1
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Moussa SM, Mahmoud SS, Aly EM, Talaat MS. Bio-spectroscopic analysis of corneal structural alterations in dry eye disease: A study of collagen, co-enzymes, lipids, and proteins with emphasis on phytotherapy intervention. Int J Biol Macromol 2024; 280:136010. [PMID: 39326615 DOI: 10.1016/j.ijbiomac.2024.136010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/06/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Dry eye disease (DED) stands as a prevalent cause for ophthalmology consultations, securing the third position following refractive errors and cataracts. Moreover, the likelihood of experiencing DED escalates with advancing age. In this experimental study corneal tissue alterations due to DED were investigated over different periods by applying both infrared and synchronous fluorescence spectroscopy. The potential effects of instillation of pomegranate and green tea water extracts as green-friendly treatment modalities were also evaluated. The obtained results collectively indicate that DED affects the OH bearing constituents (collagen, glycosaminoglycans, and proteoglycans) of cornea leading to changes in protein secondary structure and the collagen fibrils. Additionally, enhanced dehydrated environment, and reduced energetic/metabolic state, as indicated by co-enzymes, was observed. Phyto-therapeutic administration can contain these alterations with enhanced energetic/metabolic state and increased hydration environment. In conclusion, instillation of green tea extract can protect/restore the collagen fibrils and its potential effects, in general, exceeds that of pomegranate extract.
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Affiliation(s)
- Shaimaa M Moussa
- Physics department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sherif S Mahmoud
- Biophysics and Laser Science Unit, Research Institute of Ophthalmology, Giza, Egypt.
| | - Eman M Aly
- Biophysics and Laser Science Unit, Research Institute of Ophthalmology, Giza, Egypt
| | - Mona S Talaat
- Physics department, Faculty of Science, Ain Shams University, Cairo, Egypt
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2
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Engl W, Kunstar-Thomas A, Chen S, Ng WS, Sielaff H, Zhao ZW. Single-molecule imaging of SWI/SNF chromatin remodelers reveals bromodomain-mediated and cancer-mutants-specific landscape of multi-modal DNA-binding dynamics. Nat Commun 2024; 15:7646. [PMID: 39223123 PMCID: PMC11369179 DOI: 10.1038/s41467-024-52040-y] [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: 12/30/2023] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Despite their prevalent cancer implications, the in vivo dynamics of SWI/SNF chromatin remodelers and how misregulation of such dynamics underpins cancer remain poorly understood. Using live-cell single-molecule tracking, we quantify the intranuclear diffusion and chromatin-binding of three key subunits common to all major human SWI/SNF remodeler complexes (BAF57, BAF155 and BRG1), and resolve two temporally distinct stable binding modes for the fully assembled complex. Super-resolved density mapping reveals heterogeneous, nanoscale remodeler binding "hotspots" across the nucleoplasm where multiple binding events (especially longer-lived ones) preferentially cluster. Importantly, we uncover distinct roles of the bromodomain in modulating chromatin binding/targeting in a DNA-accessibility-dependent manner, pointing to a model where successive longer-lived binding within "hotspots" leads to sustained productive remodeling. Finally, systematic comparison of six common BRG1 mutants implicated in various cancers unveils alterations in chromatin-binding dynamics unique to each mutant, shedding insight into a multi-modal landscape regulating the spatio-temporal organizational dynamics of SWI/SNF remodelers.
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Affiliation(s)
- Wilfried Engl
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Aliz Kunstar-Thomas
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Siyi Chen
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 119543, Singapore.
- Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore, 117557, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- Integrative Sciences and Engineering Programme, National University of Singapore, Singapore, 119077, Singapore.
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3
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Unger BA, Wu CY, Choi AA, He C, Xu K. Hypersensitivity of the vimentin cytoskeleton to net-charge states and Coulomb repulsion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602555. [PMID: 39026705 PMCID: PMC11257561 DOI: 10.1101/2024.07.08.602555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
As with most intermediate filament systems, the hierarchical self-assembly of vimentin into nonpolar filaments requires no nucleators or energy input. Utilizing a set of live-cell, single-molecule, and super-resolution microscopy tools, here we show that in mammalian cells, the assembly and disassembly of the vimentin cytoskeleton is highly sensitive to the protein net charge state. Starting with the intriguing observation that the vimentin cytoskeleton fully disassembles under hypotonic stress yet reassembles within seconds upon osmotic pressure recovery, we pinpoint ionic strength as its underlying driving factor. Further modulating the pH and expressing differently charged constructs, we converge on a model in which the vimentin cytoskeleton is destabilized by Coulomb repulsion when its mass-accumulated negative charges (-18 per vimentin protein) along the filament are less screened or otherwise intensified, and stabilized when the charges are better screened or otherwise reduced. Generalizing this model to other intermediate filaments, we further show that whereas the negatively charged GFAP cytoskeleton is similarly subject to fast disassembly under hypotonic stress, the cytokeratin, as a copolymer of negatively and positively charged subunits, does not exhibit this behavior. Thus, in cells containing both vimentin and keratin cytoskeletons, hypotonic stress disassembles the former but not the latter. Together, our results both provide new handles for modulating cell behavior and call for new attention to the effects of net charges in intracellular protein interactions.
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Affiliation(s)
- Bret A. Unger
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Alexander A. Choi
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Changdong He
- Department of Chemistry & California Institute for Quantitative Biosciences
- University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Corresponding author: (K.X.)
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4
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Saladin L, Breton V, Le Berruyer V, Nazac P, Lequeu T, Didier P, Danglot L, Collot M. Targeted Photoconvertible BODIPYs Based on Directed Photooxidation-Induced Conversion for Applications in Photoconversion and Live Super-Resolution Imaging. J Am Chem Soc 2024; 146:17456-17473. [PMID: 38861358 DOI: 10.1021/jacs.4c05231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Photomodulable fluorescent probes are drawing increasing attention due to their applications in advanced bioimaging. Whereas photoconvertible probes can be advantageously used in tracking, photoswitchable probes constitute key tools for single-molecule localization microscopy to perform super-resolution imaging. Herein, we shed light on a red and far-red BODIPY, namely, BDP-576 and BDP-650, which possess both properties of conversion and switching. Our study demonstrates that these pyrrolyl-BODIPYs convert into typical green- and red-emitting BODIPYs that are perfectly adapted to microscopy. We also showed that this pyrrolyl-BODIPYs undergo Directed Photooxidation Induced Conversion, a photoconversion mechanism that we recently introduced, where the pyrrole moiety plays a central role. These unique features were used to develop targeted photoconvertible probes toward different organelles or subcellular units (plasma membrane, mitochondria, nucleus, actin, Golgi apparatus, etc.) using chemical targeting moieties and a Halo tag. We notably showed that BDP-650 could be used to track intracellular vesicles over more than 20 min in two-color imagings with laser scanning confocal microscopy, demonstrating its robustness. The switching properties of these photoconverters were studied at the single-molecule level and were then successfully used in live single-molecule localization microscopy in epithelial cells and neurons. Both membrane- and mitochondria- targeted probes could be used to decipher membrane 3D architecture and mitochondrial dynamics at the nanoscale. This study builds a bridge between the photoconversion and photoswitching properties of probes undergoing directed photooxidation and shows the versatility and efficacy of this mechanism in advanced live imaging.
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Affiliation(s)
- Lazare Saladin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Victor Breton
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in Healthy and Diseased Brain team; NeurImag core facility scientific director, 75014 Paris, France
| | - Valentine Le Berruyer
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
- Chemistry of Photoresponsive Systems, Laboratoire de Chémo-Biologie Synthétique et Thérapeutique (CBST) UMR 7199, CNRS, Université de Strasbourg, F-67400 Illkirch, France
| | - Paul Nazac
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in Healthy and Diseased Brain team; NeurImag core facility scientific director, 75014 Paris, France
| | - Thiebault Lequeu
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Lydia Danglot
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in healthy and Diseased brain team; NeurImag core facility scientific director, 75014 Paris, France
| | - Mayeul Collot
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, CNRS/Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Graffenstaden, France
- Chemistry of Photoresponsive Systems, Laboratoire de Chémo-Biologie Synthétique et Thérapeutique (CBST) UMR 7199, CNRS, Université de Strasbourg, F-67400 Illkirch, France
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5
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Steves MA, He C, Xu K. Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. Annu Rev Phys Chem 2024; 75:163-183. [PMID: 38360526 DOI: 10.1146/annurev-physchem-070623-034225] [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] [Indexed: 02/17/2024]
Abstract
By superlocalizing the positions of millions of single molecules over many camera frames, a class of super-resolution fluorescence microscopy methods known as single-molecule localization microscopy (SMLM) has revolutionized how we understand subcellular structures over the past decade. In this review, we highlight emerging studies that transcend the outstanding structural (shape) information offered by SMLM to extract and map physicochemical parameters in living mammalian cells at single-molecule and super-resolution levels. By encoding/decoding high-dimensional information-such as emission and excitation spectra, motion, polarization, fluorescence lifetime, and beyond-for every molecule, and mass accumulating these measurements for millions of molecules, such multidimensional and multifunctional super-resolution approaches open new windows into intracellular architectures and dynamics, as well as their underlying biophysical rules, far beyond the diffraction limit.
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Affiliation(s)
- Megan A Steves
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Changdong He
- Department of Chemistry, University of California, Berkeley, California, USA;
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California, USA;
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6
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Cha HJ, He C, Glover DJ, Xu K, Clark DS. STORM Super-Resolution Visualization of Self-Assembled γPFD Chaperone Ultrastructures in Methanocaldococcus jannaschii. NANO LETTERS 2024; 24:6078-6083. [PMID: 38723608 PMCID: PMC11117396 DOI: 10.1021/acs.nanolett.4c01043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Gamma-prefoldin (γPFD), a unique chaperone found in the extremely thermophilic methanogen Methanocaldococcus jannaschii, self-assembles into filaments in vitro, which so far have been observed using transmission electron microscopy and cryo-electron microscopy. Utilizing three-dimensional stochastic optical reconstruction microscopy (3D-STORM), here we achieve ∼20 nm resolution by precisely locating individual fluorescent molecules, hence resolving γPFD ultrastructure both in vitro and in vivo. Through CF647 NHS ester labeling, we first demonstrate the accurate visualization of filaments and bundles with purified γPFD. Next, by implementing immunofluorescence labeling after creating a 3xFLAG-tagged γPFD strain, we successfully visualize γPFD in M. jannaschii cells. Through 3D-STORM and two-color STORM imaging with DNA, we show the widespread distribution of filamentous γPFD structures within the cell. These findings provide valuable insights into the structure and localization of γPFD, opening up possibilities for studying intriguing nanoscale components not only in archaea but also in other microorganisms.
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Affiliation(s)
- Hee-Jeong Cha
- Department
of Chemical and Biomolecular Engineering, University of California—Berkeley, Berkeley, California 94720, United States
| | - Changdong He
- Department
of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
| | - Dominic J. Glover
- School
of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ke Xu
- Department
of Chemistry, University of California—Berkeley, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Douglas S. Clark
- Department
of Chemical and Biomolecular Engineering, University of California—Berkeley, Berkeley, California 94720, United States
- Molecular
Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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7
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Choi AA, Xu K. Single-Molecule Diffusivity Quantification Unveils Ubiquitous Net Charge-Driven Protein-Protein Interaction. J Am Chem Soc 2024; 146:10973-10978. [PMID: 38576203 PMCID: PMC11023747 DOI: 10.1021/jacs.4c02475] [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: 04/06/2024]
Abstract
Recent microscopy and nuclear magnetic resonance (NMR) studies have noticed substantial suppression of intracellular diffusion for positively charged proteins, suggesting an overlooked role of electrostatic attraction in nonspecific protein interactions in a predominantly negatively charged intracellular environment. Utilizing single-molecule detection and statistics, here, we quantify in aqueous solutions how protein diffusion, in the limit of low diffuser concentration to avoid aggregate/coacervate formation, is modulated by differently charged interactor proteins over wide concentration ranges. We thus report substantially suppressed diffusion when oppositely charged interactors are added at parts per million levels, yet unvaried diffusivities when same-charge interactors are added beyond 1%. The electrostatic attraction-driven suppression of diffusion is sensitive to the protein net charge states, as probed by varying the solution pH and ionic strength or chemically modifying the proteins and is robust across different diffuser-interactor pairs. By converting the measured diffusivities to diffuser diameters, we further show that in the limit of excess interactors, a positively charged diffuser molecule effectively drags along just one monolayer of negatively charged interactors, where further interactions stop. We thus unveil ubiquitous, net charge-driven protein-protein interactions and shed new light on the mechanism of charge-based diffusion suppression in living cells.
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Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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8
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An K, Qiao Q, Zhou W, Jiang W, Li J, Xu Z. Stable Super-Resolution Imaging of Cell Membrane Nanoscale Subcompartment Dynamics with a Buffering Cyanine Dye. Anal Chem 2024; 96:5985-5991. [PMID: 38557031 DOI: 10.1021/acs.analchem.4c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Super-resolution fluorescence imaging is a crucial method for visualizing the dynamics of the cell membrane involved in various physiological and pathological processes. This requires bright fluorescent dyes with excellent photostability and labeling stability to enable long-term imaging. In this context, we introduce a buffering-strategy-based cyanine dye, SA-Cy5, designed to identify and label carbonic anhydrase IX (CA IX) located in the cell membrane. The unique feature of SA-Cy5 lies in its ability to overcome photobleaching. When the dye on the cell membrane undergoes photobleaching, it is rapidly replaced by an intact probe from the buffer pool outside the cell membrane. This dynamic replacement ensures that the fluorescence intensity on the cell membrane remains stable over time. Under the super-resolution structured illumination microscopy (SIM), the cell membrane can be continuously imaged for 60 min with a time resolution of 20 s. This extended imaging period allows for the observation of substructural dynamics of the cell membrane, including the growth and fusion of filamentous pseudopodia and the fusion of vesicles. Additionally, this buffering strategy introduces a novel approach to address the issue of poor photostability associated with the cyanine dyes.
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Affiliation(s)
- Kai An
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wei Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Wenchao Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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9
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [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: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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10
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Rentsch J, Bandstra S, Sezen B, Sigrist P, Bottanelli F, Schmerl B, Shoichet S, Noé F, Sadeghi M, Ewers H. Sub-membrane actin rings compartmentalize the plasma membrane. J Cell Biol 2024; 223:e202310138. [PMID: 38252080 PMCID: PMC10807028 DOI: 10.1083/jcb.202310138] [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: 10/27/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
The compartmentalization of the plasma membrane (PM) is a fundamental feature of cells. The diffusivity of membrane proteins is significantly lower in biological than in artificial membranes. This is likely due to actin filaments, but assays to prove a direct dependence remain elusive. We recently showed that periodic actin rings in the neuronal axon initial segment (AIS) confine membrane protein motion between them. Still, the local enrichment of ion channels offers an alternative explanation. Here we show, using computational modeling, that in contrast to actin rings, ion channels in the AIS cannot mediate confinement. Furthermore, we show, employing a combinatorial approach of single particle tracking and super-resolution microscopy, that actin rings are close to the PM and that they confine membrane proteins in several neuronal cell types. Finally, we show that actin disruption leads to loss of compartmentalization. Taken together, we here develop a system for the investigation of membrane compartmentalization and show that actin rings compartmentalize the PM.
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Affiliation(s)
- Jakob Rentsch
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Selle Bandstra
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Batuhan Sezen
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Philipp Sigrist
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Francesca Bottanelli
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Bettina Schmerl
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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11
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Islam MM, Nawagamuwage SU, Parshin IV, Richard MC, Burin AL, Rubtsov IV. Probing the Hydrophobic Region of a Lipid Bilayer at Specific Depths Using Vibrational Spectroscopy. J Am Chem Soc 2023; 145:26363-26373. [PMID: 37982703 DOI: 10.1021/jacs.3c10178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
A novel spectroscopic approach for studying the flexibility and mobility in the hydrophobic interior of lipid bilayers at specific depths is proposed. A set of test compounds featuring an azido moiety and a cyano or carboxylic acid moiety, connected by an alkyl chain of different lengths, was synthesized. FTIR data and molecular dynamics calculations indicated that the test compounds in a bilayer are oriented so that the cyano or carboxylic acid moiety is located in the lipid head-group region, while the azido group stays inside the bilayer at the depth determined by its alkyl chain length. We found that the asymmetric stretching mode of the azido group (νN3) can serve as a reporter of the membrane interior dynamics. FTIR and two-dimensional infrared (2DIR) studies were performed at different temperatures, ranging from 22 to 45 °C, covering the Lβ-Lα phase transition temperature of dipalmitoylphosphatidylcholine (∼41 °C). The width of the νN3 peak was found to be very sensitive to the phase transition and to the temperature in general. We introduced an order parameter, SN3, which characterizes restrictions to motion inside the bilayer. 2DIR spectra of νN3 showed different extents of inhomogeneity at different depths in the bilayer, with the smallest inhomogeneity in the middle of the leaflet. The spectral diffusion dynamics of the N3 peak was found to be dependent on the depth of the N3 group location in the bilayer. The obtained results enhance our understanding of the bilayer dynamics and can be extended to investigate membranes with more complex compositions.
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Affiliation(s)
- Md Muhaiminul Islam
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | | | - Igor V Parshin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Margaret C Richard
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Igor V Rubtsov
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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12
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He C, Wu CY, Li W, Xu K. Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates. J Am Chem Soc 2023; 145:24240-24248. [PMID: 37782826 PMCID: PMC10691933 DOI: 10.1021/jacs.3c08674] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remains unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here, we uncover nanoscale heterogeneities in FUS condensates and elucidate their evolution over aging. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems at the nanoscale.
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Affiliation(s)
- Changdong He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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13
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Park J, Ahn Y, Lee WJ, Jin S, Jeong S, Kim J, Lee YS, Lee JC, Seo D. Analysis of Phase Heterogeneity in Lipid Membranes Using Single-Molecule Tracking in Live Cells. Anal Chem 2023; 95:15924-15932. [PMID: 37774148 DOI: 10.1021/acs.analchem.3c02655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
In live cells, the plasma membrane is composed of lipid domains separated by hundreds of nanometers in dynamic equilibrium. Lipid phase separation regulates the trafficking and spatiotemporal organization of membrane molecules that promote signal transduction. However, visualizing domains with adequate spatiotemporal accuracy remains challenging because of their subdiffraction limit size and highly dynamic properties. Here, we present a single lipid-molecular motion analysis pipeline (lipid-MAP) for analyzing the phase heterogeneity of lipid membranes by detecting the instantaneous velocity change of a single lipid molecule using the excellent optical properties of nanoparticles, high spatial localization accuracy of single-molecule localization microscopy, and separation capability of the diffusion state of the hidden Markov model algorithm. Using lipid-MAP, individual lipid molecules were found to be in dynamic equilibrium between two statistically distinguishable phases, leading to the formation of small (∼170 nm), viscous (2.5× more viscous than surrounding areas), and transient domains in live cells. Moreover, our findings provide an understanding of how membrane compositional changes, i.e., cholesterol and phospholipids, affect domain formation. This imaging method can contribute to an improved understanding of spatiotemporal-controlled membrane dynamics at the molecular level.
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Affiliation(s)
- Jiseong Park
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Yongdeok Ahn
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Wonhee John Lee
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Siwoo Jin
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Sejoo Jeong
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Jaeyong Kim
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Young-Sam Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Jong-Chan Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
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14
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Liu Y, Shahid MA, Mao H, Chen J, Waddington M, Song KH, Zhang Y. Switchable and Functional Fluorophores for Multidimensional Single-Molecule Localization Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:403-413. [PMID: 37655169 PMCID: PMC10466381 DOI: 10.1021/cbmi.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 09/02/2023]
Abstract
Multidimensional single-molecule localization microscopy (mSMLM) represents a paradigm shift in the realm of super-resolution microscopy techniques. It affords the simultaneous detection of single-molecule spatial locations at the nanoscale and functional information by interrogating the emission properties of switchable fluorophores. The latter is finely tuned to report its local environment through carefully manipulated laser illumination and single-molecule detection strategies. This Perspective highlights recent strides in mSMLM with a focus on fluorophore designs and their integration into mSMLM imaging systems. Particular interests are the accomplishments in simultaneous multiplexed super-resolution imaging, nanoscale polarity and hydrophobicity mapping, and single-molecule orientational imaging. Challenges and prospects in mSMLM are also discussed, which include the development of more vibrant and functional fluorescent probes, the optimization of optical implementation to judiciously utilize the photon budget, and the advancement of imaging analysis and machine learning techniques.
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Affiliation(s)
- Yunshu Liu
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Md Abul Shahid
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Hongjing Mao
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Jiahui Chen
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Michael Waddington
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Ki-Hee Song
- Quantum
Optics Research Division, Korea Atomic Energy
Research Institute, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Yang Zhang
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
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15
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He C, Wu CY, Li W, Xu K. Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548239. [PMID: 37503034 PMCID: PMC10369965 DOI: 10.1101/2023.07.12.548239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remain unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here we uncover nanoscale heterogeneities in the aging process of FUS condensates. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SM d M), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating nanoscale structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems.
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16
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Zhang Z, Chen H, Hu M, Wang D. Single-Molecule Tracking of Reagent Diffusion during Chemical Reactions. J Am Chem Soc 2023; 145:10512-10521. [PMID: 37079767 DOI: 10.1021/jacs.2c13172] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Recent experiments have shown that the diffusion of reagent molecules is inconsistent with what the Stokes-Einstein equation predicts during a chemical reaction. Here, we used single-molecule tracking to observe the diffusion of reactive reagent molecules during click and Diels-Alder (DA) reactions. We found that the diffusion coefficient of the reagents remained unchanged within the experimental uncertainty upon the DA reaction. Yet, diffusion of reagent molecules is faster than predicted during the click reaction when the reagent concentration and catalyst concentration exceed a threshold. A stepwise analysis suggested that the fast diffusion scenario is due to the reaction but not the involvement of the tracer with the reaction itself. The present results provide experimental evidence on the faster-than-expected reagent diffusion during a CuAAC reaction in specific conditions and propose new insights into understanding this unexpected behavior.
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Affiliation(s)
- Zhengfu Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| | - Hongbo Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
| | - Ming Hu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
| | - Dapeng Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, P. R. China
- University of Science and Technology of China, Hefei 230026, Anhui, P. R. China
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17
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Choi AA, Xiang L, Li W, Xu K. Single-Molecule Displacement Mapping Indicates Unhindered Intracellular Diffusion of Small (≲1 kDa) Solutes. J Am Chem Soc 2023; 145:10.1021/jacs.3c00597. [PMID: 37027457 PMCID: PMC10558625 DOI: 10.1021/jacs.3c00597] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
While fundamentally important, the intracellular diffusion of small (≲1 kDa) solutes has been difficult to elucidate due to challenges in both labeling and measurement. Here we quantify and spatially map the translational diffusion patterns of small solutes in mammalian cells by integrating several recent advances. In particular, by executing tandem stroboscopic illumination pulses down to 400 μs separation, we extend single-molecule displacement/diffusivity mapping (SMdM), a super-resolution diffusion quantification tool, to small solutes with high diffusion coefficients D of >300 μm2/s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ∼60-70% of that in vitro, up to ∼250 μm2/s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments.
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Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Limin Xiang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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18
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Park HH, Choi AA, Xu K. Size-Dependent Suppression of Molecular Diffusivity in Expandable Hydrogels: A Single-Molecule Study. J Phys Chem B 2023; 127:3333-3339. [PMID: 37011131 DOI: 10.1021/acs.jpcb.3c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
By repurposing the recently popularized expansion microscopy to control the meshwork size of hydrogels, we examine the size-dependent suppression of molecular diffusivity in the resultant tuned hydrogel nanomatrices over a wide range of polymer fractions of ∼0.14-7 wt %. With our recently developed single-molecule displacement/diffusivity mapping (SMdM) microscopy methods, we thus show that with a fixed meshwork size, larger molecules exhibit more impeded diffusion and that, for the same molecule, diffusion is progressively more suppressed as the meshwork size is reduced; this effect is more prominent for the larger molecules. Moreover, we show that the meshwork-induced obstruction of diffusion is uncoupled from the suppression of diffusion due to increased solution viscosities. Thus, the two mechanisms, respectively, being diffuser-size-dependent and independent, may separately scale down molecular diffusivity to produce the final diffusion slowdown in complex systems like the cell.
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Affiliation(s)
- Ha H Park
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
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19
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Park HH, Wang B, Moon S, Jepson T, Xu K. Machine-learning-powered extraction of molecular diffusivity from single-molecule images for super-resolution mapping. Commun Biol 2023; 6:336. [PMID: 36977778 PMCID: PMC10050076 DOI: 10.1038/s42003-023-04729-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
While critical to biological processes, molecular diffusion is difficult to quantify, and spatial mapping of local diffusivity is even more challenging. Here we report a machine-learning-enabled approach, pixels-to-diffusivity (Pix2D), to directly extract the diffusion coefficient D from single-molecule images, and consequently enable super-resolved D spatial mapping. Working with single-molecule images recorded at a fixed framerate under typical single-molecule localization microscopy (SMLM) conditions, Pix2D exploits the often undesired yet evident motion blur, i.e., the convolution of single-molecule motion trajectory during the frame recording time with the diffraction-limited point spread function (PSF) of the microscope. Whereas the stochastic nature of diffusion imprints diverse diffusion trajectories to different molecules diffusing at the same given D, we construct a convolutional neural network (CNN) model that takes a stack of single-molecule images as the input and evaluates a D-value as the output. We thus validate robust D evaluation and spatial mapping with simulated data, and with experimental data successfully characterize D differences for supported lipid bilayers of different compositions and resolve gel and fluidic phases at the nanoscale.
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Affiliation(s)
- Ha H Park
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Bowen Wang
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Suhong Moon
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA, 94720, USA
| | - Tyler Jepson
- QB3-Berkeley, University of California, Berkeley, CA, 94720, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- QB3-Berkeley, University of California, Berkeley, CA, 94720, USA.
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20
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Brenner B, Sun C, Raymo FM, Zhang HF. Spectroscopic single-molecule localization microscopy: applications and prospective. NANO CONVERGENCE 2023; 10:14. [PMID: 36943541 PMCID: PMC10030755 DOI: 10.1186/s40580-023-00363-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/05/2023] [Indexed: 05/25/2023]
Abstract
Single-molecule localization microscopy (SMLM) breaks the optical diffraction limit by numerically localizing sparse fluorescence emitters to achieve super-resolution imaging. Spectroscopic SMLM or sSMLM further allows simultaneous spectroscopy and super-resolution imaging of fluorescence molecules. Hence, sSMLM can extract spectral features with single-molecule sensitivity, higher precision, and higher multiplexity than traditional multicolor microscopy modalities. These new capabilities enabled advanced multiplexed and functional cellular imaging applications. While sSMLM suffers from reduced spatial precision compared to conventional SMLM due to splitting photons to form spatial and spectral images, several methods have been reported to mitigate these weaknesses through innovative optical design and image processing techniques. This review summarizes the recent progress in sSMLM, its applications, and our perspective on future work.
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Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Françisco M Raymo
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
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21
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-Molecule Displacement Mapping Unveils Sign-Asymmetric Protein Charge Effects on Intraorganellar Diffusion. NANO LETTERS 2023; 23:1711-1716. [PMID: 36802676 PMCID: PMC10044514 DOI: 10.1021/acs.nanolett.2c04379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SMdM), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ∼40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, hence a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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Affiliation(s)
- Limin Xiang
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
- College of Chemistry and Molecular Sciences & TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Rui Yan
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Kun Chen
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Wan Li
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
| | - Ke Xu
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720
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22
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Han K, Huang S, Kong J, Yang Y, Shi L, Ci Y. A novel fluorescent endoplasmic reticulum marker for super-resolution imaging in live cells. FEBS Lett 2023; 597:693-701. [PMID: 36694281 DOI: 10.1002/1873-3468.14581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/26/2023]
Abstract
Endoplasmic reticulum (ER) is a highly complicated and dynamic organelle that actively changes its shape and communicates with other organelles. Visualization of ER in live cells is of great importance to understand cellular activities. Here, we designed a novel ER marker, RR-mNeonGreen, which comprised an N-terminal ER retention signal, a bright fluorescent protein (mNeonGreen), and a C-terminal transmembrane region. Colocalization of RR-mNeonGreen with mCherry-KDEL verified that RR-mNeonGreen perfectly labeled the ER. RR-mNeonGreen showed better continuity of ER tubules when imaged by super-resolution microscopy. Moreover, RR-mNeonGreen is competent for live-cell imaging of ER dynamics and tracing of the interaction between ER and mitochondria at high spatiotemporal resolution. In summary, RR-mNeonGreen is a novel ER marker for super-resolution live-cell imaging with multiple merits.
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Affiliation(s)
- Kai Han
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Shuhan Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jie Kong
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yali Ci
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
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23
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Du Y, Lyu Y, Li S, Ding D, Chen J, Yang C, Sun Y, Qu F, Xiao Z, Jiang J, Tan W. Ligand Dilution Analysis Facilitates Aptamer Binding Characterization at the Single-Molecule Level. Angew Chem Int Ed Engl 2023; 62:e202215387. [PMID: 36479802 DOI: 10.1002/anie.202215387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
Cell-specific aptamers offer a powerful tool to study membrane receptors at the single-molecule level. Most target receptors of aptamers are highly expressed on the cell surface, but difficult to analyze in situ because of dense distribution and fast velocity. Therefore, we herein propose a random sampling-based analysis strategy termed ligand dilution analysis (LDA) for easily implemented aptamer-based receptor study. Receptor density on the cell surface can be calculated based on a regression model. By using a synergistic ligand dilution design, colocalization and differentiation of aptamer and monoclonal antibody (mAb) binding on a single receptor can be realized. Once this is accomplished, precise binding site and detailed aptamer-receptor binding mode can be further determined using molecular docking and molecular dynamics simulation. The ligand dilution strategy also sets the stage for an aptamer-based dynamics analysis of two- and three-dimensional motion and fluctuation of highly expressed receptors on the live cell membrane.
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Affiliation(s)
- Yulin Du
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Shenzhen Research Institute, Hunan University, Shenzhen, Guangdong 518000, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ding Ding
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianghuai Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cai Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fengli Qu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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24
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Xiang L, Yan R, Chen K, Li W, Xu K. Single-molecule displacement mapping unveils sign-asymmetric protein charge effects on intraorganellar diffusion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525611. [PMID: 36747807 PMCID: PMC9900983 DOI: 10.1101/2023.01.26.525611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Using single-molecule displacement/diffusivity mapping (SM d M), an emerging super-resolution microscopy method, here we quantify, at nanoscale resolution, the diffusion of a typical fluorescent protein (FP) in the endoplasmic reticulum (ER) and mitochondrion of living mammalian cells. We thus show that the diffusion coefficients D in both organelles are ~40% of that in the cytoplasm, with the latter exhibiting higher spatial inhomogeneities. Moreover, we unveil that diffusions in the ER lumen and the mitochondrial matrix are markedly impeded when the FP is given positive, but not negative, net charges. Calculation shows most intraorganellar proteins as negatively charged, thus a mechanism to impede the diffusion of positively charged proteins. However, we further identify the ER protein PPIB as an exception with a positive net charge, and experimentally show that the removal of this positive charge elevates its intra-ER diffusivity. We thus unveil a sign-asymmetric protein charge effect on the nanoscale intraorganellar diffusion.
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25
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Choi AA, Xiang L, Li W, Xu K. Single-molecule displacement mapping indicates unhindered intracellular diffusion of small (<~1 kDa) solutes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525579. [PMID: 36747694 PMCID: PMC9900885 DOI: 10.1101/2023.01.26.525579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
While fundamentally important, the intracellular diffusion of small (<~1 kDa) solutes has been difficult to elucidate due to challenges in both labeling and measurement. Here we quantify and spatially map the translational diffusion patterns of small solutes in mammalian cells by integrating several recent advances. In particular, by executing tandem stroboscopic illumination pulses down to 400-μs separation, we extend single-molecule displacement/diffusivity mapping (SM d M), a super-resolution diffusion quantification tool, to small solutes with high diffusion coefficients D of >300 μm 2 /s. We thus show that for multiple water-soluble dyes and dye-tagged nucleotides, intracellular diffusion is dominated by vast regions of high diffusivity ~60-70% of that in vitro , up to ~250 μm 2 /s in the fastest cases. Meanwhile, we also visualize sub-micrometer foci of substantial slowdowns in diffusion, thus underscoring the importance of spatially resolving the local diffusion behavior. Together, these results suggest that the intracellular diffusion of small solutes is only modestly scaled down by the slightly higher viscosity of the cytosol over water, but otherwise not further hindered by macromolecular crowding. We thus lift a paradoxically low speed limit for intracellular diffusion suggested by previous experiments. Abstract Graphic
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26
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Tran BM, Linnik DS, Punter CM, Śmigiel WM, Mantovanelli L, Iyer A, O’Byrne C, Abee T, Johansson J, Poolman B. Super-resolving microscopy reveals the localizations and movement dynamics of stressosome proteins in Listeria monocytogenes. Commun Biol 2023; 6:51. [PMID: 36641529 PMCID: PMC9840623 DOI: 10.1038/s42003-023-04423-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
The human pathogen Listeria monocytogenes can cope with severe environmental challenges, for which the high molecular weight stressosome complex acts as the sensing hub in a complicated signal transduction pathway. Here, we show the dynamics and functional roles of the stressosome protein RsbR1 and its paralogue, the blue-light receptor RsbL, using photo-activated localization microscopy combined with single-particle tracking and single-molecule displacement mapping and supported by physiological studies. In live cells, RsbR1 is present in multiple states: in protomers with RsbS, large clusters of stressosome complexes, and in connection with the plasma membrane via Prli42. RsbL diffuses freely in the cytoplasm but forms clusters upon exposure to light. The clustering of RsbL is independent of the presence of Prli42. Our work provides a comprehensive view of the spatial organization and intracellular dynamics of the stressosome proteins in L. monocytogenes, which paves the way towards uncovering the stress-sensing mechanism of this signal transduction pathway.
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Affiliation(s)
- Buu Minh Tran
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Dmitrii Sergeevich Linnik
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Christiaan Michiel Punter
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Wojciech Mikołaj Śmigiel
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Luca Mantovanelli
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Aditya Iyer
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Conor O’Byrne
- Microbiology, School of Biological & Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Tjakko Abee
- grid.4818.50000 0001 0791 5666Laboratory of Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jörgen Johansson
- grid.12650.300000 0001 1034 3451Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Bert Poolman
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
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27
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Nieto-Garai JA, Olazar-Intxausti J, Anso I, Lorizate M, Terrones O, Contreras FX. Super-Resolution Microscopy to Study Interorganelle Contact Sites. Int J Mol Sci 2022; 23:15354. [PMID: 36499680 PMCID: PMC9739495 DOI: 10.3390/ijms232315354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/29/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Interorganelle membrane contact sites (MCS) are areas of close vicinity between the membranes of two organelles that are maintained by protein tethers. Recently, a significant research effort has been made to study MCS, as they are implicated in a wide range of biological functions, such as organelle biogenesis and division, apoptosis, autophagy, and ion and phospholipid homeostasis. Their composition, characteristics, and dynamics can be studied by different techniques, but in recent years super-resolution fluorescence microscopy (SRFM) has emerged as a powerful tool for studying MCS. In this review, we first explore the main characteristics and biological functions of MCS and summarize the different approaches for studying them. Then, we center on SRFM techniques that have been used to study MCS. For each of the approaches, we summarize their working principle, discuss their advantages and limitations, and explore the main discoveries they have uncovered in the field of MCS.
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Affiliation(s)
- Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Itxaso Anso
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Maier Lorizate
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Oihana Terrones
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Francesc-Xabier Contreras
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
- Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, 48940 Leioa, Spain
- Ikerbasque, Basque Foundation of Science, 48011 Bilbao, Spain
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28
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Liu X, Jiang Y, Cui Y, Yuan J, Fang X. Deep learning in single-molecule imaging and analysis: recent advances and prospects. Chem Sci 2022; 13:11964-11980. [PMID: 36349113 PMCID: PMC9600384 DOI: 10.1039/d2sc02443h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/19/2022] [Indexed: 09/19/2023] Open
Abstract
Single-molecule microscopy is advantageous in characterizing heterogeneous dynamics at the molecular level. However, there are several challenges that currently hinder the wide application of single molecule imaging in bio-chemical studies, including how to perform single-molecule measurements efficiently with minimal run-to-run variations, how to analyze weak single-molecule signals efficiently and accurately without the influence of human bias, and how to extract complete information about dynamics of interest from single-molecule data. As a new class of computer algorithms that simulate the human brain to extract data features, deep learning networks excel in task parallelism and model generalization, and are well-suited for handling nonlinear functions and extracting weak features, which provide a promising approach for single-molecule experiment automation and data processing. In this perspective, we will highlight recent advances in the application of deep learning to single-molecule studies, discuss how deep learning has been used to address the challenges in the field as well as the pitfalls of existing applications, and outline the directions for future development.
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Affiliation(s)
- Xiaolong Liu
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yifei Jiang
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences Hangzhou 310022 Zhejiang China
| | - Yutong Cui
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Jinghe Yuan
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
| | - Xiaohong Fang
- Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences Hangzhou 310022 Zhejiang China
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29
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Aparin IO, Yan R, Pelletier R, Choi AA, Danylchuk DI, Xu K, Klymchenko AS. Fluorogenic Dimers as Bright Switchable Probes for Enhanced Super-Resolution Imaging of Cell Membranes. J Am Chem Soc 2022; 144:18043-18053. [PMID: 36153973 DOI: 10.1021/jacs.2c07542] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Super-resolution fluorescence imaging based on single-molecule localization microscopy (SMLM) enables visualizing cellular structures with nanometric precision. However, its spatial and temporal resolution largely relies on the brightness of ON/OFF switchable fluorescent dyes. Moreover, in cell plasma membranes, the single-molecule localization is hampered by the fast lateral diffusion of membrane probes. Here, to address these two fundamental problems, we propose a concept of ON/OFF switchable probes for SMLM (points accumulation for imaging in nanoscale topography, PAINT) based on fluorogenic dimers of bright cyanine dyes. In these probes, the two cyanine units connected with a linker were modified at their extremities with low-affinity membrane anchors. Being self-quenched in water due to intramolecular dye H-aggregation, they displayed light up on reversible binding to lipid membranes. The charged group in the linker further decreased the probe affinity to the lipid membranes, thus accelerating its dynamic reversible ON/OFF switching. The concept was validated on cyanines 3 and 5. SMLM of live cells revealed that the new probes provided higher brightness and ∼10-fold slower diffusion at the cell surface, compared to reference probes Nile Red and DiD, which boosted axial localization precision >3-fold down to 31 nm. The new probe allowed unprecedented observation of nanoscale fibrous protrusions on plasma membranes of live cells with 40 s time resolution, revealing their fast dynamics. Thus, going beyond the brightness limit of single switchable dyes by cooperative dequenching in fluorogenic dimers and slowing down probe diffusion in biomembranes open the route to significant enhancement of super-resolution fluorescence microscopy of live cells.
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Affiliation(s)
- Ilya O Aparin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Rémi Pelletier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Alexander A Choi
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, 67401 Illkirch, France
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30
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Collot M, Pfister S, Klymchenko AS. Advanced functional fluorescent probes for cell plasma membranes. Curr Opin Chem Biol 2022; 69:102161. [DOI: 10.1016/j.cbpa.2022.102161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/03/2022]
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31
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Choi AA, Park HH, Chen K, Yan R, Li W, Xu K. Displacement Statistics of Unhindered Single Molecules Show no Enhanced Diffusion in Enzymatic Reactions. J Am Chem Soc 2022; 144:4839-4844. [PMID: 35258969 PMCID: PMC8975259 DOI: 10.1021/jacs.1c12328] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent studies have sparked debate over whether catalytic reactions enhance the diffusion coefficients D of enzymes. Through high statistics of the transient (600 μs) displacements of unhindered single molecules freely diffusing in common buffers, we here quantify D for four enzymes under catalytic turnovers. We thus formulate how ∼ ±1% precisions may be achieved for D, and show no changes in diffusivity for catalase, urease, aldolase, and alkaline phosphatase under the application of wide concentration ranges of substrates. Our single-molecule approach thus overcomes potential limitations and artifacts underscored by recent studies to show no enhanced diffusion in enzymatic reactions.
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Affiliation(s)
- Alexander A. Choi
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ha H. Park
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kun Chen
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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32
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Yan R, Chen K, Wang B, Xu K. SURF4-induced tubular ERGIC selectively expedites ER-to-Golgi transport. Dev Cell 2022; 57:512-525.e8. [PMID: 35051356 PMCID: PMC8891076 DOI: 10.1016/j.devcel.2021.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022]
Abstract
The endoplasmic reticulum (ER)-to-Golgi transport is critical to protein secretion and intracellular sorting. Here, we report a highly elongated tubular ER-Golgi intermediate compartment (t-ERGIC) that selectively expedites the ER-to-Golgi transport for soluble cargoes of the receptor SURF4. Lacking the canonical ERGIC marker ERGIC-53 yet positive for the small GTPases Rab1A/B, the t-ERGIC is further marked by its extraordinarily elongated and thinned shape. With its large surface-to-volume ratio, high intracellular traveling speeds, and ER-Golgi recycling capabilities, the t-ERGIC accelerates the trafficking of SURF4-bound cargoes. The biogenesis and cargo selectivity of t-ERGIC both depend on SURF4, which recognizes the N terminus of soluble cargoes and co-clusters with the selected cargoes to expand the ER-exit site. In the steady state, the t-ERGIC-mediated fast ER-to-Golgi transport is antagonized by the KDEL-mediated ER retrieval. Together, our results argue that specific cargo-receptor interactions give rise to distinct transport carriers that regulate the trafficking kinetics.
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Affiliation(s)
- Rui Yan
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Kun Chen
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720,Chan Zuckerberg Biohub, San Francisco, CA, USA, 94158
| | - Bowen Wang
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA, 94720,Chan Zuckerberg Biohub, San Francisco, CA, USA, 94158
| | - Ke Xu
- Department of Chemistry & California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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33
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Jeong D, Kim D. Super‐resolution fluorescence microscopy‐based single‐molecule spectroscopy. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dokyung Jeong
- Department of Chemistry Hanyang University Seoul Republic of Korea
| | - Doory Kim
- Department of Chemistry Hanyang University Seoul Republic of Korea
- Research Institute for Convergence of Basic Science, Institute of Nano Science and Technology, and Research Institute for Natural Sciences Hanyang University Seoul Republic of Korea
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34
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Carravilla P, Dasgupta A, Zhurgenbayeva G, Danylchuk DI, Klymchenko AS, Sezgin E, Eggeling C. Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes. BIOPHYSICAL REPORTS 2021; 1:None. [PMID: 34939048 PMCID: PMC8651516 DOI: 10.1016/j.bpr.2021.100023] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 12/28/2022]
Abstract
Understanding the plasma membrane nanoscale organization and dynamics in living cells requires microscopy techniques with high spatial and temporal resolution that permit for long acquisition times and allow for the quantification of membrane biophysical properties, such as lipid ordering. Among the most popular super-resolution techniques, stimulated emission depletion (STED) microscopy offers one of the highest temporal resolutions, ultimately defined by the scanning speed. However, monitoring live processes using STED microscopy is significantly limited by photobleaching, which recently has been circumvented by exchangeable membrane dyes that only temporarily reside in the membrane. Here, we show that NR4A, a polarity-sensitive exchangeable plasma membrane probe based on Nile red, permits the super-resolved quantification of membrane biophysical parameters in real time with high temporal and spatial resolution as well as long acquisition times. The potential of this polarity-sensitive exchangeable dye is showcased by live-cell real-time three-dimensional STED recordings of bleb formation and lipid exchange during membrane fusion as well as by STED-fluorescence correlation spectroscopy experiments for the simultaneous quantification of membrane dynamics and lipid packing that correlate in model and live-cell membranes.
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Affiliation(s)
- Pablo Carravilla
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Anindita Dasgupta
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Gaukhar Zhurgenbayeva
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Dmytro I. Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian Eggeling
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Jena Center for Soft Matter, Jena, Germany
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35
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Xiang L, Chen K, Xu K. Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. ACS NANO 2021; 15:12483-12496. [PMID: 34304562 PMCID: PMC8789943 DOI: 10.1021/acsnano.1c04708] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.
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