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Harju J, van Teeseling MCF, Broedersz CP. Loop-extruders alter bacterial chromosome topology to direct entropic forces for segregation. Nat Commun 2024; 15:4618. [PMID: 38816445 PMCID: PMC11139863 DOI: 10.1038/s41467-024-49039-w] [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: 11/28/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
Entropic forces have been argued to drive bacterial chromosome segregation during replication. In many bacterial species, however, specifically evolved mechanisms, such as loop-extruding SMC complexes and the ParABS origin segregation system, contribute to or are even required for chromosome segregation, suggesting that entropic forces alone may be insufficient. The interplay between and the relative contributions of these segregation mechanisms remain unclear. Here, we develop a biophysical model showing that purely entropic forces actually inhibit bacterial chromosome segregation until late replication stages. By contrast, our model reveals that loop-extruders loaded at the origins of replication, as observed in many bacterial species, alter the effective topology of the chromosome, thereby redirecting and enhancing entropic forces to enable accurate chromosome segregation during replication. We confirm our model predictions with polymer simulations: purely entropic forces do not allow for concurrent replication and segregation, whereas entropic forces steered by specifically loaded loop-extruders lead to robust, global chromosome segregation during replication. Finally, we show how loop-extruders can complement locally acting origin separation mechanisms, such as the ParABS system. Together, our results illustrate how changes in the geometry and topology of the polymer, induced by DNA-replication and loop-extrusion, impact the organization and segregation of bacterial chromosomes.
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Affiliation(s)
- Janni Harju
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Muriel C F van Teeseling
- Junior research group Prokaryotic Cell Biology, Department for Microbial Interactions, Institute of Microbiology, Friedrich-Schiller-Universität, Jena, Germany
| | - Chase P Broedersz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilian-University Munich, Munich, Germany.
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2
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: Compaction, segregation, and entanglement suppression. Proc Natl Acad Sci U S A 2024; 121:e2401494121. [PMID: 38753513 PMCID: PMC11127048 DOI: 10.1073/pnas.2401494121] [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: 01/26/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross-over between two and four at contour lengths on the order of 30 kilo-base pairs. The anomalously high fractal dimension [Formula: see text] is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ([Formula: see text]) longer than tens of minutes to be proportional to [Formula: see text]. We validate our results with hybrid molecular dynamics-Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, NC27708
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, NC27708
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
- Department of Physics, Duke University, Durham, NC27708
- Department of Chemistry, Duke University, Durham, NC27708
- World Premier International Research Center Initiative–Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo001-0021, Japan
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3
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Losa J, Heinemann M. Contribution of different macromolecules to the diffusion of a 40 nm particle in Escherichia coli. Biophys J 2024; 123:1211-1221. [PMID: 38555507 PMCID: PMC11140462 DOI: 10.1016/j.bpj.2024.03.040] [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: 01/19/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Due to the high concentration of proteins, nucleic acids, and other macromolecules, the bacterial cytoplasm is typically described as a crowded environment. However, the extent to which each of these macromolecules individually affects the mobility of macromolecular complexes, and how this depends on growth conditions, is presently unclear. In this study, we sought to quantify the crowding experienced by an exogenous 40 nm fluorescent particle in the cytoplasm of E. coli under different growth conditions. By performing single-particle tracking measurements in cells selectively depleted of DNA and/or mRNA, we determined the contribution to crowding of mRNA, DNA, and remaining cellular components, i.e., mostly proteins and ribosomes. To estimate this contribution to crowding, we quantified the difference of the particle's diffusion coefficient in conditions with and without those macromolecules. We found that the contributions of the three classes of components were of comparable magnitude, being largest in the case of proteins and ribosomes. We further found that the contributions of mRNA and DNA to crowding were significantly larger than expected based on their volumetric fractions alone. Finally, we found that the crowding contributions change only slightly with the growth conditions. These results reveal how various cellular components partake in crowding of the cytoplasm and the consequences this has for the mobility of large macromolecular complexes.
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Affiliation(s)
- José Losa
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
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4
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Meschichi A, Rosa S. Plant chromatin on the move: an overview of chromatin mobility during transcription and DNA repair. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:953-962. [PMID: 36811211 DOI: 10.1111/tpj.16159] [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: 01/10/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
It has become increasingly clear in recent years that chromosomes are highly dynamic entities. Chromatin mobility and re-arrangement are involved in many biological processes, including gene regulation and the maintenance of genome stability. Despite extensive studies on chromatin mobility in yeast and animal systems, up until recently, not much had been investigated at this level in plants. For plants to achieve proper growth and development, they need to respond rapidly and appropriately to environmental stimuli. Therefore, understanding how chromatin mobility can support plant responses may offer profound insights into the functioning of plant genomes. In this review, we discuss the state of the art related to chromatin mobility in plants, including the available technologies for their role in various cellular processes.
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Affiliation(s)
- Anis Meschichi
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
| | - Stefanie Rosa
- Plant Biology Department, Swedish University of Agricultural Sciences (SLU), Almas Allé 5, Uppsala, Sweden
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5
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Shaban HA, Friman ET, Deluz C, Tollenaere A, Katanayeva N, Suter DM. Individual transcription factors modulate both the micromovement of chromatin and its long-range structure. Proc Natl Acad Sci U S A 2024; 121:e2311374121. [PMID: 38648478 PMCID: PMC11067044 DOI: 10.1073/pnas.2311374121] [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: 07/05/2023] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here, we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine high-resolution diffusion mapping and dense flow reconstruction and correlation in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.
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Affiliation(s)
- Haitham A. Shaban
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
- Spectroscopy Department, Institute of Physics Research, National Research Centre, Cairo12622, Egypt
| | - Elias T. Friman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Cédric Deluz
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Armelle Tollenaere
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
| | - David M. Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, LausanneCH-1015, Switzerland
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6
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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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7
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Yuan T, Yan H, Bailey MLP, Williams JF, Surovtsev I, King MC, Mochrie SGJ. Effect of loops on the mean-square displacement of Rouse-model chromatin. Phys Rev E 2024; 109:044502. [PMID: 38755928 DOI: 10.1103/physreve.109.044502] [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: 04/24/2023] [Accepted: 02/16/2024] [Indexed: 05/18/2024]
Abstract
Chromatin polymer dynamics are commonly described using the classical Rouse model. The subsequent discovery, however, of intermediate-scale chromatin organization known as topologically associating domains (TADs) in experimental Hi-C contact maps for chromosomes across the tree of life, together with the success of loop extrusion factor (LEF) model in explaining TAD formation, motivates efforts to understand the effect of loops and loop extrusion on chromatin dynamics. This paper seeks to fulfill this need by combining LEF-model simulations with extended Rouse-model polymer simulations to investigate the dynamics of chromatin with loops and dynamic loop extrusion. We show that loops significantly suppress the averaged mean-square displacement (MSD) of a gene locus, consistent with recent experiments that track fluorescently labeled chromatin loci. We also find that loops reduce the MSD's stretching exponent from the classical Rouse-model value of 1/2 to a loop-density-dependent value in the 0.45-0.40 range. Remarkably, stretching exponent values in this range have also been observed in recent experiments [Weber et al., Phys. Rev. Lett. 104, 238102 (2010)0031-900710.1103/PhysRevLett.104.238102; Bailey et al., Mol. Biol. Cell 34, ar78 (2023)1059-152410.1091/mbc.E23-04-0119]. We also show that the dynamics of loop extrusion itself negligibly affects chromatin mobility. By studying static "rosette" loop configurations, we also demonstrate that chromatin MSDs and stretching exponents depend on the location of the locus in question relative to the position of the loops and on the local friction environment.
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Affiliation(s)
- Tianyu Yuan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Hao Yan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
| | - Jessica F Williams
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Megan C King
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut 06520, USA
- Department of Physics, Yale University, New Haven, Connecticut 06520, USA
- Department of Applied Physics, Yale University, New Haven, Connecticut 06520, USA
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8
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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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9
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Dutta S, Ghosh A, Spakowitz AJ. Effect of local active fluctuations on structure and dynamics of flexible biopolymers. SOFT MATTER 2024; 20:1694-1701. [PMID: 38226903 DOI: 10.1039/d3sm01491f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Active fluctuations play a significant role in the structure and dynamics of biopolymers (e.g. chromatin and cytoskeletal proteins) that are instrumental in the functioning of living cells. For a large range of experimentally accessible length and time scales, these polymers can be represented as flexible chains that are subjected to spatially and temporally varying fluctuating forces. In this work, we introduce a mathematical framework that correlates the spatial and temporal patterns of the fluctuations to different observables that describe the dynamics and conformations of the polymer. We demonstrate the power of this approach by analyzing the case of a point fluctuation on the polymer with an exponential decay of correlation in time with a finite time constant. Specifically, we identify the length and time scale over which the behavior of the polymer exhibits a significant departure from the behavior of a Rouse chain and the range of impact of the fluctuation along the chain. Furthermore, we show that the conformation of the polymer retains the memory of the active fluctuation from earlier times. Altogether, this work sets the basis for understanding and interpreting the role of spatio-temporal patterns of fluctuations in the dynamics, conformation, and functionality of biopolymers in living cells.
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Affiliation(s)
- Sayantan Dutta
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Ashesh Ghosh
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
- Department of Material Science and Engineering, Stanford University, Stanford, California 94305, USA
- Biophysics Program, Stanford University, Stanford, California 94305, USA.
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10
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Rudyak VY, Lopushenko A, Palyulin VV, Chertovich AV. Long-range ordering of velocity-aligned active polymers. J Chem Phys 2024; 160:044905. [PMID: 38275191 DOI: 10.1063/5.0181252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
In this work, we study the effect of covalent bonding on the behavior of non-equilibrium systems with the active force acting on particles along their velocity. Self-ordering of single particles does not occur in this model. However, starting from some critical polymerization degree, the ordered state is observed. It is homogeneous and exhibits no phase separation. In the ordered state, the chains prefer a near-two-dimensional configuration and all move in one direction. Importantly, the self-ordering is obtained only at intermediate active force magnitudes. At high magnitudes, the transition from the disordered to ordered state is suppressed by the swelling of the chains during the transition, as we show by the transition kinetics analysis. We demonstrate the bistable behavior of the system in a particular range of polymerization degrees, amplitudes of active force, densities, and thermostat temperatures. Overall, we show that covalent bonding greatly aids the self-ordering in this active particle model, in contrast to active Brownian particles.
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Affiliation(s)
- Vladimir Yu Rudyak
- Semenov Federal Research Center for Chemical Physics, Kosygina, 4, 119991 Moscow, Russia
| | - Alexander Lopushenko
- Semenov Federal Research Center for Chemical Physics, Kosygina, 4, 119991 Moscow, Russia
| | - Vladimir V Palyulin
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Alexander V Chertovich
- Semenov Federal Research Center for Chemical Physics, Kosygina, 4, 119991 Moscow, Russia
- Faculty of Physics, Lomonosov Moscow State University, Moscow 119991, Russia
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11
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Chan B, Rubinstein M. Activity-driven chromatin organization during interphase: compaction, segregation, and entanglement suppression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576729. [PMID: 38328091 PMCID: PMC10849557 DOI: 10.1101/2024.01.22.576729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In mammalian cells, the cohesin protein complex is believed to translocate along chromatin during interphase to form dynamic loops through a process called active loop extrusion. Chromosome conformation capture and imaging experiments have suggested that chromatin adopts a compact structure with limited interpenetration between chromosomes and between chromosomal sections. We developed a theory demonstrating that active loop extrusion causes the apparent fractal dimension of chromatin to cross over between two and four at contour lengths on the order of 30 kilo-base pairs (kbp). The anomalously high fractal dimension D = 4 is due to the inability of extruded loops to fully relax during active extrusion. Compaction on longer contour length scales extends within topologically associated domains (TADs), facilitating gene regulation by distal elements. Extrusion-induced compaction segregates TADs such that overlaps between TADs are reduced to less than 35% and increases the entanglement strand of chromatin by up to a factor of 50 to several Mega-base pairs. Furthermore, active loop extrusion couples cohesin motion to chromatin conformations formed by previously extruding cohesins and causes the mean square displacement of chromatin loci during lag times ( Δ t ) longer than tens of minutes to be proportional to Δ t 1 / 3 . We validate our results with hybrid molecular dynamics - Monte Carlo simulations and show that our theory is consistent with experimental data. This work provides a theoretical basis for the compact organization of interphase chromatin, explaining the physical reason for TAD segregation and suppression of chromatin entanglements which contribute to efficient gene regulation.
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Affiliation(s)
- Brian Chan
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
| | - Michael Rubinstein
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, United States
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina, 27708, United States
- Department of Physics, Duke University, Durham, North Carolina, 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina, 27708, United States
- World Premier International Research Center Initiative — Institute for Chemical Reaction Design and Discovery, Hokkaido University, Sapporo, 001-0021, Japan
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12
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Kwon E, Baek Y. α-divergence improves the entropy production estimation via machine learning. Phys Rev E 2024; 109:014143. [PMID: 38366477 DOI: 10.1103/physreve.109.014143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 01/05/2024] [Indexed: 02/18/2024]
Abstract
Recent years have seen a surge of interest in the algorithmic estimation of stochastic entropy production (EP) from trajectory data via machine learning. A crucial element of such algorithms is the identification of a loss function whose minimization guarantees the accurate EP estimation. In this study we show that there exists a host of loss functions, namely, those implementing a variational representation of the α-divergence, which can be used for the EP estimation. By fixing α to a value between -1 and 0, the α-NEEP (Neural Estimator for Entropy Production) exhibits a much more robust performance against strong nonequilibrium driving or slow dynamics, which adversely affects the existing method based on the Kullback-Leibler divergence (α=0). In particular, the choice of α=-0.5 tends to yield the optimal results. To corroborate our findings, we present an exactly solvable simplification of the EP estimation problem, whose loss function landscape and stochastic properties give deeper intuition into the robustness of the α-NEEP.
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Affiliation(s)
- Euijoon Kwon
- Department of Physics and Astronomy & Center for Theoretical Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Yongjoo Baek
- Department of Physics and Astronomy & Center for Theoretical Physics, Seoul National University, Seoul 08826, Republic of Korea
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13
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Yu KKH, Basu S, Baquer G, Ahn R, Gantchev J, Jindal S, Regan MS, Abou-Mrad Z, Prabhu MC, Williams MJ, D'Souza AD, Malinowski SW, Hopland K, Elhanati Y, Stopka SA, Stortchevoi A, He Z, Sun J, Chen Y, Espejo AB, Chow KH, Yerrum S, Kao PL, Kerrigan BP, Norberg L, Nielsen D, Puduvalli VK, Huse J, Beroukhim R, Kim YSB, Goswami S, Boire A, Frisken S, Cima MJ, Holdhoff M, Lucas CHG, Bettegowda C, Levine SS, Bale TA, Brennan C, Reardon DA, Lang FF, Antonio Chiocca E, Ligon KL, White FM, Sharma P, Tabar V, Agar NYR. Investigative needle core biopsies for multi-omics in Glioblastoma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.29.23300541. [PMID: 38234840 PMCID: PMC10793534 DOI: 10.1101/2023.12.29.23300541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Glioblastoma (GBM) is a primary brain cancer with an abysmal prognosis and few effective therapies. The ability to investigate the tumor microenvironment before and during treatment would greatly enhance both understanding of disease response and progression, as well as the delivery and impact of therapeutics. Stereotactic biopsies are a routine surgical procedure performed primarily for diagnostic histopathologic purposes. The role of investigative biopsies - tissue sampling for the purpose of understanding tumor microenvironmental responses to treatment using integrated multi-modal molecular analyses ('Multi-omics") has yet to be defined. Secondly, it is unknown whether comparatively small tissue samples from brain biopsies can yield sufficient information with such methods. Here we adapt stereotactic needle core biopsy tissue in two separate patients. In the first patient with recurrent GBM we performed highly resolved multi-omics analysis methods including single cell RNA sequencing, spatial-transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics from biopsy tissue that was obtained from a single procedure. In a second patient we analyzed multi-regional core biopsies to decipher spatial and genomic variance. We also investigated the utility of stereotactic biopsies as a method for generating patient derived xenograft models in a separate patient cohort. Dataset integration across modalities showed good correspondence between spatial modalities, highlighted immune cell associated metabolic pathways and revealed poor correlation between RNA expression and the tumor MHC Class I immunopeptidome. In conclusion, stereotactic needle biopsy cores are of sufficient quality to generate multi-omics data, provide data rich insight into a patient's disease process and tumor immune microenvironment and can be of value in evaluating treatment responses. One sentence summary Integrative multi-omics analysis of stereotactic needle core biopsies in glioblastoma.
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14
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Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Ebata H, Mizuno D. Activity-dependent glassy cell mechanics II: Nonthermal fluctuations under metabolic activity. Biophys J 2023; 122:4395-4413. [PMID: 37865819 PMCID: PMC10698330 DOI: 10.1016/j.bpj.2023.10.018] [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: 04/05/2023] [Revised: 08/28/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
The glassy cytoplasm, crowded with bio-macromolecules, is fluidized in living cells by mechanical energy derived from metabolism. Characterizing the living cytoplasm as a nonequilibrium system is crucial in elucidating the intricate mechanism that relates cell mechanics to metabolic activities. In this study, we conducted active and passive microrheology in eukaryotic cells, and quantified nonthermal fluctuations by examining the violation of the fluctuation-dissipation theorem. The power spectral density of active force generation was estimated following the Langevin theory extended to nonequilibrium systems. However, experiments performed while regulating cellular metabolic activity showed that the nonthermal displacement fluctuation, rather than the active nonthermal force, is linked to metabolism. We discuss that mechano-enzymes in living cells do not act as microscopic objects. Instead, they generate meso-scale collective fluctuations with displacements controlled by enzymatic activity. The activity induces structural relaxations in glassy cytoplasm. Even though the autocorrelation of nonthermal fluctuations is lost at long timescales due to the structural relaxations, the nonthermal displacement fluctuation remains regulated by metabolic reactions. Our results therefore demonstrate that nonthermal fluctuations serve as a valuable indicator of a cell's metabolic activities, regardless of the presence or absence of structural relaxations.
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Affiliation(s)
| | | | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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15
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Dutta S, Ghosh A, Boettiger AN, Spakowitz AJ. Leveraging polymer modeling to reconstruct chromatin connectivity from live images. Biophys J 2023; 122:3532-3540. [PMID: 37542372 PMCID: PMC10502477 DOI: 10.1016/j.bpj.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/19/2023] [Accepted: 08/01/2023] [Indexed: 08/06/2023] Open
Abstract
Chromosomal dynamics plays a central role in a number of critical biological processes, such as transcriptional regulation, genetic recombination, and DNA replication. However, visualization of chromatin is generally limited to live imaging of a few fluorescently labeled chromosomal loci or high-resolution reconstruction of multiple loci from a single time frame. To aid in mapping the underlying chromosomal structure based on parsimonious experimental measurements, we present an exact analytical expression for the evolution of the polymer configuration based on a flexible-polymer model, and we propose an algorithm that tracks the polymer configuration from live images of chromatin marked with several fluorescent marks. Our theory identifies the resolution of microscopy needed to achieve high-accuracy tracking for a given spacing of markers, establishing the statistical confidence in the assignment of genome identity to the visualized marks. We then leverage experimental data of locus-tracking measurements to demonstrate the validity of our modeling approach and to establish a basis for the design of experiments with a desired resolution. Altogether, this work provides a computational approach founded on polymer physics that vastly improves the interpretation of in vivo measurements of biopolymer dynamics.
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Affiliation(s)
- Sayantan Dutta
- Department of Chemical Engineering, Stanford University, Stanford, California
| | - Ashesh Ghosh
- Department of Chemical Engineering, Stanford University, Stanford, California
| | | | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Program in Biophysics, Stanford University, Stanford, California.
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16
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Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023; 11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.
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Affiliation(s)
- Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - John E. Stone
- NVIDIA Corporation, Santa Clara, CA, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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17
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Eshghi I, Zidovska A, Grosberg AY. Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:69. [PMID: 37540478 DOI: 10.1140/epje/s10189-023-00327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of motors having polar symmetry, both in the linear response regime as well as in the long-term, fully nonlinear regime of the flows. The introduction of a boundary induces a particular geometry in the flows of chromatin, which we describe using vector spherical harmonics, a tool which greatly simplifies both our analytical and numerical approaches. We find that the long-term behavior of this model in confinement is dominated by steady, transverse flows of chromatin which circulate around the spherical domain. These circulating flows are found to be robust to perturbations, and their characteristic size is set by the size of the domain. This gives us further insight into active chromatin dynamics in the cell nucleus, and provides a foundation for development of further, more complex models of active chromatin dynamics.
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Affiliation(s)
- Iraj Eshghi
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexandra Zidovska
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA
| | - Alexander Y Grosberg
- Center for Soft Matter Research, Department of Physics, New York University, New York, NY, 10003, USA.
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18
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Bailey MLP, Surovtsev I, Williams JF, Yan H, Yuan T, Li K, Duseau K, Mochrie SGJ, King MC. Loops and the activity of loop extrusion factors constrain chromatin dynamics. Mol Biol Cell 2023; 34:ar78. [PMID: 37126401 PMCID: PMC10398873 DOI: 10.1091/mbc.e23-04-0119] [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: 04/05/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
The chromosomes-DNA polymers and their binding proteins-are compacted into a spatially organized, yet dynamic, three-dimensional structure. Recent genome-wide chromatin conformation capture experiments reveal a hierarchical organization of the DNA structure that is imposed, at least in part, by looping interactions arising from the activity of loop extrusion factors. The dynamics of chromatin reflects the response of the polymer to a combination of thermal fluctuations and active processes. However, how chromosome structure and enzymes acting on chromatin together define its dynamics remains poorly understood. To gain insight into the structure-dynamics relationship of chromatin, we combine high-precision microscopy in living Schizosaccharomyces pombe cells with systematic genetic perturbations and Rouse model polymer simulations. We first investigated how the activity of two loop extrusion factors, the cohesin and condensin complexes, influences chromatin dynamics. We observed that deactivating cohesin, or to a lesser extent condensin, increased chromatin mobility, suggesting that loop extrusion constrains rather than agitates chromatin motion. Our corresponding simulations reveal that the introduction of loops is sufficient to explain the constraining activity of loop extrusion factors, highlighting that the conformation adopted by the polymer plays a key role in defining its dynamics. Moreover, we find that the number of loops or residence times of loop extrusion factors influence the dynamic behavior of the chromatin polymer. Last, we observe that the activity of the INO80 chromatin remodeler, but not the SWI/SNF or RSC complexes, is critical for ATP-dependent chromatin mobility in fission yeast. Taking the data together, we suggest that thermal and INO80-dependent activities exert forces that drive chromatin fluctuations, which are constrained by the organization of the chromosome into loops.
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Affiliation(s)
- Mary Lou P. Bailey
- Department of Applied Physics, Yale University, New Haven, CT 06511
- Integrated Graduate Program in Physics Engineering Biology, Yale University, New Haven, CT 06511
| | - Ivan Surovtsev
- Department of Physics, Yale University, New Haven, CT 06511
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | | | - Hao Yan
- Integrated Graduate Program in Physics Engineering Biology, Yale University, New Haven, CT 06511
- Department of Physics, Yale University, New Haven, CT 06511
| | - Tianyu Yuan
- Integrated Graduate Program in Physics Engineering Biology, Yale University, New Haven, CT 06511
- Department of Physics, Yale University, New Haven, CT 06511
| | - Kevin Li
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - Katherine Duseau
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
| | - Simon G. J. Mochrie
- Department of Applied Physics, Yale University, New Haven, CT 06511
- Integrated Graduate Program in Physics Engineering Biology, Yale University, New Haven, CT 06511
- Department of Physics, Yale University, New Haven, CT 06511
| | - Megan C. King
- Integrated Graduate Program in Physics Engineering Biology, Yale University, New Haven, CT 06511
- Department of Molecular, Cell and Developmental Biology, Yale University, New Haven, CT 06511
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520
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19
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Stella AL, Chechkin A, Teza G. Anomalous Dynamical Scaling Determines Universal Critical Singularities. PHYSICAL REVIEW LETTERS 2023; 130:207104. [PMID: 37267558 DOI: 10.1103/physrevlett.130.207104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/19/2023] [Indexed: 06/04/2023]
Abstract
Anomalous diffusion phenomena occur on length scales spanning from intracellular to astrophysical ranges. A specific form of decay at a large argument of the probability density function of rescaled displacement (scaling function) is derived and shown to imply universal singularities in the normalized cumulant generator. Exact calculations for continuous time random walks provide paradigmatic examples connected with singularities of second order phase transitions. In the biased case scaling is restricted to displacements in the drift direction and singularities have no equilibrium analogue.
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Affiliation(s)
- Attilio L Stella
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy and INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Aleksei Chechkin
- Institute of Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany, Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, University of Science and Technology, Wyspianskiego 27, 50-370 Wrocław, Poland, and Akhiezer Institute for Theoretical Physics National Science Center ''Kharkov Institute of Physics and Technology,'' 61108, Kharkiv, Ukraine
| | - Gianluca Teza
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
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20
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Ebata H, Umeda K, Nishizawa K, Nagao W, Inokuchi S, Sugino Y, Miyamoto T, Mizuno D. Activity-dependent glassy cell mechanics Ⅰ: Mechanical properties measured with active microrheology. Biophys J 2023; 122:1781-1793. [PMID: 37050875 PMCID: PMC10209042 DOI: 10.1016/j.bpj.2023.04.011] [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: 08/22/2022] [Revised: 01/27/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
Active microrheology was conducted in living cells by applying an optical-trapping force to vigorously fluctuating tracer beads with feedback-tracking technology. The complex shear modulus G(ω)=G'(ω)-iG″(ω) was measured in HeLa cells in an epithelial-like confluent monolayer. We found that G(ω)∝(-iω)1/2 over a wide range of frequencies (1 Hz < ω/2π < 10 kHz). Actin disruption and cell-cycle progression from G1 to S and G2 phases only had a limited effect on G(ω) in living cells. On the other hand, G(ω) was found to be dependent on cell metabolism; ATP-depleted cells showed an increased elastic modulus G'(ω) at low frequencies, giving rise to a constant plateau such that G(ω)=G0+A(-iω)1/2. Both the plateau and the additional frequency dependency ∝(-iω)1/2 of ATP-depleted cells are consistent with a rheological response typical of colloidal jamming. On the other hand, the plateau G0 disappeared in ordinary metabolically active cells, implying that living cells fluidize their internal states such that they approach the critical jamming point.
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Affiliation(s)
- Hiroyuki Ebata
- Department of Physics, Kyushu University, Fukuoka, Japan
| | | | - Kenji Nishizawa
- Institute of Developmental Biology of Marseille, Marseille, France
| | - Wataru Nagao
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Shono Inokuchi
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Yujiro Sugino
- Department of Physics, Kyushu University, Fukuoka, Japan
| | - Takafumi Miyamoto
- Department of Endocrinology and Metabolism, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; Transborder Medical Research Center, University of Tsukuba, Ibaraki, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, Japan.
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21
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Goychuk A, Kannan D, Chakraborty AK, Kardar M. Polymer folding through active processes recreates features of genome organization. Proc Natl Acad Sci U S A 2023; 120:e2221726120. [PMID: 37155885 PMCID: PMC10194017 DOI: 10.1073/pnas.2221726120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate. Moreover, chromatin motion varies with genomic coordinate, pointing toward a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers nonequilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward exploring whether active mechanisms contribute to shaping genome conformations, we discuss a data-driven approach.
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Affiliation(s)
- Andriy Goychuk
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Deepti Kannan
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
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22
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Stella AL, Chechkin A, Teza G. Universal singularities of anomalous diffusion in the Richardson class. Phys Rev E 2023; 107:054118. [PMID: 37329006 DOI: 10.1103/physreve.107.054118] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/21/2023] [Indexed: 06/18/2023]
Abstract
Inhomogeneous environments are rather ubiquitous in nature, often implying anomalies resulting in deviation from Gaussianity of diffusion processes. While sub- and superdiffusion are usually due to contrasting environmental features (hindering or favoring the motion, respectively), they are both observed in systems ranging from the micro- to the cosmological scale. Here we show how a model encompassing sub- and superdiffusion in an inhomogeneous environment exhibits a critical singularity in the normalized generator of the cumulants. The singularity originates directly and exclusively from the asymptotics of the non-Gaussian scaling function of displacement, and the independence from other details confers it a universal character. Our analysis, based on the method first applied by Stella et al. [Phys. Rev. Lett. 130, 207104 (2023)10.1103/PhysRevLett.130.207104], shows that the relation connecting the scaling function asymptotics to the diffusion exponent characteristic of processes in the Richardson class implies a nonstandard extensivity in time of the cumulant generator. Numerical tests fully confirm the results.
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Affiliation(s)
- Attilio L Stella
- Department of Physics and Astronomy, University of Padova, Via Marzolo 8, I-35131 Padova, Italy and INFN, Sezione di Padova, Via Marzolo 8, I-35131 Padova, Italy
| | - Aleksei Chechkin
- Institute of Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany; Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, University of Science and Technology, Wyspianskiego 27, 50-370 Wrocław, Poland; and Akhiezer Institute for Theoretical Physics, National Science Center "Kharkov Institute of Physics and Technology", 61108 Kharkiv, Ukraine
| | - Gianluca Teza
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
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23
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Garner RM, Molines AT, Theriot JA, Chang F. Vast heterogeneity in cytoplasmic diffusion rates revealed by nanorheology and Doppelgänger simulations. Biophys J 2023; 122:767-783. [PMID: 36739478 PMCID: PMC10027447 DOI: 10.1016/j.bpj.2023.01.040] [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: 07/28/2022] [Revised: 12/22/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The cytoplasm is a complex, crowded, actively driven environment whose biophysical characteristics modulate critical cellular processes such as cytoskeletal dynamics, phase separation, and stem cell fate. Little is known about the variance in these cytoplasmic properties. Here, we employed particle-tracking nanorheology on genetically encoded multimeric 40 nm nanoparticles (GEMs) to measure diffusion within the cytoplasm of individual fission yeast (Schizosaccharomyces pombe) cellscells. We found that the apparent diffusion coefficients of individual GEM particles varied over a 400-fold range, while the differences in average particle diffusivity among individual cells spanned a 10-fold range. To determine the origin of this heterogeneity, we developed a Doppelgänger simulation approach that uses stochastic simulations of GEM diffusion that replicate the experimental statistics on a particle-by-particle basis, such that each experimental track and cell had a one-to-one correspondence with their simulated counterpart. These simulations showed that the large intra- and inter-cellular variations in diffusivity could not be explained by experimental variability but could only be reproduced with stochastic models that assume a wide intra- and inter-cellular variation in cytoplasmic viscosity. The simulation combining intra- and inter-cellular variation in viscosity also predicted weak nonergodicity in GEM diffusion, consistent with the experimental data. To probe the origin of this variation, we found that the variance in GEM diffusivity was largely independent of factors such as temperature, the actin and microtubule cytoskeletons, cell-cyle stage, and spatial locations, but was magnified by hyperosmotic shocks. Taken together, our results provide a striking demonstration that the cytoplasm is not "well-mixed" but represents a highly heterogeneous environment in which subcellular components at the 40 nm size scale experience dramatically different effective viscosities within an individual cell, as well as in different cells in a genetically identical population. These findings carry significant implications for the origins and regulation of biological noise at cellular and subcellular levels.
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Affiliation(s)
- Rikki M Garner
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Arthur T Molines
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts.
| | - Julie A Theriot
- Biophysics Program, Stanford University School of Medicine, Stanford, California; Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, Washington; Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California; Marine Biological Laboratory, Woods Hole, Massachusetts
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24
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Escudero-Pérez B, Lalande A, Mathieu C, Lawrence P. Host–Pathogen Interactions Influencing Zoonotic Spillover Potential and Transmission in Humans. Viruses 2023; 15:v15030599. [PMID: 36992308 PMCID: PMC10060007 DOI: 10.3390/v15030599] [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] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Emerging infectious diseases of zoonotic origin are an ever-increasing public health risk and economic burden. The factors that determine if and when an animal virus is able to spill over into the human population with sufficient success to achieve ongoing transmission in humans are complex and dynamic. We are currently unable to fully predict which pathogens may appear in humans, where and with what impact. In this review, we highlight current knowledge of the key host–pathogen interactions known to influence zoonotic spillover potential and transmission in humans, with a particular focus on two important human viruses of zoonotic origin, the Nipah virus and the Ebola virus. Namely, key factors determining spillover potential include cellular and tissue tropism, as well as the virulence and pathogenic characteristics of the pathogen and the capacity of the pathogen to adapt and evolve within a novel host environment. We also detail our emerging understanding of the importance of steric hindrance of host cell factors by viral proteins using a “flytrap”-type mechanism of protein amyloidogenesis that could be crucial in developing future antiviral therapies against emerging pathogens. Finally, we discuss strategies to prepare for and to reduce the frequency of zoonotic spillover occurrences in order to minimize the risk of new outbreaks.
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Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Alexandre Lalande
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Cyrille Mathieu
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
- Correspondence:
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25
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Chaki S, Theeyancheri L, Chakrabarti R. A polymer chain with dipolar active forces in connection to spatial organization of chromatin. SOFT MATTER 2023; 19:1348-1355. [PMID: 36723034 DOI: 10.1039/d2sm01170k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A living cell is an active environment where the organization and dynamics of chromatin are affected by different forms of activity. Optical experiments report that loci show subdiffusive dynamics and the chromatin fiber is seen to be coherent over micrometer-scale regions. Using a bead-spring polymer chain with dipolar active forces, we study how the subdiffusive motion of the loci generate large-scale coherent motion of the chromatin. We show that in the presence of extensile (contractile) activity, the dynamics of the loci grows faster (slower) and the spatial correlation length increases (decreases) compared to the case with no dipolar forces. Hence, both the dipolar active forces modify the elasticity of the chain. Interestingly in our model, the dynamics and organization of such dipolar active chains largely differ from the passive chain with renormalized elasticity.
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Affiliation(s)
- Subhasish Chaki
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois, 61801, USA.
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Ligesh Theeyancheri
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India.
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26
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Arbel-Goren R, McKeithen-Mead SA, Voglmaier D, Afremov I, Teza G, Grossman AD, Stavans J. Target search by an imported conjugative DNA element for a unique integration site along a bacterial chromosome during horizontal gene transfer. Nucleic Acids Res 2023; 51:3116-3129. [PMID: 36762480 PMCID: PMC10123120 DOI: 10.1093/nar/gkad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/18/2023] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are mobile genetic elements that can transfer by conjugation to recipient cells. Some ICEs integrate into a unique site in the genome of their hosts. We studied quantitatively the process by which an ICE searches for its unique integration site in the Bacillus subtilis chromosome. We followed the motion of both ICEBs1 and the chromosomal integration site in real time within individual cells. ICEBs1 exhibited a wide spectrum of dynamical behaviors, ranging from rapid sub-diffusive displacements crisscrossing the cell, to kinetically trapped states. The chromosomal integration site moved sub-diffusively and exhibited pronounced dynamical asymmetry between longitudinal and transversal motions, highlighting the role of chromosomal structure and the heterogeneity of the bacterial interior in the search. The successful search for and subsequent recombination into the integration site is a key step in the acquisition of integrating mobile genetic elements. Our findings provide new insights into intracellular transport processes involving large DNA molecules.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Dominik Voglmaier
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idana Afremov
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gianluca Teza
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alan D Grossman
- Department of Biology Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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27
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Guan Y, Xu X, Liu C, Wang J, Niu C, Zheng F, Li Q. Evaluating the physiology and fermentation performance of the lager yeast during very high gravity brewing with increased temperature. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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28
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Chen ZR, Zhou W, Shen L. Scaling Behaviors of Polymers on Lipid Membranes: Coupling of Polymer Chain Dynamics and Surface Thermal Fluctuations. CHINESE JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1007/s10118-022-2848-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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29
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Yang S, Zhao J, Cui X, Zhan Q, Yi K, Wang Q, Xiao M, Tan Y, Hong B, Fang C, Kang C. TCA-phospholipid-glycolysis targeted triple therapy effectively suppresses ATP production and tumor growth in glioblastoma. Theranostics 2022; 12:7032-7050. [PMID: 36276638 PMCID: PMC9576613 DOI: 10.7150/thno.74197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/14/2022] [Indexed: 11/14/2022] Open
Abstract
Rationale: Glioblastoma (GBM) displays a complex metabolic reprogramming in cancer cells. Adenosine triphosphate (ATP) is one of the central mediators of cell metabolism and signaling. GBM cells generate ATP by glycolysis and the tricarboxylic acid (TCA) cycle associated with oxidative phosphorylation (OXPHOS) through the breaking-down of pyruvate or fatty acids to meet the growing energy demand of cancer cells. Therefore, it's urgent to develop novel treatments targeting energy metabolism to hinder tumor cell proliferation in GBM. Methods: Non-targeted metabolomic profiling analysis was utilized to evaluate cell metabolic reprogramming using a small molecule inhibitor (SMI) EPIC-0412 treatment. Cellular oxygen consumption rate (OCR) and the total proton efflux rate (PER), as well as ATP concentration, were tracked to study metabolic responses to specifically targeted inhibitors, including EPIC-0412, arachidonyl trifluoromethyl ketone (AACOCF3), and 2 deoxy-D-glucose (2-DG). Cancer cell proliferation was assessed by CCK-8 measurements and colony formation assay. Additionally, flow cytometry, immunoblotting (IB), and immunofluorescence (IF) analyses were performed with GBM cells to understand their tumorigenic properties under treatments. Finally, the anticancer effects of this combination therapy were evaluated in the GBM mouse model by convection-enhanced delivery (CED). Results: We found that SMI EPIC-0412 could effectively perturb the TCA cycle, which participated in the combination therapy of cytosolic phospholipase A2 (cPLA2)-inhibitor AACOCF3, and hexokinase II (HK2)-inhibitor 2-DG to disrupt the GBM energy metabolism for targeted metabolic treatments. ATP production was significantly declined in glioma cells when treated with monotherapy (EPIC-0412 or AACOCF3), dual therapy (EPIC-0412 + AACOCF3), or triple therapy (EPIC-0412 + AACOCF3 +2-DG) regimen. Our experiments revealed that these therapies hindered glioma cell proliferation and growth, leading to the reduction in ATP production and G0/G1 cell cycle arrest. We demonstrated that the combination therapy effectively extended the survival of cerebral tumor-bearing mice. Conclusion: Our findings indicate that the TCA-phospholipid-glycolysis metabolism axis can be blocked by specific inhibitors that significantly disrupt the tumor energy metabolism and suppress tumor proliferation in vitro and in vivo, suggesting that targeting ATP synthesis inhibition in cancer cells might be an attractive therapeutic avenue in GBM management.
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Affiliation(s)
- Shixue Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Tianjin, 300052, China.,Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
| | - Jixing Zhao
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Tianjin, 300052, China.,Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
| | - Xiaoteng Cui
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Tianjin, 300052, China.,Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
| | - Qi Zhan
- Tianjin Key Laboratory of Composite and Functional Materials, School of Material Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Kaikai Yi
- Department of Neuro-Oncology and Neurosurgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Qixue Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Tianjin, 300052, China.,Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
| | - Menglin Xiao
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding, 071000, China
| | - Yanli Tan
- Department of Pathology, Affiliated Hospital of Hebei University, Department of Pathology, Hebei University School of Basic Medical Sciences, Baoding, 071000, China
| | - Biao Hong
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Tianjin, 300052, China.,Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Hebei Key Laboratory of Precise Diagnosis and Treatment of Glioma, Baoding, 071000, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Lab of Neuro-oncology, Tianjin Neurological Institute, Tianjin, 300052, China.,Key Laboratory of Post-Neuro Injury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, 300052, China
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30
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Huang WYC, Cheng X, Ferrell JE. Cytoplasmic organization promotes protein diffusion in Xenopus extracts. Nat Commun 2022; 13:5599. [PMID: 36151204 PMCID: PMC9508076 DOI: 10.1038/s41467-022-33339-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
The cytoplasm is highly organized. However, the extent to which this organization influences the dynamics of cytoplasmic proteins is not well understood. Here, we use Xenopus laevis egg extracts as a model system to study diffusion dynamics in organized versus disorganized cytoplasm. Such extracts are initially homogenized and disorganized, and self-organize into cell-like units over the course of tens of minutes. Using fluorescence correlation spectroscopy, we observe that as the cytoplasm organizes, protein diffusion speeds up by about a factor of two over a length scale of a few hundred nanometers, eventually approaching the diffusion time measured in organelle-depleted cytosol. Even though the ordered cytoplasm contained organelles and cytoskeletal elements that might interfere with diffusion, the convergence of protein diffusion in the cytoplasm toward that in organelle-depleted cytosol suggests that subcellular organization maximizes protein diffusivity. The effect of organization on diffusion varies with molecular size, with the effects being largest for protein-sized molecules, and with the time scale of the measurement. These results show that cytoplasmic organization promotes the efficient diffusion of protein molecules in a densely packed environment. Cytoplasmic organization is a hallmark of living cells. Here, the authors make use of self-organizing cell extracts to examine how the emergence of large-scale organizations influences the microscopic diffusion of protein molecules in the cytoplasm.
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Affiliation(s)
- William Y C Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Xianrui Cheng
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
| | - James E Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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31
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Ghosh A, Spakowitz AJ. Active and thermal fluctuations in multi-scale polymer structure and dynamics. SOFT MATTER 2022; 18:6629-6637. [PMID: 36000419 DOI: 10.1039/d2sm00593j] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The presence of athermal noise or biological fluctuations control and maintain crucial life-processes. In this work, we present an exact analytical treatment of the dynamic behavior of a flexible polymer chain that is subjected to both thermal and active forces. Our model for active forces incorporates temporal correlation associated with the characteristic time scale and processivity of enzymatic function (driven by ATP hydrolysis), leading to an active-force time scale that competes with relaxation processes within the polymer chain. We analyze the structure and dynamics of an active-Brownian polymer using our exact results for the dynamic structure factor and the looping time for the chain ends. The spectrum of relaxation times within a polymer chain implies two different behaviors at small and large length scales. Small length-scale relaxation is faster than the active-force time scale, and the dynamic and structural behavior at these scales are oblivious to active forces and, are thus governed by the true thermal temperature. Large length-scale behavior is governed by relaxation times that are much longer than the active-force time scale, resulting in an effective active-Brownian temperature that dramatically alters structural and dynamic behavior. These complex multi-scale effects imply a time-dependent temperature that governs living and non-equilibrium systems, serving as a unifying concept for interpreting and predicting their physical behavior.
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Affiliation(s)
- Ashesh Ghosh
- Department of Chemical Engineering, Stanford University, Stanford, California, USA.
| | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California, USA.
- Biophysics Program, Stanford University, Stanford, California, USA
- Department of Materials Science & Engineering, Stanford University, Stanford, California, USA
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32
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Locatelli M, Lawrimore J, Lin H, Sanaullah S, Seitz C, Segall D, Kefer P, Salvador Moreno N, Lietz B, Anderson R, Holmes J, Yuan C, Holzwarth G, Bloom KS, Liu J, Bonin K, Vidi PA. DNA damage reduces heterogeneity and coherence of chromatin motions. Proc Natl Acad Sci U S A 2022; 119:e2205166119. [PMID: 35858349 PMCID: PMC9304018 DOI: 10.1073/pnas.2205166119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 01/14/2023] Open
Abstract
Chromatin motions depend on and may regulate genome functions, in particular the DNA damage response. In yeast, DNA double-strand breaks (DSBs) globally increase chromatin diffusion, whereas in higher eukaryotes the impact of DSBs on chromatin dynamics is more nuanced. We mapped the motions of chromatin microdomains in mammalian cells using diffractive optics and photoactivatable chromatin probes and found a high level of spatial heterogeneity. DNA damage reduces heterogeneity and imposes spatially defined shifts in motions: Distal to DNA breaks, chromatin motions are globally reduced, whereas chromatin retains higher mobility at break sites. These effects are driven by context-dependent changes in chromatin compaction. Photoactivated lattices of chromatin microdomains are ideal to quantify microscale coupling of chromatin motion. We measured correlation distances up to 2 µm in the cell nucleus, spanning chromosome territories, and speculate that this correlation distance between chromatin microdomains corresponds to the physical separation of A and B compartments identified in chromosome conformation capture experiments. After DNA damage, chromatin motions become less correlated, a phenomenon driven by phase separation at DSBs. Our data indicate tight spatial control of chromatin motions after genomic insults, which may facilitate repair at the break sites and prevent deleterious contacts of DSBs, thereby reducing the risk of genomic rearrangements.
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Affiliation(s)
- Maëlle Locatelli
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Hua Lin
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Sarvath Sanaullah
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Clayton Seitz
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
| | - Dave Segall
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Paul Kefer
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Naike Salvador Moreno
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Benton Lietz
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Rebecca Anderson
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Julia Holmes
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47907
| | - George Holzwarth
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
| | - Kerry S. Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jing Liu
- Department of Physics, Indiana University–Purdue University Indianapolis, Indianapolis, IN 46202
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202
- Center for Computational Biology and Bioinformatics, Indiana University, Indianapolis, IN 46202
| | - Keith Bonin
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
| | - Pierre-Alexandre Vidi
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157
- Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC 27157
- Laboratoire InGenO, Institut de Cancérologie de l’Ouest, 49055 Angers, France
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33
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Sadoon AA, Oliver WF, Wang Y. Revisiting the Temperature Dependence of Protein Diffusion inside Bacteria: Validity of the Stokes-Einstein Equation. PHYSICAL REVIEW LETTERS 2022; 129:018101. [PMID: 35841576 DOI: 10.1103/physrevlett.129.018101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Although the transport and mixing of proteins and other molecules inside bacteria rely on the diffusion of molecules, many aspects of the molecular diffusion in bacterial cytoplasm remain unclear or controversial, including how the diffusion-temperature relation follows the Stokes-Einstein equation. In this study, we applied single-particle tracking photoactivated localization microscopy to investigate the diffusion of histonelike nucleoid structuring (HNS) proteins and free dyes in bacterial cytoplasm at different temperatures. Although the diffusion of HNS proteins in both live and dead bacteria increased at higher temperatures and appeared to follow the Arrhenius equation, the diffusion of free dyes decreased at higher temperatures, questioning the previously proposed theories based on superthermal fluctuations. To understand the measured diffusion-temperature relations, we developed an alternative model, in which the bacterial cytoplasm is considered as a polymeric network or mesh. In our model, the Stokes-Einstein equation remains valid, while the polymeric network contributes a significant term to the viscosity experienced by the molecules diffusing in bacterial cytoplasm. Our model was successful in predicting the diffusion-temperature relations for both HNS proteins and free dyes in bacteria. In addition, we systematically examined the predicted diffusion-temperature relations with different parameters in the model, and predicted the possible existence of phase transitions.
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Affiliation(s)
- Asmaa A Sadoon
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Department of Physics, University of Thi-Qar, Nassiriya 64001, Iraq
| | - William F Oliver
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Yong Wang
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, USA
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34
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Bera P, Wasim A, Mondal J. Hi-C embedded polymer model of Escherichia coli reveals the origin of heterogeneous subdiffusion in chromosomal loci. Phys Rev E 2022; 105:064402. [PMID: 35854496 DOI: 10.1103/physreve.105.064402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Underneath its apparently simple architecture, the circular chromosome of Escherichia coli is known for displaying complex dynamics in its cytoplasm, with past investigations hinting at inherently diverse mobilities of chromosomal loci across the genome. To decipher its origin, we simulate the dynamics of genome-wide spectrum of E. coli chromosomal loci, via integrating its experimentally derived Hi-C interaction matrix within a polymer-based model. Our analysis demonstrates that, while the dynamics of the chromosome is subdiffusive in a viscoelastic media, the diffusion constants are strongly dependent of chromosomal loci coordinates and diffusive exponents (α) are widely heterogenous with α ≈ 0.36-0.60. The loci-dependent heterogeneous dynamics and mean first-passage times of interloci encounter were found to be modulated via genetically distant interloci communications and is robust even in the presence of active, ATP-dependent noises. Control investigations reveal that the absence of Hi-C-derived interactions in the model would have abolished the traits of heterogeneous loci diffusion, underscoring the key role of loci-specific genetically distant interaction in modulating the underlying heterogeneity of the loci diffusion.
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Affiliation(s)
- Palash Bera
- Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Abdul Wasim
- Tata Institute of Fundamental Research, Hyderabad 500046, India
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35
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Lee DSW, Strom AR, Brangwynne CP. The mechanobiology of nuclear phase separation. APL Bioeng 2022; 6:021503. [PMID: 35540725 PMCID: PMC9054271 DOI: 10.1063/5.0083286] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/19/2022] [Indexed: 02/06/2023] Open
Abstract
The cell nucleus can be thought of as a complex, dynamic, living material, which functions to organize and protect the genome and coordinate gene expression. These functions are achieved via intricate mechanical and biochemical interactions among its myriad components, including the nuclear lamina, nuclear bodies, and the chromatin itself. While the biophysical organization of the nuclear lamina and chromatin have been thoroughly studied, the concept that liquid–liquid phase separation and related phase transitions play a role in establishing nuclear structure has emerged only recently. Phase transitions are likely to be intimately coupled to the mechanobiology of structural elements in the nucleus, but their interplay with one another is still not understood. Here, we review recent developments on the role of phase separation and mechanics in nuclear organization and discuss the functional implications in cell physiology and disease states.
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Affiliation(s)
- Daniel S. W. Lee
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Amy R. Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Clifford P. Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, New Jersey 08544, USA
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36
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Starr CH, Bryant Z, Spakowitz AJ. Coarse-grained modeling reveals the impact of supercoiling and loop length in DNA looping kinetics. Biophys J 2022; 121:1949-1962. [PMID: 35421389 PMCID: PMC9199097 DOI: 10.1016/j.bpj.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/19/2021] [Accepted: 04/06/2022] [Indexed: 11/02/2022] Open
Abstract
Measurements of protein-mediated DNA looping reveal that in vivo conditions favor the formation of loops shorter than those that occur in vitro, yet the precise physical mechanisms underlying this shift remain unclear. To understand the extent to which in vivo supercoiling may explain these shifts, we develop a theoretical model based on coarse-grained molecular simulation and analytical transition state theory, enabling us to map out looping energetics and kinetics as a function of two key biophysical parameters: superhelical density and loop length. We show that loops on the scale of a persistence length respond to supercoiling over a much wider range of superhelical densities and to a larger extent than longer loops. This effect arises from a tendency for loops to be centered on the plectonemic end region, which bends progressively more tightly with superhelical density. This trend reveals a mechanism by which supercoiling favors shorter loop lengths. In addition, our model predicts a complex kinetic response to supercoiling for a given loop length, governed by a competition between an enhanced rate of looping due to torsional buckling and a reduction in looping rate due to chain straightening as the plectoneme tightens at higher superhelical densities. Together, these effects lead to a flattening of the kinetic response to supercoiling within the physiological range for all but the shortest loops. Using experimental estimates for in vivo superhelical densities, we discuss our model's ability to explain available looping data, highlighting both the importance of supercoiling as a regulatory force in genetics and the additional complexities of looping phenomena in vivo.
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Affiliation(s)
- Charles H Starr
- Biophysics Program, Stanford University, Stanford, California
| | - Zev Bryant
- Biophysics Program, Stanford University, Stanford, California; Department of Bioengineering, Stanford University, Stanford, California
| | - Andrew J Spakowitz
- Biophysics Program, Stanford University, Stanford, California; Department of Chemical Engineering, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California.
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37
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Musial G, Kohlfaerber T, Ahrens M, Schulz-Hildebrandt H, Steven P, Hüttmann G. Dynamic Contrast Microscopic Optical Coherence Tomography As a Novel Method for Assessing Corneal Epithelium During Exposure to Benzalkonium Chloride. Transl Vis Sci Technol 2022; 11:28. [PMID: 35622381 PMCID: PMC9145126 DOI: 10.1167/tvst.11.5.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Microscopic optical coherence tomography (mOCT) has an imaging resolution of 1 µm in all voxel dimensions, but individual epithelial cells are difficult to resolve due to lack of scattering contrast. Adding dynamic contrast processing to mOCT (dmOCT) results in color images that enable visualization of individual cells and possibly give information on cellular function via the calculation of a motility coefficient. We propose this technique as a novel method of evaluating the ocular surface after exposure to a toxic chemical, benzalkonium chloride (BAK). Methods Ex vivo cross-section images were acquired with a custom-built, frequency-domain mOCT system. Eyes were explanted from healthy adult C57BL/6 mice and imaged every 30 minutes with five sets of dmOCT scans at each imaging time. Total epithelium and stroma thicknesses were measured from a single mOCT B-scan, and measures of color changes (hue) and the motility coefficient were acquired from dmOCT scans. Results After 30-minute exposures to 0.005% BAK, local motility decreased and total epithelium thickness increased compared to controls. For basal epithelium cells, local motility decreased after 60-minute exposures, and the hue shifted red after 90-minute exposures. Stroma thickness did not significantly swell until 150-minute exposures to BAK. Conclusions dmOCT allows us to view the behavior of the cornea epithelium under toxic stress due to BAK, revealing parallel swelling of the extracellular matrix and changes in local subcellular motion. Translational Relevance The evaluation of the cornea epithelium using dmOCT is helpful to our understanding of the toxic effects of BAK.
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Affiliation(s)
- Gwen Musial
- University Hospital Cologne, Cologne, Germany
| | | | - Martin Ahrens
- Institute of Biomedial Optics, University of Lübeck, Lübeck, Germany
| | | | | | - Gereon Hüttmann
- Institute of Biomedial Optics, University of Lübeck, Lübeck, Germany.,Airway Research Center North Member of the German Center for Lung Research, DZL, 22927 Großhansdorf, Germany.,Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany
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38
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Yesbolatova AK, Arai R, Sakaue T, Kimura A. Formulation of Chromatin Mobility as a Function of Nuclear Size during C. elegans Embryogenesis Using Polymer Physics Theories. PHYSICAL REVIEW LETTERS 2022; 128:178101. [PMID: 35570447 DOI: 10.1103/physrevlett.128.178101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
During early embryogenesis of the nematode, Caenorhabditis elegans, the chromatin motion markedly decreases. Despite its biological implications, the underlying mechanism for this transition was unclear. By combining theory and experiment, we analyze the mean-square displacement (MSD) of the chromatin loci, and demonstrate that MSD-vs-time relationships in various nuclei collapse into a single master curve by normalizing them with the mesh size and the corresponding time scale. This enables us to identify the onset of the entangled dynamics with the size of tube diameter of chromatin polymer in the C. elegans embryo. Our dynamical scaling analysis predicts the transition between unentangled and entangled dynamics of chromatin polymers, the quantitative formula for MSD as a function of nuclear size and timescale, and provides testable hypotheses on chromatin mobility in other cell types and species.
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Affiliation(s)
- Aiya K Yesbolatova
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Ritsuko Arai
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Akatsuki Kimura
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Mishima 411-8540, Japan
- Cell Architecture Laboratory, Department of Chromosome Science, National Institute of Genetics, Mishima 411-8540, Japan
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39
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Losa J, Leupold S, Alonso-Martinez D, Vainikka P, Thallmair S, Tych KM, Marrink SJ, Heinemann M. Perspective: a stirring role for metabolism in cells. Mol Syst Biol 2022; 18:e10822. [PMID: 35362256 PMCID: PMC8972047 DOI: 10.15252/msb.202110822] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self‐propel or to break free from supramolecular structures. This catalysis‐induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research.
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Affiliation(s)
- José Losa
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Simeon Leupold
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Diego Alonso-Martinez
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Petteri Vainikka
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Katarzyna M Tych
- Chemical Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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40
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Diffusion and distal linkages govern interchromosomal dynamics during meiotic prophase. Proc Natl Acad Sci U S A 2022; 119:e2115883119. [PMID: 35302885 PMCID: PMC8944930 DOI: 10.1073/pnas.2115883119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceEssential for sexual reproduction, meiosis is a specialized cell division required for the production of haploid gametes. Critical to this process are the pairing, recombination, and segregation of homologous chromosomes (homologs). While pairing and recombination are linked, it is not known how many linkages are sufficient to hold homologs in proximity. Here, we reveal that random diffusion and the placement of a small number of linkages are sufficient to establish the apparent "pairing" of homologs. We also show that colocalization between any two loci is more dynamic than anticipated. Our study provides observations of live interchromosomal dynamics during meiosis and illustrates the power of combining single-cell measurements with theoretical polymer modeling.
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41
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Saurabh S, Chong TN, Bayas C, Dahlberg PD, Cartwright HN, Moerner WE, Shapiro L. ATP-responsive biomolecular condensates tune bacterial kinase signaling. SCIENCE ADVANCES 2022; 8:eabm6570. [PMID: 35171683 PMCID: PMC8849385 DOI: 10.1126/sciadv.abm6570] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Biomolecular condensates formed via liquid-liquid phase separation enable spatial and temporal organization of enzyme activity. Phase separation in many eukaryotic condensates has been shown to be responsive to intracellular adenosine triphosphate (ATP) levels, although the consequences of these mechanisms for enzymes sequestered within the condensates are unknown. Here, we show that ATP depletion promotes phase separation in bacterial condensates composed of intrinsically disordered proteins. Enhanced phase separation promotes the sequestration and activity of a client kinase enabling robust signaling and maintenance of viability under the stress posed by nutrient scarcity. We propose that a diverse repertoire of condensates can serve as control knobs to tune enzyme sequestration and reactivity in response to the metabolic state of bacterial cells.
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Affiliation(s)
- Saumya Saurabh
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Corresponding author. (S.S.); (L.S.)
| | - Trisha N. Chong
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Camille Bayas
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | | | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Corresponding author. (S.S.); (L.S.)
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42
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Mechanisms of DNA Mobilization and Sequestration. Genes (Basel) 2022; 13:genes13020352. [PMID: 35205396 PMCID: PMC8872102 DOI: 10.3390/genes13020352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 12/04/2022] Open
Abstract
The entire genome becomes mobilized following DNA damage. Understanding the mechanisms that act at the genome level requires that we embrace experimental and computational strategies to capture the behavior of the long-chain DNA polymer, which is the building block for the chromosome. Long-chain polymers exhibit constrained, sub-diffusive motion in the nucleus. Cross-linking proteins, including cohesin and condensin, have a disproportionate effect on genome organization in their ability to stabilize transient interactions. Cross-linking proteins can segregate the genome into sub-domains through polymer–polymer phase separation (PPPS) and can drive the formation of gene clusters through small changes in their binding kinetics. Principles from polymer physics provide a means to unravel the mysteries hidden in the chains of life.
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43
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Kim JY, Jin CR, Kim HS, Park J, Choi YE. Fluorogenic "on-off" nanosensor based on dual-quenching effect for imaging intracellular metabolite of various microalgae. Biosens Bioelectron 2022; 198:113839. [PMID: 34856515 DOI: 10.1016/j.bios.2021.113839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/23/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022]
Abstract
Sensing intracellular compounds such as ATP in living microalgal cells is of great importance in diverse fields. To achieve this, nanosensing platform composed of graphene oxide (GO) and ATP aptamer (APT) was applied to diverse microalgal cells (Chlamydomonas reinhardtii, Chlorella vulgaris, Anabaena flos-aquae, and Ochromonas danica). The nanosized GO was characterized with atomic force microscopy (AFM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). The nanosensing platform (GO-APT) was prepared by attaching fluorophore-labeled APT to GO. GO-APT was applicable to only cell wall-deficient species (O. danica and mutant strains of C. reinhardtii) and the existence of flagella did not affect the uptake of the GO-APT by the cells. These results indicate that the cell wall is the primary barrier of GO-APT internalization for sensing application. To reduce the background fluorescence signal elicited by nonspecific displacement of the fluorophore-labeled probe, APT was modified as molecular beacon (MB) type (APTMB). Owing to the double quenching effect (by GO and quencher-labeled complementary sequence), the background signal significantly reduced. Cytotoxicity of GO-APTMB on the microalgal species was also tested. The application of GO-APTMB had no effect on the growth of microalgae. Given that diverse aptamer sequences had been screened, the sensing platform is not limited for detecting ATP only, but also can be applied to other metabolite imaging by simply changing the aptamer sequences. Our research will contribute to broadening the application of GO and aptamer beacon complex for intracellular metabolite imaging and detecting.
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Affiliation(s)
- Jee Young Kim
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul, 02841, South Korea
| | - Cho Rok Jin
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul, 02841, South Korea
| | - Hyun Soo Kim
- Department of Electronic Engineering, Kwangwoon University, Seoul, 01897, South Korea
| | - Jaewon Park
- School of Microelectronics, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yoon-E Choi
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul, 02841, South Korea.
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44
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Simultaneous probing of dual intracellular metabolites (ATP and paramylon) in live microalgae using graphene oxide/aptamer nanocomplex. Mikrochim Acta 2022; 189:88. [DOI: 10.1007/s00604-022-05198-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/21/2022] [Indexed: 11/28/2022]
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45
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Eisenstecken T, Winkler RG. Path integral description of semiflexible active Brownian polymers. J Chem Phys 2022; 156:064105. [DOI: 10.1063/5.0081020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Roland G. Winkler
- Institute for Advanced Simulation, Forschungszentrum Jülich, Germany
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46
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Phipps J, Dubrana K. DNA Repair in Space and Time: Safeguarding the Genome with the Cohesin Complex. Genes (Basel) 2022; 13:198. [PMID: 35205243 PMCID: PMC8872453 DOI: 10.3390/genes13020198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 12/04/2022] Open
Abstract
DNA double-strand breaks (DSBs) are a deleterious form of DNA damage, which must be robustly addressed to ensure genome stability. Defective repair can result in chromosome loss, point mutations, loss of heterozygosity or chromosomal rearrangements, which could lead to oncogenesis or cell death. We explore the requirements for the successful repair of DNA DSBs by non-homologous end joining and homology-directed repair (HDR) mechanisms in relation to genome folding and dynamics. On the occurrence of a DSB, local and global chromatin composition and dynamics, as well as 3D genome organization and break localization within the nuclear space, influence how repair proceeds. The cohesin complex is increasingly implicated as a key regulator of the genome, influencing chromatin composition and dynamics, and crucially genome organization through folding chromosomes by an active loop extrusion mechanism, and maintaining sister chromatid cohesion. Here, we consider how this complex is now emerging as a key player in the DNA damage response, influencing repair pathway choice and efficiency.
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Affiliation(s)
| | - Karine Dubrana
- UMR Stabilité Génétique Cellules Souches et Radiations, INSERM, iRCM/IBFJ CEA, Université de Paris and Université Paris-Saclay, F-92265 Fontenay-aux-Roses, France;
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47
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Zhang M, Seitz C, Chang G, Iqbal F, Lin H, Liu J. A guide for single-particle chromatin tracking in live cell nuclei. Cell Biol Int 2022; 46:683-700. [PMID: 35032142 PMCID: PMC9035067 DOI: 10.1002/cbin.11762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/29/2021] [Accepted: 01/08/2022] [Indexed: 11/09/2022]
Abstract
The emergence of labeling strategies and live cell imaging methods enables the imaging of chromatin in living cells at single digit nanometer resolution as well as milliseconds temporal resolution. These technical breakthroughs revolutionize our understanding of chromatin structure, dynamics and functions. Single molecule tracking algorithms are usually preferred to quantify the movement of these intranucleus elements to interpret the spatiotemporal evolution of the chromatin. In this review, we will first summarize the fluorescent labeling strategy of chromatin in live cells which will be followed by a sys-tematic comparison of live cell imaging instrumentation. With the proper microscope, we will discuss the image analysis pipelines to extract the biophysical properties of the chromatin. Finally, we expect to give practical suggestions to broad biologists on how to select methods and link to the model properly according to different investigation pur-poses. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mengdi Zhang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Clayton Seitz
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Garrick Chang
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Fadil Iqbal
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Hua Lin
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Jing Liu
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA.,Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN, USA.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
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48
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Sakaue T, Kimura A. Scaling Relationship in Chromatin as a Polymer. Results Probl Cell Differ 2022; 70:263-277. [PMID: 36348110 DOI: 10.1007/978-3-031-06573-6_8] [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: 06/16/2023]
Abstract
Genomic DNA, which controls genetic information, is stored in the cell nucleus in eukaryotes. Chromatin moves dynamically in the nucleus, and this movement is closely related to the function of chromatin. However, the driving force of chromatin movement, its control mechanism, and the functional significance of movement are unclear. In addition to biochemical and genetic approaches such as identification and analysis of regulators, approaches based on the physical properties of chromatin and cell nuclei are indispensable for this understanding. In particular, the idea of polymer physics is expected to be effective. This paper introduces our efforts to combine biological experiments on chromatin kinetics with theoretical analysis based on polymer physics.
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Affiliation(s)
- Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan.
| | - Akatsuki Kimura
- Cell Architecture Laboratory, National Institute of Genetics, Mishima, Japan.
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Japan.
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49
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Mancini L, Crozat E, Javer A, Lagomarsino MC, Cicuta P. Dynamics of Bacterial Chromosomes by Locus Tracking in Fluorescence Microscopy. Methods Mol Biol 2022; 2476:155-170. [PMID: 35635703 DOI: 10.1007/978-1-0716-2221-6_12] [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: 06/15/2023]
Abstract
In the last two decades, it has been shown that bacterial chromosomes have remarkable spatial organization at various scales, and they display well-defined movements during the cell cycle, for example to reliably segregate daughter chromosomes. More recently, various labs have begun investigating also the short time dynamics (displacements during time intervals of 0.1 s-100 s), which should be related to the molecular structure. Probing these dynamics is analogous to "microrheology" approaches that have been applied successfully to study mechanical response of complex fluids. These studies of chromosome fluctuation dynamics have revealed differences of fluctuation amplitude across the chromosome, and different characters of motion depending on the time window of interest. Different fluctuation amplitudes have also been observed for the same chromosomal loci under antibiotic treatments, with magnitudes that are correlated to changes in intracellular density and thus crowding. We describe how to carry out tracking experiments of single loci and how to analyze locus motility. We point out the importance of considering in the analysis the number of GFP molecules per fluorescent locus, as well as the nature of the protein they are fused to, and also how to measure intracellular density.
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Affiliation(s)
- Leonardo Mancini
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Estelle Crozat
- Centre de Biologie Intégrative de Toulouse, Laboratoire de Microbiologie et de Génétique Moléculaires, Université de Toulouse, CNRS, UPS, Toulouse, France
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Avelino Javer
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Marco Cosentino Lagomarsino
- IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
- Physics Department, University of Milan, and INFN, Milan, Italy
| | - Pietro Cicuta
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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50
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Ghosh A, Spakowitz AJ. Statistical behavior of nonequilibrium and living biological systems subjected to active and thermal fluctuations. Phys Rev E 2022; 105:014415. [PMID: 35193230 DOI: 10.1103/physreve.105.014415] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
We present a path-integral formulation of the motion of a particle subjected to fluctuating active and thermal forces. This general framework predicts the statistical behavior associated with the stochastic trajectories of the particle, accounting for all possible realizations of Brownian and active forces, over an arbitrary potential landscape. Temporal correlations in the active forces result in non-Markovian statistics, necessitating the inclusion of a fixed active-force value at specified times within the statistical treatment. We specialize our theory to that of exponentially correlated active forces for a particle in a harmonic potential. We find the exact results for the statistical distributions for the initial position of the particle, accounting for the impact of the correlated active forces at all times prior to the initial time. Our theory is then used to find the two-point distribution for the active Brownian particle, which governs the joint probability that a particle begins and ends at specified locations. Analyses of the active Brownian statistics demonstrate that the impact of active forces can be interpreted through a time-dependent temperature whose influence depends on the competition of timescales of the active-force correlation and the relaxation time of the particle in the harmonic potential. The general results presented in this work are transferable to a broad range of nonequilibrium systems with active and Brownian motion, and the time-dependent temperature serves as a governing principle to describe the competition of timescales associated with active forces and internal relaxation processes.
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Affiliation(s)
- Ashesh Ghosh
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Andrew J Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, USA
- Department of Materials Science, Stanford University, Stanford, California 94305, USA
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Biophysics Program, Stanford University, Stanford, California 94305, USA
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