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Di Terlizzi I, Gironella M, Herraez-Aguilar D, Betz T, Monroy F, Baiesi M, Ritort F. Variance sum rule for entropy production. Science 2024; 383:971-976. [PMID: 38422150 DOI: 10.1126/science.adh1823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 01/09/2024] [Indexed: 03/02/2024]
Abstract
Entropy production is the hallmark of nonequilibrium physics, quantifying irreversibility, dissipation, and the efficiency of energy transduction processes. Despite many efforts, its measurement at the nanoscale remains challenging. We introduce a variance sum rule (VSR) for displacement and force variances that permits us to measure the entropy production rate σ in nonequilibrium steady states. We first illustrate it for directly measurable forces, such as an active Brownian particle in an optical trap. We then apply the VSR to flickering experiments in human red blood cells. We find that σ is spatially heterogeneous with a finite correlation length, and its average value agrees with calorimetry measurements. The VSR paves the way to derive σ using force spectroscopy and time-resolved imaging in living and active matter.
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Affiliation(s)
- I Di Terlizzi
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden, Germany
- Dipartimento di Fisica e Astronomia, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - M Gironella
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, C/ Marti i Franques 1, 08028 Barcelona, Spain
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden
| | - D Herraez-Aguilar
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Ctra. Pozuelo-Majadahonda Km 1,800, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - T Betz
- Third Institute of Physics, Georg August Universität Göttingen, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - F Monroy
- Departamento de Química Física, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
- Translational Biophysics, Instituto de Investigación Sanitaria Hospital Doce de Octubre (IMAS12), Av. Andalucía, 28041 Madrid, Spain
| | - M Baiesi
- Dipartimento di Fisica e Astronomia, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
- INFN, Sezione di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, C/ Marti i Franques 1, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
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Liu L, Tang S, Liu T, Zhang Z, Wang X, Bilal M, Liu S, Luo H, Zhao Y, Duan X. Transcriptomic analysis approach towards an improved tolerance of Escherichia coli to gallic acid stress. Arch Microbiol 2023; 205:372. [PMID: 37934297 DOI: 10.1007/s00203-023-03708-4] [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: 09/08/2023] [Revised: 10/01/2023] [Accepted: 10/13/2023] [Indexed: 11/08/2023]
Abstract
As a natural green additive, gallic acid has been widely used in food production. However, it can inhibit the physiological metabolism of Escherichia coli, which severely limits the ability and efficiency of gallic acid production. To explore the adaptation mechanism of E. coli under gallic acid stress and further explore the target of genetic modification, the effects of gallic acid stress on the fermentation characteristics of E. coli W3110 ATCC (82057) were investigated by cell biomass and cell morphometry. Moreover, transcriptome analysis was used to analyze the gene transcription level of E. coli W3110 ATCC (82057) to explore effects of gallic acid stress on important essential physiological processes. The results showed that under high concentration of gallic acid, the biomass of E. coli W3110 ATCC (82057) decreased significantly and the cells showed irregular morphology. Transcriptome analysis showed that E. coli W3110 ATCC (82057) improved its adaptive capacity through three strategies. First, genes of bamD, ompC, and ompF encoding outer membrane protein BamD, OmpC, and OmpC were decreased 5-, 31.1- and 8.1-fold, respectively, under gallic acid stress compared to the control, leading to the reduction of gallic acid absorption. Moreover, genes (mdtA, mdtB, mdtC, mdtD, mdtE, and mdtF) related to MdtABC multidrug efflux system and multidrug efflux pump MdtEF were up-regulated by1.0-53.0 folds, respectively, and genes (aaeA, aaeB, and aaeX) related to AaeAB efflux system were up-regulated by 8.0-13.3 folds, respectively, which contributed to the excretion of gallic acid. In addition, genes of acid fitness island also were up-regulated by different degrees under the stress of an acidic environment to maintain the stability of the intracellular environment. In conclusion, E. coli W3110 ATCC (82057) would enhance its tolerance to gallic acid by reducing absorption, increasing excretion, and maintaining intracellular environment stability. This study provides research ideas for the construction of engineered strains with high gallic acid yield.
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Affiliation(s)
- Lina Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China.
| | - Shijie Tang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Tingting Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Zihao Zhang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Xuefeng Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Shuai Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Xuguo Duan
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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Gupta S, Soni J, Kumar A, Mandal T. Origin of the nonlinear structural and mechanical properties in oppositely curved lipid mixtures. J Chem Phys 2023; 159:165102. [PMID: 37873964 DOI: 10.1063/5.0167144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023] Open
Abstract
Structural and mechanical properties of membranes such as thickness, tail order, bending modulus and curvature energetics play crucial role in controlling various cellular functions that depend on the local lipid organization and membrane reshaping. While behavior of these biophysical properties are well understood in single component membranes, very little is known about how do they change in the mixed lipid membranes. Often various properties of the mixed lipid bilayers are assumed to change linearly with the mole fractions of the constituent lipids which, however, is true for "ideal" mixing only. In this study, using molecular dynamics simulations, we show that structural and mechanical properties of binary lipid mixture change nonlinearly with the lipid mole fractions, and the strength of the nonlinearity depends on two factors - spontaneous curvature difference and locally inhomogeneous interactions between the lipid components.
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Affiliation(s)
- Shivam Gupta
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Jatin Soni
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Awneesh Kumar
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Taraknath Mandal
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
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Surveying membrane landscapes: a new look at the bacterial cell surface. Nat Rev Microbiol 2023:10.1038/s41579-023-00862-w. [PMID: 36828896 DOI: 10.1038/s41579-023-00862-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 02/26/2023]
Abstract
Recent studies applying advanced imaging techniques are changing the way we understand bacterial cell surfaces, bringing new knowledge on everything from single-cell heterogeneity in bacterial populations to their drug sensitivity and mechanisms of antimicrobial resistance. In both Gram-positive and Gram-negative bacteria, the outermost surface of the bacterial cell is being imaged at nanoscale; as a result, topographical maps of bacterial cell surfaces can be constructed, revealing distinct zones and specific features that might uniquely identify each cell in a population. Functionally defined assembly precincts for protein insertion into the membrane have been mapped at nanoscale, and equivalent lipid-assembly precincts are suggested from discrete lipopolysaccharide patches. As we review here, particularly for Gram-negative bacteria, the applications of various modalities of nanoscale imaging are reawakening our curiosity about what is conceptually a 3D cell surface landscape: what it looks like, how it is made and how it provides resilience to respond to environmental impacts.
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Defeat undefeatable: ionic liquids as novel antimicrobial agents. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Turbant F, Waeytens J, Campidelli C, Bombled M, Martinez D, Grélard A, Habenstein B, Raussens V, Velez M, Wien F, Arluison V. Unraveling Membrane Perturbations Caused by the Bacterial Riboregulator Hfq. Int J Mol Sci 2022; 23:ijms23158739. [PMID: 35955871 PMCID: PMC9369112 DOI: 10.3390/ijms23158739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Hfq is a pleiotropic regulator that mediates several aspects of bacterial RNA metabolism. The protein notably regulates translation efficiency and RNA decay in Gram-negative bacteria, usually via its interaction with small regulatory RNAs. Previously, we showed that the Hfq C-terminal region forms an amyloid-like structure and that these fibrils interact with membranes. The immediate consequence of this interaction is a disruption of the membrane, but the effect on Hfq structure was unknown. To investigate details of the mechanism of interaction, the present work uses different in vitro biophysical approaches. We show that the Hfq C-terminal region influences membrane integrity and, conversely, that the membrane specifically affects the amyloid assembly. The reported effect of this bacterial master regulator on membrane integrity is discussed in light of the possible consequence on small regulatory RNA-based regulation.
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Affiliation(s)
- Florian Turbant
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jehan Waeytens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
- Institut de Chimie Physique, CNRS UMR8000, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Camille Campidelli
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Marianne Bombled
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Axelle Grélard
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), University of Bordeaux, CNRS, Bordeaux INP, 33600 Pessac, France
| | - Vincent Raussens
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Marisela Velez
- Instituto de Catálisis y Petroleoquímica, CSIC, c/Marie Curie, 2, Cantoblanco, E-28049 Madrid, Spain
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France
- Correspondence: (F.W.); (V.A.)
| | - Véronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR SDV, Université Paris Cité, 75006 Paris, France
- Correspondence: (F.W.); (V.A.)
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