1
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Boyd-Shiwarski CR, Shiwarski DJ, Subramanya AR. A New Phase for WNK Kinase Signaling Complexes as Biomolecular Condensates. Physiology (Bethesda) 2024; 39:0. [PMID: 38624245 DOI: 10.1152/physiol.00013.2024] [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: 02/22/2024] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024] Open
Abstract
The purpose of this review is to highlight transformative advances that have been made in the field of biomolecular condensates, with special emphasis on condensate material properties, physiology, and kinases, using the With-No-Lysine (WNK) kinases as a prototypical example. To convey how WNK kinases illustrate important concepts for biomolecular condensates, we start with a brief history, focus on defining features of biomolecular condensates, and delve into some examples of how condensates are implicated in cellular physiology (and pathophysiology). We then highlight how WNK kinases, through the action of "WNK droplets" that ubiquitously regulate intracellular volume and kidney-specific "WNK bodies" that are implicated in distal tubule salt reabsorption and potassium homeostasis, exemplify many of the defining features of condensates. Finally, this review addresses the controversies within this emerging field and questions to address.
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Affiliation(s)
- Cary R Boyd-Shiwarski
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
| | - Daniel J Shiwarski
- Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Arohan R Subramanya
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Pittsburgh Heart, Lung, Blood Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
- VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States
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2
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Wang G, Huang L, Zhuang S, Han F, Huang Q, Hao M, Lin G, Chen L, Shen B, Li F, Li X, Chen C, Gao Y, Mock T, Liang J. Resting cell formation in the marine diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2024; 243:1347-1360. [PMID: 38402560 DOI: 10.1111/nph.19646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/08/2024] [Indexed: 02/26/2024]
Abstract
Resting cells represent a survival strategy employed by diatoms to endure prolonged periods of unfavourable conditions. In the oceans, many diatoms sink at the end of their blooming season and therefore need to endure cold and dark conditions in the deeper layers of the water column. How they survive these conditions is largely unknown. We conducted an integrative analysis encompassing methods from histology, physiology, biochemistry, and genetics to reveal the biological mechanism of resting-cell formation in the model diatom Thalassiosira pseudonana. Resting-cell formation was triggered by a decrease in light and temperature with subsequent catabolism of storage compounds. Resting cells were characterised by an acidic and viscous cytoplasm and altered morphology of the chloroplast ultrastructure. The formation of resting cells in T. pseudonana is an energy demanding process required for a biophysical alteration of the cytosol and chloroplasts to endure the unfavourable conditions of the deeper ocean as photosynthetic organisms. However, most resting cells (> 90%) germinate upon return to favorable growth conditions.
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Affiliation(s)
- Guangning Wang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lu Huang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Shanshan Zhuang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Fang Han
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qianqian Huang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Mengyuan Hao
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Guifang Lin
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Longnan Chen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Biying Shen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Feng Li
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xuesong Li
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Changping Chen
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
| | - Yahui Gao
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
- State Key Laboratory of Marine Environment Science, Xiamen University, Xiamen, 361102, Fujian, China
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Junrong Liang
- School of Life Sciences, Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen Key Laboratory of Plant Genetics, Xiamen University, Xiamen, 361102, Fujian, China
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3
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Walker RM, Sanabria VC, Youk H. Microbial life in slow and stopped lanes. Trends Microbiol 2024; 32:650-662. [PMID: 38123400 PMCID: PMC11187706 DOI: 10.1016/j.tim.2023.11.014] [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: 10/16/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Microbes in nature often lack nutrients and face extreme or widely fluctuating temperatures, unlike microbes in growth-optimized settings in laboratories that much of the literature examines. Slowed or suspended lives are the norm for microbes. Studying them is important for understanding the consequences of climate change and for addressing fundamental questions about life: are there limits to how slowly a cell's life can progress, and how long cells can remain viable without self-replicating? Recent studies began addressing these questions with single-cell-level measurements and mathematical models. Emerging principles that govern slowed or suspended lives of cells - including lives of dormant spores and microbes at extreme temperatures - are re-defining discrete cellular states as continuums and revealing intracellular dynamics at new timescales. Nearly inactive, lifeless-appearing microbes are transforming our understanding of life.
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Affiliation(s)
- Rachel M Walker
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Valeria C Sanabria
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hyun Youk
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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4
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Ding M, Xu W, Pei G, Li P. Long way up: rethink diseases in light of phase separation and phase transition. Protein Cell 2024; 15:475-492. [PMID: 38069453 PMCID: PMC11214837 DOI: 10.1093/procel/pwad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/24/2023] [Indexed: 07/02/2024] Open
Abstract
Biomolecular condensation, driven by multivalency, serves as a fundamental mechanism within cells, facilitating the formation of distinct compartments, including membraneless organelles that play essential roles in various cellular processes. Perturbations in the delicate equilibrium of condensation, whether resulting in gain or loss of phase separation, have robustly been associated with cellular dysfunction and physiological disorders. As ongoing research endeavors wholeheartedly embrace this newly acknowledged principle, a transformative shift is occurring in our comprehension of disease. Consequently, significant strides have been made in unraveling the profound relevance and potential causal connections between abnormal phase separation and various diseases. This comprehensive review presents compelling recent evidence that highlight the intricate associations between aberrant phase separation and neurodegenerative diseases, cancers, and infectious diseases. Additionally, we provide a succinct summary of current efforts and propose innovative solutions for the development of potential therapeutics to combat the pathological consequences attributed to aberrant phase separation.
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Affiliation(s)
- Mingrui Ding
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- NuPhase Therapeutics, Beijing 100083, China
| | - Weifan Xu
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
- NuPhase Therapeutics, Beijing 100083, China
| | - Gaofeng Pei
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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5
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Urbanska M, Guck J. Single-Cell Mechanics: Structural Determinants and Functional Relevance. Annu Rev Biophys 2024; 53:367-395. [PMID: 38382116 DOI: 10.1146/annurev-biophys-030822-030629] [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: 02/23/2024]
Abstract
The mechanical phenotype of a cell determines its ability to deform under force and is therefore relevant to cellular functions that require changes in cell shape, such as migration or circulation through the microvasculature. On the practical level, the mechanical phenotype can be used as a global readout of the cell's functional state, a marker for disease diagnostics, or an input for tissue modeling. We focus our review on the current knowledge of structural components that contribute to the determination of the cellular mechanical properties and highlight the physiological processes in which the mechanical phenotype of the cells is of critical relevance. The ongoing efforts to understand how to efficiently measure and control the mechanical properties of cells will define the progress in the field and drive mechanical phenotyping toward clinical applications.
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Affiliation(s)
- Marta Urbanska
- Max Planck Institute for the Science of Light, Erlangen, Germany; ,
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jochen Guck
- Max Planck Institute for the Science of Light, Erlangen, Germany; ,
- Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
- Department of Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
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6
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Cairo LV, Hong X, Müller MBD, Yuste-Checa P, Jagadeesan C, Bracher A, Park SH, Hayer-Hartl M, Hartl FU. Stress-dependent condensate formation regulated by the ubiquitin-related modifier Urm1. Cell 2024:S0092-8674(24)00649-4. [PMID: 38942013 DOI: 10.1016/j.cell.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 04/12/2024] [Accepted: 06/08/2024] [Indexed: 06/30/2024]
Abstract
The ability of proteins and RNA to coalesce into phase-separated assemblies, such as the nucleolus and stress granules, is a basic principle in organizing membraneless cellular compartments. While the constituents of biomolecular condensates are generally well documented, the mechanisms underlying their formation under stress are only partially understood. Here, we show in yeast that covalent modification with the ubiquitin-like modifier Urm1 promotes the phase separation of a wide range of proteins. We find that the drop in cellular pH induced by stress triggers Urm1 self-association and its interaction with both target proteins and the Urm1-conjugating enzyme Uba4. Urmylation of stress-sensitive proteins promotes their deposition into stress granules and nuclear condensates. Yeast cells lacking Urm1 exhibit condensate defects that manifest in reduced stress resilience. We propose that Urm1 acts as a reversible molecular "adhesive" to drive protective phase separation of functionally critical proteins under cellular stress.
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Affiliation(s)
- Lucas V Cairo
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Xiaoyu Hong
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martin B D Müller
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Patricia Yuste-Checa
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Chandhuru Jagadeesan
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Bracher
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sae-Hun Park
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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7
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Sakai K, Kondo Y, Goto Y, Aoki K. Cytoplasmic fluidization contributes to breaking spore dormancy in fission yeast. Proc Natl Acad Sci U S A 2024; 121:e2405553121. [PMID: 38889144 PMCID: PMC11214080 DOI: 10.1073/pnas.2405553121] [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: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/20/2024] Open
Abstract
The cytoplasm is a complex, crowded environment that influences myriad cellular processes including protein folding and metabolic reactions. Recent studies have suggested that changes in the biophysical properties of the cytoplasm play a key role in cellular homeostasis and adaptation. However, it still remains unclear how cells control their cytoplasmic properties in response to environmental cues. Here, we used fission yeast spores as a model system of dormant cells to elucidate the mechanisms underlying regulation of the cytoplasmic properties. By tracking fluorescent tracer particles, we found that particle mobility decreased in spores compared to vegetative cells and rapidly increased at the onset of dormancy breaking upon glucose addition. This cytoplasmic fluidization depended on glucose-sensing via the cyclic adenosine monophosphate-protein kinase A pathway. PKA activation led to trehalose degradation through trehalase Ntp1, thereby increasing particle mobility as the amount of trehalose decreased. In contrast, the rapid cytoplasmic fluidization did not require de novo protein synthesis, cytoskeletal dynamics, or cell volume increase. Furthermore, the measurement of diffusion coefficients with tracer particles of different sizes suggests that the spore cytoplasm impedes the movement of larger protein complexes (40 to 150 nm) such as ribosomes, while allowing free diffusion of smaller molecules (~3 nm) such as second messengers and signaling proteins. Our experiments have thus uncovered a series of signaling events that enable cells to quickly fluidize the cytoplasm at the onset of dormancy breaking.
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Affiliation(s)
- Keiichiro Sakai
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
| | - Yohei Kondo
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Yuhei Goto
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
| | - Kazuhiro Aoki
- Quantitative Biology Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Quantitative Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji-cho, Okazaki, Aichi444-8787, Japan
- Division of Integrated Life Science, Department of Gene Mechanisms, Laboratory of Cell Cycle Regulation, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
- Center for Living Systems Information Science, Graduate School of Biostudies, Kyoto University, Kyoto606-8315, Japan
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8
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Hugener J, Xu J, Wettstein R, Ioannidi L, Velikov D, Wollweber F, Henggeler A, Matos J, Pilhofer M. FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis. Cell 2024; 187:3303-3318.e18. [PMID: 38906101 DOI: 10.1016/j.cell.2024.04.026] [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: 08/11/2023] [Revised: 02/06/2024] [Accepted: 04/19/2024] [Indexed: 06/23/2024]
Abstract
Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly understood. Here, we visualized budding yeast cells undergoing meiosis by cryo-electron tomography (cryoET) and discovered elaborate filamentous assemblies decorating the nucleus, cytoplasm, and mitochondria. To determine filament composition, we developed a "filament identification" (FilamentID) workflow that combines multiscale cryoET/cryo-electron microscopy (cryoEM) analyses of partially lysed cells or organelles. FilamentID identified the mitochondrial filaments as being composed of the conserved aldehyde dehydrogenase Ald4ALDH2 and the nucleoplasmic/cytoplasmic filaments as consisting of acetyl-coenzyme A (CoA) synthetase Acs1ACSS2. Structural characterization further revealed the mechanism underlying polymerization and enabled us to genetically perturb filament formation. Acs1 polymerization facilitates the recovery of chronologically aged spores and, more generally, the cell cycle re-entry of starved cells. FilamentID is broadly applicable to characterize filaments of unknown identity in diverse cellular contexts.
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Affiliation(s)
- Jannik Hugener
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Jingwei Xu
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Rahel Wettstein
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Lydia Ioannidi
- Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Daniel Velikov
- Max Perutz Labs, University of Vienna, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Florian Wollweber
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Adrian Henggeler
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Joao Matos
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
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9
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Boersma AJ. DNA and mRNA as molecular speed bumps in Escherichia coli's cytoplasm. Biophys J 2024; 123:1165-1166. [PMID: 38616488 PMCID: PMC11140458 DOI: 10.1016/j.bpj.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024] Open
Affiliation(s)
- Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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10
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Cereghetti G, Kissling VM, Koch LM, Arm A, Schmidt CC, Thüringer Y, Zamboni N, Afanasyev P, Linsenmeier M, Eichmann C, Kroschwald S, Zhou J, Cao Y, Pfizenmaier DM, Wiegand T, Cadalbert R, Gupta G, Boehringer D, Knowles TPJ, Mezzenga R, Arosio P, Riek R, Peter M. An evolutionarily conserved mechanism controls reversible amyloids of pyruvate kinase via pH-sensing regions. Dev Cell 2024:S1534-5807(24)00271-5. [PMID: 38788715 DOI: 10.1016/j.devcel.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/15/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024]
Abstract
Amyloids are known as irreversible aggregates associated with neurodegenerative diseases. However, recent evidence shows that a subset of amyloids can form reversibly and fulfill essential cellular functions. Yet, the molecular mechanisms regulating functional amyloids and distinguishing them from pathological aggregates remain unclear. Here, we investigate the conserved principles of amyloid reversibility by studying the essential metabolic enzyme pyruvate kinase (PK) in yeast and human cells. We demonstrate that yeast PK (Cdc19) and human PK (PKM2) form reversible amyloids through a pH-sensitive amyloid core. Stress-induced cytosolic acidification promotes aggregation via protonation of specific glutamate (yeast) or histidine (human) residues within the amyloid core. Mutations mimicking protonation cause constitutive PK aggregation, while non-protonatable PK mutants remain soluble even upon stress. Physiological PK aggregation is coupled to metabolic rewiring and glycolysis arrest, causing severe growth defects when misregulated. Our work thus identifies an evolutionarily conserved, potentially widespread mechanism regulating functional amyloids during stress.
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Affiliation(s)
- Gea Cereghetti
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK.
| | - Vera M Kissling
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland; Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | - Lisa M Koch
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Alexandra Arm
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Claudia C Schmidt
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yannik Thüringer
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Pavel Afanasyev
- Cryo-EM Knowledge Hub (CEMK), ETH Zurich, 8093 Zürich, Switzerland
| | - Miriam Linsenmeier
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Sonja Kroschwald
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jiangtao Zhou
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Yiping Cao
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Dorota M Pfizenmaier
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Thomas Wiegand
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland; Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Govind Gupta
- Particles-Biology Interactions Laboratory, Department of Materials Meet Life, Empa, 9014 St. Gallen, Switzerland
| | | | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, UK
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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11
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Pouliquen DL. The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research. Front Cell Dev Biol 2024; 12:1403037. [PMID: 38803391 PMCID: PMC11128620 DOI: 10.3389/fcell.2024.1403037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.
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Affiliation(s)
- Daniel L. Pouliquen
- Inserm, CNRS, CRCINA, Nantes Université, University of Angers, Angers, France
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12
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Jung HJ, Pham TD, Su XT, Grigore TV, Hoenderop JG, Olauson H, Wall SM, Ellison DH, Welling PA, Al-Qusairi L. Klotho is highly expressed in the chief sites of regulated potassium secretion, and it is stimulated by potassium intake. Sci Rep 2024; 14:10740. [PMID: 38729987 PMCID: PMC11087591 DOI: 10.1038/s41598-024-61481-w] [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: 10/27/2023] [Accepted: 05/06/2024] [Indexed: 05/12/2024] Open
Abstract
Klotho regulates many pathways in the aging process, but it remains unclear how it is physiologically regulated. Because Klotho is synthesized, cleaved, and released from the kidney; activates the chief urinary K+ secretion channel (ROMK) and stimulates urinary K+ secretion, we explored if Klotho protein is regulated by dietary K+ and the potassium-regulatory hormone, Aldosterone. Klotho protein along the nephron was evaluated in humans and in wild-type (WT) mice; and in mice lacking components of Aldosterone signaling, including the Aldosterone-Synthase KO (AS-KO) and the Mineralocorticoid-Receptor KO (MR-KO) mice. We found the specific cells of the distal nephron in humans and mice that are chief sites of regulated K+ secretion have the highest Klotho protein expression along the nephron. WT mice fed K+-rich diets increased Klotho expression in these cells. AS-KO mice exhibit normal Klotho under basal conditions but could not upregulate Klotho in response to high-K+ intake in the K+-secreting cells. Similarly, MR-KO mice exhibit decreased Klotho protein expression. Together, i) Klotho is highly expressed in the key sites of regulated K+ secretion in humans and mice, ii) In mice, K+-rich diets increase Klotho expression specifically in the potassium secretory cells of the distal nephron, iii) Aldosterone signaling is required for Klotho response to high K+ intake.
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Affiliation(s)
- Hyun Jun Jung
- Department of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Truyen D Pham
- Department of Nephrology, Emory University School of Medicine, Atlanta, GA, USA
| | - Xiao-Tong Su
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health and Science University, Portland, USA
| | - Teodora Veronica Grigore
- Department of Medical BioSciences, Radboud Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost G Hoenderop
- Department of Medical BioSciences, Radboud Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannes Olauson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Susan M Wall
- Department of Nephrology, Emory University School of Medicine, Atlanta, GA, USA
| | - David H Ellison
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health and Science University, Portland, USA
| | - Paul A Welling
- Department of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lama Al-Qusairi
- Department of Nephrology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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13
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Wu W, Ishamuddin SH, Quinn TW, Yerrum S, Zhang Y, Debaize LL, Kao PL, Duquette SM, Murakami MA, Mohseni M, Chow KH, Miettinen TP, Ligon KL, Manalis SR. Measuring single-cell density with high throughput enables dynamic profiling of immune cell and drug response from patient samples. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591092. [PMID: 38712225 PMCID: PMC11071500 DOI: 10.1101/2024.04.25.591092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Cell density, the ratio of cell mass to volume, is an indicator of molecular crowding and therefore a fundamental determinant of cell state and function. However, existing density measurements lack the precision or throughput to quantify subtle differences in cell states, particularly in primary samples. Here we present an approach for measuring the density of 30,000 single cells per hour with a precision of 0.03% (0.0003 g/mL) by integrating fluorescence exclusion microscopy with a suspended microchannel resonator. Applying this approach to human lymphocytes, we discovered that cell density and its variation decrease as cells transition from quiescence to a proliferative state, suggesting that the level of molecular crowding decreases and becomes more regulated upon entry into the cell cycle. Using a pancreatic cancer patient-derived xenograft model, we found that the ex vivo density response of primary tumor cells to drug treatment can predict in vivo tumor growth response. Our method reveals unexpected behavior in molecular crowding during cell state transitions and suggests density as a new biomarker for functional precision medicine.
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Affiliation(s)
- Weida Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St building 76, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames St #56-651, Cambridge, MA 02139, USA
| | - Sarah H. Ishamuddin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St building 76, Cambridge, MA 02139, USA
| | - Thomas W. Quinn
- Center for Patient-Derived Models, Dana-Farber Cancer Institute, 21 Burlington Ave, Boston, MA 02215, USA
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Smitha Yerrum
- Center for Patient-Derived Models, Dana-Farber Cancer Institute, 21 Burlington Ave, Boston, MA 02215, USA
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Ye Zhang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St building 76, Cambridge, MA 02139, USA
| | - Lydie L. Debaize
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Pei-Lun Kao
- Center for Patient-Derived Models, Dana-Farber Cancer Institute, 21 Burlington Ave, Boston, MA 02215, USA
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Sarah Marie Duquette
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St building 76, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames St #56-651, Cambridge, MA 02139, USA
| | - Mark A. Murakami
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Morvarid Mohseni
- Oncology Discovery, Bristol-Myers Squibb, 250 Water St, Cambridge, MA 02141, USA
| | - Kin-Hoe Chow
- Center for Patient-Derived Models, Dana-Farber Cancer Institute, 21 Burlington Ave, Boston, MA 02215, USA
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Teemu P. Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St building 76, Cambridge, MA 02139, USA
| | - Keith L. Ligon
- Center for Patient-Derived Models, Dana-Farber Cancer Institute, 21 Burlington Ave, Boston, MA 02215, USA
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
- Department of Pathology, Brigham & Women’s Hospital, Harvard Medical School, 75 Francis St, Boston, MA 02215, USA
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
| | - Scott R. Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St building 76, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 21 Ames St #56-651, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, 415 Main St, Cambridge, MA 02142, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 33 Massachusetts Ave, Cambridge, MA 02139, USA
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14
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Vizjak P, Kamp D, Hepp N, Scacchetti A, Gonzalez Pisfil M, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. Nat Struct Mol Biol 2024:10.1038/s41594-024-01290-x. [PMID: 38664566 DOI: 10.1038/s41594-024-01290-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/25/2024] [Indexed: 05/07/2024]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. Here we investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner, qualitatively agree with our data. We speculate that monkey-bar mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
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Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Early Stage Bioprocess Development, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- ViraTherapeutics GmbH, Rum, Austria
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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15
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Magkiriadou S, Stepp WL, Newman DK, Manley S, Racki LR. Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2024; 121:e2313004121. [PMID: 38564631 PMCID: PMC11009631 DOI: 10.1073/pnas.2313004121] [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: 08/21/2023] [Accepted: 01/26/2024] [Indexed: 04/04/2024] Open
Abstract
Polyphosphate (polyP) synthesis is a ubiquitous stress and starvation response in bacteria. In diverse species, mutants unable to make polyP have a wide variety of physiological defects, but the mechanisms by which this simple polyanion exerts its effects remain unclear. One possibility is that polyP's many functions stem from global effects on the biophysical properties of the cell. We characterize the effect of polyphosphate on cytoplasmic mobility under nitrogen-starvation conditions in the opportunistic pathogen Pseudomonas aeruginosa. Using fluorescence microscopy and particle tracking, we quantify the motion of chromosomal loci and cytoplasmic tracer particles. In the absence of polyP and upon starvation, we observe a 2- to 10-fold increase in mean cytoplasmic diffusivity. Tracer particles reveal that polyP also modulates the partitioning between a "more mobile" and a "less mobile" population: Small particles in cells unable to make polyP are more likely to be "mobile" and explore more of the cytoplasm, particularly during starvation. Concomitant with this larger freedom of motion in polyP-deficient cells, we observe decompaction of the nucleoid and an increase in the steady-state concentration of ATP. The dramatic polyP-dependent effects we observe on cytoplasmic transport properties occur under nitrogen starvation, but not carbon starvation, suggesting that polyP may have distinct functions under different types of starvation.
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Affiliation(s)
- Sofia Magkiriadou
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Willi L. Stepp
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Dianne K. Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA91125
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA91125
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of Physics, École Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Lisa R. Racki
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, San Diego, CA92037
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16
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Sun X, Zhou Y, Wang Z, Peng M, Wei X, Xie Y, Wen C, Liu J, Ye M. Biomolecular Condensates Decipher Molecular Codes of Cell Fate: From Biophysical Fundamentals to Therapeutic Practices. Int J Mol Sci 2024; 25:4127. [PMID: 38612940 PMCID: PMC11012904 DOI: 10.3390/ijms25074127] [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: 02/29/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
Cell fate is precisely modulated by complex but well-tuned molecular signaling networks, whose spatial and temporal dysregulation commonly leads to hazardous diseases. Biomolecular condensates (BCs), as a newly emerging type of biophysical assemblies, decipher the molecular codes bridging molecular behaviors, signaling axes, and clinical prognosis. Particularly, physical traits of BCs play an important role; however, a panoramic view from this perspective toward clinical practices remains lacking. In this review, we describe the most typical five physical traits of BCs, and comprehensively summarize their roles in molecular signaling axes and corresponding major determinants. Moreover, establishing the recent observed contribution of condensate physics on clinical therapeutics, we illustrate next-generation medical strategies by targeting condensate physics. Finally, the challenges and opportunities for future medical development along with the rapid scientific and technological advances are highlighted.
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Affiliation(s)
- Xing Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Yangyang Zhou
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Zhiyan Wang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Menglan Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Xianhua Wei
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
| | - Yifang Xie
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Chengcai Wen
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Jing Liu
- Molecular Biology Research Center and Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410000, China; (Y.X.); (C.W.)
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China; (X.S.); (Y.Z.); (Z.W.); (M.P.); (X.W.)
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17
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Ye Y, Homer HA. A surge in cytoplasmic viscosity triggers nuclear remodeling required for Dux silencing and pre-implantation embryo development. Cell Rep 2024; 43:113917. [PMID: 38446665 DOI: 10.1016/j.celrep.2024.113917] [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: 08/23/2023] [Revised: 12/17/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Embryonic genome activation (EGA) marks the transition from dependence on maternal transcripts to an embryonic transcriptional program. The precise temporal regulation of gene expression, specifically the silencing of the Dux/murine endogenous retrovirus type L (MERVL) program during late 2-cell interphase, is crucial for developmental progression in mouse embryos. How this finely tuned regulation is achieved within this specific window is poorly understood. Here, using particle-tracking microrheology throughout the mouse oocyte-to-embryo transition, we identify a surge in cytoplasmic viscosity specific to late 2-cell interphase brought about by high microtubule and endomembrane density. Importantly, preventing the rise in 2-cell viscosity severely impairs nuclear reorganization, resulting in a persistently open chromatin configuration and failure to silence Dux/MERVL. This, in turn, derails embryo development beyond the 2- and 4-cell stages. Our findings reveal a mechanical role of the cytoplasm in regulating Dux/MERVL repression via nuclear remodeling during a temporally confined period in late 2-cell interphase.
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Affiliation(s)
- Yunan Ye
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia
| | - Hayden Anthony Homer
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia.
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18
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Laporte D, Massoni-Laporte A, Lefranc C, Dompierre J, Mauboules D, Nsamba ET, Royou A, Gal L, Schuldiner M, Gupta ML, Sagot I. A stable microtubule bundle formed through an orchestrated multistep process controls quiescence exit. eLife 2024; 12:RP89958. [PMID: 38527106 PMCID: PMC10963028 DOI: 10.7554/elife.89958] [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] [Indexed: 03/27/2024] Open
Abstract
Cells fine-tune microtubule assembly in both space and time to give rise to distinct edifices with specific cellular functions. In proliferating cells, microtubules are highly dynamics, and proliferation cessation often leads to their stabilization. One of the most stable microtubule structures identified to date is the nuclear bundle assembled in quiescent yeast. In this article, we characterize the original multistep process driving the assembly of this structure. This Aurora B-dependent mechanism follows a precise temporality that relies on the sequential actions of kinesin-14, kinesin-5, and involves both microtubule-kinetochore and kinetochore-kinetochore interactions. Upon quiescence exit, the microtubule bundle is disassembled via a cooperative process involving kinesin-8 and its full disassembly is required prior to cells re-entry into proliferation. Overall, our study provides the first description, at the molecular scale, of the entire life cycle of a stable microtubule structure in vivo and sheds light on its physiological function.
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Affiliation(s)
| | | | | | | | | | - Emmanuel T Nsamba
- Genetics, Development, and Cell Biology, Iowa State UniversityAmesUnited States
| | - Anne Royou
- Univ. Bordeaux, CNRS, IBGC, UMR 5095BordeauxFrance
| | - Lihi Gal
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Mohan L Gupta
- Genetics, Development, and Cell Biology, Iowa State UniversityAmesUnited States
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19
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [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] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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20
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Sposini V, Nampoothiri S, Chechkin A, Orlandini E, Seno F, Baldovin F. Being Heterogeneous Is Advantageous: Extreme Brownian Non-Gaussian Searches. PHYSICAL REVIEW LETTERS 2024; 132:117101. [PMID: 38563912 DOI: 10.1103/physrevlett.132.117101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/15/2023] [Accepted: 02/01/2024] [Indexed: 04/04/2024]
Abstract
Redundancy in biology may be explained by the need to optimize extreme searching processes, where one or few among many particles are requested to reach the target like in human fertilization. We show that non-Gaussian rare fluctuations in Brownian diffusion dominates such searches, introducing drastic corrections to the known Gaussian behavior. Our demonstration entails different physical systems and pinpoints the relevance of diversity within redundancy to boost fast targeting. We sketch an experimental context to test our results: polydisperse systems.
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Affiliation(s)
- Vittoria Sposini
- Faculty of Physics, University of Vienna, Kolingasse 14-16, 1090 Vienna, Austria
| | - Sankaran Nampoothiri
- Department of Physics, Gandhi Institute of Technology and Management (GITAM) University, Bengaluru 561203, India
| | - Aleksei Chechkin
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wroclaw University of Science and Technology, Wyspianskiego Str. 27, 50-370 Wroclaw, Poland
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Akhiezer Institute for Theoretical Physics, 61108 Kharkov, Ukraine
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia 'G. Galilei' - DFA, Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova (PD), Italy
| | - Flavio Seno
- Dipartimento di Fisica e Astronomia 'G. Galilei' - DFA, Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova (PD), Italy
| | - Fulvio Baldovin
- Dipartimento di Fisica e Astronomia 'G. Galilei' - DFA, Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova (PD), Italy
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21
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Sposini V, Nampoothiri S, Chechkin A, Orlandini E, Seno F, Baldovin F. Being heterogeneous is disadvantageous: Brownian non-Gaussian searches. Phys Rev E 2024; 109:034120. [PMID: 38632764 DOI: 10.1103/physreve.109.034120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/01/2024] [Indexed: 04/19/2024]
Abstract
Diffusing diffusivity models, polymers in the grand canonical ensemble and polydisperse, and continuous-time random walks all exhibit stages of non-Gaussian diffusion. Is non-Gaussian targeting more efficient than Gaussian? We address this question, central to, e.g., diffusion-limited reactions and some biological processes, through a general approach that makes use of Jensen's inequality and that encompasses all these systems. In terms of customary mean first-passage time, we show that Gaussian searches are more effective than non-Gaussian ones. A companion paper argues that non-Gaussianity becomes instead highly more efficient in applications where only a small fraction of tracers is required to reach the target.
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Affiliation(s)
- Vittoria Sposini
- Faculty of Physics, University of Vienna, Kolingasse 14-16, 1090 Vienna, Austria
| | - Sankaran Nampoothiri
- Department of Physics, Gandhi Institute of Technology and Management (GITAM) University, Bengaluru 561203, India
| | - Aleksei Chechkin
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wroclaw University of Science and Technology, Wyspianskiego Street 27, 50-370 Wroclaw, Poland
- Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Akhiezer Institute for Theoretical Physics, 61108 Kharkov, Ukraine
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia 'G. Galilei' - DFA, Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova (PD), Italy
| | - Flavio Seno
- Dipartimento di Fisica e Astronomia 'G. Galilei' - DFA, Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova (PD), Italy
| | - Fulvio Baldovin
- Dipartimento di Fisica e Astronomia 'G. Galilei' - DFA, Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova (PD), Italy
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22
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Cui H, Shi Q, Macarios CM, Schimmel P. Metabolic regulation of mRNA splicing. Trends Cell Biol 2024:S0962-8924(24)00025-4. [PMID: 38431493 DOI: 10.1016/j.tcb.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
Alternative mRNA splicing enables the diversification of the proteome from a static genome and confers plasticity and adaptiveness on cells. Although this is often explored in development, where hard-wired programs drive the differentiation and specialization, alternative mRNA splicing also offers a way for cells to react to sudden changes in outside stimuli such as small-molecule metabolites. Fluctuations in metabolite levels and availability in particular convey crucial information to which cells react and adapt. We summarize and highlight findings surrounding the metabolic regulation of mRNA splicing. We discuss the principles underlying the biochemistry and biophysical properties of mRNA splicing, and propose how these could intersect with metabolite levels. Further, we present examples in which metabolites directly influence RNA-binding proteins and splicing factors. We also discuss the interplay between alternative mRNA splicing and metabolite-responsive signaling pathways. We hope to inspire future research to obtain a holistic picture of alternative mRNA splicing in response to metabolic cues.
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Affiliation(s)
- Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada.
| | - Qingyu Shi
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | | | - Paul Schimmel
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA 92037, USA.
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23
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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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24
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Sugiyama S, Suda K, Kono K. Cytoplasmic zoning by protein phase transition after membrane permeabilization. J Biochem 2024; 175:147-153. [PMID: 37972304 PMCID: PMC10873517 DOI: 10.1093/jb/mvad094] [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: 08/30/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Biological membranes, including plasma membrane (PM) and organelle membranes, restrict the flux of ions, molecules and organelles. However, the barrier function of biological membranes is frequently compromised by various perturbations, including physical membrane damage and protein- or chemical-induced pore formation. Recent evidence suggests that, upon PM damage, protein gelation and solid condensation are utilized to restrict ion/molecule/organelle flux across the damaged membranes by zoning the cytoplasm. In addition, membrane permeabilization dramatically alters intramembrane and extramembrane ion/molecule concentrations via the flux across the permeabilized membrane. The changes in ion/molecule concentration and their downstream pathways induce protein phase transition to form zones for biological processes or protein sequestration. Here, we review the mechanisms and functions of protein phase transition after biological membrane permeabilization.
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Affiliation(s)
- Shinju Sugiyama
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Kojiro Suda
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Keiko Kono
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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25
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Wang S, Lim S, Tasmim S, Kalairaj MS, Rivera-Tarazona LK, Abdelrahman MK, Javed M, George SM, Lee YJ, Jawed MK, Ware TH. Reconfigurable Growth of Engineered Living Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2309818. [PMID: 38288578 DOI: 10.1002/adma.202309818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/11/2024] [Indexed: 02/10/2024]
Abstract
The growth of multicellular organisms is a process akin to additive manufacturing where cellular proliferation and mechanical boundary conditions, among other factors, drive morphogenesis. Engineers have limited ability to engineer morphogenesis to manufacture goods or to reconfigure materials comprised of biomass. Herein, a method that uses biological processes to grow and regrow magnetic engineered living materials (mELMs) into desired geometries is reported. These composites contain Saccharomyces cerevisiae and magnetic particles within a hydrogel matrix. The reconfigurable manufacturing process relies on the growth of living cells, magnetic forces, and elastic recovery of the hydrogel. The mELM then adopts a form in an external magnetic field. Yeast within the material proliferates, resulting in 259 ± 14% volume expansion. Yeast proliferation fixes the magnetic deformation, even when the magnetic field is removed. The shape fixity can be up to 99.3 ± 0.3%. The grown mELM can recover up to 73.9 ± 1.9% of the original form by removing yeast cell walls. The directed growth and recovery process can be repeated at least five times. This work enables ELMs to be processed and reprocessed into user-defined geometries without external material deposition.
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Affiliation(s)
- Suitu Wang
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, 77840, USA
| | - Sangmin Lim
- Department of Mechanical & Aerospace Engineering, University of California, Los Angeles, CA, 90095, USA
| | - Seelay Tasmim
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77840, USA
| | | | | | - Mustafa K Abdelrahman
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, 77840, USA
| | - Mahjabeen Javed
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77840, USA
| | - Sasha M George
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, 77840, USA
| | - Yoo Jin Lee
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77840, USA
| | - M Khalid Jawed
- Department of Mechanical & Aerospace Engineering, University of California, Los Angeles, CA, 90095, USA
| | - Taylor H Ware
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX, 77840, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, 77840, USA
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26
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Jacobs-Wagner C. Through the looking glass: An adventure into the metastable world of the bacterial cytoplasm. Cell 2024; 187:228-234. [PMID: 38242080 DOI: 10.1016/j.cell.2023.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024]
Abstract
This personal story recounts the accidental observation, the struggles, the breakthroughs, and the collaborative spirit of a few individuals that led to the discovery that bacterial cells expend energy to effectively fluidize their otherwise "glass-like" cytoplasm and promote the dispersal of large cytoplasmic components. This adventure, which led us into an uncharted world at the intersection of cell biology and condensed matter physics about ten years ago, forever transformed the way I view cells and conduct research.
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Affiliation(s)
- Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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27
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Kosmachevskaya OV, Novikova NN, Yakunin SN, Topunov AF. Formation of Supplementary Metal-Binding Centers in Proteins under Stress Conditions. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S180-S204. [PMID: 38621750 DOI: 10.1134/s0006297924140104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/21/2023] [Accepted: 10/29/2023] [Indexed: 04/17/2024]
Abstract
In many proteins, supplementary metal-binding centers appear under stress conditions. They are known as aberrant or atypical sites. Physico-chemical properties of proteins are significantly changed after such metal binding, and very stable protein aggregates are formed, in which metals act as "cross-linking" agents. Supplementary metal-binding centers in proteins often arise as a result of posttranslational modifications caused by reactive oxygen and nitrogen species and reactive carbonyl compounds. New chemical groups formed as a result of these modifications can act as ligands for binding metal ions. Special attention is paid to the role of cysteine SH-groups in the formation of supplementary metal-binding centers, since these groups are the main target for the action of reactive species. Supplementary metal binding centers may also appear due to unmasking of amino acid residues when protein conformation changing. Appearance of such centers is usually considered as a pathological process. Such unilateral approach does not allow to obtain an integral view of the phenomenon, ignoring cases when formation of metal complexes with altered proteins is a way to adjust protein properties, activity, and stability under the changed redox conditions. The role of metals in protein aggregation is being studied actively, since it leads to formation of non-membranous organelles, liquid condensates, and solid conglomerates. Some proteins found in such aggregates are typical for various diseases, such as Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and some types of cancer.
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Affiliation(s)
- Olga V Kosmachevskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | | | - Sergey N Yakunin
- National Research Center "Kurchatov Institute", Moscow, 123182, Russia
| | - Alexey F Topunov
- Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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28
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Gorsheneva NA, Sopova JV, Azarov VV, Grizel AV, Rubel AA. Biomolecular Condensates: Structure, Functions, Methods of Research. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S205-S223. [PMID: 38621751 DOI: 10.1134/s0006297924140116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 04/17/2024]
Abstract
The term "biomolecular condensates" is used to describe membraneless compartments in eukaryotic cells, accumulating proteins and nucleic acids. Biomolecular condensates are formed as a result of liquid-liquid phase separation (LLPS). Often, they demonstrate properties of liquid-like droplets or gel-like aggregates; however, some of them may appear to have a more complex structure and high-order organization. Membraneless microcompartments are involved in diverse processes both in cytoplasm and in nucleus, among them ribosome biogenesis, regulation of gene expression, cell signaling, and stress response. Condensates properties and structure could be highly dynamic and are affected by various internal and external factors, e.g., concentration and interactions of components, solution temperature, pH, osmolarity, etc. In this review, we discuss variety of biomolecular condensates and their functions in live cells, describe their structure variants, highlight domain and primary sequence organization of the constituent proteins and nucleic acids. Finally, we describe current advances in methods that characterize structure, properties, morphology, and dynamics of biomolecular condensates in vitro and in vivo.
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Affiliation(s)
| | - Julia V Sopova
- St. Petersburg State University, St. Petersburg, 199034, Russia.
| | | | - Anastasia V Grizel
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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29
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Vizjak P, Kamp D, Hepp N, Scacchetti A, Pisfil MG, Bartho J, Halic M, Becker PB, Smolle M, Stigler J, Mueller-Planitz F. ISWI catalyzes nucleosome sliding in condensed nucleosome arrays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.04.569516. [PMID: 38106060 PMCID: PMC10723341 DOI: 10.1101/2023.12.04.569516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
How chromatin enzymes work in condensed chromatin and how they maintain diffusional mobility inside remains unexplored. We investigated these challenges using the Drosophila ISWI remodeling ATPase, which slides nucleosomes along DNA. Folding of chromatin fibers did not affect sliding in vitro. Catalytic rates were also comparable in- and outside of chromatin condensates. ISWI cross-links and thereby stiffens condensates, except when ATP hydrolysis is possible. Active hydrolysis is also required for ISWI's mobility in condensates. Energy from ATP hydrolysis therefore fuels ISWI's diffusion through chromatin and prevents ISWI from cross-linking chromatin. Molecular dynamics simulations of a 'monkey-bar' model in which ISWI grabs onto neighboring nucleosomes, then withdraws from one before rebinding another in an ATP hydrolysis-dependent manner qualitatively agree with our data. We speculate that 'monkey-bar' mechanisms could be shared with other chromatin factors and that changes in chromatin dynamics caused by mutations in remodelers could contribute to pathologies.
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Affiliation(s)
- Petra Vizjak
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Dieter Kamp
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Nicola Hepp
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Alessandro Scacchetti
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- Current address: Epigenetics Institute & Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia (PA), USA
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Joseph Bartho
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Peter B Becker
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Michaela Smolle
- Department of Physiological Chemistry, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
- BioPhysics Core Facility, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhadernerstr. 9, 82152 Planegg-Martinsried, Germany
| | - Johannes Stigler
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str 25, 81377 München, Germany
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
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30
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Romero-Romero ML, Garcia-Seisdedos H. Agglomeration: when folded proteins clump together. Biophys Rev 2023; 15:1987-2003. [PMID: 38192350 PMCID: PMC10771401 DOI: 10.1007/s12551-023-01172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/25/2023] [Indexed: 01/10/2024] Open
Abstract
Protein self-association is a widespread phenomenon that results in the formation of multimeric protein structures with critical roles in cellular processes. Protein self-association can lead to finite protein complexes or open-ended, and potentially, infinite structures. This review explores the concept of protein agglomeration, a process that results from the infinite self-assembly of folded proteins. We highlight its differences from other better-described processes with similar macroscopic features, such as aggregation and liquid-liquid phase separation. We review the sequence, structural, and biophysical factors influencing protein agglomeration. Lastly, we briefly discuss the implications of agglomeration in evolution, disease, and aging. Overall, this review highlights the need to study protein agglomeration for a better understanding of cellular processes.
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Affiliation(s)
- M. L. Romero-Romero
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology, Dresden, Germany
| | - H. Garcia-Seisdedos
- Department of Structural and Molecular Biology, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
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31
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Holt LJ, Delarue M. Macromolecular crowding: Sensing without a sensor. Curr Opin Cell Biol 2023; 85:102269. [PMID: 37897928 DOI: 10.1016/j.ceb.2023.102269] [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: 08/23/2023] [Revised: 09/28/2023] [Accepted: 10/01/2023] [Indexed: 10/30/2023]
Abstract
All living cells are crowded with macromolecules. Crowding can directly modulate biochemical reactions to various degrees depending on the sizes, shapes, and binding affinities of the reactants. Here, we explore the possibility that cells can sense and adapt to changes in crowding through the widespread modulation of biochemical reactions without the need for a dedicated sensor. Additionally, we explore phase separation as a general physicochemical response to changes in crowding, and a mechanism to both transduce information and physically restore crowding homeostasis.
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Affiliation(s)
- Liam J Holt
- New York University Grossman School of Medicine, Institute for Systems Genetics, New York, NY, USA
| | - Morgan Delarue
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.
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32
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Arjona MI, Najafi J, Minc N. Cytoplasm mechanics and cellular organization. Curr Opin Cell Biol 2023; 85:102278. [PMID: 37979412 DOI: 10.1016/j.ceb.2023.102278] [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: 07/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/20/2023]
Abstract
As cells organize spatially or divide, they translocate many micron-scale organelles in their cytoplasm. These include endomembrane vesicles, nuclei, microtubule asters, mitotic spindles, or chromosomes. Organelle motion is powered by cytoskeleton forces but is opposed by viscoelastic forces imparted by the surrounding crowded cytoplasm medium. These resistive forces associated to cytoplasm physcial properties remain generally underappreciated, yet reach significant values to slow down organelle motion or even limit their displacement by springing them back towards their original position. The cytoplasm may also be itself organized in time and space, being for example stiffer or more fluid at certain locations or during particular cell cycle phases. Thus, cytoplasm mechanics may be viewed as a labile module that contributes to organize cells. We here review emerging methods, mechanisms, and concepts to study cytoplasm mechanical properties and their function in organelle positioning, cellular organization and division.
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Affiliation(s)
- María Isabel Arjona
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Javad Najafi
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France
| | - Nicolas Minc
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France; Equipe Labellisée LIGUE Contre le Cancer, France.
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33
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Mouton SN, Boersma AJ, Veenhoff LM. A physicochemical perspective on cellular ageing. Trends Biochem Sci 2023; 48:949-962. [PMID: 37716870 DOI: 10.1016/j.tibs.2023.08.007] [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: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Cellular ageing described at the molecular level is a multifactorial process that leads to a spectrum of ageing trajectories. There has been recent discussion about whether a decline in physicochemical homeostasis causes aberrant phase transitions, which are a driver of ageing. Indeed, the function of all biological macromolecules, regardless of their participation in biomolecular condensates, depends on parameters such as pH, crowding, and redox state. We expand on the physicochemical homeostasis hypothesis and summarise recent evidence that the intracellular milieu influences molecular processes involved in ageing.
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Affiliation(s)
- Sara N Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Liesbeth M Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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34
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Bonucci M, Shu T, Holt LJ. How it feels in a cell. Trends Cell Biol 2023; 33:924-938. [PMID: 37286396 PMCID: PMC10592589 DOI: 10.1016/j.tcb.2023.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Life emerges from thousands of biochemical processes occurring within a shared intracellular environment. We have gained deep insights from in vitro reconstitution of isolated biochemical reactions. However, the reaction medium in test tubes is typically simple and diluted. The cell interior is far more complex: macromolecules occupy more than a third of the space, and energy-consuming processes agitate the cell interior. Here, we review how this crowded, active environment impacts the motion and assembly of macromolecules, with an emphasis on mesoscale particles (10-1000 nm diameter). We describe methods to probe and analyze the biophysical properties of cells and highlight how changes in these properties can impact physiology and signaling, and potentially contribute to aging, and diseases, including cancer and neurodegeneration.
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Affiliation(s)
- Martina Bonucci
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA.
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35
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Kim H, Choi Y, Kim SY, Pahk KJ. Increased intracellular diffusivity of macromolecules within a mammalian cell by low-intensity pulsed ultrasound. ULTRASONICS SONOCHEMISTRY 2023; 100:106644. [PMID: 37844347 PMCID: PMC10587770 DOI: 10.1016/j.ultsonch.2023.106644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/18/2023]
Abstract
Whilst a number of studies have demonstrated that low-intensity pulsed ultrasound (LIPUS) is a promising therapeutic ultrasound technique that can be used for delivering mild mechanical stimuli to target tissue non-invasively, the underlying biophysical mechanisms still remain unclear. Most mechanism studies have focused explicitly on the effects of LIPUS on the cell membrane and mechanosensitive receptors. In the present study, we propose an additional mechanism by which LIPUS propagation through living cells may directly impact intracellular dynamics, particularly the diffusion transport of biomolecules. To support our hypothesis, human epithelial-like cells (SaOS-2 and HeLa) seeded on a confocal dish placed on a microscope stage were exposed to LIPUS with various exposure conditions (ultrasound frequencies of 0.5, 1 and 3 MHz, peak acoustic pressure of 200 and 400 kPa, a pulse repetition frequency of 1 kHz and a 20 % duty cycle), and the diffusivities of various sizes of biomolecules in the cytoplasm area were measured using fluorescence recovery after photobleaching (FRAP). Furthermore, giant unilamellar vesicles (GUVs) filled with macromolecules were used to examine the physical causal relationship between LIPUS and molecular diffusion changes. Nucleocytoplasmic transport coefficients were also measured by modified FRAP that bleaches the whole cell nuclear region. Extracellular signal-regulated kinases (ERK) activity (the phosphorylation dynamics) was monitored using fluorescence resonance energy transfer (FRET) microscopy. All the measurements were taken during, before and after the LIPUS exposure. Our experimental results clearly showed that the diffusion coefficients of macromolecules within the cell increased with acoustic pressure by 12.1 to 33.5 % during the sonication, and the increments were proportional to their molecular sizes regardless of the ultrasound frequency used. This observation in living cells was consistent with the GUVs exposed to the LIPUS, which indicated that the diffusivity increase was a passive physical response to the acoustic energy of LIPUS. Under the 1 MHz LIPUS exposure with 400 kPa, the passive nucleocytoplasmic transport of enhanced green fluorescent protein (EGFP) was accelerated by 21.4 %. With the same LIPUS exposure condition, both the diffusivity and phosphorylation of ERK induced by EGF treatment were significantly elevated simultaneously, which implied that LIPUS could also modify the kinase kinetics in the signal transduction process. Taken together, this study is the first attempt to uncover the physical link between LIPUS and the dynamics of intracellular macromolecules and related biological processes that LIPUS can possibly increase the diffusivity of intracellular macromolecules, leading to the changes in the basic cellular processes: passive nucleocytoplasmic transport and ERK. Our findings can provide a novel perspective that the mechanotransduction process that the intracellular region, in addition to the cell membrane, can convert the acoustic stimuli of LIPUS to biochemical signals.
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Affiliation(s)
- Hyojun Kim
- LAAS-CNRS, University of Toulouse, CNRS, Toulouse, France
| | - Yeonho Choi
- Department of Bioengineering, Korea University, Seoul, Republic of Korea
| | - So Yeon Kim
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea.
| | - Ki Joo Pahk
- Department of Biomedical Engineering, Kyung Hee University, Yongin 17104, Republic of Korea.
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Watson JL, Seinkmane E, Styles CT, Mihut A, Krüger LK, McNally KE, Planelles-Herrero VJ, Dudek M, McCall PM, Barbiero S, Vanden Oever M, Peak-Chew SY, Porebski BT, Zeng A, Rzechorzek NM, Wong DCS, Beale AD, Stangherlin A, Riggi M, Iwasa J, Morf J, Miliotis C, Guna A, Inglis AJ, Brugués J, Voorhees RM, Chambers JE, Meng QJ, O'Neill JS, Edgar RS, Derivery E. Macromolecular condensation buffers intracellular water potential. Nature 2023; 623:842-852. [PMID: 37853127 PMCID: PMC10665201 DOI: 10.1038/s41586-023-06626-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 09/08/2023] [Indexed: 10/20/2023]
Abstract
Optimum protein function and biochemical activity critically depends on water availability because solvent thermodynamics drive protein folding and macromolecular interactions1. Reciprocally, macromolecules restrict the movement of 'structured' water molecules within their hydration layers, reducing the available 'free' bulk solvent and therefore the total thermodynamic potential energy of water, or water potential. Here, within concentrated macromolecular solutions such as the cytosol, we found that modest changes in temperature greatly affect the water potential, and are counteracted by opposing changes in osmotic strength. This duality of temperature and osmotic strength enables simple manipulations of solvent thermodynamics to prevent cell death after extreme cold or heat shock. Physiologically, cells must sustain their activity against fluctuating temperature, pressure and osmotic strength, which impact water availability within seconds. Yet, established mechanisms of water homeostasis act over much slower timescales2,3; we therefore postulated the existence of a rapid compensatory response. We find that this function is performed by water potential-driven changes in macromolecular assembly, particularly biomolecular condensation of intrinsically disordered proteins. The formation and dissolution of biomolecular condensates liberates and captures free water, respectively, quickly counteracting thermal or osmotic perturbations of water potential, which is consequently robustly buffered in the cytoplasm. Our results indicate that biomolecular condensation constitutes an intrinsic biophysical feedback response that rapidly compensates for intracellular osmotic and thermal fluctuations. We suggest that preserving water availability within the concentrated cytosol is an overlooked evolutionary driver of protein (dis)order and function.
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Affiliation(s)
| | | | | | - Andrei Mihut
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Michal Dudek
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK
| | - Patrick M McCall
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | | | | | | | | | - Aiwei Zeng
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Alessandra Stangherlin
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Margot Riggi
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Jörg Morf
- Laboratory of Nuclear Dynamics, Babraham Institute, Cambridge, UK
| | | | - Alina Guna
- California Institute of Technology, Pasadena, CA, USA
| | | | - Jan Brugués
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | | | | | - Qing-Jun Meng
- Wellcome Centre for Cell Matrix Research, University of Manchester, Manchester, UK
| | | | - Rachel S Edgar
- Department of Infectious Disease, Imperial College London, London, UK.
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Liu X, Mokarizadeh AH, Narayanan A, Mane P, Pandit A, Tseng YM, Tsige M, Joy A. Multiphasic Coacervates Assembled by Hydrogen Bonding and Hydrophobic Interactions. J Am Chem Soc 2023; 145:23109-23120. [PMID: 37820374 DOI: 10.1021/jacs.3c06675] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Coacervation has emerged as a prevalent mechanism to compartmentalize biomolecules in living cells. Synthetic coacervates help in understanding the assembly process and mimic the functions of biological coacervates as simplified artificial systems. Though the molecular mechanism and mesoscopic properties of coacervates formed from charged coacervates have been well investigated, the details of the assembly and stabilization of nonionic coacervates remain largely unknown. Here, we describe a library of coacervate-forming polyesteramides and show that the water-tertiary amide bridging hydrogen bonds and hydrophobic interactions stabilize these nonionic, single-component coacervates. Analogous to intracellular biological coacervates, these coacervates exhibit "liquid-like" features with low viscosity and low interfacial energy, and form coacervates with as few as five repeating units. By controlling the temperature and engineering the molar ratio between hydrophobic interaction sites and bridging hydrogen bonding sites, we demonstrate the tuneability of the viscosity and interfacial tension of polyesteramide-based coacervates. Taking advantage of the differences in the mesoscopic properties of these nonionic coacervates, we engineered multiphasic coacervates with core-shell architectures similar to those of intracellular biological coacervates, such as nucleoli and stress granule-p-body complexes. The multiphasic structures produced from these synthetic nonionic polyesteramide coacervates may serve as a valuable tool for investigating physicochemical principles deployed by living cells to spatiotemporally control cargo partitioning, biochemical reaction rates, and interorganellar signal transport.
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Affiliation(s)
- Xinhao Liu
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Abdol Hadi Mokarizadeh
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Amal Narayanan
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Prathamesh Mane
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Avanti Pandit
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Yen-Ming Tseng
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Mesfin Tsige
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Abraham Joy
- School of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325, United States
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38
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Feng J, Gabryelczyk B, Tunn I, Osmekhina E, Linder MB. A Minispidroin Guides the Molecular Design for Cellular Condensation Mechanisms in S. cerevisiae. ACS Synth Biol 2023; 12:3050-3063. [PMID: 37688556 PMCID: PMC10594646 DOI: 10.1021/acssynbio.3c00374] [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: 06/18/2023] [Indexed: 09/11/2023]
Abstract
Structural engineering of molecules for condensation is an emerging technique within synthetic biology. Liquid-liquid phase separation of biomolecules leading to condensation is a central step in the assembly of biological materials into their functional forms. Intracellular condensates can also function within cells in a regulatory manner to facilitate reaction pathways and to compartmentalize interactions. We need to develop a strong understanding of how to design molecules for condensates and how their in vivo-in vitro properties are related. The spider silk protein NT2RepCT undergoes condensation during its fiber-forming process. Using parallel in vivo and in vitro characterization, in this study, we mapped the effects of intracellular conditions for NT2RepCT and its several structural variants. We found that intracellular conditions may suppress to some extent condensation whereas molecular crowding affects both condensate properties and their formation. Intracellular characterization of protein condensation allowed experiments on pH effects and solubilization to be performed within yeast cells. The growth of intracellular NT2RepCT condensates was restricted, and Ostwald ripening was not observed in yeast cells, in contrast to earlier observations in E. coli. Our results lead the way to using intracellular condensation to screen for properties of molecular assembly. For characterizing different structural variants, intracellular functional characterization can eliminate the need for time-consuming batch purification and in vitro condensation. Therefore, we suggest that the in vivo-in vitro understanding will become useful in, e.g., high-throughput screening for molecular functions and in strategies for designing tunable intracellular condensates.
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Affiliation(s)
- Jianhui Feng
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Bartosz Gabryelczyk
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Isabell Tunn
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Ekaterina Osmekhina
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
| | - Markus B. Linder
- Department of Bioproducts
and Biosystems, School of Chemical Engineering and Academy of Finland
Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, Espoo 02150, Finland
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39
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Ferreira PA. Nucleocytoplasmic transport at the crossroads of proteostasis, neurodegeneration and neuroprotection. FEBS Lett 2023; 597:2567-2589. [PMID: 37597509 DOI: 10.1002/1873-3468.14722] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/21/2023]
Abstract
Nucleocytoplasmic transport comprises the multistep assembly, transport, and disassembly of protein and RNA cargoes entering and exiting nuclear pores. Accruing evidence supports that impairments to nucleocytoplasmic transport are a hallmark of neurodegenerative diseases. These impairments cause dysregulations in nucleocytoplasmic partitioning and proteostasis of nuclear transport receptors and client substrates that promote intracellular deposits - another hallmark of neurodegeneration. Disturbances in liquid-liquid phase separation (LLPS) between dense and dilute phases of biomolecules implicated in nucleocytoplasmic transport promote micrometer-scale coacervates, leading to proteinaceous aggregates. This Review provides historical and emerging principles of LLPS at the interface of nucleocytoplasmic transport, proteostasis, aging and noxious insults, whose dysregulations promote intracellular aggregates. E3 SUMO-protein ligase Ranbp2 constitutes the cytoplasmic filaments of nuclear pores, where it acts as a molecular hub for rate-limiting steps of nucleocytoplasmic transport. A vignette is provided on the roles of Ranbp2 in nucleocytoplasmic transport and at the intersection of proteostasis in the survival of photoreceptor and motor neurons under homeostatic and pathophysiological environments. Current unmet clinical needs are highlighted, including therapeutics aiming to manipulate aggregation-dissolution models of purported neurotoxicity in neurodegeneration.
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Affiliation(s)
- Paulo A Ferreira
- Department of Ophthalmology, Department of Pathology, Duke University Medical Center, NC, Durham, USA
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40
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Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ. Mesoscale molecular assembly is favored by the active, crowded cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558334. [PMID: 37781612 PMCID: PMC10541124 DOI: 10.1101/2023.09.19.558334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The mesoscale organization of molecules into membraneless biomolecular condensates is emerging as a key mechanism of rapid spatiotemporal control in cells1. Principles of biomolecular condensation have been revealed through in vitro reconstitution2. However, intracellular environments are much more complex than test-tube environments: They are viscoelastic, highly crowded at the mesoscale, and are far from thermodynamic equilibrium due to the constant action of energy-consuming processes3. We developed synDrops, a synthetic phase separation system, to study how the cellular environment affects condensate formation. Three key features enable physical analysis: synDrops are inducible, bioorthogonal, and have well-defined geometry. This design allows kinetic analysis of synDrop assembly and facilitates computational simulation of the process. We compared experiments and simulations to determine that macromolecular crowding promotes condensate nucleation but inhibits droplet growth through coalescence. ATP-dependent cellular activities help overcome the frustration of growth. In particular, actomyosin dynamics potentiate droplet growth by reducing confinement and elasticity in the mammalian cytoplasm, thereby enabling synDrop coarsening. Our results demonstrate that mesoscale molecular assembly is favored by the combined effects of crowding and active matter in the cytoplasm. These results move toward a better predictive understanding of condensate formation in vivo.
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Affiliation(s)
- Tong Shu
- Institute for Systems Genetics, NYU Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
| | - Gaurav Mitra
- Department of Chemistry, New York University, New York, New York, USA
| | | | | | - Emmanuel D. Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Glen M. Hocky
- Department of Chemistry, New York University, New York, New York, USA
- Simons Center for Computational Physical Chemistry, New York University, New York, New York, USA
| | - Liam J. Holt
- Institute for Systems Genetics, NYU Langone Medical Center, 435 E 30th Street, New York, NY 10016, USA
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41
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Grimes B, Jacob W, Liberman AR, Kim N, Zhao X, Masison DC, Greene LE. The Properties and Domain Requirements for Phase Separation of the Sup35 Prion Protein In Vivo. Biomolecules 2023; 13:1370. [PMID: 37759770 PMCID: PMC10526957 DOI: 10.3390/biom13091370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The Sup35 prion protein of budding yeast has been reported to undergo phase separation to form liquid droplets both at low pH in vitro and when energy depletion decreases the intracellular pH in vivo. It also has been shown using purified proteins that this phase separation is driven by the prion domain of Sup35 and does not re-quire its C-terminal domain. In contrast, we now find that a Sup35 fragment consisting of only the N-terminal prion domain and the M-domain does not phase separate in vivo; this phase separation of Sup35 requires the C-terminal domain, which binds Sup45 to form the translation termination complex. The phase-separated Sup35 not only colocalizes with Sup45 but also with Pub1, a stress granule marker protein. In addition, like stress granules, phase separation of Sup35 appears to require mRNA since cycloheximide treatment, which inhibits mRNA release from ribosomes, prevents phase separation of Sup35. Finally, unlike Sup35 in vitro, Sup35 condensates do not disassemble in vivo when the intracellular pH is increased. These results suggest that, in energy-depleted cells, Sup35 forms supramolecular assemblies that differ from the Sup35 liquid droplets that form in vitro.
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Affiliation(s)
- Bryan Grimes
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Walter Jacob
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amanda R. Liberman
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathan Kim
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong Zhao
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Masison
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lois E. Greene
- Laboratory of Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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42
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Xie Y, Liu T, Gresham D, Holt LJ. mRNA condensation fluidizes the cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542963. [PMID: 37398029 PMCID: PMC10312499 DOI: 10.1101/2023.05.30.542963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The intracellular environment is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cell physiology. When exposed to stress, mRNAs released after translational arrest condense with RNA binding proteins, resulting in the formation of membraneless RNA protein (RNP) condensates known as processing bodies (P-bodies) and stress granules (SGs). However, the impact of the assembly of these condensates on the biophysical properties of the crowded cytoplasmic environment remains unclear. Here, we find that upon exposure to stress, polysome collapse and condensation of mRNAs increases mesoscale particle diffusivity in the cytoplasm. Increased mesoscale diffusivity is required for the efficient formation of Q-bodies, membraneless organelles that coordinate degradation of misfolded peptides that accumulate during stress. Additionally, we demonstrate that polysome collapse and stress granule formation has a similar effect in mammalian cells, fluidizing the cytoplasm at the mesoscale. We find that synthetic, light-induced RNA condensation is sufficient to fluidize the cytoplasm, demonstrating a causal effect of RNA condensation. Together, our work reveals a new functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to effectively respond to stressful conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Department of Biology, New York University, New York, New York, United States
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
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43
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Merotto E, Pavan PG, Piccoli M. Three-Dimensional Bioprinting of Naturally Derived Hydrogels for the Production of Biomimetic Living Tissues: Benefits and Challenges. Biomedicines 2023; 11:1742. [PMID: 37371837 DOI: 10.3390/biomedicines11061742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/07/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Three-dimensional bioprinting is the process of manipulating cell-laden bioinks to fabricate living structures. Three-dimensional bioprinting techniques have brought considerable innovation in biomedicine, especially in the field of tissue engineering, allowing the production of 3D organ and tissue models for in vivo transplantation purposes or for in-depth and precise in vitro analyses. Naturally derived hydrogels, especially those obtained from the decellularization of biological tissues, are promising bioinks for 3D printing purposes, as they present the best biocompatibility characteristics. Despite this, many natural hydrogels do not possess the necessary mechanical properties to allow a simple and immediate application in the 3D printing process. In this review, we focus on the bioactive and mechanical characteristics that natural hydrogels may possess to allow efficient production of organs and tissues for biomedical applications, emphasizing the reinforcement techniques to improve their biomechanical properties.
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Affiliation(s)
- Elena Merotto
- Tissue Engineering Lab, Istituto di Ricerca Pediatrica Città della Speranza, Corso Statu Uniti 4, 35127 Padova, Italy
- Department of Industrial Engineering, University of Padova, Via Gradenigo 6a, 35129 Padova, Italy
| | - Piero G Pavan
- Tissue Engineering Lab, Istituto di Ricerca Pediatrica Città della Speranza, Corso Statu Uniti 4, 35127 Padova, Italy
- Department of Industrial Engineering, University of Padova, Via Gradenigo 6a, 35129 Padova, Italy
| | - Martina Piccoli
- Tissue Engineering Lab, Istituto di Ricerca Pediatrica Città della Speranza, Corso Statu Uniti 4, 35127 Padova, Italy
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44
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Opalek M, Tutaj H, Pirog A, Smug BJ, Rutkowska J, Wloch-Salamon D. A Systematic Review on Quiescent State Research Approaches in S. cerevisiae. Cells 2023; 12:1608. [PMID: 37371078 DOI: 10.3390/cells12121608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast Saccharomyces cerevisiae. We group research articles into those that consider all cells comprising the stationary-phase (SP) population as quiescent and those that recognize heterogeneity within the SP by distinguishing phenotypically distinct subpopulations. Furthermore, we investigate the chronological age of the quiescent populations under study and the methods used to induce the quiescent state, such as gradual starvation or abrupt environmental change. We also assess whether the strains used in research are prototrophic or auxotrophic. By combining the above features, we identify 48 possible experimental setups that can be used to study quiescence, which can be misleading when drawing general conclusions. We therefore summarize our review by proposing guidelines and recommendations pertaining to the information included in research articles. We believe that more rigorous reporting on the features of quiescent populations will facilitate knowledge transfer within and between disciplines, thereby stimulating valuable scientific discussion.
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Affiliation(s)
- Monika Opalek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Hanna Tutaj
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Rutkowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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45
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Schulte T, Panas MD, Han X, Williams L, Kedersha N, Fleck JS, Tan TJC, Dopico XC, Olsson A, Morro AM, Hanke L, Nilvebrant J, Giang KA, Nygren PÅ, Anderson P, Achour A, McInerney GM. Caprin-1 binding to the critical stress granule protein G3BP1 is influenced by pH. Open Biol 2023; 13:220369. [PMID: 37161291 PMCID: PMC10170197 DOI: 10.1098/rsob.220369] [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: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/11/2023] Open
Abstract
G3BP is the central node within stress-induced protein-RNA interaction networks known as stress granules (SGs). The SG-associated proteins Caprin-1 and USP10 bind mutually exclusively to the NTF2 domain of G3BP1, promoting and inhibiting SG formation, respectively. Herein, we present the crystal structure of G3BP1-NTF2 in complex with a Caprin-1-derived short linear motif (SLiM). Caprin-1 interacts with His-31 and His-62 within a third NTF2-binding site outside those covered by USP10, as confirmed using biochemical and biophysical-binding assays. Nano-differential scanning fluorimetry revealed reduced thermal stability of G3BP1-NTF2 at acidic pH. This destabilization was counterbalanced significantly better by bound USP10 than Caprin-1. The G3BP1/USP10 complex immunoprecipated from human U2OS cells was more resistant to acidic buffer washes than G3BP1/Caprin-1. Acidification of cellular condensates by approximately 0.5 units relative to the cytosol was detected by ratiometric fluorescence analysis of pHluorin2 fused to G3BP1. Cells expressing a Caprin-1/FGDF chimera with higher G3BP1-binding affinity had reduced Caprin-1 levels and slightly reduced condensate sizes. This unexpected finding may suggest that binding of the USP10-derived SLiM to NTF2 reduces the propensity of G3BP1 to enter condensates.
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Affiliation(s)
- Tim Schulte
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Marc D. Panas
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Lucy Williams
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Nancy Kedersha
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Simon Fleck
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Timothy J. C. Tan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Anders Olsson
- Protein Expression and Characterization, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
| | - Ainhoa Moliner Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Johan Nilvebrant
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Kim Anh Giang
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, 114 21, Stockholm
- Science for Life Laboratory, Tomtebodavägen 23A, 171 65, Sweden
| | - Paul Anderson
- Division of Rheumatology, Immunity, and Inflammation, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, and Division of Infectious Diseases, Karolinska University Hospital, Stockholm, 171 77, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
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46
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Li Y, Liang W, Li C. Exogenous adenosine and/or guanosine enhances tetracycline sensitivity of persister cells. Microbiol Res 2023; 270:127321. [PMID: 36773473 DOI: 10.1016/j.micres.2023.127321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/25/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023]
Abstract
Vibrio splendidus is an opportunistic pathogen, its pathogenicity continues to be a major aquaculture disease infection problem in many parts of the world. Bacteria can form dormant and persister cells, which may be responsible for the difficulty in treating latent infections. Bacterial persister cells are a small subpopulation with high phenotypic heterogeneity that have the ability to persist in response to high concentrations of antibiotics. In our previous work, we have confirmed tetracycline could induce V. splendidus AJ01 persister cells formation. Here, we show that exogenous adenosine and/or guanosine supply restores susceptibility of AJ01 persister cells to tetracycline, leading to effective killing of this persist subpopulation upon wake-up. Mechanistically, exogenous adenosine and/or guanosine promotes the intracellular ATP level, reduces percentage of cells with protein aggresomes, and destroys membrane stability. In addition, when cells were exposed to tetracycline, we found that cells with small nucleocytoplasmic ratio is easy to survive. Overall, our results support that exogenous adenosine or guanosine could be an effective strategy for treating infections with antibiotic-persist bacteria via regulating persisters cells formation.
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Affiliation(s)
- Yanan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China
| | - Weikang Liang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China
| | - Chenghua Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, PR China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, PR China.
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47
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Frittoli E, Palamidessi A, Iannelli F, Zanardi F, Villa S, Barzaghi L, Abdo H, Cancila V, Beznoussenko GV, Della Chiara G, Pagani M, Malinverno C, Bhattacharya D, Pisati F, Yu W, Galimberti V, Bonizzi G, Martini E, Mironov AA, Gioia U, Ascione F, Li Q, Havas K, Magni S, Lavagnino Z, Pennacchio FA, Maiuri P, Caponi S, Mattarelli M, Martino S, d'Adda di Fagagna F, Rossi C, Lucioni M, Tancredi R, Pedrazzoli P, Vecchione A, Petrini C, Ferrari F, Lanzuolo C, Bertalot G, Nader G, Foiani M, Piel M, Cerbino R, Giavazzi F, Tripodo C, Scita G. Tissue fluidification promotes a cGAS-STING cytosolic DNA response in invasive breast cancer. NATURE MATERIALS 2023; 22:644-655. [PMID: 36581770 PMCID: PMC10156599 DOI: 10.1038/s41563-022-01431-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/02/2022] [Indexed: 05/05/2023]
Abstract
The process in which locally confined epithelial malignancies progressively evolve into invasive cancers is often promoted by unjamming, a phase transition from a solid-like to a liquid-like state, which occurs in various tissues. Whether this tissue-level mechanical transition impacts phenotypes during carcinoma progression remains unclear. Here we report that the large fluctuations in cell density that accompany unjamming result in repeated mechanical deformations of cells and nuclei. This triggers a cellular mechano-protective mechanism involving an increase in nuclear size and rigidity, heterochromatin redistribution and remodelling of the perinuclear actin architecture into actin rings. The chronic strains and stresses associated with unjamming together with the reduction of Lamin B1 levels eventually result in DNA damage and nuclear envelope ruptures, with the release of cytosolic DNA that activates a cGAS-STING (cyclic GMP-AMP synthase-signalling adaptor stimulator of interferon genes)-dependent cytosolic DNA response gene program. This mechanically driven transcriptional rewiring ultimately alters the cell state, with the emergence of malignant traits, including epithelial-to-mesenchymal plasticity phenotypes and chemoresistance in invasive breast carcinoma.
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Affiliation(s)
| | | | - Fabio Iannelli
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Stefano Villa
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
- Max Plank Institute for Dynamics and Self-Organization, Göttingen, Germany
| | | | - Hind Abdo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Valeria Cancila
- Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy
| | | | | | - Massimiliano Pagani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
| | | | | | - Federica Pisati
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Weimiao Yu
- Institute of Molecular and Cell Biology, A*STAR, Singapore, & Bioinformatics Institute, A*STAR, Singapore, Singapore
| | | | | | | | | | - Ubaldo Gioia
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Flora Ascione
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Qingsen Li
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Kristina Havas
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Serena Magni
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Zeno Lavagnino
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Paolo Maiuri
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Silvia Caponi
- Istituto Officina dei Materiali, National Research Council (IOM-CNR), Unit of Perugia, c/o Department of Physics and Geology, University of Perugia, Perugia, Italy
| | | | - Sabata Martino
- Department of Chemistry, Biology and Biotechnology, Biochemical and Biotechnological Sciences, University of Perugia, Perugia, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Chiara Rossi
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Marco Lucioni
- Unit of Anatomic Pathology, Department of Molecular Medicine, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Richard Tancredi
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- S.C. Oncologia Medica, ASST Melegnano e della Martesana, Ospedale Uboldo, Cernusco sul Naviglio, Milan, Italy
| | - Paolo Pedrazzoli
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Internal Medicine and Medical Therapy, University of Pavia, Pavia, Italy
| | - Andrea Vecchione
- Department of Clinical and Molecular Medicine, University of Roma, La Sapienza, Rome, Italy
| | | | - Francesco Ferrari
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
- National Institute of Molecular Genetics Romeo and Enrica Invernizzi, INGM, Milan, Italy
| | - Giovanni Bertalot
- Department of Pathology, S. Chiara Hospital, Azienda Provinciale per i Servizi Sanitari, Trento, Italy
- CISMed University of Trento, University of Trento, Trento, Italy
| | - Guilherme Nader
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR-144, Paris, France
- Cell Pathology Children's Hospital of Philadelphia, Research Institute Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marco Foiani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy
| | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR-144, Paris, France
| | - Roberto Cerbino
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy
- Faculty of Physics, University of Vienna, Vienna, Austria
| | - Fabio Giavazzi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, Italy.
| | - Claudio Tripodo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Health Sciences, Human Pathology Section, University of Palermo School of Medicine, Palermo, Italy.
| | - Giorgio Scita
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
- Department of Oncology and Haemato-Oncology, University of Milan, Milan, Italy.
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48
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Gavrilova AA, Fefilova AS, Vishnyakov IE, Kuznetsova IM, Turoverov KK, Uversky VN, Fonin AV. On the Roles of the Nuclear Non-Coding RNA-Dependent Membrane-Less Organelles in the Cellular Stress Response. Int J Mol Sci 2023; 24:ijms24098108. [PMID: 37175815 PMCID: PMC10179167 DOI: 10.3390/ijms24098108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
At the beginning of the 21st century, it became obvious that radical changes had taken place in the concept of living matter and, in particular, in the concept of the organization of intracellular space. The accumulated data testify to the essential importance of phase transitions of biopolymers (first of all, intrinsically disordered proteins and RNA) in the spatiotemporal organization of the intracellular space. Of particular interest is the stress-induced reorganization of the intracellular space. Examples of organelles formed in response to stress are nuclear A-bodies and nuclear stress bodies. The formation of these organelles is based on liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) and non-coding RNA. Despite their overlapping composition and similar mechanism of formation, these organelles have different functional activities and physical properties. In this review, we will focus our attention on these membrane-less organelles (MLOs) and describe their functions, structure, and mechanism of formation.
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Affiliation(s)
- Anastasia A Gavrilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Innokentii E Vishnyakov
- Group of Molecular Cytology of Prokaryotes and Bacterial Invasion, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia
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49
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Baquero F, Martínez JL, Sánchez A, Fernández-de-Bobadilla MD, San-Millán A, Rodríguez-Beltrán J. Bacterial Subcellular Architecture, Structural Epistasis, and Antibiotic Resistance. BIOLOGY 2023; 12:biology12050640. [PMID: 37237454 DOI: 10.3390/biology12050640] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Epistasis refers to the way in which genetic interactions between some genetic loci affect phenotypes and fitness. In this study, we propose the concept of "structural epistasis" to emphasize the role of the variable physical interactions between molecules located in particular spaces inside the bacterial cell in the emergence of novel phenotypes. The architecture of the bacterial cell (typically Gram-negative), which consists of concentrical layers of membranes, particles, and molecules with differing configurations and densities (from the outer membrane to the nucleoid) determines and is in turn determined by the cell shape and size, depending on the growth phases, exposure to toxic conditions, stress responses, and the bacterial environment. Antibiotics change the bacterial cell's internal molecular topology, producing unexpected interactions among molecules. In contrast, changes in shape and size may alter antibiotic action. The mechanisms of antibiotic resistance (and their vectors, as mobile genetic elements) also influence molecular connectivity in the bacterial cell and can produce unexpected phenotypes, influencing the action of other antimicrobial agents.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), 28034 Madrid, Spain
| | | | - Alvaro Sánchez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
| | - Miguel D Fernández-de-Bobadilla
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFECT), 28034 Madrid, Spain
| | - Alvaro San-Millán
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFECT), 28034 Madrid, Spain
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), 28034 Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFECT), 28034 Madrid, Spain
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50
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Corci B, Hooiveld O, Dolga AM, Åberg C. Extending the analogy between intracellular motion in mammalian cells and glassy dynamics. SOFT MATTER 2023; 19:2529-2538. [PMID: 36939775 DOI: 10.1039/d2sm01672a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
How molecules, organelles, and foreign objects move within living cells has been studied in organisms ranging from bacteria to human cells. In mammalian cells, in particular, cellular vesicles move across the cell using motor proteins that carry the vesicle down the cytoskeleton to their destination. We have recently noted several similarities between the motion of such vesicles and that in disordered, "glassy", systems, but the generality of this observation remains unclear. Here we follow the motion of mitochondria, the organelles responsible for cell energy production, in mammalian cells over timescales from 50 ms to 70 s. Qualitative observations show that single mitochondria remain within a spatially limited region for extended periods of time, before moving longer distances relatively quickly. The displacement distribution is roughly Gaussian for shorter distances (≲0.05 μm) but exhibits exponentially decaying tails at longer distances (up to 0.40 μm). This behaviour is well-described by a model developed to describe the motion in glassy systems. These observations are extended to in total 3 different objects (mitochondria, lysosomes and nano-sized beads enclosed in vesicles), 3 different mammalian cell types (HEK 293, HeLa, and HT22), from 2 different organisms (human and mouse). Further evidence that supports glass-like characteristics of the motion is a difference between the time it takes to move a longer distance for the first time and subsequent times, as well as a weak ergodicity breaking of the motion. Overall, we demonstrate the ubiquity of glass-like motion in mammalian cells, providing a different perspective on intracellular motion.
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Affiliation(s)
- Beatrice Corci
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Oscar Hooiveld
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Amalia M Dolga
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Christoffer Åberg
- Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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