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Moores AN, Uphoff S. Robust Quantification of Live-Cell Single-Molecule Tracking Data for Fluorophores with Different Photophysical Properties. J Phys Chem B 2024; 128:7291-7303. [PMID: 38859654 PMCID: PMC11301680 DOI: 10.1021/acs.jpcb.4c01454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
High-speed single-molecule tracking in live cells is becoming an increasingly popular method for quantifying the spatiotemporal behavior of proteins in vivo. The method provides a wealth of quantitative information, but users need to be aware of biases that can skew estimates of molecular mobilities. The range of suitable fluorophores for live-cell single-molecule imaging has grown substantially over the past few years, but it remains unclear to what extent differences in photophysical properties introduce biases. Here, we tested two fluorophores with entirely different photophysical properties, one that photoswitches frequently between bright and dark states (TMR) and one that shows exceptional photostability without photoswitching (JFX650). We used a fusion of the Escherichia coli DNA repair enzyme MutS to the HaloTag and optimized sample preparation and imaging conditions for both types of fluorophore. We then assessed the reliability of two common data analysis algorithms, mean-square displacement (MSD) analysis and Hidden Markov Modeling (HMM), to estimate the diffusion coefficients and fractions of MutS molecules in different states of motion. We introduce a simple approach that removes discrepancies in the data analyses and show that both algorithms yield consistent results, regardless of the fluorophore used. Nevertheless, each dye has its own strengths and weaknesses, with TMR being more suitable for sampling the diffusive behavior of many molecules, while JFX650 enables prolonged observation of only a few molecules per cell. These characterizations and recommendations should help to standardize measurements for increased reproducibility and comparability across studies.
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Affiliation(s)
- Amy N Moores
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, U.K
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Rd, Oxford OX1 3QU, U.K
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2
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Deinum EE, Jacobs B. Rho of Plants patterning: linking mathematical models and molecular diversity. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1274-1288. [PMID: 37962515 PMCID: PMC10901209 DOI: 10.1093/jxb/erad447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/08/2023] [Indexed: 11/15/2023]
Abstract
ROPs (Rho of Plants) are plant specific small GTPases involved in many membrane patterning processes and play important roles in the establishment and communication of cell polarity. These small GTPases can produce a wide variety of patterns, ranging from a single cluster in tip-growing root hairs and pollen tubes to an oriented stripe pattern controlling protoxylem cell wall deposition. For an understanding of what controls these various patterns, models are indispensable. Consequently, many modelling studies on small GTPase patterning exist, often focusing on yeast or animal cells. Multiple patterns occurring in plants, however, require the stable co-existence of multiple active ROP clusters, which does not occur with the most common yeast/animal models. The possibility of such patterns critically depends on the precise model formulation. Additionally, different small GTPases are usually treated interchangeably in models, even though plants possess two types of ROPs with distinct molecular properties, one of which is unique to plants. Furthermore, the shape and even the type of ROP patterns may be affected by the cortical cytoskeleton, and cortex composition and anisotropy differ dramatically between plants and animals. Here, we review insights into ROP patterning from modelling efforts across kingdoms, as well as some outstanding questions arising from these models and recent experimental findings.
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Affiliation(s)
- Eva E Deinum
- Mathematical and Statistical Methods (Biometris), Plant Science Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Bas Jacobs
- Mathematical and Statistical Methods (Biometris), Plant Science Group, Wageningen University, 6708 PB Wageningen, The Netherlands
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3
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Wagh K, Stavreva DA, Jensen RAM, Paakinaho V, Fettweis G, Schiltz RL, Wüstner D, Mandrup S, Presman DM, Upadhyaya A, Hager GL. Dynamic switching of transcriptional regulators between two distinct low-mobility chromatin states. SCIENCE ADVANCES 2023; 9:eade1122. [PMID: 37315128 PMCID: PMC10954219 DOI: 10.1126/sciadv.ade1122] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 05/10/2023] [Indexed: 06/16/2023]
Abstract
How chromatin dynamics relate to transcriptional activity remains poorly understood. Using single-molecule tracking, coupled with machine learning, we show that histone H2B and multiple chromatin-bound transcriptional regulators display two distinct low-mobility states. Ligand activation results in a marked increase in the propensity of steroid receptors to bind in the lowest-mobility state. Mutational analysis revealed that interactions with chromatin in the lowest-mobility state require an intact DNA binding domain and oligomerization domains. These states are not spatially separated as previously believed, but individual H2B and bound-TF molecules can dynamically switch between them on time scales of seconds. Single bound-TF molecules with different mobilities exhibit different dwell time distributions, suggesting that the mobility of TFs is intimately coupled with their binding dynamics. Together, our results identify two unique and distinct low-mobility states that appear to represent common pathways for transcription activation in mammalian cells.
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Affiliation(s)
- Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rikke A. M. Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - R. Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Diego M. Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires C1428EGA, Argentina
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Bailey MLP, Pratt SE, Hinrichsen M, Zhang Y, Bewersdorf J, Regan LJ, Mochrie SGJ. Uncovering diffusive states of the yeast membrane protein, Pma1, and how labeling method can change diffusive behavior. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:42. [PMID: 37294385 PMCID: PMC10369454 DOI: 10.1140/epje/s10189-023-00301-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
We present and analyze video-microscopy-based single-particle-tracking measurements of the budding yeast (Saccharomyces cerevisiae) membrane protein, Pma1, fluorescently labeled either by direct fusion to the switchable fluorescent protein, mEos3.2, or by a novel, light-touch, labeling scheme, in which a 5 amino acid tag is directly fused to the C-terminus of Pma1, which then binds mEos3.2. The track diffusivity distributions of these two populations of single-particle tracks differ significantly, demonstrating that labeling method can be an important determinant of diffusive behavior. We also applied perturbation expectation maximization (pEMv2) (Koo and Mochrie in Phys Rev E 94(5):052412, 2016), which sorts trajectories into the statistically optimum number of diffusive states. For both TRAP-labeled Pma1 and Pma1-mEos3.2, pEMv2 sorts the tracks into two diffusive states: an essentially immobile state and a more mobile state. However, the mobile fraction of Pma1-mEos3.2 tracks is much smaller ([Formula: see text]) than the mobile fraction of TRAP-labeled Pma1 tracks ([Formula: see text]). In addition, the diffusivity of Pma1-mEos3.2's mobile state is several times smaller than the diffusivity of TRAP-labeled Pma1's mobile state. Thus, the two different labeling methods give rise to very different overall diffusive behaviors. To critically assess pEMv2's performance, we compare the diffusivity and covariance distributions of the experimental pEMv2-sorted populations to corresponding theoretical distributions, assuming that Pma1 displacements realize a Gaussian random process. The experiment-theory comparisons for both the TRAP-labeled Pma1 and Pma1-mEos3.2 reveal good agreement, bolstering the pEMv2 approach.
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Affiliation(s)
- Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
| | - Susan E Pratt
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
| | | | - Yongdeng Zhang
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
| | - Joerg Bewersdorf
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
| | - Lynne J Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, 06511, UK
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA.
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA.
- Department of Physics, Yale University, New Haven, CT, 06511, USA.
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5
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Abstract
Some dividing cells sense their shape by becoming polarized along their long axis. Cell polarity is controlled in part by polarity proteins, like Rho GTPases, cycling between active membrane-bound forms and inactive cytosolic forms, modeled as a "wave-pinning" reaction-diffusion process. Does shape sensing emerge from wave pinning? We show that wave pinning senses the cell's long axis. Simulating wave pinning on a curved surface, we find that high-activity domains migrate to peaks and troughs of the surface. For smooth surfaces, a simple rule of minimizing the domain perimeter while keeping its area fixed predicts the final position of the domain and its shape. However, when we introduce roughness to our surfaces, shape sensing can be disrupted, and high-activity domains can become localized to locations other than the global peaks and valleys of the surface. On rough surfaces, the domains of the wave-pinning model are more robust in finding the peaks and troughs than the minimization rule, although both can become trapped in steady states away from the peaks and valleys. We can control the robustness of shape sensing by altering the Rho GTPase diffusivity and the domain size. We also find that the shape-sensing properties of cell polarity models can explain how domains localize to curved regions of deformed cells. Our results help to understand the factors that allow cells to sense their shape-and the limits that membrane roughness can place on this process.
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Rinaldi L, Fettweis G, Kim S, Garcia DA, Fujiwara S, Johnson TA, Tettey TT, Ozbun L, Pegoraro G, Puglia M, Blagoev B, Upadhyaya A, Stavreva DA, Hager GL. The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation. SCIENCE ADVANCES 2022; 8:eabj8360. [PMID: 35353576 PMCID: PMC8967222 DOI: 10.1126/sciadv.abj8360] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 02/07/2022] [Indexed: 05/13/2023]
Abstract
The cohesin complex is central to chromatin looping, but mechanisms by which these long-range chromatin interactions are formed and persist remain unclear. We demonstrate that interactions between a transcription factor (TF) and the cohesin loader NIPBL regulate enhancer-dependent gene activity. Using mass spectrometry, genome mapping, and single-molecule tracking methods, we demonstrate that the glucocorticoid (GC) receptor (GR) interacts with NIPBL and the cohesin complex at the chromatin level, promoting loop extrusion and long-range gene regulation. Real-time single-molecule experiments show that loss of cohesin markedly diminishes the concentration of TF molecules at specific nuclear confinement sites, increasing TF local concentration and promoting gene regulation. Last, patient-derived acute myeloid leukemia cells harboring cohesin mutations exhibit a reduced response to GCs, suggesting that the GR-NIPBL-cohesin interaction is defective in these patients, resulting in poor response to GC treatment.
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Affiliation(s)
- Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sohyoung Kim
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David A. Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Saori Fujiwara
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas A. Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Theophilus T. Tettey
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laurent Ozbun
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- High-Throughput Imaging Facility (HiTIF), Center for Cancer Research (CCR), NCI/NIH, Bethesda, MD 20892, USA
| | - Michele Puglia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Diana A. Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Chatterjee M, Sain A. Dynamic surface patterns on cells. J Chem Phys 2022; 156:084117. [DOI: 10.1063/5.0077311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dynamic pattern formations are commonly observed in multicellular systems, such as cardiac tissue and slime molds, and modeled using reaction–diffusion systems. Recent experiments have revealed dynamic patterns in the concentration profile of various cortical proteins at a much smaller scale, namely, embryos at their single-cell stage. Spiral waves of Rho and F-actin proteins have been reported in Xenopus frog and starfish oocytes [Bement et al., Nat. Cell Biol. 17, 1471 (2015)], while a pulsatile pattern of Rho and myosin proteins has been found in C. elegans embryo [Nishikawa et al., eLife 6, e30537 (2017)]. Here, we propose that these two seemingly distinct dynamic patterns are signatures of a single reaction–diffusion network involving active-Rho, inactive-Rho, actin, and myosin. We show that a small variation in the concentration of other ancillary proteins can give rise to different dynamical states from the same chemical network.
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Affiliation(s)
- Mainak Chatterjee
- Physics Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anirban Sain
- Physics Department, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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8
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Eroumé KS, Cavill R, Staňková K, de Boer J, Carlier A. Exploring the influence of cytosolic and membrane FAK activation on YAP/TAZ nuclear translocation. Biophys J 2021; 120:4360-4377. [PMID: 34509508 PMCID: PMC8553670 DOI: 10.1016/j.bpj.2021.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/16/2021] [Accepted: 09/07/2021] [Indexed: 11/12/2022] Open
Abstract
Membrane binding and unbinding dynamics play a crucial role in the biological activity of several nonintegral membrane proteins, which have to be recruited to the membrane to perform their functions. By localizing to the membrane, these proteins are able to induce downstream signal amplification in their respective signaling pathways. Here, we present a 3D computational approach using reaction-diffusion equations to investigate the relation between membrane localization of focal adhesion kinase (FAK), Ras homolog family member A (RhoA), and signal amplification of the YAP/TAZ signaling pathway. Our results show that the theoretical scenarios in which FAK is membrane bound yield robust and amplified YAP/TAZ nuclear translocation signals. Moreover, we predict that the amount of YAP/TAZ nuclear translocation increases with cell spreading, confirming the experimental findings in the literature. In summary, our in silico predictions show that when the cell membrane interaction area with the underlying substrate increases, for example, through cell spreading, this leads to more encounters between membrane-bound signaling partners and downstream signal amplification. Because membrane activation is a motif common to many signaling pathways, this study has important implications for understanding the design principles of signaling networks.
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Affiliation(s)
- Kerbaï Saïd Eroumé
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, the Netherlands
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, Faculty of Science and Engineering, Maastricht University, Maastricht, the Netherlands
| | - Katerina Staňková
- Department of Data Science and Knowledge Engineering, Faculty of Science and Engineering, Maastricht University, Maastricht, the Netherlands
| | - Jan de Boer
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Aurélie Carlier
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, the Netherlands.
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9
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Bailey MLP, Yan H, Surovtsev I, Williams JF, King MC, Mochrie SGJ. Covariance distributions in single particle tracking. Phys Rev E 2021; 103:032405. [PMID: 33862686 PMCID: PMC9115892 DOI: 10.1103/physreve.103.032405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/12/2021] [Indexed: 11/07/2022]
Abstract
Several recent experiments, including our own experiments in the fission yeast, Schizosaccharomyces pombe, have characterized the motions of gene loci within living nuclei by measuring the locus position over time, then proceeding to obtain the statistical properties of this motion. To address the question of whether a population of such single-particle tracks, obtained from many different cells, corresponds to a single mode of diffusion, we derive theoretical equations describing the probability distribution of the displacement covariance, assuming the displacement itself is a zero-mean multivariate Gaussian random variable. We also determine the corresponding theoretical means, variances, and third central moments. Bolstering the theory is good agreement between its predictions and the results obtained for various simulated and measured data sets, including simulated particle trajectories undergoing simple and anomalous diffusion, and the measured trajectories of an optically trapped bead in water, and in a viscoelastic polymer solution. We also show that, for sufficiently long tracks, each covariance distribution in all of these examples is well-described by a skew-normal distribution with mean, variance, and skewness given by the theory. However, for the experimentally measured motion of a gene locus in S. pombe, we find that the first two covariance distributions are wider than predicted, although the third and subsequent covariance distributions are well-described by theory. This observation suggests that the origin of the theory-experiment discrepancy in this case is associated with localization noise, which influences only the first two covariances. Thus, we hypothesized that the discrepancy is caused by locus-to-locus heterogeneity in the localization noise, of independent measurements of the same tagged site. Indeed, simulations implementing heterogeneous localization noise revealed that the excess covariance widths can be largely recreated on the basis of heterogeneous noise. Thus, we conclude that the motion of gene loci in fission yeast is consistent with a single mode of diffusion.
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Affiliation(s)
- Mary Lou P. Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Hao Yan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Jessica F. Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Megan C. King
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Simon G. J. Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
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10
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Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol Cell 2021; 81:1484-1498.e6. [PMID: 33561389 DOI: 10.1016/j.molcel.2021.01.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within the local chromatin context. The mechanisms by which TFs navigate the nuclear environment as they search for binding sites remain unclear. Here, we used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic low-mobility populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), implicated in liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Together, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Rikke A M Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.
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11
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Karslake JD, Donarski ED, Shelby SA, Demey LM, DiRita VJ, Veatch SL, Biteen JS. SMAUG: Analyzing single-molecule tracks with nonparametric Bayesian statistics. Methods 2020; 193:16-26. [PMID: 32247784 DOI: 10.1016/j.ymeth.2020.03.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/08/2023] Open
Abstract
Single-molecule fluorescence microscopy probes nanoscale, subcellular biology in real time. Existing methods for analyzing single-particle tracking data provide dynamical information, but can suffer from supervisory biases and high uncertainties. Here, we develop a method for the case of multiple interconverting species undergoing free diffusion and introduce a new approach to analyzing single-molecule trajectories: the Single-Molecule Analysis by Unsupervised Gibbs sampling (SMAUG) algorithm, which uses nonparametric Bayesian statistics to uncover the whole range of information contained within a single-particle trajectory dataset. Even in complex systems where multiple biological states lead to a number of observed mobility states, SMAUG provides the number of mobility states, the average diffusion coefficient of single molecules in that state, the fraction of single molecules in that state, the localization noise, and the probability of transitioning between two different states. In this paper, we provide the theoretical background for the SMAUG analysis and then we validate the method using realistic simulations of single-particle trajectory datasets as well as experiments on a controlled in vitro system. Finally, we demonstrate SMAUG on real experimental systems in both prokaryotes and eukaryotes to measure the motions of the regulatory protein TcpP in Vibrio cholerae and the dynamics of the B-cell receptor antigen response pathway in lymphocytes. Overall, SMAUG provides a mathematically rigorous approach to measuring the real-time dynamics of molecular interactions in living cells.
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Affiliation(s)
- Joshua D Karslake
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
| | - Eric D Donarski
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
| | - Sarah A Shelby
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
| | - Lucas M Demey
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Victor J DiRita
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Sarah L Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA
| | - Julie S Biteen
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48104 USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48104 USA.
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Falcao RC, Coombs D. Diffusion analysis of single particle trajectories in a Bayesian nonparametrics framework. Phys Biol 2020; 17:025001. [DOI: 10.1088/1478-3975/ab64b3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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14
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Rey-Suarez I, Wheatley BA, Koo P, Bhanja A, Shu Z, Mochrie S, Song W, Shroff H, Upadhyaya A. WASP family proteins regulate the mobility of the B cell receptor during signaling activation. Nat Commun 2020; 11:439. [PMID: 31974357 PMCID: PMC6978525 DOI: 10.1038/s41467-020-14335-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 12/23/2019] [Indexed: 12/13/2022] Open
Abstract
Regulation of membrane receptor mobility tunes cellular response to external signals, such as in binding of B cell receptors (BCR) to antigen, which initiates signaling. However, whether BCR signaling is regulated by BCR mobility, and what factors mediate this regulation, are not well understood. Here we use single molecule imaging to examine BCR movement during signaling activation and a novel machine learning method to classify BCR trajectories into distinct diffusive states. Inhibition of actin dynamics downstream of the actin nucleating factors, Arp2/3 and formin, decreases BCR mobility. Constitutive loss or acute inhibition of the Arp2/3 regulator, N-WASP, which is associated with enhanced signaling, increases the proportion of BCR trajectories with lower diffusivity. Furthermore, loss of N-WASP reduces the diffusivity of CD19, a stimulatory co-receptor, but not that of FcγRIIB, an inhibitory co-receptor. Our results implicate a dynamic actin network in fine-tuning receptor mobility and receptor-ligand interactions for modulating B cell signaling. B cell receptors (BCR) capture antigen and initiate downstream antibody responses, but whether and how BCR signaling is regulated by BCR mobility is still unclear. Here the authors show, using single molecule imaging and machine learning analyses, that BCR and CD19 mobility is modulated by the actin nucleation regulators Arp2/3 and N-WASP to control BCR signaling.
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Affiliation(s)
- Ivan Rey-Suarez
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA.,National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Brittany A Wheatley
- Department of Physics, University of Maryland, College Park, MD, 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA
| | - Peter Koo
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Anshuman Bhanja
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Zhou Shu
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.,Division of Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Simon Mochrie
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Wenxia Song
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Arpita Upadhyaya
- Biophysics Program, University of Maryland, College Park, MD, 20742, USA. .,Department of Physics, University of Maryland, College Park, MD, 20742, USA. .,Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA.
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15
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Slator PJ, Burroughs NJ. A Hidden Markov Model for Detecting Confinement in Single-Particle Tracking Trajectories. Biophys J 2018; 115:1741-1754. [PMID: 30274829 PMCID: PMC6226389 DOI: 10.1016/j.bpj.2018.09.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/20/2018] [Accepted: 09/04/2018] [Indexed: 01/08/2023] Open
Abstract
State-of-the-art single-particle tracking (SPT) techniques can generate long trajectories with high temporal and spatial resolution. This offers the possibility of mechanistically interpreting particle movements and behavior in membranes. To this end, a number of statistical techniques have been developed that partition SPT trajectories into states with distinct diffusion signatures, allowing a statistical analysis of diffusion state dynamics and switching behavior. Here, we develop a confinement model, within a hidden Markov framework, that switches between phases of free diffusion and confinement in a harmonic potential well. By using a Markov chain Monte Carlo algorithm to fit this model, automated partitioning of individual SPT trajectories into these two phases is achieved, which allows us to analyze confinement events. We demonstrate the utility of this algorithm on a previously published interferometric scattering microscopy data set, in which gold-nanoparticle-tagged ganglioside GM1 lipids were tracked in model membranes. We performed a comprehensive analysis of confinement events, demonstrating that there is heterogeneity in the lifetime, shape, and size of events, with confinement size and shape being highly conserved within trajectories. Our observations suggest that heterogeneity in confinement events is caused by both individual nanoparticle characteristics and the binding-site environment. The individual nanoparticle heterogeneity ultimately limits the ability of interferometric scattering microscopy to resolve molecule dynamics to the order of the tag size; homogeneous tags could potentially allow the resolution to be taken below this limit by deconvolution methods. In a wider context, the presented harmonic potential well confinement model has the potential to detect and characterize a wide variety of biological phenomena, such as hop diffusion, receptor clustering, and lipid rafts.
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Affiliation(s)
- Paddy J Slator
- Centre for Medical Image Computing and Department of Computer Science, University College London, London, United Kingdom; Systems Biology Doctoral Training Centre, University of Warwick, Coventry, United Kingdom
| | - Nigel J Burroughs
- Mathematics Institute, University of Warwick, Coventry, United Kingdom.
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Abstract
Single-particle tracking (SPT) enables the ability to noninvasively probe the diffusive motions of individual proteins inside living cells at sub-diffraction-limit resolution. The stochastic motions of diffusing Rho GTPases encode information concerning its interactions with binding partners and with its local environment. By identifying Rho GTPases' diffusive states, insight can thus be gained into the spatiotemporal in vivo biochemistry inside live cells at a single-molecule resolution. Here we present perturbation expectation-maximization (pEM), a computational method which simultaneously analyzes a population of protein trajectories to uncover the system of diffusive behaviors: (1) the number of diffusive states, (2) the properties of each such diffusive state, and (3) the probabilities of each trajectory to a respective diffusive state. We provide a step-by-step guide to pEM and discuss considerations for its practical applications, including pEM's capabilities and limitations.
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17
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Pointwise error estimates in localization microscopy. Nat Commun 2017; 8:15115. [PMID: 28466844 PMCID: PMC5418599 DOI: 10.1038/ncomms15115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 03/01/2017] [Indexed: 01/21/2023] Open
Abstract
Pointwise localization of individual fluorophores is a critical step in super-resolution localization microscopy and single particle tracking. Although the methods are limited by the localization errors of individual fluorophores, the pointwise localization precision has so far been estimated using theoretical best case approximations that disregard, for example, motion blur, defocus effects and variations in fluorescence intensity. Here, we show that pointwise localization precision can be accurately estimated directly from imaging data using the Bayesian posterior density constrained by simple microscope properties. We further demonstrate that the estimated localization precision can be used to improve downstream quantitative analysis, such as estimation of diffusion constants and detection of changes in molecular motion patterns. Finally, the quality of actual point localizations in live cell super-resolution microscopy can be improved beyond the information theoretic lower bound for localization errors in individual images, by modelling the movement of fluorophores and accounting for their pointwise localization uncertainty.
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Rowland DJ, Biteen JS. Measuring molecular motions inside single cells with improved analysis of single-particle trajectories. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Koo PK, Mochrie SGJ. Systems-level approach to uncovering diffusive states and their transitions from single-particle trajectories. Phys Rev E 2016; 94:052412. [PMID: 27967069 DOI: 10.1103/physreve.94.052412] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Indexed: 06/06/2023]
Abstract
The stochastic motions of a diffusing particle contain information concerning the particle's interactions with binding partners and with its local environment. However, an accurate determination of the underlying diffusive properties, beyond normal diffusion, has remained challenging when analyzing particle trajectories on an individual basis. Here, we introduce the maximum-likelihood estimator (MLE) for confined diffusion and fractional Brownian motion. We demonstrate that this MLE yields improved estimation over traditional mean-square displacement analyses. We also introduce a model selection scheme (that we call mleBIC) that classifies individual trajectories to a given diffusion mode. We demonstrate the statistical limitations of classification via mleBIC using simulated data. To overcome these limitations, we introduce a version of perturbation expectation-maximization (pEMv2), which simultaneously analyzes a collection of particle trajectories to uncover the system of interactions that give rise to unique normal and/or non-normal diffusive states within the population. We test and evaluate the performance of pEMv2 on various sets of simulated particle trajectories, which transition among several modes of normal and non-normal diffusion, highlighting the key considerations for employing this analysis methodology.
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Affiliation(s)
- Peter K Koo
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Simon G J Mochrie
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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Patel A, Williams-Perez S, Peyton N, Reicks A, Buzick J, Farley J, Shirar S, Ellerbroek SM. Arg188 drives RhoC membrane binding. Small GTPases 2016; 8:114-121. [PMID: 27355867 DOI: 10.1080/21541248.2016.1205334] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
RhoA and RhoC GTPases are 92% identical but demonstrate unique regulation and function. Phosphorylation of Ser188 has widely been reported to inhibit RhoA activity. RhoC possesses Arg188 in place of Ser188 but retains a canonical upstream PKA recognition sequence. We report here that RhoC-R188S was a PKA substrate in vitro and exhibited less GTP loading compared to wild-type RhoC when expressed in cells. Transiently expressed RhoC was found to be significantly more membrane associated than RhoA. Membrane association of RhoC-R188S and RhoC-R188A were similar to each other and wild-type RhoA, suggesting that Arg188 directly promotes RhoC membrane binding. The positive influence of Arg188 on RhoC membrane association was evident in a constitutively active (Q63L) background. In accordance, RhoA-S188R was significantly more membrane associated than either RhoA or RhoA-S188A. Altogether, these data suggest that swapping residue 188 identity effectively flips the membrane binding profile of wild-type RhoA and RhoC through positive arginine contribution rather than negative phosphoserine regulation.
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Affiliation(s)
- Aditi Patel
- a Department of BCES , Wartburg College , Waverly , IA , USA
| | | | - Nicole Peyton
- a Department of BCES , Wartburg College , Waverly , IA , USA
| | - Amy Reicks
- a Department of BCES , Wartburg College , Waverly , IA , USA
| | - Justin Buzick
- a Department of BCES , Wartburg College , Waverly , IA , USA
| | - Janean Farley
- a Department of BCES , Wartburg College , Waverly , IA , USA
| | - Sarah Shirar
- a Department of BCES , Wartburg College , Waverly , IA , USA
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Affiliation(s)
- Ji Yu
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut 06030;
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