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Xiu F, Knežević A, Huskens J, Kudernac T. Interplay of Depletion Forces and Biomolecular Recognition in the Hierarchical Assembly of Supramolecular Tubes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207098. [PMID: 36840672 DOI: 10.1002/smll.202207098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/27/2023] [Indexed: 05/25/2023]
Abstract
Crowding effects have a profound impact on the hierarchical organization of cellular architectures. In the fields of systems chemistry and soft matter, this effect has not received much attention so far. Here, it is explored how poly(ethylene glycol) (PEG) as a crowding agent invokes depletion forces that act on synthetic supramolecular tubes. Hence, supramolecular tubes are pushed from their random orientation into hierarchically assembled bundles due to the PEG-induced crowded environment. The resulting morphology of formed bundled architectures can be tuned by the concentrations of both the supramolecular tubes and the PEG. The introduction of biotin groups at the surface of the tubes allows the engineering of biotin-streptavidin crosslinks between them. The order of introducing PEG and streptavidin in the system further affects the formed hierarchical assemblies, as well as their resistance toward dilution. The strategy described here provides a new route to establish hierarchically organized supramolecular architectures, combining crowding and specific biomolecular interactions, which shows the potential for controlling the structure of supramolecular materials and other soft matter systems.
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Affiliation(s)
- Fangyuan Xiu
- Molecular Nanofabrication Group, MESA+ Institute, University of Twente, PO Box 207, Enschede, 7500 AE, The Netherlands
| | - Anamarija Knežević
- Molecular Nanofabrication Group, MESA+ Institute, University of Twente, PO Box 207, Enschede, 7500 AE, The Netherlands
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, 10000, Croatia
| | - Jurriaan Huskens
- Molecular Nanofabrication Group, MESA+ Institute, University of Twente, PO Box 207, Enschede, 7500 AE, The Netherlands
| | - Tibor Kudernac
- Molecular Nanofabrication Group, MESA+ Institute, University of Twente, PO Box 207, Enschede, 7500 AE, The Netherlands
- Faculty of Science and Engineering, Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
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Boiero Sanders M, Toret CP, Guillotin A, Antkowiak A, Vannier T, Robinson RC, Michelot A. Specialization of actin isoforms derived from the loss of key interactions with regulatory factors. EMBO J 2022; 41:e107982. [PMID: 35178724 PMCID: PMC8886540 DOI: 10.15252/embj.2021107982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
A paradox of eukaryotic cells is that while some species assemble a complex actin cytoskeleton from a single ortholog, other species utilize a greater diversity of actin isoforms. The physiological consequences of using different actin isoforms, and the molecular mechanisms by which highly conserved actin isoforms are segregated into distinct networks, are poorly known. Here, we sought to understand how a simple biological system, composed of a unique actin and a limited set of actin‐binding proteins, reacts to a switch to heterologous actin expression. Using yeast as a model system and biomimetic assays, we show that such perturbation causes drastic reorganization of the actin cytoskeleton. Our results indicate that defective interaction of a heterologous actin for important regulators of actin assembly limits certain actin assembly pathways while reinforcing others. Expression of two heterologous actin variants, each specialized in assembling a different network, rescues cytoskeletal organization and confers resistance to external perturbation. Hence, while species using a unique actin have homeostatic actin networks, actin assembly pathways in species using several actin isoforms may act more independently.
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Affiliation(s)
| | - Christopher P Toret
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Audrey Guillotin
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Adrien Antkowiak
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Thomas Vannier
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Alphée Michelot
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
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Hagan MF, Grason GM. Equilibrium mechanisms of self-limiting assembly. REVIEWS OF MODERN PHYSICS 2021; 93:025008. [PMID: 35221384 PMCID: PMC8880259 DOI: 10.1103/revmodphys.93.025008] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of self-limiting assembly, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories: self-closing assemblies and open-boundary assemblies. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.
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Affiliation(s)
- Michael F Hagan
- Martin Fisher School of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Gregory M Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA
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Abstract
As discovered over the past 25 years, the cytoskeletons of bacteria and archaea are complex systems of proteins whose central components are dynamic cytomotive filaments. They perform roles in cell division, DNA partitioning, cell shape determination and the organisation of intracellular components. The protofilament structures and polymerisation activities of various actin-like, tubulin-like and ESCRT-like proteins of prokaryotes closely resemble their eukaryotic counterparts but show greater diversity. Their activities are modulated by a wide range of accessory proteins but these do not include homologues of the motor proteins that supplement filament dynamics to aid eukaryotic cell motility. Numerous other filamentous proteins, some related to eukaryotic IF-proteins/lamins and dynamins etc, seem to perform structural roles similar to those in eukaryotes.
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Affiliation(s)
- Linda A Amos
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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Benetatos P, Jho Y. Bundling in semiflexible polymers: A theoretical overview. Adv Colloid Interface Sci 2016; 232:114-126. [PMID: 26813628 DOI: 10.1016/j.cis.2016.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 12/07/2015] [Accepted: 01/02/2016] [Indexed: 01/07/2023]
Abstract
Supramolecular assemblies of polymers are key modules to sustain the structure of cells and their function. The main elements of these assemblies are charged semiflexible polymers (polyelectrolytes) generally interacting via a long(er)-range repulsion and a short(er)-range attraction. The most common supramolecular structure formed by these polymers is the bundle. In the present paper, we critically review some recent theoretical and computational advances on the problem of bundle formation, and point a few promising directions for future work.
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Affiliation(s)
- Panayotis Benetatos
- Department of Physics, Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 702-701, South Korea
| | - YongSeok Jho
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, 790-784, South Korea; Department of Physics, Pohang University of Science and Technology, 790-784, South Korea.
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Türmer K, Orbán J, Gróf P, Nyitrai M. FASCIN and alpha-actinin can regulate the conformation of actin filaments. Biochim Biophys Acta Gen Subj 2015; 1850:1855-61. [PMID: 26025636 DOI: 10.1016/j.bbagen.2015.05.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 05/21/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND Actin filament bundling proteins mediate numerous processes in cells such as the formation of cell membrane protrusions or cell adhesions and stress fiber based locomotion. Among them alpha-actinin and fascin are the most abundant ones. This work characterizes differences in molecular motions in actin filaments due to the binding of these two actin bundling proteins. METHODS We investigated how alpha-actinin and fascin binding modify the conformation of actin filaments by using conventional and saturation transfer EPR methods. RESULTS The result characteristic for motions on the microsecond time scale showed that both actin bundling proteins made the bending and torsional twisting of the actin filaments slower. When nanosecond time scale molecular motions were described the two proteins were found to induce opposite changes in the actin filaments. The binding of one molecule of alpha-actinin or fascin modified the conformation of numerous actin protomers. CONCLUSION As fascin and alpha-actinin participates in different cellular processes their binding can serve the proper tuning of the structure of actin by establishing the right conformation for the interactions with other actin binding proteins. Our observations are in correlation with the model where actin filaments fulfill their biological functions under the regulation by actin-binding proteins. GENERAL SIGNIFICANCE Supporting the general model for the cellular regulation of the actin cytoskeleton we showed that two abundant actin bundling proteins, fascin and alpha-actinin, alter the conformation of actin filaments through long range allosteric interactions in two different ways providing the structural framework for the adaptation to specific biological functions.
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Affiliation(s)
- Katalin Türmer
- Department of Biophysics, Medical School, University of Pécs, Szigeti u. 12, Pécs H-7624, Hungary; János Szentágothai Research Center, Pécs H-7624, Hungary
| | - József Orbán
- Department of Biophysics, Medical School, University of Pécs, Szigeti u. 12, Pécs H-7624, Hungary; János Szentágothai Research Center, Pécs H-7624, Hungary; MTA-PTE High Intensity Terahertz Research Group, Hungary
| | - Pál Gróf
- Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, IX. Tűzoltó u. 37-47, Budapest H-1095, Hungary
| | - Miklós Nyitrai
- Department of Biophysics, Medical School, University of Pécs, Szigeti u. 12, Pécs H-7624, Hungary; János Szentágothai Research Center, Pécs H-7624, Hungary; MTA-PTE Nuclear-Mitochondrial Interactions Research Group, Hungary.
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Ku C, Lo WS, Kuo CH. Molecular evolution of the actin-like MreB protein gene family in wall-less bacteria. Biochem Biophys Res Commun 2014; 446:927-32. [DOI: 10.1016/j.bbrc.2014.03.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/10/2014] [Indexed: 01/01/2023]
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Saier MH. Microcompartments and protein machines in prokaryotes. J Mol Microbiol Biotechnol 2013; 23:243-69. [PMID: 23920489 DOI: 10.1159/000351625] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The prokaryotic cell was once thought of as a 'bag of enzymes' with little or no intracellular compartmentalization. In this view, most reactions essential for life occurred as a consequence of random molecular collisions involving substrates, cofactors and cytoplasmic enzymes. Our current conception of a prokaryote is far from this view. We now consider a bacterium or an archaeon as a highly structured, nonrandom collection of functional membrane-embedded and proteinaceous molecular machines, each of which serves a specialized function. In this article we shall present an overview of such microcompartments including (1) the bacterial cytoskeleton and the apparati allowing DNA segregation during cell division; (2) energy transduction apparati involving light-driven proton pumping and ion gradient-driven ATP synthesis; (3) prokaryotic motility and taxis machines that mediate cell movements in response to gradients of chemicals and physical forces; (4) machines of protein folding, secretion and degradation; (5) metabolosomes carrying out specific chemical reactions; (6) 24-hour clocks allowing bacteria to coordinate their metabolic activities with the daily solar cycle, and (7) proteinaceous membrane compartmentalized structures such as sulfur granules and gas vacuoles. Membrane-bound prokaryotic organelles were considered in a recent Journal of Molecular Microbiology and Biotechnology written symposium concerned with membranous compartmentalization in bacteria [J Mol Microbiol Biotechnol 2013;23:1-192]. By contrast, in this symposium, we focus on proteinaceous microcompartments. These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple noncompartmentalized cell.
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Affiliation(s)
- Milton H Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, Calif. 92093-0116, USA.
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Ludueña RF. A Hypothesis on the Origin and Evolution of Tubulin. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:41-185. [DOI: 10.1016/b978-0-12-407699-0.00002-9] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Baskin TI, Gu Y. Making parallel lines meet: transferring information from microtubules to extracellular matrix. Cell Adh Migr 2012; 6:404-8. [PMID: 22902763 PMCID: PMC3496676 DOI: 10.4161/cam.21121] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The extracellular matrix is constructed beyond the plasma membrane, challenging mechanisms for its control by the cell. In plants, the cell wall is highly ordered, with cellulose microfibrils aligned coherently over a scale spanning hundreds of cells. To a considerable extent, deploying aligned microfibrils determines mechanical properties of the cell wall, including strength and compliance. Cellulose microfibrils have long been seen to be aligned in parallel with an array of microtubules in the cell cortex. How do these cortical microtubules affect the cellulose synthase complex? This question has stood for as many years as the parallelism between the elements has been observed, but now an answer is emerging. Here, we review recent work establishing that the link between microtubules and microfibrils is mediated by a protein named cellulose synthase-interacting protein 1 (CSI1). The protein binds both microtubules and components of the cellulose synthase complex. In the absence of CSI1, microfibrils are synthesized but their alignment becomes uncoupled from the microtubules, an effect that is phenocopied in the wild type by depolymerizing the microtubules. The characterization of CSI1 significantly enhances knowledge of how cellulose is aligned, a process that serves as a paradigmatic example of how cells dictate the construction of their extracellular environment.
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Affiliation(s)
- Tobias I Baskin
- Biology Department, University of Massachusetts; Amherst, MA, USA.
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