1
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Sedeh AB, Kobitski A, Dai S, Eroğlu-Kayıkçı S, Nienhaus K, Hilbert L, Nienhaus GU. Stimulated emission double depletion nanoscopy with background correction at the single-pixel level. Opt Lett 2023; 48:5791-5794. [PMID: 37910760 DOI: 10.1364/ol.502001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/12/2023] [Indexed: 11/03/2023]
Abstract
Fluorescence microscopy images are inevitably tainted by background contributions including emission from out-of-focus planes, scattered light, and detector noise. In stimulated emission depletion (STED) nanoscopy, an additional, method-specific background arises from incomplete depletion and re-excitation by the depletion beam. Various approaches have been proposed to remove the background from a STED image, some of which rely on the acquisition of a separate background image that is subtracted from the STED image with a weighting factor. Using stimulated emission double depletion (STEDD) nanoscopy, we observed that the weighting factor varies locally in densely labeled samples, so that background removal with a single (global) weighting factor generates local image artifacts due to incorrect background subtraction. Here we present an algorithm that computes the optimal weighting factor at the single-pixel level, yielding a difference image with excellent suppression of low-frequency background.
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2
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Englert D, Burger EM, Grün F, Verma MS, Lackner J, Lampe M, Bühler B, Schokolowski J, Nienhaus GU, Jäschke A, Sunbul M. Fast-exchanging spirocyclic rhodamine probes for aptamer-based super-resolution RNA imaging. Nat Commun 2023; 14:3879. [PMID: 37391423 PMCID: PMC10313827 DOI: 10.1038/s41467-023-39611-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
Live-cell RNA imaging with high spatial and temporal resolution remains a major challenge. Here we report the development of RhoBAST:SpyRho, a fluorescent light-up aptamer (FLAP) system ideally suited for visualizing RNAs in live or fixed cells with various advanced fluorescence microscopy modalities. Overcoming problems associated with low cell permeability, brightness, fluorogenicity, and signal-to-background ratio of previous fluorophores, we design a novel probe, SpyRho (Spirocyclic Rhodamine), which tightly binds to the RhoBAST aptamer. High brightness and fluorogenicity is achieved by shifting the equilibrium between spirolactam and quinoid. With its high affinity and fast ligand exchange, RhoBAST:SpyRho is a superb system for both super-resolution SMLM and STED imaging. Its excellent performance in SMLM and the first reported super-resolved STED images of specifically labeled RNA in live mammalian cells represent significant advances over other FLAPs. The versatility of RhoBAST:SpyRho is further demonstrated by imaging endogenous chromosomal loci and proteins.
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Affiliation(s)
- Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Eva-Maria Burger
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Franziska Grün
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Mrigank S Verma
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Jens Lackner
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bastian Bühler
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Janin Schokolowski
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
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3
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Kuznik NC, Solozobova V, Lee II, Jung N, Yang L, Nienhaus K, Ntim EA, Rottenberg JT, Muhle-Goll C, Kumar AR, Peravali R, Gräßle S, Gourain V, Deville C, Cato L, Neeb A, Dilger M, Cramer von Clausbruch CA, Weiss C, Kieffer B, Nienhaus GU, Brown M, Bräse S, Cato ACB. A chemical probe for BAG1 targets androgen receptor-positive prostate cancer through oxidative stress signaling pathway. iScience 2022; 25:104175. [PMID: 35479411 PMCID: PMC9036123 DOI: 10.1016/j.isci.2022.104175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/01/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
BAG1 is a family of polypeptides with a conserved C-terminal BAG domain that functions as a nucleotide exchange factor for the molecular chaperone HSP70. BAG1 proteins also control several signaling processes including proteostasis, apoptosis, and transcription. The largest isoform, BAG1L, controls the activity of the androgen receptor (AR) and is upregulated in prostate cancer. Here, we show that BAG1L regulates AR dynamics in the nucleus and its ablation attenuates AR target gene expression especially those involved in oxidative stress and metabolism. We show that a small molecule, A4B17, that targets the BAG domain downregulates AR target genes similar to a complete BAG1L knockout and upregulates the expression of oxidative stress-induced genes involved in cell death. Furthermore, A4B17 outperformed the clinically approved antagonist enzalutamide in inhibiting cell proliferation and prostate tumor development in a mouse xenograft model. BAG1 inhibitors therefore offer unique opportunities for antagonizing AR action and prostate cancer growth. BAG1L interacts with a sequence overlapping a polyalanine tract in the AR NTD Knockdown of BAG1L increase AR dynamics in the nucleus BAG1L uses ROS pathway to regulate AR+ prostate cancer cell proliferation A small molecule BAG1 inhibitor inhibits prostate tumor growth in mouse xenografts
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Affiliation(s)
- Nane C Kuznik
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Valeria Solozobova
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Irene I Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nicole Jung
- Institute of Biological and Chemical Systems, Functional Molecular Systems, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Linxiao Yang
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Emmanuel A Ntim
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Jaice T Rottenberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Claudia Muhle-Goll
- Institute of Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Amrish Rajendra Kumar
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ravindra Peravali
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Simone Gräßle
- Institute of Biological and Chemical Systems, Functional Molecular Systems, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Victor Gourain
- LabEx IGO "Immunotherapy, Graft, Oncology", Centre de Recherche en Transplantation et Immunologie - UMR1064, 44093 Nantes, France
| | - Célia Deville
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U964, CNRS, UMR-7104, Université de Strasbourg, 67404 Illkirch-Graffenstaden, France
| | - Laura Cato
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Antje Neeb
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Marco Dilger
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Christina A Cramer von Clausbruch
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Carsten Weiss
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
| | - Bruno Kieffer
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM, U964, CNRS, UMR-7104, Université de Strasbourg, 67404 Illkirch-Graffenstaden, France
| | - G Ulrich Nienhaus
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Applied Physics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stefan Bräse
- Institute of Biological and Chemical Systems, Functional Molecular Systems, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Andrew C B Cato
- Institute of Biological and Chemical Systems, Biological Information Processing, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen, Germany
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4
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Ambrosi G, Voloshanenko O, Eckert AF, Kranz D, Nienhaus GU, Boutros M. Allele-specific endogenous tagging and quantitative analysis of β-catenin in colorectal cancer cells. eLife 2022; 11:64498. [PMID: 35014953 PMCID: PMC8752093 DOI: 10.7554/elife.64498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/30/2020] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
Wnt signaling plays important roles in development, homeostasis, and tumorigenesis. Mutations in β-catenin that activate Wnt signaling have been found in colorectal and hepatocellular carcinomas. However, the dynamics of wild-type and mutant forms of β-catenin are not fully understood. Here, we genome-engineered fluorescently tagged alleles of endogenous β-catenin in a colorectal cancer cell line. Wild-type and oncogenic mutant alleles were tagged with different fluorescent proteins, enabling the analysis of both variants in the same cell. We analyzed the properties of both β-catenin alleles using immunoprecipitation, immunofluorescence, and fluorescence correlation spectroscopy approaches, revealing distinctly different biophysical properties. In addition, activation of Wnt signaling by treatment with a GSK3β inhibitor or a truncating APC mutation modulated the wild-type allele to mimic the properties of the mutant β-catenin allele. The one-step tagging strategy demonstrates how genome engineering can be employed for the parallel functional analysis of different genetic variants.
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Affiliation(s)
- Giulia Ambrosi
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
| | - Oksana Voloshanenko
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
| | - Antonia F Eckert
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dominique Kranz
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
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5
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Hüpfel M, Fernández Merino M, Bennemann J, Takamiya M, Rastegar S, Tursch A, Holstein TW, Nienhaus GU. Two plus one is almost three: a fast approximation for multi-view deconvolution. Biomed Opt Express 2022; 13:147-158. [PMID: 35154860 PMCID: PMC8803020 DOI: 10.1364/boe.443660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/25/2021] [Accepted: 11/28/2021] [Indexed: 05/04/2023]
Abstract
Multi-view deconvolution is a powerful image-processing tool for light sheet fluorescence microscopy, providing isotropic resolution and enhancing the image content. However, performing these calculations on large datasets is computationally demanding and time-consuming even on high-end workstations. Especially in long-time measurements on developing animals, huge amounts of image data are acquired. To keep them manageable, redundancies should be removed right after image acquisition. To this end, we report a fast approximation to three-dimensional multi-view deconvolution, denoted 2D+1D multi-view deconvolution, which is able to keep up with the data flow. It first operates on the two dimensions perpendicular and subsequently on the one parallel to the rotation axis, exploiting the rotational symmetry of the point spread function along the rotation axis. We validated our algorithm and evaluated it quantitatively against two-dimensional and three-dimensional multi-view deconvolution using simulated and real image data. 2D+1D multi-view deconvolution takes similar computation time but performs markedly better than the two-dimensional approximation only. Therefore, it will be most useful for image processing in time-critical applications, where the full 3D multi-view deconvolution cannot keep up with the data flow.
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Affiliation(s)
- Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Manuel Fernández Merino
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Johannes Bennemann
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), 76021 Eggenstein-Leopoldshafen, Germany
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), 76021 Eggenstein-Leopoldshafen, Germany
| | - Anja Tursch
- Centre for Organismal Studies (COS), Universität Heidelberg, 69120 Heidelberg, Germany
| | - Thomas W. Holstein
- Centre for Organismal Studies (COS), Universität Heidelberg, 69120 Heidelberg, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Centre for Organismal Studies (COS), Universität Heidelberg, 69120 Heidelberg, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76021 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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6
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Gao P, Nienhaus GU. Axial line-scanning stimulated emission depletion fluorescence correlation spectroscopy. Opt Lett 2021; 46:2184-2187. [PMID: 33929450 DOI: 10.1364/ol.420765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Investigating the dynamics and interactions of biomolecules within or attached to membranes of living cells is crucial for understanding biology at the molecular level. In this pursuit, classical, diffraction-limited optical fluorescence microscopy is widely used, but it faces limitations due to (1) the heterogeneity of biomembranes on the nanoscale and (2) the intrinsic motion of membranes with respect to the focus. Here we introduce a new confocal microscopy-based fluctuation spectroscopy technique aimed at alleviating these two problems, called axial line-scanning stimulated emission depletion fluorescence correlation spectroscopy (axial ls-STED-FCS). Axial line scanning by means of a tunable acoustic gradient index of refraction lens provides a time resolution of a few microseconds, which is more than two orders of magnitude greater than that of conventional, lateral line-scanning fluorescence correlation spectroscopy (typically around 1 ms). Using STED excitation, the observation area on the membrane can be reduced 10-100 fold, resulting in sub-diffraction spatial resolution and the ability to study samples with densely labeled membranes. Due to these attractive properties, we expect that the axial ls-STED-FCS will find wide application, especially in the biomolecular sciences.
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7
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Sunbul M, Lackner J, Martin A, Englert D, Hacene B, Grün F, Nienhaus K, Nienhaus GU, Jäschke A. Super-resolution RNA imaging using a rhodamine-binding aptamer with fast exchange kinetics. Nat Biotechnol 2021; 39:686-690. [PMID: 33574610 DOI: 10.1038/s41587-020-00794-3] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/10/2020] [Indexed: 11/09/2022]
Abstract
Overcoming limitations of previous fluorescent light-up RNA aptamers for super-resolution imaging, we present RhoBAST, an aptamer that binds a fluorogenic rhodamine dye with fast association and dissociation kinetics. Its intermittent fluorescence emission enables single-molecule localization microscopy with a resolution not limited by photobleaching. We use RhoBAST to image subcellular structures of RNA in live and fixed cells with about 10-nm localization precision and a high signal-to-noise ratio.
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Affiliation(s)
- Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
| | - Jens Lackner
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Annabell Martin
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Daniel Englert
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Benjamin Hacene
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Franziska Grün
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Karin Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Institute of Biological and Chemical Systems (IBCS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany.
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8
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Gao P, Nienhaus K, Nienhaus GU. Axial Line-Scanning STED-FCS. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1264] [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] [Indexed: 10/22/2022] Open
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9
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Hüpfel M, Kobitski AY, Zhang W, Nienhaus GU. Wavelet-Based Background and Noise Removal for Fluorescence Microscopy Images. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.2221] [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] [Indexed: 10/22/2022] Open
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10
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Hüpfel M, Yu. Kobitski A, Zhang W, Nienhaus GU. Wavelet-based background and noise subtraction for fluorescence microscopy images. Biomed Opt Express 2021; 12:969-980. [PMID: 33680553 PMCID: PMC7901331 DOI: 10.1364/boe.413181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/27/2020] [Accepted: 01/15/2021] [Indexed: 05/20/2023]
Abstract
Fluorescence microscopy images are inevitably contaminated by background intensity contributions. Fluorescence from out-of-focus planes and scattered light are important sources of slowly varying, low spatial frequency background, whereas background varying from pixel to pixel (high frequency noise) is introduced by the detection system. Here we present a powerful, easy-to-use software, wavelet-based background and noise subtraction (WBNS), which effectively removes both of these components. To assess its performance, we apply WBNS to synthetic images and compare the results quantitatively with the ground truth and with images processed by other background removal algorithms. We further evaluate WBNS on real images taken with a light-sheet microscope and a super-resolution stimulated emission depletion microscope. For both cases, we compare the WBNS algorithm with hardware-based background removal techniques and present a quantitative assessment of the results. WBNS shows an excellent performance in all these applications and significantly enhances the visual appearance of fluorescence images. Moreover, it may serve as a pre-processing step for further quantitative analysis.
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Affiliation(s)
- Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Andrei Yu. Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Weichun Zhang
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA
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11
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Affiliation(s)
- Sarah Wieghold
- Department of Chemistry and BiochemistryFlorida State University 95 Chieftan Way Tallahassee FL 32306 USA
| | - Alexander S. Bieber
- Department of Chemistry and BiochemistryFlorida State University 95 Chieftan Way Tallahassee FL 32306 USA
| | - Jens Lackner
- Institute of Applied Physics (APH)Karlsruhe Institute of Technology (KIT) Wolfgang-Gaede-Str. 1 76131 Karlsruhe Germany
| | - Karin Nienhaus
- Institute of Applied Physics (APH)Karlsruhe Institute of Technology (KIT) Wolfgang-Gaede-Str. 1 76131 Karlsruhe Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics (APH)Karlsruhe Institute of Technology (KIT) Wolfgang-Gaede-Str. 1 76131 Karlsruhe Germany
- Institute of Nanotechnology (INT)Karlsruhe Institute of Technology (KIT) 76344 Eggenstein-Leopoldshafen Germany
- Institute of Biological and Chemical Systems (IBCS)Karlsruhe Institute of Technology (KIT) 76344 Eggenstein-Leopoldshafen Germany
- Department of PhysicsUniversity of Illinois at Urbana−Champaign 1110 West Green Street Urbana IL 61801 USA
| | - Lea Nienhaus
- Department of Chemistry and BiochemistryFlorida State University 95 Chieftan Way Tallahassee FL 32306 USA
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12
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Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. Confocal and Super-resolution Imaging of RNA in Live Bacteria Using a Fluorogenic Silicon Rhodamine-binding Aptamer. Bio Protoc 2020; 10:e3603. [PMID: 33659569 DOI: 10.21769/bioprotoc.3603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/15/2020] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
Genetically encoded light-up RNA aptamers have been shown to be promising tools for the visualization of RNAs in living cells, helping us to advance our understanding of the broad and complex life of RNA. Although a handful of light-up aptamers spanning the visible wavelength region have been developed, none of them have yet been reported to be compatible with advanced super-resolution techniques, mainly due to poor photophysical properties of their small-molecule fluorogens. Here, we describe a detailed protocol for fluorescence microscopy of mRNA in live bacteria using the recently reported fluorogenic silicon rhodamine binding aptamer (SiRA) featuring excellent photophysical properties. Notably, with SiRA, we demonstrated the first aptamer-based RNA visualization using super-resolution (STED) microscopy. This imaging method can be especially valuable for visualization of RNA in prokaryotes since the size of a bacterium is only a few times greater than the optical resolution of a conventional microscope.
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Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Peng Gao
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120 Heidelberg, Germany
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13
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Gao P, Wirth R, Lackner J, Sunbul M, Jaeschke A, Nienhaus GU. Superresolution Imaging of Live Cells with Genetically Encoded Silicon Rhodamine-Binding RNA Aptamers. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.916] [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] [Indexed: 10/25/2022] Open
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14
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Wang H, Ma R, Nienhaus K, Nienhaus GU. Protein Adsorption Onto Polystyrene Nanoparticles and its Effect on Nanoparticle Agglomeration. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Nienhaus K, Nienhaus GU. Towards a molecular-level understanding of the protein corona around nanoparticles – Recent advances and persisting challenges. Current Opinion in Biomedical Engineering 2019. [DOI: 10.1016/j.cobme.2019.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Adams M, Kozlowska M, Baroni N, Oldenburg M, Ma R, Busko D, Turshatov A, Emandi G, Senge MO, Haldar R, Wöll C, Nienhaus GU, Richards BS, Howard IA. Highly Efficient One-Dimensional Triplet Exciton Transport in a Palladium-Porphyrin-Based Surface-Anchored Metal-Organic Framework. ACS Appl Mater Interfaces 2019; 11:15688-15697. [PMID: 30938507 DOI: 10.1021/acsami.9b03079] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Efficient photon-harvesting materials require easy-to-deposit materials exhibiting good absorption and excited-state transport properties. We demonstrate an organic thin-film material system, a palladium-porphyrin-based surface-anchored metal-organic framework (SURMOF) thin film that meets these requirements. Systematic investigations using transient absorption spectroscopy confirm that triplets are very mobile within single crystalline domains; a detailed analysis reveals a triplet transfer rate on the order of 1010 s-1. The crystalline nature of the SURMOFs also allows a thorough theoretical analysis using the density functional theory. The theoretical results reveal that the intermolecular exciton transfer can be described by a Dexter electron exchange mechanism that is considerably enhanced by virtual charge-transfer exciton intermediates. On the basis of the photophysical results, we predict exciton diffusion lengths on the order of several micrometers in perfectly ordered, single-crystalline SURMOFs. In the presently available samples, strong interactions of excitons with domain boundaries present in these metal-organic thin films limit the diffusion length to the diameter of these two-dimensional grains, which amount to about 100 nm. Our results demonstrate high potential of SURMOFs for light-harvesting applications.
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Affiliation(s)
| | | | | | | | - Rui Ma
- Institute of Applied Physics , Karlsruhe Institute of Technology , Wolfgang-Gaede-Straße 1 , 76131 Karlsruhe , Germany
| | | | | | - Ganapathi Emandi
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin , The University of Dublin , 152-160 Pearse Street , 2 Dublin , Ireland
| | - Mathias O Senge
- School of Chemistry, SFI Tetrapyrrole Laboratory, Trinity Biomedical Sciences Institute, Trinity College Dublin , The University of Dublin , 152-160 Pearse Street , 2 Dublin , Ireland
| | | | | | - G Ulrich Nienhaus
- Institute of Applied Physics , Karlsruhe Institute of Technology , Wolfgang-Gaede-Straße 1 , 76131 Karlsruhe , Germany
- Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , 61801 Illinois , United States
| | - Bryce S Richards
- Light Technology Institute , Karlsruhe Institute of Technology , Wolfgang-Gaede-Straße 1 , 76131 Karlsruhe , Germany
| | - Ian A Howard
- Light Technology Institute , Karlsruhe Institute of Technology , Wolfgang-Gaede-Straße 1 , 76131 Karlsruhe , Germany
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17
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Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. SiRA: A Silicon Rhodamine-Binding Aptamer for Live-Cell Super-Resolution RNA Imaging. J Am Chem Soc 2019; 141:7562-7571. [PMID: 30986047 DOI: 10.1021/jacs.9b02697] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although genetically encoded light-up RNA aptamers have become promising tools for visualizing and tracking RNAs in living cells, aptamer/ligand pairs that emit in the far-red and near-infrared (NIR) regions are still rare. In this work, we developed a light-up RNA aptamer that binds silicon rhodamines (SiRs). SiRs are photostable, NIR-emitting fluorophores that change their open-closed equilibrium between the noncolored spirolactone and the fluorescent zwitterion in response to their environment. This property is responsible for their high cell permeability and fluorogenic behavior. Aptamers binding to SiR were in vitro selected from a combinatorial RNA library. Sequencing, bioinformatic analysis, truncation, and mutational studies revealed a 50-nucleotide minimal aptamer, SiRA, which binds with nanomolar affinity to the target SiR. In addition to silicon rhodamines, SiRA binds structurally related rhodamines and carborhodamines, making it a versatile tool spanning the far-red region of the spectrum. Photophysical characterization showed that SiRA is remarkably resistant to photobleaching and constitutes the brightest far-red light-up aptamer system known to date owing to its favorable features: a fluorescence quantum yield of 0.98 and an extinction coefficient of 86 000 M-1cm-1. Using the SiRA system, we visualized the expression of RNAs in bacteria in no-wash live-cell imaging experiments and also report stimulated emission depletion (STED) super-resolution microscopy images of aptamer-based, fluorescently labeled mRNA in live cells. This work represents, to our knowledge, the first application of the popular SiR dyes and of intramolecular spirocyclization as a means of background reduction in the field of aptamer-based RNA imaging. We anticipate a high potential for this novel RNA labeling tool to address biological questions.
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Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Peng Gao
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Institute of Toxicology and Genetics (ITG) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
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18
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Gao P, Gao X, Nienhaus K, Nienhaus GU. Line-Scanning Spatial Correlation Spectroscopy for Studying Dynamics in Biomembranes. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.750] [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] [Indexed: 11/29/2022] Open
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19
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Abstract
Nitric oxide synthases (NOSs) are heme enzymes that generate highly reactive nitric oxide from l-arginine (l-Arg) in a complex mechanism that is still only partially understood. We have studied carbon monoxide (CO) binding to the oxygenase domain of murine inducible NOS (iNOS) by using flash photolysis. The P420 and P450 forms of the enzyme, assigned to a protonated and unprotonated proximal cysteine, through which the heme is anchored to the protein, show markedly different CO rebinding properties. The data suggest that P420 has a widely open distal pocket that admits water. CO rebinding to the P450 form strongly depends on the presence of the substrate l-Arg, the intermediate Nω-hydroxy-l-arginine, and the cofactor tetrahydrobiopterin. After adding these small molecules to the enzyme solution, the CO kinetics change slowly over the hours. This process can be described as a relaxation from a fast rebinding, metastable species to a slowly rebinding, thermodynamically stable species, which we associate with the enzymatically active form. Our results allow us to determine kinetic parameters of l-Arg binding to the ferrous deoxy iNOS protein for the first time and also provide clues regarding the nature of structural differences between the two interconverting species.
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Affiliation(s)
- Michael Horn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
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20
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Zheng J, Zuo C, Gao P, Nienhaus GU. Dual-mode phase and fluorescence imaging with a confocal laser scanning microscope. Opt Lett 2018; 43:5689-5692. [PMID: 30439929 DOI: 10.1364/ol.43.005689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 06/09/2023]
Abstract
We present dual-mode phase and fluorescence imaging in a confocal laser scanning microscopy (CLSM) system. For phase imaging, the depth of field of the CLSM system is extended by fast axial scanning with a tunable acoustic gradient index of refraction lens. Under transillumination, intensity images of the sample are recorded at a few different defocusing distances. The phase image is reconstructed from these intensity images by using the transport-of-intensity equation. The 3D fluorescence image is obtained by confocal scanning. The dual-mode images with pixel-to-pixel correspondence yield complementary quantitative structural and functional information. Combination of the two imaging modalities enables standalone determination of the refractive index of live cells.
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21
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Zhou L, Middel V, Reischl M, Strähle U, Nienhaus GU. Distinct amino acid motifs carrying multiple positive charges regulate membrane targeting of dysferlin and MG53. PLoS One 2018; 13:e0202052. [PMID: 30092031 PMCID: PMC6084962 DOI: 10.1371/journal.pone.0202052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 04/12/2018] [Accepted: 07/26/2018] [Indexed: 11/17/2022] Open
Abstract
Dysferlin (Dysf) and mitsugumin53 (MG53) are two key proteins involved in membrane repair of muscle cells which are efficiently recruited to the sarcolemma upon lesioning. Plasma membrane localization and recruitment of a Dysf fragment to membrane lesions in zebrafish myofibers relies on the presence of a short, polybasic amino acid motif, WRRFK. Here we show that the positive charges carried by this motif are responsible for this function. In mouse MG53, we have identified a similar motif with multiple basic residues, WKKMFR. A single amino acid replacement, K279A, leads to severe aggregation of MG53 in inclusion bodies in HeLa cells. This result is due to the loss of positive charge, as shown by studying the effects of other neutral amino acids at position 279. Consequently, our data suggest that positively charged amino acid stretches play an essential role in the localization and function of Dysf and MG53.
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Affiliation(s)
- Lu Zhou
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Volker Middel
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Markus Reischl
- Institute for Applied Computer Science, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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22
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Schott B, Traub M, Schlagenhauf C, Takamiya M, Antritter T, Bartschat A, Löffler K, Blessing D, Otte JC, Kobitski AY, Nienhaus GU, Strähle U, Mikut R, Stegmaier J. EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos. PLoS Comput Biol 2018; 14:e1006128. [PMID: 29672531 PMCID: PMC5929571 DOI: 10.1371/journal.pcbi.1006128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/01/2018] [Accepted: 04/08/2018] [Indexed: 01/13/2023] Open
Abstract
State-of-the-art light-sheet and confocal microscopes allow recording of entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be segmented and tracked automatically in these terabyte-scale 3D+t images, resulting in thousands of cell migration trajectories that provide detailed insights to large-scale tissue reorganization at the cellular level. Here we present EmbryoMiner, a new interactive open-source framework suitable for in-depth analyses and comparisons of entire embryos, including an extensive set of trajectory features. Starting at the whole-embryo level, the framework can be used to iteratively focus on a region of interest within the embryo, to investigate and test specific trajectory-based hypotheses and to extract quantitative features from the isolated trajectories. Thus, the new framework provides a valuable new way to quantitatively compare corresponding anatomical regions in different embryos that were manually selected based on biological prior knowledge. As a proof of concept, we analyzed 3D+t light-sheet microscopy images of zebrafish embryos, showcasing potential user applications that can be performed using the new framework.
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Affiliation(s)
- Benjamin Schott
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- * E-mail: (BS); (JS)
| | - Manuel Traub
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Cornelia Schlagenhauf
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Masanari Takamiya
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Thomas Antritter
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Andreas Bartschat
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Katharina Löffler
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Denis Blessing
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jens C. Otte
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Andrei Y. Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - G. Ulrich Nienhaus
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ralf Mikut
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Johannes Stegmaier
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Imaging and Computer Vision, RWTH Aachen University, Aachen, Germany
- * E-mail: (BS); (JS)
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23
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Manz C, Kobitski AY, Samanta A, Jäschke A, Nienhaus GU. The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study. J Chem Phys 2018; 148:123324. [DOI: 10.1063/1.5003783] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Christoph Manz
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrei Yu. Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Ayan Samanta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Andres Jäschke
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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24
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Zhou L, Obhof T, Schneider K, Feldbrügge M, Nienhaus GU, Kämper J. Cytoplasmic Transport Machinery of the SPF27 Homologue Num1 in Ustilago maydis. Sci Rep 2018; 8:3611. [PMID: 29483520 PMCID: PMC5832149 DOI: 10.1038/s41598-018-21628-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 10/25/2017] [Accepted: 02/07/2018] [Indexed: 01/15/2023] Open
Abstract
In the phytopathogenic basidiomycete Ustilago maydis, the Num1 protein has a pivotal function in hyphal morphogenesis. Num1 functions as a core component of the spliceosome-associated Prp19/CDC5 complex (NTC). The interaction of Num1 with the kinesin motor Kin1 suggests a connection between a component of the splicing machinery and cytoplasmic trafficking processes. Previously it was shown that Num1 localizes predominantly in the nucleus; however, due to the diffraction-limited spatial resolution of conventional optical microscopy, it was not possible to attribute the localization to specific structures within the cytoplasm. We have now employed super-resolution localization microscopy to visualize Num1 in the cytoplasm by fusing it to a tandem dimeric Eos fluorescent protein (tdEosFP). The Num1 protein is localized within the cytoplasm with an enhanced density in the vicinity of microtubules. Num1 movement is found predominantly close to the nucleus. Movement is dependent on its interaction partner Kin1, but independent of Kin3. Our results provide strong evidence that, in addition to its involvement in splicing in the nucleus, Num1 has an additional functional role in the cytosol connected to the Kin1 motor protein.
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Affiliation(s)
- Lu Zhou
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Theresa Obhof
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Karina Schneider
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Michael Feldbrügge
- Institute of Microbiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine-University, Düsseldorf, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany. .,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany.
| | - Jörg Kämper
- Department of Genetics, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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25
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Nienhaus K, Mohr MA, Yu Kobitski A, Rullan Sabater L, Obara CJ, Lippincott-Schwartz J, Nienhaus GU, Pantazis P. Primed Green-to-Red Photoconversion of Fluorescent Proteins Occurs via a Triplet State. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2916] [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] [Indexed: 11/27/2022] Open
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26
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Manz C, Yu Kobitski A, Samanta A, Keller BG, Jäschke A, Nienhaus GU. Energy Landscape Analysis of the Full-Length SAM-I Riboswitch using Single-Molecule FRET Spectroscopy. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3692] [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] [Indexed: 11/26/2022] Open
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27
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Nienhaus K, Nienhaus GU. Different Mechanisms of Catalytic Complex Formation in Two L-Tryptophan Processing Dioxygenases. Front Mol Biosci 2018; 4:94. [PMID: 29354636 PMCID: PMC5758539 DOI: 10.3389/fmolb.2017.00094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 10/24/2017] [Accepted: 12/18/2017] [Indexed: 01/25/2023] Open
Abstract
The human heme enzymes tryptophan 2,3-dioxygenase (hTDO) and indoleamine 2,3 dioxygenase (hIDO) catalyze the initial step in L-tryptophan (L-Trp) catabolism, the insertion of dioxygen into L-Trp. Overexpression of these enzymes causes depletion of L-Trp and accumulation of metabolic products, and thereby contributes to tumor immune tolerance and immune dysregulation in a variety of disease pathologies. Understanding the assembly of the catalytically active, ternary enzyme-substrate-ligand complexes is not yet fully resolved, but an essential prerequisite for designing efficient and selective de novo inhibitors. Evidence is mounting that the ternary complex forms by sequential binding of ligand and substrate in a specific order. In hTDO, the apolar L-Trp binds first, decreasing active-site solvation and, as a result, reducing non-productive oxidation of the heme iron by the dioxygen ligand, which may leave the substrate bound to a ferric heme iron. In hIDO, by contrast, dioxygen must first coordinate to the heme iron because a bound substrate would occlude ligand access to the heme iron, so the ternary complex can no longer form. Consequently, faster association of L-Trp at high concentrations results in substrate inhibition. Here, we summarize our present knowledge of ternary complex formation in hTDO and hIDO and relate these findings to structural peculiarities of their active sites.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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28
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Zhou L, Evangelinos M, Wernet V, Eckert AF, Ishitsuka Y, Fischer R, Nienhaus GU, Takeshita N. Superresolution and pulse-chase imaging reveal the role of vesicle transport in polar growth of fungal cells. Sci Adv 2018; 4:e1701798. [PMID: 29387789 PMCID: PMC5787382 DOI: 10.1126/sciadv.1701798] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 12/27/2017] [Indexed: 06/07/2023]
Abstract
Polarized growth of filamentous fungi requires continuous transport of biomolecules to the hyphal tip. To this end, construction materials are packaged in vesicles and transported by motor proteins along microtubules and actin filaments. We have studied these processes with quantitative superresolution localization microscopy of live Aspergillus nidulans cells expressing the photoconvertible protein mEosFPthermo fused to the chitin synthase ChsB. ChsB is mainly located at the Spitzenkörper near the hyphal tip and produces chitin, a key component of the cell wall. We have visualized the pulsatory dynamics of the Spitzenkörper, reflecting vesicle accumulation before exocytosis and their subsequent fusion with the apical plasma membrane. Furthermore, high-speed pulse-chase imaging after photoconversion of mEosFPthermo in a tightly focused spot revealed that ChsB is transported with two different speeds from the cell body to the hyphal tip and vice versa. Comparative analysis using motor protein deletion mutants allowed us to assign the fast movements (7 to 10 μm s-1) to transport of secretory vesicles by kinesin-1, and the slower ones (2 to 7 μm s-1) to transport by kinesin-3 on early endosomes. Our results show how motor proteins ensure the supply of vesicles to the hyphal tip, where temporally regulated exocytosis results in stepwise tip extension.
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Affiliation(s)
- Lu Zhou
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Nanotechnology, KIT, Karlsruhe, Germany
| | - Minoas Evangelinos
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
- Faculty of Biology, University of Athens, Athens, Greece
- Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, Gosselies, Belgium
| | - Valentin Wernet
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
| | - Antonia F. Eckert
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Yuji Ishitsuka
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Nanotechnology, KIT, Karlsruhe, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute of Toxicology and Genetics, KIT, Eggenstein-Leopoldshafen, Germany
| | - Norio Takeshita
- Department of Microbiology, Institute for Applied Biosciences, KIT, Karlsruhe, Germany
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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Zheng J, Gao P, Shao X, Nienhaus GU. Refractive index measurement of suspended cells using opposed-view digital holographic microscopy. Appl Opt 2017; 56:9000-9005. [PMID: 29131185 DOI: 10.1364/ao.56.009000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/13/2017] [Indexed: 06/07/2023]
Abstract
Opposed-view digital holographic microscopy (OV-DHM) with autofocusing and out-of-focus background suppression was demonstrated and applied to measure the refractive index (RI) of suspended HeLa cells. In OV-DHM, a specimen is illuminated from two sides in a 4π-like configuration. The generated two opposite-view object waves, which have orthogonal polarization orientations, interfere with a common reference wave, and the generated holograms are recorded by a CMOS camera. The image plane of the sample was determined by finding the minimal variation between the two object waves. The out-of-focus background was suppressed by averaging the two object waves. Simultaneous determination of both the cell thickness and the phase retardation was avoided by using a spheroidal model for the detached cell obtained from confocal microscopy. Thus, the RI of suspended HeLa cells was measured from phase images of OV-DHM, with the thickness of the cells estimated by using a constant axial-to-lateral ratio. This measurement strategy reveals the RI with an accuracy of ∼10% of the RI difference between cells and surrounding medium.
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Wang H, Lin Y, Nienhaus K, Nienhaus GU. The protein corona on nanoparticles as viewed from a nanoparticle‐sizing perspective. WIREs Nanomed Nanobiotechnol 2017; 10:e1500. [DOI: 10.1002/wnan.1500] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/28/2017] [Accepted: 09/18/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Haixia Wang
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Youhui Lin
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
| | - Karin Nienhaus
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
| | - G. Ulrich Nienhaus
- Institute of Applied PhysicsKarlsruhe Institute of TechnologyKarlsruheGermany
- Institute of NanotechnologyKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Institute of Toxicology and GeneticsKarlsruhe Institute of TechnologyEggenstein‐LeopoldshafenGermany
- Department of PhysicsUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
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Manz C, Kobitski AY, Samanta A, Keller BG, Jäschke A, Nienhaus GU. Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat Chem Biol 2017; 13:1172-1178. [DOI: 10.1038/nchembio.2476] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
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Abstract
The human heme enzyme tryptophan 2,3-dioxygenase (hTDO) catalyzes the insertion of dioxygen into its cognate substrate, l-tryptophan (l-Trp). Its active site structure is highly dynamic, and the mechanism of enzyme-substrate-ligand complex formation and the ensuing enzymatic reaction is not yet understood. Here we have studied complex formation in hTDO by using time-resolved optical and infrared spectroscopy with carbon monoxide (CO) as a ligand. We have observed that both substrate-free and substrate-bound hTDO coexist in two discrete conformations with greatly different ligand binding rates. In the fast rebinding hTDO conformation, there is facile ligand access to the heme iron, but it is greatly hindered in the slowly rebinding conformation. Spectroscopic evidence implicates active site solvation as playing a crucial role for the observed kinetic differences. Substrate binding shifts the conformational equilibrium markedly toward the fast species and thus primes the active site for subsequent ligand binding, ensuring that formation of the ternary complex occurs predominantly by first binding l-Trp and then the ligand. Consequently, the efficiency of catalysis is enhanced because O2 binding prior to substrate binding, resulting in nonproductive oxidation of the heme iron, is greatly suppressed.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Vincent Hahn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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Nienhaus K, Nickel E, Nienhaus GU. Substrate binding in human indoleamine 2,3-dioxygenase 1: A spectroscopic analysis. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2017; 1865:453-463. [DOI: 10.1016/j.bbapap.2017.02.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/22/2017] [Accepted: 02/07/2017] [Indexed: 11/27/2022]
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Abstract
Nanotechnology holds great promise for applications in many fields including biology and medicine. Unfortunately, the processes occurring at the interface between nanomaterials and living systems are exceedingly complex and not yet well understood, which has significantly hampered the realization of many nanobiotechnology applications. Whenever nanoparticles (NPs) are incorporated by a living organism, a protein adsorption layer, also known as the "protein corona", forms on the NP surface. Accordingly, living organisms interact with protein-coated rather than bare NPs, and their biological responses depend on the nature of the protein corona. In recent years, a wide variety of biophysical techniques have been employed to elucidate mechanistic aspects of NP-protein interactions. In most studies, NPs are immersed in protein or biofluid (e.g., blood serum) solutions and then separated from the liquid for analysis. Because this approach may modify the composition and structure of the protein corona, our group has pioneered the use of fluorescence correlation spectroscopy (FCS) as an in situ technique, capable of examining NP-protein interactions while the NPs are suspended in biological fluids. FCS allows us to measure, with subnanometer precision and as a function of protein concentration, the increase in hydrodynamic radius of the NPs due to protein adsorption. This Account aims at reviewing recent progress in the exploration of NP-protein interactions by using FCS. In vitro FCS studies of the adsorption of important serum proteins onto water-solubilized luminescent NPs always showed a stepwise increase of the NP radius upon protein binding in the form of a binding isotherm, regardless of the type of NP and its specific surface functionalization. This observation indicates formation of a protein monolayer on the NP. Structure-based calculations of protein surface potentials revealed that positively charged patches on the proteins interact electrostatically with negatively charged NP surfaces, and the observed protein layer thickness always matched the known molecular dimensions of the proteins binding in certain orientations. Temperature and NP surface functionalization have also been identified as important parameters controlling protein corona formation. Notably, while the corona formed from a single type of serum protein was reversible, protein adsorption from complex biological media such as blood serum was entirely irreversible. These quantitative in vitro studies are of great relevance to the bio-nano community and especially to researchers developing engineered nanomaterials for biological and biomedical applications. Future efforts will be directed toward elucidating kinetic aspects of protein corona formation and the detailed structure of the adsorbed proteins at the molecular level. To better appreciate the biological responses triggered by NP exposure, more efforts will be devoted to the exploration of the biomolecular corona as it forms on NPs in contact with living cells, tissues, and even entire model organisms. These studies are challenging when performed in a well-controlled and quantitative fashion and rely on the availability of sophisticated analytical tools, particularly, quantitative optical imaging techniques including FCS and related fluctuation methods.
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Affiliation(s)
- Li Shang
- Institute
of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
- Center
for Nano Energy Materials, School of Materials Science and Engineering, Northwestern Polytechnical University, Xi’an 710072, China
| | - G. Ulrich Nienhaus
- Institute
of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
- Institute
of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute
of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Gao P, Nienhaus GU. Precise background subtraction in stimulated emission double depletion nanoscopy. Opt Lett 2017; 42:831-834. [PMID: 28198876 DOI: 10.1364/ol.42.000831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
Low-resolution background in stimulated emission depletion (STED) nanoscopy can arise from incomplete depletion or re-excitation by the STED beam. We have recently introduced stimulated emission double depletion (STEDD), a technique to efficiently suppress this background. In STEDD, the conventional, doughnut-shaped STED pulse, which depletes excited fluorophores outside the center of the focal region, is followed by a second Gaussian STED pulse, which specifically depletes the central region. The background is removed by calculating a weighted difference of photon events collected before and after the second STED pulse. Here, we present a simple, yet powerful, method to determine the weight factor, which depends on the fluorescence decay, from a direct analysis of the acquired data. We vary the weight factor to identify its optimal value as the one for which the weight of high-frequency components in the spectrum of the acquired STEDD image is maximized. This strategy is also applicable to other differential approaches for background suppression in imaging.
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Zhou L, Middel V, Strähle U, Nienhaus GU. Single Molecule Imaging Reveals Dysferlin-Mediated Recruitment of Phosphatidylserine in Cell Membrane Repair. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.804] [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] [Indexed: 10/20/2022] Open
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Matela G, Gao P, Guigas G, Eckert AF, Nienhaus K, Nienhaus GU. A far-red emitting fluorescent marker protein, mGarnet2, for microscopy and STED nanoscopy. Chem Commun (Camb) 2017; 53:979-982. [PMID: 28044150 DOI: 10.1039/c6cc09081h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Here we present mGarnet2, a monomeric, far-red fluorescent marker protein derived from mRuby, with absorption and emission bands peaking at 598 and 671 nm, respectively. The protein shows excellent performance as a live-cell fusion marker for STED nanoscopy with 640 nm excitation and 780 nm depletion wavelengths.
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Affiliation(s)
- Gabriela Matela
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Peng Gao
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany and Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Gernot Guigas
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Antonia F Eckert
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - G U Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany and Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Abstract
Proteins of the green fluorescent protein (GFP) family are indispensable for fluorescence imaging experiments in the life sciences, particularly of living specimens. Their essential role as genetically encoded fluorescence markers has motivated many researchers over the last 20 years to further advance and optimize these proteins by using protein engineering. Amino acids can be exchanged by site-specific mutagenesis, starting with naturally occurring proteins as templates. Optical properties of the fluorescent chromophore are strongly tuned by the surrounding protein environment, and a targeted modification of chromophore-protein interactions requires a profound knowledge of the underlying photophysics and photochemistry, which has by now been well established from a large number of structural and spectroscopic experiments and molecular-mechanical and quantum-mechanical computations on many variants of fluorescent proteins. Nevertheless, such rational engineering often does not meet with success and thus is complemented by random mutagenesis and selection based on the optical properties. In this topical review, we present an overview of the key structural and spectroscopic properties of fluorescent proteins. We address protein-chromophore interactions that govern ground state optical properties as well as processes occurring in the electronically excited state. Special emphasis is placed on photoactivation of fluorescent proteins. These light-induced reactions result in large structural changes that drastically alter the fluorescence properties of the protein, which enables some of the most exciting applications, including single particle tracking, pulse chase imaging and super-resolution imaging. We also present a few examples of fluorescent protein application in live-cell imaging experiments.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Straße 1, 76131 Karlsruhe, Germany
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Bergs A, Ishitsuka Y, Evangelinos M, Nienhaus GU, Takeshita N. Dynamics of Actin Cables in Polarized Growth of the Filamentous Fungus Aspergillus nidulans. Front Microbiol 2016; 7:682. [PMID: 27242709 PMCID: PMC4860496 DOI: 10.3389/fmicb.2016.00682] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 02/24/2016] [Accepted: 04/26/2016] [Indexed: 12/20/2022] Open
Abstract
Highly polarized growth of filamentous fungi requires a continuous supply of proteins and lipids to the hyphal tip. This transport is managed by vesicle trafficking via the actin and microtubule cytoskeletons and their associated motor proteins. Particularly, actin cables originating from the hyphal tip are essential for hyphal growth. Although, specific marker proteins have been developed to visualize actin cables in filamentous fungi, the exact organization and dynamics of actin cables has remained elusive. Here, we observed actin cables using tropomyosin (TpmA) and Lifeact fused to fluorescent proteins in living Aspergillus nidulans hyphae and studied the dynamics and regulation. GFP tagged TpmA visualized dynamic actin cables formed from the hyphal tip with cycles of elongation and shrinkage. The elongation and shrinkage rates of actin cables were similar and approximately 0.6 μm/s. Comparison of actin markers revealed that high concentrations of Lifeact reduced actin dynamics. Simultaneous visualization of actin cables and microtubules suggests temporally and spatially coordinated polymerization and depolymerization between the two cytoskeletons. Our results provide new insights into the molecular mechanism of ordered polarized growth regulated by actin cables and microtubules.
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Affiliation(s)
- Anna Bergs
- Department of Microbiology, Institute for Applied Bioscience, Karlsruhe Institute of Technology Karlsruhe, Germany
| | - Yuji Ishitsuka
- Institute of Applied Physics, Karlsruhe Institute of Technology Karlsruhe, Germany
| | - Minoas Evangelinos
- Department of Microbiology, Institute for Applied Bioscience, Karlsruhe Institute of TechnologyKarlsruhe, Germany; Faculty of Biology, University of AthensAthens, Greece
| | - G U Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of TechnologyKarlsruhe, Germany; Institute of Toxicology and Genetics, Karlsruhe Institute of TechnologyEggenstein-Leopoldshafen, Germany; Institute of Nanotechnology, Karlsruhe Institute of TechnologyEggenstein-Leopoldshafen, Germany; Department of Physics, University of Illinois at Urbana-ChampaignUrbana-Champaign, IL, USA
| | - Norio Takeshita
- Department of Microbiology, Institute for Applied Bioscience, Karlsruhe Institute of TechnologyKarlsruhe, Germany; Faculty of Life and Environmental Sciences, University of TsukubaTsukuba, Japan
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40
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Li Y, Shang L, Nienhaus GU. Super-resolution imaging-based single particle tracking reveals dynamics of nanoparticle internalization by live cells. Nanoscale 2016; 8:7423-9. [PMID: 27001905 DOI: 10.1039/c6nr01495j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
By combining super-resolution photoactivation localization microscopy with single particle tracking, we have visualized the endocytic process in the live-cell environment with nanoparticles (NPs) of different size and surface functionalization. This allowed us to analyze the dynamics of NPs interacting with cells with high spatial and temporal resolution. We identified two distinctly different types of pathways by which NPs are internalized via clathrin-coated pits (CCPs). Predominantly, NPs first bind to the membrane and, subsequently, CCPs form at this site. However, there are also instances where a NP diffuses on the membrane and utilizes a preformed CCP. Moreover, we have applied this new method to further explore the effects of size and surface functionalization on the NP dynamics on the plasma membrane and the ensuing endocytosis.
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Affiliation(s)
- Yiming Li
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany. and Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Li Shang
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany. and Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany. and Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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41
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Gao P, Nienhaus GU. Confocal laser scanning microscopy with spatiotemporal structured illumination. Opt Lett 2016; 41:1193-1196. [PMID: 26977667 DOI: 10.1364/ol.41.001193] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
Confocal laser scanning microscopy (CLSM), which is widely utilized in the biological and biomedical sciences, is limited in spatial resolution due to diffraction to about half the light wavelength. Here we have combined structured illumination with CLSM to enhance its spatial resolution. To this end, we have used a spatial light modulator (SLM) to generate fringe patterns of different orientations and phase shifts in the excitation spot without any mechanical movement. We have achieved 1.8 and 1.7 times enhanced lateral and axial resolutions, respectively, by synthesizing the object spectrum along different illumination directions. This technique is thus a promising tool for high-resolution morphological or fluorescence imaging, especially in deep tissue.
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42
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Zhou L, Middel V, Nienhaus GU, Uwe Strähle U. Super-Resolution Imaging of Plasma Membrane Lesions Inflicted by 405-nm Laser Light. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2609] [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] [Indexed: 10/22/2022] Open
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43
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Hense A, Prunsche B, Gao P, Ishitsuka Y, Nienhaus K, Nienhaus GU. mGarnet, A Far-Red Fluorescent Protein for Live-Cell Sted Imaging. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2608] [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] [Indexed: 11/30/2022] Open
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44
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Nienhaus K, Nienhaus GU. Where Do We Stand with Super-Resolution Optical Microscopy? J Mol Biol 2016; 428:308-322. [DOI: 10.1016/j.jmb.2015.12.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
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Hense A, Prunsche B, Gao P, Ishitsuka Y, Nienhaus K, Ulrich Nienhaus G. Monomeric Garnet, a far-red fluorescent protein for live-cell STED imaging. Sci Rep 2015; 5:18006. [PMID: 26648024 PMCID: PMC4673609 DOI: 10.1038/srep18006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/10/2015] [Indexed: 01/25/2023] Open
Abstract
The advancement of far-red emitting variants of the green fluorescent protein (GFP) is crucially important for imaging live cells, tissues and organisms. Despite notable efforts, far-red marker proteins still need further optimization to match the performance of their green counterparts. Here we present mGarnet, a robust monomeric marker protein with far-red fluorescence peaking at 670 nm. Thanks to its large extinction coefficient of 95,000 M(-1)cm(-1), mGarnet can be efficiently excited with 640-nm light on the red edge of its 598-nm excitation band. A large Stokes shift allows essentially the entire fluorescence emission to be collected even with 640-nm excitation, counterbalancing the lower fluorescence quantum yield of mGarnet, 9.1%, that is typical of far-red FPs. We demonstrate an excellent performance as a live-cell fusion marker in STED microscopy, using 640 nm excitation and 780 nm depletion wavelengths.
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Affiliation(s)
- Anika Hense
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Benedikt Prunsche
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Peng Gao
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Yuji Ishitsuka
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana IL 61801, USA
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46
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Ishitsuka Y, Savage N, Li Y, Bergs A, Grün N, Kohler D, Donnelly R, Nienhaus GU, Fischer R, Takeshita N. Superresolution microscopy reveals a dynamic picture of cell polarity maintenance during directional growth. Sci Adv 2015; 1:e1500947. [PMID: 26665168 PMCID: PMC4673053 DOI: 10.1126/sciadv.1500947] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/14/2015] [Indexed: 05/02/2023]
Abstract
Polar (directional) cell growth, a key cellular mechanism shared among a wide range of species, relies on targeted insertion of new material at specific locations of the plasma membrane. How these cell polarity sites are stably maintained during massive membrane insertion has remained elusive. Conventional live-cell optical microscopy fails to visualize polarity site formation in the crowded cell membrane environment because of its limited resolution. We have used advanced live-cell imaging techniques to directly observe the localization, assembly, and disassembly processes of cell polarity sites with high spatiotemporal resolution in a rapidly growing filamentous fungus, Aspergillus nidulans. We show that the membrane-associated polarity site marker TeaR is transported on microtubules along with secretory vesicles and forms a protein cluster at that point of the apical membrane where the plus end of the microtubule touches. There, a small patch of membrane is added through exocytosis, and the TeaR cluster gets quickly dispersed over the membrane. There is an incessant disassembly and reassembly of polarity sites at the growth zone, and each new polarity site locus is slightly offset from preceding ones. On the basis of our imaging results and computational modeling, we propose a transient polarity model that explains how cell polarity is stably maintained during highly active directional growth.
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Affiliation(s)
- Yuji Ishitsuka
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Natasha Savage
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Yiming Li
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Anna Bergs
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
| | - Nathalie Grün
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
| | - Daria Kohler
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Rebecca Donnelly
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
- Institute of Nanotechnology, KIT, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Toxicology and Genetics, KIT, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
| | - Reinhard Fischer
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
| | - Norio Takeshita
- Department of Microbiology, Institute for Applied Biosciences, KIT, 76187 Karlsruhe, Germany
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Corresponding author. E-mail: (G.U.N.); (R.F.); (N.T.)
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Manck R, Ishitsuka Y, Herrero S, Takeshita N, Nienhaus GU, Fischer R. Genetic evidence for a microtubule-capture mechanism during polarised growth of Aspergillus nidulans. Development 2015. [DOI: 10.1242/dev.131144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Manck R, Ishitsuka Y, Herrero S, Takeshita N, Nienhaus GU, Fischer R. Genetic evidence for a microtubule-capture mechanism during polarised growth of Aspergillus nidulans. J Cell Sci 2015; 128:3569-82. [PMID: 26272919 DOI: 10.1242/jcs.169094] [Citation(s) in RCA: 18] [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: 01/26/2015] [Accepted: 08/10/2015] [Indexed: 12/13/2022] Open
Abstract
The cellular switch from symmetry to polarity in eukaryotes depends on the microtubule (MT) and actin cytoskeletons. In fungi such as Schizosaccharomyces pombe or Aspergillus nidulans, the MT cytoskeleton determines the sites of actin polymerization through cortical cell-end marker proteins. Here we describe A. nidulans MT guidance protein A (MigA) as the first ortholog of the karyogamy protein Kar9 from Saccharomyces cerevisiae in filamentous fungi. A. nidulans MigA interacts with the cortical ApsA protein and is involved in spindle positioning during mitosis. MigA is also associated with septal and nuclear MT organizing centers (MTOCs). Super-resolution photoactivated localization microscopy (PALM) analyses revealed that MigA is recruited to assembling and retracting MT plus ends in an EbA-dependent manner. MigA is required for MT convergence in hyphal tips and plays a role in correct localization of the cell-end markers TeaA and TeaR. In addition, MigA interacts with a class-V myosin, suggesting that an active mechanism exists to capture MTs and to pull the ends along actin filaments. Hence, the organization of MTs and actin depend on each other, and positive feedback loops ensure robust polar growth.
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Affiliation(s)
- Raphael Manck
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany
| | - Yuji Ishitsuka
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Physics and Center for Functional Nanostructures, Karlsruhe 76131, Germany
| | - Saturnino Herrero
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany
| | - Norio Takeshita
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany University of Tsukuba, Faculty of Life and Environmental Sciences, Tsukuba, Ibaraki 305-8572, Japan
| | - G Ulrich Nienhaus
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Physics and Center for Functional Nanostructures, Karlsruhe 76131, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Hertzstrasse 16, Karlsruhe D-76187, Germany
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Pelaz B, del Pino P, Maffre P, Hartmann R, Gallego M, Rivera-Fernández S, de la Fuente JM, Nienhaus GU, Parak WJ. Surface Functionalization of Nanoparticles with Polyethylene Glycol: Effects on Protein Adsorption and Cellular Uptake. ACS Nano 2015; 9:6996-7008. [PMID: 26079146 DOI: 10.1021/acsnano.5b01326] [Citation(s) in RCA: 563] [Impact Index Per Article: 62.6] [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: 05/17/2023]
Abstract
Here we have investigated the effect of enshrouding polymer-coated nanoparticles (NPs) with polyethylene glycol (PEG) on the adsorption of proteins and uptake by cultured cells. PEG was covalently linked to the polymer surface to the maximal grafting density achievable under our experimental conditions. Changes in the effective hydrodynamic radius of the NPs upon adsorption of human serum albumin (HSA) and fibrinogen (FIB) were measured in situ using fluorescence correlation spectroscopy. For NPs without a PEG shell, a thickness increase of around 3 nm, corresponding to HSA monolayer adsorption, was measured at high HSA concentration. Only 50% of this value was found for NPs with PEGylated surfaces. While the size increase clearly reveals formation of a protein corona also for PEGylated NPs, fluorescence lifetime measurements and quenching experiments suggest that the adsorbed HSA molecules are buried within the PEG shell. For FIB adsorption onto PEGylated NPs, even less change in NP diameter was observed. In vitro uptake of the NPs by 3T3 fibroblasts was reduced to around 10% upon PEGylation with PEG chains of 10 kDa. Thus, even though the PEG coatings did not completely prevent protein adsorption, the PEGylated NPs still displayed a pronounced reduction of cellular uptake with respect to bare NPs, which is to be expected if the adsorbed proteins are not exposed on the NP surface.
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Affiliation(s)
- Beatriz Pelaz
- †Fachbereich Physik, Philipps Universität Marburg, 35037 Marburg, Germany
| | | | - Pauline Maffre
- §Institute of Applied Physics and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Raimo Hartmann
- †Fachbereich Physik, Philipps Universität Marburg, 35037 Marburg, Germany
| | | | | | - Jesus M de la Fuente
- ⊥Instituto de Ciencia de Materiales de Aragon, CSIC/University of Zaragoza, 50018 Zaragoza, Spain
| | - G Ulrich Nienhaus
- §Institute of Applied Physics and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- #Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Wolfgang J Parak
- †Fachbereich Physik, Philipps Universität Marburg, 35037 Marburg, Germany
- ‡CIC biomaGUNE, 20009 San Sebastian, Spain
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Klapper Y, Maffre P, Shang L, Ekdahl KN, Nilsson B, Hettler S, Dries M, Gerthsen D, Nienhaus GU. Low affinity binding of plasma proteins to lipid-coated quantum dots as observed by in situ fluorescence correlation spectroscopy. Nanoscale 2015; 7:9980-9984. [PMID: 25975280 DOI: 10.1039/c5nr01694k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein binding to lipid-coated nanoparticles has been pursued quantitatively by using fluorescence correlation spectroscopy. The binding of three important plasma proteins to lipid-enwrapped quantum dots (QDs) shows very low affinity, with an apparent dissociation coefficient in the range of several hundred micromolar. Thus, the tendency to adsorb is orders of magnitude weaker than for QDs coated with dihydrolipoic acid.
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Affiliation(s)
- Yvonne Klapper
- Institute of Applied Physics and Center for Functional Nanostructures, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.
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