1
|
Bestsennaia E, Maslov I, Balandin T, Alekseev A, Yudenko A, Abu Shamseye A, Zabelskii D, Baumann A, Catapano C, Karathanasis C, Gordeliy V, Heilemann M, Gensch T, Borshchevskiy V. Channelrhodopsin-2 Oligomerization in Cell Membrane Revealed by Photo-Activated Localization Microscopy. Angew Chem Int Ed Engl 2024; 63:e202307555. [PMID: 38226794 DOI: 10.1002/anie.202307555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 01/03/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Microbial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2±0.9 proteins/μm2 . Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.
Collapse
Affiliation(s)
- Ekaterina Bestsennaia
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Maslov
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and the Biomedical Research Institute, Hasselt University, B3590, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001, Leuven, Belgium
| | - Taras Balandin
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexey Alekseev
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Anna Yudenko
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Assalla Abu Shamseye
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Dmitrii Zabelskii
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
- European XFEL, 22869, Schenefeld, Germany
| | - Arnd Baumann
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Claudia Catapano
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, 60438, Frankfurt, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing 1, IBI-1 (Molecular and Cellular Physiology), Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing 7, IBI-7 (Structural Biochemistry), Forschungszentrum Jülich, 52428, Jülich, Germany
| |
Collapse
|
2
|
Sun N, Jia Y, Bai S, Yang Y, Dai L, Li J. Spatial mapping and quantitative evaluation of protein corona on PEGylated mesoporous silica particles by super-resolution fluorescence microscopy. J Colloid Interface Sci 2024; 653:351-358. [PMID: 37717435 DOI: 10.1016/j.jcis.2023.09.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/01/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Nanoparticles (NPs) adsorb serum proteins when exposed to biological fluids, forming a dynamic protein corona that has a profound impact on their overall biological profile and fate. Polyethylene glycol (PEG) modification is the most widely used strategy to mitigate and inhibit protein corona formation. Nevertheless, the accurate mapping and quantification of PEG inhibition effects on protein corona formation have scarcely been reported. Herein, we demonstrate the direct observation and quantification of protein corona adsorbed onto PEGylated mesoporous silica particles by direct stochastic optical reconstruction microscopy (dSTORM). The variation tendency of protein penetration depth in terms of PEG molecular weights and incubated time is investigated for the first time. The maximum penetration depths present slight increase with the prolonged incubation time, while they tend to remarkably decrease with increased chain length of modified PEG. Moreover, the co-localization of preformed protein corona with lysosomes and the destination of adsorbed protein are demonstrated. Our method provides important technical characterization information and in-depth understanding of protein corona adsorbed onto PEGylated mesoporous silica particles. This shines new light on the behaviors of silica materials in cells and may promote their practical applications in biomedicine.
Collapse
Affiliation(s)
- Nan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Luru Dai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
3
|
Matamouros S, Gensch T, Cerff M, Sachs CC, Abdollahzadeh I, Hendriks J, Horst L, Tenhaef N, Tenhaef J, Noack S, Graf M, Takors R, Nöh K, Bott M. Growth-rate dependency of ribosome abundance and translation elongation rate in Corynebacterium glutamicum differs from that in Escherichia coli. Nat Commun 2023; 14:5611. [PMID: 37699882 PMCID: PMC10497606 DOI: 10.1038/s41467-023-41176-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Bacterial growth rate (µ) depends on the protein synthesis capacity of the cell and thus on the number of active ribosomes and their translation elongation rate. The relationship between these fundamental growth parameters have only been described for few bacterial species, in particular Escherichia coli. Here, we analyse the growth-rate dependency of ribosome abundance and translation elongation rate for Corynebacterium glutamicum, a gram-positive model species differing from E. coli by a lower growth temperature optimum and a lower maximal growth rate. We show that, unlike in E. coli, there is little change in ribosome abundance for µ <0.4 h-1 in C. glutamicum and the fraction of active ribosomes is kept above 70% while the translation elongation rate declines 5-fold. Mathematical modelling indicates that the decrease in the translation elongation rate can be explained by a depletion of translation precursors.
Collapse
Affiliation(s)
- Susana Matamouros
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Martin Cerff
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Christian C Sachs
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Iman Abdollahzadeh
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Johnny Hendriks
- Institute of Biological Information Processing, IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich, Jülich, Germany
| | - Lucas Horst
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Niklas Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Julia Tenhaef
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michaela Graf
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Katharina Nöh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
| |
Collapse
|
4
|
Tan HL, Bungert-Plümke S, Kortzak D, Fahlke C, Stölting G. Dual-color Colocalization in Single-molecule Localization Microscopy to Determine the Oligomeric State of Proteins in the Plasma Membrane. Bio Protoc 2023; 13:e4749. [PMID: 37456335 PMCID: PMC10339340 DOI: 10.21769/bioprotoc.4749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/15/2023] [Accepted: 05/21/2023] [Indexed: 07/18/2023] Open
Abstract
Determining the oligomeric state of membrane proteins is critical for understanding their function. However, traditional ex situ methods like clear native gel electrophoresis can disrupt protein subunit interactions during sample preparation. In situ methods such as stepwise photobleaching have limitations due to high expression levels and limitations of optical resolution in microscopy. Super-resolution microscopy techniques such as single-molecule localization microscopy (SMLM) have the potential to overcome these limitations, but the stochastic nature of signals can lead to miscounting due to over-expression, background noise, and temporal separation of signals. Additionally, this technique has limited application due to the limited selection of fluorescent labels and the demanding control of laser power. To address these issues, we developed a dual color colocalization (DCC) strategy that offers higher tolerance to background noise and simplifies data acquisition and processing for high-throughput and reliable counting. The DCC strategy was used to determine the oligomeric states of membrane proteins of the SLC17 and SLC26 family with SMLM, providing a robust and efficient method for studying protein interactions.
Collapse
Affiliation(s)
- Hua Leonhard Tan
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Stefanie Bungert-Plümke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Daniel Kortzak
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Christoph Fahlke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Gabriel Stölting
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Center of Functional Genomics, Hypertension and Molecular Biology of Endocrine Tumors, Berlin, Germany
| |
Collapse
|
5
|
Sun N, Jia Y, Bai S, Li Q, Dai L, Li J. The power of super-resolution microscopy in modern biomedical science. Adv Colloid Interface Sci 2023; 314:102880. [PMID: 36965225 DOI: 10.1016/j.cis.2023.102880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
Super-resolution microscopy (SRM) technology that breaks the diffraction limit has revolutionized the field of cell biology since its appearance, which enables researchers to visualize cellular structures with nanometric resolution, multiple colors and single-molecule sensitivity. With the flourishing development of hardware and the availability of novel fluorescent probes, the impact of SRM has already gone beyond cell biology and extended to nanomedicine, material science and nanotechnology, and remarkably boosted important breakthroughs in these fields. In this review, we will mainly highlight the power of SRM in modern biomedical science, discussing how these SRM techniques revolutionize the way we understand cell structures, biomaterials assembly and how assembled biomaterials interact with cellular organelles, and finally their promotion to the clinical pre-diagnosis. Moreover, we also provide an outlook on the current technical challenges and future improvement direction of SRM. We hope this review can provide useful information, inspire new ideas and propel the development both from the perspective of SRM techniques and from the perspective of SRM's applications.
Collapse
Affiliation(s)
- Nan Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Yi Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Shiwei Bai
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049
| | - Qi Li
- State Key Laboratory of Biochemical Engineering Institute of Process Engineering Chinese Academy of Sciences, Beijing 100190, China
| | - Luru Dai
- Wenzhou Institute and Wenzhou Key Laboratory of Biophysics, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049.
| |
Collapse
|
6
|
Steffen A, Reusch B, Gruteser N, Mainz D, Roncarati R, Baumann A, Stradal TEB, Knebel-Mörsdorf D. Baculovirus Actin Rearrangement-Inducing Factor 1 Can Remodel the Mammalian Actin Cytoskeleton. Microbiol Spectr 2023; 11:e0518922. [PMID: 36779726 PMCID: PMC10100760 DOI: 10.1128/spectrum.05189-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 01/23/2023] [Indexed: 02/14/2023] Open
Abstract
The actin rearrangement-inducing factor 1 (Arif-1) of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an early viral protein that manipulates the actin cytoskeleton of host insect cells. Arif-1 is conserved among alphabaculoviruses and is responsible for the accumulation of F-actin at the plasma membrane during the early phase of infection. However, the molecular mechanism underlying Arif-1-induced cortical actin accumulation is still open. Recent studies have demonstrated the formation of invadosome-like structures induced by Arif-1, suggesting a function in systemic virus spread. Here, we addressed whether Arif-1 is able to manipulate the actin cytoskeleton of mammalian cells comparably to insect cells. Strikingly, transient overexpression of Arif-1 in B16-F1 mouse melanoma cells revealed pronounced F-actin remodeling. Actin assembly was increased, and intense membrane ruffling occurred at the expense of substrate-associated lamellipodia. Deletion mutagenesis studies of Arif-1 confirmed that the C-terminal cytoplasmic region was not sufficient to induce F-actin remodeling, supporting that the transmembrane region for Arif-1 function is also required in mammalian cells. The similarities between Arif-1-induced actin remodeling in insect and mammalian cells indicate that Arif-1 function relies on conserved cellular interaction partners and signal transduction pathways, thus providing an experimental tool to elucidate the underlying mechanism. IMPORTANCE Virus-induced changes of the host cell cytoskeleton play a pivotal role in the pathogenesis of viral infections. The baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is known for intervening with the regulation of the host actin cytoskeleton in a wide manner throughout the infection cycle. The actin rearrangement-inducing factor 1 (Arif-1) is a viral protein that causes actin rearrangement during the early phase of AcMNPV infection. Here, we performed overexpression studies of Arif-1 in mammalian cells to establish an experimental tool that allows elucidation of the mechanism underlying the Arif-1-induced remodeling of actin dynamics in a well-characterized and genetically accessible system.
Collapse
Affiliation(s)
- Anika Steffen
- Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Björn Reusch
- Center for Biochemistry, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Nadine Gruteser
- Institute of Biological Information Processing, Molecular and Cellular Physiology, Research Center Juelich, Juelich, Germany
| | - Daniela Mainz
- Center for Biochemistry, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Renza Roncarati
- Center for Biochemistry, University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Arnd Baumann
- Institute of Biological Information Processing, Molecular and Cellular Physiology, Research Center Juelich, Juelich, Germany
| | - Theresia E. B. Stradal
- Department of Cell Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dagmar Knebel-Mörsdorf
- Center for Biochemistry, University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Pediatrics, University Hospital Cologne, University of Cologne, Cologne, Germany
| |
Collapse
|
7
|
Sun N, Jia Y, Wang C, Xia J, Cao H, Dai L, Li C, Zhang X, Li J. Monitoring the distribution of internalized silica nanoparticles inside cells via direct stochastic optical reconstruction microscopy. J Colloid Interface Sci 2022; 615:248-255. [DOI: 10.1016/j.jcis.2022.01.196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/25/2022]
|
8
|
Cao F, Li Y, Wu J, Liu W, Ngai T. Measurements of interactions between fluorescent molecules and polyethylene glycol self-assembled monolayers. Soft Matter 2021; 18:236-243. [PMID: 34874390 DOI: 10.1039/d1sm01329g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Blocking the non-specific binding of fluorescent biomolecules to substrates is one of the most important approaches to minimize the background noise in single-molecule fluorescence detection. Polyethylene glycol (PEG) and its derivatives are the most frequently used self-assembled monolayers (SAMs) for surface passivation because they are particularly effective to reduce the adsorption of a majority of biomolecules. Most studies related to PEG SAMs focus only on the interactions between biomolecules and substrates, while few reports exist in which the interactions between fluorophores and organosilane SAMs are directly examined. The objective of this study is to try to clarify the interactions between fluorescein isothiocyanate (FITC) and PEG SAMs at different ionic strengths. Total internal reflection microscopy (TIRM) was utilized for quantitative analysis of the interactions. At low ionic strength, long-range attractions between FITC-modified polystyrene-silica particles and PEG SAM grafting substrates were observed, even though both of them had an ensemble-averaged negative charge. The origin of this attraction could be correlated to their nonuniformly charged surfaces. At high ionic strength, van der Waals attraction at short distances was measured as the electrostatic interactions were completely screened. Due to the polarizability of the FITC molecule, the van der Waals attractions increased with the thickness of the PEG SAMs. This phenomenon is explained by the hydration shell of the PEG SAMs.
Collapse
Affiliation(s)
- Feng Cao
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - Yinan Li
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - Jiahao Wu
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - Wei Liu
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| | - To Ngai
- Department of Chemistry, The Chinese University of Hong Kong, N.T., Shatin, Hong Kong, China.
| |
Collapse
|
9
|
Hauser F, Jacak J. Real-time 3D single-molecule localization microscopy analysis using lookup tables. Biomed Opt Express 2021; 12:4955-4968. [PMID: 34513235 PMCID: PMC8407837 DOI: 10.1364/boe.424016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/14/2021] [Accepted: 06/20/2021] [Indexed: 05/11/2023]
Abstract
Herein, we present a new algorithm for real-time analysis of 3D single molecule localization microscopy images with a small impact on fitting accuracy using lookup-tables with discrete xyz-positions. The algorithm realizes real-time visualization during acquisition. We demonstrate its performance on simulated and measured data. Additionally, combining real-time fitting with a feedback loop controlling the activation laser pulse keeps the number of emitters per image frame constant.
Collapse
Affiliation(s)
- Fabian Hauser
- University of Applied Sciences, Upper Austria School of Medical Engineering and Applied Social Sciences, Garnisonstraße 21, 4020 Linz, Austria
- Austrian Cluster for Tissue Regeneration, Vienna 1200, Austria
| | - Jaroslaw Jacak
- University of Applied Sciences, Upper Austria School of Medical Engineering and Applied Social Sciences, Garnisonstraße 21, 4020 Linz, Austria
- Austrian Cluster for Tissue Regeneration, Vienna 1200, Austria
| |
Collapse
|
10
|
Rivas Aiello MB, Azcárate JC, Zelaya E, David Gara P, Bosio GN, Gensch T, Mártire DO. Photothermal therapy with silver nanoplates in HeLa cells studied by in situ fluorescence microscopy. Biomater Sci 2021; 9:2608-2619. [PMID: 33595000 DOI: 10.1039/d0bm01952f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Photothermal therapy (PTT) is a noninvasive treatment for cancer relying on the incorporation of NIR-light absorbing nanomaterials into cells, which upon illumination release heat causing thermally induced cell death. We prove that irradiation of aqueous suspensions of poly(vinylpyrrolidone)-coated silver nanoplates (PVPAgNP) or PVPAgNP in HeLa cells with red or NIR lasers causes a sizeable photothermal effect, which in cells can be visualized with the temperature sensing fluorophore Rhodamine B (RhB) using spinning disk confocal fluorescence microscopy or fluorescence lifetime imaging. Upon red-light irradiation of cells that were incubated with both, RhB and PVPAgNP at concentrations with no adverse effects on cell viability, a substantial heat release is detected. Initiation of cell death by photothermal effect is observed by positive signals of fluorescent markers for early and late apoptosis. Surprisingly, a new nanomaterial-assisted cell killing mode is operating when PVPAgNP-loaded HeLa cells are excited with moderate powers of fs-pulsed NIR light. Small roundish areas are generated with bright and fast (<1 ns) decaying emission, which expand fast and destroy the whole cell in seconds. This characteristic emission is assigned to efficient optical breakdown initiation around the strongly absorbing PVPAgNP leading to plasma formation that spreads fast through the cell.
Collapse
Affiliation(s)
- María Belén Rivas Aiello
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, C. C. 16, Suc. 4, (1900) La Plata, Argentina.
| | | | | | | | | | | | | |
Collapse
|
11
|
Yao Q, Wang C, Fu M, Dai L, Li J, Gao Y. Dynamic Detection of Active Enzyme Instructed Supramolecular Assemblies In Situ via Super-Resolution Microscopy. ACS Nano 2020; 14:4882-4889. [PMID: 32233450 DOI: 10.1021/acsnano.0c00883] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Inspired by the self-assembly phenomena in nature, the instructed self-assembly of exogenous small molecules in a biological environment has become a prevalent process to control cell fate. Despite mounting examples of versatile bioactivities, the underlying mechanism remains less understood, which is in large hindered by the difficulties in the identification of those dynamic assemblies in situ. Here, with direct stochastic optical reconstruction microscopy, we are able to elucidate the dynamic morphology transformation of the enzyme-instructed supramolecular assemblies in situ inside cancer cells with a resolution below 50 nm. It indicates that the assembling molecules endure drastically different pathways between cell lines with different phosphatase activities and distribution. In HeLa cells, the direct formation of intracellular supramolecular nanofibers showed slight cytotoxicity, which was due to the possible cellular secretory pathway to excrete those exogenous molecules assemblies. In contrast, in Saos-2 cells with active phosphatase on the cell surface, assemblies with granular morphology first formed on the cell membranes, followed by a transformation into nanofibers and accumulation in cells, which induced Saos-2 cell death eventually. Overall, we provided a convenient method to reveal the in situ dynamic nanomorphology transformation of the supramolecular assemblies in a biological environment, in order to decipher their diverse biological activities.
Collapse
Affiliation(s)
- Qingxin Yao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenlei Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meifang Fu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Luru Dai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Lab of Colloid, Interface and Thermodynamics Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yuan Gao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
12
|
Fan X, Hendriks J, Comini M, Katranidis A, Büldt G, Gensch T. Spatial filter and its application in three-dimensional single molecule localization microscopy. Methods Appl Fluoresc 2020; 8:025008. [PMID: 32150730 DOI: 10.1088/2050-6120/ab7e0f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Single molecule localization microscopy (SMLM) allows the imaging of cellular structures with resolutions five to ten times below the diffraction limit of optical microscopy. It was originally introduced as a two-dimensional technique based on the localization of single emitters as projection onto the x-y imaging plane. The determination of the axial position of a fluorescent emitter is only possible by additional information. Here we report a method (spatial filter SMLM (SFSMLM)) that allows to determine the axial positions of fluorescent molecules and nanoparticles on the nanometer scale by the usage of two spatial filters, which are placed in two otherwise identical emission detection channels. SFSMLM allows axial localization in a range of ca. 1.5 μm with a localization precision of 15 - 30 nm in axial direction. The technique was utilized for localizing and imaging small cellular structures - e.g. actin filaments, vesicles and mitochondria - in three dimensions.
Collapse
Affiliation(s)
- Xiaoming Fan
- Institute of Complex Systems (ICS-4, Cellular Biophysics), Forschungszentrum Jülich, Leo-Brandt-Str., 52428 Jülich, Germany. Institute of Complex Systems (ICS-5, Molecular Biophysics), Forschungszentrum Jülich, Leo-Brandt-Str., 52428 Jülich, Germany. Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, People's Republic of China
| | | | | | | | | | | |
Collapse
|
13
|
Babcock HP, Huang F, Speer CM. Correcting Artifacts in Single Molecule Localization Microscopy Analysis Arising from Pixel Quantum Efficiency Differences in sCMOS Cameras. Sci Rep 2019; 9:18058. [PMID: 31792238 PMCID: PMC6889274 DOI: 10.1038/s41598-019-53698-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
Optimal analysis of single molecule localization microscopy (SMLM) data acquired with a scientific Complementary Metal-Oxide-Semiconductor (sCMOS) camera relies on statistical compensation for its pixel-dependent gain, offset and readout noise. In this work we show that it is also necessary to compensate for differences in the relative quantum efficiency (RQE) of each pixel. We found differences in RQE on the order of 4% in our tested sCMOS sensors. These differences were large enough to have a noticeable effect on analysis algorithm results, as seen both in simulations and biological imaging data. We discuss how the RQE differences manifest themselves in the analysis results and present the modifications to the Poisson maximum likelihood estimation (MLE) sCMOS analysis algorithm that are needed to correct for the RQE differences.
Collapse
Affiliation(s)
- Hazen P Babcock
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA.
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Colenso M Speer
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| |
Collapse
|
14
|
Abdollahzadeh I, Hendriks J, Sanwald JL, Simons IM, Hoffmann S, Weiergräber OH, Willbold D, Gensch T. Autophagy-Related Proteins GABARAP and LC3B Label Structures of Similar Size but Different Shape in Super-Resolution Imaging. Molecules 2019; 24:E1833. [PMID: 31086037 DOI: 10.3390/molecules24091833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 12/19/2022] Open
Abstract
Subcellular structures containing autophagy-related proteins of the Atg8 protein family have been investigated with conventional wide-field fluorescence and single molecule localisation microscopy. Fusion proteins of GABARAP and LC3B, respectively, with EYFP were overexpressed in HEK293 cells. While size distributions of structures labelled by the two proteins were found to be similar, shape distributions appeared quite disparate, with EYFP-GABARAP favouring circular structures and elliptical structures being dominant for EYFP-LC3B. The latter also featured a nearly doubled fraction of U-shape structures. The experimental results point towards highly differential localisation of the two proteins, which appear to label structures representing distinct stages or even specific channels of vesicular trafficking pathways. Our data also demonstrate that the application of super-resolution techniques expands the possibilities of fluorescence-based methods in autophagy studies and in some cases can rectify conclusions obtained from conventional fluorescence microscopy with diffraction-limited resolution.
Collapse
|
15
|
Conrad R, Stölting G, Hendriks J, Ruello G, Kortzak D, Jordan N, Gensch T, Hidalgo P. Rapid Turnover of the Cardiac L-Type Ca V1.2 Channel by Endocytic Recycling Regulates Its Cell Surface Availability. iScience 2018; 7:1-15. [PMID: 30267672 PMCID: PMC6135870 DOI: 10.1016/j.isci.2018.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/18/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Calcium entry through CaV1.2 L-type calcium channels regulates cardiac contractility. Here, we study the impact of exocytic and post-endocytic trafficking on cell surface channel abundance in cardiomyocytes. Single-molecule localization and confocal microscopy reveal an intracellular CaV1.2 pool tightly associated with microtubules from the perinuclear region to the cell periphery, and with actin filaments at the cell cortex. Channels newly inserted into the plasma membrane become internalized with an average time constant of 7.5 min and are sorted out to the Rab11a-recycling compartment. CaV1.2 recycling suffices for maintaining stable L-type current amplitudes over 20 hr independent of de novo channel transport along microtubules. Disruption of the actin cytoskeleton re-routes CaV1.2 from recycling toward lysosomal degradation. We identify endocytic recycling as essential for the homeostatic regulation of voltage-dependent calcium influx into cardiomyocytes. This mechanism provides the basis for a dynamic adjustment of the channel's surface availability and thus, of heart's contraction.
Collapse
Affiliation(s)
- Rachel Conrad
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gabriel Stölting
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Johnny Hendriks
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giovanna Ruello
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Daniel Kortzak
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Nadine Jordan
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Thomas Gensch
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Patricia Hidalgo
- Institute of Complex Systems 4, Zelluläre Biophysik, Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany.
| |
Collapse
|
16
|
Babcock HP. Multiplane and Spectrally-Resolved Single Molecule Localization Microscopy with Industrial Grade CMOS cameras. Sci Rep 2018; 8:1726. [PMID: 29379074 PMCID: PMC5789017 DOI: 10.1038/s41598-018-19981-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/04/2018] [Indexed: 01/04/2023] Open
Abstract
This work explores the use of industrial grade CMOS cameras for single molecule localization microscopy (SMLM). We show that industrial grade CMOS cameras approach the performance of scientific grade CMOS cameras at a fraction of the cost. This makes it more economically feasible to construct high-performance imaging systems with multiple cameras that are capable of a diversity of applications. In particular we demonstrate the use of industrial CMOS cameras for biplane, multiplane and spectrally resolved SMLM. We also provide open-source software for simultaneous control of multiple CMOS cameras and for the reduction of the movies that are acquired to super-resolution images.
Collapse
Affiliation(s)
- Hazen P Babcock
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA.
| |
Collapse
|
17
|
Kube S, Hersch N, Naumovska E, Gensch T, Hendriks J, Franzen A, Landvogt L, Siebrasse JP, Kubitscheck U, Hoffmann B, Merkel R, Csiszár A. Fusogenic Liposomes as Nanocarriers for the Delivery of Intracellular Proteins. Langmuir 2017; 33:1051-1059. [PMID: 28059515 DOI: 10.1021/acs.langmuir.6b04304] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Direct delivery of proteins and peptides into living mammalian cells has been accomplished using phospholipid liposomes as carrier particles. Such liposomes are usually taken up via endocytosis where the main part of their cargo is degraded in lysosomes before reaching its destination. Here, fusogenic liposomes, a newly developed molecular carrier system, were used for protein delivery. When such liposomes were loaded with water-soluble proteins and brought into contact with mammalian cells, the liposomal membrane efficiently fused with the cellular plasma membrane delivering the liposomal content to the cytoplasm without degradation. To explore the key factors of proteofection processes, the complex formation of fusogenic liposomes and proteins of interest and the size and zeta potential of the formed fusogenic proteoliposoms were monitored. Intracellular protein delivery was analyzed using fluorescence microscopy and flow cytometry. Proteins such as EGFP, Dendra2, and R-phycoerythrin or peptides such as LifeAct-FITC and NTF2-AlexaFluor488 were successfully incorporated into mammalian cells with high efficiency. Moreover, correct functionality and faithful transport to binding sites were also proven for the imported proteins.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Lisa Landvogt
- Biophysical Chemistry, Friedrich-Wilhelms-University Bonn , D-53012 Bonn, Germany
| | - Jan-Peter Siebrasse
- Biophysical Chemistry, Friedrich-Wilhelms-University Bonn , D-53012 Bonn, Germany
| | - Ulrich Kubitscheck
- Biophysical Chemistry, Friedrich-Wilhelms-University Bonn , D-53012 Bonn, Germany
| | | | | | | |
Collapse
|
18
|
Tang Y, Hendriks J, Gensch T, Dai L, Li J. Automatic Bayesian single molecule identification for localization microscopy. Sci Rep 2016; 6:33521. [PMID: 27641933 DOI: 10.1038/srep33521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/30/2016] [Indexed: 01/03/2023] Open
Abstract
Single molecule localization microscopy (SMLM) is on its way to become a mainstream imaging technique in the life sciences. However, analysis of SMLM data is biased by user provided subjective parameters required by the analysis software. To remove this human bias we introduce here the Auto-Bayes method that executes the analysis of SMLM data automatically. We demonstrate the success of the method using the photoelectron count of an emitter as selection characteristic. Moreover, the principle can be used for any characteristic that is bimodally distributed with respect to false and true emitters. The method also allows generation of an emitter reliability map for estimating quality of SMLM-based structures. The potential of the Auto-Bayes method is shown by the fact that our first basic implementation was able to outperform all software packages that were compared in the ISBI online challenge in 2015, with respect to molecule detection (Jaccard index).
Collapse
|
19
|
Fu M, Dai L, Jiang Q, Tang Y, Zhang X, Ding B, Li J. Observation of intracellular interactions between DNA origami and lysosomes by the fluorescence localization method. Chem Commun (Camb) 2016; 52:9240-2. [DOI: 10.1039/c6cc00484a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The combined image (b) of the fluorescence localization image of DNA origami and the TIRF image of lysosomes illustrates detailed interactions between them.
Collapse
Affiliation(s)
- Meifang Fu
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Lab of Colloid
- Interface and Chemical Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
| | - Luru Dai
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Qiao Jiang
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Yunqing Tang
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Xiaoming Zhang
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Baoquan Ding
- National Center for Nanoscience and Technology
- Beijing 100190
- China
| | - Junbai Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- CAS Key Lab of Colloid
- Interface and Chemical Thermodynamics
- Institute of Chemistry
- Chinese Academy of Sciences
| |
Collapse
|
20
|
Zhang X, Dai L, Wang A, Wölk C, Dobner B, Brezesinski G, Tang Y, Wang X, Li J. The Directional Observation of Highly Dynamic Membrane Tubule Formation Induced by Engulfed Liposomes. Sci Rep 2015; 5:16559. [PMID: 26548331 DOI: 10.1038/srep16559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 10/01/2015] [Indexed: 11/09/2022] Open
Abstract
Highly dynamic tubular structures in cells are responsible for exchanges between organelles. Compared with bacterial invasion, the most affordable and least toxic lipids were found in this study to be gentle and safe exogenous stimuli for the triggering of membrane tubules. A specific lipid system was internalized by NIH3T3 cells. Following cellular uptake, the constructed liposomes traveled towards the nucleus in aggregations and were gradually distributed into moving vesicles and tubules in the cytosol. The triggered tubules proceeded, retreated or fluctuated along the cytoskeleton and were highly dynamic, moving quickly (up to several microns per second), and breaking and fusing frequently. These elongated tubules could also fuse with one another, giving rise to polygonal membrane networks. These lipid systems, with the novel property of accelerating intracellular transport, provide a new paradigm for investigating cellular dynamics.
Collapse
|