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Mayer I, Karimian T, Gordiyenko K, Angelin A, Kumar R, Hirtz M, Mikut R, Reischl M, Stegmaier J, Zhou L, Ma R, Nienhaus GU, Rabe KS, Lanzerstorfer P, Domínguez CM, Niemeyer CM. Surface-Patterned DNA Origami Rulers Reveal Nanoscale Distance Dependency of the Epidermal Growth Factor Receptor Activation. NANO LETTERS 2024; 24:1611-1619. [PMID: 38267020 PMCID: PMC10853960 DOI: 10.1021/acs.nanolett.3c04272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The nanoscale arrangement of ligands can have a major effect on the activation of membrane receptor proteins and thus cellular communication mechanisms. Here we report on the technological development and use of tailored DNA origami-based molecular rulers to fabricate "Multiscale Origami Structures As Interface for Cells" (MOSAIC), to enable the systematic investigation of the effect of the nanoscale spacing of epidermal growth factor (EGF) ligands on the activation of the EGF receptor (EGFR). MOSAIC-based analyses revealed that EGF distances of about 30-40 nm led to the highest response in EGFR activation of adherent MCF7 and Hela cells. Our study emphasizes the significance of DNA-based platforms for the detailed investigation of the molecular mechanisms of cellular signaling cascades.
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Affiliation(s)
- Ivy Mayer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Tina Karimian
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Klavdiya Gordiyenko
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Alessandro Angelin
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ravi Kumar
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Michael Hirtz
- Institute
of Nanotechnology (INT) & Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Ralf Mikut
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Markus Reischl
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Johannes Stegmaier
- Institute
for Automation and Applied Informatics (IAI), Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
- Institute
of Imaging and Computer Vision, RWTH Aachen
University, 52074 Aachen, Germany
| | - Lu Zhou
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Rui Ma
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute
of Applied Physics (APH), Karlsruhe Institute
of Technology (KIT), 76049 Karlsruhe, Germany
- Institute
of Biological and Chemical Systems (IBCS) and Institute of Nanotechnology
(INT), Karlsruhe Institute of Technology
(KIT), 76021 Karlsruhe, Germany
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Kersten S. Rabe
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Peter Lanzerstorfer
- School
of Engineering, University of Applied Sciences
Upper Austria, 4600 Wels, Austria
| | - Carmen M. Domínguez
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Christof M. Niemeyer
- Institute
for Biological Interfaces (IBG-1), Karlsruhe
Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
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2
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Wollman AJM, Syeda AH, Howard JAL, Payne-Dwyer A, Leech A, Warecka D, Guy C, McGlynn P, Hawkins M, Leake MC. Tetrameric UvrD Helicase Is Located at the E. Coli Replisome due to Frequent Replication Blocks. J Mol Biol 2024; 436:168369. [PMID: 37977299 DOI: 10.1016/j.jmb.2023.168369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/19/2023]
Abstract
DNA replication in all organisms must overcome nucleoprotein blocks to complete genome duplication. Accessory replicative helicases in Escherichia coli, Rep and UvrD, help remove these blocks and aid the re-initiation of replication. Mechanistic details of Rep function have emerged from recent live cell studies; however, the division of UvrD functions between its activities in DNA repair and role as an accessory helicase remain unclear in live cells. By integrating super-resolved single-molecule fluorescence microscopy with biochemical analysis, we find that UvrD self-associates into tetrameric assemblies and, unlike Rep, is not recruited to a specific replisome protein despite being found at approximately 80% of replication forks. Instead, its colocation with forks is likely due to the very high frequency of replication blocks composed of DNA-bound proteins, including RNA polymerase and factors involved in repairing DNA damage. Deleting rep and DNA repair factor genes mutS and uvrA, and inhibiting transcription through RNA polymerase mutation and antibiotic inhibition, indicates that the level of UvrD at the fork is dependent on UvrD's function. Our findings show that UvrD is recruited to sites of nucleoprotein blocks via different mechanisms to Rep and plays a multi-faceted role in ensuring successful DNA replication.
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Affiliation(s)
- Adam J M Wollman
- School of Physics, Engineering and Technology, University of York, York YO10 5DD, United Kingdom; Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Aisha H Syeda
- School of Physics, Engineering and Technology, University of York, York YO10 5DD, United Kingdom; Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Jamieson A L Howard
- School of Physics, Engineering and Technology, University of York, York YO10 5DD, United Kingdom; Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Alex Payne-Dwyer
- School of Physics, Engineering and Technology, University of York, York YO10 5DD, United Kingdom; Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Andrew Leech
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Dominika Warecka
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Colin Guy
- Covance Laboratories Ltd., Otley Road, Harrogate HG3 1PY, United Kingdom
| | - Peter McGlynn
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Michelle Hawkins
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Mark C Leake
- School of Physics, Engineering and Technology, University of York, York YO10 5DD, United Kingdom; Department of Biology, University of York, York YO10 5DD, United Kingdom.
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3
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Adler L, Lau CS, Shaikh KM, van Maldegem KA, Payne-Dwyer AL, Lefoulon C, Girr P, Atkinson N, Barrett J, Emrich-Mills TZ, Dukic E, Blatt MR, Leake MC, Peltier G, Spetea C, Burlacot A, McCormick AJ, Mackinder LCM, Walker CE. The role of BST4 in the pyrenoid of Chlamydomonas reinhardtii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.15.545204. [PMID: 38014171 PMCID: PMC10680556 DOI: 10.1101/2023.06.15.545204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
In many eukaryotic algae, CO2 fixation by Rubisco is enhanced by a CO2-concentrating mechanism, which utilizes a Rubisco-rich organelle called the pyrenoid. The pyrenoid is traversed by a network of thylakoid-membranes called pyrenoid tubules, proposed to deliver CO2. In the model alga Chlamydomonas reinhardtii (Chlamydomonas), the pyrenoid tubules have been proposed to be tethered to the Rubisco matrix by a bestrophin-like transmembrane protein, BST4. Here, we show that BST4 forms a complex that localizes to the pyrenoid tubules. A Chlamydomonas mutant impaired in the accumulation of BST4 (bst4) formed normal pyrenoid tubules and heterologous expression of BST4 in Arabidopsis thaliana did not lead to the incorporation of thylakoids into a reconstituted Rubisco condensate. Chlamydomonas bst4 mutant did not show impaired growth at air level CO2. By quantifying the non-photochemical quenching (NPQ) of chlorophyll fluorescence, we show that bst4 displays a transiently lower thylakoid lumenal pH during dark to light transition compared to control strains. When acclimated to high light, bst4 had sustained higher NPQ and elevated levels of light-induced H2O2 production. We conclude that BST4 is not a tethering protein, but rather is an ion channel involved in lumenal pH regulation possibly by mediating bicarbonate transport across the pyrenoid tubules.
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Affiliation(s)
- Liat Adler
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, University of Edinburgh, EH9 3BF, United Kingdom
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, 94305 USA
| | - Chun Sing Lau
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Kashif M Shaikh
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg 40530, Sweden
| | - Kim A van Maldegem
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg 40530, Sweden
| | - Alex L Payne-Dwyer
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
- School of Physics, Engineering and Technology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Cecile Lefoulon
- Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, United Kingdom
| | - Philipp Girr
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Nicky Atkinson
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, University of Edinburgh, EH9 3BF, United Kingdom
| | - James Barrett
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Tom Z Emrich-Mills
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Emilija Dukic
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg 40530, Sweden
| | - Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, United Kingdom
| | - Mark C Leake
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
- School of Physics, Engineering and Technology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Gilles Peltier
- Aix-Marseille Université, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108 Saint-Paul-lez-Durance, France
| | - Cornelia Spetea
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg 40530, Sweden
| | - Adrien Burlacot
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, 94305 USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, University of Edinburgh, EH9 3BF, United Kingdom
| | - Luke C M Mackinder
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Charlotte E Walker
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, Heslington, York YO10 5DD, United Kingdom
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4
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Refinement of Singer-Nicolson fluid-mosaic model by microscopy imaging: Lipid rafts and actin-induced membrane compartmentalization. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184093. [PMID: 36423676 DOI: 10.1016/j.bbamem.2022.184093] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
This year celebrates the 50th anniversary of the Singer-Nicolson fluid mosaic model for biological membranes. The next level of sophistication we have achieved for understanding plasma membrane (PM) structures, dynamics, and functions during these 50 years includes the PM interactions with cortical actin filaments and the partial demixing of membrane constituent molecules in the PM, particularly raft domains. Here, first, we summarize our current knowledge of these two structures and emphasize that they are interrelated. Second, we review the structure, molecular dynamics, and function of raft domains, with main focuses on raftophilic glycosylphosphatidylinositol-anchored proteins (GPI-APs) and their signal transduction mechanisms. We pay special attention to the results obtained by single-molecule imaging techniques and other advanced microscopy methods. We also clarify the limitations of present optical microscopy methods for visualizing raft domains, but emphasize that single-molecule imaging techniques can "detect" raft domains associated with molecules of interest in the PM.
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5
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Single-molecule and super-resolved imaging deciphers membrane behavior of onco-immunogenic CCR5. iScience 2022; 25:105675. [PMID: 36561885 PMCID: PMC9763858 DOI: 10.1016/j.isci.2022.105675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/20/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
The ability of tumors to establish a pro-tumorigenic microenvironment is an important point of investigation in the search for new therapeutics. Tumors form microenvironments in part by the "education" of immune cells attracted via chemotactic axes such as that of CCR5-CCL5. Further, CCR5 upregulation by cancer cells, coupled with its association with pro-tumorigenic features such as drug resistance and metastasis, has suggested CCR5 as a therapeutic target. However, with several conformational "pools" being reported, phenotypic investigations must be capable of unveiling conformational heterogeneity. Addressing this challenge, we performed super-resolution structured illumination microscopy (SIM) and single molecule partially TIRF-coupled HILO (PaTCH) microscopy of CCR5 in fixed cells. SIM data revealed a non-random spatial distribution of CCR5 assemblies, while Intensity-tracking of CCR5 assemblies from PaTCH images indicated dimeric sub-units independent of CCL5 perturbation. These biophysical methods can provide important insights into the structure and function of onco-immunogenic receptors and many other biomolecules.
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6
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Abstract
The epidermal growth factor (EGF) system has allowed chemists, biologists, and clinicians to improve our understanding of cell production and cancer therapy. The discovery of EGF led to the recognition of cell surface receptors capable of controlling the proliferation and survival of cells. The detailed structures of the EGF-like ligand and the responses of their receptors (EGFR-family) has revealed the conformational and aggregation changes whereby ligands activate the intracellular kinase domains. Biophysical analysis has revealed the preformed clustering of different EGFR-family members and the processes which occur on ligand binding. Understanding these receptor activation processes and the consequential cytoplasmic signaling has allowed the development of inhibitors which are revolutionizing cancer therapy. This Review describes the recent progress in our understanding of the activation of the EGFR-family, the effects of signaling from the EGFR-family on cell proliferation, and the targeting of the EGFR-family in cancer treatment.
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Affiliation(s)
- Antony W Burgess
- Honorary Laboratory Head, Personalized Oncology Division, WEHI, Parkville3050, Australia.,Professor Emeritus, Departments of Medical Biology and Surgery (Royal Melbourne Hospital), University of Melbourne, Melbourne3052, Australia.,The Brain Cancer Centre at WEHI, Parkville3052, Australia
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7
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Payne-Dwyer AL, Syeda AH, Shepherd JW, Frame L, Leake MC. RecA and RecB: probing complexes of DNA repair proteins with mitomycin C in live Escherichia coli with single-molecule sensitivity. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220437. [PMID: 35946163 PMCID: PMC9363994 DOI: 10.1098/rsif.2022.0437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The RecA protein and RecBCD complex are key bacterial components for the maintenance and repair of DNA. RecBCD is a helicase-nuclease that uses homologous recombination to resolve double-stranded DNA breaks. It also facilitates coating of single-stranded DNA with RecA to form RecA filaments, a vital step in the double-stranded break DNA repair pathway. However, questions remain about the mechanistic roles of RecA and RecBCD in live cells. Here, we use millisecond super-resolved fluorescence microscopy to pinpoint the spatial localization of fluorescent reporters of RecA or RecB at physiological levels of expression in individual live Escherichia coli cells. By introducing the DNA cross-linker mitomycin C, we induce DNA damage and quantify the resulting steady state changes in stoichiometry, cellular protein copy number and molecular mobilities of RecA and RecB. We find that both proteins accumulate in molecular hotspots to effect repair, resulting in RecA stoichiometries equivalent to several hundred molecules that assemble largely in dimeric subunits before DNA damage, but form periodic subunits of approximately 3-4 molecules within mature filaments of several thousand molecules. Unexpectedly, we find that the physiologically predominant forms of RecB are not only rapidly diffusing monomers, but slowly diffusing dimers.
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Affiliation(s)
- Alex L Payne-Dwyer
- Department of Physics, University of York, York YO10 5DD, UK.,Department of Biology, University of York, York YO10 5DD, UK
| | - Aisha H Syeda
- Department of Physics, University of York, York YO10 5DD, UK.,Department of Biology, University of York, York YO10 5DD, UK
| | - Jack W Shepherd
- Department of Physics, University of York, York YO10 5DD, UK.,Department of Biology, University of York, York YO10 5DD, UK
| | - Lewis Frame
- School of Natural Sciences, University of York, York YO10 5DD, UK
| | - Mark C Leake
- Department of Physics, University of York, York YO10 5DD, UK.,Department of Biology, University of York, York YO10 5DD, UK
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8
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Wollman AJM, Fournier C, Llorente-Garcia I, Harriman O, Payne-Dwyer AL, Shashkova S, Zhou P, Liu TC, Ouaret D, Wilding J, Kusumi A, Bodmer W, Leake MC. Critical roles for EGFR and EGFR-HER2 clusters in EGF binding of SW620 human carcinoma cells. J R Soc Interface 2022; 19:20220088. [PMID: 35612280 PMCID: PMC9131850 DOI: 10.1098/rsif.2022.0088] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Epidermal growth factor (EGF) signalling regulates normal epithelial and other cell growth, with EGF receptor (EGFR) overexpression reported in many cancers. However, the role of EGFR clusters in cancer and their dependence on EGF binding is unclear. We present novel single-molecule total internal reflection fluorescence microscopy of (i) EGF and EGFR in living cancer cells, (ii) the action of anti-cancer drugs that separately target EGFR and human EGFR2 (HER2) on these cells and (iii) EGFR–HER2 interactions. We selected human epithelial SW620 carcinoma cells for their low level of native EGFR expression, for stable transfection with fluorescent protein labelled EGFR, and imaged these using single-molecule localization microscopy to quantify receptor architectures and dynamics upon EGF binding. Prior to EGF binding, we observe pre-formed EGFR clusters. Unexpectedly, clusters likely contain both EGFR and HER2, consistent with co-diffusion of EGFR and HER2 observed in a different model CHO-K1 cell line, whose stoichiometry increases following EGF binding. We observe a mean EGFR : EGF stoichiometry of approximately 4 : 1 for plasma membrane-colocalized EGFR–EGF that we can explain using novel time-dependent kinetics modelling, indicating preferential ligand binding to monomers. Our results may inform future cancer drug developments.
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Affiliation(s)
- Adam J M Wollman
- Department of Physics, University of York, York, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Charlotte Fournier
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK.,Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919 Tancha, Onna-son, Okinawa 904-0495, Japan
| | | | - Oliver Harriman
- Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, UK
| | | | | | - Peng Zhou
- Membrane Cooperativity Unit, OIST, 1919 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Ta-Chun Liu
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Djamila Ouaret
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Jenny Wilding
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Akihiro Kusumi
- Membrane Cooperativity Unit, OIST, 1919 Tancha, Onna-son, Okinawa 904-0495, Japan
| | - Walter Bodmer
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mark C Leake
- Department of Physics, University of York, York, UK.,Department of Biology, University of York, York, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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