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Szoke T, Goldberger O, Albocher-Kedem N, Barsheshet M, Dezorella N, Nussbaum-Shochat A, Wiener R, Schuldiner M, Amster-Choder O. Regulation of major bacterial survival strategies by transcripts sequestration in a membraneless organelle. Cell Rep 2023; 42:113393. [PMID: 37934665 DOI: 10.1016/j.celrep.2023.113393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/10/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
TmaR, the only known pole-localizer protein in Escherichia coli, was shown to cluster at the cell poles and control localization and activity of the major sugar regulator in a tyrosine phosphorylation-dependent manner. Here, we show that TmaR assembles by phase separation (PS) via heterotypic interactions with RNA in vivo and in vitro. An unbiased automated mutant screen combined with directed mutagenesis and genetic manipulations uncovered the importance of a predicted nucleic-acid-binding domain, a disordered region, and charged patches, one containing the phosphorylated tyrosine, for TmaR condensation. We demonstrate that, by protecting flagella-related transcripts, TmaR controls flagella production and, thus, cell motility and biofilm formation. These results connect PS in bacteria to survival and provide an explanation for the linkage between metabolism and motility. Intriguingly, a point mutation or increase in its cellular concentration induces irreversible liquid-to-solid transition of TmaR, similar to human disease-causing proteins, which affects cell morphology and division.
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Affiliation(s)
- Tamar Szoke
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Omer Goldberger
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Nitsan Albocher-Kedem
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Meshi Barsheshet
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Nili Dezorella
- Electron Microscopy Unit, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Nussbaum-Shochat
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel.
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Norris V, Kayser C, Muskhelishvili G, Konto-Ghiorghi Y. The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. FEMS Microbiol Rev 2023; 47:fuac049. [PMID: 36549664 DOI: 10.1093/femsre/fuac049] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organize their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the nucleoid-associated proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs, and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU, and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes, and hence in the phenotypes of daughter cells.
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Affiliation(s)
- Vic Norris
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Clara Kayser
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Georgi Muskhelishvili
- Agricultural University of Georgia, School of Natural Sciences, 0159 Tbilisi, Georgia
| | - Yoan Konto-Ghiorghi
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
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T N, Govindarajan S, Munavar MH. trans-translation system is important for maintaining genome integrity during DNA damage in bacteria. Res Microbiol 2023; 174:104136. [PMID: 37690591 DOI: 10.1016/j.resmic.2023.104136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
DNA integrity in bacteria is regulated by various factors that act on the DNA. trans-translation has previously been shown to be important for the survival of Escherichia coli cells exposed to certain DNA-damaging agents. However, the mechanisms underlying this sensitivity are poorly understood. In this study, we explored the involvement of the trans-translation system in the maintenance of genome integrity using various DNA-damaging agents and mutant backgrounds. Relative viability assays showed that SsrA-defective cells were sensitive to DNA-damaging agents, such as nalidixic acid (NA), ultraviolet radiation (UV), and methyl methanesulfonate (MMS). The viability of SsrA-defective cells was rescued by deleting sulA, although the expression of SulA was not more pronounced in SsrA-defective cells than in wild-type cells. Live cell imaging using a Gam-GFP fluorescent reporter showed increased double-strand breaks (DSBs) in SsrA-defective cells during DNA damage. We also showed that the ribosome rescue function of SsrA was sufficient for DNA damage tolerance. DNA damage sensitivity can be alleviated by partial uncoupling of transcription and translation by using sub-lethal concentrations of ribosome inhibiting antibiotic (tetracycline) or by mutating the gene coding for RNase H (rnhA). Taken together, our results highlight the importance of trans-translation system in maintaining genome integrity and bacterial survival during DNA damage.
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Affiliation(s)
- Nagarajan T
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India; Department of Biological Sciences, SRM University-AP, Amaravati, India
| | | | - M Hussain Munavar
- Department of Molecular Biology, School of Biological Sciences, Madurai Kamaraj University, Madurai, India.
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Competitive Coherence Generates Qualia in Bacteria and Other Living Systems. BIOLOGY 2021; 10:biology10101034. [PMID: 34681133 PMCID: PMC8533353 DOI: 10.3390/biology10101034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022]
Abstract
The relevance of bacteria to subjective experiences or qualia is underappreciated. Here, I make four proposals. Firstly, living systems traverse sequences of active states that determine their behaviour; these states result from competitive coherence, which depends on connectivity-based competition between a Next process and a Now process, whereby elements in the active state at time n+1 are chosen between the elements in the active state at time n and those elements in the developing n+1 state. Secondly, bacteria should help us link the mental to the physical world given that bacteria were here first, are highly complex, influence animal behaviour and dominate the Earth. Thirdly, the operation of competitive coherence to generate active states in bacteria, brains and other living systems is inseparable from qualia. Fourthly, these qualia become particularly important to the generation of active states in the highest levels of living systems, namely, the ecosystem and planetary levels.
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Tyrosine phosphorylation-dependent localization of TmaR that controls activity of a major bacterial sugar regulator by polar sequestration. Proc Natl Acad Sci U S A 2021; 118:2016017118. [PMID: 33376208 DOI: 10.1073/pnas.2016017118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The poles of Escherichia coli cells are emerging as hubs for major sensory systems, but the polar determinants that allocate their components to the pole are largely unknown. Here, we describe the discovery of a previously unannotated protein, TmaR, which localizes to the E. coli cell pole when phosphorylated on a tyrosine residue. TmaR is shown here to control the subcellular localization and activity of the general PTS protein Enzyme I (EI) by binding and polar sequestration of EI, thus regulating sugar uptake and metabolism. Depletion or overexpression of TmaR results in EI release from the pole or enhanced recruitment to the pole, which leads to increasing or decreasing the rate of sugar consumption, respectively. Notably, phosphorylation of TmaR is required to release EI and enable its activity. Like TmaR, the ability of EI to be recruited to the pole depends on phosphorylation of one of its tyrosines. In addition to hyperactivity in sugar consumption, the absence of TmaR also leads to detrimental effects on the ability of cells to survive in mild acidic conditions. Our results suggest that this survival defect, which is sugar- and EI-dependent, reflects the difficulty of cells lacking TmaR to enter stationary phase. Our study identifies TmaR as the first, to our knowledge, E. coli protein reported to localize in a tyrosine-dependent manner and to control the activity of other proteins by their polar sequestration and release.
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Belkahla H, Boudjemaa R, Caorsi V, Pineau D, Curcio A, Lomas JS, Decorse P, Chevillot-Biraud A, Azaïs T, Wilhelm C, Randriamahazaka H, Hémadi M. Carbon dots, a powerful non-toxic support for bioimaging by fluorescence nanoscopy and eradication of bacteria by photothermia. NANOSCALE ADVANCES 2019; 1:2571-2579. [PMID: 36132715 PMCID: PMC9418816 DOI: 10.1039/c9na00140a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/17/2019] [Indexed: 05/02/2023]
Abstract
Carbon Dots (CDs) are innovative materials which have potential applications in many fields, including nanomedicine, energy and catalysis. Here CDs were produced by the alkali-assisted ultrasonic route and characterized by several techniques to determine their composition and properties. Fluorescence nanoscopy using single-molecule localization microscopy shows that they have very good photophysical properties and a remarkable blinking behaviour at 405 nm. Moreover, these CDs are a safe material, non-toxic towards different cell lines (cancer and non-cancer cells) even at very high concentration, reflecting an excellent biocompatibility. Photothermia, i.e. their heating capacity under laser irradiation, was evaluated at two wavelengths and at several power densities. The resulting temperature increment was high (5 < ΔT < 45 °C) and appropriate for biomedical applications. Bioimaging and photothermia were then performed on E. coli, a Gram(-) bacterium, incubated with CDs. Remarkably, by photothermia at 680 nm (0.3, 1 and 1.9 W cm-2) or 808 nm (1.9 W cm-2), CDs are able to eradicate bacteria in their exponential and stationary phases. Images obtained by 3D super-resolution microscopy clearly show the different CD distributions in surviving bacteria after mild photothermal treatment. These results confirm that CDs are multifunctional materials with a wide range of biomedical applications.
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Affiliation(s)
- H Belkahla
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - R Boudjemaa
- Abbelight 6 rue Jean Calvin 75005 Paris France
| | - V Caorsi
- Abbelight 6 rue Jean Calvin 75005 Paris France
| | - D Pineau
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - A Curcio
- Laboratoire Matières et Systèmes Complexes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7057, 10 rue Alice Domon et Léonie Duquet 75205 Paris Cedex 13 France
| | - J S Lomas
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - P Decorse
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - A Chevillot-Biraud
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - T Azaïs
- Laboratoire de Chimie de la Matière Condensée de Paris, Sorbonne Université, CNRS-UMR 7574, Collège de France 4 place Jussieu 75005 Paris France
| | - C Wilhelm
- Laboratoire Matières et Systèmes Complexes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7057, 10 rue Alice Domon et Léonie Duquet 75205 Paris Cedex 13 France
| | - H Randriamahazaka
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
| | - M Hémadi
- Interfaces, Traitements, Organisation et Dynamique des Systèmes, Université Paris Diderot, Sorbonne Paris Cité CNRS-UMR 7086, 15 rue Jean-Antoine de Baïf 75205 Paris Cedex 13 France
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Norris V. Successive Paradigm Shifts in the Bacterial Cell Cycle and Related Subjects. Life (Basel) 2019; 9:E27. [PMID: 30866455 PMCID: PMC6462897 DOI: 10.3390/life9010027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 02/28/2019] [Accepted: 03/04/2019] [Indexed: 11/26/2022] Open
Abstract
A paradigm shift in one field can trigger paradigm shifts in other fields. This is illustrated by the paradigm shifts that have occurred in bacterial physiology following the discoveries that bacteria are not unstructured, that the bacterial cell cycle is not controlled by the dynamics of peptidoglycan, and that the growth rates of bacteria in the same steady-state population are not at all the same. These paradigm shifts are having an effect on longstanding hypotheses about the regulation of the bacterial cell cycle, which appear increasingly to be inadequate. I argue that, just as one earthquake can trigger others, an imminent paradigm shift in the regulation of the bacterial cell cycle will have repercussions or "paradigm quakes" on hypotheses about the origins of life and about the regulation of the eukaryotic cell cycle.
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Affiliation(s)
- Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, University of Rouen, 76821 Mont Saint Aignan, France.
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Jeckelmann JM, Erni B. Carbohydrate Transport by Group Translocation: The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System. Subcell Biochem 2019; 92:223-274. [PMID: 31214989 DOI: 10.1007/978-3-030-18768-2_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Bacterial Phosphoenolpyruvate (PEP) : Sugar Phosphotransferase System (PTS) mediates the uptake and phosphorylation of carbohydrates, and controls the carbon- and nitrogen metabolism in response to the availability of sugars. PTS occur in eubacteria and in a few archaebacteria but not in animals and plants. All PTS comprise two cytoplasmic phosphotransferase proteins (EI and HPr) and a species-dependent, variable number of sugar-specific enzyme II complexes (IIA, IIB, IIC, IID). EI and HPr transfer phosphorylgroups from PEP to the IIA units. Cytoplasmic IIA and IIB units sequentially transfer phosphates to the sugar, which is transported by the IIC and IICIID integral membrane protein complexes. Phosphorylation by IIB and translocation by IIC(IID) are tightly coupled. The IIC(IID) sugar transporters of the PTS are in the focus of this review. There are four structurally different PTS transporter superfamilies (glucose, glucitol, ascorbate, mannose) . Crystal structures are available for transporters of two superfamilies: bcIICmal (MalT, 5IWS, 6BVG) and bcIICchb (ChbC, 3QNQ) of B. subtilis from the glucose family, and IICasc (UlaA, 4RP9, 5ZOV) of E. coli from the ascorbate superfamily . They are homodimers and each protomer has an independent transport pathway which functions by an elevator-type alternating-access mechanism. bcIICmal and bcIICchb have the same fold, IICasc has a completely different fold. Biochemical and biophysical data accumulated in the past with the transporters for mannitol (IICBAmtl) and glucose (IICBglc) are reviewed and discussed in the context of the bcIICmal crystal structures. The transporters of the mannose superfamily are dimers of protomers consisting of a IIC and a IID protein chain. The crystal structure is not known and the topology difficult to predict. Biochemical data indicate that the IICIID complex employs a different transport mechanism . Species specific IICIID serve as a gateway for the penetration of bacteriophage lambda DNA across, and insertion of class IIa bacteriocins into the inner membrane. PTS transporters are inserted into the membrane by SecYEG translocon and have specific lipid requirements. Immunoelectron- and fluorescence microscopy indicate a non-random distribution and supramolecular complexes of PTS proteins.
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Affiliation(s)
- Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
| | - Bernhard Erni
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
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