small, femtoliter to sub-femtoliter, usually confocal volume at high time resolution. A time-dependent autocorrelation function is generated and evaluated to obtain time constants of photophysical and photochemical reactions, as well as of molecular diffusion and in the observation volume. Molecules in various subcellular compartments-including the nucleus, the cytoplasm, and the membrane-can be observed after labeling them with antibodies, ligands, or fluorescent proteins. The anomaly of diffusion, the local concentration, and the average fluorescence per diffusing particle can also be determined, all of which can be characteristic of molecular interactions. A two-color version of FCS, fluorescence cross-correlation spectroscopy, can also be applied to observe co-diffusion, i.e., stable association of two distinct molecular species in their cellular environment.
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Affiliation(s)
- György Vámosi
- Cell Biology and Signaling Research Group of the Hungarian Academy of Sciences, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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27
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Michelman-Ribeiro A, Mazza D, Rosales T, Stasevich TJ, Boukari H, Rishi V, Vinson C, Knutson JR, McNally JG. Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy. Biophys J 2009; 97:337-46. [PMID: 19580772 PMCID: PMC2711375 DOI: 10.1016/j.bpj.2009.04.027] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 04/07/2009] [Accepted: 04/22/2009] [Indexed: 10/20/2022] Open
Abstract
Measurement of live-cell binding interactions is vital for understanding the biochemical reactions that drive cellular processes. Here, we develop, characterize, and apply a new procedure to extract information about binding to an immobile substrate from fluorescence correlation spectroscopy (FCS) autocorrelation data. We show that existing methods for analyzing such data by two-component diffusion fits can produce inaccurate estimates of diffusion constants and bound fractions, or even fail altogether to fit FCS binding data. By analyzing live-cell FCS measurements, we show that our new model can satisfactorily account for the binding interactions introduced by attaching a DNA binding domain to the dimerization domain derived from a site-specific transcription factor (the vitellogenin binding protein (VBP)). We find that our FCS estimates are quantitatively consistent with our fluorescence recovery after photobleaching (FRAP) measurements on the same VBP domains. However, due to the fast binding interactions introduced by the DNA binding domain, FCS generates independent estimates for the diffusion constant (6.7 +/- 2.4 microm2/s) and the association (2 +/- 1.2 s(-1)) and dissociation (19 +/- 7 s(-1)) rates, whereas FRAP produces only a single, but a consistent, estimate, the effective-diffusion constant (4.4 +/- 1.4 microm2/s), which depends on all three parameters. We apply this new FCS method to evaluate the efficacy of a potential anticancer drug that inhibits DNA binding of VBP in vitro and find that in vivo the drug inhibits DNA binding in only a subset of cells. In sum, we provide a straightforward approach to directly measure binding rates from FCS data.
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Affiliation(s)
- Ariel Michelman-Ribeiro
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Davide Mazza
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Tilman Rosales
- Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Timothy J. Stasevich
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hacene Boukari
- Laboratory of Cell Biophysics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Vikas Rishi
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jay R. Knutson
- Laboratory of Molecular Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - James G. McNally
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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28
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Westphal V, Rizzoli SO, Lauterbach MA, Kamin D, Jahn R, Hell SW. Video-Rate Far-Field Optical Nanoscopy Dissects Synaptic Vesicle Movement. Science 2008; 320:246-9. [DOI: 10.1126/science.1154228] [Citation(s) in RCA: 626] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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29
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Abstract
We measured synaptic vesicle mobility using fluorescence recovery after photobleaching of FM 1-43 [N-(3-triethylammoniumpropyl)-4-(4-(dibutylamino)styryl) pyridinium dibromide] stained mouse motor nerve terminals obtained from wild-type (WT) and synapsin triple knock-out (TKO) mice at room temperature and physiological temperature. Vesicles were mobile in resting terminals at physiological temperature but virtually immobile at room temperature. Mobility was increased at both temperatures by blocking phosphatases with okadaic acid, decreased at physiological temperature by blocking kinases with staurosporine, and unaffected by disrupting actin filaments with latrunculin A or reducing intracellular calcium concentration with BAPTA-AM. Synapsin TKO mice showed reduced numbers of synaptic vesicles and reduced FM 1-43 staining intensity. Synaptic transmission, however, was indistinguishable from WT, as was synaptic vesicle mobility under all conditions tested. Thus, in TKO mice, and perhaps WT mice, a phospho-protein different from synapsin but otherwise of unknown identity is the primary regulator of synaptic vesicle mobility.
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