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Maillard J, Grassin E, Bestsennaia E, Silaghi M, Straková K, García-Calvo J, Sakai N, Matile S, Fürstenberg A. Single-Molecule Localization Microscopy and Tracking with a Fluorescent Mechanosensitive Probe. J Phys Chem B 2024; 128:7997-8006. [PMID: 39119910 DOI: 10.1021/acs.jpcb.4c02506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
A milestone in optical imaging of mechanical forces in cells has been the development of the family of flipper fluorescent probes able to report membrane tension noninvasively in living cells through their fluorescence lifetime. The specifically designed Flipper-CF3 probe with an engineered inherent blinking mechanism was recently introduced for super-resolution fluorescence microscopy of lipid ordered membranes but was too dim to be detected in lipid disordered membranes at the single-molecule level (García-Calvo, J. J. Am. Chem. Soc. 2020, 142(28), 12034-12038). We show here that the original and commercially available probe Flipper-TR is compatible with single-molecule based super-resolution imaging and resolves both liquid ordered and liquid disordered membranes of giant unilamellar vesicles below the diffraction limit. Single probe molecules were additionally tracked in lipid bilayers, enabling to distinguish membranes of varying composition from the diffusion coefficient of the probe. Differences in brightness between Flipper-CF3 and Flipper-TR originate in their steady-state absorption and fluorescence properties. The general compatibility of the Flipper-TR scaffold with single-molecule detection is further shown in super-resolution experiments with targetable Flipper-TR derivatives.
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Affiliation(s)
- Jimmy Maillard
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Ewa Grassin
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Ekaterina Bestsennaia
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Melinda Silaghi
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Karolina Straková
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - José García-Calvo
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Alexandre Fürstenberg
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
- Department of Inorganic and Analytical Chemistry, University of Geneva, 1211 Geneva, Switzerland
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2
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Lee S, Chung M. DNA-Tethered Lipid Membrane Formation via Solvent-Assisted Self-Assembly. J Phys Chem B 2023; 127:1350-1356. [PMID: 36733188 DOI: 10.1021/acs.jpcb.2c07978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
DNA-tethered lipid bilayers have been used in many studies, based on the controllable and well-defined properties of DNA tethers. However, their application has been limited, because it is difficult to cover a wide range of surfaces and achieve electrical insulation. We implemented an existing method, where a DNA hybrid chip on a silica or glass surface supports a lipid membrane using solvent-assisted self-assembly. The formation of a continuous lipid bilayer was confirmed through the change in quartz crystal microbalance dissipation results, depending on the presence or absence of DNA hybrids. The fluidity of the DNA-tethered lipid membranes was analyzed using a fluorescence microscope. The electrochemical analysis demonstrated the versatility of this new technique, which can be used for sensor or electrode surface modification for biosensors or bioelectronics.
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Affiliation(s)
- Sangmin Lee
- Department of Chemical Engineering, Hongik University, Mapo-gu, Seoul 04066, Republic of Korea
| | - Minsub Chung
- Department of Chemical Engineering, Hongik University, Mapo-gu, Seoul 04066, Republic of Korea
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3
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Toyota T, Zhang Y. Identifying and Manipulating Giant Vesicles: Review of Recent Approaches. MICROMACHINES 2022; 13:644. [PMID: 35630111 PMCID: PMC9144095 DOI: 10.3390/mi13050644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 12/20/2022]
Abstract
Giant vesicles (GVs) are closed bilayer membranes that primarily comprise amphiphiles with diameters of more than 1 μm. Compared with regular vesicles (several tens of nanometers in size), GVs are of greater scientific interest as model cell membranes and protocells because of their structure and size, which are similar to those of biological systems. Biopolymers and nano-/microparticles can be encapsulated in GVs at high concentrations, and their application as artificial cell bodies has piqued interest. It is essential to develop methods for investigating and manipulating the properties of GVs toward engineering applications. In this review, we discuss current improvements in microscopy, micromanipulation, and microfabrication technologies for progress in GV identification and engineering tools. Combined with the advancement of GV preparation technologies, these technological advancements can aid the development of artificial cell systems such as alternative tissues and GV-based chemical signal processing systems.
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Affiliation(s)
- Taro Toyota
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan;
- Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yiting Zhang
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan;
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4
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Puza S, Caesar S, Poojari C, Jung M, Seemann R, Hub JS, Schrul B, Fleury JB. Lipid Droplets Embedded in a Model Cell Membrane Create a Phospholipid Diffusion Barrier. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106524. [PMID: 35072348 DOI: 10.1002/smll.202106524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Lipid droplets (LDs) are ubiquitous, cytoplasmic fat storage organelles that originate from the endoplasmic reticulum (ER) membrane. They are composed of a core of neutral lipids surrounded by a phospholipid monolayer. Proteins embedded into this monolayer membrane adopt a monotopic topology and are crucial for regulated lipid storage and consumption. A key question is, which collective properties of protein-intrinsic and lipid-mediated features determine spatio-temporal protein partitioning between phospholipid bilayer and LD monolayer membranes. To address this question, a freestanding phospholipid bilayer with physiological lipidic composition is produced using microfluidics and micrometer-sized LDs are dispersed around the bilayer that spontaneously insert into the bilayer. Using confocal microscopy, the 3D geometry of the reconstituted LDs is determined with high spatial resolution. The micrometer-sized bilayer-embedded LDs present a characteristic lens shape that obeys predictions from equilibrium wetting theory. Fluorescence recovery after photobleaching measurements reveals the existence of a phospholipid diffusion barrier at the monolayer-bilayer interface. Coarse-grained molecular dynamics simulation reveals lipid specific density distributions along the pore rim, which may rationalize the diffusion barrier. The lipid diffusion barrier between the LD covering monolayer and the bilayer may be a key phenomenon influencing protein partitioning between the ER membrane and LDs in living cells.
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Affiliation(s)
- Sevde Puza
- Saarland University, Experimental Physics and Center for Biophysics (ZBP), Saarland University, 66123, Saarbrücken, Germany
| | - Stefanie Caesar
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Faculty of Medicine, Saarland University, 66421, Homburg, Germany
| | - Chetan Poojari
- Saarland University, Theoretical Physics and Center for Biophysics (ZBP), Saarland University, 66123, Saarbrücken, Germany
| | - Michael Jung
- Saarland University, Experimental Physics and Center for Biophysics (ZBP), Saarland University, 66123, Saarbrücken, Germany
| | - Ralf Seemann
- Saarland University, Experimental Physics and Center for Biophysics (ZBP), Saarland University, 66123, Saarbrücken, Germany
| | - Jochen S Hub
- Saarland University, Theoretical Physics and Center for Biophysics (ZBP), Saarland University, 66123, Saarbrücken, Germany
| | - Bianca Schrul
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling (PZMS), Faculty of Medicine, Saarland University, 66421, Homburg, Germany
| | - Jean-Baptiste Fleury
- Saarland University, Experimental Physics and Center for Biophysics (ZBP), Saarland University, 66123, Saarbrücken, Germany
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5
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Laskowski PR, Pluhackova K, Haase M, Lang BM, Nagler G, Kuhn A, Müller DJ. Monitoring the binding and insertion of a single transmembrane protein by an insertase. Nat Commun 2021; 12:7082. [PMID: 34873152 PMCID: PMC8648943 DOI: 10.1038/s41467-021-27315-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 11/11/2021] [Indexed: 11/27/2022] Open
Abstract
Cells employ highly conserved families of insertases and translocases to insert and fold proteins into membranes. How insertases insert and fold membrane proteins is not fully known. To investigate how the bacterial insertase YidC facilitates this process, we here combine single-molecule force spectroscopy and fluorescence spectroscopy approaches, and molecular dynamics simulations. We observe that within 2 ms, the cytoplasmic α-helical hairpin of YidC binds the polypeptide of the membrane protein Pf3 at high conformational variability and kinetic stability. Within 52 ms, YidC strengthens its binding to the substrate and uses the cytoplasmic α-helical hairpin domain and hydrophilic groove to transfer Pf3 to the membrane-inserted, folded state. In this inserted state, Pf3 exposes low conformational variability such as typical for transmembrane α-helical proteins. The presence of YidC homologues in all domains of life gives our mechanistic insight into insertase-mediated membrane protein binding and insertion general relevance for membrane protein biogenesis.
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Affiliation(s)
- Pawel R Laskowski
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Kristyna Pluhackova
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Maximilian Haase
- Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599, Stuttgart, Germany
| | - Brian M Lang
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Gisela Nagler
- Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599, Stuttgart, Germany
| | - Andreas Kuhn
- Molecular Microbiology, Biology Institute, Universität Hohenheim, 70599, Stuttgart, Germany
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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Aden S, Snoj T, Anderluh G. The use of giant unilamellar vesicles to study functional properties of pore-forming toxins. Methods Enzymol 2021; 649:219-251. [PMID: 33712188 DOI: 10.1016/bs.mie.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pore-forming toxins (PFTs) act upon lipid membranes and appropriate model systems are of great importance in researching these proteins. Giant unilamellar vesicles (GUVs) are an excellent model membrane system to study interactions between lipids and proteins. Their main advantage is the size comparable to cells, which means that GUVs can be observed directly under the light microscope. Many PFTs properties can be studied by using GUVs, such as binding specificity, membrane reorganization upon protein binding and oligomerization, pore properties and mechanism of pore formation. GUVs also represent a good model for biotechnological approaches, e.g., in applications in synthetic biology and medicine. Each research area has its own demands for GUVs properties, so several different approaches for GUVs preparations have been developed and will be discussed in this chapter.
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Affiliation(s)
- Saša Aden
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tina Snoj
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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7
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Kataoka-Hamai C, Kawakami K. Domain Sorting in Giant Unilamellar Vesicles Adsorbed on Glass. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1082-1088. [PMID: 33440115 DOI: 10.1021/acs.langmuir.0c02843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Giant unilamellar vesicles (GUVs) adsorb to a solid surface and rupture to form a planar bilayer patch. These bilayer patches are used to investigate the properties and functions of biological membranes. Therefore, it is crucial to understand the mechanisms of GUV adsorption. In this study, we investigate the adsorption of phase-separated GUVs on glass using fluorescence microscopy. GUVs containing liquid-ordered (Lo) and liquid-disordered (Ld) phases underwent domain sorting after adsorption. The Ld domain in the unbound region migrated to the highly curved region near the edge of the adsorbed region. Additionally, the Lo phase grew linearly along the edge of the adsorbed region, creating a thin ring-like domain. After the domain sorting event, the GUV ruptured to form a planar bilayer patch with circular-patterned domains in the initially adsorbed area. We found that domain sorting was promoted by increasing the extent of GUV deformation. These results suggest that both the Ld and Lo domains are reorganized for stabilizing the curved bilayer region in adsorbed GUVs.
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Affiliation(s)
- Chiho Kataoka-Hamai
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Kohsaku Kawakami
- Research Center for Functional Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
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8
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Mohammed L, Nourddine H, Saad EF, Abdelali D, Hamid R. Chitosan-covered liposomes as a promising drug transporter: nanoscale investigations. RSC Adv 2021; 11:1503-1516. [PMID: 35424127 PMCID: PMC8693526 DOI: 10.1039/d0ra08305d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/11/2020] [Indexed: 01/11/2023] Open
Abstract
Liposomes are small artificial vesicles spherical shaped of 50-1000 nm in diameter. They are created from natural non-toxic phospholipids membranes. Externally, they are decorated with biocompatible polymers. Chitosan, a natural polymer, demonstrates exceptional advantages in drug delivery, in particular, as liposome cover. In this paper, Molecular Dynamics simulations (MD) are performed in the coupled NPT-NPH and NVT-NVE statistical ensembles to study the static and dynamic properties of DPPC membrane-bilayer with grafted cationic chitosan chains, with added Cl- anions to neutralize the environment, using the Martini coarse-grained force-field. From the NPT-NPH MD simulations we found a chitosan layer L DM ranging from 3.2 to 6.6 nm for graft chains of a degree of polymerization n p = 45 and different grafting molar fractions X p = 0.005, X p = 0.014 and X p = 0.1. Also, the chitosan chains showed three essential grafting regimes: mushroom, critic, and brush depending on X p. The DPPC bilayer thickness D B and the area per lipid A l increased proportionally to X p. From the NVT-NVE MD simulations, the analysis of the radial distribution function showed that the increase of X p gives a more close-packed and rigid liposome. The analysis of the mean square displacement revealed that the diffusion of lipids is anomalous. In contrast, the diffusion of chitosan chains showed a normal diffusion, just after 100 ps. The diffusion regime of ions is found to be normal and independent of time. For the three identified regimes, the chitosan showed a tendency to adhere to the membrane surface and therefore affect the properties of the liposomal membrane.
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Affiliation(s)
- Lemaalem Mohammed
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Hadrioui Nourddine
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - El Fassi Saad
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Derouiche Abdelali
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
| | - Ridouane Hamid
- Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences, Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco
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9
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Oropeza-Guzman E, Ríos-Ramírez M, Ruiz-Suárez JC. Leveraging the Coffee Ring Effect for a Defect-Free Electroformation of Giant Unilamellar Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:16528-16535. [PMID: 31747518 DOI: 10.1021/acs.langmuir.9b02488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We took advantage of the microflow hydrodynamics in the evaporation of sessile droplets to increase the height uniformity of thin lipid films for the subsequent electroformation of defect-free giant unilamellar vesicles (GUV). By serially casting progressively larger liposome suspension droplets on the same spot of an indium-tin-oxide (ITO) electrode, we managed to leverage the coffee ring effect (CRE) in the evaporation of each droplet to generate a smeared multilayer film of uniform thickness. This multidroplet technique of lipid film formation outperformed the traditional single-droplet deposition, improving the final quality of electroformed GUV samples. The proposed film formation technique constitutes a solvent-free method that results in a dramatic reduction (∼20×) in the appearance of undesirable structures like nonspherical (NSV), multilamellar (MLV), and multivesicular (MVV) vesicles.
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Affiliation(s)
- Eric Oropeza-Guzman
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV) Unidad Monterrey , Apodaca , Nuevo León 66600 , México
| | - Maricarmen Ríos-Ramírez
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV) Unidad Monterrey , Apodaca , Nuevo León 66600 , México
| | - Jesús Carlos Ruiz-Suárez
- Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV) Unidad Monterrey , Apodaca , Nuevo León 66600 , México
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10
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Okumus B, Landgraf D, Lai GC, Bakshi S, Arias-Castro JC, Yildiz S, Huh D, Fernandez-Lopez R, Peterson CN, Toprak E, El Karoui M, Paulsson J. Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells. Nat Commun 2016; 7:11641. [PMID: 27189321 PMCID: PMC4873973 DOI: 10.1038/ncomms11641] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/15/2016] [Indexed: 11/18/2022] Open
Abstract
Many key regulatory proteins in bacteria are present in too low numbers to be detected with conventional methods, which poses a particular challenge for single-cell analyses because such proteins can contribute greatly to phenotypic heterogeneity. Here we develop a microfluidics-based platform that enables single-molecule counting of low-abundance proteins by mechanically slowing-down their diffusion within the cytoplasm of live Escherichia coli (E. coli) cells. Our technique also allows for automated microscopy at high throughput with minimal perturbation to native physiology, as well as viable enrichment/retrieval. We illustrate the method by analysing the control of the master regulator of the E. coli stress response, RpoS, by its adapter protein, SprE (RssB). Quantification of SprE numbers shows that though SprE is necessary for RpoS degradation, it is expressed at levels as low as 3–4 molecules per average cell cycle, and fluctuations in SprE are approximately Poisson distributed during exponential phase with no sign of bursting. Several proteins are expressed at too low abundance in the Escherichia coli (E. coli) proteome to be detected by standard methods. Here, the authors create a microfluidics-based platform enabling single-molecule counting of low-abundance proteins by mechanically slowing-down their diffusion in live E. coli.
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Affiliation(s)
- Burak Okumus
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dirk Landgraf
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ghee Chuan Lai
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Somenath Bakshi
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Juan Carlos Arias-Castro
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Physics, Universidad de los Andes, Bogota 4976-12340, Colombia
| | - Sadik Yildiz
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dann Huh
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Raul Fernandez-Lopez
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Celeste N Peterson
- Department of Biology, Suffolk University, Boston, Massachusetts 02108, USA
| | - Erdal Toprak
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Meriem El Karoui
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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11
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Bakshi S, Choi H, Weisshaar JC. The spatial biology of transcription and translation in rapidly growing Escherichia coli. Front Microbiol 2015; 6:636. [PMID: 26191045 PMCID: PMC4488752 DOI: 10.3389/fmicb.2015.00636] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/12/2015] [Indexed: 11/21/2022] Open
Abstract
Single-molecule fluorescence provides high resolution spatial distributions of ribosomes and RNA polymerase (RNAP) in live, rapidly growing Escherichia coli. Ribosomes are more strongly segregated from the nucleoids (chromosomal DNA) than previous widefield fluorescence studies suggested. While most transcription may be co-translational, the evidence indicates that most translation occurs on free mRNA copies that have diffused from the nucleoids to a ribosome-rich region. Analysis of time-resolved images of the nucleoid spatial distribution after treatment with the transcription-halting drug rifampicin and the translation-halting drug chloramphenicol shows that both drugs cause nucleoid contraction on the 0–3 min timescale. This is consistent with the transertion hypothesis. We suggest that the longer-term (20–30 min) nucleoid expansion after Rif treatment arises from conversion of 70S-polysomes to 30S and 50S subunits, which readily penetrate the nucleoids. Monte Carlo simulations of a polymer bead model built to mimic the chromosomal DNA and ribosomes (either 70S-polysomes or 30S and 50S subunits) explain spatial segregation or mixing of ribosomes and nucleoids in terms of excluded volume and entropic effects alone. A comprehensive model of the transcription-translation-transertion system incorporates this new information about the spatial organization of the E. coli cytoplasm. We propose that transertion, which radially expands the nucleoids, is essential for recycling of 30S and 50S subunits from ribosome-rich regions back into the nucleoids. There they initiate co-transcriptional translation, which is an important mechanism for maintaining RNAP forward progress and protecting the nascent mRNA chain. Segregation of 70S-polysomes from the nucleoid may facilitate rapid growth by shortening the search time for ribosomes to find free mRNA concentrated outside the nucleoid and the search time for RNAP concentrated within the nucleoid to find transcription initiation sites.
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Affiliation(s)
- Somenath Bakshi
- Department of Chemistry and Molecular Biophysics Program, University of Wisconsin-Madison, Madison WI, USA
| | - Heejun Choi
- Department of Chemistry and Molecular Biophysics Program, University of Wisconsin-Madison, Madison WI, USA
| | - James C Weisshaar
- Department of Chemistry and Molecular Biophysics Program, University of Wisconsin-Madison, Madison WI, USA
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12
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Bakshi S, Dalrymple RM, Li W, Choi H, Weisshaar JC. Partitioning of RNA polymerase activity in live Escherichia coli from analysis of single-molecule diffusive trajectories. Biophys J 2014; 105:2676-86. [PMID: 24359739 DOI: 10.1016/j.bpj.2013.10.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/20/2013] [Accepted: 10/23/2013] [Indexed: 11/28/2022] Open
Abstract
Superresolution fluorescence microscopy is used to locate single copies of RNA polymerase (RNAP) in live Escherichia coli and track their diffusive motion. On a timescale of 0.1-1 s, most copies separate remarkably cleanly into two diffusive states. The "slow" RNAPs, which move indistinguishably from DNA loci, are assigned to specifically bound copies (with fractional population ftrxn) that are initiating transcription, elongating, pausing, or awaiting termination. The "mixed-state" RNAP copies, with effective diffusion constant Dmixed = 0.21 μm(2) s(-1), are assigned as a rapidly exchanging mixture of nonspecifically bound copies (fns) and copies undergoing free, three-dimensional diffusion within the nucleoids (ffree). Longer trajectories of 7-s duration reveal transitions between the slow and mixed states, corroborating the assignments. Short trajectories of 20-ms duration enable direct observation of the freely diffusing RNAP copies, yielding Dfree = 0.7 μm(2) s(-1). Analysis of single-particle trajectories provides quantitative estimates of the partitioning of RNAP into different states of activity: ftrxn = 0.54 ± 0.07, fns = 0.28 ± 0.05, ffree = 0.12 ± 0.03, and fnb = 0.06 ± 0.05 (fraction unable to bind to DNA on a 1-s timescale). These fractions disagree with earlier estimates.
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Affiliation(s)
- Somenath Bakshi
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Renée M Dalrymple
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Wenting Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Heejun Choi
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - James C Weisshaar
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin; Molecular Biophysics Program, University of Wisconsin-Madison, Madison, Wisconsin.
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13
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Kusters I, van Oijen AM, Driessen AJM. Membrane-on-a-chip: microstructured silicon/silicon-dioxide chips for high-throughput screening of membrane transport and viral membrane fusion. ACS NANO 2014; 8:3380-92. [PMID: 24601516 DOI: 10.1021/nn405884a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Screening of transport processes across biological membranes is hindered by the challenge to establish fragile supported lipid bilayers and the difficulty to determine at which side of the membrane reactants reside. Here, we present a method for the generation of suspended lipid bilayers with physiological relevant lipid compositions on microstructured Si/SiO2 chips that allow for high-throughput screening of both membrane transport and viral membrane fusion. Simultaneous observation of hundreds of single-membrane channels yields statistical information revealing population heterogeneities of the pore assembly and conductance of the bacterial toxin α-hemolysin (αHL). The influence of lipid composition and ionic strength on αHL pore formation was investigated at the single-channel level, resolving features of the pore-assembly pathway. Pore formation is inhibited by a specific antibody, demonstrating the applicability of the platform for drug screening of bacterial toxins and cell-penetrating agents. Furthermore, fusion of H3N2 influenza viruses with suspended lipid bilayers can be observed directly using a specialized chip architecture. The presented micropore arrays are compatible with fluorescence readout from below using an air objective, thus allowing high-throughput screening of membrane transport in multiwell formats in analogy to plate readers.
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Affiliation(s)
- Ilja Kusters
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, Groningen, The Netherlands
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14
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Hughes LD, Boxer SG. DNA-based patterning of tethered membrane patches. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:12220-7. [PMID: 23992147 PMCID: PMC3815428 DOI: 10.1021/la402537p] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Solid-supported lipid bilayers are useful model systems for mimicking cellular membranes; however, the interaction of the bilayer with the surface can disrupt the function of integral membrane proteins and impede topological transformations such as membrane fusion. As a result, a variety of tethered or cushioned lipid bilayer architectures have been described, which retain the proximity to the surface, enabling surface-sensitive techniques, but physically distance the bilayer from the surface. We have recently developed a method for spatially separating a lipid bilayer from a solid support using DNA lipids. In this system, a DNA strand is covalently attached to a glass slide or SiO2 wafer, and giant unilamellar vesicles (GUVs) displaying the complement rupture to form a planar lipid bilayer tethered above the surface. However, the location of the patch is random, determined by where the DNA-GUV initially binds to its complement. To allow greater versatility and control, we sought a way to pattern tethered membrane patches. We present a method for creating spatially distinct tethered membrane patches on a glass slide using microarray printing. Surface-reactive DNA sequences are spotted onto the slide, incubated to covalently link the DNA to the surface, and DNA-GUVs patches are formed selectively on the printed DNA. By interfacing the bilayers with microfluidic flow cells, materials can be added on top of or fused into the membrane to change the composition of the bilayers. With further development, this approach would enable rapid screening of different patches in protein binding assays and would enable interfacing patches with electrical detectors.
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Affiliation(s)
- Laura D. Hughes
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
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15
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Ott M, Shai Y, Haran G. Single-particle tracking reveals switching of the HIV fusion peptide between two diffusive modes in membranes. J Phys Chem B 2013; 117:13308-21. [PMID: 23915358 DOI: 10.1021/jp4039418] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fusion of the HIV membrane with that of a target T cell is an essential first step in the viral infection process. Here we describe single-particle tracking (SPT) studies of a 16-amino-acid peptide derived from the HIV fusion protein (FP16), as it interacts with a supported lipid bilayer. FP16 was found to spontaneously insert into and move within the bilayer with two different modes of diffusion, a fast mode with a diffusion coefficient typical of protein motion in membranes and a much slower one. We observed transitions between the two modes: slow peptides were found to speed up, and fast peptides could slow down. Hidden Markov model analysis was employed as a method for the identification of the two modes in single-molecule trajectories and analysis of their interconversion rates. Surprisingly, the diffusion coefficients of the two modes were found to depend differently on solution viscosity. Thus, whereas the fast diffusive mode behaved as predicted by the Saffman-Delbrück theory, the slow mode behaved according to the Stokes-Einstein relation. To further characterize the two diffusive modes, FP16 molecules were studied in bilayers cooled through their liquid crystalline-to-gel phase transition. Our analysis suggested that the slow diffusive mode might originate from the formation of large objects, such as lipid domains or local protrusions, which are induced by the peptides and move together with them.
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Affiliation(s)
- Maria Ott
- Departments of Chemical Physics and ‡Biological Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
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16
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Waichman S, Roder F, Richter CP, Birkholz O, Piehler J. Diffusion and interaction dynamics of individual membrane protein complexes confined in micropatterned polymer-supported membranes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:570-577. [PMID: 23109503 DOI: 10.1002/smll.201201530] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/12/2012] [Indexed: 06/01/2023]
Abstract
Micropatterned polymer-supported membranes (PSM) are established as a tool for confining the diffusion of transmembrane proteins for single molecule studies. To this end, a photochemical surface modification with hydrophobic tethers on a PEG polymer brush is implemented for capturing of lipid vesicles and subsequent fusion. Formation of contiguous membranes within micropatterns is confirmed by scanning force microscopy, fluorescence recovery after photobleaching (FRAP), and super-resolved single-molecule tracking and localization microscopy. Free diffusion of transmembrane proteins reconstituted into micropatterned PSM is demonstrated by FRAP and by single-molecule tracking. By exploiting the confinement of diffusion within micropatterned PSM, the diffusion and interaction dynamics of individual transmembrane receptors are quantitatively resolved.
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Affiliation(s)
- Sharon Waichman
- Department of Biology, University of Osnabrück, Osnabrück, Germany
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