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Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024; 124:8550-8595. [PMID: 38885177 PMCID: PMC11260227 DOI: 10.1021/acs.chemrev.4c00138] [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] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
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2
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Leyden MR, Michalik P, Baruffaldi L, Mahmood S, Kalani L, Hunt DF, Eirin-Lopez JM, Andrade MC, Shabanowitz J, Ausió J. The protamines of the noble false widow spider Steatoda nobilis provide an example of liquid-liquid phase separation chromatin transitions during spermiogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597381. [PMID: 38895387 PMCID: PMC11185589 DOI: 10.1101/2024.06.04.597381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
While there is extensive information about sperm nuclear basic proteins (SNBP) in vertebrates, there is very little information about Arthropoda by comparison. This paper aims to contribute to filling this gap by analyzing these proteins in the sperm of the noble false widow spider Steatoda nobilis (Order Araneae, Family Theridiidae). To this end, we have developed a protein extraction method that allows the extraction of cysteine-containing protamines suitable for the preparation and analysis of SNBPs from samples where the amount of starting tissue material is limited. We carried out top-down mass spectrometry sequencing and molecular phylogenetic analyses to characterize the protamines of S. nobilis and other spiders. We also used electron microscopy to analyze the chromatin organization of the sperm, and we found it to exhibit liquid-liquid phase spinodal decomposition during the late stages of spermiogenesis. These studies further our knowledge of the distribution of SNBPs within the animal kingdom and provide additional support for a proposed evolutionary origin of many protamines from a histone H1 (H5) replication-independent precursor.
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Affiliation(s)
- Melissa R. Leyden
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Peter Michalik
- Zoologisches Institut und Museum, Universität Greifswald, Greifswald, Germany
| | - Luciana Baruffaldi
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Susheen Mahmood
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Ladan Kalani
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 2Y2, Canada
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Jose Maria Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, Florida, USA
| | - Maydianne C.B. Andrade
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON, M1C 1A4, Canada
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC V8W 2Y2, Canada
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3
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Leyden MR, Gowen B, Gonzalez-Romero R, Eirin-Lopez JM, Kim BH, Hayashi F, McCartney J, Zhang PC, Kubo-Irie M, Shabanowitz J, Hunt DF, Ferree P, Kasinsky H, Ausió J. Protamines and the sperm nuclear basic proteins Pandora's Box of insects. Biochem Cell Biol 2024; 102:238-251. [PMID: 38408323 DOI: 10.1139/bcb-2023-0363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Insects are the largest group of animals when it comes to the number and diversity of species. Yet, with the exception of Drosophila, no information is currently available on the primary structure of their sperm nuclear basic proteins (SNBPs). This paper represents the first attempt in this regard and provides information about six species of Neoptera: Poecillimon thessalicus, Graptosaltria nigrofuscata, Apis mellifera, Nasonia vitripennis, Parachauliodes continentalis, and Tribolium castaneum. The SNBPs of these species were characterized by acetic acid urea gel electrophoresis (AU-PAGE) and high-performance liquid chromatography fractionated. Protein sequencing was obtained using a combination of mass spectrometry sequencing, Edman N-terminal degradation sequencing and genome mining. While the SNBPs of several of these species exhibit a canonical arginine-rich protamine nature, a few of them exhibit a protamine-like composition. They appear to be the products of extensive cleavage processing from a precursor protein which are sometimes further processed by other post-translational modifications that are likely involved in the chromatin transitions observed during spermiogenesis in these organisms.
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Affiliation(s)
- Melissa R Leyden
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Brent Gowen
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Rodrigo Gonzalez-Romero
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Jose Maria Eirin-Lopez
- Environmental Epigenetics Laboratory, Institute of Environment, Florida International University, Miami, FL, USA
- Florida International University, Miami, FL, USA
| | - Bo-Hyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Fumio Hayashi
- Department of Biology, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji, Tokyo 192-0397, Japan
| | - Jay McCartney
- Institute of Natural Sciences, Massey University, Palmerston North, Manawatu, New Zealand
| | - Patrick C Zhang
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - Miyoko Kubo-Irie
- Biological Laboratory, The Open University of Japan, Wakaba, Mihama-ku, Chiba, 261-8506, Japan
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA
| | - Patrick Ferree
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711, USA
| | - Harold Kasinsky
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
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Kaur R, Meier CJ, McGraw EA, Hillyer JF, Bordenstein SR. The mechanism of cytoplasmic incompatibility is conserved in Wolbachia-infected Aedes aegypti mosquitoes deployed for arbovirus control. PLoS Biol 2024; 22:e3002573. [PMID: 38547237 PMCID: PMC11014437 DOI: 10.1371/journal.pbio.3002573] [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: 11/20/2023] [Revised: 04/12/2024] [Accepted: 03/01/2024] [Indexed: 04/13/2024] Open
Abstract
The rising interest and success in deploying inherited microorganisms and cytoplasmic incompatibility (CI) for vector control strategies necessitate an explanation of the CI mechanism. Wolbachia-induced CI manifests in the form of embryonic lethality when sperm from Wolbachia-bearing testes fertilize eggs from uninfected females. Embryos from infected females however survive to sustain the maternally inherited symbiont. Previously in Drosophila melanogaster flies, we demonstrated that CI modifies chromatin integrity in developing sperm to bestow the embryonic lethality. Here, we validate these findings using wMel-transinfected Aedes aegypti mosquitoes released to control vector-borne diseases. Once again, the prophage WO CI proteins, CifA and CifB, target male gametic nuclei to modify chromatin integrity via an aberrant histone-to-protamine transition. Cifs are not detected in the embryo, and thus elicit CI via the nucleoprotein modifications established pre-fertilization. The rescue protein CifA in oogenesis localizes to stem cell, nurse cell, and oocyte nuclei, as well as embryonic DNA during embryogenesis. Discovery of the nuclear targeting Cifs and altered histone-to-protamine transition in both Aedes aegypti mosquitoes and D. melanogaster flies affirm the Host Modification Model of CI is conserved across these host species. The study also newly uncovers the cell biology of Cif proteins in the ovaries, CifA localization in the embryos, and an impaired histone-to-protamine transition during spermiogenesis of any mosquito species. Overall, these sperm modification findings may enable future optimization of CI efficacy in vectors or pests that are refractory to Wolbachia transinfections.
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Affiliation(s)
- Rupinder Kaur
- Pennsylvania State University, Departments of Biology and Entomology, University Park, Pennsylvania, United States of America
- Pennsylvania State University, One Health Microbiome Center, Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
| | - Cole J. Meier
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
| | - Elizabeth A. McGraw
- Pennsylvania State University, Departments of Biology and Entomology, University Park, Pennsylvania, United States of America
- Pennsylvania State University, One Health Microbiome Center, Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America
- Pennsylvania State University, Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America
| | - Julian F. Hillyer
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Pennsylvania State University, Departments of Biology and Entomology, University Park, Pennsylvania, United States of America
- Pennsylvania State University, One Health Microbiome Center, Huck Institutes of the Life Sciences, University Park, Pennsylvania, United States of America
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
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5
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Orsi GA, Tortora MMC, Horard B, Baas D, Kleman JP, Bucevičius J, Lukinavičius G, Jost D, Loppin B. Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis. Nat Commun 2023; 14:4187. [PMID: 37443316 PMCID: PMC10345107 DOI: 10.1038/s41467-023-39908-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Spermiogenesis is a radical process of differentiation whereby sperm cells acquire a compact and specialized morphology to cope with the constraints of sexual reproduction while preserving their main cargo, an intact copy of the paternal genome. In animals, this often involves the replacement of most histones by sperm-specific nuclear basic proteins (SNBPs). Yet, how the SNBP-structured genome achieves compaction and accommodates shaping remain largely unknown. Here, we exploit confocal, electron and super-resolution microscopy, coupled with polymer modeling to identify the higher-order architecture of sperm chromatin in the needle-shaped nucleus of the emerging model cricket Gryllus bimaculatus. Accompanying spermatid differentiation, the SNBP-based genome is strikingly reorganized as ~25nm-thick fibers orderly coiled along the elongated nucleus axis. This chromatin spool is further found to achieve large-scale helical twisting in the final stages of spermiogenesis, favoring its ultracompaction. We reveal that these dramatic transitions may be recapitulated by a surprisingly simple biophysical principle based on a nucleated rigidification of chromatin linked to the histone-to-SNBP transition within a confined nuclear space. Our work highlights a unique, liquid crystal-like mode of higher-order genome organization in ultracompact cricket sperm, and establishes a multidisciplinary methodological framework to explore the diversity of non-canonical modes of DNA organization.
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Affiliation(s)
- Guillermo A Orsi
- Institute for Advanced Biosciences, University Grenoble Alpes, Inserm U 1209, CNRS UMR 5309, 38000, Grenoble, France.
| | - Maxime M C Tortora
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Béatrice Horard
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France
| | - Dominique Baas
- Laboratoire MeLiS, CNRS UMR 52684, Inserm U 1314, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Philippe Kleman
- Institut de Biologie Structurale, UMR5075, University Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Jonas Bucevičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Daniel Jost
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS UMR5239, Inserm U1293, Université Claude Bernard Lyon 1, Lyon, France.
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Zhao P, Han W, Shu Y, Li M, Sun Y, Sui X, Liu B, Tian B, Liu Y, Fu Q. Liquid-liquid phase separation drug aggregate: Merit for oral delivery of amorphous solid dispersions. J Control Release 2023; 353:42-50. [PMID: 36414193 DOI: 10.1016/j.jconrel.2022.11.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
As a promising strategy, amorphous solid dispersion has been extensively employed in improving the oral bioavailability of insoluble drugs. Despite the numerous advantages, the problems associated with supersaturation stability limit its further application. Recently, the formation and stability of the liquid-liquid phase separation drug aggregate (LLPS-DA) have been found to be vital for supersaturation maintenance. An in-depth review of LLPS-DA was required to further explore the supersaturation maintenance mechanism in vivo. Hence, this study aimed to present a short review to introduce the LLPS-DA, highlight the in vivo advantages for oral administration, and discuss the prospects to help understand the in vivo behavior of LLPS-DA.
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Affiliation(s)
- Peixu Zhao
- Wuya College of Innovation, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China
| | - Wen Han
- Wuya College of Innovation, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China
| | - Yecheng Shu
- Wuya College of Innovation, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China
| | - Mo Li
- Liaoning Institute for Drug Control, No. 7 Chongshan West Road, Shenyang 110016, China
| | - Yichi Sun
- School of Pharmacy, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China
| | - Xiaofan Sui
- Liaoning Institute for Drug Control, No. 7 Chongshan West Road, Shenyang 110016, China
| | - Bingyang Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China
| | - Baocheng Tian
- School of Pharmacy, Binzhou Medical University, No. 346, Guanhai Road, Yantai 264003, China
| | - Yanhua Liu
- Department of Pharmaceutics, Ningxia Medical University, 1160 Shengli Street, Yinchuan 750004, China
| | - Qiang Fu
- Wuya College of Innovation, Shenyang Pharmaceutical University, No. 103, Wenhua Road, Shenyang 110016, China.
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Mazarakos K, Prasad R, Zhou HX. SpiDec: Computing binodals and interfacial tension of biomolecular condensates from simulations of spinodal decomposition. Front Mol Biosci 2022; 9:1021939. [PMID: 36353733 PMCID: PMC9637972 DOI: 10.3389/fmolb.2022.1021939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/12/2022] [Indexed: 08/31/2023] Open
Abstract
Phase separation of intrinsically disordered proteins (IDPs) is a phenomenon associated with many essential cellular processes, but a robust method to compute the binodal from molecular dynamics simulations of IDPs modeled at the all-atom level in explicit solvent is still elusive, due to the difficulty in preparing a suitable initial dense configuration and in achieving phase equilibration. Here we present SpiDec as such a method, based on spontaneous phase separation via spinodal decomposition that produces a dense slab when the system is initiated at a homogeneous, low density. After illustrating the method on four model systems, we apply SpiDec to a tetrapeptide modeled at the all-atom level and solvated in TIP3P water. The concentrations in the dense and dilute phases agree qualitatively with experimental results and point to binodals as a sensitive property for force-field parameterization. SpiDec may prove useful for the accurate determination of the phase equilibrium of IDPs.
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Affiliation(s)
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
| | - Huan-Xiang Zhou
- Department of Physics, University of Illinois at Chicago, Chicago, IL, United States
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, United States
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