1
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Chen H, Yan G, Wen MH, Brooks KN, Zhang Y, Huang PS, Chen TY. Advancements and Practical Considerations for Biophysical Research: Navigating the Challenges and Future of Super-resolution Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:331-344. [PMID: 38817319 PMCID: PMC11134610 DOI: 10.1021/cbmi.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024]
Abstract
The introduction of super-resolution microscopy (SRM) has significantly advanced our understanding of cellular and molecular dynamics, offering a detailed view previously beyond our reach. Implementing SRM in biophysical research, however, presents numerous challenges. This review addresses the crucial aspects of utilizing SRM effectively, from selecting appropriate fluorophores and preparing samples to analyzing complex data sets. We explore recent technological advancements and methodological improvements that enhance the capabilities of SRM. Emphasizing the integration of SRM with other analytical methods, we aim to overcome inherent limitations and expand the scope of biological insights achievable. By providing a comprehensive guide for choosing the most suitable SRM methods based on specific research objectives, we aim to empower researchers to explore complex biological processes with enhanced precision and clarity, thereby advancing the frontiers of biophysical research.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Guangjie Yan
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Kameron N. Brooks
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Pei-San Huang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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2
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Munshi R, Ling J, Ryabichko S, Wieschaus E, Gregor T. Transcription factor clusters as information transfer agents. ARXIV 2024:arXiv:2403.02943v1. [PMID: 38495568 PMCID: PMC10942473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Deciphering how genes interpret information from the concentration of transcription factors (TFs) within the cell nucleus remains a fundamental question in gene regulation. Recent advancements have unveiled the heterogeneous distribution of TF molecules in the nucleus, posing challenges to the precise decoding of concentration signals. To explore this phenomenon, we employ high-resolution single-cell imaging of a fluorescently tagged TF protein, Bicoid, in living fly embryos. We show that accumulation of Bicoid in submicron clusters preserves the spatial information of the maternal Bicoid gradient, and that cluster intensity, size, and frequency offer remarkably precise spatial cues. We further discover that various known gene targets of Bicoid activation colocalize with clusters and that for the target gene Hunchback, this colocalization is dependent on its enhancer binding affinity. Modeling information transfer through these clusters suggests that clustering offers a more rapid sensing mechanism for global nuclear concentrations than freely diffusing TF molecules detected by simple enhancers.
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Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jia Ling
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sergey Ryabichko
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Eric Wieschaus
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA
| | - Thomas Gregor
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Stem Cell and Developmental Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
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3
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Ye R, Sun X, Mao X, Alfonso FS, Baral S, Liu C, Coates GW, Chen P. Optical sequencing of single synthetic polymers. Nat Chem 2024; 16:210-217. [PMID: 37945834 DOI: 10.1038/s41557-023-01363-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023]
Abstract
Microscopic sequences of synthetic polymers play crucial roles in the polymer properties, but are generally unknown and inaccessible to traditional measurements. Here we report real-time optical sequencing of single synthetic copolymer chains under living polymerization conditions. We achieve this by carrying out multi-colour imaging of polymer growth by single catalysts at single-monomer resolution using CREATS (coupled reaction approach toward super-resolution imaging). CREATS makes a reaction effectively fluorogenic, enabling single-molecule localization microscopy of chemical reactions at higher reactant concentrations. Our data demonstrate that the chain propagation kinetics of surface-grafted polymerization contains temporal fluctuations with a defined memory time (which can be attributed to neighbouring monomer interactions) and chain-length dependence (due to surface electrostatic effects). Furthermore, the microscopic sequences of individual copolymers reveal their tendency to form block copolymers, and, more importantly, quantify the size distribution of individual blocks for comparison with theoretically random copolymers. Such sequencing capability paves the way for single-chain-level structure-function correlation studies of synthetic polymers.
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Affiliation(s)
- Rong Ye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Chemical Engineering and Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI, USA
| | - Xiangcheng Sun
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Chemical Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Xianwen Mao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Materials Science and Engineering, Institute of Functional Intelligent Materials, and Centre for Advanced 2D Materials, National University of Singapore, Singapore, Singapore
| | - Felix S Alfonso
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Susil Baral
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Chemistry, Illinois State University, Normal, IL, USA
| | - Chunming Liu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- School of Polymer Science and Polymer Engineering and Department of Chemistry, University of Akron, Akron, OH, USA
| | - Geoffrey W Coates
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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4
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Chen H, Chen TY. From Monomers to Hexamers: A Theoretical Probability of the Neighbor Density Approach to Dissect Protein Oligomerization in Cells. Anal Chem 2024; 96:895-903. [PMID: 38156958 PMCID: PMC10842889 DOI: 10.1021/acs.analchem.3c04728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Deciphering the oligomeric state of proteins within cells is pivotal to understanding their role in intricate cellular processes. With the recent advances in single-molecule localization microscopy, previous efforts have harnessed protein location density approaches, coupled with simulations, to extract membrane protein oligomeric states in cells, highlighting the value of such techniques. However, a comprehensive theoretical approach that can be universally applied across different proteins (e.g., membrane and cytosolic proteins) remains elusive. Here, we introduce the theoretical probability of neighbor density (PND) as a robust tool to discern protein oligomeric states in cellular environments. Utilizing our approach, the theoretical PND was validated against simulated data for both membrane and cytosolic proteins, consistently aligning with experimental baselines for membrane proteins. This congruence was maintained even when adjusting for protein concentrations or exploring proteins of various oligomeric states. The strength of our method lies not only in its precision but also in its adaptability, accommodating diverse cellular protein scenarios without compromising the accuracy. The development and validation of the theoretical PND facilitate accurate protein oligomeric state determination and bolster our understanding of protein-mediated cellular functions.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204
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5
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Lewis JS, van Oijen AM, Spenkelink LM. Embracing Heterogeneity: Challenging the Paradigm of Replisomes as Deterministic Machines. Chem Rev 2023; 123:13419-13440. [PMID: 37971892 PMCID: PMC10790245 DOI: 10.1021/acs.chemrev.3c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/15/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]
Abstract
The paradigm of cellular systems as deterministic machines has long guided our understanding of biology. Advancements in technology and methodology, however, have revealed a world of stochasticity, challenging the notion of determinism. Here, we explore the stochastic behavior of multi-protein complexes, using the DNA replication system (replisome) as a prime example. The faithful and timely copying of DNA depends on the simultaneous action of a large set of enzymes and scaffolding factors. This fundamental cellular process is underpinned by dynamic protein-nucleic acid assemblies that must transition between distinct conformations and compositional states. Traditionally viewed as a well-orchestrated molecular machine, recent experimental evidence has unveiled significant variability and heterogeneity in the replication process. In this review, we discuss recent advances in single-molecule approaches and single-particle cryo-EM, which have provided insights into the dynamic processes of DNA replication. We comment on the new challenges faced by structural biologists and biophysicists as they attempt to describe the dynamic cascade of events leading to replisome assembly, activation, and progression. The fundamental principles uncovered and yet to be discovered through the study of DNA replication will inform on similar operating principles for other multi-protein complexes.
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Affiliation(s)
- Jacob S. Lewis
- Macromolecular
Machines Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Antoine M. van Oijen
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M. Spenkelink
- Molecular
Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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6
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Chakraborty UK, Park Y, Sengupta K, Jung W, Joshi CP, Francis DH, Chen P. A 'through-DNA' mechanism for metal uptake-vs.-efflux regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570191. [PMID: 38105935 PMCID: PMC10723295 DOI: 10.1101/2023.12.05.570191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Transition metals like Zn are essential for all organisms including bacteria, but fluctuations of their concentrations in the cell can be lethal. Organisms have thus evolved complex mechanisms for cellular metal homeostasis. One mechanistic paradigm involves pairs of transcription regulators sensing intracellular metal concentrations to regulate metal uptake and efflux. Here we report that Zur and ZntR, a prototypical pair of regulators for Zn uptake and efflux in E. coli , respectively, can coordinate their regulation through DNA, besides sensing cellular Zn 2+ concentrations. Using a combination of live-cell single-molecule tracking and in vitro single-molecule FRET measurements, we show that unmetallated ZntR can enhance the unbinding kinetics of Zur from DNA by directly acting on Zur-DNA complexes, possibly through forming heteromeric ternary and quaternary complexes that involve both protein-DNA and protein-protein interactions. This 'through-DNA' mechanism may functionally facilitate the switching in Zn uptake regulation when bacteria encounter changing Zn environments; it could also be relevant for regulating the uptake-vs.-efflux of various metals across different bacterial species and yeast.
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7
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Fu B, Mao X, Park Y, Zhao Z, Yan T, Jung W, Francis DH, Li W, Pian B, Salimijazi F, Suri M, Hanrath T, Barstow B, Chen P. Single-cell multimodal imaging uncovers energy conversion pathways in biohybrids. Nat Chem 2023; 15:1400-1407. [PMID: 37500951 DOI: 10.1038/s41557-023-01285-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Microbe-semiconductor biohybrids, which integrate microbial enzymatic synthesis with the light-harvesting capabilities of inorganic semiconductors, have emerged as promising solar-to-chemical conversion systems. Improving the electron transport at the nano-bio interface and inside cells is important for boosting conversion efficiencies, yet the underlying mechanism is challenging to study by bulk measurements owing to the heterogeneities of both constituents. Here we develop a generalizable, quantitative multimodal microscopy platform that combines multi-channel optical imaging and photocurrent mapping to probe such biohybrids down to single- to sub-cell/particle levels. We uncover and differentiate the critical roles of different hydrogenases in the lithoautotrophic bacterium Ralstonia eutropha for bioplastic formation, discover this bacterium's surprisingly large nanoampere-level electron-uptake capability, and dissect the cross-membrane electron-transport pathways. This imaging platform, and the associated analytical framework, can uncover electron-transport mechanisms in various types of biohybrid, and potentially offers a means to use and engineer R. eutropha for efficient chemical production coupled with photocatalytic materials.
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Affiliation(s)
- Bing Fu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Xianwen Mao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Materials Science and Engineering, Institute of Functional Intelligent Materials, and Centre for Advanced 2D Materials, National University of Singapore, Singapore, Singapore
| | - Youngchan Park
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zhiheng Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Tianlei Yan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Danielle H Francis
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Friends School of Baltimore, Baltimore, MD, USA
| | - Wenjie Li
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Brooke Pian
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Farshid Salimijazi
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Mokshin Suri
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA
| | - Tobias Hanrath
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Buz Barstow
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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8
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Harper CE, Zhang W, Lee J, Shin JH, Keller MR, van Wijngaarden E, Chou E, Wang Z, Dörr T, Chen P, Hernandez CJ. Mechanical stimuli activate gene expression via a cell envelope stress sensing pathway. Sci Rep 2023; 13:13979. [PMID: 37633922 PMCID: PMC10460444 DOI: 10.1038/s41598-023-40897-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/17/2023] [Indexed: 08/28/2023] Open
Abstract
Mechanosensitive mechanisms are often used to sense damage to tissue structure, stimulating matrix synthesis and repair. While this kind of mechanoregulatory process is well recognized in eukaryotic systems, it is not known whether such a process occurs in bacteria. In Vibrio cholerae, antibiotic-induced damage to the load-bearing cell wall promotes increased signaling by the two-component system VxrAB, which stimulates cell wall synthesis. Here we show that changes in mechanical stress within the cell envelope are sufficient to stimulate VxrAB signaling in the absence of antibiotics. We applied mechanical forces to individual bacteria using three distinct loading modalities: extrusion loading within a microfluidic device, direct compression and hydrostatic pressure. In all cases, VxrAB signaling, as indicated by a fluorescent protein reporter, was increased in cells submitted to greater magnitudes of mechanical loading, hence diverse forms of mechanical stimuli activate VxrAB signaling. Reduction in cell envelope stiffness following removal of the endopeptidase ShyA led to large increases in cell envelope deformation and substantially increased VxrAB response, further supporting the responsiveness of VxrAB. Our findings demonstrate a mechanosensitive gene regulatory system in bacteria and suggest that mechanical signals may contribute to the regulation of cell wall homeostasis.
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Affiliation(s)
- Christine E Harper
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Wenyao Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Junsung Lee
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Jung-Ho Shin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Megan R Keller
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Ellen van Wijngaarden
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Chou
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Zhaohong Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA.
- Department of Microbiology, Cornell University, Ithaca, NY, 14853, USA.
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY, 14853, USA.
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.
| | - Christopher J Hernandez
- Department of Bioengineering and Therapeutic Sciences and Orthopaedic Surgery, University of California, San Francisco, CA, 94143, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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9
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Chen H, Chen TY. Probing Oxidant Effects on Superoxide Dismutase 1 Oligomeric States in Live Cells Using Single-Molecule Fluorescence Anisotropy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:49-57. [PMID: 37122833 PMCID: PMC10131266 DOI: 10.1021/cbmi.3c00002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 05/02/2023]
Abstract
The protein Cu/Zn superoxide dismutase (SOD1) is known to function as a dimer, but its concentration in cells (∼50 μM) and the dimerization constant (K d of 500 μM) results suggest that it exists in a monomer-dimer equilibrium. It is unclear how the oligomeric state of SOD1 changes when cells are initially exposed to high levels of extracellular oxidative stress. To address this problem, we introduced the single-molecule fluorescence anisotropy (smFA) assay to explore SOD1 oligomeric states in live COS7 cells. smFA specifically probes the fluorescence polarization changes caused by molecular rotations where the fast-rotating molecules (either due to smaller hydrodynamic volume or less viscous environments) deteriorate the emission polarization and thus lower the anisotropy. After validating that smFA is effective in distinguishing monomeric and dimeric fluorescence proteins, we overexpressed SOD1 in live COS7 cells and investigated how its oligomeric state changes under basal, 2 h, and 24 h 100 μM H2O2 treatments. We found that treating cells with H2O2 promotes SOD1 dimerization and decreases cellular viscosity in 2 h. Interestingly, prolonged H2O2 treatments show similar results as the basal conditions, indicating that cells return to a steady state similar to the basal state after 24 h, despite the presence of H2O2. Our results demonstrate that SOD1 changes its oligomeric state equilibrium in response to extracellular oxidative stresses. smFA will open new opportunities to explore the relationship between the SOD1 oligomer state and its H2O2-based signaling and transcription regulation roles.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University
of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University
of Houston, Houston, Texas 77204, United States
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10
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Zhang Y, Wen MH, Qin G, Cai C, Chen TY. Subcellular redox responses reveal different Cu-dependent antioxidant defenses between mitochondria and cytosol. Metallomics 2022; 14:mfac087. [PMID: 36367501 PMCID: PMC9686363 DOI: 10.1093/mtomcs/mfac087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2023]
Abstract
Excess intracellular Cu perturbs cellular redox balance and thus causes diseases. However, the relationship between cellular redox status and Cu homeostasis and how such an interplay is coordinated within cellular compartments has not yet been well established. Using combined approaches of organelle-specific redox sensor Grx1-roGFP2 and non-targeted proteomics, we investigate the real-time Cu-dependent antioxidant defenses of mitochondria and cytosol in live HEK293 cells. The Cu-dependent real-time imaging experiments show that CuCl2 treatment results in increased oxidative stress in both cytosol and mitochondria. In contrast, subsequent excess Cu removal by bathocuproine sulfonate, a Cu chelating reagent, lowers oxidative stress in mitochondria but causes even higher oxidative stress in the cytosol. The proteomic data reveal that several mitochondrial proteins, but not cytosolic ones, undergo significant abundance change under Cu treatments. The proteomic analysis also shows that proteins with significant changes are related to mitochondrial oxidative phosphorylation and glutathione synthesis. The differences in redox behaviors and protein profiles in different cellular compartments reveal distinct mitochondrial and cytosolic response mechanisms upon Cu-induced oxidative stress. These findings provide insights into how redox and Cu homeostasis interplay by modulating specific protein expressions at the subcellular levels, shedding light on understanding the effects of Cu-induced redox misregulation on the diseases.
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Affiliation(s)
- Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Guoting Qin
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
- College of Optometry, University of Houston, Houston, TX 77204, USA
| | - Chengzhi Cai
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
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11
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Brown JWP, Alford RG, Walsh JC, Spinney RE, Xu SY, Hertel S, Berengut JF, Spenkelink LM, van Oijen AM, Böcking T, Morris RG, Lee LK. Rapid Exchange of Stably Bound Protein and DNA Cargo on a DNA Origami Receptor. ACS NANO 2022; 16:6455-6467. [PMID: 35316035 DOI: 10.1021/acsnano.2c00699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.
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Affiliation(s)
- James W P Brown
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Rokiah G Alford
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - James C Walsh
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard E Spinney
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Stephanie Y Xu
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Sophie Hertel
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Jonathan F Berengut
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Chemistry, University of Sydney, Sydney 2006, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
- Illawarra Health & Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Till Böcking
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Richard G Morris
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- School of Physics, University of New South Wales, Sydney 2052, Australia
| | - Lawrence K Lee
- EMBL Australia Node for Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
- ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney 2052, Australia
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12
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Mao X, Chen P. Inter-facet junction effects on particulate photoelectrodes. NATURE MATERIALS 2022; 21:331-337. [PMID: 34952940 DOI: 10.1038/s41563-021-01161-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 10/21/2021] [Indexed: 06/14/2023]
Abstract
Particulate semiconductor photocatalysts are paramount for many solar energy conversion technologies. In anisotropically shaped photocatalyst particles, the different constituent facets may form inter-facet junctions at their adjoining edges, analogous to lateral two-dimensional (2D) heterojunctions or pseudo-2D junctions made of few-layer 2D materials. Using subfacet-level multimodal functional imaging, we uncover inter-facet junction effects on anisotropically shaped bismuth vanadate (BiVO4) particles and identify the characteristics of near-edge transition zones on the particle surface, which underpin the whole-particle photoelectrochemistry. We further show that chemical doping modulates the widths of such near-edge surface transition zones, consequently altering particles' performance. Decoupled facet-size scaling laws further translate inter-facet junction effects into quantitative particle-size engineering principles, revealing surprising multiphasic size dependences of whole-particle photoelectrode performance. The imaging tools, the analytical framework and the inter-facet junction concept pave new avenues towards understanding, predicting and engineering (opto)electronic and photoelectrochemical properties of faceted semiconducting materials, with broad implications in energy science and semiconductor technology.
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Affiliation(s)
- Xianwen Mao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Department of Materials Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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13
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Facilitated Dissociation of Nucleoid Associated Proteins from DNA in the Bacterial Confinement. Biophys J 2022; 121:1119-1133. [PMID: 35257784 PMCID: PMC9034294 DOI: 10.1016/j.bpj.2022.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 03/01/2022] [Indexed: 11/20/2022] Open
Abstract
Transcription machinery depends on the temporal formation of protein-DNA complexes. Recent experiments demonstrated that not only the formation but also the lifetime of such complexes can affect the transcriptional machinery. In parallel, in vitro single-molecule studies showed that nucleoid-associated proteins (NAPs) leave the DNA rapidly as the bulk concentration of the protein increases via facilitated dissociation (FD). Nevertheless, whether such a concentration-dependent mechanism is functional in a bacterial cell, in which NAP levels and the 3d chromosomal structure are often coupled, is not clear a priori. Here, by using extensive coarse-grained molecular simulations, we model the unbinding of specific and nonspecific dimeric NAPs from a high-molecular-weight circular DNA molecule in a cylindrical structure mimicking the cellular confinement of a bacterial chromosome. Our simulations confirm that physiologically relevant peak protein levels (tens of micromolar) lead to highly compact chromosomal structures. This compaction results in rapid off rates (shorter DNA residence times) for specifically DNA-binding NAPs, such as the factor for inversion stimulation, which mostly dissociate via a segmental jump mechanism. Contrarily, for nonspecific NAPs, which are more prone to leave their binding sites via 1d sliding, the off rates decrease as the protein levels increase. The simulations with restrained chromosome models reveal that chromosome compaction is in favor of faster dissociation but only for specific proteins, and nonspecific proteins are not affected by the chromosome compaction. Overall, our results suggest that the cellular concentration level of a structural DNA-binding protein can be highly intermingled with its DNA residence time.
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14
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Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. Int J Mol Sci 2022; 23:ijms23042179. [PMID: 35216300 PMCID: PMC8879271 DOI: 10.3390/ijms23042179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.
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15
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Natesan R, Gowrishankar K, Kuttippurathu L, Kumar PBS, Rao M. Active Remodeling of Chromatin and Implications for In Vivo Folding. J Phys Chem B 2021; 126:100-109. [DOI: 10.1021/acs.jpcb.1c08655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Lakshmi Kuttippurathu
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, United States
| | - P. B. Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai 600036, India
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 668557, Kerala, India
| | - Madan Rao
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bengaluru 560065, India
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16
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Appling FD, Berlow RB, Stanfield RL, Dyson HJ, Wright PE. The molecular basis of allostery in a facilitated dissociation process. Structure 2021; 29:1327-1338.e5. [PMID: 34520739 PMCID: PMC8642270 DOI: 10.1016/j.str.2021.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/22/2021] [Accepted: 07/21/2021] [Indexed: 12/29/2022]
Abstract
Facilitated dissociation provides a mechanism by which high-affinity complexes can be rapidly disassembled. The negative feedback regulator CITED2 efficiently downregulates the hypoxic response by displacing the hypoxia-inducible transcription factor HIF-1α from the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300. Displacement occurs by a facilitated dissociation mechanism involving a transient ternary intermediate formed by binding of the intrinsically disordered CITED2 activation domain to the TAZ1:HIF-1α complex. The short lifetime of the intermediate precludes straightforward structural investigations. To obtain insights into the molecular determinants of facilitated dissociation, we model the ternary intermediate by generating a fusion peptide composed of the primary CITED2 and HIF-1α binding motifs. X-ray crystallographic and NMR studies of the fusion peptide complex reveal TAZ1-mediated negative cooperativity that results in nearly mutually exclusive binding of specific CITED2 and HIF-1α interaction motifs, providing molecular-level insights into the allosteric switch that terminates the hypoxic response.
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Affiliation(s)
- Francis D Appling
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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17
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Wen MH, Xie X, Huang PS, Yang K, Chen TY. Crossroads between membrane trafficking machinery and copper homeostasis in the nerve system. Open Biol 2021; 11:210128. [PMID: 34847776 PMCID: PMC8633785 DOI: 10.1098/rsob.210128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Imbalanced copper homeostasis and perturbation of membrane trafficking are two common symptoms that have been associated with the pathogenesis of neurodegenerative and neurodevelopmental diseases. Accumulating evidence from biophysical, cellular and in vivo studies suggest that membrane trafficking orchestrates both copper homeostasis and neural functions-however, a systematic review of how copper homeostasis and membrane trafficking interplays in neurons remains lacking. Here, we summarize current knowledge of the general trafficking itineraries for copper transporters and highlight several critical membrane trafficking regulators in maintaining copper homeostasis. We discuss how membrane trafficking regulators may alter copper transporter distribution in different membrane compartments to regulate intracellular copper homeostasis. Using Parkinson's disease and MEDNIK as examples, we further elaborate how misregulated trafficking regulators may interplay parallelly or synergistically with copper dyshomeostasis in devastating pathogenesis in neurodegenerative diseases. Finally, we explore multiple unsolved questions and highlight the existing challenges to understand how copper homeostasis is modulated through membrane trafficking.
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Affiliation(s)
- Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Xihong Xie
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Pei-San Huang
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Karen Yang
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
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18
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Ye R, Zhao M, Mao X, Wang Z, Garzón DA, Pu H, Zhao Z, Chen P. Nanoscale cooperative adsorption for materials control. Nat Commun 2021; 12:4287. [PMID: 34257300 PMCID: PMC8277846 DOI: 10.1038/s41467-021-24590-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/16/2021] [Indexed: 11/29/2022] Open
Abstract
Adsorption plays vital roles in many processes including catalysis, sensing, and nanomaterials design. However, quantifying molecular adsorption, especially at the nanoscale, is challenging, hindering the exploration of its utilization on nanomaterials that possess heterogeneity across different length scales. Here we map the adsorption of nonfluorescent small molecule/ion and polymer ligands on gold nanoparticles of various morphologies in situ under ambient solution conditions, in which these ligands are critical for the particles’ physiochemical properties. We differentiate at nanometer resolution their adsorption affinities among different sites on the same nanoparticle and uncover positive/negative adsorption cooperativity, both essential for understanding adsorbate-surface interactions. Considering the surface density of adsorbed ligands, we further discover crossover behaviors of ligand adsorption between different particle facets, leading to a strategy and its implementation in facet-controlled synthesis of colloidal metal nanoparticles by merely tuning the concentration of a single ligand. Adsorption is a fundamentally important process but challenging to quantify, especially at the nanoscale. Here, the authors map the adsorption affinity and cooperativity of various ligands on single gold nanoparticles and discover adsorption crossover behaviors between different facets, leading to a strategy to control particle shape.
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Affiliation(s)
- Rong Ye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Ming Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Xianwen Mao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Zhaohong Wang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Diego A Garzón
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.,Departamento de Química, Universidad de Los Andes, Bogotá, Colombia
| | - Heting Pu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhiheng Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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19
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Single-Molecule Fluorescence Methods to Study Protein Exchange Kinetics in Supramolecular Complexes. Methods Mol Biol 2021; 2281:49-65. [PMID: 33847951 DOI: 10.1007/978-1-0716-1290-3_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Recent single-molecule studies have demonstrated that the composition of multi-protein complexes can strike a balance between stability and dynamics. Proteins can dynamically exchange in and out of the complex depending on their concentration in solution. These exchange dynamics are a key determinant of the molecular pathways available to multi-protein complexes. It is therefore important that we develop robust and reproducible assays to study protein exchange. Using DNA replication as an example, we describe three single-molecule fluorescence assays used to study protein exchange dynamics. In the chase exchange assay, fluorescently labeled proteins are challenged by unlabeled proteins, where exchange results in the disappearance of the fluorescence signal. In the FRAP exchange assay, fluorescently labeled proteins are photobleached before exchange is measured by an increase in fluorescence as non-bleached proteins exchange into the complex. Finally, in the two-color exchange assay, proteins are labeled with two different fluorophores and exchange is visualized by detecting changes in color. All three assays compliment in their ability to elucidate the dynamic behavior of proteins in large biological systems.
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20
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Huang PS, Wen MH, Xie X, Xu A, Lee DF, Chen TY. Generation of a homozygous knock-in human embryonic stem cell line expressing SNAP-tagged SOD1. Stem Cell Res 2021; 54:102415. [PMID: 34118566 PMCID: PMC8330834 DOI: 10.1016/j.scr.2021.102415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 05/11/2021] [Accepted: 05/31/2021] [Indexed: 11/16/2022] Open
Abstract
Superoxide Dismutase 1 (SOD1) is an antioxidant enzyme that protects the cells from radical oxygen species. To study the behavior of endogenous SOD1 under a microscope, we genetically modified H1 human embryonic stem cells (hESCs) to express SOD1 fused with a SNAP-tag, a protein tag that can be covalently labeled with a variety of synthetic probes. The engineered homozygous clone expressing SOD1-SNAP fusion proteins has normal stem cell morphology and karyotype, expresses pluripotency markers, and can be differentiated into all three germ layers in vitro, providing a versatile platform for imaging-based studies of SOD1.
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Affiliation(s)
- Pei-San Huang
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Xihong Xie
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA.
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21
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Balogh RK, Németh E, Jones NC, Hoffmann SV, Jancsó A, Gyurcsik B. A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:491-500. [PMID: 33907862 DOI: 10.1007/s00249-021-01539-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/13/2021] [Accepted: 04/14/2021] [Indexed: 11/30/2022]
Abstract
The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.
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Affiliation(s)
- Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Eszter Németh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.,Institute of Enzymology, Genome Stability Research Group, Research Centre for Natural Sciences, Magyar tudósok körútja 2, Budapest, 1117, Hungary
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Søren Vrønning Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary.
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22
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Lagage V, Uphoff S. Pulses and delays, anticipation and memory: seeing bacterial stress responses from a single-cell perspective. FEMS Microbiol Rev 2021; 44:565-571. [PMID: 32556120 DOI: 10.1093/femsre/fuaa022] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
Stress responses are crucial for bacteria to survive harmful conditions that they encounter in the environment. Although gene regulatory mechanisms underlying stress responses in bacteria have been thoroughly characterised for decades, recent advances in imaging technologies helped to uncover previously hidden dynamics and heterogeneity that become visible at the single-cell level. Despite the diversity of stress response mechanisms, certain dynamic regulatory features are frequently seen in single cells, such as pulses, delays, stress anticipation and memory effects. Often, these dynamics are highly variable across cells. While any individual cell may not achieve an optimal stress response, phenotypic diversity can provide a benefit at the population level. In this review, we highlight microscopy studies that offer novel insights into how bacteria sense stress, regulate protective mechanisms, cope with response delays and prepare for future environmental challenges. These studies showcase developments in the single-cell imaging toolbox including gene expression reporters, FRET, super-resolution microscopy and single-molecule tracking, as well as microfluidic techniques to manipulate cells and create defined stress conditions.
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Affiliation(s)
- Valentine Lagage
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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23
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Stracy M, Schweizer J, Sherratt DJ, Kapanidis AN, Uphoff S, Lesterlin C. Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins. Mol Cell 2021; 81:1499-1514.e6. [PMID: 33621478 PMCID: PMC8022225 DOI: 10.1016/j.molcel.2021.01.039] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/24/2020] [Accepted: 01/27/2021] [Indexed: 12/18/2022]
Abstract
Despite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Toward identifying universal mechanisms of the target search, we used single-molecule tracking of 11 diverse DNA-binding proteins in living Escherichia coli. The mobility of these proteins during the target search was dictated by DNA interactions rather than by their molecular weights. By generating cells devoid of all chromosomal DNA, we discovered that the nucleoid is not a physical barrier for protein diffusion but significantly slows the motion of DNA-binding proteins through frequent short-lived DNA interactions. The representative DNA-binding proteins (irrespective of their size, concentration, or function) spend the majority (58%–99%) of their search time bound to DNA and occupy as much as ∼30% of the chromosomal DNA at any time. Chromosome crowding likely has important implications for the function of all DNA-binding proteins. Protein motion was compared between unperturbed cells and DNA-free cells Protein mobility was dictated by DNA interactions rather than molecular weight The nucleoid is not a physical barrier for protein diffusion The proteins studied spend most (58%–99%) of their search time bound to DNA
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Affiliation(s)
- Mathew Stracy
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Jakob Schweizer
- Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | - David J Sherratt
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Christian Lesterlin
- Molecular Microbiology and Structural Biochemistry (MMSB), Université Lyon 1, CNRS, INSERM, UMR5086, 69007 Lyon, France.
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24
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Chen H, Xie X, Chen TY. Single-molecule microscopy for in-cell quantification of protein oligomeric stoichiometry. Curr Opin Struct Biol 2020; 66:112-118. [PMID: 33242727 DOI: 10.1016/j.sbi.2020.10.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Protein organization modification plays a vital role in initiating signaling pathways, transcriptional regulation, and cell apoptosis regulation. Simultaneous quantification of oligomeric state and cellular parameters in the same cell, even though challenging, is required to understand their correlation at the molecular level. Recent advances of fluorescence protein and single-molecule localization microscopy enables the determination of localizations and oligomeric states of target proteins in cells. We reviewed the fluorescence intensity-based, localization-based, and photophysical property-based approaches for in-cell quantification of protein oligomeric stoichiometry. We discussed their working principles, applications, advantages, and limitations. These results also imply the combination of methodologies targeting different biological parameters at the single-cell level is essential to uncover the structure-function relationship at the molecular level.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, United States
| | - Xihong Xie
- Department of Chemistry, University of Houston, Houston, TX 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, United States.
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25
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The Major Chromosome Condensation Factors Smc, HBsu, and Gyrase in Bacillus subtilis Operate via Strikingly Different Patterns of Motion. mSphere 2020; 5:5/5/e00817-20. [PMID: 32907955 PMCID: PMC7485690 DOI: 10.1128/msphere.00817-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
All types of cells need to compact their chromosomes containing their genomic information several-thousand-fold in order to fit into the cell. In eukaryotes, histones achieve a major degree of compaction and bind very tightly to DNA such that they need to be actively removed to allow access of polymerases to the DNA. Bacteria have evolved a basic, highly dynamic system of DNA compaction, accommodating rapid adaptability to changes in environmental conditions. We show that the Bacillus subtilis histone-like protein HBsu exchanges on DNA on a millisecond scale and moves through the entire nucleoid containing the genome as a slow-mobility fraction and a dynamic fraction, both having short dwell times. Thus, HBsu achieves compaction via short and transient DNA binding, thereby allowing rapid access of DNA replication or transcription factors to DNA. Topoisomerase gyrase and B. subtilis Smc show different interactions with DNA in vivo, displaying continuous loading or unloading from DNA, or using two fractions, one moving through the genome and one statically bound on a time scale of minutes, respectively, revealing three different modes of DNA compaction in vivo. Although DNA-compacting proteins have been extensively characterized in vitro, knowledge of their DNA binding dynamics in vivo is greatly lacking. We have employed single-molecule tracking to characterize the motion of the three major chromosome compaction factors in Bacillus subtilis, Smc (structural maintenance of chromosomes) proteins, topoisomerase DNA gyrase, and histone-like protein HBsu. We show that these three proteins display strikingly different patterns of interaction with DNA; while Smc displays two mobility fractions, one static and one moving through the chromosome in a constrained manner, gyrase operates as a single slow-mobility fraction, suggesting that all gyrase molecules are catalytically actively engaged in DNA binding. Conversely, bacterial histone-like protein HBsu moves through the nucleoid as a larger, slow-mobility fraction and a smaller, high-mobility fraction, with both fractions having relatively short dwell times. Turnover within the SMC complex that makes up the static fraction is shown to be important for its function in chromosome compaction. Our report reveals that chromosome compaction in bacteria can occur via fast, transient interactions in vivo, avoiding clashes with RNA and DNA polymerases. IMPORTANCE All types of cells need to compact their chromosomes containing their genomic information several-thousand-fold in order to fit into the cell. In eukaryotes, histones achieve a major degree of compaction and bind very tightly to DNA such that they need to be actively removed to allow access of polymerases to the DNA. Bacteria have evolved a basic, highly dynamic system of DNA compaction, accommodating rapid adaptability to changes in environmental conditions. We show that the Bacillus subtilis histone-like protein HBsu exchanges on DNA on a millisecond scale and moves through the entire nucleoid containing the genome as a slow-mobility fraction and a dynamic fraction, both having short dwell times. Thus, HBsu achieves compaction via short and transient DNA binding, thereby allowing rapid access of DNA replication or transcription factors to DNA. Topoisomerase gyrase and B. subtilis Smc show different interactions with DNA in vivo, displaying continuous loading or unloading from DNA, or using two fractions, one moving through the genome and one statically bound on a time scale of minutes, respectively, revealing three different modes of DNA compaction in vivo.
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26
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Pan M, Zhang Y, Yan G, Chen TY. Dissection of Interaction Kinetics through Single-Molecule Interaction Simulation. Anal Chem 2020; 92:11582-11589. [PMID: 32786469 DOI: 10.1021/acs.analchem.0c01014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability to extract kinetic interaction parameters from single-molecule fluorescence resonance energy transfer trajectories without the need for solving complex single-molecule differential equations has the potential to address some of the critical biophysical questions. Here, we provide a noise-free single-molecule interaction simulation (SMIS) tool to give the expected dwell-time distributions and relative populations of each FRET level based on the assigned kinetic model and to dissect kinetic interaction parameters from single-molecule FRET trajectories. The method provides the expected dwell-time distributions, average transition rates, and relative populations of each FRET level based on the assigned kinetic model. By comparing with ground truth data and experimental data, we demonstrated that SMIS is useful to quantify the interaction kinetic rate constants without using the traditional single-molecule analytical solution approach.
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Affiliation(s)
- Manhua Pan
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Guangjie Yan
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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27
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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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Jung W, Sengupta K, Wendel BM, Helmann JD, Chen P. Biphasic unbinding of a metalloregulator from DNA for transcription (de)repression in Live Bacteria. Nucleic Acids Res 2020; 48:2199-2208. [PMID: 32009151 PMCID: PMC7049717 DOI: 10.1093/nar/gkaa056] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/06/2020] [Accepted: 01/17/2020] [Indexed: 11/12/2022] Open
Abstract
Microorganisms use zinc-sensing regulators to alter gene expression in response to changes in the availability of zinc, an essential micronutrient. Under zinc-replete conditions, the Fur-family metalloregulator Zur binds to DNA tightly in its metallated repressor form to Zur box operator sites, repressing the transcription of zinc uptake transporters. Derepression comes from unbinding of the regulator, which, under zinc-starvation conditions, exists in its metal-deficient non-repressor forms having no significant affinity with Zur box. While the mechanism of transcription repression by Zur is well-studied, little is known on how derepression by Zur could be facilitated. Using single-molecule/single-cell measurements, we find that in live Escherichia coli cells, Zur's unbinding rate from DNA is sensitive to Zur protein concentration in a first-of-its-kind biphasic manner, initially impeded and then facilitated with increasing Zur concentration. These results challenge conventional models of protein unbinding being unimolecular processes and independent of protein concentration. The facilitated unbinding component likely occurs via a ternary complex formation mechanism. The impeded unbinding component likely results from Zur oligomerization on chromosome involving inter-protein salt-bridges. Unexpectedly, a non-repressor form of Zur is found to bind chromosome tightly, likely at non-consensus sequence sites. These unusual behaviors could provide functional advantages in Zur's facile switching between repression and derepression.
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Affiliation(s)
- Won Jung
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Kushal Sengupta
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Brian M Wendel
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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29
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Baksh KA, Zamble DB. Allosteric control of metal-responsive transcriptional regulators in bacteria. J Biol Chem 2020; 295:1673-1684. [PMID: 31857375 PMCID: PMC7008368 DOI: 10.1074/jbc.rev119.011444] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many transition metals are essential trace nutrients for living organisms, but they are also cytotoxic in high concentrations. Bacteria maintain the delicate balance between metal starvation and toxicity through a complex network of metal homeostasis pathways. These systems are coordinated by the activities of metal-responsive transcription factors-also known as metal-sensor proteins or metalloregulators-that are tuned to sense the bioavailability of specific metals in the cell in order to regulate the expression of genes encoding proteins that contribute to metal homeostasis. Metal binding to a metalloregulator allosterically influences its ability to bind specific DNA sequences through a variety of intricate mechanisms that lie on a continuum between large conformational changes and subtle changes in internal dynamics. This review summarizes recent advances in our understanding of how metal sensor proteins respond to intracellular metal concentrations. In particular, we highlight the allosteric mechanisms used for metal-responsive regulation of several prokaryotic single-component metalloregulators, and we briefly discuss current open questions of how metalloregulators function in bacterial cells. Understanding the regulation and function of metal-responsive transcription factors is a fundamental aspect of metallobiochemistry and is important for gaining insights into bacterial growth and virulence.
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Affiliation(s)
- Karina A Baksh
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Deborah B Zamble
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.
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30
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Erbaş A, Marko JF. How do DNA-bound proteins leave their binding sites? The role of facilitated dissociation. Curr Opin Chem Biol 2019; 53:118-124. [PMID: 31586479 PMCID: PMC6926143 DOI: 10.1016/j.cbpa.2019.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/11/2019] [Accepted: 08/24/2019] [Indexed: 10/25/2022]
Abstract
Dissociation of a protein from DNA is often assumed to be described by an off rate that is independent of other molecules in solution. Recent experiments and computational analyses have challenged this view by showing that unbinding rates (residence times) of DNA-bound proteins can depend on concentrations of nearby molecules that are competing for binding. This 'facilitated dissociation' (FD) process can occur at the single-binding site level via formation of a ternary complex, and can dominate over 'spontaneous dissociation' at low (submicromolar) concentrations. In the crowded intracellular environment FD introduces new regulatory possibilities at the level of individual biomolecule interactions.
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Affiliation(s)
- Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Physics & Astronomy, Northwestern University, Evanston, IL 60208, USA
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31
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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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32
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Spenkelink LM, Lewis JS, Jergic S, Xu ZQ, Robinson A, Dixon NE, van Oijen AM. Recycling of single-stranded DNA-binding protein by the bacterial replisome. Nucleic Acids Res 2019; 47:4111-4123. [PMID: 30767010 PMCID: PMC6486552 DOI: 10.1093/nar/gkz090] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/30/2019] [Accepted: 02/09/2019] [Indexed: 02/06/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) support DNA replication by protecting single-stranded DNA from nucleolytic attack, preventing intra-strand pairing events and playing many other regulatory roles within the replisome. Recent developments in single-molecule approaches have led to a revised picture of the replisome that is much more complex in how it retains or recycles protein components. Here, we visualize how an in vitro reconstituted Escherichia coli replisome recruits SSB by relying on two different molecular mechanisms. Not only does it recruit new SSB molecules from solution to coat newly formed single-stranded DNA on the lagging strand, but it also internally recycles SSB from one Okazaki fragment to the next. We show that this internal transfer mechanism is balanced against recruitment from solution in a manner that is concentration dependent. By visualizing SSB dynamics in live cells, we show that both internal transfer and external exchange mechanisms are physiologically relevant.
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Affiliation(s)
- Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747 AG, the Netherlands
| | - Jacob S Lewis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Slobodan Jergic
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Andrew Robinson
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
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33
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Dahlke K, Sing CE. Influence of Nucleoid-Associated Proteins on DNA Supercoiling. J Phys Chem B 2019; 123:10152-10162. [PMID: 31710235 DOI: 10.1021/acs.jpcb.9b07436] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
DNA supercoiling, where the DNA strand forms a writhe to relieve torsional stress, plays a vital role in packaging the genetic material in cells. Experiment, simulation, and theory have all demonstrated how supercoiling emerges due to the over- or underwinding of the DNA strand. Nucleoid-associated proteins (NAPs) help structure DNA in prokaryotes, yet the role that they play in the supercoiling process has not been as thoroughly investigated. We develop a coarse-grained simulation to model DNA supercoiling in the presence of proteins, providing a rigorous physical understanding of how NAPs affect supercoiling behavior. Specifically, we demonstrate how the force and torque necessary to form supercoils are affected by the presence of NAPs. NAPs that bend DNA stabilize the supercoil, thus shifting the transition between extended and supercoiled DNAs. We develop a theory to explain how NAP binding affects DNA supercoiling. This provides insight into how NAPs modulate DNA compaction via a combination of supercoiling and local protein-dependent deformations.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering , University of Illinois Urbana-Champaign , Urbana , Illinois 61801 , United States
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34
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Li L, Chen X, Cui C, Pan X, Li X, Yazd HS, Wu Q, Qiu L, Li J, Tan W. Aptamer Displacement Reaction from Live-Cell Surfaces and Its Applications. J Am Chem Soc 2019; 141:17174-17179. [PMID: 31539233 DOI: 10.1021/jacs.9b07191] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The DNA strand displacement reaction has had sustained scientific interest in building complicated nucleic acid-based networks. However, extending the fundamental mechanism to more diverse biomolecules in a complex environment remains challenging. Aptamers bind with targeted biomolecules with high affinity and selectivity, thus offering a promising route to link the powers of nucleic acid with diverse cues. Here, we describe three methods that allow facile and efficient displacement reaction of aptamers from the living cell surface using complement DNA (cDNA), toehold-labeled cDNA (tcDNA), and single-stranded binding protein (SSB). The kinetics of the DNA strand displacement reaction is severely affected by complex physicochemical properties of the natural membrane. Toehold-mediated and SSB-mediated aptamer displacement exhibited significantly enhanced kinetics, and they completely removed the aptamer quickly to avoid a false signal caused by aptamer internalization. Because of its simplicity, aptamer displacement enabled detection of membrane protein post-translation and improved selection efficiency of cell-SELEX.
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Affiliation(s)
- Long Li
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Xigao Chen
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Cheng Cui
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xiaoshu Pan
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Xiaowei Li
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Hoda Safari Yazd
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Qiong Wu
- Department of Chemistry, Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute , University of Florida , Gainesville , Florida 32611 , United States
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , China
| | - Juan Li
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences , The Cancer Hospital of the University of Chinese Academy of Sciences , Hangzhou , Zhejiang 310022 , China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha 410082 , China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences , The Cancer Hospital of the University of Chinese Academy of Sciences , Hangzhou , Zhejiang 310022 , China
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35
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Generation of a genetically modified human embryonic stem cells expressing fluorescence tagged ATOX1. Stem Cell Res 2019; 41:101631. [PMID: 31704540 PMCID: PMC6939864 DOI: 10.1016/j.scr.2019.101631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/26/2019] [Accepted: 10/14/2019] [Indexed: 11/23/2022] Open
Abstract
ATOX1 is a copper chaperone involved in intracellular copper homeostasis, cell proliferation, and tumor progression. To investigate the physiologically relevant molecular mechanism of ATOX1 by using imaging-based approaches, we genetically modified ATOX1 in H1 hESCs to express mCherry-ATOX1 fusion protein under endogenous regulatory machinery. The fluorescence engineered hESC clone maintains characteristic stem cell features and can differentiate to all three germ layers, serving as a unique tool to dissect the role of ATOX1 in various cellular processes.
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36
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Tsai MY, Zheng W, Chen M, Wolynes PG. Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation. J Am Chem Soc 2019; 141:18113-18126. [DOI: 10.1021/jacs.9b08287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Min-Yeh Tsai
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan (R.O.C.)
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37
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Dahlke K, Zhao J, Sing CE, Banigan EJ. Force-Dependent Facilitated Dissociation Can Generate Protein-DNA Catch Bonds. Biophys J 2019; 117:1085-1100. [PMID: 31427067 DOI: 10.1016/j.bpj.2019.07.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/08/2019] [Accepted: 07/29/2019] [Indexed: 12/31/2022] Open
Abstract
Cellular structures are continually subjected to forces, which may serve as mechanical signals for cells through their effects on biomolecule interaction kinetics. Typically, molecular complexes interact via "slip bonds," so applied forces accelerate off rates by reducing transition energy barriers. However, biomolecules with multiple dissociation pathways may have considerably more complicated force dependencies. This is the case for DNA-binding proteins that undergo "facilitated dissociation," in which competitor biomolecules from solution enhance molecular dissociation in a concentration-dependent manner. Using simulations and theory, we develop a generic model that shows that proteins undergoing facilitated dissociation can form an alternative type of molecular bond, known as a "catch bond," for which applied forces suppress protein dissociation. This occurs because the binding by protein competitors responsible for the facilitated dissociation pathway can be inhibited by applied forces. Within the model, we explore how the force dependence of dissociation is regulated by intrinsic factors, including molecular sensitivity to force and binding geometry and the extrinsic factor of competitor protein concentration. We find that catch bonds generically emerge when the force dependence of the facilitated unbinding pathway is stronger than that of the spontaneous unbinding pathway. The sharpness of the transition between slip- and catch-bond kinetics depends on the degree to which the protein bends its DNA substrate. This force-dependent kinetics is broadly regulated by the concentration of competitor biomolecules in solution. Thus, the observed catch bond is mechanistically distinct from other known physiological catch bonds because it requires an extrinsic factor-competitor proteins-rather than a specific intrinsic molecular structure. We hypothesize that this mechanism for regulating force-dependent protein dissociation may be used by cells to modulate protein exchange, regulate transcription, and facilitate diffusive search processes.
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Affiliation(s)
- Katelyn Dahlke
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Jing Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Charles E Sing
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Edward J Banigan
- Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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38
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Itoh Y, Murata A, Takahashi S, Kamagata K. Intrinsically disordered domain of tumor suppressor p53 facilitates target search by ultrafast transfer between different DNA strands. Nucleic Acids Res 2019; 46:7261-7269. [PMID: 29986056 PMCID: PMC6101536 DOI: 10.1093/nar/gky586] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/19/2018] [Indexed: 01/23/2023] Open
Abstract
Intersegmental transfer (IST) is an important strategy in the target search used by sequence-specific DNA-binding proteins (DBPs), enabling DBPs to search for targets between multiple DNA strands without dissociation. We examined the IST of the tumor suppressor p53 using ensemble stopped-flow and single-molecule fluorescence measurements. The ensemble measurements demonstrated that p53 exhibits very fast IST, whose rate constant was ∼108 M-1 s-1. To determine the domains of p53 responsible for IST, two mutants with deletions of one of its two DNA binding domains were generated. The mutant lacking the disordered C-terminal (CT) domain (the CoreTet mutant) abolished IST, whereas the mutant lacking the structured core domain (the TetCT mutant) maintained IST, clearly demonstrating the importance of the CT domain. Single-molecule fluorescence measurements further demonstrated the transfer of p53 between two tethered DNA strands. The pseudo-wild-type p53 and the TetCT mutant showed significant transfer efficiencies, whereas the transfer efficiency for the CoreTet mutant was zero. These results suggest that ultrafast IST might be promoted by four copies of the CT domain, by binding to two DNA strands simultaneously. Such ultrafast IST might be important to avoid nearby-bound DBPs during the target search process of p53 in nucleus.
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Affiliation(s)
- Yuji Itoh
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Agato Murata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Kiyoto Kamagata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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39
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Mao X, Liu C, Hesari M, Zou N, Chen P. Super-resolution imaging of non-fluorescent reactions via competition. Nat Chem 2019; 11:687-694. [DOI: 10.1038/s41557-019-0288-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/31/2019] [Indexed: 11/09/2022]
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40
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Padmanabhan P, Martínez-Mármol R, Xia D, Götz J, Meunier FA. Frontotemporal dementia mutant Tau promotes aberrant Fyn nanoclustering in hippocampal dendritic spines. eLife 2019; 8:45040. [PMID: 31237563 PMCID: PMC6592683 DOI: 10.7554/elife.45040] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/13/2019] [Indexed: 12/14/2022] Open
Abstract
The Src kinase Fyn plays critical roles in memory formation and Alzheimer’s disease. Its targeting to neuronal dendrites is regulated by Tau via an unknown mechanism. As nanoclustering is essential for efficient signaling, we used single-molecule tracking to characterize the nanoscale distribution of Fyn in mouse hippocampal neurons, and manipulated the expression of Tau to test whether it controls Fyn nanoscale organization. We found that dendritic Fyn exhibits at least three distinct motion states, two of them associated with nanodomains. Fyn mobility decreases in dendrites during neuronal maturation, suggesting a dynamic synaptic reorganization. Removing Tau increases Fyn mobility in dendritic shafts, an effect that is rescued by re-expressing wildtype Tau. By contrast, expression of frontotemporal dementia P301L mutant Tau immobilizes Fyn in dendritic spines, affecting its motion state distribution and nanoclustering. Tau therefore controls the nanoscale organization of Fyn in dendrites, with the pathological Tau P301L mutation potentially contributing to synaptic dysfunction by promoting aberrant Fyn nanoclustering in spines.
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Affiliation(s)
- Pranesh Padmanabhan
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), University of Queensland, Brisbane, Australia
| | - Ramón Martínez-Mármol
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), University of Queensland, Brisbane, Australia
| | - Di Xia
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), University of Queensland, Brisbane, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), University of Queensland, Brisbane, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), University of Queensland, Brisbane, Australia
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41
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Jiang Z, Tian L, Fang X, Zhang K, Liu Q, Dong Q, Wang E, Wang J. The emergence of the two cell fates and their associated switching for a negative auto-regulating gene. BMC Biol 2019; 17:49. [PMID: 31202264 PMCID: PMC6570905 DOI: 10.1186/s12915-019-0666-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/20/2019] [Indexed: 01/24/2023] Open
Abstract
Background Decisions in the cell that lead to its ultimate fate are important for fundamental cellular functions such as proliferation, growth, differentiation, development, and death. These cell fate decisions can be influenced by both the gene regulatory network and also environmental factors and can be modeled using simple gene feedback circuits. Negative auto-regulation is a common feedback motif in the gene circuits. It can act to reduce gene expression noise or induce oscillatory expression and is thought to lead to only one cell fate. Here, we present experimental and modeling data to suggest that a self-repressor circuit can lead to two cell fates under specific conditions. Results We show that the introduction of inducers capable of binding and unbinding to a self-repressing gene product (protein), thus regulating the associated gene, can lead to the emergence of two cell states. We suggest that the inducers can alter the effective regulatory binding and unbinding speed of the self-repressor regulatory protein to its destination DNA without changing the gene itself. The corresponding simulation results are consistent with the experimental findings. We propose physical and quantitative explanations for the origin of the two phenotypic cell fates. Conclusions Our results suggest a mechanism for the emergence of multiple cell fates. This may explain the heterogeneity often observed among cell states, while illustrating that altering gene regulation strength can influence cell fates and their decision-making processes without genetic changes. Electronic supplementary material The online version of this article (10.1186/s12915-019-0666-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenlong Jiang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China.,College of Physics, Jilin University, Changchun, Jilin, 130012, China
| | - Li Tian
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiaona Fang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Qiong Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Qingzhe Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jin Wang
- Department of Chemistry, Physics and Applied Mathematics, State University of New York at Stony Brook, Stony Brook, New York, 11794-3400, USA.
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42
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Erbaş A, Olvera de la Cruz M, Marko JF. Receptor-Ligand Rebinding Kinetics in Confinement. Biophys J 2019; 116:1609-1624. [PMID: 31029377 PMCID: PMC6506716 DOI: 10.1016/j.bpj.2019.02.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 02/05/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022] Open
Abstract
Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in design of drugs and high-precision biosensors. In this study, we investigate initial release and rebinding of ligands to their binding sites grafted on a planar surface, a situation commonly observed in single-molecule experiments and that occurs in vivo, e.g., during exocytosis. Via scaling arguments and molecular dynamic simulations, we analyze the dependence of nonequilibrium rebinding kinetics on two intrinsic length scales: the average separation distance between the binding sites and the total diffusible volume (i.e., height of the experimental reservoir in which diffusion takes place or average distance between receptor-bearing surfaces). We obtain time-dependent scaling laws for on rates and for the cumulative number of rebinding events. For diffusion-limited binding, the (rebinding) on rate decreases with time via multiple power-law regimes before the terminal steady-state (constant on-rate) regime. At intermediate times, when particle density has not yet become uniform throughout the diffusible volume, the cumulative number of rebindings exhibits a novel, to our knowledge, plateau behavior because of the three-dimensional escape process of ligands from binding sites. The duration of the plateau regime depends on the average separation distance between binding sites. After the three-dimensional diffusive escape process, a one-dimensional diffusive regime describes on rates. In the reaction-limited scenario, ligands with higher affinity to their binding sites (e.g., longer residence times) delay entry to the power-law regimes. Our results will be useful for extracting hidden timescales in experiments such as kinetic rate measurements for ligand-receptor interactions in microchannels, as well as for cell signaling via diffusing molecules.
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Affiliation(s)
- Aykut Erbaş
- UNAM-National Nanotechnology Research Center and Institute of Materials Science & Nanotechnology, Bilkent University, Ankara, Turkey.
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois; Department of Physics and Astronomy, Northwestern University, Evanston, Illinois; Department of Chemistry, Northwestern University, Evanston, Illinois
| | - John F Marko
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois; Department of Molecular Biosciences, Northwestern University, Evanston, Illinois.
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43
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Liew ATF, Foo YH, Gao Y, Zangoui P, Singh MK, Gulvady R, Kenney LJ. Single cell, super-resolution imaging reveals an acid pH-dependent conformational switch in SsrB regulates SPI-2. eLife 2019; 8:e45311. [PMID: 31033442 PMCID: PMC6557628 DOI: 10.7554/elife.45311] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/28/2019] [Indexed: 12/29/2022] Open
Abstract
After Salmonella is phagocytosed, it resides in an acidic vacuole. Its cytoplasm acidifies to pH 5.6; acidification activates pathogenicity island 2 (SPI-2). SPI-2 encodes a type three secretion system whose effectors modify the vacuole, driving endosomal tubulation. Using super-resolution imaging in single bacterial cells, we show that low pH induces expression of the SPI-2 SsrA/B signaling system. Single particle tracking, atomic force microscopy, and single molecule unzipping assays identified pH-dependent stimulation of DNA binding by SsrB. A so-called phosphomimetic form (D56E) was unable to bind to DNA in live cells. Acid-dependent DNA binding was not intrinsic to regulators, as PhoP and OmpR binding was not pH-sensitive. The low level of SPI-2 injectisomes observed in single cells is not due to fluctuating SsrB levels. This work highlights the surprising role that acid pH plays in virulence and intracellular lifestyles of Salmonella; modifying acid survival pathways represents a target for inhibiting Salmonella.
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Affiliation(s)
- Andrew Tze Fui Liew
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yong Hwee Foo
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Yunfeng Gao
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Parisa Zangoui
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | | | - Ranjit Gulvady
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
| | - Linda J Kenney
- Mechanobiology Institute, T-LabNational University of SingaporeSingaporeSingapore
- Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonUnited States
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44
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Uluşeker C, Torres-Bacete J, García JL, Hanczyc MM, Nogales J, Kahramanoğulları O. Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels. Sci Rep 2019; 9:2076. [PMID: 30765722 PMCID: PMC6376016 DOI: 10.1038/s41598-018-38223-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 12/13/2018] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli have developed one of the most efficient regulatory response mechanisms to phosphate starvation. The machinery involves a cascade with a two-component system (TCS) that relays the external signal to the genetic circuit, resulting in a feedback response. Achieving a quantitative understanding of this system has implications in synthetic biology and biotechnology, for example, in applications for wastewater treatment. To this aim, we present a computational model and experimental results with a detailed description of the TCS, consisting of PhoR and PhoB, together with the mechanisms of gene expression. The model is parameterised within the feasible range, and fitted to the dynamic response of our experimental data on PhoB as well as PhoA, the product of this network that is used in alkaline phosphatase production. Deterministic and stochastic simulations with our model predict the regulation dynamics in higher external phosphate concentrations while reproducing the experimental observations. In a cycle of simulations and experimental verification, our model predicts and explores phenotypes with various synthetic promoter designs that can optimise the inorganic phosphate intake in E. coli. Sensitivity analysis demonstrates that the Pho-controlled genes have a significant influence over the phosphate response. Together with experimental findings, our model should thus provide insights for the investigations on engineering new sensors and regulators for living technologies.
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Affiliation(s)
- Cansu Uluşeker
- University of Trento, Centre for Integrative Biology, Trento, 38123, Italy.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto, 38068, Italy
| | - Jesús Torres-Bacete
- Centro Nacional de Biotecnología (CNB-CSIC), Systems Biology Department, Madrid, 28049, Spain
| | - José L García
- Centro de Investigaciones Biológicas (CIB-CSIC), Microbial and Plant Biotechnology Department, Madrid, 28040, Spain.,Institute for Integrative Systems Biology (I2Sysbio-CSIC-UV), Applied Systems Biology and Synthetic Biology Department, Paterna, 46980, Spain
| | - Martin M Hanczyc
- University of Trento, Centre for Integrative Biology, Trento, 38123, Italy.,Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Juan Nogales
- Centro Nacional de Biotecnología (CNB-CSIC), Systems Biology Department, Madrid, 28049, Spain
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45
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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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46
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Xie X, Cheng YS, Wen MH, Calindi A, Yang K, Chiu CW, Chen TY. Quantifying the Oligomeric States of Membrane Proteins in Cells through Super-Resolution Localizations. J Phys Chem B 2018; 122:10496-10504. [PMID: 30384609 DOI: 10.1021/acs.jpcb.8b10402] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Transitions between different oligomeric states of membrane proteins are essential for proper cellular functions. However, the quantification of their oligomeric states in cells is technically challenging. Here we developed a new method to quantify oligomeric state(s) of highly expressed membrane proteins using the probability density function of molecule density ( PDFMD) calculated from super-resolution localizations. We provided the theoretical model of PDFMD, discussed the effects of protein concentration, cell geometry, and photophysics of fluorescent proteins on PDFMD, and provided experimental criteria for proper quantification of oligomeric states. This method was further validated using simulated single-molecule fluorescent movies and applied to two membrane proteins, UhpT and SbmA in E. coli. The study shows that PDFMD is useful in quantifying oligomeric states of membrane proteins in cells that can help in understanding cellular tasks. Potential applications to proteins with higher oligomeric states under high concentration and limitations of our methodology were also discussed.
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Affiliation(s)
- Xihong Xie
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
| | - Yu-Shan Cheng
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
| | - Meng-Hsuan Wen
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
| | - Aparna Calindi
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
| | - Karen Yang
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
| | - Chi-Wei Chiu
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
| | - Tai-Yen Chen
- Department of Chemistry , University of Houston , Houston , Texas 77204 , United States
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47
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Zhu Q, Smith EA. Diaphanous-1 affects the nanoscale clustering and lateral diffusion of receptor for advanced glycation endproducts (RAGE). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1861:43-49. [PMID: 30401627 DOI: 10.1016/j.bbamem.2018.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 12/22/2022]
Abstract
The interactions between the cytoplasmic protein diaphanous-1 (Diaph1) and the receptor for advanced glycation endproducts (RAGE) drive the negative consequences of RAGE signaling in several disease processes. Reported in this work is how Diaph1 affects the nanoscale clustering and diffusion of RAGE measured using super-resolution stochastic optical reconstruction microscopy (STORM) and single particle tracking (SPT). Altering the Diaph1 binding site has a different impact on RAGE diffusion compared to when Diaph1 expression is reduced in HEK293 cells. In cells with reduced Diaph1 expression (RAGE-Diaph1-/-), the average RAGE diffusion coefficient is increased by 35%. RAGE diffusion is known to be influenced by the dynamics of the actin cytoskeleton. Actin labeling shows that a reduced Diaph1 expression leads to cells with reduced filopodia density and length. In contrast, when two RAGE amino acids that interact with Diaph1 are mutated (RAGERQ/AA), the average RAGE diffusion coefficient is decreased by 16%. Since RAGE diffusion is slowed when the interaction between Diaph1 and RAGE is disrupted, the interaction of the two proteins results in faster RAGE diffusion. In both RAGERQ/AA and RAGE-Diaph1-/- cells the number and size of RAGE clusters are decreased compared to cells expressing RAGE and native concentrations of Diaph1. This work shows that Diaph1 has a role in affecting RAGE clusters and diffusion.
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Affiliation(s)
- Qiaochu Zhu
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States
| | - Emily A Smith
- Department of Chemistry, Iowa State University, Ames, IA 50011, United States.
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48
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Xu ZQ, Dixon NE. Bacterial replisomes. Curr Opin Struct Biol 2018; 53:159-168. [PMID: 30292863 DOI: 10.1016/j.sbi.2018.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 01/18/2023]
Abstract
Bacterial replisomes are dynamic multiprotein DNA replication machines that are inherently difficult for structural studies. However, breakthroughs continue to come. The structures of Escherichia coli DNA polymerase III (core)-clamp-DNA subcomplexes solved by single-particle cryo-electron microscopy in both polymerization and proofreading modes and the discovery of the stochastic nature of the bacterial replisomes represent notable progress. The structures reveal an intricate interaction network in the polymerase-clamp subassembly, providing insights on how replisomes may work. Meantime, ensemble and single-molecule functional assays and fluorescence microscopy show that the bacterial replisomes can work in a decoupled and uncoordinated way, with polymerases quickly exchanging and both leading-strand and lagging-strand polymerases and the helicase working independently, contradictory to the elegant textbook view of a highly coordinated machine.
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Affiliation(s)
- Zhi-Qiang Xu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, and Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia.
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49
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Chen TY, Cheng YS, Huang PS, Chen P. Facilitated Unbinding via Multivalency-Enabled Ternary Complexes: New Paradigm for Protein-DNA Interactions. Acc Chem Res 2018; 51:860-868. [PMID: 29368512 DOI: 10.1021/acs.accounts.7b00541] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dynamic protein-DNA interactions constitute highly robust cellular machineries to fulfill cellular functions. A vast number of studies have focused on how DNA-binding proteins search for and interact with their target DNA segments and on what cellular cues can regulate protein binding, for which protein concentration is a most obvious one. In contrast, how protein unbinding could be regulated by protein concentration has evaded attention because protein unbinding from DNA is typically a unimolecular reaction and thus concentration independent. Recent single-molecule studies from multiple research groups have uncovered that protein concentration can facilitate the unbinding of DNA-bound proteins, revealing regulation of protein unbinding as another mechanistic paradigm for gene regulation. In this Account, we review these recent in vitro and in vivo single-molecule experiments that uncovered the concentration-facilitated protein unbinding by multiple types of DNA-binding proteins, including sequence-nonspecific DNA-binding proteins (e.g., nucleoid-associated proteins, NAP), sequence-specific DNA-binding proteins (e.g., metal-responsive transcription regulators CueR and ZntR), sequence-neutral single-stranded DNA-binding proteins (e.g., Replication protein A, RPA), and DNA polymerases. For the in vitro experiments, Marko's group investigated the exchange of GFP-tagged DNA-bound NAPs with nontagged NAPs in solution of increasing concentration using single-molecule magnetic-tweezers fluorescence microscopy. The faster fluorescence intensity decrease with higher nontagged NAP concentrations suggests that DNA-bound NAPs undergo faster exchange with higher free NAP concentrations. Chen's group used single-molecule fluorescence resonance energy transfer measurements to study the unbinding of CueR from its cognate oligomeric DNA. The average microscopic dwell times of DNA-bound states become shorter with increasing CueR concentrations in the surroundings, demonstrating that free CueR proteins can facilitate the unbinding of the incumbent one on DNA through either assisted dissociation or direct substitution. Greene's group studied the unbinding of RPAs from single-stranded DNA using total internal reflection fluorescence microscopy and DNA curtain techniques. The fluorescence intensity versus time traces show faster decay with higher wild-type RPA concentrations, indicating that DNA-bound RPAs can undergo a concentration-facilitated exchange when encountering excess free RPA. van Oijen's group investigated the leading/lagging-strand polymerase exchange events in the bacteriophage T7 and E. coli replication systems using a combination of single-molecule fluorescence microscopy and DNA-flow-stretching assay. The processivity was observed to have larger decrease when the concentration of the Y526F polymerase mutant increases, indicating that the unbinding of the polymerase is also concentration-dependent. Using stroboscopic imaging and single-molecule tracking, Chen's group further advanced their study into living bacterial cells. They found CueR, as well as its homologue ZntR, shows concentration-enhanced unbinding from its DNA-binding site in vivo. Mechanistic consensus has emerged from these in vitro and in vivo single-molecule studies that encompass a range of proteins with distinct biological functions. It involves multivalent contacts between protein and DNA. The multivalency enables the formation of ternary complexes as intermediates, which subsequently give rise to concentration-enhanced protein unbinding. As multivalent contacts are ubiquitous among DNA-interacting proteins, this multivalency-enabled facilitated unbinding mechanism thus provides a potentially general mechanistic paradigm in regulating protein-DNA interactions.
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Affiliation(s)
- Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Yu-Shan Cheng
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Pei-San Huang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Peng Chen
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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50
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Moringo NA, Shen H, Bishop LDC, Wang W, Landes CF. Enhancing Analytical Separations Using Super-Resolution Microscopy. Annu Rev Phys Chem 2018; 69:353-375. [PMID: 29490205 DOI: 10.1146/annurev-physchem-052516-045018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution microscopy is becoming an invaluable tool to investigate structure and dynamics driving protein interactions at interfaces. In this review, we highlight the applications of super-resolution microscopy for quantifying the physics and chemistry that occur between target proteins and stationary-phase supports during chromatographic separations. Our discussion concentrates on the newfound ability of super-resolved single-protein spectroscopy to inform theoretical parameters via quantification of adsorption-desorption dynamics, protein unfolding, and nanoconfined transport.
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Affiliation(s)
| | - Hao Shen
- Department of Chemistry, Rice University, Houston, Texas 77251, USA;
| | - Logan D C Bishop
- Department of Chemistry, Rice University, Houston, Texas 77251, USA;
| | - Wenxiao Wang
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, USA
| | - Christy F Landes
- Department of Chemistry, Rice University, Houston, Texas 77251, USA; .,Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77251, USA.,Smalley-Curl Institute, Rice University, Houston, Texas 77251, USA
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