1
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Meschichi A, Rosa S. Plant chromatin on the move: an overview of chromatin mobility during transcription and DNA repair. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:953-962. [PMID: 36811211 DOI: 10.1111/tpj.16159] [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: 01/10/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
It has become increasingly clear in recent years that chromosomes are highly dynamic entities. Chromatin mobility and re-arrangement are involved in many biological processes, including gene regulation and the maintenance of genome stability. Despite extensive studies on chromatin mobility in yeast and animal systems, up until recently, not much had been investigated at this level in plants. For plants to achieve proper growth and development, they need to respond rapidly and appropriately to environmental stimuli. Therefore, understanding how chromatin mobility can support plant responses may offer profound insights into the functioning of plant genomes. In this review, we discuss the state of the art related to chromatin mobility in plants, including the available technologies for their role in various cellular processes.
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Affiliation(s)
- Anis Meschichi
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
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2
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Tran BM, Linnik DS, Punter CM, Śmigiel WM, Mantovanelli L, Iyer A, O’Byrne C, Abee T, Johansson J, Poolman B. Super-resolving microscopy reveals the localizations and movement dynamics of stressosome proteins in Listeria monocytogenes. Commun Biol 2023; 6:51. [PMID: 36641529 PMCID: PMC9840623 DOI: 10.1038/s42003-023-04423-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
The human pathogen Listeria monocytogenes can cope with severe environmental challenges, for which the high molecular weight stressosome complex acts as the sensing hub in a complicated signal transduction pathway. Here, we show the dynamics and functional roles of the stressosome protein RsbR1 and its paralogue, the blue-light receptor RsbL, using photo-activated localization microscopy combined with single-particle tracking and single-molecule displacement mapping and supported by physiological studies. In live cells, RsbR1 is present in multiple states: in protomers with RsbS, large clusters of stressosome complexes, and in connection with the plasma membrane via Prli42. RsbL diffuses freely in the cytoplasm but forms clusters upon exposure to light. The clustering of RsbL is independent of the presence of Prli42. Our work provides a comprehensive view of the spatial organization and intracellular dynamics of the stressosome proteins in L. monocytogenes, which paves the way towards uncovering the stress-sensing mechanism of this signal transduction pathway.
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Affiliation(s)
- Buu Minh Tran
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Dmitrii Sergeevich Linnik
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Christiaan Michiel Punter
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Wojciech Mikołaj Śmigiel
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Luca Mantovanelli
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Aditya Iyer
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Conor O’Byrne
- Microbiology, School of Biological & Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Tjakko Abee
- grid.4818.50000 0001 0791 5666Laboratory of Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jörgen Johansson
- grid.12650.300000 0001 1034 3451Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Bert Poolman
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
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3
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Miné-Hattab J, Liu S, Taddei A. Repair Foci as Liquid Phase Separation: Evidence and Limitations. Genes (Basel) 2022; 13:1846. [PMID: 36292731 PMCID: PMC9602295 DOI: 10.3390/genes13101846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 07/26/2023] Open
Abstract
In response to DNA double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less condensates or "foci". The formation of these foci and their disassembly within the proper time window are essential for genome integrity. However, how these membrane-less sub-compartments are formed, maintained and disassembled remains unclear. Recently, several studies across different model organisms proposed that DNA repair foci form via liquid phase separation. In this review, we discuss the current research investigating the physical nature of repair foci. First, we present the different models of condensates proposed in the literature, highlighting the criteria to differentiate them. Second, we discuss evidence of liquid phase separation at DNA repair sites and the limitations of this model to fully describe structures formed in response to DNA damage. Finally, we discuss the origin and possible function of liquid phase separation for DNA repair processes.
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4
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Lin TS, Kojima S, Fukuoka H, Ishijima A, Homma M, Lo CJ. Stator Dynamics Depending on Sodium Concentration in Sodium-Driven Bacterial Flagellar Motors. Front Microbiol 2021; 12:765739. [PMID: 34899649 PMCID: PMC8661058 DOI: 10.3389/fmicb.2021.765739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Bacterial flagellar motor (BFM) is a large membrane-spanning molecular rotary machine for swimming motility. Torque is generated by the interaction between the rotor and multiple stator units powered by ion-motive force (IMF). The number of bound stator units is dynamically changed in response to the external load and the IMF. However, the detailed dynamics of stator unit exchange process remains unclear. Here, we directly measured the speed changes of sodium-driven chimeric BFMs under fast perfusion of different sodium concentration conditions using computer-controlled, high-throughput microfluidic devices. We found the sodium-driven chimeric BFMs maintained constant speed over a wide range of sodium concentrations by adjusting stator units in compensation to the sodium-motive force (SMF) changes. The BFM has the maximum number of stator units and is most stable at 5 mM sodium concentration rather than higher sodium concentration. Upon rapid exchange from high to low sodium concentration, the number of functional stator units shows a rapidly excessive reduction and then resurrection that is different from predictions of simple absorption model. This may imply the existence of a metastable hidden state of the stator unit during the sudden loss of sodium ions.
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Affiliation(s)
- Tsai-Shun Lin
- Department of Physics and Center for Complex Systems, National Central University, Taoyuan City, Taiwan
| | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hajime Fukuoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Akihiko Ishijima
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Chien-Jung Lo
- Department of Physics and Center for Complex Systems, National Central University, Taoyuan City, Taiwan
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5
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Miné-Hattab J, Heltberg M, Villemeur M, Guedj C, Mora T, Walczak AM, Dahan M, Taddei A. Single molecule microscopy reveals key physical features of repair foci in living cells. eLife 2021; 10:60577. [PMID: 33543712 PMCID: PMC7924958 DOI: 10.7554/elife.60577] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 01/26/2021] [Indexed: 12/20/2022] Open
Abstract
In response to double strand breaks (DSB), repair proteins accumulate at damaged sites, forming membrane-less sub-compartments or foci. Here we explored the physical nature of these foci, using single molecule microscopy in living cells. Rad52, the functional homolog of BRCA2 in yeast, accumulates at DSB sites and diffuses ~6 times faster within repair foci than the focus itself, exhibiting confined motion. The Rad52 confinement radius coincides with the focus size: foci resulting from 2 DSBs are twice larger in volume that the ones induced by a unique DSB and the Rad52 confinement radius scales accordingly. In contrast, molecules of the single strand binding protein Rfa1 follow anomalous diffusion similar to the focus itself or damaged chromatin. We conclude that while most Rfa1 molecules are bound to the ssDNA, Rad52 molecules are free to explore the entire focus reflecting the existence of a liquid droplet around damaged DNA.
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Affiliation(s)
- Judith Miné-Hattab
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Mathias Heltberg
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Marie Villemeur
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Chloé Guedj
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France
| | - Thierry Mora
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL University, CNRS, Sorbonne Université , Université de Paris, Paris, France
| | - Maxime Dahan
- Institut Curie, PSL University, Sorbonne Université, CNRS, Physico Chimie Curie, Paris, France
| | - Angela Taddei
- Institut Curie, PSL University, Sorbonne Université, CNRS, Nuclear Dynamics, Paris, France.,Cogitamus Laboratory, Paris, France
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6
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Martini L, Brameyer S, Hoyer E, Jung K, Gerland U. Dynamics of chromosomal target search by a membrane-integrated one-component receptor. PLoS Comput Biol 2021; 17:e1008680. [PMID: 33539417 PMCID: PMC7888679 DOI: 10.1371/journal.pcbi.1008680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/17/2021] [Accepted: 01/07/2021] [Indexed: 12/03/2022] Open
Abstract
Membrane proteins account for about one third of the cellular proteome, but it is still unclear how dynamic they are and how they establish functional contacts with cytoplasmic interaction partners. Here, we consider a membrane-integrated one-component receptor that also acts as a transcriptional activator, and analyze how it kinetically locates its specific binding site on the genome. We focus on the case of CadC, the pH receptor of the acid stress response Cad system in E. coli. CadC is a prime example of a one-component signaling protein that directly binds to its cognate target site on the chromosome to regulate transcription. We combined fluorescence microscopy experiments, mathematical analysis, and kinetic Monte Carlo simulations to probe this target search process. Using fluorescently labeled CadC, we measured the time from activation of the receptor until successful binding to the DNA in single cells, exploiting that stable receptor-DNA complexes are visible as fluorescent spots. Our experimental data indicate that CadC is highly mobile in the membrane and finds its target by a 2D diffusion and capture mechanism. DNA mobility is constrained due to the overall chromosome organization, but a labeled DNA locus in the vicinity of the target site appears sufficiently mobile to randomly come close to the membrane. Relocation of the DNA target site to a distant position on the chromosome had almost no effect on the mean search time, which was between four and five minutes in either case. However, a mutant strain with two binding sites displayed a mean search time that was reduced by about a factor of two. This behavior is consistent with simulations of a coarse-grained lattice model for the coupled dynamics of DNA within a cell volume and proteins on its surface. The model also rationalizes the experimentally determined distribution of search times. Overall our findings reveal that DNA target search does not present a much bigger kinetic challenge for membrane-integrated proteins than for cytoplasmic proteins. More generally, diffusion and capture mechanisms may be sufficient for bacterial membrane proteins to establish functional contacts with cytoplasmic targets. Adaptation to changing environments is vital to bacteria and is enabled by sophisticated signal transduction systems. While signal transduction by two-component systems is well studied, the signal transduction of membrane-integrated one-component systems, where one protein performs both sensing and response regulation, are insufficiently understood. How can a membrane-integrated protein bind to specific sites on the genome to regulate transcription? Here, we study the kinetics of this process, which involves both protein diffusion within the membrane and conformational fluctuations of the genomic DNA. A well-suited model system for this question is CadC, the signaling protein of the E. coli Cad system involved in pH stress response. Fluorescently labeled CadC forms visible spots in single cells upon stable DNA-binding, marking the end of the protein-DNA search process. Moreover, the start of the search is triggered by a medium shift exposing cells to pH stress. We probe the underlying mechanism by varying the number and position of DNA target sites. We combine these experiments with mathematical analysis and kinetic Monte Carlo simulations of lattice models for the search process. Our results suggest that CadC diffusion in the membrane is pivotal for this search, while the DNA target site is just mobile enough to reach the membrane.
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Affiliation(s)
- Linda Martini
- Physics of Complex Biosystems, Technical University of Munich, Garching, Germany
| | - Sophie Brameyer
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Elisabeth Hoyer
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Kirsten Jung
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
- * E-mail: (KJ); (UG)
| | - Ulrich Gerland
- Physics of Complex Biosystems, Technical University of Munich, Garching, Germany
- * E-mail: (KJ); (UG)
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7
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Miné-Hattab J, Chiolo I. Complex Chromatin Motions for DNA Repair. Front Genet 2020; 11:800. [PMID: 33061931 PMCID: PMC7481375 DOI: 10.3389/fgene.2020.00800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/06/2020] [Indexed: 12/26/2022] Open
Abstract
A number of studies across different model systems revealed that chromatin undergoes significant changes in dynamics in response to DNA damage. These include local motion changes at damage sites, increased nuclear exploration of both damaged and undamaged loci, and directed motions to new nuclear locations associated with certain repair pathways. These studies also revealed the need for new analytical methods to identify directed motions in a context of mixed trajectories, and the importance of investigating nuclear dynamics over different time scales to identify diffusion regimes. Here we provide an overview of the current understanding of this field, including imaging and analytical methods developed to investigate nuclear dynamics in different contexts. These dynamics are essential for genome integrity. Identifying the molecular mechanisms responsible for these movements is key to understanding how their misregulation contributes to cancer and other genome instability disorders.
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Affiliation(s)
- Judith Miné-Hattab
- UMR 3664, CNRS, Institut Curie, PSL Research University, Paris, France
- UMR 3664, CNRS, Institut Curie, Sorbonne Université, Paris, France
| | - Irene Chiolo
- Molecular and Computational Biology Department, University of Southern California, Los Angeles, CA, United States
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8
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Metal-induced sensor mobilization turns on affinity to activate regulator for metal detoxification in live bacteria. Proc Natl Acad Sci U S A 2020; 117:13248-13255. [PMID: 32467170 DOI: 10.1073/pnas.1919816117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Metal detoxification is essential for bacteria's survival in adverse environments and their pathogenesis in hosts. Understanding the underlying mechanisms is crucial for devising antibacterial treatments. In the Gram-negative bacterium Escherichia coli, membrane-bound sensor CusS and its response regulator CusR together regulate the transcription of the cus operon that plays important roles in cells' resistance to copper/silver, and they belong to the two-component systems (TCSs) that are ubiquitous across various organisms and regulate diverse cellular functions. In vitro protein reconstitution and associated biochemical/physical studies have provided significant insights into the functions and mechanisms of CusS-CusR and related TCSs. Such studies are challenging regarding multidomain membrane proteins like CusS and also lack the physiological environment, particularly the native spatial context of proteins inside a cell. Here, we use stroboscopic single-molecule imaging and tracking to probe the dynamic behaviors of both CusS and CusR in live cells, in combination with protein- or residue-specific genetic manipulations. We find that copper stress leads to a cellular protein concentration increase and a concurrent mobilization of CusS out of clustered states in the membrane. We show that the mobilized CusS has significant interactions with CusR for signal transduction and that CusS's affinity toward CusR switches on upon sensing copper at the interfacial metal-binding sites in CusS's periplasmic sensor domains, prior to ATP binding and autophosphorylation at CusS's cytoplasmic kinase domain(s). The observed CusS mobilization upon stimulation and its surprisingly early interaction with CusR likely ensure an efficient signal transduction by providing proper conformation and avoiding futile cross talks.
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9
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Mechanical stress compromises multicomponent efflux complexes in bacteria. Proc Natl Acad Sci U S A 2019; 116:25462-25467. [PMID: 31772020 DOI: 10.1073/pnas.1909562116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Physical forces have a profound effect on growth, morphology, locomotion, and survival of organisms. At the level of individual cells, the role of mechanical forces is well recognized in eukaryotic physiology, but much less is known about prokaryotic organisms. Recent findings suggest an effect of physical forces on bacterial shape, cell division, motility, virulence, and biofilm initiation, but it remains unclear how mechanical forces applied to a bacterium are translated at the molecular level. In Gram-negative bacteria, multicomponent protein complexes can form rigid links across the cell envelope and are therefore subject to physical forces experienced by the cell. Here we manipulate tensile and shear mechanical stress in the bacterial cell envelope and use single-molecule tracking to show that octahedral shear (but not hydrostatic) stress within the cell envelope promotes disassembly of the tripartite efflux complex CusCBA, a system used by Escherichia coli to resist copper and silver toxicity. By promoting disassembly of this protein complex, mechanical forces within the cell envelope make the bacteria more susceptible to metal toxicity. These findings demonstrate that mechanical forces can inhibit the function of cell envelope protein assemblies in bacteria and suggest the possibility that other multicomponent, transenvelope efflux complexes may be sensitive to mechanical forces including complexes involved in antibiotic resistance, cell division, and translocation of outer membrane components. By modulating the function of proteins within the cell envelope, mechanical stress has the potential to regulate multiple processes required for bacterial survival and growth.
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10
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Qin X, Liu L, Lee SK, Alsina A, Liu T, Wu C, Park H, Yu C, Kim H, Chu J, Triller A, Tang BZ, Hyeon C, Park CY, Park H. Increased Confinement and Polydispersity of STIM1 and Orai1 after Ca 2+ Store Depletion. Biophys J 2019; 118:70-84. [PMID: 31818466 DOI: 10.1016/j.bpj.2019.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/14/2019] [Accepted: 11/18/2019] [Indexed: 12/18/2022] Open
Abstract
STIM1 (a Ca2+ sensor in the endoplasmic reticulum (ER) membrane) and Orai1 (a pore-forming subunit of the Ca2+-release-activated calcium channel in the plasma membrane) diffuse in the ER membrane and plasma membrane, respectively. Upon depletion of Ca2+ stores in the ER, STIM1 translocates to the ER-plasma membrane junction and binds Orai1 to trigger store-operated Ca2+ entry. However, the motion of STIM1 and Orai1 during this process and its roles to Ca2+ entry is poorly understood. Here, we report real-time tracking of single STIM1 and Orai1 particles in the ER membrane and plasma membrane in living cells before and after Ca2+ store depletion. We found that the motion of single STIM1 and Orai1 particles exhibits anomalous diffusion both before and after store depletion, and their mobility-measured by the radius of gyration of the trajectories, mean-square displacement, and generalized diffusion coefficient-decreases drastically after store depletion. We also found that the measured displacement distribution is non-Gaussian, and the non-Gaussian parameter drastically increases after store depletion. Detailed analyses and simulations revealed that single STIM1 and Orai1 particles are confined in the compartmentalized membrane both before and after store depletion, and the changes in the motion after store depletion are explained by increased confinement and polydispersity of STIM1-Orai1 complexes formed at the ER-plasma membrane junctions. Further simulations showed that this increase in the confinement and polydispersity after store depletion localizes a rapid increase of Ca2+ influx, which can facilitate the rapid activation of local Ca2+ signaling pathways and the efficient replenishing of Ca2+ store in the ER in store-operated Ca2+ entry.
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Affiliation(s)
- Xianan Qin
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Lei Liu
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Sang Kwon Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Adolfo Alsina
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Teng Liu
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | | | - Hojeong Park
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | | | - Hajin Kim
- Department of Biomedical Engineering and Department of Physics, Ulsan National Institute of Science and Technology, Ulsan, Korea
| | - Jun Chu
- Research Lab for Biomedical Optics and Molecular Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Antoine Triller
- Biologie Cellulaire de la Synapse N&P, IBENS, Institut de Biologie de L'ENS, Ecole Normale Supérieure, Paris, France
| | - Ben Zhong Tang
- Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Department of Chemistry, Kowloon, Hong Kong, China, Kowloon, Hong Kong, China
| | - Changbong Hyeon
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
| | - Chan Young Park
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea.
| | - Hyokeun Park
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Division of Life Science; State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
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11
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Maia P, Pérez-Rodríguez G, Pérez-Pérez M, Fdez-Riverola F, Lourenço A, Azevedo NF. Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli. Comput Biol Med 2019; 107:218-226. [DOI: 10.1016/j.compbiomed.2019.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 01/16/2023]
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12
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Turkowyd B, Müller-Esparza H, Climenti V, Steube N, Endesfelder U, Randau L. Live-cell single-particle tracking photoactivated localization microscopy of Cascade-mediated DNA surveillance. Methods Enzymol 2019; 616:133-171. [PMID: 30691641 DOI: 10.1016/bs.mie.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Type I CRISPR-Cas systems utilize small CRISPR RNA (crRNA) molecules to scan DNA strands for target regions. Different crRNAs are bound by several CRISPR-associated (Cas) protein subunits that form the stable ribonucleoprotein complex Cascade. The Cascade-mediated DNA surveillance process requires a sufficient degree of base-complementarity between crRNA and target sequences and relies on the recognition of small DNA motifs, termed protospacer adjacent motifs. Recently, super-resolution microscopy and single-particle tracking methods have been developed to follow individual protein complexes in live cells. Here, we described how this technology can be adapted to visualize the DNA scanning process of Cascade assemblies in Escherichia coli cells. The activity of recombinant Type I-Fv Cascade complexes of Shewanella putrefaciens CN-32 serves as a model system that facilitates comparative studies for many of the diverse CRISPR-Cas systems.
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Affiliation(s)
- Bartosz Turkowyd
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Hanna Müller-Esparza
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Vanessa Climenti
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Niklas Steube
- Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| | - Lennart Randau
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany; Prokaryotic Small RNA Biology Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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13
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Sarkar P, Chattopadhyay A. Exploring membrane organization at varying spatiotemporal resolutions utilizing fluorescence-based approaches: implications in membrane biology. Phys Chem Chem Phys 2019; 21:11554-11563. [DOI: 10.1039/c9cp02087j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Representative experimental approaches based on dynamic fluorescence microscopy to analyze organization and dynamics of membrane lipids and proteins.
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Affiliation(s)
- Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad 500 007
- India
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14
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Lucena D, Mauri M, Schmidt F, Eckhardt B, Graumann PL. Microdomain formation is a general property of bacterial membrane proteins and induces heterogeneity of diffusion patterns. BMC Biol 2018; 16:97. [PMID: 30173665 PMCID: PMC6120080 DOI: 10.1186/s12915-018-0561-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 08/08/2018] [Indexed: 11/22/2022] Open
Abstract
Background Proteins within the cytoplasmic membrane display distinct localization patterns and arrangements. While multiple models exist describing the dynamics of membrane proteins, to date, there have been few systematic studies, particularly in bacteria, to evaluate how protein size, number of transmembrane domains, and temperature affect their diffusion, and if conserved localization patterns exist. Results We have used fluorescence microscopy, single-molecule tracking (SMT), and computer-aided visualization methods to obtain a better understanding of the three-dimensional organization of bacterial membrane proteins, using the model bacterium Bacillus subtilis. First, we carried out a systematic study of the localization of over 200 B. subtilis membrane proteins, tagged with monomeric mVenus-YFP at their original gene locus. Their subcellular localization could be discriminated in polar, septal, patchy, and punctate patterns. Almost 20% of membrane proteins specifically localized to the cell poles, and a vast majority of all proteins localized in distinct structures, which we term microdomains. Dynamics were analyzed for selected membrane proteins, using SMT. Diffusion coefficients of the analyzed transmembrane proteins did not correlate with protein molecular weight, but correlated inversely with the number of transmembrane helices, i.e., transmembrane radius. We observed that temperature can strongly influence diffusion on the membrane, in that upon growth temperature upshift, diffusion coefficients of membrane proteins increased and still correlated inversely to the number of transmembrane domains, following the Saffman–Delbrück relation. Conclusions The vast majority of membrane proteins localized to distinct multimeric assemblies. Diffusion of membrane proteins can be suitably described by discriminating diffusion coefficients into two protein populations, one mobile and one immobile, the latter likely constituting microdomains. Our results show there is high heterogeneity and yet structural order in the cell membrane, and provide a roadmap for our understanding of membrane organization in prokaryotes. Electronic supplementary material The online version of this article (10.1186/s12915-018-0561-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniella Lucena
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Marco Mauri
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,INRIA Grenoble - Rhône-Alpes, Montbonnot, France
| | - Felix Schmidt
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Fachbereich Physik, Philipps-Universität Marburg, Marburg, Germany
| | - Bruno Eckhardt
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Fachbereich Physik, Philipps-Universität Marburg, Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany. .,Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany.
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15
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Shearer J, Khalid S. Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations. Sci Rep 2018; 8:1805. [PMID: 29379141 PMCID: PMC5789016 DOI: 10.1038/s41598-018-20227-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/04/2018] [Indexed: 01/09/2023] Open
Abstract
We use coarse-grain molecular simulations to investigate the structural and dynamics differences between an asymmetric and a symmetrical membrane, both containing beta barrel transmembrane proteins. We find in where the dynamics of the two leaflets differ greatly, the slowest leaflet dominates the structural effects and importance of protein-lipid interactions.
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Affiliation(s)
- Jonathan Shearer
- University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Syma Khalid
- University of Southampton, Southampton, SO17 1BJ, United Kingdom.
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16
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Abstract
Here, we describe protocols for three-dimensional tracking of single quantum dot-conjugated molecules with nanometer accuracy in living cells using conventional fluorescence microscopy. The technique exploits out-of-focus images of single emitters combined with an automated pattern-recognition open-source software that fits the images with proper model functions to extract the emitter coordinates. We describe protocols for targeting quantum dots to both membrane components and cytosolic proteins.
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17
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Single-Molecule Imaging of Escherichia coli Transmembrane Proteins. Methods Mol Biol 2017. [PMID: 28940067 DOI: 10.1007/978-1-4939-7271-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Single-molecule imaging in living cells can provide unique information about biological processes. Bacteria offer some particular challenges for single-molecule imaging due to their small size, only slightly larger than the diffraction limit of visible light. Here, we describe how reliable and reproducible single-molecule data can be obtained for a transmembrane protein in the Gram-negative bacterium Escherichia coli by using live-cell fluorescence microscopy. Fluorescent labeling of a protein by genetic fusion, cell culturing, sample preparation, imaging, and data analysis are discussed.
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18
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Multi-color single-molecule tracking and subtrajectory analysis for quantification of spatiotemporal dynamics and kinetics upon T cell activation. Sci Rep 2017; 7:6994. [PMID: 28765585 PMCID: PMC5539329 DOI: 10.1038/s41598-017-06960-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/20/2017] [Indexed: 11/08/2022] Open
Abstract
The dynamic properties of molecules in living cells are attracting increasing interest. We propose a new method, moving subtrajectory analysis using single-molecule tracking, and demonstrate its utility in the spatiotemporal quantification of not only dynamics but also the kinetics of interactions using single-color images. Combining this technique with three-color simultaneous single-molecule imaging, we quantified the dynamics and kinetics of molecules in spatial relation to T cell receptor (TCR) microclusters, which trigger TCR signaling. CD3ε, a component of the TCR/CD3 complex, and CD45, a phosphatase positively and negatively regulating signaling, were each found in two mobility states: faster (associated) and slower (dissociated) states. Dynamics analysis suggests that the microclusters are loosely composed of heterogeneous nanoregions, possibly surrounded by a weak barrier. Kinetics analysis quantified the association and dissociation rates of interactions with the microclusters. The associations of both CD3ε and CD45 were single-step processes. In contrast, their dissociations were each composed of two components, indicating transient and stable associated states. Inside the microclusters, the association was accelerated, and the stable association was increased. Only CD45 showed acceleration of association at the microcluster boundary, suggesting specific affinity on the boundary. Thus, this method is an innovative and versatile tool for spatiotemporal quantification.
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19
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Adrian M, Kusters R, Storm C, Hoogenraad CC, Kapitein LC. Probing the Interplay between Dendritic Spine Morphology and Membrane-Bound Diffusion. Biophys J 2017; 113:2261-2270. [PMID: 28750887 PMCID: PMC5700248 DOI: 10.1016/j.bpj.2017.06.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 11/17/2022] Open
Abstract
Dendritic spines are protrusions along neuronal dendrites that harbor the majority of excitatory postsynapses. Their distinct morphology, often featuring a bulbous head and small neck that connects to the dendritic shaft, has been shown to facilitate compartmentalization of electrical and cytoplasmic signaling stimuli elicited at the synapse. The extent to which spine morphology also forms a barrier for membrane-bound diffusion has remained unclear. Recent simulations suggested that especially the diameter of the spine neck plays a limiting role in this process. Here, we examine the connection between spine morphology and membrane-bound diffusion through a combination of photoconversion, live-cell superresolution experiments, and numerical simulations. Local photoconversion was used to obtain the timescale of diffusive equilibration in spines and followed by global sparse photoconversion to determine spine morphologies with nanoscopic resolution. These morphologies were subsequently used to assess the role of morphology on the diffusive equilibration. From the simulations, we could determine a robust relation between the equilibration timescale and a generalized shape factor calculated using both spine neck width and neck length, as well as spine head size. Experimentally, we found that diffusive equilibration was often slower, but rarely faster than predicted from the simulations, indicating that other biological confounders further reduce membrane-bound diffusion in these spines. This shape-dependent membrane-bound diffusion in mature spines may contribute to spine-specific compartmentalization of neurotransmitter receptors and signaling molecules and thereby support long-term plasticity of synaptic contacts.
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Affiliation(s)
- Max Adrian
- Division of Cell Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Remy Kusters
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Cornelis Storm
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Casper C Hoogenraad
- Division of Cell Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Lukas C Kapitein
- Division of Cell Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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20
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Adaptor protein mediates dynamic pump assembly for bacterial metal efflux. Proc Natl Acad Sci U S A 2017; 114:6694-6699. [PMID: 28607072 DOI: 10.1073/pnas.1704729114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Multicomponent efflux complexes constitute a primary mechanism for Gram-negative bacteria to expel toxic molecules for survival. As these complexes traverse the periplasm and link inner and outer membranes, it remains unclear how they operate efficiently without compromising periplasmic plasticity. Combining single-molecule superresolution imaging and genetic engineering, we study in living Escherichia coli cells the tripartite efflux complex CusCBA of the resistance-nodulation-division family that is essential for bacterial resistance to drugs and toxic metals. We find that CusCBA complexes are dynamic structures and shift toward the assembled form in response to metal stress. Unexpectedly, the periplasmic adaptor protein CusB is a key metal-sensing element that drives the assembly of the efflux complex ahead of the transcription activation of the cus operon for defending against metals. This adaptor protein-mediated dynamic pump assembly allows the bacterial cell for efficient efflux upon cellular demand while still maintaining periplasmic plasticity; this could be broadly relevant to other multicomponent efflux systems.
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21
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Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CF. Single Particle Tracking: From Theory to Biophysical Applications. Chem Rev 2017; 117:7331-7376. [PMID: 28520419 DOI: 10.1021/acs.chemrev.6b00815] [Citation(s) in RCA: 264] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After three decades of developments, single particle tracking (SPT) has become a powerful tool to interrogate dynamics in a range of materials including live cells and novel catalytic supports because of its ability to reveal dynamics in the structure-function relationships underlying the heterogeneous nature of such systems. In this review, we summarize the algorithms behind, and practical applications of, SPT. We first cover the theoretical background including particle identification, localization, and trajectory reconstruction. General instrumentation and recent developments to achieve two- and three-dimensional subdiffraction localization and SPT are discussed. We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT.
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Affiliation(s)
- Hao Shen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Lawrence J Tauzin
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Rashad Baiyasi
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Wenxiao Wang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Nicholas Moringo
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Bo Shuang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Christy F Landes
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
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22
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Oswald F, Varadarajan A, Lill H, Peterman EJG, Bollen YJM. MreB-Dependent Organization of the E. coli Cytoplasmic Membrane Controls Membrane Protein Diffusion. Biophys J 2016; 110:1139-49. [PMID: 26958890 PMCID: PMC4788719 DOI: 10.1016/j.bpj.2016.01.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/05/2016] [Accepted: 01/11/2016] [Indexed: 01/13/2023] Open
Abstract
The functional organization of prokaryotic cell membranes, which is essential for many cellular processes, has been challenging to analyze due to the small size and nonflat geometry of bacterial cells. Here, we use single-molecule fluorescence microscopy and three-dimensional quantitative analyses in live Escherichia coli to demonstrate that its cytoplasmic membrane contains microdomains with distinct physical properties. We show that the stability of these microdomains depends on the integrity of the MreB cytoskeletal network underneath the membrane. We explore how the interplay between cytoskeleton and membrane affects trans-membrane protein (TMP) diffusion and reveal that the mobility of the TMPs tested is subdiffusive, most likely caused by confinement of TMP mobility by the submembranous MreB network. Our findings demonstrate that the dynamic architecture of prokaryotic cell membranes is controlled by the MreB cytoskeleton and regulates the mobility of TMPs.
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Affiliation(s)
- Felix Oswald
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, the Netherlands; Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, the Netherlands; LaserLaB Amsterdam, the Netherlands
| | - Aravindan Varadarajan
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, the Netherlands; LaserLaB Amsterdam, the Netherlands
| | - Holger Lill
- Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, the Netherlands; LaserLaB Amsterdam, the Netherlands
| | - Erwin J G Peterman
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, the Netherlands; LaserLaB Amsterdam, the Netherlands
| | - Yves J M Bollen
- Department of Molecular Cell Biology, Vrije Universiteit Amsterdam, the Netherlands; LaserLaB Amsterdam, the Netherlands.
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23
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Yang F, Chen TY, Krzemiński Ł, Santiago AG, Jung W, Chen P. Single-molecule dynamics of the molecular chaperone trigger factor in living cells. Mol Microbiol 2016; 102:992-1003. [PMID: 27626893 DOI: 10.1111/mmi.13529] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 09/10/2016] [Indexed: 01/20/2023]
Abstract
In bacteria, trigger factor (TF) is the molecular chaperone that interacts with the ribosome to assist the folding of nascent polypeptides. Studies in vitro have provided insights into the function and mechanism of TF. Much is to be elucidated, however, about how TF functions in vivo. Here, we use single-molecule tracking, in combination with genetic manipulations, to study the dynamics and function of TF in living E. coli cells. We find that TF, besides interacting with the 70S ribosome, may also bind to ribosomal subunits and form TF-polypeptide complexes that may include DnaK/DnaJ proteins. The TF-70S ribosome interactions are highly dynamic inside cells, with an average residence time of ∼0.2 s. Our results confirm that the signal recognition particle weakens TF's interaction with the 70S ribosome, and further identify that this weakening mainly results from a change in TF's binding to the 70S ribosome, rather than its unbinding. Moreover, using photoconvertible bimolecular fluorescence complementation, we selectively probe TF2 dimers in the cell and show that TF2 does not bind to the 70S ribosome but is involved in the post-translational interactions with polypeptides. These findings contribute to the fundamental understanding of molecular chaperones in assisting protein folding in living cells.
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Affiliation(s)
- Feng Yang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tai-Yen Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Łukasz Krzemiński
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ace George Santiago
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
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24
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On the mobility, membrane location and functionality of mechanosensitive channels in Escherichia coli. Sci Rep 2016; 6:32709. [PMID: 27596282 PMCID: PMC5011748 DOI: 10.1038/srep32709] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/12/2016] [Indexed: 11/23/2022] Open
Abstract
Bacterial mechanosensitive channels protect cells from structural damage during hypoosmotic shock. MscS, MscL and MscK are the most abundant channels in E. coli and arguably the most important ones in osmoprotection. By combining physiological assays with quantitative photo-activated localization microscopy (qPALM), we find an almost linear relationship between channel abundance and cell survival. A minimum of 100 MscL (or MscS) channels is needed for protection when a single type of channel is expressed. Under native-like conditions MscL, MscS as well as MscK distribute homogeneously over the cytoplasmic membrane and the lateral diffusion of the channels is in accordance with their relative protein mass. However, we observe cluster formation and a reduced mobility of MscL when the majority of the subunits of the pentameric channel contain the fluorescent mEos3.2 protein. These data provide new insights into the quantitative biology of mechanosensitive channels and emphasizes the need for care in analysing protein complexes even when the fluorescent tag has been optimized for monomeric behaviour.
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25
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Shuang B, Wang W, Shen H, Tauzin LJ, Flatebo C, Chen J, Moringo NA, Bishop LDC, Kelly KF, Landes CF. Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions. Sci Rep 2016; 6:30826. [PMID: 27488312 PMCID: PMC4973222 DOI: 10.1038/srep30826] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/11/2016] [Indexed: 01/17/2023] Open
Abstract
Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions.
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Affiliation(s)
- Bo Shuang
- Department of Chemistry, Rice University, Houston, TX 77251, USA
| | - Wenxiao Wang
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
| | - Hao Shen
- Department of Chemistry, Rice University, Houston, TX 77251, USA
| | | | | | - Jianbo Chen
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
| | | | | | - Kevin F. Kelly
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
| | - Christy F. Landes
- Department of Chemistry, Rice University, Houston, TX 77251, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77251, USA
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26
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Kleanthous C, Rassam P, Baumann CG. Protein-protein interactions and the spatiotemporal dynamics of bacterial outer membrane proteins. Curr Opin Struct Biol 2015; 35:109-15. [PMID: 26629934 PMCID: PMC4684144 DOI: 10.1016/j.sbi.2015.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/26/2015] [Accepted: 10/30/2015] [Indexed: 01/14/2023]
Abstract
We discuss spatiotemporal patterning in the bacterial outer membrane. Promiscuous interactions between outer membrane proteins govern their behaviour. Turnover and biogenesis of outer membrane proteins linked to formation of clusters. Implications of spatiotemporal patterning for bacterial physiology discussed.
It has until recently been unclear whether outer membrane proteins (OMPs) of Gram-negative bacteria are organized or distributed randomly. Studies now suggest promiscuous protein–protein interactions (PPIs) between β-barrel OMPs in Escherichia coli govern their local and global dynamics, engender spatiotemporal patterning of the outer membrane into micro-domains and are the basis of β-barrel protein turnover. We contextualize these latest advances, speculate on areas of bacterial cell biology that might be influenced by the organization of OMPs into supramolecular assemblies, and highlight the new questions and controversies this revised view of the bacterial outer membrane raises.
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Affiliation(s)
- Colin Kleanthous
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Patrice Rassam
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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27
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Gardini L, Capitanio M, Pavone FS. 3D tracking of single nanoparticles and quantum dots in living cells by out-of-focus imaging with diffraction pattern recognition. Sci Rep 2015; 5:16088. [PMID: 26526410 PMCID: PMC4630642 DOI: 10.1038/srep16088] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022] Open
Abstract
Live cells are three-dimensional environments where biological molecules move to find their targets and accomplish their functions. However, up to now, most single molecule investigations have been limited to bi-dimensional studies owing to the complexity of 3d-tracking techniques. Here, we present a novel method for three-dimensional localization of single nano-emitters based on automatic recognition of out-of-focus diffraction patterns. Our technique can be applied to track the movements of single molecules in living cells using a conventional epifluorescence microscope. We first demonstrate three-dimensional localization of fluorescent nanobeads over 4 microns depth with accuracy below 2 nm in vitro. Remarkably, we also establish three-dimensional tracking of Quantum Dots, overcoming their anisotropic emission, by adopting a ligation strategy that allows rotational freedom of the emitter combined with proper pattern recognition. We localize commercially available Quantum Dots in living cells with accuracy better than 7 nm over 2 microns depth. We validate our technique by tracking the three-dimensional movements of single protein-conjugated Quantum Dots in living cell. Moreover, we find that important localization errors can occur in off-focus imaging when improperly calibrated and we give indications to avoid them. Finally, we share a Matlab script that allows readily application of our technique by other laboratories.
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Affiliation(s)
- Lucia Gardini
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Marco Capitanio
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Francesco S Pavone
- LENS - European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino, Italy.,National Institute of Optics-National Research Council, Largo Fermi 6, 50125 Florence, Italy.,International Center of Computational Neurophotonics, Via Nello Carrara 1, 50019, Sesto Fiorentino (FI), Italy
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28
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Chen TY, Jung W, Santiago AG, Yang F, Krzemiński Ł, Chen P. Quantifying Multistate Cytoplasmic Molecular Diffusion in Bacterial Cells via Inverse Transform of Confined Displacement Distribution. J Phys Chem B 2015; 119:14451-9. [PMID: 26491971 PMCID: PMC4645974 DOI: 10.1021/acs.jpcb.5b08654] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Single-molecule tracking (SMT) of
fluorescently tagged cytoplasmic
proteins can provide valuable information on the underlying biological
processes in living cells via subsequent analysis of the displacement
distributions; however, the confinement effect originated from the
small size of a bacterial cell skews the protein’s displacement
distribution and complicates the quantification of the intrinsic diffusive
behaviors. Using the inverse transformation method, we convert the
skewed displacement distribution (for both 2D and 3D imaging conditions)
back to that in free space for systems containing one or multiple
(non)interconverting Brownian diffusion states, from which we can
reliably extract the number of diffusion states as well as their intrinsic
diffusion coefficients and respective fractional populations. We further
demonstrate a successful application to experimental SMT data of a
transcription factor in living E. coli cells. This
work allows a direct quantitative connection between cytoplasmic SMT
data with diffusion theory for analyzing molecular diffusive behavior
in live bacteria.
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Affiliation(s)
- Tai-Yen Chen
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Won Jung
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Ace George Santiago
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Feng Yang
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Łukasz Krzemiński
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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29
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Gameiro D, Pérez-Pérez M, Pérez-Rodríguez G, Monteiro G, Azevedo NF, Lourenço A. Computational resources and strategies to construct single-molecule metabolic models of microbial cells. Brief Bioinform 2015; 17:863-76. [DOI: 10.1093/bib/bbv096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Indexed: 11/12/2022] Open
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30
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Milenkovic L, Weiss LE, Yoon J, Roth TL, Su YS, Sahl SJ, Scott MP, Moerner WE. Single-molecule imaging of Hedgehog pathway protein Smoothened in primary cilia reveals binding events regulated by Patched1. Proc Natl Acad Sci U S A 2015; 112:8320-5. [PMID: 26100903 PMCID: PMC4500289 DOI: 10.1073/pnas.1510094112] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Accumulation of the signaling protein Smoothened (Smo) in the membrane of primary cilia is an essential step in Hedgehog (Hh) signal transduction, yet the molecular mechanisms of Smo movement and localization are poorly understood. Using ultrasensitive single-molecule tracking with high spatial/temporal precision (30 nm/10 ms), we discovered that binding events disrupt the primarily diffusive movement of Smo in cilia at an array of sites near the base. The affinity of Smo for these binding sites was modulated by the Hh pathway activation state. Activation, by either a ligand or genetic loss of the negatively acting Hh receptor Patched-1 (Ptch), reduced the affinity and frequency of Smo binding at the base. Our findings quantify activation-dependent changes in Smo dynamics in cilia and highlight a previously unknown step in Hh pathway activation.
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Affiliation(s)
- Ljiljana Milenkovic
- Department of Developmental Biology, Genetics and Bioengineering, Stanford University, Stanford, CA 94305
| | - Lucien E Weiss
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Joshua Yoon
- Department of Chemistry, Stanford University, Stanford, CA 94305; Department of Applied Physics, Stanford University, Stanford, CA 94305
| | - Theodore L Roth
- Department of Developmental Biology, Genetics and Bioengineering, Stanford University, Stanford, CA 94305
| | - YouRong S Su
- Department of Developmental Biology, Genetics and Bioengineering, Stanford University, Stanford, CA 94305
| | - Steffen J Sahl
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Matthew P Scott
- Department of Developmental Biology, Genetics and Bioengineering, Stanford University, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305;
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Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells. Nat Commun 2015; 6:7445. [PMID: 26145755 PMCID: PMC4507017 DOI: 10.1038/ncomms8445] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 05/11/2015] [Indexed: 02/04/2023] Open
Abstract
Binding and unbinding of transcription regulators at operator sites constitute a primary mechanism for gene regulation. While many cellular factors are known to regulate their binding, little is known on how cells can modulate their unbinding for regulation. Using nanometer-precision single-molecule tracking, we study the unbinding kinetics from DNA of two metal-sensing transcription regulators in living Escherichia coli cells. We find that they show unusual concentration-dependent unbinding kinetics from chromosomal recognition sites in both their apo and holo forms. Unexpectedly, their unbinding kinetics further varies with the extent of chromosome condensation, and more surprisingly, varies in opposite ways for their apo-repressor versus holo-activator forms. These findings suggest likely broadly relevant mechanisms for facile switching between transcription activation and deactivation in vivo and in coordinating transcription regulation of resistance genes with the cell cycle. Binding and unbinding of transcription regulators at operator sites regulates gene expression. By single-molecule tracking of metal-sensing regulators, here the authors show that the unbinding kinetics depends on regulator concentration and chromosome condensation, and varies with their metal-binding states.
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32
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Affiliation(s)
- Lydia Kisley
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
| | - Christy F. Landes
- Department of Chemistry and Department of Electrical and Computer
Engineering,
Rice Quantum Institute, Rice University, 6100 Main Street, MS-60, Houston, Texas 77005, United States
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