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Morra R, Pratama F, Butterfield T, Tomazetto G, Young K, Lopez R, Dixon N. arfA antisense RNA regulates MscL excretory activity. Life Sci Alliance 2023; 6:e202301954. [PMID: 37012050 PMCID: PMC10070815 DOI: 10.26508/lsa.202301954] [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: 01/27/2023] [Revised: 03/20/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Excretion of cytoplasmic protein (ECP) is a commonly observed phenomenon in bacteria, and this partial extracellular localisation of the intracellular proteome has been implicated in a variety of stress response mechanisms. In response to hypoosmotic shock and ribosome stalling in Escherichia coli, ECP is dependent upon the presence of the large-conductance mechanosensitive channel and the alternative ribosome-rescue factor A gene products. However, it is not known if a mechanistic link exists between the corresponding genes and the respective stress response pathways. Here, we report that the corresponding mscL and arfA genes are commonly co-located on the genomes of Gammaproteobacteria and display overlap in their respective 3' UTR and 3' CDS. We show this unusual genomic arrangement permits an antisense RNA-mediated regulatory control between mscL and arfA, and this modulates MscL excretory activity in E. coli These findings highlight a mechanistic link between osmotic, translational stress responses and ECP in E. coli, further elucidating the previously unknown regulatory function of arfA sRNA.
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Affiliation(s)
- Rosa Morra
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Fenryco Pratama
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Institut Teknologi Bandung, Bandung, Indonesia
| | - Thomas Butterfield
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Geizecler Tomazetto
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Kate Young
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Ruth Lopez
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
| | - Neil Dixon
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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Gomez D, Peña Ccoa WJ, Singh Y, Rojas E, Hocky GM. Molecular Paradigms for Biological Mechanosensing. J Phys Chem B 2021; 125:12115-12124. [PMID: 34709040 DOI: 10.1021/acs.jpcb.1c06330] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many proteins in living cells are subject to mechanical forces, which can be generated internally by molecular machines, or externally, e.g., by pressure gradients. In general, these forces fall in the piconewton range, which is similar in magnitude to forces experienced by a molecule due to thermal fluctuations. While we would naively expect such moderate forces to produce only minimal changes, a wide variety of "mechanosensing" proteins have evolved with functions that are responsive to forces in this regime. The goal of this article is to provide a physical chemistry perspective on protein-based molecular mechanosensing paradigms used in living systems, and how these paradigms can be explored using novel computational methods.
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Affiliation(s)
- David Gomez
- Department of Biology, New York University, New York, New York 10003, United States.,Department of Chemistry, New York University, New York, New York 10003, United States
| | - Willmor J Peña Ccoa
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yuvraj Singh
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Enrique Rojas
- Department of Biology, New York University, New York, New York 10003, United States
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, New York 10003, United States
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3
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Phase separation in the outer membrane of Escherichia coli. Proc Natl Acad Sci U S A 2021; 118:2112237118. [PMID: 34716276 DOI: 10.1073/pnas.2112237118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/20/2021] [Indexed: 11/18/2022] Open
Abstract
Gram-negative bacteria are surrounded by a protective outer membrane (OM) with phospholipids in its inner leaflet and lipopolysaccharides (LPS) in its outer leaflet. The OM is also populated with many β-barrel outer-membrane proteins (OMPs), some of which have been shown to cluster into supramolecular assemblies. However, it remains unknown how abundant OMPs are organized across the entire bacterial surface and how this relates to the lipids in the membrane. Here, we reveal how the OM is organized from molecular to cellular length scales, using atomic force microscopy to visualize the OM of live bacteria, including engineered Escherichia coli strains and complemented by specific labeling of abundant OMPs. We find that a predominant OMP in the E. coli OM, the porin OmpF, forms a near-static network across the surface, which is interspersed with barren patches of LPS that grow and merge with other patches during cell elongation. Embedded within the porin network is OmpA, which forms noncovalent interactions to the underlying cell wall. When the OM is destabilized by mislocalization of phospholipids to the outer leaflet, a new phase appears, correlating with bacterial sensitivity to harsh environments. We conclude that the OM is a mosaic of phase-separated LPS-rich and OMP-rich regions, the maintenance of which is essential to the integrity of the membrane and hence to the lifestyle of a gram-negative bacterium.
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4
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Boldini A, Porfiri M. Inversion of Solvent Migration in Charged Membranes. PHYSICAL REVIEW LETTERS 2021; 127:156001. [PMID: 34678022 DOI: 10.1103/physrevlett.127.156001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/14/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
We theoretically demonstrate the possibility of inversion of solvent migration in charged membranes, opposing osmosis. Inversion of solvent migration is ascribed to the finite volume of ions in the solution permeating the membrane, a quantity that has been neglected in the literature so far. We propose a model of the electrochemistry in the proximity of an electrode, illustrating the range of the molar volume of ions that can yield the inversion of solvent migration. This study poses the basis for novel applications in microfluidics, nanofluidics, and electrochemistry, along with new inquiries in biology.
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Affiliation(s)
- Alain Boldini
- Department of Mechanical and Aerospace Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA
| | - Maurizio Porfiri
- Center for Urban Science and Progress, Department of Mechanical and Aerospace Engineering, and Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, USA
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Holt JR, Zeng WZ, Evans EL, Woo SH, Ma S, Abuwarda H, Loud M, Patapoutian A, Pathak MM. Spatiotemporal dynamics of PIEZO1 localization controls keratinocyte migration during wound healing. eLife 2021; 10:65415. [PMID: 34569935 PMCID: PMC8577841 DOI: 10.7554/elife.65415] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 09/24/2021] [Indexed: 12/17/2022] Open
Abstract
Keratinocytes, the predominant cell type of the epidermis, migrate to reinstate the epithelial barrier during wound healing. Mechanical cues are known to regulate keratinocyte re-epithelialization and wound healing; however, the underlying molecular transducers and biophysical mechanisms remain elusive. Here, we show through molecular, cellular, and organismal studies that the mechanically activated ion channel PIEZO1 regulates keratinocyte migration and wound healing. Epidermal-specific Piezo1 knockout mice exhibited faster wound closure while gain-of-function mice displayed slower wound closure compared to littermate controls. By imaging the spatiotemporal localization dynamics of endogenous PIEZO1 channels, we find that channel enrichment at some regions of the wound edge induces a localized cellular retraction that slows keratinocyte collective migration. In migrating single keratinocytes, PIEZO1 is enriched at the rear of the cell, where maximal retraction occurs, and we find that chemical activation of PIEZO1 enhances retraction during single as well as collective migration. Our findings uncover novel molecular mechanisms underlying single and collective keratinocyte migration that may suggest a potential pharmacological target for wound treatment. More broadly, we show that nanoscale spatiotemporal dynamics of Piezo1 channels can control tissue-scale events, a finding with implications beyond wound healing to processes as diverse as development, homeostasis, disease, and repair.
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Affiliation(s)
- Jesse R Holt
- Departmentof Physiology & Biophysics, UC Irvine, Irvine, United States.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, United States.,Center for Complex Biological Systems, UC Irvine, Irvine, United States
| | - Wei-Zheng Zeng
- Howard Hughes Medical Institute, Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Elizabeth L Evans
- Departmentof Physiology & Biophysics, UC Irvine, Irvine, United States.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, United States
| | - Seung-Hyun Woo
- Howard Hughes Medical Institute, Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Shang Ma
- Howard Hughes Medical Institute, Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Hamid Abuwarda
- Departmentof Physiology & Biophysics, UC Irvine, Irvine, United States.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, United States
| | - Meaghan Loud
- Howard Hughes Medical Institute, Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Ardem Patapoutian
- Howard Hughes Medical Institute, Department of Neuroscience, The Scripps Research Institute, La Jolla, United States
| | - Medha M Pathak
- Departmentof Physiology & Biophysics, UC Irvine, Irvine, United States.,Sue and Bill Gross Stem Cell Research Center, UC Irvine, Irvine, United States.,Center for Complex Biological Systems, UC Irvine, Irvine, United States.,Department of Biomedical Engineering, UC Irvine, Irvine, United States
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Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. SOFT MATTER 2021; 17:3798-3806. [PMID: 33629089 DOI: 10.1039/d0sm02012e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.
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Affiliation(s)
- Christian Vanhille-Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK.
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Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. SOFT MATTER 2020; 16:10628-10639. [PMID: 33084724 DOI: 10.1039/d0sm00712a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.
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Affiliation(s)
- V E Debets
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands.
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