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Kobayashi R, Nabika H. Liquid-liquid phase separation induced by crowding condition affects amyloid-β aggregation mechanism. SOFT MATTER 2024; 20:5331-5342. [PMID: 38847095 DOI: 10.1039/d4sm00470a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is common in the aggregation of proteins associated with neurodegenerative diseases. Many efforts have been made to reproduce crowded conditions with artificial polymeric materials to understand the effect of LLPS in physiological conditions with significantly highly concentrated proteins, such as intrinsically disordered proteins. Although the possibility that LLPS is involved in intracellular amyloid-β (Aβ) aggregation, a protein related to the pathogenesis of Alzheimer's disease, has been investigated, the relationship between LLPS and the aggregation of Aβ is poorly characterized. Thus, in this study, we mimicked the intracellular crowding environment using polyethylene glycol and dextran, used commonly as model polymers, to examine the relationship of Aβ with LLPS and aggregation dynamics in vitro. We confirmed that Aβ undergoes LLPS under specific polymer coexistence conditions. Moreover, the addition of different electrolytes modulated LLPS and fibril formation. These results suggest that hydrophobic and electrostatic interactions are the driving forces for the LLPS of Aβ. Similar to the role of the liposome interface, the interface of droplets induced by LLPS functioned as the site for heterogeneous nucleation. These findings offer valuable insights into the complex mechanisms of Aβ aggregation in vivo and may be useful in establishing therapeutic methods for Alzheimer's disease.
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Affiliation(s)
- Ryuki Kobayashi
- Department of Science, Graduate School of Science and Engineering, Yamagata University, 1-4-12, Kojirakawa, Yamagata 990-8560, Japan
| | - Hideki Nabika
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa, Yamagata 990-8560, Japan.
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2
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Chekulaeva M. Mechanistic insights into the basis of widespread RNA localization. Nat Cell Biol 2024; 26:1037-1046. [PMID: 38956277 DOI: 10.1038/s41556-024-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/20/2024] [Indexed: 07/04/2024]
Abstract
The importance of subcellular mRNA localization is well established, but the underlying mechanisms mostly remain an enigma. Early studies suggested that specific mRNA sequences recruit RNA-binding proteins (RBPs) to regulate mRNA localization. However, despite the observation of thousands of localized mRNAs, only a handful of these sequences and RBPs have been identified. This suggests the existence of alternative, and possibly predominant, mechanisms for mRNA localization. Here I re-examine currently described mRNA localization mechanisms and explore alternative models that could account for its widespread occurrence.
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Affiliation(s)
- Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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3
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Hao S, Lee YJ, Benhamou Goldfajn N, Flores E, Liang J, Fuehrer H, Demmerle J, Lippincott-Schwartz J, Liu Z, Sukenik S, Cai D. YAP condensates are highly organized hubs. iScience 2024; 27:109927. [PMID: 38784009 PMCID: PMC11111833 DOI: 10.1016/j.isci.2024.109927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 10/24/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
YAP/TEAD signaling is essential for organismal development, cell proliferation, and cancer progression. As a transcriptional coactivator, how YAP activates its downstream target genes is incompletely understood. YAP forms biomolecular condensates in response to hyperosmotic stress, concentrating transcription-related factors to activate downstream target genes. However, whether YAP forms condensates under other signals, how YAP condensates organize and function, and how YAP condensates activate transcription in general are unknown. Here, we report that endogenous YAP forms sub-micron scale condensates in response to Hippo pathway regulation and actin cytoskeletal tension. YAP condensates are stabilized by the transcription factor TEAD1, and recruit BRD4, a coactivator that is enriched at active enhancers. Using single-particle tracking, we found that YAP condensates slowed YAP diffusion within condensate boundaries, a possible mechanism for promoting YAP target search. These results reveal that YAP condensate formation is a highly regulated process that is critical for YAP/TEAD target gene expression.
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Affiliation(s)
- Siyuan Hao
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ye Jin Lee
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nadav Benhamou Goldfajn
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Eduardo Flores
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, CA 95343, USA
| | - Jindayi Liang
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Hannah Fuehrer
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Justin Demmerle
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | | | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shahar Sukenik
- Department of Chemistry and Chemical Biology, University of California, Merced, Merced, CA 95343, USA
| | - Danfeng Cai
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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4
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Giudice J, Jiang H. Splicing regulation through biomolecular condensates and membraneless organelles. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00739-7. [PMID: 38773325 DOI: 10.1038/s41580-024-00739-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Biomolecular condensates, sometimes also known as membraneless organelles (MLOs), can form through weak multivalent intermolecular interactions of proteins and nucleic acids, a process often associated with liquid-liquid phase separation. Biomolecular condensates are emerging as sites and regulatory platforms of vital cellular functions, including transcription and RNA processing. In the first part of this Review, we comprehensively discuss how alternative splicing regulates the formation and properties of condensates, and conversely the roles of biomolecular condensates in splicing regulation. In the second part, we focus on the spatial connection between splicing regulation and nuclear MLOs such as transcriptional condensates, splicing condensates and nuclear speckles. We then discuss key studies showing how splicing regulation through biomolecular condensates is implicated in human pathologies such as neurodegenerative diseases, different types of cancer, developmental disorders and cardiomyopathies, and conclude with a discussion of outstanding questions pertaining to the roles of condensates and MLOs in splicing regulation and how to experimentally study them.
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Affiliation(s)
- Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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5
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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Sandhu A, Lyu X, Wan X, Meng X, Tang NH, Gonzalez G, Syed IN, Chen L, Jin Y, Chisholm AD. The microtubule regulator EFA-6 forms spatially restricted cortical foci dependent on its intrinsically disordered region and interactions with tubulins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.14.588158. [PMID: 38645057 PMCID: PMC11030407 DOI: 10.1101/2024.04.14.588158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Microtubules (MTs) are dynamic components of the cytoskeleton and play essential roles in morphogenesis and maintenance of tissue and cell integrity. Despite recent advances in understanding MT ultrastructure, organization, and growth control, how cells regulate MT organization at the cell cortex remains poorly understood. The EFA-6/EFA6 proteins are recently identified membrane-associated proteins that inhibit cortical MT dynamics. Here, combining visualization of endogenously tagged C. elegans EFA-6 with genetic screening, we uncovered tubulin-dependent regulation of EFA-6 patterning. In the mature epidermal epithelium, EFA-6 forms punctate foci in specific regions of the apical cortex, dependent on its intrinsically disordered region (IDR). We further show the EFA-6 IDR is sufficient to form biomolecular condensates in vitro. In screens for mutants with altered GFP::EFA-6 localization, we identified a novel gain-of-function (gf) mutation in an α-tubulin tba-1 that induces ectopic EFA-6 foci in multiple cell types. tba-1(gf) animals exhibit temperature-sensitive embryonic lethality, which is partially suppressed by efa-6(lf), indicating the interaction between tubulins and EFA-6 is important for normal development. TBA-1(gf) shows reduced incorporation into filamentous MTs but has otherwise mild effects on cellular MT organization. The ability of TBA-1(gf) to trigger ectopic EFA-6 foci formation requires β-tubulin TBB-2 and the chaperon EVL-20/Arl2. The tba-1(gf)-induced EFA-6 foci display slower turnover, contain the MT-associated protein TAC-1/TACC, and require the EFA-6 MTED. Our results reveal a novel crosstalk between cellular tubulins and cortical MT regulators in vivo.
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Affiliation(s)
- Anjali Sandhu
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA 92093 USA
| | - Xiaohui Lyu
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA 92093 USA
| | - Xinghaoyun Wan
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA 92093 USA
| | - Xuefeng Meng
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA 92093 USA
| | - Ngang Heok Tang
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, CA 92093 USA
| | - Gilberto Gonzalez
- Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Ishana N. Syed
- Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lizhen Chen
- Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA 92093 USA
| | - Andrew D. Chisholm
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, CA 92093 USA
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, CA 92093 USA
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7
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Dudas EF, Tully MD, Foldes T, Kelly G, Tartaglia GG, Pastore A. The structural properties of full-length annexin A11. Front Mol Biosci 2024; 11:1347741. [PMID: 38516187 PMCID: PMC10955470 DOI: 10.3389/fmolb.2024.1347741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/17/2024] [Indexed: 03/23/2024] Open
Abstract
Annexin A11 (ANXA11) is a calcium-dependent phospholipid-binding protein belonging to the annexin protein family and implicated in the neurodegenerative amyotrophic lateral sclerosis. Structurally, ANXA11 contains a conserved calcium-binding C-terminal domain common to all annexins and a putative intrinsically unfolded N-terminus specific for ANXA11. Little is known about the structure and functions of this region of the protein. By analogy with annexin A1, it was suggested that residues 38 to 59 within the ANXA11 N-terminus could form a helical region that would be involved in interactions. Interestingly, this region contains residues that, when mutated, may lead to clinical manifestations. In the present study, we have studied the structural features of the full-length protein with special attention to the N-terminal region using a combination of biophysical techniques which include nuclear magnetic resonance and small angle X-ray scattering. We show that the N-terminus is intrinsically disordered and that the overall features of the protein are not markedly affected by the presence of calcium. We also analyzed the 38-59 helix hypothesis using synthetic peptides spanning both the wild-type sequence and clinically relevant mutations. We show that the peptides have a remarkable character typical of a native helix and that mutations do not alter the behaviour suggesting that they are required for interactions rather than being structurally important. Our work paves the way to a more thorough understanding of the ANXA11 functions.
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Affiliation(s)
- Erika F. Dudas
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
| | - Mark D. Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Tamas Foldes
- University College London, Department of Physics and Astronomy, University College London, London, United Kingdom
- Institut de Biologie Structurale (IBS), Institut Laue-Langevin, University Grenoble Alpes, Grenoble, France
| | - Geoff Kelly
- MRC Biomedical NMR Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- European Synchrotron Radiation Facility, Grenoble, France
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8
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Lee SE, Chang S. nArgBP2 together with GKAP and SHANK3 forms a dynamic layered structure. Front Cell Neurosci 2024; 18:1354900. [PMID: 38440150 PMCID: PMC10909995 DOI: 10.3389/fncel.2024.1354900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
nArgBP2, a protein whose disruption is implicated in intellectual disability, concentrates in excitatory spine-synapses. By forming a triad with GKAP and SHANK, it regulates spine structural rearrangement. We here find that GKAP and SHANK3 concentrate close to the synaptic contact, whereas nArgBP2 concentrates more centrally in the spine. The three proteins collaboratively form biomolecular condensates in living fibroblasts, exhibiting distinctive layered localizations. nArgBP2 concentrates in the inner phase, SHANK3 in the outer phase, and GKAP partially in both. Upon co-expression of GKAP and nArgBP2, they evenly distribute within condensates, with a notable peripheral localization of SHANK3 persisting when co-expressed with either GKAP or nArgBP2. Co-expression of SHANK3 and GKAP with CaMKIIα results in phase-in-phase condensates, with CaMKIIα at the central locus and SHANK3 and GKAP exhibiting peripheral localization. Additional co-expression of nArgBP2 maintains the layered organizational structure within condensates. Subsequent CaMKIIα activation disperses a majority of the condensates, with an even distribution of all proteins within the extant deformed condensates. Our findings suggest that protein segregation via phase separation may contribute to establishing layered organization in dendritic spines.
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Affiliation(s)
- Sang-Eun Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
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9
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Du C, Zhao X. Screening and characterization of a denitrifying Chelatococcus with strong desulfurization capacity. Heliyon 2024; 10:e25135. [PMID: 38333781 PMCID: PMC10850526 DOI: 10.1016/j.heliyon.2024.e25135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
A denitrifying bacteria, which we named Chelatococcus DNB-15, was screened and isolated from the Shengli Oilfield polymer-containing wastewater. The strain was characterized by 16S rDNA analysis and the effects of nutrient substrate type, pH, mineralization and temperature on the activity of the strain were also investigated. The strain was identified as Chelatococcus, of which the most efficient carbon source is sodium citrate, the most suitable nitrogen source is potassium nitrate, the suitable temperature for growth is 35~45 °C, the suitable pH range for growth is 7.0~9.0, and the maximal tolerable mineralization is 4 × 104 mg/L. The desulfurization experiment showed that Chelatococcus DNB-15 has desulfurization ability to some extent. When the initial sulfide concentration is lower than 50 mg/L, Chelatococcus DNB-15 grows rapidly, and the sulfides are removed quickly within 24 h, displaying a sulfur removal rate higher than 99 %; When the initial sulfide concentration is higher than 150 mg/L, the growth of Chelatococcus DNB-15 is severely restricted, the desulfurization effect is not obvious, and the desulfurization rate is almost stagnant.
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Affiliation(s)
- Chunan Du
- College of Chemical Engineering, Shandong Institute of Petroleumand Chemical Technology, Dongying, 257000, China
| | - Xiaolong Zhao
- China University of Petroleum–Beijing at Karamay, Karamay, 834000, China
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10
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罗 国, 周 陈. [Latest Findings on Phase Separation of Cytomechanical Proteins]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:19-23. [PMID: 38322526 PMCID: PMC10839485 DOI: 10.12182/20240160206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Indexed: 02/08/2024]
Abstract
The cellular response to mechanical stimuli depends largely on the structure of the cell itself and the abundance of intracellular cytomechanical proteins also plays a key role in the response to the stimulation of external mechanical signals. Liquid-liquid phase separation (LLPS) is the process by which proteins or protein-RNA complexes spontaneously separate and form two distinct "phases", ie, a low-concentration phase coexisting with a high-concentration phase. According to published findings, membrane-free organelles form and maintain their structures and regulate their internal biochemical activities through LLPS. LLPS, a novel mechanism for intracellular regulation of the biochemical reactions of biomacromolecules, plays a crucial role in modulating the responses of cytomechanical proteins. LLPS leads to the formation of highly concentrated liquid-phase condensates through multivalent interactions between biomacromolecules, thereby regulating a series of intracellular life activities. It has been reported that a variety of cytomechanical proteins respond to external mechanical signals through LLPS, which in turn affects biological behaviors such as cell growth, proliferation, spreading, migration, and apoptosis. Herein, we introduced the mechanisms of cytomechanics and LLPS. In addition, we presented the latest findings on cytomechanical protein phase separation, covering such issues as the regulation of focal adhesion maturation and mechanical signal transduction by LIM domain-containing protein 1 (LIMD1) phase separation, the regulation of intercellular tight junctions by zonula occludens (ZO) phase separation, and the regulation of cell proliferation and apoptosis by cytomechanical protein phase separation of the Hippo signaling pathway. The proposition of LLPS provides an explanation for the formation mechanism of intracellular membraneless organelles and supplies new approaches to understanding the biological functions of intracellular physiology or pathology. However, the molecular mechanisms by which LLPS drives focal adhesions and cell-edge dynamics are still not fully understood. It is not clear whether LLPS under in vitro conditions can occur under physiological conditions of organisms. There are still difficulties to be overcome in using LLPS to explain the interactions of multiple intracellular molecules. Researchers should pursue answers to these questions in the future.
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Affiliation(s)
- 国文 罗
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - 陈晨 周
- 口腔疾病研究国家重点实验室 国家口腔疾病临床医学研究中心 四川大学华西口腔医院 (成都 610041)State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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11
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Lavering ED, Gandhamaneni M, Weeks DL. Intrinsically disordered regions are not sufficient to direct the compartmental localization of nucleolar proteins in the nucleus. PLoS Biol 2023; 21:e3002378. [PMID: 37943867 PMCID: PMC10662738 DOI: 10.1371/journal.pbio.3002378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 11/21/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
The nucleolus is a non-membrane bound organelle central to ribosome biogenesis. The nucleolus contains a mix of proteins and RNA and has 3 known nucleolar compartments: the fibrillar center (FC), the dense fibrillar component (DFC), and the granular component (GC). The spatial organization of the nucleolus is influenced by the phase separation properties of nucleolar proteins, the presence of RNA, protein modification, and cellular activity. Many nucleolar proteins appear to concentrate within the borders of the compartments. We investigated whether the intrinsically disordered regions from several proteins provided the information needed to establish specific compartment localization using Xenopus laevis oocytes. For the proteins we tested, the disordered regions were not sufficient to direct specific domain localization and appear dispensable with respect to compartmentalization. Among the proteins that colocalize to the DFC are the quartet that comprise the box H/ACA pseudouridylation complex. In contrast to the insufficiency of IDRs to direct compartment localization, we found that the DFC accumulation of 2 box H/ACA proteins, Gar1 and Nhp2, was disrupted by mutations that were previously shown to reduce their ability to join the box H/ACA complex. Using a nanobody to introduce novel binding to a different DFC localized protein, we restored the localization of the mutated forms of Gar1 and Nhp2.
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Affiliation(s)
- Emily D. Lavering
- Biochemistry and Molecular Biology Department, Carver College of Medicine, University of Iowa, Iowa City, United States of America
| | | | - Daniel L. Weeks
- Biochemistry and Molecular Biology Department, Carver College of Medicine, University of Iowa, Iowa City, United States of America
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12
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Kim N, Kim TH, Kim C, Lee JE, Kang MG, Shin S, Jung M, Kim JS, Mun JY, Rhee HW, Park SY, Shin Y, Yoo JY. Intrinsically disordered region-mediated condensation of IFN-inducible SCOTIN/SHISA-5 inhibits ER-to-Golgi vesicle transport. Dev Cell 2023; 58:1950-1966.e8. [PMID: 37816329 DOI: 10.1016/j.devcel.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/27/2023] [Accepted: 08/25/2023] [Indexed: 10/12/2023]
Abstract
Newly synthesized proteins in the endoplasmic reticulum (ER) are sorted by coat protein complex II (COPII) at the ER exit site en route to the Golgi. Under cellular stresses, COPII proteins become targets of regulation to control the transport. Here, we show that the COPII outer coat proteins Sec31 and Sec13 are selectively sequestered into the biomolecular condensate of SCOTIN/SHISA-5, which interferes with COPII vesicle formation and inhibits ER-to-Golgi transport. SCOTIN is an ER transmembrane protein with a cytosolic intrinsically disordered region (IDR), which is required and essential for the formation of condensates. Upon IFN-γ stimulation, which is a cellular condition that induces SCOTIN expression and condensation, ER-to-Golgi transport was inhibited in a SCOTIN-dependent manner. Furthermore, cancer-associated mutations of SCOTIN perturb its ability to form condensates and control transport. Together, we propose that SCOTIN impedes the ER-to-Golgi transport through its ability to form biomolecular condensates at the ER membrane.
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Affiliation(s)
- Nari Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
| | - Tae-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Chaelim Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jee-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghee Shin
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea; Center for RNA Research, Institute for Basic Science (IBS), Seoul 08826, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Yongdae Shin
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Joo-Yeon Yoo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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13
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Chen L, Zhang Z, Han Q, Maity BK, Rodrigues L, Zboril E, Adhikari R, Ko SH, Li X, Yoshida SR, Xue P, Smith E, Xu K, Wang Q, Huang THM, Chong S, Liu Z. Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions. Mol Cell 2023; 83:3438-3456.e12. [PMID: 37738977 PMCID: PMC10592010 DOI: 10.1016/j.molcel.2023.08.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 07/11/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023]
Abstract
Transcription factors (TFs) activate enhancers to drive cell-specific gene programs in response to signals, but our understanding of enhancer assembly during signaling events is incomplete. Here, we show that androgen receptor (AR) forms condensates through multivalent interactions mediated by its N-terminal intrinsically disordered region (IDR) to orchestrate enhancer assembly in response to androgen signaling. AR IDR can be substituted by IDRs from selective proteins for AR condensation capacity and its function on enhancers. Expansion of the poly(Q) track within AR IDR results in a higher AR condensation propensity as measured by multiple methods, including live-cell single-molecule microscopy. Either weakening or strengthening AR condensation propensity impairs its heterotypic multivalent interactions with other enhancer components and diminishes its transcriptional activity. Our work reveals the requirement of an optimal level of AR condensation in mediating enhancer assembly and suggests that alteration of the fine-tuned multivalent IDR-IDR interactions might underlie AR-related human pathologies.
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Affiliation(s)
- Lizhen Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Qinyu Han
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Barun K Maity
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leticia Rodrigues
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Emily Zboril
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rashmi Adhikari
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Su-Hyuk Ko
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xin Li
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Shawn R Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pengya Xue
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Emilie Smith
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kexin Xu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Qianben Wang
- Department of Pathology, Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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14
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Poudyal M, Patel K, Gadhe L, Sawner AS, Kadu P, Datta D, Mukherjee S, Ray S, Navalkar A, Maiti S, Chatterjee D, Devi J, Bera R, Gahlot N, Joseph J, Padinhateeri R, Maji SK. Intermolecular interactions underlie protein/peptide phase separation irrespective of sequence and structure at crowded milieu. Nat Commun 2023; 14:6199. [PMID: 37794023 PMCID: PMC10550955 DOI: 10.1038/s41467-023-41864-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a crucial biological phenomenon underlying the sequestration of macromolecules (such as proteins and nucleic acids) into membraneless organelles in cells. Unstructured and intrinsically disordered domains are known to facilitate multivalent interactions driving protein LLPS. We hypothesized that LLPS could be an intrinsic property of proteins/polypeptides but with distinct phase regimes irrespective of their sequence and structure. To examine this, we studied many (a total of 23) proteins/polypeptides with different structures and sequences for LLPS study in the presence and absence of molecular crowder, polyethylene glycol (PEG-8000). We showed that all proteins and even highly charged polypeptides (under study) can undergo liquid condensate formation, however with different phase regimes and intermolecular interactions. We further demonstrated that electrostatic, hydrophobic, and H-bonding or a combination of such intermolecular interactions plays a crucial role in individual protein/peptide LLPS.
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Affiliation(s)
- Manisha Poudyal
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Siddhartha Maiti
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Department of Bioengineering, VIT Bhopal University, Bhopal-Indore Highway, Kothrikalan, Sehore, Madhya Pradesh, 466114, India
| | - Debdeep Chatterjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jyoti Devi
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Riya Bera
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jennifer Joseph
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India.
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15
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Flores-Solis D, Lushpinskaia IP, Polyansky AA, Changiarath A, Boehning M, Mirkovic M, Walshe J, Pietrek LM, Cramer P, Stelzl LS, Zagrovic B, Zweckstetter M. Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nat Commun 2023; 14:5979. [PMID: 37749095 PMCID: PMC10519987 DOI: 10.1038/s41467-023-41633-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 09/10/2023] [Indexed: 09/27/2023] Open
Abstract
Eukaryotic gene regulation and pre-mRNA transcription depend on the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. Due to its highly repetitive, intrinsically disordered sequence, the CTD enables clustering and phase separation of Pol II. The molecular interactions that drive CTD phase separation and Pol II clustering are unclear. Here, we show that multivalent interactions involving tyrosine impart temperature- and concentration-dependent self-coacervation of the CTD. NMR spectroscopy, molecular ensemble calculations and all-atom molecular dynamics simulations demonstrate the presence of diverse tyrosine-engaging interactions, including tyrosine-proline contacts, in condensed states of human CTD and other low-complexity proteins. We further show that the network of multivalent interactions involving tyrosine is responsible for the co-recruitment of the human Mediator complex and CTD during phase separation. Our work advances the understanding of the driving forces of CTD phase separation and thus provides the basis to better understand CTD-mediated Pol II clustering in eukaryotic gene transcription.
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Affiliation(s)
- David Flores-Solis
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Irina P Lushpinskaia
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany
| | - Anton A Polyansky
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Arya Changiarath
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
| | - Marc Boehning
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Milana Mirkovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - James Walshe
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lisa M Pietrek
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Strasße 3, 60438, Frankfurt am Main, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany
| | - Lukas S Stelzl
- Faculty of Biology, Johannes Gutenberg University Mainz (JGU), Gresemundweg 2, 55128, Mainz, Germany
- KOMET1, Institute of Physics, Johannes Gutenberg University Mainz (JGU), Staudingerweg 9, 55099, Mainz, Germany
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany
| | - Bojan Zagrovic
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Campus Vienna Biocenter 5, 1030, Vienna, Austria
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Campus Vienna Biocenter 5, 1030, Vienna, Austria
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 35075, Göttingen, Germany.
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077, Göttingen, Germany.
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16
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Khandwala CB, Sarkar P, Schmidt HB, Ma M, Kinnebrew M, Pusapati GV, Patel BB, Tillo D, Lebensohn AM, Rohatgi R. Direct ionic stress sensing and mitigation by the transcription factor NFAT5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.23.559074. [PMID: 37886503 PMCID: PMC10602047 DOI: 10.1101/2023.09.23.559074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Homeostatic control of intracellular ionic strength is essential for protein, organelle and genome function, yet mechanisms that sense and enable adaptation to ionic stress remain poorly understood in animals. We find that the transcription factor NFAT5 directly senses solution ionic strength using a C-terminal intrinsically disordered region. Both in intact cells and in a purified system, NFAT5 forms dynamic, reversible biomolecular condensates in response to increasing ionic strength. This self-associative property, conserved from insects to mammals, allows NFAT5 to accumulate in the nucleus and activate genes that restore cellular ion content. Mutations that reduce condensation or those that promote aggregation both reduce NFAT5 activity, highlighting the importance of optimally tuned associative interactions. Remarkably, human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic or hypertonic stress in yeast. Thus NFAT5 is both the sensor and effector of a cell-autonomous ionic stress response pathway in animal cells.
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Affiliation(s)
- Chandni B. Khandwala
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Parijat Sarkar
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - H. Broder Schmidt
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mengxiao Ma
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maia Kinnebrew
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ganesh V. Pusapati
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bhaven B. Patel
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Desiree Tillo
- Center for Cancer Research Genomics Core, National Cancer Institute, National Institutes of Health, NIH, Building 37, RM 2056B, Bethesda, MD, 20892, USA
| | - Andres M. Lebensohn
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NIH, Building 37, RM 2056B, Bethesda, MD, 20892, USA
| | - Rajat Rohatgi
- Departments of Biochemistry and Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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17
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Loedige I, Baranovskii A, Mendonsa S, Dantsuji S, Popitsch N, Breimann L, Zerna N, Cherepanov V, Milek M, Ameres S, Chekulaeva M. mRNA stability and m 6A are major determinants of subcellular mRNA localization in neurons. Mol Cell 2023; 83:2709-2725.e10. [PMID: 37451262 PMCID: PMC10529935 DOI: 10.1016/j.molcel.2023.06.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
For cells to perform their biological functions, they need to adopt specific shapes and form functionally distinct subcellular compartments. This is achieved in part via an asymmetric distribution of mRNAs within cells. Currently, the main model of mRNA localization involves specific sequences called "zipcodes" that direct mRNAs to their proper locations. However, while thousands of mRNAs localize within cells, only a few zipcodes have been identified, suggesting that additional mechanisms contribute to localization. Here, we assess the role of mRNA stability in localization by combining the isolation of the soma and neurites of mouse primary cortical and mESC-derived neurons, SLAM-seq, m6A-RIP-seq, the perturbation of mRNA destabilization mechanisms, and the analysis of multiple mRNA localization datasets. We show that depletion of mRNA destabilization elements, such as m6A, AU-rich elements, and suboptimal codons, functions as a mechanism that mediates the localization of mRNAs associated with housekeeping functions to neurites in several types of neurons.
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Affiliation(s)
- Inga Loedige
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Artem Baranovskii
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Samantha Mendonsa
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Sayaka Dantsuji
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Niko Popitsch
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Laura Breimann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nadja Zerna
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Vsevolod Cherepanov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Miha Milek
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany
| | - Stefan Ameres
- Max Perutz Labs, University of Vienna, Vienna BioCenter, 1030 Vienna, Austria
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin 10115, Germany.
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18
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Wu SA, Shen C, Wei X, Zhang X, Wang S, Chen X, Torres M, Lu Y, Lin LL, Wang HH, Hunter AH, Fang D, Sun S, Ivanova MI, Lin Y, Qi L. The mechanisms to dispose of misfolded proteins in the endoplasmic reticulum of adipocytes. Nat Commun 2023; 14:3132. [PMID: 37253728 PMCID: PMC10229581 DOI: 10.1038/s41467-023-38690-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
Endoplasmic reticulum (ER)-associated degradation (ERAD) and ER-phagy are two principal degradative mechanisms for ER proteins and aggregates, respectively; however, the crosstalk between these two pathways under physiological settings remains unexplored. Using adipocytes as a model system, here we report that SEL1L-HRD1 protein complex of ERAD degrades misfolded ER proteins and limits ER-phagy and that, only when SEL1L-HRD1 ERAD is impaired, the ER becomes fragmented and cleared by ER-phagy. When both are compromised, ER fragments containing misfolded proteins spatially coalesce into a distinct architecture termed Coalescence of ER Fragments (CERFs), consisted of lipoprotein lipase (LPL, a key lipolytic enzyme and an endogenous SEL1L-HRD1 substrate) and certain ER chaperones. CERFs enlarge and become increasingly insoluble with age. Finally, we reconstitute the CERFs through LPL and BiP phase separation in vitro, a process influenced by both redox environment and C-terminal tryptophan loop of LPL. Hence, our findings demonstrate a sequence of events centered around SEL1L-HRD1 ERAD to dispose of misfolded proteins in the ER of adipocytes, highlighting the profound cellular adaptability to misfolded proteins in the ER in vivo.
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Affiliation(s)
- Shuangcheng Alivia Wu
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Chenchen Shen
- Tsinghua-Peking Center for Life Science, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaoqiong Wei
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Xiawei Zhang
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Siwen Wang
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Xinxin Chen
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Mauricio Torres
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - You Lu
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Liangguang Leo Lin
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Huilun Helen Wang
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA
| | - Allen H Hunter
- College of Engineering and Michigan Center for Materials Characterization, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Shengyi Sun
- Center for Molecular Medicine and Genetics, Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Magdalena I Ivanova
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109-5622, USA
- Biophysics Program, University of Michigan, Ann Arbor, MI, USA
| | - Yi Lin
- Tsinghua-Peking Center for Life Science, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Ling Qi
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48105, USA.
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48105, USA.
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19
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Savinkova LK, Sharypova EB, Kolchanov NA. On the Role of TATA Boxes and TATA-Binding Protein in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:1000. [PMID: 36903861 PMCID: PMC10005294 DOI: 10.3390/plants12051000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/13/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
For transcription initiation by RNA polymerase II (Pol II), all eukaryotes require assembly of basal transcription machinery on the core promoter, a region located approximately in the locus spanning a transcription start site (-50; +50 bp). Although Pol II is a complex multi-subunit enzyme conserved among all eukaryotes, it cannot initiate transcription without the participation of many other proteins. Transcription initiation on TATA-containing promoters requires the assembly of the preinitiation complex; this process is triggered by an interaction of TATA-binding protein (TBP, a component of the general transcription factor TFIID (transcription factor II D)) with a TATA box. The interaction of TBP with various TATA boxes in plants, in particular Arabidopsis thaliana, has hardly been investigated, except for a few early studies that addressed the role of a TATA box and substitutions in it in plant transcription systems. This is despite the fact that the interaction of TBP with TATA boxes and their variants can be used to regulate transcription. In this review, we examine the roles of some general transcription factors in the assembly of the basal transcription complex, as well as functions of TATA boxes of the model plant A. thaliana. We review examples showing not only the involvement of TATA boxes in the initiation of transcription machinery assembly but also their indirect participation in plant adaptation to environmental conditions in responses to light and other phenomena. Examples of an influence of the expression levels of A. thaliana TBP1 and TBP2 on morphological traits of the plants are also examined. We summarize available functional data on these two early players that trigger the assembly of transcription machinery. This information will deepen the understanding of the mechanisms underlying transcription by Pol II in plants and will help to utilize the functions of the interaction of TBP with TATA boxes in practice.
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20
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Leube RE, Quinlan RA. Editorial: The wetware credentials of intermediate filaments involves coordinating, organising and networking in cells and tissues. Front Cell Dev Biol 2023; 11:1146618. [PMID: 36861037 PMCID: PMC9969193 DOI: 10.3389/fcell.2023.1146618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Affiliation(s)
- Rudolf E. Leube
- Institute of Molecular and Cellular Anatomy, RWTH Aachen University, Aachen, Germany,*Correspondence: Rudolf E. Leube, ; Roy A. Quinlan,
| | - Roy A. Quinlan
- Department of Biosciences, University of Durham, Upper Mountjoy Science Site, Durham, United Kingdom,Biophysical Sciences Institute, University of Durham, Durham, United Kingdom,Department of Biological Structure, University of Washington, Seattle, WA, United States,*Correspondence: Rudolf E. Leube, ; Roy A. Quinlan,
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21
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Synaptic vesicle proteins and ATG9A self-organize in distinct vesicle phases within synapsin condensates. Nat Commun 2023; 14:455. [PMID: 36709207 PMCID: PMC9884207 DOI: 10.1038/s41467-023-36081-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/16/2023] [Indexed: 01/30/2023] Open
Abstract
Ectopic expression in fibroblasts of synapsin 1 and synaptophysin is sufficient to generate condensates of vesicles highly reminiscent of synaptic vesicle (SV) clusters and with liquid-like properties. Here we show that unlike synaptophysin, other major integral SV membrane proteins fail to form condensates with synapsin, but co-assemble into the clusters formed by synaptophysin and synapsin in this ectopic expression system. Another vesicle membrane protein, ATG9A, undergoes activity-dependent exo-endocytosis at synapses, raising questions about the relation of ATG9A traffic to the traffic of SVs. We find that both in fibroblasts and in nerve terminals ATG9A does not co-assemble into synaptophysin-positive vesicle condensates but localizes on a distinct class of vesicles that also assembles with synapsin but into a distinct phase. Our findings suggest that ATG9A undergoes differential sorting relative to SV proteins and also point to a dual role of synapsin in controlling clustering at synapses of SVs and ATG9A vesicles.
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22
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Liquid-liquid Phase Separation of α-Synuclein: A New Mechanistic Insight for α-Synuclein Aggregation Associated with Parkinson's Disease Pathogenesis. J Mol Biol 2023; 435:167713. [PMID: 35787838 DOI: 10.1016/j.jmb.2022.167713] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023]
Abstract
Aberrant aggregation of the misfolded presynaptic protein, α-Synuclein (α-Syn) into Lewy body (LB) and Lewy neuritis (LN) is a major pathological hallmark of Parkinson's disease (PD) and other synucleinopathies. Numerous studies have suggested that prefibrillar and fibrillar species of the misfolded α-Syn aggregates are responsible for cell death in PD pathogenesis. However, the precise molecular events during α-Syn aggregation, especially in the early stages, remain elusive. Emerging evidence has demonstrated that liquid-liquid phase separation (LLPS) of α-Syn occurs in the nucleation step of α-Syn aggregation, which offers an alternate non-canonical aggregation pathway in the crowded microenvironment. The liquid-like α-Syn droplets gradually undergo an irreversible liquid-to-solid phase transition into amyloid-like hydrogel entrapping oligomers and fibrils. This new mechanism of α-Syn LLPS and gel formation might represent the molecular basis of cellular toxicity associated with PD. This review aims to demonstrate the recent development of α-Syn LLPS, the underlying mechanism along with the microscopic events of aberrant phase transition. This review further discusses how several intrinsic and extrinsic factors regulate the thermodynamics and kinetics of α-Syn LLPS and co-LLPS with other proteins, which might explain the pathophysiology of α-Syn in various neurodegenerative diseases.
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23
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Biomolecular condensate assembly of nArgBP2 tunes its functionality to manifest the structural plasticity of dendritic spines. Exp Mol Med 2023; 55:108-119. [PMID: 36599935 PMCID: PMC9898538 DOI: 10.1038/s12276-022-00918-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 01/05/2023] Open
Abstract
nArgBP2, a candidate gene for intellectual disability, is a postsynaptic protein critical for dendritic spine development and morphogenesis, and its knockdown (KD) in developing neurons severely impairs spine-bearing excitatory synapse formation. Surprisingly, nArgBP2 KD in mature neurons did not cause morphological defects in the existing spines at rest, raising questions of how it functions in mature neurons. We found that unlike its inaction at rest, nArgBP2 KD completely inhibited the enlargement of dendritic spines during chemically induced long-term potentiation (cLTP) in mature neurons. We further found that nArgBP2 forms condensates in dendritic spines and that these condensates are dispersed by cLTP, which spatiotemporally coincides with spine head enlargement. Condensates with CaMKII phosphorylation-deficient mutant or CaMKII inhibition are neither dispersed nor accompanied by spine enlargement during cLTP. We found that nArgBP2 condensates in spines exhibited liquid-like properties, and in heterologous and in vitro expression systems, nArgBP2 undergoes liquid-liquid phase separation via multivalent intermolecular interactions between SH3 domains and proline-rich domains. It also forms coacervates with CaMKIIα, which is rapidly dissembled by calcium/CaMKIIα-dependent phosphorylation. We further showed that the interaction between nArgBP2 and WAVE1 competes with nArgBP2 phase separation and that blocking the nArgBP2-WAVE1 interaction prevents spine enlargement during cLTP. Together, our results suggest that nArgBP2 at rest is confined to the condensates but is released by CaMKIIα-mediated phosphorylation during synaptic plasticity, which regulates its timely interaction with WAVE1 to induce spine head enlargement in mature neurons.
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Sequence-Based Prediction of Protein Phase Separation: The Role of Beta-Pairing Propensity. Biomolecules 2022; 12:biom12121771. [PMID: 36551199 PMCID: PMC9775558 DOI: 10.3390/biom12121771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The formation of droplets of bio-molecular condensates through liquid-liquid phase separation (LLPS) of their component proteins is a key factor in the maintenance of cellular homeostasis. Different protein properties were shown to be important in LLPS onset, making it possible to develop predictors, which try to discriminate a positive set of proteins involved in LLPS against a negative set of proteins not involved in LLPS. On the other hand, the redundancy and multivalency of the interactions driving LLPS led to the suggestion that the large conformational entropy associated with non specific side-chain interactions is also a key factor in LLPS. In this work we build a LLPS predictor which combines the ability to form pi-pi interactions, with an unrelated feature, the propensity to stabilize the β-pairing interaction mode. The cross-β structure is formed in the amyloid aggregates, which are involved in degenerative diseases and may be the final thermodynamically stable state of protein condensates. Our results show that the combination of pi-pi and β-pairing propensity yields an improved performance. They also suggest that protein sequences are more likely to be involved in phase separation if the main chain conformational entropy of the β-pairing maintained droplet state is increased. This would stabilize the droplet state against the more ordered amyloid state. Interestingly, the entropic stabilization of the droplet state appears to proceed according to different mechanisms, depending on the fraction of "droplet-driving" proteins present in the positive set.
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25
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A brief guideline for studies of phase-separated biomolecular condensates. Nat Chem Biol 2022; 18:1307-1318. [DOI: 10.1038/s41589-022-01204-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/10/2022] [Indexed: 11/20/2022]
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26
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Chowdhary S, Kainth AS, Paracha S, Gross DS, Pincus D. Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response. Mol Cell 2022; 82:4386-4399.e7. [PMID: 36327976 PMCID: PMC9701134 DOI: 10.1016/j.molcel.2022.10.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 08/28/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Mammalian developmental and disease-associated genes concentrate large quantities of the transcriptional machinery by forming membrane-less compartments known as transcriptional condensates. However, it is unknown whether these structures are evolutionarily conserved or involved in 3D genome reorganization. Here, we identify inducible transcriptional condensates in the yeast heat shock response (HSR). HSR condensates are biophysically dynamic spatiotemporal clusters of the sequence-specific transcription factor heat shock factor 1 (Hsf1) with Mediator and RNA Pol II. Uniquely, HSR condensates drive the coalescence of multiple Hsf1 target genes, even those located on different chromosomes. Binding of the chaperone Hsp70 to a site on Hsf1 represses clustering, whereas an intrinsically disordered region on Hsf1 promotes condensate formation and intergenic interactions. Mutation of both Hsf1 determinants reprograms HSR condensates to become constitutively active without intergenic coalescence, which comes at a fitness cost. These results suggest that transcriptional condensates are ancient and flexible compartments of eukaryotic gene control.
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Affiliation(s)
- Surabhi Chowdhary
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Amoldeep S Kainth
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Sarah Paracha
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA; Center for Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA.
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Wessén J, Das S, Pal T, Chan HS. Analytical Formulation and Field-Theoretic Simulation of Sequence-Specific Phase Separation of Protein-Like Heteropolymers with Short- and Long-Spatial-Range Interactions. J Phys Chem B 2022; 126:9222-9245. [PMID: 36343363 DOI: 10.1021/acs.jpcb.2c06181] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A theory for sequence-dependent liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study of biomolecular condensates is formulated by extending the random phase approximation (RPA) and field-theoretic simulation (FTS) of heteropolymers with spatially long-range Coulomb interactions to include the fundamental effects of short-range, hydrophobic-like interactions between amino acid residues. To this end, short-range effects are modeled by Yukawa interactions between multiple nonelectrostatic charges derived from an eigenvalue decomposition of pairwise residue-residue contact energies. Chain excluded volume is afforded by incompressibility constraints. A mean-field approximation leads to an effective Flory-Huggins χ parameter, which, in conjunction with RPA, accounts for the contact-interaction effects of amino acid composition and the sequence-pattern effects of long-range electrostatics in IDP LLPS, whereas FTS based on the formulation provides full sequence dependence for both short- and long-range interactions. This general approach is illustrated here by applications to variants of a natural IDP in the context of several different amino-acid interaction schemes as well as a set of different model hydrophobic-polar sequences sharing the same composition. Effectiveness of the methodology is verified by coarse-grained explicit-chain molecular dynamics simulations.
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Affiliation(s)
- Jonas Wessén
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Suman Das
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tanmoy Pal
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Wang L, Choi K, Su T, Li B, Wu X, Zhang R, Driskill JH, Li H, Lei H, Guo P, Chen EH, Zheng Y, Pan D. Multiphase coalescence mediates Hippo pathway activation. Cell 2022; 185:4376-4393.e18. [PMID: 36318920 PMCID: PMC9669202 DOI: 10.1016/j.cell.2022.09.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 05/29/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
The function of biomolecular condensates is often restricted by condensate dissolution. Whether condensates can be suppressed without condensate dissolution is unclear. Here, we show that upstream regulators of the Hippo signaling pathway form functionally antagonizing condensates, and their coalescence into a common phase provides a mode of counteracting the function of biomolecular condensates without condensate dissolution. Specifically, the negative regulator SLMAP forms Hippo-inactivating condensates to facilitate pathway inhibition by the STRIPAK complex. In response to cell-cell contact or osmotic stress, the positive regulators AMOT and KIBRA form Hippo-activating condensates to facilitate pathway activation. The functionally antagonizing SLMAP and AMOT/KIBRA condensates further coalesce into a common phase to inhibit STRIPAK function. These findings provide a paradigm for restricting the activity of biomolecular condensates without condensate dissolution, shed light on the molecular principles of multiphase organization, and offer a conceptual framework for understanding upstream regulation of the Hippo signaling pathway.
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Affiliation(s)
- Li Wang
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kyungsuk Choi
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ting Su
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Bing Li
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaofeng Wu
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ruihui Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jordan H Driskill
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hongde Li
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Huiyan Lei
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pengfei Guo
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth H Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yonggang Zheng
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Horvath A, Vendruscolo M, Fuxreiter M. Sequence-based Prediction of the Cellular Toxicity Associated with Amyloid Aggregation within Protein Condensates. Biochemistry 2022; 61:2461-2469. [DOI: 10.1021/acs.biochem.2c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Attila Horvath
- John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Canberra2600, Australia
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, UK
| | - Monika Fuxreiter
- Department of Biomedical Sciences, University of Padova, Padova, PD35131Italy
- Department of Physics and Astronomy, University of Padova, Padova, PD35131Italy
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30
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Ren J, Zhang Z, Zong Z, Zhang L, Zhou F. Emerging Implications of Phase Separation in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202855. [PMID: 36117111 PMCID: PMC9631093 DOI: 10.1002/advs.202202855] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 08/26/2022] [Indexed: 05/19/2023]
Abstract
In eukaryotic cells, biological activities are executed in distinct cellular compartments or organelles. Canonical organelles with membrane-bound structures are well understood. Cells also inherently contain versatile membrane-less organelles (MLOs) that feature liquid or gel-like bodies. A biophysical process termed liquid-liquid phase separation (LLPS) elucidates how MLOs form through dynamic biomolecule assembly. LLPS-related molecules often have multivalency, which is essential for low-affinity inter- or intra-molecule interactions to trigger phase separation. Accumulating evidence shows that LLPS concentrates and organizes desired molecules or segregates unneeded molecules in cells. Thus, MLOs have tunable functional specificity in response to environmental stimuli and metabolic processes. Aberrant LLPS is widely associated with several hallmarks of cancer, including sustained proliferative signaling, growth suppressor evasion, cell death resistance, telomere maintenance, DNA damage repair, etc. Insights into the molecular mechanisms of LLPS provide new insights into cancer therapeutics. Here, the current understanding of the emerging concepts of LLPS and its involvement in cancer are comprehensively reviewed.
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Affiliation(s)
- Jiang Ren
- School of MedicineZhejiang University City CollegeHangzhou215123China
- The Eighth Affiliated HospitalSun Yat‐sen UniversityShenzhen518033China
| | - Zhenyu Zhang
- Department of NeurosurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan450003China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
| | - Long Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkLife Sciences InstituteZhejiang UniversityHangzhou310058China
- International Biomed‐X Research Center, Second Affiliated Hospital of Zhejiang University School of MedicineZhejiang UniversityHangzhouChina
- Cancer CenterZhejiang UniversityHangzhou215123China
| | - Fangfang Zhou
- School of MedicineZhejiang University City CollegeHangzhou215123China
- Institutes of Biology and Medical SciencesSoochow UniversitySuzhou215123China
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31
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“Structure”-function relationships in eukaryotic transcription factors: The role of intrinsically disordered regions in gene regulation. Mol Cell 2022; 82:3970-3984. [DOI: 10.1016/j.molcel.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/19/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
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32
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Lee J, Cho H, Kwon I. Phase separation of low-complexity domains in cellular function and disease. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1412-1422. [PMID: 36175485 PMCID: PMC9534829 DOI: 10.1038/s12276-022-00857-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
In this review, we discuss the ways in which recent studies of low-complexity (LC) domains have challenged our understanding of the mechanisms underlying cellular organization. LC sequences, long believed to function in the absence of a molecular structure, are abundant in the proteomes of all eukaryotic organisms. Over the past decade, the phase separation of LC domains has emerged as a fundamental mechanism driving dynamic multivalent interactions of many cellular processes. We review the key evidence showing the role of phase separation of individual proteins in organizing cellular assemblies and facilitating biological function while implicating the dynamics of phase separation as a key to biological validity and functional utility. We also highlight the evidence showing that pathogenic LC proteins alter various phase separation-dependent interactions to elicit debilitating human diseases, including cancer and neurodegenerative diseases. Progress in understanding the biology of phase separation may offer useful hints toward possible therapeutic interventions to combat the toxicity of pathogenic proteins.
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Affiliation(s)
- Jiwon Lee
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea
| | - Hana Cho
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
| | - Ilmin Kwon
- Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, 16419, Korea.
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33
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Wang H, Li B, Zuo L, Wang B, Yan Y, Tian K, Zhou R, Wang C, Chen X, Jiang Y, Zheng H, Qin F, Zhang B, Yu Y, Liu CP, Xu Y, Gao J, Qi Z, Deng W, Ji X. The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors. Nat Commun 2022; 13:5703. [PMID: 36171202 PMCID: PMC9519968 DOI: 10.1038/s41467-022-33433-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 09/16/2022] [Indexed: 11/10/2022] Open
Abstract
RNA polymerase II (Pol II) apparatuses are compartmentalized into transcriptional clusters. Whether protein factors control these clusters remains unknown. In this study, we find that the ATPase-associated with diverse cellular activities (AAA + ) ATPase RUVBL2 co-occupies promoters with Pol II and various transcription factors. RUVBL2 interacts with unphosphorylated Pol II in chromatin to promote RPB1 carboxy-terminal domain (CTD) clustering and transcription initiation. Rapid depletion of RUVBL2 leads to a decrease in the number of Pol II clusters and inhibits nascent RNA synthesis, and tethering RUVBL2 to an active promoter enhances Pol II clustering at the promoter. We also identify target genes that are directly linked to the RUVBL2-Pol II axis. Many of these genes are hallmarks of cancers and encode proteins with diverse cellular functions. Our results demonstrate an emerging activity for RUVBL2 in regulating Pol II cluster formation in the nucleus. RNA polymerase II (Pol II) transcription factories play a central role in gene expression and 3D chromatin organization. Here, the authors demonstrate that RUVBL2 directly regulates Pol II clustering at active gene promoters.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,Department of Pathogenic Biology, Chengdu Medical College, Chengdu, 610500, China
| | - Boyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Linyu Zuo
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Bo Wang
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Yan
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Rong Zhou
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chenlu Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Fangfei Qin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Bin Zhang
- Departments of Pathology and Laboratory Medicine, and Pediatrics, University of Rochester Medical Center, 601 Elmwood Ave, Box 608, Rochester, NY, 14642, USA
| | - Yang Yu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Juntao Gao
- Institute for TCM-X; MOE Key Laboratory of Bioinformatics; Bioinformatics Division, BNRist (Beijing National Research Center for Information Science and Technology); Department of Automation, Tsinghua University, Beijing, 100084, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
| | - Zhi Qi
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Wulan Deng
- Biomedical Pioneering Innovation Center (BIOPIC), Academy for Advanced Interdisciplinary Studies, Beijing Advanced Innovation Center for Genomics (ICG), Peking-Tsinghua Center for Life Sciences (CLS), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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Ahmad A, Uversky VN, Khan RH. Aberrant liquid-liquid phase separation and amyloid aggregation of proteins related to neurodegenerative diseases. Int J Biol Macromol 2022; 220:703-720. [PMID: 35998851 DOI: 10.1016/j.ijbiomac.2022.08.132] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/05/2022]
Abstract
Recent evidence has shown that the processes of liquid-liquid phase separation (LLPS) or liquid-liquid phase transitions (LLPTs) are a crucial and prevalent phenomenon that underlies the biogenesis of numerous membrane-less organelles (MLOs) and biomolecular condensates within the cells. Findings show that processes associated with LLPS play an essential role in physiology and disease. In this review, we discuss the physical and biomolecular factors that contribute to the development of LLPS, the associated functions, as well as their consequences for cell physiology and neurological disorders. Additionally, the finding of mis-regulated proteins, which have long been linked to aggregates in neuropathology, are also known to induce LLPS/LLPTs, prompting a lot of interest in understanding the connection between aberrant phase separation and disorder conditions. Moreover, the methods used in recent and ongoing studies in this field are also explored, as is the possibility that these findings will encourage new lines of inquiry into the molecular causes of neurodegenerative diseases.
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Affiliation(s)
- Azeem Ahmad
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P. 202002, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P. 202002, India.
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Saha K, Ghosh G. Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly. Nucleic Acids Res 2022; 50:8262-8278. [PMID: 35871302 PMCID: PMC9371905 DOI: 10.1093/nar/gkac636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
We recently reported that serine–arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions in vivo, we show that the SR proteins bind the pre-mRNAs cooperatively generating a substrate that recruits U1 snRNP and U2AF65 in a splice signal-independent manner. Excess U1 snRNP selectively displaces some of the SR protein molecules from the pre-mRNA generating the substrate for splice signal-specific, sequential recognition by U1 snRNP, U2AF65 and U2AF35. Our work thus identifies a novel function of U1 snRNP in mammalian splicing substrate definition, explains the need for excess U1 snRNP compared to other U snRNPs in vivo, demonstrates how excess SR proteins could inhibit splicing, and provides a conceptual basis to examine if this mechanism of splicing substrate definition is employed by other splicing regulatory proteins.
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Affiliation(s)
- Kaushik Saha
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive , La Jolla , CA 92093-0375, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive , La Jolla , CA 92093-0375, USA
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36
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Xie L, Dong P, Qi Y, Hsieh THS, English BP, Jung S, Chen X, De Marzio M, Casellas R, Chang HY, Zhang B, Tjian R, Liu Z. BRD2 compartmentalizes the accessible genome. Nat Genet 2022; 54:481-491. [PMID: 35410381 PMCID: PMC9099420 DOI: 10.1038/s41588-022-01044-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/01/2022] [Indexed: 12/15/2022]
Abstract
Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associated domains (TADs). While the formation of TADs is dependent on Cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after Cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on one hand by Cohesin and on the other by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-Cohesin interplay model of nuclear topology, where genome compartmentalization results from a competition between loop extrusion and chromatin state-specific affinity interactions.
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37
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Zhang Q, Tan W, Xu B. Enzymatic Noncovalent Synthesis for Targeting Subcellular Organelles. Chempluschem 2022; 87:e202200060. [PMID: 35420712 PMCID: PMC9508291 DOI: 10.1002/cplu.202200060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/23/2022] [Indexed: 11/09/2022]
Abstract
Enzymatic noncovalent synthesis (ENS) exploits enzymatic reactions to produce spatially organized higher-order supramolecular assemblies that modulate cellular processes. While ENS is a general mechanism to create higher-order assemblies of proteins for diverse cellular functions, the exploration of ENS of other bioactive molecules, such as peptides or small organic molecules, is rather limited. Since ENS generates non-diffusive supramolecular assemblies locally, it provides a unique approach to targeting subcellular organelles. In this Review, we highlight the recent progress of the application of ENS of peptide assemblies for targeting subcellular organelles. After a brief introduction of the concept of ENS, we introduce the case of generating artificial filaments by ENS in cell cytosol, then discuss the use of ENS for targeting endoplasmic reticulum, mitochondria, Golgi apparatus, and lysosomes, and finally we describe the targeting of nucleus by ENS. We hope to illustrate the promise of ENS, as a localized molecular process in an open system, for understanding diseases, controlling cell behaviors, and developing new therapeutics.
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Affiliation(s)
- Qiuxin Zhang
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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38
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Levone BR, Lombardi S, Barabino SM. Laser microirradiation as a tool to investigate the role of liquid-liquid phase separation in DNA damage repair. STAR Protoc 2022; 3:101146. [PMID: 35146448 PMCID: PMC8819395 DOI: 10.1016/j.xpro.2022.101146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Here we describe a protocol for the generation of site-specific DNA damage, including double and single strand breaks, using the 405 nm laser of a confocal microscope in cells pre-sensitized with Hoechst. This is a simple approach, particularly useful to assess the involvement of proteins and the roles of liquid-liquid phase separation in DNA damage repair. Examples of transfection protocol, drug concentrations, and microscopy are provided, although optimization may be needed for specific experimental setups and cell lines used. For complete details on the use and execution of this protocol, please refer to Levone et al. (2021). Protocol for the generation of site-specific DNA damage in living cells Using a 405 nm laser of a confocal microscope in pre-sensitized cells Analysis of the kinetics of proteins in DNA damage repair Analysis of the roles of liquid–liquid phase separation in DNA damage repair
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Affiliation(s)
- Brunno Rocha Levone
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20125 Milan, Italy
- Corresponding author
| | - Silvia Lombardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20125 Milan, Italy
| | - Silvia M.L. Barabino
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20125 Milan, Italy
- Corresponding author
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39
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Weis K, Hondele M. The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA-Protein Condensates. Annu Rev Biochem 2022; 91:197-219. [PMID: 35303788 DOI: 10.1146/annurev-biochem-032620-105429] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DEAD-box ATPases constitute a very large protein family present in all cells, often in great abundance. From bacteria to humans, they play critical roles in many aspects of RNA metabolism, and due to their widespread importance in RNA biology, they have been characterized in great detail at both the structural and biochemical levels. DEAD-box proteins function as RNA-dependent ATPases that can unwind short duplexes of RNA, remodel ribonucleoprotein (RNP) complexes, or act as clamps to promote RNP assembly. Yet, it often remains enigmatic how individual DEAD-box proteins mechanistically contribute to specific RNA-processing steps. Here, we review the role of DEAD-box ATPases in the regulation of gene expression and propose that one common function of these enzymes is in the regulation of liquid-liquid phase separation of RNP condensates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland;
| | - Maria Hondele
- Biozentrum, University of Basel, Basel, Switzerland;
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40
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Musacchio A. On the role of phase separation in the biogenesis of membraneless compartments. EMBO J 2022; 41:e109952. [PMID: 35107832 PMCID: PMC8886532 DOI: 10.15252/embj.2021109952] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/16/2022] Open
Abstract
Molecular mechanistic biology has ushered us into the world of life’s building blocks, revealing their interactions in macromolecular complexes and inspiring strategies for detailed functional interrogations. The biogenesis of membraneless cellular compartments, functional mesoscale subcellular locales devoid of strong internal order and delimiting membranes, is among mechanistic biology’s most demanding current challenges. A developing paradigm, biomolecular phase separation, emphasizes solvation of the building blocks through low‐affinity, weakly adhesive unspecific interactions as the driver of biogenesis of membraneless compartments. Here, I discuss the molecular underpinnings of the phase separation paradigm and demonstrate that validating its assumptions is much more challenging than hitherto appreciated. I also discuss that highly specific interactions, rather than unspecific ones, appear to be the main driver of biogenesis of subcellular compartments, while phase separation may be harnessed locally in selected instances to generate material properties tailored for specific functions, as exemplified by nucleocytoplasmic transport.
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Affiliation(s)
- Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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41
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Lin YH, Wu H, Jia B, Zhang M, Chan HS. Assembly of model postsynaptic densities involves interactions auxiliary to stoichiometric binding. Biophys J 2022; 121:157-171. [PMID: 34637756 PMCID: PMC8758407 DOI: 10.1016/j.bpj.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 01/07/2023] Open
Abstract
The assembly of functional biomolecular condensates often involves liquid-liquid phase separation (LLPS) of proteins with multiple modular domains, which can be folded or conformationally disordered to various degrees. To understand the LLPS-driving domain-domain interactions, a fundamental question is how readily the interactions in the condensed phase can be inferred from interdomain interactions in dilute solutions. In particular, are the interactions leading to LLPS exclusively those underlying the formation of discrete interdomain complexes in homogeneous solutions? We address this question by developing a mean-field LLPS theory of two stoichiometrically constrained solute species. The theory is applied to the neuronal proteins SynGAP and PSD-95, whose complex coacervate serves as a rudimentary model for neuronal postsynaptic densities (PSDs). The predicted phase behaviors are compared with experiments. Previously, a three SynGAP/two PSD-95 ratio was determined for SynGAP/PSD-95 complexes in dilute solutions. However, when this 3:2 stoichiometry is uniformly imposed in our theory encompassing both dilute and condensed phases, the tie-line pattern of the predicted SynGAP/PSD-95 phase diagram differs drastically from that obtained experimentally. In contrast, theories embodying alternate scenarios postulating auxiliary SynGAP-PSD-95 as well as SynGAP-SynGAP and PSD-95-PSD-95 interactions, in addition to those responsible for stoichiometric SynGAP/PSD-95 complexes, produce tie-line patterns consistent with experiment. Hence, our combined theoretical-experimental analysis indicates that weaker interactions or higher-order complexes beyond the 3:2 stoichiometry, but not yet documented, are involved in the formation of SynGAP/PSD-95 condensates, imploring future efforts to ascertain the nature of these auxiliary interactions in PSD-like LLPS and underscoring a likely general synergy between stoichiometric, structurally specific binding and stochastic, multivalent "fuzzy" interactions in the assembly of functional biomolecular condensates.
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Affiliation(s)
- Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada,Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Haowei Wu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Bowen Jia
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China,School of Life Sciences, Southern University of Science and Technology, Shenzhen, China,Corresponding author
| | - Hue Sun Chan
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada,Corresponding author
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42
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Irgen-Gioro S, Yoshida S, Walling V, Chong S. Fixation can change the appearance of phase separation in living cells. eLife 2022; 11:79903. [PMID: 36444977 PMCID: PMC9817179 DOI: 10.7554/elife.79903] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/28/2022] [Indexed: 11/30/2022] Open
Abstract
Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed-cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.
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Affiliation(s)
- Shawn Irgen-Gioro
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shawn Yoshida
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States,Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Victoria Walling
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Shasha Chong
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
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43
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Abstract
This review covers research findings reported over the past decade concerning the ability of low complexity (LC) domains to self-associate in a manner leading to their phase separation from aqueous solution. We focus our message upon the reductionist use of two forms of phase separation as biochemical assays to study how LC domains might function in living cells. Cells and their varied compartments represent extreme examples of material condensates. Over the past half century, biochemists, structural biologists, and molecular biologists have resolved the mechanisms driving innumerable forms of macromolecular condensation. In contrast, we remain largely ignorant as to how 10%-20% of our proteins actually work to assist in cell organization. This enigmatic 10%-20% of the proteome corresponds to gibberish-like LC sequences. We contend that many of these LC sequences move in and out of a structurally ordered, self-associated state as a means of offering a combination of organizational specificity and dynamic pliability to living cells. Finally, we speculate that ancient proteins may have behaved similarly, helping to condense, organize, and protect RNA early during evolution.
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Affiliation(s)
- Masato Kato
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, USA
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Xiaoming Zhou
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Steven L McKnight
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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44
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Wang J, Hu L, Zhang H, Fang Y, Wang T, Wang H. Intracellular Condensates of Oligopeptide for Targeting Lysosome and Addressing Multiple Drug Resistance of Cancer. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2104704. [PMID: 34632634 DOI: 10.1002/adma.202104704] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular condensates have been demonstrated as a ubiquitous phenomenon in biological systems and play a crucial role in controlling cellular functions. However, the spatiotemporal construction of artificial biomolecular condensates with functions remains challenging and has been less explored. Herein, a general approach is reported to construct biomolecular condensates (e.g., hydrogel) in the lysosome of living cells for cancer therapy and address multiple drug resistance induced by lysosome sequestration. Aromatic-motif-appended pH-responsive hexapeptide (LTP) derived from natural insulin can be uptaken by cancer cells mainly through caveolae-dependent endocytosis, ensuring the proton-triggered phase transformation (solution to hydrogel) of LTP inside the lysosome specifically. Lysosomal hydrogelation further leads to enlargement of the lysosome in cancer cells and increases the permeability of the lysosome, resulting in cancer cell death. Importantly, lysosomal assemblies can significantly improve the efficiency of current chemotherapy drugs toward multidrug resistance (MDR) cells in vitro and in xenograft tumor models. As an example of functional artificial condensates in lysosomes, this work provides a new strategy for controlling functional condensates formation precisely in the organelles of living cells and addressing MDR in cancer therapy.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Liangbo Hu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China
| | - Hongyue Zhang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China
| | - Yu Fang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China
| | - Tingliang Wang
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
| | - Huaimin Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, Institute of Natural Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang Province, 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China
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45
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Distinct roles of hnRNPH1 low-complexity domains in splicing and transcription. Proc Natl Acad Sci U S A 2021; 118:2109668118. [PMID: 34873036 PMCID: PMC8685725 DOI: 10.1073/pnas.2109668118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2021] [Indexed: 12/21/2022] Open
Abstract
Phase separation of low-complexity (LC) domains appended to most RNA-binding proteins (RBPs) emerges as a principle underlying spatiotemporal protein recruitment. Yet, how LC domains regulate the function of RBPs in cells remains unclear. An alternative-splicing regulator, hnRNPH1, contains two LC domains (LC1 and LC2). Here, we show that phase separation of the LC1 can exert control over hnRNPH1 function in RNA-splicing possibly by facilitating interactions between hnRNPH1 and a variety of RBPs. In contrast, the LC2 lacking in vitro phase properties, is required for aberrant transcriptional activation in the context of fusion oncoproteins. These results have broad implications for understanding how phase separation contributes to distinct roles of LC domains in control of physiological as well as oncogenic functions. Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins that control key events in RNA biogenesis under both normal and diseased cellular conditions. The low-complexity (LC) domain of hnRNPs can become liquid-like droplets or reversible amyloid-like polymers by phase separation. Yet, whether phase separation of the LC domains contributes to physiological functions of hnRNPs remains unclear. hnRNPH1 contains two LC domains, LC1 and LC2. Here, we show that reversible phase separation of the LC1 domain is critical for both interaction with different kinds of RNA-binding proteins and control of the alternative-splicing activity of hnRNPH1. Interestingly, although not required for phase separation, the LC2 domain contributes to the robust transcriptional activation of hnRNPH1 when fused to the DNA-binding domain, as found recently in acute lymphoblastic leukemia. Our data suggest that the ability of the LC1 domain to phase-separate into reversible polymers or liquid-like droplets is essential for function of hnRNPH1 as an alternative RNA-splicing regulator, whereas the LC2 domain may contribute to the aberrant transcriptional activity responsible for cancer transformation.
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46
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Yi M, Tan W, Guo J, Xu B. Enzymatic noncovalent synthesis of peptide assemblies generates multimolecular crowding in cells for biomedical applications. Chem Commun (Camb) 2021; 57:12870-12879. [PMID: 34817487 PMCID: PMC8711086 DOI: 10.1039/d1cc05565h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymatic noncovalent synthesis enables the spatiotemporal control of multimolecular crowding in cells, thus offering a unique opportunity for modulating cellular functions. This article introduces some representative enzymes and molecular building blocks for generating peptide assemblies as multimolecular crowding in cells, highlights the relevant biomedical applications, such as anticancer therapy, molecular imaging, trafficking proteins, genetic engineering, artificial intracellular filaments, cell morphogenesis, and antibacterial, and briefly discusses the promises of ENS as a multistep molecular process in biology and medicine.
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Affiliation(s)
- Meihui Yi
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
| | - Jiaqi Guo
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
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47
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Fassler JS, Skuodas S, Weeks DL, Phillips BT. Protein Aggregation and Disaggregation in Cells and Development. J Mol Biol 2021; 433:167215. [PMID: 34450138 PMCID: PMC8530975 DOI: 10.1016/j.jmb.2021.167215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 08/01/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a feature of numerous neurodegenerative diseases. However, regulated, often reversible, formation of protein aggregates, also known as condensates, helps control a wide range of cellular activities including stress response, gene expression, memory, cell development and differentiation. This review presents examples of aggregates found in biological systems, how they are used, and cellular strategies that control aggregation and disaggregation. We include features of the aggregating proteins themselves, environmental factors, co-aggregates, post-translational modifications and well-known aggregation-directed activities that influence their formation, material state, stability and dissolution. We highlight the emerging roles of biomolecular condensates in early animal development, and disaggregation processing proteins that have recently been shown to play key roles in gametogenesis and embryogenesis.
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Affiliation(s)
- Jan S Fassler
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States.
| | - Sydney Skuodas
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@sskuodas
| | - Daniel L Weeks
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, United States
| | - Bryan T Phillips
- Department of Biology, University of Iowa, Iowa City, IA 52242, United States. https://twitter.com/@bt4phillips
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48
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Müntjes K, Devan SK, Reichert AS, Feldbrügge M. Linking transport and translation of mRNAs with endosomes and mitochondria. EMBO Rep 2021; 22:e52445. [PMID: 34402186 PMCID: PMC8490996 DOI: 10.15252/embr.202152445] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic cells, proteins are targeted to their final subcellular locations with precise timing. A key underlying mechanism is the active transport of cognate mRNAs, which in many systems can be linked intimately to membrane trafficking. A prominent example is the long-distance endosomal transport of mRNAs and their local translation. Here, we describe current highlights of fundamental mechanisms of the underlying transport process as well as of biological functions ranging from endosperm development in plants to fungal pathogenicity and neuronal processes. Translation of endosome-associated mRNAs often occurs at the cytoplasmic surface of endosomes, a process that is needed for membrane-assisted formation of heteromeric protein complexes and for accurate subcellular targeting of proteins. Importantly, endosome-coupled translation of mRNAs encoding mitochondrial proteins, for example, seems to be particularly important for efficient organelle import and for regulating subcellular mitochondrial activity. In essence, these findings reveal a new mechanism of loading newly synthesised proteins onto endocytic membranes enabling intimate crosstalk between organelles. The novel link between endosomes and mitochondria adds an inspiring new level of complexity to trafficking and organelle biology.
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Affiliation(s)
- Kira Müntjes
- Institute of MicrobiologyCluster of Excellence on Plant SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Senthil Kumar Devan
- Institute of MicrobiologyCluster of Excellence on Plant SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology IMedical Faculty and University Hospital DüsseldorfHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Michael Feldbrügge
- Institute of MicrobiologyCluster of Excellence on Plant SciencesHeinrich Heine University DüsseldorfDüsseldorfGermany
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49
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Prevalence and species distribution of the low-complexity, amyloid-like, reversible, kinked segment structural motif in amyloid-like fibrils. J Biol Chem 2021; 297:101194. [PMID: 34537246 PMCID: PMC8551513 DOI: 10.1016/j.jbc.2021.101194] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022] Open
Abstract
Membraneless organelles (MLOs) are vital and dynamic reaction centers in cells that compartmentalize the cytoplasm in the absence of a membrane. Multivalent interactions between protein low-complexity domains contribute to MLO organization. Previously, we used computational methods to identify structural motifs termed low-complexity amyloid-like reversible kinked segments (LARKS) that promote phase transition to form hydrogels and that are common in human proteins that participate in MLOs. Here, we searched for LARKS in the proteomes of six model organisms: Homo sapiens, Drosophila melanogaster, Plasmodium falciparum, Saccharomyces cerevisiae, Mycobacterium tuberculosis, and Escherichia coli to gain an understanding of the distribution of LARKS in the proteomes of various species. We found that LARKS are abundant in M. tuberculosis, D. melanogaster, and H. sapiens but not in S. cerevisiae or P. falciparum. LARKS have high glycine content, which enables kinks to form as exemplified by the known LARKS-rich amyloidogenic structures of TDP43, FUS, and hnRNPA2, three proteins that are known to participate in MLOs. These results support the idea of LARKS as an evolved structural motif. Based on these results, we also established the LARKSdb Web server, which permits users to search for LARKS in their protein sequences of interest.
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50
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Kim G, Lee SE, Jeong S, Lee J, Park D, Chang S. Multivalent electrostatic pi-cation interaction between synaptophysin and synapsin is responsible for the coacervation. Mol Brain 2021; 14:137. [PMID: 34496937 PMCID: PMC8424992 DOI: 10.1186/s13041-021-00846-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/24/2021] [Indexed: 12/26/2022] Open
Abstract
We recently showed that synaptophysin (Syph) and synapsin (Syn) can induce liquid-liquid phase separation (LLPS) to cluster small synaptic-like microvesicles in living cells which are highly reminiscent of SV cluster. However, as there is no physical interaction between them, the underlying mechanism for their coacervation remains unknown. Here, we showed that the coacervation between Syph and Syn is primarily governed by multivalent pi-cation electrostatic interactions among tyrosine residues of Syph C-terminal (Ct) and positively charged Syn. We found that Syph Ct is intrinsically disordered and it alone can form liquid droplets by interactions among themselves at high concentration in a crowding environment in vitro or when assisted by additional interactions by tagging with light-sensitive CRY2PHR or subunits of a multimeric protein in living cells. Syph Ct contains 10 repeated sequences, 9 of them start with tyrosine, and mutating 9 tyrosine to serine (9YS) completely abolished the phase separating property of Syph Ct, indicating tyrosine-mediated pi-interactions are critical. We further found that 9YS mutation failed to coacervate with Syn, and since 9YS retains Syph's negative charge, the results indicate that pi-cation interactions rather than simple charge interactions are responsible for their coacervation. In addition to revealing the underlying mechanism of Syph and Syn coacervation, our results also raise the possibility that physiological regulation of pi-cation interactions between Syph and Syn during synaptic activity may contribute to the dynamics of synaptic vesicle clustering.
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Affiliation(s)
- Goeun Kim
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Sang-Eun Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
- UK Dementia Research Institute, University College London, Cruciform Building, Gower St, London, WC1E 6BT, UK
| | - Seonyoung Jeong
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Jeongkun Lee
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Daehun Park
- Departments of Neuroscience and Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea.
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