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Lee C, Kang SW. Influence of citric acid concentrations on the porosity and performance of cellulose acetate-based porous membranes: A comprehensive study. Int J Biol Macromol 2024; 263:130243. [PMID: 38378111 DOI: 10.1016/j.ijbiomac.2024.130243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/22/2024]
Abstract
This study investigates the influence of citric acid concentration on the fabrication of porous cellulose acetate (CA) membranes using the Non-Solvent Induced Phase Separation (NIPS) method. A notable aspect is the precise control over membrane properties, particularly pore size and porosity, achieved solely through the adjustment of citric acid concentration, serving as the additive. Higher concentrations of citric acid increase pore size by rendering polymer chains more pliable, whereas lower concentrations lead to smaller, denser pores due to improved dispersion in the CA matrix and altered water interactions during phase separation. A decrease in porosity and Gurley values with reducing citric acid concentrations (from 5 × 10-2 to 1 × 10-3 M ratios) indicates less plasticization of CA chains. However, at very low concentrations (1 × 10-4 and 1 × 10-5), porosity increases, despite the presence of smaller pores, and Gurley values approach those of pure CA in terms of gas permeability. Fourier Transform Infrared (FT-IR) spectroscopy confirms the presence of citric acid and its interaction with carbonyl groups, consistent with the pore size observations from Scanning Electron Microscopy (SEM). Spectral data deconvolution reveals weakened carbonyl bonds due to the reduced presence of citric acid, correlating with the smaller pores observed in SEM. Thermal Gravimetric Analysis (TGA) demonstrates that composite membranes are more thermally stable than pure CA, attributed to the citric acid-induced crosslinking within the polymer chains. Stability increases with decreasing citric acid concentration, with some anomalies at the lowest levels. In conclusion, this study highlights the capability of adjusting citric acid concentration to tailor membrane properties, offering valuable insights for the creation of porous materials across diverse industrial applications.
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Affiliation(s)
- Chaeyeon Lee
- Department of Chemistry and Energy Engineering, Sangmyung University, Seoul 03016, Republic of Korea
| | - Sang Wook Kang
- Department of Chemistry and Energy Engineering, Sangmyung University, Seoul 03016, Republic of Korea.
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2
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Wu L, Cui B, Dong D, Wu Z, Li J, Lu L, Wang N, Nishinari K, Zhao M. Effect of mixture microstructure/compatibility on the properties of type-A gelatin-dextran edible films. Carbohydr Polym 2024; 329:121733. [PMID: 38286534 DOI: 10.1016/j.carbpol.2023.121733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/03/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024]
Abstract
The influence of phase separation behavior on bio-based film properties has attracted more and more attention. This work investigated the effects of microstructure and compatibility of the type-A gelatin (GE)-dextran (DE) mixtures on GE-DE edible film properties. Three kinds of GE-DE edible films with different textures were prepared via modulating the microstructure and compatibility of film-forming mixtures using the method of gelation-drying, e.g., homogeneous films, microphase separated films with relatively homogeneous texture, and microphase separated films with uneven texture. The optical, mechanical, water barrier, and thermal properties of films were characterized. Results showed that microstructure and compatibility significantly affected the film properties. In general, films with DE-in-GE microstructure exhibited the best film properties, followed by films with water-in-water-in-water/bicontinuous microstructure, and then films with GE-in-DE microstructure. And homogeneous films showed the best film properties, followed by films with relatively homogeneous texture, and then films with uneven texture. The weight loss results suggested the potential of GE-DE edible films for application in cherry tomato preservation. This work provided interesting information for the design of film with fabricated microstructure and properties.
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Affiliation(s)
- Ling Wu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Glyn O. Phillips Hydrocolloid Research Centre at HUT, Hubei University of Technology, Wuhan 430068, China
| | - Bo Cui
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Die Dong
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Zhengzong Wu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Jianpeng Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Lu Lu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Na Wang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China
| | - Katsuyoshi Nishinari
- Glyn O. Phillips Hydrocolloid Research Centre at HUT, Hubei University of Technology, Wuhan 430068, China
| | - Meng Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China.
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Fakim H, Vande Velde C. The implications of physiological biomolecular condensates in amyotrophic lateral sclerosis. Semin Cell Dev Biol 2024; 156:176-189. [PMID: 37268555 DOI: 10.1016/j.semcdb.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
In recent years, there has been an emphasis on the role of phase-separated biomolecular condensates, especially stress granules, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). This is largely due to several ALS-associated mutations occurring in genes involved in stress granule assembly and observations that pathological inclusions detected in ALS patient neurons contain stress granule proteins, including the ALS-linked proteins TDP-43 and FUS. However, protein components of stress granules are also found in numerous other phase-separated biomolecular condensates under physiological conditions which are inadequately discussed in the context of ALS. In this review, we look beyond stress granules and describe the roles of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites, such as the nucleolus, Cajal bodies, paraspeckles and neuronal RNA transport granules. We also discuss the consequences of ALS-linked mutations in TDP-43 and FUS on their ability to phase separate into these stress-independent biomolecular condensates and perform their respective functions. Importantly, biomolecular condensates sequester multiple overlapping protein and RNA components, and their dysregulation could contribute to the observed pleiotropic effects of both sporadic and familial ALS on RNA metabolism.
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Affiliation(s)
- Hana Fakim
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada.
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Wang Y, Li H, Xie Y, Li X, Sun S, Jing X, Mi HY, Wang Y, Liu C, Shen C. Regulating microstructures of aerogels by controlling phase separation mechanism for improving specific surface area and energy harvesting. J Colloid Interface Sci 2024; 658:772-782. [PMID: 38154240 DOI: 10.1016/j.jcis.2023.12.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/30/2023]
Abstract
Aerogels with 3D porous structures have been attracting increasing attention among functional materials due to their advantages of being lightweight and high specific surface area. Precise control of the porous structure of aerogel is essential to improve its performance. In this work, polylactic acid (PLA) aerogels with distinctly different microstructures were fabricated by precisely controlling the phase separation behavior of the ternary solution system. Rheological and theoretical analyses have revealed that the interactions between polymer molecules, solvents and non-solvents play a crucial role in determining the nucleation and growth of poor olymer and rich polymer phases. By adjusting the non-solvent type and the solution composition, aerogels with spider network structure, bead-like connected microsphere structure, and cluster petal structure were obtained. Ideal spinodal phase separation conditions were obtained to produce aerogels with a homogeneous fiber network structure. The optimum PLA aerogel achieved an extremely porosity of 96 % and a high specific surface area of 114 m2/g, which rendered it with excellent triboelectric generation performance. Thus, this work provides fundamental insights into the precise regulation of the phase separation behavior and the structure of the aerogel, which can help boost the performance and expand the applications of PLA aerogels.
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Affiliation(s)
- Yameng Wang
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Hui Li
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Yibing Xie
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Xijue Li
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Shuangjie Sun
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Xin Jing
- Key Laboratory of Advanced Packaging Materials and Technology of Hunan Province, Hunan University of Technology, Zhuzhou, 412007, China
| | - Hao-Yang Mi
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China; Key Laboratory of Advanced Packaging Materials and Technology of Hunan Province, Hunan University of Technology, Zhuzhou, 412007, China.
| | - Yaming Wang
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China.
| | - Chuntai Liu
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
| | - Changyu Shen
- National Engineering Research Center for Advanced Polymer Processing Technology, The Key Laboratory of Advanced Materials Processing & Mold of Ministry of Education, Zhengzhou University, Zhengzhou 450001, China
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Mao Y, Liang X, Zhao J, Jiang L, Liang Q, Ngai T, Gong X, Wu M. 3D monitoring of the micro phase separations inside the intraocular lens. Acta Biomater 2024; 177:178-188. [PMID: 38307480 DOI: 10.1016/j.actbio.2024.01.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024]
Abstract
Glistenings often occur after implanting the intraocular lens (IOL) due to the formation of numerous microvacuoles (MVs) and may lead to deterioration of vision quality. Previous studies showed the formation of MVs was associated with the hydrophobicity of IOL materials. Yet, the mechanism remains an open question due to the complexity of IOL polymer networks. In this study, two commercialized IOLs with similar hydrophobicity are found distinct in the formation of MVs. The 3D growth kinetics of MVs during cooling processes are captured for the first time by digital holographic microscopy (DHM) and the components of MVs are measured by DHM and Raman spectroscopy. The results reveal that the growth of MVs stems from the microphase separation of water and surrounding IOL polymers. A polymer swelling model is thus proposed to describe the microphase separation process which is found dependent on the elasticity of IOL polymer networks. The total volume of MVs is determined by the IOL hydrophobicity, while the elastic force of IOL polymer networks determines the number density and size of MVs. This study demonstrates an approach for characterizing the phase separation of crosslinked polymeric materials in biosystems and sheds lights on the refinement of IOL materials. STATEMENT OF SIGNIFICANCE: Glistenings due to the formation of numerous microvacuoles (MVs) in intraocular lens (IOL) can occur after IOL implantation, which may induce poor quality of vision. However, the underlying mechanism of MVs formation is still an open question. This study establishes an in-situ 3D imaging platform to monitor growth kinetics of the MVs in IOLs, which allows to uncover the mechanism of glistenings formation resulting from the microphase separation. The findings imply the material hydrophobicity influences the total volume of MVs, while the local elasticity of IOL polymer networks determines the number density and the size of MVs. This study offers a new approach for characterizing phase separation in crosslinking biosystems and sheds lights on the refinement of IOL materials.
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Affiliation(s)
- Yan Mao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China
| | - Xiao Liang
- Faculty of Material Science and Engineering, South China University of Technology, Guangzhou 510640, PR China
| | - Junpeng Zhao
- Faculty of Material Science and Engineering, South China University of Technology, Guangzhou 510640, PR China
| | - Lingxiang Jiang
- South China Advanced Institute for Soft Matter Science and Technology (AISMST), School of Emergent Soft Matter, South China University of Technology, Guangzhou 510640, PR China
| | - Qingyou Liang
- Faculty of Material Science and Engineering, South China University of Technology, Guangzhou 510640, PR China; Analytical and Testing Center, South China University of Technology, Guangzhou 510640, PR China
| | - To Ngai
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong 999077, PR China
| | - Xiangjun Gong
- Faculty of Material Science and Engineering, South China University of Technology, Guangzhou 510640, PR China; Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, Guangzhou 510640, PR China.
| | - Mingxing Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China.
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Liang Q, Yang S, Mai M, Chen X, Zhu X. Mining phase separation-related diagnostic biomarkers for endometriosis through WGCNA and multiple machine learning techniques: a retrospective and nomogram study. J Assist Reprod Genet 2024:10.1007/s10815-024-03079-9. [PMID: 38456992 DOI: 10.1007/s10815-024-03079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
OBJECTIVE The objective of this study was to investigate the role of phase separation-related genes in the development of endometriosis (EMs) and to identify potential characteristic genes associated with the condition. METHODS We used GEO database data, including 74 non-endometriosis and 74 varying-degree EMs patients. Our approach involved identifying significant gene modules, exploring gene intersections, identifying core genes, and screening for potential EMs biomarkers using weighted gene co-expression network analysis (WGCNA) and various machine learning approaches. We also performed gene set enrichment analysis (GSEA) to understand relevant pathways. This comprehensive approach helps investigate EMs genetics and potential biomarkers. RESULTS Nine genes were identified at the intersection, suggesting their involvement in EMs. GSEA linked DEGs to pathways like complement and coagulation cascades, DNA replication, chemokines, apical plasma membrane processes, and diseases such as Hepatitis B, Human T-cell leukemia virus 1 infection, and COVID-19. Five feature genes (FOS, CFD, CCNA1, CA4, CST1) were selected by machine learning for an effective EMs diagnostic nomogram. GSEA indicated their roles in mismatch repair, cell cycle regulation, complement and coagulation cascades, and IL-17 inflammation. Notable differences in immune cell proportions (CD4 T cells, CD8 T cells, DCs, macrophages) were observed between normal and disease groups, suggesting immune involvement. CONCLUSIONS This study suggests the potential involvement of phase separation-related genes in the pathogenesis of endometriosis (EMs) and identifies promising biomarkers for diagnosis. These findings have implications for further research and the development of new therapeutic strategies for EMs.
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Affiliation(s)
- Qiuyi Liang
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Shengmei Yang
- Obstetrical Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Meiyi Mai
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiurong Chen
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Medicine and Epidemiology Laboratory (CMEL), The Marine Biomedical Research Institute of Guangdong Zhanjiang, School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, China.
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7
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Mao S, Xie C, Liu Y, Zhao Y, Li M, Gao H, Xiao Y, Zou Y, Zheng Z, Gao Y, Xie J, Tian B, Wang L, Hua Y, Xu H. Apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) promotes stress granule formation via YBX1 phosphorylation in ovarian cancer. Cell Mol Life Sci 2024; 81:113. [PMID: 38436697 PMCID: PMC10912283 DOI: 10.1007/s00018-023-05086-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/30/2023] [Accepted: 12/12/2023] [Indexed: 03/05/2024]
Abstract
APE1 is an essential gene involved in DNA damage repair, the redox regulation of transcriptional factors (TFs) and RNA processing. APE1 overexpression is common in cancers and correlates with poor patient survival. Stress granules (SGs) are phase-separated cytoplasmic assemblies that cells form in response to environmental stresses. Precise regulation of SGs is pivotal to cell survival, whereas their dysregulation is increasingly linked to diseases. Whether APE1 engages in modulating SG dynamics is worthy of investigation. In this study, we demonstrate that APE1 colocalizes with SGs and promotes their formation. Through phosphoproteome profiling, we discover that APE1 significantly alters the phosphorylation landscape of ovarian cancer cells, particularly the phosphoprofile of SG proteins. Notably, APE1 promotes the phosphorylation of Y-Box binding protein 1 (YBX1) at S174 and S176, leading to enhanced SG formation and cell survival. Moreover, expression of the phosphomutant YBX1 S174/176E mimicking hyperphosphorylation in APE1-knockdown cells recovered the impaired SG formation. These findings shed light on the functional importance of APE1 in SG regulation and highlight the importance of YBX1 phosphorylation in SG dynamics.
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Affiliation(s)
- Shuyu Mao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Chong Xie
- Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518107, China
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Yufeng Liu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Mengxia Li
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinses Academy of Sciences, Hangzhou, China
| | - Han Gao
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinses Academy of Sciences, Hangzhou, China
| | - Yue Xiao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yongkang Zou
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Zhiguo Zheng
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Ya Gao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Juan Xie
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China.
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China.
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Man J, Zhang Q, Zhao T, Sun D, Sun W, Long K, Zhang Z. Oxidative Stress Induced by Arsenite is Involved in YTHDF2 Phase Separation. Biol Trace Elem Res 2024; 202:885-899. [PMID: 37310554 DOI: 10.1007/s12011-023-03728-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
YTH N6-methyladenosine RNA binding protein 2 (YTHDF2) undergoes phase separation in response to the stimulation of high concentration of arsenite, suggesting that oxidative stress, the major mechanism of arsenite toxicity, may play a role in YTHDF2 phase separation. However, whether arsenite-induced oxidative stress is involved in phase separation of YTHDF2 has yet to be established. To explore the effect of arsenite-induced oxidative stress on YTHDF2 phase separation, the levels of oxidative stress, YTHDF2 phase separation, and N6-methyladenosine (m6A) in human keratinocytes were detected after exposure to various concentrations of sodium arsenite (0-500 µM; 1 h) and antioxidant N-acetylcysteine (0-10 mM; 2 h). We found that arsenite promoted oxidative stress and YTHDF2 phase separation in a concentration-dependent manner. In contrast, pretreatment with N-acetylcysteine significantly relieved arsenate-induced oxidative stress and inhibited YTHDF2 phase separation. As one of the key factors to YTHDF2 phase separation, N6-methyladenosine (m6A) levels in human keratinocytes were significantly increased after arsenite exposure, accompanied by upregulation of m6A methylesterase levels and downregulation of m6A demethylases levels. On the contrary, N-acetylcysteine mitigated the arsenite-induced increase of m6A and m6A methylesterase and the arsenite-induced decrease in m6A demethylase. Collectively, our study firstly revealed that oxidative stress induced by arsenite plays an important role in YTHDF2 phase separation driven by m6A modification, which provides new insights into the arsenite toxicity from the phase-separation perspective.
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Affiliation(s)
- Jin Man
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Qian Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Weilian Sun
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Keyan Long
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, Sichuan University, Chengdu, 610041, Sichuan, China.
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9
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Chen X, Gao M, Xia Y, Wang X, Qin J, He H, Liu W, Zhang X, Peng S, Zeng Z, Su Y, Zhang X. Phase separation of Nur77 mediates XS561-induced apoptosis by promoting the formation of Nur77/Bcl-2 condensates. Acta Pharm Sin B 2024; 14:1204-1221. [PMID: 38486987 PMCID: PMC10935061 DOI: 10.1016/j.apsb.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/15/2023] [Accepted: 10/24/2023] [Indexed: 03/17/2024] Open
Abstract
The orphan nuclear receptor Nur77 is a critical regulator of the survival and death of tumor cells. The pro-death effect of Nur77 can be regulated by its interaction with Bcl-2, resulting in conversion of Bcl-2 from a survival to killer. As Bcl-2 is overexpressed in various cancers preventing them from apoptosis and promoting their resistance to chemotherapy, targeting the apoptotic pathway of Nur77/Bcl-2 may lead to new cancer therapeutics. Here, we report our identification of XS561 as a novel Nur77 ligand that induces apoptosis of tumor cells by activating the Nur77/Bcl-2 pathway. In vitro and animal studies revealed an apoptotic effect of XS561 in a range of tumor cell lines including MDA-MB-231 triple-negative breast cancer (TNBC) and MCF-7/LCC2 tamoxifen-resistant breast cancer (TAMR) in a Nur77-dependent manner. Mechanistic studies showed XS561 potently induced the translocation of Nur77 from the nucleus to mitochondria, resulting in mitochondria-related apoptosis. Interestingly, XS561-induced accumulation of Nur77 at mitochondria was associated with XS561 induction of Nur77 phase separation and the formation of Nur77/Bcl-2 condensates. Together, our studies identify XS561 as a new activator of the Nur77/Bcl-2 apoptotic pathway and reveal a role of phase separation in mediating the apoptotic effect of Nur77 at mitochondria.
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Affiliation(s)
- Xiaohui Chen
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
- Department of Clinical Laboratory, the Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai 519000, China
| | - Meichun Gao
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Yongzhen Xia
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Xin Wang
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Jingbo Qin
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Hongying He
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Weirong Liu
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Xiaowei Zhang
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Shuangzhou Peng
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Zhiping Zeng
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
| | - Ying Su
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
- NucMito Pharmaceuticals Co., Ltd., Xiamen 361000, China
| | - Xiaokun Zhang
- School of Pharmaceutical Science, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361002, China
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10
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Hirano A, Wada M, Sato TK, Kameda T. N-acetyl amino acid amide solubility in aqueous 1,6-hexanediol solutions: Insights into the protein droplet deformation mechanism. Int J Biol Macromol 2024; 261:129724. [PMID: 38272403 DOI: 10.1016/j.ijbiomac.2024.129724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Proteinaceous liquid droplets, generated by liquid-liquid phase separation, function as membraneless compartments that are essential for diverse biological functions. Studies addressing droplet generation have used 1,6-hexanediol (1,6-HD) as a droplet-discerning agent owing to its capacity to induce droplet deformation. Despite the empirical utility of 1,6-HD, the mechanism underlying 1,6-HD-induced droplet deformation remains unknown. In this study, the solubilities of N-acetyl amino acid amides, which correspond to proteinogenic amino acid residues, were examined in the presence of 1,6-HD at 25 °C. Other solvents included ethanol, 1-propanol, and amides. Remarkably, 1,6-HD effectively solubilized hydrophobic species (particularly aromatic species) and exhibited reduced efficacy in solubilizing hydrophilic species and peptide bond moieties. These solubilizing effects are reflected in changes in protein solubility and structure. Specifically, 1,6-HD primarily targets the hydrophobic regions of a protein, increasing protein solubility without causing substantial structural changes. This solubilization mechanism is essential for elucidating the role of 1,6-HD as a droplet-discerning agent and recognizing its potential limitations.
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Affiliation(s)
- Atsushi Hirano
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan.
| | - Momoyo Wada
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Takehiro K Sato
- Spiber, Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Koto, Tokyo 135-0064, Japan
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11
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Chen Y, Lan Q. Experimental evidence for immiscibility of enantiomeric polymers: Phase separation of high-molecular-weight poly(ʟ-lactide)/poly(ᴅ-lactide) blends and its impact on hindering stereocomplex crystallization. Int J Biol Macromol 2024; 260:129459. [PMID: 38232890 DOI: 10.1016/j.ijbiomac.2024.129459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/01/2024] [Accepted: 01/11/2024] [Indexed: 01/19/2024]
Abstract
Although polymers tend not to mix, it remains challenging to characterize the immiscibility of enantiomeric poly(ʟ-lactide) (PLLA) and poly(ᴅ-lactide) (PDLA), particularly with equivalent and high molecular weight (high MW), which frustratingly disfavors the exclusive stereocomplexation. By introducing a random copolymer (PLC) of ʟ-lactide and caprolactone to form binary blends with PLLA and PDLA, the phase behavior of high-MW PLLA/PDLA blends was investigated mainly by using differential scanning calorimetry (DSC) and atomic force microscopy (AFM). DSC results showed that PLLA/PLC blends exhibited a single glass transition temperature (Tg), which depended on the blending ratio and precisely corresponded with the theoretical values calculated from the Fox equation. In comparison, PDLA/PLC blends showed composition-dependent heat-capacity increment at two unchanged Tg values of pure PLC and PDLA. AFM observation revealed that PLC is completely miscible with PLLA at high MW but is immiscible with PDLA, logically suggesting immiscibility of high-MW PLLA and PDLA. Moreover, AFM results demonstrated that high-MW PLLA/PDLA blends exhibited spherical droplets in asymmetric blends and bicontinuous interpenetrating worm-like patterns in symmetric counterparts, showing distinct and well-defined interfaces, confirming the microphase separation. Additionally, different MWs fundamentally led to significant differences in miscibility, which consequently affected the crystallization behaviors of PLLA/PDLA blends. This work provides evidence for (im)miscibility and its crucial impact on the crystallization of PLLA/PDLA blends and has important implications for understanding the stereocomplexation of polymers.
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Affiliation(s)
- Yujing Chen
- Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - Qiaofeng Lan
- Biomaterials Research Center, School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China.
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12
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Guan J, Jakob U. The Protein Scaffolding Functions of Polyphosphate. J Mol Biol 2024:168504. [PMID: 38423453 DOI: 10.1016/j.jmb.2024.168504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 03/02/2024]
Abstract
Inorganic polyphosphate (polyP), one of the first high-energy compound on earth, defies its extreme compositional and structural simplicity with an astoundingly wide array of biological activities across all domains of life. However, the underlying mechanism of such functional pleiotropy remains largely elusive. In this review, we will summarize recent studies demonstrating that this simple polyanion stabilizes protein folding intermediates and scaffolds select native proteins. These functions allow polyP to act as molecular chaperone that protects cells against protein aggregation, as pro-amyloidogenic factor that accelerates both physiological and disease-associated amyloid formation, and as a modulator of liquid-liquid phase separation processes. These activities help to explain polyP's known roles in bacterial stress responses and pathogenicity, provide the mechanistic foundation for its potential role in human neurodegenerative diseases, and open a new direction regarding its influence on gene expression through condensate formation. We will highlight critical unanswered questions and point out potential directions that will help to further understand the pleiotropic functions of this ancient and ubiquitous biopolymer.
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Affiliation(s)
- Jian Guan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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13
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Wang X, Liu J, Mao C, Mao Y. Phase separation-mediated biomolecular condensates and their relationship to tumor. Cell Commun Signal 2024; 22:143. [PMID: 38383403 PMCID: PMC10880379 DOI: 10.1186/s12964-024-01518-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
Phase separation is a cellular phenomenon where macromolecules aggregate or segregate, giving rise to biomolecular condensates resembling "droplets" and forming distinct, membrane-free compartments. This process is pervasive in biological cells, contributing to various essential cellular functions. However, when phase separation goes awry, leading to abnormal molecular aggregation, it can become a driving factor in the development of diseases, including tumor. Recent investigations have unveiled the intricate connection between dysregulated phase separation and tumor pathogenesis, highlighting its potential as a novel therapeutic target. This article provides an overview of recent phase separation research, with a particular emphasis on its role in tumor, its therapeutic implications, and outlines avenues for further exploration in this intriguing field.
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Affiliation(s)
- Xi Wang
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Jiameng Liu
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China
| | - Chaoming Mao
- Department of Nuclear Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
| | - Yufei Mao
- Department of Ultrasound Medicine, The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, China.
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14
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Garg A, Kumar G, Singh V, Sinha S. Doxorubicin catalyses self-assembly of p53 by phase separation. Curr Res Struct Biol 2024; 7:100133. [PMID: 38435052 PMCID: PMC10906149 DOI: 10.1016/j.crstbi.2024.100133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/29/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
Liquid-liquid phase separation plays a crucial role in cellular physiology, as it leads to the formation of membrane-less organelles in response to various internal stimuli, contributing to various cellular functions. However, the influence of exogenous stimuli on this process in the context of disease intervention remains unexplored. In this current investigation, we explore the impact of doxorubicin on the abnormal self-assembly of p53 using a combination of biophysical and imaging techniques. Additionally, we shed light on the potential mechanisms behind chemoresistance in cancer cells carrying mutant p53. Our findings reveal that doxorubicin co-localizes with both wild-type p53 (WTp53) and its mutant variants. Our in vitro experiments indicate that doxorubicin interacts with the N-terminal-deleted form of WTp53 (WTp53ΔNterm), inducing liquid-liquid phase separation, ultimately leading to protein aggregation. Notably, the p53 variants at the R273 position exhibit a propensity for phase separation even in the absence of doxorubicin, highlighting the destabilizing effects of point mutations at this position. The strong interaction between doxorubicin and p53 variants, along with its localization within the protein condensates, provides a potential explanation for the development of chemotherapy resistance. Collectively, our cellular and in vitro studies emphasize the role of exogenous agents in driving phase separation-mediated p53 aggregation.
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Affiliation(s)
- Ankush Garg
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
| | - Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
| | - Varinder Singh
- Indian Institute of Science Education and Research, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Sector- 81, Mohali (SAS Nagar), Punjab, 140306, India
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15
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Ueno N, Sato H. Visualization of isothermal crystallization and phase separation in poly[(R)-3-hydroxybutyrate]/poly(L-lactic acid) by low-frequency Raman imaging. Spectrochim Acta A Mol Biomol Spectrosc 2024; 312:124052. [PMID: 38394883 DOI: 10.1016/j.saa.2024.124052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/24/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024]
Abstract
The visualization of the variation of the inter/intra molecular interaction (C = O⋯CH3) between poly[(R)-3-hydroxybutyrate] (PHB) and poly-L-lactic acid (PLLA) in the PHB/PLLA miscible blend during phase separation and crystallization process was successfully investigated using Raman imaging. Images of the blend were developed using high- and low-frequency Raman spectra acquired during the isothermal crystallization of the blend, and both of them were compared. The low-frequency region allowed to observe the changes in the hydrogen bonds between the molecular chains in the blend during phase separation and crystallization via a band at 75 cm-1 derived from PHB. The imaging results obtained using the band at 75 cm-1 due to hydrogen bonding (C = O⋯CH3) between molecular chains were in good agreement with the results obtained using the C = O stretching band at 1720 cm-1. Herein, we demonstrated that the low-frequency region of the Raman spectrum is more sensitive to detecting the start of the phase separation and crystallization of PHB than the corresponding high-frequency region.
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Affiliation(s)
- Nami Ueno
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto, Nada-Ku, Kobe 657-8501, Japan
| | - Harumi Sato
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto, Nada-Ku, Kobe 657-8501, Japan; Molecular Photoscience Research Center, Kobe University, Rokkoudai, Nada-Ku, Kobe 657-8501, Japan.
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16
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Lv H, Duan X, Han Z, Yu H, Liu B. Quencher-free fluorescent assays by controlled DNA partitioning in the aqueous two-phase system with crowding-enhanced kinetics. Biosens Bioelectron 2024; 246:115864. [PMID: 38039730 DOI: 10.1016/j.bios.2023.115864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
Fluorescent DNA assays are promising in disease diagnosis, environmental monitoring, and drug screening, encompassing both heterogeneous and homogeneous assay types. Nevertheless, heterogeneous assays suffer from tedious washing steps and slow reaction kinetics, whereas homogenous assays require well-designed fluorophore pairs to modulate signal off/on. Herein, we developed a cost-effective and efficient quencher-free fluorescent DNA assay using an aqueous two-phase system (ATPS). Using a strand-displacement reaction, we showed that similar sensing performance could be achieved at a much lower cost. Furthermore, the unique crowding environment in ATPS accelerated strand-displacement reactions by up to six-fold and reduced DNA amplification time from 120 min to 30 min. Our assay demonstrated robust sensing in serum environments and successful detection of miRNA extracted from cells. This innovative assay format has the potential for biosensor development with both heterogeneous readout and rapid reaction kinetics in various applications.
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Affiliation(s)
- Haoyue Lv
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Xiaoman Duan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Zhaoyu Han
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Haozhen Yu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China
| | - Biwu Liu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, PR China.
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17
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Yao RW, Rosen MK. Advanced Surface Passivation for High-Sensitivity Studies of Biomolecular Condensates. bioRxiv 2024:2024.02.12.580000. [PMID: 38405951 PMCID: PMC10888978 DOI: 10.1101/2024.02.12.580000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Biomolecular condensates are cellular compartments that concentrate biomolecules without an encapsulating membrane. In recent years, significant advances have been made in the understanding of condensates through biochemical reconstitution and microscopic detection of these structures. Quantitative visualization and biochemical assays of biomolecular condensates rely on surface passivation to minimize background and artifacts due to condensate adhesion. However, the challenge of undesired interactions between condensates and glass surfaces, which can alter material properties and impair observational accuracy, remains a critical hurdle. Here, we introduce an efficient, generically applicable, and simple passivation method employing self-assembly of the surfactant Pluronic F127 (PF127). The method greatly reduces nonspecific binding across a range of condensates systems for both phase-separated droplets and biomolecules in dilute phase. Additionally, by integrating PF127 passivation with the Biotin-NeutrAvidin system, we achieve controlled multi-point attachment of condensates to surfaces. This not only preserves condensate properties but also facilitates long-time FRAP imaging and high-precision single-molecule analyses. Using this method, we have explored the dynamics of polySIM molecules within polySUMO/polySIM condensates at the single-molecule level. Our observations suggest a potential heterogeneity in the distribution of available polySIM-binding sites within the condensates.
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Affiliation(s)
- Run-Wen Yao
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Michael K. Rosen
- Department of Biophysics, Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, 75390, USA
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18
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Liu Y, Feng W, Wang Y, Wu B. Crosstalk between protein post-translational modifications and phase separation. Cell Commun Signal 2024; 22:110. [PMID: 38347544 PMCID: PMC10860296 DOI: 10.1186/s12964-023-01380-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024] Open
Abstract
The phenomenon of phase separation is quite common in cells, and it is involved in multiple processes of life activities. However, the current research on the correlation between protein modifications and phase separation and the interference with the tendency of phase separation has some limitations. Here we focus on several post-translational modifications of proteins, including protein phosphorylation modification at multiple sites, methylation modification, acetylation modification, ubiquitination modification, SUMOylation modification, etc., which regulate the formation of phase separation and the stability of phase separation structure through multivalent interactions. This regulatory role is closely related to the development of neurodegenerative diseases, tumors, viral infections, and other diseases, and also plays essential functions in environmental stress, DNA damage repair, transcriptional regulation, signal transduction, and cell homeostasis of living organisms, which provides an idea to explore the interaction between novel protein post-translational modifications and phase separation. Video Abstract.
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Affiliation(s)
- Yang Liu
- Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenjuan Feng
- Department of Reproductive Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yunshan Wang
- Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Basic Medical Research Center, Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Bin Wu
- Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Department of Reproductive Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China.
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19
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Nisar J, Mir MS, Vivek. Exploring the potential of waste plastic-modified asphalt: a systematic review of blending ratios, mixing conditions, and rheological properties. Environ Sci Pollut Res Int 2024; 31:11507-11528. [PMID: 38206466 DOI: 10.1007/s11356-023-31806-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024]
Abstract
In the present study, a systematic literature review (SLR) is conducted to collect, compile, and summarize the findings of previous studies in a meaningful and systematic way. This review focuses on the ideal blending ratios, mixing parameters, and the physical, thermal, and rheological performance of waste plastic-modified asphalt. It highlights the most significant research results about the challenges like phase separation, low-temperature performance, and workability for waste plastic-modified asphalt and progress in this domain. The results point out that the use of chemical and physical additives can help in the reduction of phase separation. Furthermore, this paper debates the aging characteristics and it was seen that the integration of waste plastic in asphalt has shown to slow down the aging process of the binder. The review article put forward details of various field projects across the globe utilizing waste plastic. The review concludes by presenting key findings, identifying research gaps, and suggesting future directions to advance the knowledge and to fully comprehend the possible application of waste plastic-modified bitumen in sustainable road construction.
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Affiliation(s)
- Jasim Nisar
- Department of Civil Engineering, National Institute of Technology Srinagar, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India.
| | - Mohammad Shafi Mir
- Department of Civil Engineering, National Institute of Technology Srinagar, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
| | - Vivek
- Department of Civil Engineering, National Institute of Technology Srinagar, Hazratbal, Srinagar, Jammu and Kashmir, 190006, India
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20
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Zhang D, Ni QQ, Wang SY, He WF, Hong ZX, Liu HY, Chen XH, Chen LJ, Han FY, Zhang LJ, Li XM, Ding YQ, Jiao HL, Ye YP. APC mutations disrupt β-catenin destruction complex condensates organized by Axin phase separation. Cell Mol Life Sci 2024; 81:57. [PMID: 38279052 PMCID: PMC10817841 DOI: 10.1007/s00018-023-05068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 01/28/2024]
Abstract
The Wnt/β-catenin pathway is critical to maintaining cell fate decisions. Recent study showed that liquid-liquid-phase separation (LLPS) of Axin organized the β-catenin destruction complex condensates in a normal cellular state. Mutations inactivating the APC gene are found in approximately 80% of all human colorectal cancer (CRC). However, the molecular mechanism of the formation of β-catenin destruction complex condensates organized by Axin phase separation and how APC mutations impact the condensates are still unclear. Here, we report that the β-catenin destruction complex, which is constructed by Axin, was assembled condensates via a phase separation process in CRC cells. The key role of wild-type APC is to stabilize destruction complex condensates. Surprisingly, truncated APC did not affect the formation of condensates, and GSK 3β and CK1α were unsuccessfully recruited, preventing β-catenin phosphorylation and resulting in accumulation in the cytoplasm of CRCs. Besides, we propose that the phase separation ability of Axin participates in the nucleus translocation of β-catenin and be incorporated and concentrated into transcriptional condensates, affecting the transcriptional activity of Wnt signaling pathway.
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Affiliation(s)
- Dan Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Qi-Qi Ni
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Shu-Yang Wang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Wen-Feng He
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ze-Xuan Hong
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Hui-Ye Liu
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Xiao-Hong Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Li-Jie Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Fang-Yi Han
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Ling-Jie Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China
| | - Xiao-Ming Li
- Department of Pathology, The People's Hospital of Baoan Shenzhen, Shenzhen, Guangdong, China.
| | - Yan-Qing Ding
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
- Jinfeng Laboratory, Chongqing, China.
| | - Hong-Li Jiao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
| | - Ya-Ping Ye
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, Guangdong, China.
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21
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Lee C, Lee S, Kang SW. Enhanced porous membrane fabrication using cellulose acetate and citric acid: Improved structural integrity, thermal stability, and gas permeability. Carbohydr Polym 2024; 324:121571. [PMID: 37985069 DOI: 10.1016/j.carbpol.2023.121571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
In this study, our primary objective was to enhance the properties of porous membranes by addressing the limitations associated with phase separation. We employed a non-solvent induced phase separation (NIPS) method, utilizing cellulose acetate (CA) in conjunction with citric acid to fabricate these membranes. Citric acid played a dual role: ensuring a uniform pore structure and cross-linking the CA polymer, thereby enhancing its mechanical strength. This approach resulted in the development of a more robust membrane with superior structural integrity. Thermogravimetric analysis (TGA) confirmed enhanced thermal stability, particularly up to 150 °C, as a result of citric acid's cross-linking effect. Beyond 150 °C, the decomposition temperatures of the CA/citric acid membrane were found to be comparable to those of pure CA. Remarkably, a CA/citric acid ratio of 1:0.05 exhibited the slowest decomposition rate as the temperature increased. Scanning electron microscopy (SEM) examination unveiled a sponge-like membrane structure with numerous evenly distributed fine pores. Through the use of citric acid as a plasticizer, we were able to effectively control the penetration of water molecules, preventing the formation of macrovoids and promoting the creation of fine pores. This resulted in the fabrication of a high-porosity membrane, boasting an impressive porosity measurement of 84.9 %. Furthermore, measurements of the Gurley value confirmed efficient gas permeation, a critical characteristic for applications requiring effective gas transport. Fourier transform infrared (FT-IR) spectroscopy attested to the presence of citric acid in the membrane post-phase separation, indicating its successful integration. Our work presents a novel approach to enhance porous membranes, providing improvements in mechanical strength, thermal stability, and gas permeability. These findings offer valuable insights for the development of advanced materials with diverse applications in various fields.
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Affiliation(s)
- Chaeyeon Lee
- Department of Chemistry and Energy Engineering, Sangmyung University, Seoul 03016, Republic of Korea
| | - Sojeong Lee
- Department of Chemistry and Energy Engineering, Sangmyung University, Seoul 03016, Republic of Korea
| | - Sang Wook Kang
- Department of Chemistry and Energy Engineering, Sangmyung University, Seoul 03016, Republic of Korea.
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22
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Wang J, Devarajan DS, Kim YC, Nikoubashman A, Mittal J. Sequence-Dependent Conformational Transitions of Disordered Proteins During Condensation. bioRxiv 2024:2024.01.11.575294. [PMID: 38260590 PMCID: PMC10802556 DOI: 10.1101/2024.01.11.575294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Intrinsically disordered proteins (IDPs) can form biomolecular condensates through phase separation. It is recognized that the conformation of IDPs in the dense and dilute phases as well as at the interfaces of condensates can critically impact the resulting properties associated with their functionality. However, a comprehensive understanding of the conformational transitions of IDPs during condensation remains elusive. In this study, we employ a coarse-grained polyampholyte model, comprising an equal number of oppositely charged residues-glutamic acid and lysine-whereby conformations and phase behavior can be readily tuned by altering the protein sequence. By manipulating the sequence patterns from perfectly alternating to block-like, we obtain chains with ideal-like conformations to semi-compact structures in the dilute phase, while in the dense phase, the chain conformation is approximately that of an ideal chain, irrespective of the protein sequence. By performing simulations at different concentrations, we find that the chains assemble from the dilute phase through small oligomeric clusters to the dense phase, accompanied by a gradual swelling of the individual chains. We further demonstrate that these findings are applicable to several naturally occurring proteins involved in the formation of biological condensates. Concurrently, we delve deeper into the chain conformations within the condensate, revealing that chains at the interface show a strong sequence dependence, but remain more collapsed than those in the bulk-like dense phase. This study addresses critical gaps in our knowledge of IDP conformations within condensates as a function of protein sequence.
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Affiliation(s)
- Jiahui Wang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | | | - Young C. Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375, United States
| | - Arash Nikoubashman
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany
- Institut für Theoretische Physik, Technische Universität Dresden, 01069 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01062 Dresden, Germany
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
- Department of Chemistry, Texas A&M University, College Station, TX 77843, United States
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843, United States
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23
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Gabarayeva NI, Britski DA, Grigorjeva VV. Pollen wall development in Impatiens glandulifera: exine substructure and underlying mechanisms. Protoplasma 2024; 261:111-124. [PMID: 37542569 DOI: 10.1007/s00709-023-01887-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/26/2023] [Indexed: 08/07/2023]
Abstract
The aim of this study was to investigate in detail the pollen wall ontogeny in Impatiens glandulifera, with emphasis on the substructure and the underlying mechanisms of development. Sporopollenin-containing pollen wall, the exine, consists of two parts, ectexine and endexine. By determining the sequence of developing substructures with TEM, we have in mind to understand in which way the exine substructure is connected with function. We have shown earlier that physical processes of self-assembly and phase separation are universally involved in ectexine development; currently, we try to clear up whether these processes participate in endexine development. The data received were compared with those on other species. The ectexine ontogeny of I. glandulifera followed the main stages observed in many other species, including the late tetrad stage named "Golden gates". It turned out that the same physico-chemical processes act in endexine development, especially expressed in aperture sites. Another peculiar phenomenon observed in exine development was the recurrency of micellar sequence at near-aperture and aperture sites where the periplasmic space is widened. It should be noted that, in the whole, the developmental substructures observed during the tetrad and early post-tetrad period are similar in species with columellate exines. Evidently, these basic physical processes proceed, reiterating again and again in different species, resulting in an enormous variety of exine structures on the base of a relatively modest number of genes. Granular and alveolar exines emerge on the base of the same basic processes but are arrested at spherical and cylindrical micelle mesophases correspondingly.
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24
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Hellebois T, Addiego F, Gaiani C, Shaplov AS, Soukoulis C. Unravelling the functionality of anionic and non-ionic plant seed gums on milk protein cryogels conveying Lacticaseibacillus rhamnosus GG. Carbohydr Polym 2024; 323:121376. [PMID: 37940272 DOI: 10.1016/j.carbpol.2023.121376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 11/10/2023]
Abstract
Cryogels offer a promising macroporous platform that can be employed as either a functional ingredient in food composites or a colloidal template for incorporating bioactives, including probiotic living cells. The aim of the present work is to explore the functionality of two plant seed polysaccharides, flaxseed gum (FG) and alfalfa galactomannan (AAG), in individual and combined (1:1 ratio) milk protein-based cryogels, namely sodium caseinate (NaCas) and whey protein isolate (WPI). These cryogels were created by freeze-drying hydrogels formed via L.rhamnosus GG - a human gut-relevant probiotic strain - fermentation. Our findings showed that including gum in the composition limited volume contraction during lyophilisation, reduced macropore size and thickened cryogel skeleton vessels. Furthermore, gum-containing cryogels displayed improved thermal stability and slower water disintegration rates. The AAG-stabilised cryogels specifically showed a notable reduction in monolayer water content compared to FG. From a mechanistic viewpoint, AAG influenced the physicochemical and microstructural properties of the cryogels, most probably via its self-association during cryogenic processing, promoting the development of intertwined protein-gum networks. FG, on the other hand, enhanced these properties through electrostatic complexation with proteins. Cryogels made from protein-polysaccharide blends exhibited promising techno-functional properties for enhancing and diversifying food product innovation.
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Affiliation(s)
- Thierry Hellebois
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg; Université de Lorraine, LIBio, F-54000 Nancy, France
| | - Frédéric Addiego
- Materials Research and Technology (MRT) Department, Luxembourg Institute of Science and Technology (LIST), 5 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Claire Gaiani
- Université de Lorraine, LIBio, F-54000 Nancy, France
| | - Alexander S Shaplov
- Materials Research and Technology (MRT) Department, Luxembourg Institute of Science and Technology (LIST), 5 avenue des Hauts Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg
| | - Christos Soukoulis
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5 avenue des Hauts-Fourneaux, Esch-sur-Alzette L-4362, Luxembourg.
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25
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Chen Y, Wang Y, Wang T, Pei X, Zhang J, Liu Y. TRIM21 undergoes phase separation dependent CC domain to regulate autophagy. Biochem Biophys Res Commun 2023; 684:149101. [PMID: 37879251 DOI: 10.1016/j.bbrc.2023.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/27/2023]
Abstract
Tripartite motif (TRIM) family proteins as E3-ligases participate in various biological processes. TRIM21, as the first autoantibody protein, has been found to be associated with autophagy. However, the role of TRIM21 engaging in autophagy is still unclear. In this study, TRIM21 forms significate puncta in the cytoplasm and undergoes liquid-liquid phase separation in vitro. Furthermore, we identify phase separation of the coiled-coil (CC) domain is essential for autophagosome to mediate autophagy-related protein recruited. These findings show that phase separation of the CC domain of TRIM21 promotes autophagosome to impact cell fate.
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Affiliation(s)
- Yatao Chen
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Tan Wang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoying Pei
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jun Zhang
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China.
| | - Yan Liu
- Department of Biochemistry, School of Life Sciences, Nanjing Normal University, Nanjing, China.
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26
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Ishizaka T, Hatori K. Direct observation of oriented behavior of actin filaments interacting with desmin intermediate filaments. Biochim Biophys Acta Gen Subj 2023; 1867:130488. [PMID: 37838354 DOI: 10.1016/j.bbagen.2023.130488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
BACKGROUND Associations between actin filaments (AFs) and intermediate filaments (IFs) are frequently observed in living cells. The crosstalk between these cytoskeletal components underpins cellular organization and dynamics; however, the molecular basis of filamentous interactions is not fully understood. Here, we describe the mode of interaction between AFs and desmin IFs (DIFs) in a reconstituted in vitro system. METHODS AFs (rabbit skeletal muscle) and DIFs (chicken gizzard) were labeled with fluorescent dyes. DIFs were immobilized on a heavy meromyosin (HMM)-coated collodion surface. HMM-driven AFs with ATP hydrolysis was assessed in the presence of DIFs. Images of single filaments were obtained using fluorescence microscopy. Vector changes in the trajectories of single AFs were calculated from microscopy images. RESULTS AF speed transiently decreased upon contact with DIF. The difference between the incoming and outgoing angles of a moving AF broadened upon contact with a DIF. A smaller incoming angle tended to result in a smaller outgoing angle in a nematic manner. The percentage of moving AFs decreased with an increasing DIF density, but the speed of the moving AFs was similar to that in the no-desmin control. An abundance of DIFs tended to exclude AFs from the HMM-coated surfaces. CONCLUSIONS DIFs agitate the movement of AFs with the orientation. DIFs can bind to HMMs and weaken actin-myosin interactions. GENERAL SIGNIFICANCE The study indicates that apart from the binding strength, the accumulation of weak interactions characteristic of filamentous structures may affect the dynamic organization of cell architecture.
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Affiliation(s)
- Takumi Ishizaka
- Department of Mechanical Systems Engineering, Graduate School of Science and Engineering, Yamagata University, Japan
| | - Kuniyuki Hatori
- Department of Mechanical Systems Engineering, Graduate School of Science and Engineering, Yamagata University, Japan.
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27
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Eljebbawi A, Dolata A, Strotmann VI, Stahl Y. Unlocking nature's (sub)cellular symphony: Phase separation in plant meristems. Curr Opin Plant Biol 2023; 76:102480. [PMID: 37862837 DOI: 10.1016/j.pbi.2023.102480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/13/2023] [Accepted: 09/24/2023] [Indexed: 10/22/2023]
Abstract
Plant development is based on the balance of stem cell maintenance and differentiation in the shoot and root meristems. The necessary cell fate decisions are regulated by intricate networks of proteins and biomolecules within plant cells and require robust and dynamic compartmentalization strategies, including liquid-liquid phase separation (LLPS), which allows the formation of membrane-less compartments. This review summarizes the current knowledge about the emerging field of LLPS in plant development, with a particular focus on the shoot and root meristems. LLPS regulates not only floral transition and flowering time while integrating environmental signals in the shoots but also influences auxin signalling and is putatively involved in maintaining the stem cell niche (SCN) in the roots. Therefore, LLPS has the potential to play a crucial role in the plasticity of plant development, necessitating further research for a comprehensive understanding.
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Affiliation(s)
- Ali Eljebbawi
- Institute for Developmental Genetics, Heinrich-Heine University Duesseldorf, Germany
| | - Anika Dolata
- Institute for Developmental Genetics, Heinrich-Heine University Duesseldorf, Germany
| | - Vivien I Strotmann
- Institute for Developmental Genetics, Heinrich-Heine University Duesseldorf, Germany
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University Duesseldorf, Germany.
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28
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Abstract
The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs) harbored within transcription factors (TFs) and chromatin-modulatory proteins in inducing phase separation, a phenomenon of forming membrane-less condensates through partitioning of biomolecules. Such a process is also critically involved in the establishment of high-order chromatin structures and looping. IDR- and phase separation-driven 3D genome (re)organization often goes wrong in disease such as cancer. This review discusses about recent advances in understanding how phase separation of intrinsically disordered proteins (IDPs) modulates chromatin looping and gene expression.
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Affiliation(s)
- Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Genetics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Ling Cai Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA,CONTACT Gang Greg Wang Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599, USA
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29
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Weinmann R, Frank L, Rippe K. Approaches to characterize chromatin subcompartment organization in the cell nucleus. Curr Opin Struct Biol 2023; 83:102695. [PMID: 37722292 DOI: 10.1016/j.sbi.2023.102695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 09/20/2023]
Abstract
The mechanism of self-organization of chromatin subcompartments on the 0.1-1 μm scale and their impact on genome-associated activities has long been a key aspect of research on nuclear organization. Understanding the underlying structure-function relationship, however, remains challenging due to the complex hierarchical structure of chromatin and the polymorphic organization of subcompartments that assemble around it. Towards this goal, approaches to measure local properties and compositional dynamics of chromatin in its endogenous cellular environment are instrumental. Here, we discuss recent advancements in studying these features and their functional implications in protein and RNA enrichment and genome accessibility.
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Affiliation(s)
- Robin Weinmann
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Germany; Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Germany; Faculty of Biosciences, Heidelberg University, Germany
| | - Lukas Frank
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Germany; Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) Heidelberg, Division of Chromatin Networks, Germany; Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant), Heidelberg University, Germany.
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30
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Abstract
What did the first cells on Earth look like? This is an unanswered mystery investigated by researchers in the origins of life field. While at some point cells must have developed membranes, genetic components, and catalytic cycles and catalysts, when the earliest cells developed these is not clear. One system which could shed light into the structure and function of the first cells on Earth is membraneless compartments generated from phase separation, perhaps before or as a precursor to the advent of membrane-bound compartmentalization. Here, we briefly comment on two prebiotically relevant membraneless compartment systems: coacervates and polyester microdroplets. This discussion seeks to highlight the current understanding of these systems and to pose unanswered questions as a challenge to the field at large.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-Ku, Tokyo, 152-8550 Japan
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104 USA
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31
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Mushnoori S, Lu CY, Schmidt K, Dutt M. A coarse-grained Molecular Dynamics study of phase behavior in Co-assembled lipomimetic oligopeptides. J Mol Graph Model 2023; 125:108624. [PMID: 37699315 DOI: 10.1016/j.jmgm.2023.108624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023]
Abstract
Multicomponent biomolecular aggregates, i.e., systems consisting of more than one type of biomolecular component co-assembling into one aggregate, provide an interesting design space for engineering unique biomaterials. In this study, we examine the co-assembly of two lipomimetic oligopeptide block copolymers selected for their lipid-like amphiphilicity and highly similar architectures into nanofibers via coarse-grained MD simulations. We focus on the behavior of these peptides due to incremental differences in size by selecting two peptides that differ in length by exactly one amino acid residue. We find that the longer peptide sequence displays greater self-association properties.
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Affiliation(s)
- Srinivas Mushnoori
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ-08854, USA
| | - Chien Y Lu
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ-08854, USA
| | - Kassandra Schmidt
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ-08854, USA
| | - Meenakshi Dutt
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ-08854, USA.
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32
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Obuse C, Hirose T. Functional domains of nuclear long noncoding RNAs: Insights into gene regulation and intracellular architecture. Curr Opin Cell Biol 2023; 85:102250. [PMID: 37806294 DOI: 10.1016/j.ceb.2023.102250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/12/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023]
Abstract
Recent functional research on long noncoding RNAs (lncRNAs) has revealed their significant regulatory roles in gene expression and intracellular architecture. Well-characterized examples of such lncRNAs include Xist and NEAT1_2, which play critical roles in heterochromatin formation of inactive X-chromosomes and paraspeckle assembly, in mammalian cells. Both lncRNAs possess modular domain structures with multiple functionally distinct domains that serve as platforms for specific RNA-binding proteins (RBPs), which dictate the function of each lncRNA. Some of these RBPs bind characteristic RNA structures, which can be targeted by small chemical compounds that modulate lncRNA function by perturbing the interaction of RBPs with the RNA structures. Therefore, RNA structures hidden in lncRNAs represent a novel and potent type of therapeutic target.
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Affiliation(s)
- Chikashi Obuse
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan
| | - Tetsuro Hirose
- Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan; Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita 565-0871, Japan.
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33
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Gauthier A, Ovarlez G, Colin A. Shear thickening in presence of adhesive contact forces: The singularity of cornstarch. J Colloid Interface Sci 2023; 650:1105-1112. [PMID: 37467639 DOI: 10.1016/j.jcis.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023]
Abstract
HYPOTHESIS A number of dense particle suspensions experience a dramatic increase in viscosity with the shear stress, up to a solid-like response. This shear-thickening process is understood as a transition under flow of the nature of the contacts - from lubricated to frictional - between initially repellent particles. Most systems are now assumed to fit in with this scenario, which is questionable. EXPERIMENT Using an in-house pressure sensor array, we provide a spatio-temporal map of the normal stresses in the flows of two shear-thickening fluids: a stabilized calcium carbonate suspension, known to fit in with the standard scenario, and a cornstarch suspension, which spectacular thickening behavior remains poorly understood. FINDINGS We evidence in cornstarch a unique, stable heterogeneous structure, which moves in the velocity direction and does not appear in calcium carbonate. Its nature changes from a stress wave to a rolling solid jammed aggregate at high solid fraction and small gap width. The modeling of these heterogenities points to an adhesive force between cornstarch particles at high stress, also evidenced in microscopic measurements. Cornstarch being also attractive at low stress, it stands out of the classical shear-thickening frame, and might be part of a larger family of adhesive and attractive shear-thickening fluids.
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Affiliation(s)
- Anaïs Gauthier
- MIE - Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France.
| | | | - Annie Colin
- MIE - Chemistry, Biology and Innovation (CBI) UMR 8231, ESPCI Paris, CNRS, PSL Research University, 10 rue Vauquelin, Paris, France
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34
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Wienen D, Gries T, Cooper SL, Heath DE. An overview of polyurethane biomaterials and their use in drug delivery. J Control Release 2023; 363:376-388. [PMID: 37734672 DOI: 10.1016/j.jconrel.2023.09.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Polyurethanes are a versatile and highly tunable class of materials that possess unique properties including high tensile strength, abrasion and fatigue resistance, and flexibility at low temperatures. The tunability of polyurethane properties has allowed this class of polymers to become ubiquitous in our daily lives in fields as diverse as apparel, appliances, construction, and the automotive industry. Additionally, polyurethanes with excellent biocompatibility and hemocompatibility can be synthesized, enabling their use as biomaterials in the medical field. The tunable nature of polyurethane biomaterials also makes them excellent candidates as drug delivery vehicles, which is the focus of this review. The fundamental idea we aim to highlight in this article is the structure-property-function relationships found in polyurethane systems. Specifically, the chemical structure of the polymer determines its macroscopic properties and dictates the functions for which it will perform well. By exploring the structure-property-function relationships for polyurethanes, we aim to elucidate the fundamental properties that can be tailored to achieve controlled drug release and empower researchers to design new polyurethane systems for future drug delivery applications.
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Affiliation(s)
- David Wienen
- Institute of Textile Technology, RWTH Aachen, Germany
| | - Thomas Gries
- Institute of Textile Technology, RWTH Aachen, Germany
| | - Stuart L Cooper
- Department of Chemical and Biomolecular Engineering, The Ohio State University, USA
| | - Daniel E Heath
- Department of Biomedical Engineering, Graeme Clark Institute, University of Melbourne, Australia.
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35
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Cochard A, Safieddine A, Combe P, Benassy M, Weil D, Gueroui Z. Condensate functionalization with microtubule motors directs their nucleation in space and allows manipulating RNA localization. EMBO J 2023; 42:e114106. [PMID: 37724036 PMCID: PMC10577640 DOI: 10.15252/embj.2023114106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023] Open
Abstract
The localization of RNAs in cells is critical for many cellular processes. Whereas motor-driven transport of ribonucleoprotein (RNP) condensates plays a prominent role in RNA localization in cells, their study remains limited by the scarcity of available tools allowing to manipulate condensates in a spatial manner. To fill this gap, we reconstitute in cellula a minimal RNP transport system based on bioengineered condensates, which were functionalized with kinesins and dynein-like motors, allowing for their positioning at either the cell periphery or centrosomes. This targeting mostly occurs through the active transport of the condensate scaffolds, which leads to localized nucleation of phase-separated condensates. Then, programming the condensates to recruit specific mRNAs is able to shift the localization of these mRNAs toward the cell periphery or the centrosomes. Our method opens novel perspectives for examining the role of RNA localization as a driver of cellular functions.
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Affiliation(s)
- Audrey Cochard
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Adham Safieddine
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Pauline Combe
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
| | - Marie‐Noëlle Benassy
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris‐Seine (IBPS), Laboratoire de Biologie du DéveloppementParisFrance
| | - Zoher Gueroui
- Department of Chemistry, École Normale SupérieurePSL University, Sorbonne Université, CNRSParisFrance
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36
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Krok E, Stephan M, Dimova R, Piatkowski L. Tunable biomimetic bacterial membranes from binary and ternary lipid mixtures and their application in antimicrobial testing. Biochim Biophys Acta Biomembr 2023; 1865:184194. [PMID: 37328023 DOI: 10.1016/j.bbamem.2023.184194] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/18/2023]
Abstract
The reconstruction of accurate yet simplified mimetic models of cell membranes is a very challenging goal of synthetic biology. To date, most of the research focuses on the development of eukaryotic cell membranes, while reconstitution of their prokaryotic counterparts has not been fully addressed, and the proposed models do not reflect well the complexity of bacterial cell envelopes. Here, we describe the reconstitution of biomimetic bacterial membranes with an increasing level of complexity, developed from binary and ternary lipid mixtures. Giant unilamellar vesicles composed of phosphatidylcholine (PC) and phosphatidylethanolamine (PE); PC and phosphatidylglycerol (PG); PE and PG; PE, PG and cardiolipin (CA) at varying molar ratios were successfully prepared by the electroformation method. Each of the proposed mimetic models focuses on reproducing specific membrane features such as membrane charge, curvature, leaflets asymmetry, or the presence of phase separation. GUVs were characterized in terms of size distribution, surface charge, and lateral organization. Finally, the developed models were tested against the lipopeptide antibiotic daptomycin. The obtained results showed a clear dependency of daptomycin binding efficiency on the amount of negatively charged lipid species present in the membrane. We anticipate that the models proposed here can be applied not only in antimicrobial testing but also serve as platforms for studying fundamental biological processes in bacteria as well as their interaction with physiologically relevant biomolecules.
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Affiliation(s)
- Emilia Krok
- Poznan University of Technology, Faculty of Materials Engineering and Technical Physics, Institute of Physics, Piotrowo 3, 60-965 Poznan, Poland; Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany.
| | - Mareike Stephan
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany.
| | - Lukasz Piatkowski
- Poznan University of Technology, Faculty of Materials Engineering and Technical Physics, Institute of Physics, Piotrowo 3, 60-965 Poznan, Poland
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Dao TP, Rajendran A, Galagedera SKK, Haws W, Castañeda CA. Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4. bioRxiv 2023:2023.09.27.559790. [PMID: 37808720 PMCID: PMC10557701 DOI: 10.1101/2023.09.27.559790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Highly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2 and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2 and UBQLN4 exhibit distinct phase behaviors in vitro. Strikingly, UBQLN4 phase separates at a much lower saturation concentration than UBQLN1. However, neither UBQLN1 nor UBQLN4 phase separates with a strong temperature dependence, unlike UBQLN2. We determined that the temperature-dependent phase behavior of UBQLN2 stems from its unique proline-rich (Pxx) region, which is absent in the other UBQLNs. We found that the short N-terminal disordered regions of UBQLN1, UBQLN2 and UBQLN4 inhibit UBQLN phase separation via electrostatics interactions. Charge variants of the N-terminal regions exhibit altered phase behaviors. Consistent with the sensitivity of UBQLN phase separation to the composition of the N-terminal regions, epitope tags placed on the N-termini of the UBQLNs tune phase separation. Overall, our in vitro results have important implications for studies of UBQLNs in cells, including the identification of phase separation as a potential mechanism to distinguish the cellular roles of UBQLNs, and the need to apply caution when using epitope tags to prevent experimental artifacts.
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Affiliation(s)
- Thuy P. Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Anitha Rajendran
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | | | - William Haws
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Carlos A. Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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38
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Tschurikow X, Gadzekpo A, Tran MP, Chatterjee R, Sobucki M, Zaburdaev V, Göpfrich K, Hilbert L. Amphiphiles Formed from Synthetic DNA-Nanomotifs Mimic the Stepwise Dispersal of Transcriptional Clusters in the Cell Nucleus. Nano Lett 2023; 23:7815-7824. [PMID: 37586706 PMCID: PMC10510709 DOI: 10.1021/acs.nanolett.3c01301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/28/2023] [Indexed: 08/18/2023]
Abstract
Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and we achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Increasing amphiphile concentrations induce rounding of droplets, prevent droplet fusion, and, at high concentrations, cause full dispersal of droplets. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that the addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of transcriptional cluster formation in biological cells using relatively simple DNA sequence-programmable nanostructures, opening novel ways to control the mesoscopic organization of synthetic nanomaterials.
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Affiliation(s)
- Xenia Tschurikow
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Aaron Gadzekpo
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
| | - Mai P. Tran
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg 69120, Germany
- Max
Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Rakesh Chatterjee
- Max
Planck Zentrum für Physik und Medizin, Erlangen 91058, Germany
- Chair
of Mathematics in Life Sciences, Friedrich-Alexander
Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Marcel Sobucki
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - Vasily Zaburdaev
- Max
Planck Zentrum für Physik und Medizin, Erlangen 91058, Germany
- Chair
of Mathematics in Life Sciences, Friedrich-Alexander
Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Kerstin Göpfrich
- Center
for Molecular Biology of Heidelberg University (ZMBH), Heidelberg 69120, Germany
- Max
Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Lennart Hilbert
- Institute
of Biological and Chemical Systems, Karlsruhe
Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
- Zoological
Institute, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
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陈 一, 凌 晓, 于 浩, 丁 俊. [Role of Liquid-Liquid Phase Separation in Cell Fate Transition and Diseases]. Sichuan Da Xue Xue Bao Yi Xue Ban 2023; 54:857-862. [PMID: 37866939 PMCID: PMC10579061 DOI: 10.12182/20230960302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Indexed: 10/24/2023]
Abstract
Liquid-liquid phase separation (LLPS), a novel mechanism of the organization and formation of cellular structures, plays a vital role in regulating cell fate transitions and disease pathogenesis and is gaining widespread attention. LLPS may lead to the assemblage of cellular structures with liquid-like fluidity, such as germ granules, stress granules, and nucleoli, which are classic membraneless organelles. These structures are typically formed through the high-concentration liquid aggregation of biomacromolecules driven by weak multivalent interactions. LLPS is involved in regulating various intracellular life activities and its dysregulation may cause the disruption of cellular functions, thereby contributing to the pathogenesis and development of neurodegenerative diseases, infectious diseases, cancers, etc. Herein, we summarized published findings on the LLPS dynamics of membraneless organelles in physiological and pathological cell fate transition, revealing their crucial roles in cell differentiation, development, and various pathogenic processes. This paper provides a fresh theoretical framework and potential therapeutic targets for LLPS-related studies, opening new avenues for future research.
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Affiliation(s)
- 一龙 陈
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 生物医学大数据中心 (成都 610041)West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学“医学+信息”中心 (成都 610041)Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - 晓茹 凌
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
| | - 浩澎 于
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 生物医学大数据中心 (成都 610041)West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学“医学+信息”中心 (成都 610041)Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - 俊军 丁
- 四川大学医学大数据中心 (成都 610041)Medical Big Data Center, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 生物医学大数据中心 (成都 610041)West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学“医学+信息”中心 (成都 610041)Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
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40
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Zhu X, Wang Z, Yang Y, Ma N, Zhang X. Bioinspired Formation of Anti-Ultraviolet Micro-Goose Bump PDMAEMA/PS Coatings. Chem Asian J 2023; 18:e202300479. [PMID: 37532630 DOI: 10.1002/asia.202300479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/30/2023] [Indexed: 08/04/2023]
Abstract
In this paper, inspired by the human-giving goosebumps process, we demonstrated a rapid, versatile, and simple method to prepare anti-UV microstructures polymer blend films with good morphology based on phase separation. Through the results of characterizations, it is proved that the microstructures are formed by polymer phase separation. Then the formation possibility of microstructures is proved by thermodynamic analysis. Moreover, the phase-field model is used to simulate the formation of microstructures by the finite element method, which can illustrate the evolution process of the microstructures. Besides, the microstructures were prepared on different substrates through the simple phase separation method, which can verify the versatility of this method. In addition, the anti-UV performance of the micro-structure films was evaluated. This work proposed a simple and versatile route to prepare microstructures coating in different substrates, which exhibit well anti-UV performance, and this work has the application potential for preventing material aging caused by UV radiation.
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Affiliation(s)
- Xu Zhu
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao, 266000, China
| | - Zhen Wang
- Yusuf Hamied Department of Chemistry, Cambridge University, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Yuyun Yang
- College of Materials Science and Chemical Engineering, Harbin Engineering University, Qingdao, 266000, China
| | - Ning Ma
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao, 266000, China
- College of Materials Science and Chemical Engineering, Harbin Engineering University, Qingdao, 266000, China
| | - Xinyue Zhang
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao, 266000, China
- College of Materials Science and Chemical Engineering, Harbin Engineering University, Qingdao, 266000, China
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41
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Spicer MFD, Gerlich DW. The material properties of mitotic chromosomes. Curr Opin Struct Biol 2023; 81:102617. [PMID: 37279615 PMCID: PMC10448380 DOI: 10.1016/j.sbi.2023.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/28/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023]
Abstract
Chromosomes transform during the cell cycle, allowing transcription and replication during interphase and chromosome segregation during mitosis. Morphological changes are thought to be driven by the combined effects of DNA loop extrusion and a chromatin solubility phase transition. By extruding the chromatin fibre into loops, condensins enrich at an axial core and provide resistance to spindle pulling forces. Mitotic chromosomes are further compacted by deacetylation of histone tails, rendering chromatin insoluble and resistant to penetration by microtubules. Regulation of surface properties by Ki-67 allows independent chromosome movement in early mitosis and clustering during mitotic exit. Recent progress has provided insight into how the extraordinary material properties of chromatin emerge from these activities, and how these properties facilitate faithful chromosome segregation.
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Affiliation(s)
- Maximilian F D Spicer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria. https://twitter.com/Spicer__Max
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030, Vienna, Austria.
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Zhang L, Liu Z, Lu Y, Nie J, Chen Y. Phase Separation in Kidney Diseases: Autosomal Dominant Polycystic Kidney Disease and Beyond. Kidney Dis (Basel) 2023; 9:229-238. [PMID: 37899998 PMCID: PMC10601909 DOI: 10.1159/000530250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/15/2023] [Indexed: 10/31/2023]
Abstract
Background The formation of biomolecular condensates via phase separation has emerged as a fundamental principle underlying the spatiotemporal coordination of biological activities in cells. Aberrant biomolecular condensates often directly regulate key cellular process involved in the pathogenesis of human diseases, including kidney diseases. Summary In this review, we summarize the physiological roles of phase separation and methodologies for phase separation studies. Taking autosomal dominant polycystic kidney disease as an example, we discuss recent advances toward elucidating the multiple mechanisms involved in kidney pathology arising from aberrant phase separation. We suggest that dysregulation of phase separation contributes to the pathogenesis of other important kidney diseases, including kidney injury and fibrosis. Key Messages Phase separation provides a useful new concept to understand the mechanisms underlying kidney disease development. Targeting aberrant phase-separated condensates offers new therapeutic avenues for combating kidney diseases.
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Affiliation(s)
- Lirong Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Zhiheng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Yumei Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
| | - Jing Nie
- Division of Nephrology, State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Guangdong Provincial Institute of Nephrology, Guangdong Provincial Key Laboratory of Renal Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yupeng Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Institute of Urology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, China
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Mao S, Liu Q, Wu H, Zhu J, Xie Y, Ma J, Zhen N, Pan Q. Phase separation of YAP mediated by coiled-coil domain promotes hepatoblastoma proliferation via activation of transcription. J Gastroenterol Hepatol 2023; 38:1398-1407. [PMID: 36908026 DOI: 10.1111/jgh.16173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
AIM AND BACKGROUND Yes-associated protein (YAP), a key transcriptional co-activator associated with cell fate and tumor progression, has been reported to be a powerful driver of hepatoblastoma (HB). In this study, we investigated the mechanism underlying oncogenic role of YAP in HB. METHODS The expression of YAP in HB tissues was measured through WB and qRT-PCR. The IHC and IF were performed to determine the distribution of YAP. The phase separation of YAP was proved by living cell imaging and FRAP experiment. The effect of YAP phase separation in HB cells in vitro an in vivo were tested using CCK8, flow cytometry, and xenograft tumors. RESULTS YAP was overexpressed and activated in HB. Nuclear YAP formed an active transcriptional site via LLPS to recruit the crucial transcription factor TEAD4. Thus, YAP phase separation facilitated transcription of oncogenic genes and subsequently mediated chemoresistance of HB. Mechanistically, the phase separation ability of YAP depends on the coiled-coil domain, which is a typical phase separation domain. The electrostatic interactions and hydrophobic interactions within YAP are also vital to YAP phase separation. More importantly, YAP inhibitor verteporfin is potential treatment for HB and combination with cisplatin enhanced therapeutic efficacy. CONCLUSIONS Highly expressed and active YAP exerts an oncogenic effect in HB via phase separation and provides new insights for the treatment of HB.
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Affiliation(s)
- Siwei Mao
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qianrui Liu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
| | - Han Wu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jiabei Zhu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yi Xie
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ji Ma
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
| | - Ni Zhen
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Sanya, Hainan, China
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44
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Yuan S, Zhou G, Xu G. Translation machinery: the basis of translational control. J Genet Genomics 2023:S1673-8527(23)00161-3. [PMID: 37536497 DOI: 10.1016/j.jgg.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
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Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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45
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Cordeiro Y, Freire MHO, Wiecikowski AF, do Amaral MJ. (Dys)functional insights into nucleic acids and RNA-binding proteins modulation of the prion protein and α-synuclein phase separation. Biophys Rev 2023; 15:577-589. [PMID: 37681103 PMCID: PMC10480379 DOI: 10.1007/s12551-023-01067-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 09/09/2023] Open
Abstract
Prion diseases are prototype of infectious diseases transmitted by a protein, the prion protein (PrP), and are still not understandable at the molecular level. Heterogenous species of aggregated PrP can be generated from its monomer. α-synuclein (αSyn), related to Parkinson's disease, has also shown a prion-like pathogenic character, and likewise PrP interacts with nucleic acids (NAs), which in turn modulate their aggregation. Recently, our group and others have characterized that NAs and/or RNA-binding proteins (RBPs) modulate recombinant PrP and/or αSyn condensates formation, and uncontrolled condensation might precede pathological aggregation. Tackling abnormal phase separation of neurodegenerative disease-related proteins has been proposed as a promising therapeutic target. Therefore, understanding the mechanism by which polyanions, like NAs, modulate phase transitions intracellularly, is key to assess their role on toxicity promotion and neuronal death. Herein we discuss data on the nucleic acids binding properties and phase separation ability of PrP and αSyn with a special focus on their modulation by NAs and RBPs. Furthermore, we provide insights into condensation of PrP and/or αSyn in the light of non-trivial subcellular locations such as the nuclear and cytosolic environments.
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Affiliation(s)
- Yraima Cordeiro
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Maria Heloisa O. Freire
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Adalgisa Felippe Wiecikowski
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Mariana Juliani do Amaral
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
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Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
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Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
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Bayona-Hernandez A, Guerra S, Jiménez-Ramirez IA, Sztacho M, Hozak P, Rodriguez-Zapata LC, Pereira-Santana A, Castaño E. LIPRNAseq: a method to discover lipid interacting RNAs by sequencing. Mol Biol Rep 2023; 50:6619-6626. [PMID: 37349607 DOI: 10.1007/s11033-023-08548-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Current biological research extensively describes the interactions of molecules such as RNA with other nucleic acids or proteins. However, the relatively recent discovery of nuclear phospholipids playing biologically relevant processes outside membranes, as well as, RNA-lipid interactions shows the need for new methods to explore the identity of these RNAs. METHODS AND RESULTS In this study, we describe the method for LIPID-RNA isolation followed by sequencing and analysis of the RNA that has the ability to interact with the selected lipids. Here we utilized specific phospholipid coated beads for selective RNA binding. We tested RNA from organisms belonging to different realms (human, plant, and yeast), and tested their ability to bind a specific lipid. CONCLUSIONS The results show several RNAs differentially enriched in the pull-down of phosphatidyl Inositol 4,5 bisphosphate coated beads. This method is helpful to screen lipid-binding RNA, which may have relevant biological functions. The method can be used with different lipids and comparison of pull-downs and can narrow the selection of RNAs that interact with a particular lipid for further studies.
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Affiliation(s)
- Andrea Bayona-Hernandez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México
| | - Susana Guerra
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México
| | - Irma Angélica Jiménez-Ramirez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, Prague, 1083, 142 20, Czech Republic
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, Prague, 1083, 142 20, Czech Republic
| | - Luis Carlos Rodriguez-Zapata
- Unidad de Biotecnologia, Centro de Investigación Científica de Yucatán, Chuburná de Hidalgo, Calle 43, Número 130, Mérida, Yucatán, CP 97205, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. Subsede Sureste, Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera Sierra Papacal-Chuburná-Puerto, Mérida, 97302, Yucatán, México
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, 03940, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México.
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Riemenschneider H, Simonetti F, Sheth U, Katona E, Roth S, Hutten S, Farny D, Michaelsen M, Nuscher B, Schmidt MK, Flatley A, Schepers A, Gruijs da Silva LA, Zhou Q, Klopstock T, Liesz A, Arzberger T, Herms J, Feederle R, Gendron TF, Dormann D, Edbauer D. Targeting the glycine-rich domain of TDP-43 with antibodies prevents its aggregation in vitro and reduces neurofilament levels in vivo. Acta Neuropathol Commun 2023; 11:112. [PMID: 37434215 DOI: 10.1186/s40478-023-01592-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/31/2023] [Indexed: 07/13/2023] Open
Abstract
Cytoplasmic aggregation and concomitant nuclear clearance of the RNA-binding protein TDP-43 are found in ~ 90% of cases of amyotrophic lateral sclerosis and ~ 45% of patients living with frontotemporal lobar degeneration, but no disease-modifying therapy is available. Antibody therapy targeting other aggregating proteins associated with neurodegenerative disorders has shown beneficial effects in animal models and clinical trials. The most effective epitopes for safe antibody therapy targeting TDP-43 are unknown. Here, we identified safe and effective epitopes in TDP-43 for active and potential future passive immunotherapy. We prescreened 15 peptide antigens covering all regions of TDP-43 to identify the most immunogenic epitopes and to raise novel monoclonal antibodies in wild-type mice. Most peptides induced a considerable antibody response and no antigen triggered obvious side effects. Thus, we immunized mice with rapidly progressing TDP-43 proteinopathy ("rNLS8" model) with the nine most immunogenic peptides in five pools prior to TDP-43ΔNLS transgene induction. Strikingly, combined administration of two N-terminal peptides induced genetic background-specific sudden lethality in several mice and was therefore discontinued. Despite a strong antibody response, no TDP-43 peptide prevented the rapid body weight loss or reduced phospho-TDP-43 levels as well as the profound astrogliosis and microgliosis in rNLS8 mice. However, immunization with a C-terminal peptide containing the disease-associated phospho-serines 409/410 significantly lowered serum neurofilament light chain levels, indicative of reduced neuroaxonal damage. Transcriptomic profiling showed a pronounced neuroinflammatory signature (IL-1β, TNF-α, NfκB) in rNLS8 mice and suggested modest benefits of immunization targeting the glycine-rich region. Several novel monoclonal antibodies targeting the glycine-rich domain potently reduced phase separation and aggregation of TDP-43 in vitro and prevented cellular uptake of preformed aggregates. Our unbiased screen suggests that targeting the RRM2 domain and the C-terminal region of TDP-43 by active or passive immunization may be beneficial in TDP-43 proteinopathies by inhibiting cardinal processes of disease progression.
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Affiliation(s)
- Henrick Riemenschneider
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Francesca Simonetti
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Ludwig-Maximilians-Universität (LMU) Munich, Graduate School of Systemic Neurosciences (GSN), 81377, Munich, Germany
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-Universität (JGU), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Udit Sheth
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Eszter Katona
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Ludwig-Maximilians-Universität (LMU) Munich, Graduate School of Systemic Neurosciences (GSN), 81377, Munich, Germany
| | - Stefan Roth
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Saskia Hutten
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-Universität (JGU), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Daniel Farny
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Meike Michaelsen
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Brigitte Nuscher
- Chair of Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität (LMU) Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Michael K Schmidt
- Center for Neuropathology and Prion Research, University Hospital, LMU Munich, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Lara A Gruijs da Silva
- Ludwig-Maximilians-Universität (LMU) Munich, Graduate School of Systemic Neurosciences (GSN), 81377, Munich, Germany
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-Universität (JGU), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Qihui Zhou
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Thomas Klopstock
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Friedrich Baur Institute at the Department of Neurology, University Hospital, LMU Munich, Ziemssenstr. 1a, 80336, Munich, Germany
| | - Arthur Liesz
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Thomas Arzberger
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Center for Neuropathology and Prion Research, University Hospital, LMU Munich, Feodor-Lynen-Str. 23, 81377, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nußbaumstr. 7, 80336, Munich, Germany
| | - Jochen Herms
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Center for Neuropathology and Prion Research, University Hospital, LMU Munich, Feodor-Lynen-Str. 23, 81377, Munich, Germany
| | - Regina Feederle
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Tania F Gendron
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Dorothee Dormann
- Institute of Molecular Physiology, Faculty of Biology, Johannes Gutenberg-Universität (JGU), Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), Munich, Feodor-Lynen-Str. 17, 81377, Munich, Germany.
- Munich Cluster of Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany.
- Ludwig-Maximilians-Universität (LMU) Munich, Graduate School of Systemic Neurosciences (GSN), 81377, Munich, Germany.
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Zhou RW, Parsons RE. Etiology of super-enhancer reprogramming and activation in cancer. Epigenetics Chromatin 2023; 16:29. [PMID: 37415185 DOI: 10.1186/s13072-023-00502-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/10/2023] [Indexed: 07/08/2023] Open
Abstract
Super-enhancers are large, densely concentrated swaths of enhancers that regulate genes critical for cell identity. Tumorigenesis is accompanied by changes in the super-enhancer landscape. These aberrant super-enhancers commonly form to activate proto-oncogenes, or other genes upon which cancer cells depend, that initiate tumorigenesis, promote tumor proliferation, and increase the fitness of cancer cells to survive in the tumor microenvironment. These include well-recognized master regulators of proliferation in the setting of cancer, such as the transcription factor MYC which is under the control of numerous super-enhancers gained in cancer compared to normal tissues. This Review will cover the expanding cell-intrinsic and cell-extrinsic etiology of these super-enhancer changes in cancer, including somatic mutations, copy number variation, fusion events, extrachromosomal DNA, and 3D chromatin architecture, as well as those activated by inflammation, extra-cellular signaling, and the tumor microenvironment.
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Affiliation(s)
- Royce W Zhou
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Molecular Medicine Program, University of California San Francisco Internal Medicine Residency, San Francisco, CA, USA
| | - Ramon E Parsons
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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50
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Gabarayeva NI, Grigorjeva VV, Polevova SV, Britski DA. Ontogenesis in miniature. Pollen wall development in Campanula rapunculoides. Planta 2023; 258:38. [PMID: 37410162 DOI: 10.1007/s00425-023-04198-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
MAIN CONCLUSION Our findings suggest a reconsideration of pollen wall ontogeny process, entailing examination of physical factors, which enable a new understanding of exine developmental processes as self-formation. The pollen wall, the most complex cell wall in plants, is especially interesting as a model of ontogeny in miniature. By a detailed study of each developmental stage of Campanula rapunculoides pollen wall, we aimed to understand the establishment of complex pollen walls and the underlying developmental mechanisms. Other aim was to compare our current observations with studies in other species to reveal the common principles. We also tried to analyse the reasons for commonalities in ontogenies of exines in remote species. TEM, SEM, comparative methods were used in this study. The sequence of events leading to exine emergence from early tetrad stage to maturity is as follows: the appearance of spherical micelles in the periplasmic space and de-mixing of the mixture in periplasm (condensed and depleted layers); appearance of plasma membrane invaginations and columns of spherical micelles inside condensed layer; appearance of rod-like units, pro-tectum and thin foot layer; the appearance of spiral substructure of procolumellae and of dendritic outgrowths on the tops of procolumellae, of vast depleted zone in aperture sites; formation of the endexine lamellae on the base of laminate micelles; gradual twisting of dendritic outgrowths (macromolecule chains) into clubs on the tops of columellae and into spines; final sporopollenin accumulation. Our observations are consistent with the sequence of self-assembling micellar mesophases. Complex organisation of the exine is established through processes of self-assembly operating together with another physical process-phase separation. After genomic determination of the exine building substances, purely physical processes which are not under direct genomic control play an important role after genomic control of constructive substances. The comparison of the underlying mechanisms of exine development in remote species occurred to be general and similar to crystallisation. Our ontogenetic experience has shown the commonality of pollen wall ontogenies in remote species.
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Affiliation(s)
- Nina I Gabarayeva
- Komarov Botanical Institute, Popov St. 2, 197376, St. Petersburg, Russia.
| | | | - Svetlana V Polevova
- Department of Biology, Moscow State University, Leninski Gory, 1, 119991, Moscow, Russia
| | - Dmitri A Britski
- Komarov Botanical Institute, Popov St. 2, 197376, St. Petersburg, Russia
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