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Chakraborty S, Mishra J, Roy A, Niharika, Manna S, Baral T, Nandi P, Patra S, Patra SK. Liquid-liquid phase separation in subcellular assemblages and signaling pathways: Chromatin modifications induced gene regulation for cellular physiology and functions including carcinogenesis. Biochimie 2024; 223:74-97. [PMID: 38723938 DOI: 10.1016/j.biochi.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024]
Abstract
Liquid-liquid phase separation (LLPS) describes many biochemical processes, including hydrogel formation, in the integrity of macromolecular assemblages and existence of membraneless organelles, including ribosome, nucleolus, nuclear speckles, paraspeckles, promyelocytic leukemia (PML) bodies, Cajal bodies (all exert crucial roles in cellular physiology), and evidence are emerging day by day. Also, phase separation is well documented in generation of plasma membrane subdomains and interplay between membranous and membraneless organelles. Intrinsically disordered regions (IDRs) of biopolymers/proteins are the most critical sticking regions that aggravate the formation of such condensates. Remarkably, phase separated condensates are also involved in epigenetic regulation of gene expression, chromatin remodeling, and heterochromatinization. Epigenetic marks on DNA and histones cooperate with RNA-binding proteins through their IDRs to trigger LLPS for facilitating transcription. How phase separation coalesces mutant oncoproteins, orchestrate tumor suppressor genes expression, and facilitated cancer-associated signaling pathways are unravelling. That autophagosome formation and DYRK3-mediated cancer stem cell modification also depend on phase separation is deciphered in part. In view of this, and to linchpin insight into the subcellular membraneless organelle assembly, gene activation and biological reactions catalyzed by enzymes, and the downstream physiological functions, and how all these events are precisely facilitated by LLPS inducing organelle function, epigenetic modulation of gene expression in this scenario, and how it goes awry in cancer progression are summarized and presented in this article.
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Affiliation(s)
- Subhajit Chakraborty
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Jagdish Mishra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Tirthankar Baral
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Piyasa Nandi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India
| | - Subhajit Patra
- Department of Chemical Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, India.
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Trovato F, Fumagalli G. Molecular simulations of cellular processes. Biophys Rev 2017; 9:941-958. [PMID: 29185136 DOI: 10.1007/s12551-017-0363-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/19/2017] [Indexed: 12/12/2022] Open
Abstract
It is, nowadays, possible to simulate biological processes in conditions that mimic the different cellular compartments. Several groups have performed these calculations using molecular models that vary in performance and accuracy. In many cases, the atomistic degrees of freedom have been eliminated, sacrificing both structural complexity and chemical specificity to be able to explore slow processes. In this review, we will discuss the insights gained from computer simulations on macromolecule diffusion, nuclear body formation, and processes involving the genetic material inside cell-mimicking spaces. We will also discuss the challenges to generate new models suitable for the simulations of biological processes on a cell scale and for cell-cycle-long times, including non-equilibrium events such as the co-translational folding, misfolding, and aggregation of proteins. A prominent role will be played by the wise choice of the structural simplifications and, simultaneously, of a relatively complex energetic description. These challenging tasks will rely on the integration of experimental and computational methods, achieved through the application of efficient algorithms. Graphical abstract.
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Affiliation(s)
- Fabio Trovato
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany.
| | - Giordano Fumagalli
- Nephrology and Dialysis Unit, USL Toscana Nord Ovest, 55041, Lido di Camaiore, Lucca, Italy
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Sawyer IA, Hager GL, Dundr M. Specific genomic cues regulate Cajal body assembly. RNA Biol 2017; 14:791-803. [PMID: 27715441 PMCID: PMC5519236 DOI: 10.1080/15476286.2016.1243648] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/06/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
The assembly of specialized sub-nuclear microenvironments known as nuclear bodies (NBs) is important for promoting efficient nuclear function. In particular, the Cajal body (CB), a prominent NB that facilitates spliceosomal snRNP biogenesis, assembles in response to genomic cues. Here, we detail the factors that regulate CB assembly and structural maintenance. These include the importance of transcription at nucleating gene loci, the grouping of these genes on human chromosomes 1, 6 and 17, as well as cell cycle and biochemical regulation of CB protein function. We also speculate on the correlation between CB formation and RNA splicing levels in neurons and cancer. The timing and location of these specific molecular events is critical to CB assembly and its contribution to genome function. However, further work is required to explore the emerging biophysical characteristics of CB assembly and the impact upon subsequent genome reorganization.
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Affiliation(s)
- Iain A. Sawyer
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon L. Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, Chicago Medical School, North Chicago, IL, USA
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Jung J, Jang E, Shoaib MA, Jo K, Kim JS. Droplet formation and growth inside a polymer network: A molecular dynamics simulation study. J Chem Phys 2016; 144:134502. [PMID: 27059575 DOI: 10.1063/1.4944965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a molecular dynamics simulation study that focuses on the formation and growth of nanoscale droplets inside polymer networks. Droplet formation and growth are investigated by the liquid-vapor phase separation of a dilute Lennard-Jones (LJ) fluid inside regularly crosslinked, polymer networks with varying mesh sizes. In a polymer network with small mesh sizes, droplet formation can be suppressed, the extent of which is dependent on the attraction strength between the LJ particles. When droplets form in a polymer network with intermediate mesh sizes, subsequent growth is significantly slower when compared with that in bulk without a polymer network. Interestingly, droplet growth beyond the initial nucleation stage occurs by different mechanisms depending on the mesh size: droplets grow mainly by diffusion and coalescence inside polymer networks with large mesh sizes (as observed in bulk), whereas Ostwald ripening becomes a more dominant mechanism for droplet growth for small mesh sizes. The analysis of droplet trajectories clearly reveals the obstruction effect of the polymer network on the movement of growing droplets, which leads to Ostwald ripening of droplets. This study suggests how polymer networks can be used to control the growth of nanoscale droplets.
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Affiliation(s)
- Jiyun Jung
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Eunseon Jang
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Mahbubul Alam Shoaib
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyubong Jo
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul 04107, Republic of Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea
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