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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [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: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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2
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Kaufmann A, Vigogne M, Neuendorf TA, Reverte-López M, Rivas G, Thiele J. Studying Nucleoid-Associated Protein-DNA Interactions Using Polymer Microgels as Synthetic Mimics. ACS Synth Biol 2023; 12:3695-3703. [PMID: 37965889 DOI: 10.1021/acssynbio.3c00488] [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] [Indexed: 11/16/2023]
Abstract
Microfluidically fabricated polymer microgels are used as an experimental platform to analyze protein-DNA interactions regulating bacterial cell division. In particular, we focused on the nucleoid-associated protein SlmA, which forms a nucleoprotein complex with short DNA binding sequences (SBS) that acts as a negative regulator of the division ring stability in Escherichia coli. To mimic the bacterial nucleoid as a dense DNA region of a bacterial cell and investigate the influence of charge and permeability on protein binding and diffusion in there, we have chosen nonionic polyethylene glycol and anionic hyaluronic acid as precursor materials for hydrogel formation, previously functionalized with SBS. SlmA binds specifically to the coupled SBS for both types of microgels while preferentially accumulating at the microgels' surface. We could control the binding specificity by adjusting the buffer composition of the DNA-functionalized microgels. The microgel charge did not impact protein binding; however, hyaluronic acid-based microgels exhibit a higher permeability, promoting protein diffusion; thus, they were the preferred choice for preparing nucleoid mimics. The approaches described here provide attractive tools for bottom-up reconstitution of essential cellular processes in media that more faithfully reproduce intracellular environments.
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Affiliation(s)
- Anika Kaufmann
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden, 01069 Dresden, Germany
| | - Michelle Vigogne
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden, 01069 Dresden, Germany
| | - Talika A Neuendorf
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden, 01069 Dresden, Germany
| | - María Reverte-López
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Julian Thiele
- Institute of Physical Chemistry and Polymer Physics, Leibniz Institute of Polymer Research Dresden, 01069 Dresden, Germany
- Institute of Chemistry, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
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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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Rivas G. Biophysical Reviews' "Meet the Editors Series"-a profile of Germán Rivas. Biophys Rev 2023; 15:151-156. [PMID: 37124917 PMCID: PMC10133429 DOI: 10.1007/s12551-023-01061-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
German Rivas is an executive editor of the IUPAB Biophysical Reviews journal based in Spain. As the head of the Department of Structural and Chemical Biology at the Center for Biological Research (CIB) Margarita Salas (one of the largest research institutes devoted to life sciences of the Spanish National Research Council (CSIC)), he leads a research program aimed at understanding the structure function relationship of large macromolecular complexes (involved in bacterial cell division) when placed in physiologically complex and "crowded" media toward their reconstitution from the bottom up in cell-like compartments. In this "Meet the Editors'" piece, he briefly describes his research interests and history.
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Affiliation(s)
- Germán Rivas
- Systems Biochemistry Lab, Department of Structural and Chemical Biology, CIB Margarita Salas – CSIC, 28040 Madrid, Spain
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5
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Paccione G, Robles-Ramos MÁ, Alfonso C, Sobrinos-Sanguino M, Margolin W, Zorrilla S, Monterroso B, Rivas G. Lipid Surfaces and Glutamate Anions Enhance Formation of Dynamic Biomolecular Condensates Containing Bacterial Cell Division Protein FtsZ and Its DNA-Bound Regulator SlmA. Biochemistry 2022; 61:2482-2489. [PMID: 36315857 PMCID: PMC9670838 DOI: 10.1021/acs.biochem.2c00424] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Dynamic biomolecular condensates formed by liquid-liquid phase separation can regulate the spatial and temporal organization of proteins, thus modulating their functional activity in cells. Previous studies showed that the cell division protein FtsZ from Escherichia coli formed dynamic phase-separated condensates with nucleoprotein complexes containing the FtsZ spatial regulator SlmA under crowding conditions, with potential implications for condensate-mediated spatiotemporal control of FtsZ activity in cell division. In the present study, we assessed formation of these condensates in the presence of lipid surfaces and glutamate ions to better approximate the E. coli intracellular environment. We found that potassium glutamate substantially promoted the formation of FtsZ-containing condensates when compared to potassium chloride in crowded solutions. These condensates accumulated on supported lipid bilayers and eventually fused, resulting in a time-dependent increase in the droplet size. Moreover, the accumulated condensates were dynamic, capturing protein from the external phase. FtsZ partitioned into the condensates at the lipid surface only in its guanosine diphosphate (GDP) form, regardless of whether it came from FtsZ polymer disassembly upon guanosine triphosphate (GTP) exhaustion. These results provide insights into the behavior of these GTP-responsive condensates in minimal membrane systems, which suggest how these membraneless assemblies may tune critical bacterial division events during the cell cycle.
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Affiliation(s)
- Gianfranco Paccione
- Centro
de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Miguel Á. Robles-Ramos
- Centro
de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Carlos Alfonso
- Centro
de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Marta Sobrinos-Sanguino
- Centro
de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, Texas 77030, United States
| | - Silvia Zorrilla
- Centro
de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain,E-mail:
| | - Begoña Monterroso
- Centro
de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain,E-mail:
| | - Germán Rivas
- Centro
de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain,E-mail:
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Godino E, Doerr A, Danelon C. Min waves without MinC can pattern FtsA-anchored FtsZ filaments on model membranes. Commun Biol 2022; 5:675. [PMID: 35798943 PMCID: PMC9262947 DOI: 10.1038/s42003-022-03640-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Although the essential proteins that drive bacterial cytokinesis have been identified, the precise mechanisms by which they dynamically interact to enable symmetrical division are largely unknown. In Escherichia coli, cell division begins with the formation of a proto-ring composed of FtsZ and its membrane-tethering proteins FtsA and ZipA. In the broadly proposed molecular scenario for ring positioning, Min waves composed of MinD and MinE distribute the FtsZ-polymerization inhibitor MinC away from mid-cell, where the Z-ring can form. Therefore, MinC is believed to be an essential element connecting the Min and FtsZ subsystems. Here, by combining cell-free protein synthesis with planar lipid membranes and microdroplets, we demonstrate that MinDE drive the formation of dynamic, antiphase patterns of FtsA-anchored FtsZ filaments even in the absence of MinC. These results suggest that Z-ring positioning may be achieved with a more minimal set of proteins than previously envisaged, providing a fresh perspective about synthetic cell division. Cell-free protein synthesis of bacterial cytokinesis factors reveals that MinDE surface waves regulate FtsA-anchored FtsZ filaments in time and space independently of MinC.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Anne Doerr
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands.
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7
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Robles-Ramos MÁ, Zorrilla S, Alfonso C, Margolin W, Rivas G, Monterroso B. Assembly of bacterial cell division protein FtsZ into dynamic biomolecular condensates. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118986. [PMID: 33581219 PMCID: PMC8529516 DOI: 10.1016/j.bbamcr.2021.118986] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 11/30/2022]
Abstract
Biomolecular condensation through phase separation may be a novel mechanism to regulate bacterial processes, including cell division. Previous work revealed that FtsZ, a protein essential for cytokinesis in most bacteria, forms biomolecular condensates with SlmA, a protein that protects the chromosome from damage inflicted by the division machinery in Escherichia coli. The absence of condensates composed solely of FtsZ under the conditions used in that study suggested this mechanism was restricted to nucleoid occlusion by SlmA or to bacteria containing this protein. Here we report that FtsZ alone, under physiologically relevant conditions, can demix into condensates in bulk and when encapsulated in synthetic cell-like systems generated by microfluidics. Condensate assembly depends on FtsZ being in the GDP-bound state and on conditions mimicking the crowded environment of the cytoplasm that promote its oligomerization. Condensates are dynamic and reversibly convert into filaments upon GTP addition. Notably, FtsZ lacking its C-terminal disordered region, a structural element likely to favor biomolecular condensation, also forms condensates, albeit less efficiently. The inherent tendency of FtsZ to form condensates susceptible to modulation by physiological factors, including binding partners, suggests that such mechanisms may play a more general role in bacterial division than initially envisioned.
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Affiliation(s)
- Miguel Ángel Robles-Ramos
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Silvia Zorrilla
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, TX 77030, USA
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.
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Zorrilla S, Monterroso B, Robles-Ramos MÁ, Margolin W, Rivas G. FtsZ Interactions and Biomolecular Condensates as Potential Targets for New Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10030254. [PMID: 33806332 PMCID: PMC7999717 DOI: 10.3390/antibiotics10030254] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
FtsZ is an essential and central protein for cell division in most bacteria. Because of its ability to organize into dynamic polymers at the cell membrane and recruit other protein partners to form a “divisome”, FtsZ is a leading target in the quest for new antibacterial compounds. Strategies to potentially arrest the essential and tightly regulated cell division process include perturbing FtsZ’s ability to interact with itself and other divisome proteins. Here, we discuss the available methodologies to screen for and characterize those interactions. In addition to assays that measure protein-ligand interactions in solution, we also discuss the use of minimal membrane systems and cell-like compartments to better approximate the native bacterial cell environment and hence provide a more accurate assessment of a candidate compound’s potential in vivo effect. We particularly focus on ways to measure and inhibit under-explored interactions between FtsZ and partner proteins. Finally, we discuss recent evidence that FtsZ forms biomolecular condensates in vitro, and the potential implications of these assemblies in bacterial resistance to antibiotic treatment.
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Affiliation(s)
- Silvia Zorrilla
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Miguel-Ángel Robles-Ramos
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, TX 77030, USA;
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
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Konto-Ghiorghi Y, Norris V. Hypothesis: nucleoid-associated proteins segregate with a parental DNA strand to generate coherent phenotypic diversity. Theory Biosci 2020; 140:17-25. [PMID: 33095418 DOI: 10.1007/s12064-020-00323-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/12/2020] [Indexed: 01/07/2023]
Abstract
The generation of a phenotypic diversity that is coherent across a bacterial population is a fundamental problem. We propose here that the DNA strand-specific segregation of certain nucleoid-associated proteins or NAPs results in these proteins being asymmetrically distributed to the daughter cells. We invoke a variety of mechanisms as responsible for this asymmetrical segregation including those based on differences between the leading and lagging strands, post-translational modifications, oligomerisation and association with membrane domains.
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Affiliation(s)
- Yoan Konto-Ghiorghi
- Laboratory of Microbiology Signals and Microenvironment, EA 4312, University of Rouen, 76821, Mont Saint Aignan, France
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, EA 4312, University of Rouen, 76821, Mont Saint Aignan, France.
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