1
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Zhu Q, Ahmad A, Shi C, Tang Q, Liu C, Ouyang B, Deng Y, Li F, Cao X. Protein arginine methyltransferase 6 mediates antiviral immunity in plants. Cell Host Microbe 2024:S1931-3128(24)00273-7. [PMID: 39106871 DOI: 10.1016/j.chom.2024.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/19/2024] [Accepted: 07/12/2024] [Indexed: 08/09/2024]
Abstract
Viral suppressor RNA silencing (VSR) is essential for successful infection. Nucleotide-binding and leucine-rich repeat (NLR)-based and autophagy-mediated immune responses have been reported to target VSR as counter-defense strategies. Here, we report a protein arginine methyltransferase 6 (PRMT6)-mediated defense mechanism targeting VSR. The knockout and overexpression of PRMT6 in tomato plants lead to enhanced and reduced disease symptoms, respectively, during tomato bush stunt virus (TBSV) infection. PRMT6 interacts with and inhibits the VSR function of TBSV P19 by methylating its key arginine residues R43 and R115, thereby reducing its dimerization and small RNA-binding activities. Analysis of the natural tomato population reveals that two major alleles associated with high and low levels of PRMT6 expression are significantly associated with high and low levels of viral resistance, respectively. Our study establishes PRMT6-mediated arginine methylation of VSR as a mechanism of plant immunity against viruses.
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Affiliation(s)
- Qiangqiang Zhu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Ayaz Ahmad
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Tang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunyan Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Ouyang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingtian Deng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
| | - Xiaofeng Cao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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2
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Qin M, Fan W, Li L, Xu T, Zhang H, Chen F, Man J, Kombe AJK, Zhang J, Shi Y, Yao X, Yang Z, Hou Z, Ruan K, Liu D. PRMT1 and TDRD3 promote stress granule assembly by rebuilding the protein-RNA interaction network. Int J Biol Macromol 2024:134411. [PMID: 39097054 DOI: 10.1016/j.ijbiomac.2024.134411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/27/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Stress granules (SGs) are membrane-less organelles (MLOs) or cytosolic compartments formed upon exposure to environmental cell stress-inducing stimuli. SGs are based on ribonucleoprotein complexes from a set of cytoplasmic proteins and mRNAs, blocked in translation due to stress cell-induced polysome disassembly. Post-translational modifications (PTMs) such as methylation, are involved in SG assembly, with the methylation writer PRMT1 and its reader TDRD3 colocalizing to SGs. However, the role of this writer-reader system in SG assembly remains unclear. Here, we found that PRMT1 methylates SG constituent RNA-binding proteins (RBPs) on their RGG motifs. Besides, we report that TDRD3, as a reader of asymmetric dimethylarginines, enhances RNA binding to recruit additional RNAs and RBPs, lowering the percolation threshold and promoting SG assembly. Our study enriches our understanding of the molecular mechanism of SG formation by elucidating the functions of PRMT1 and TDRD3. We anticipate that our study will provide a new perspective for comprehensively understanding the functions of PTMs in liquid-liquid phase separation driven condensate assembly.
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Affiliation(s)
- Mengtong Qin
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Weiwei Fan
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Linge Li
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei 230026, China
| | - Tian Xu
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Hanyu Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Feng Chen
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jingwen Man
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Arnaud John Kombe Kombe
- Division of Infectious Diseases and Geographic Medicine, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiahai Zhang
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yunyu Shi
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xuebiao Yao
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Zhenye Yang
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China.
| | - Zhonghuai Hou
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; Department of Chemical Physics, iChEM, University of Science and Technology of China, Hefei 230026, China.
| | - Ke Ruan
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
| | - Dan Liu
- Hefei National Research Center for Physical Sciences at the Microscale, Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China.
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3
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Chen X, Fansler MM, Janjoš U, Ule J, Mayr C. The FXR1 network acts as a signaling scaffold for actomyosin remodeling. Cell 2024:S0092-8674(24)00775-X. [PMID: 39106863 DOI: 10.1016/j.cell.2024.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 05/24/2024] [Accepted: 07/08/2024] [Indexed: 08/09/2024]
Abstract
It is currently not known whether mRNAs fulfill structural roles in the cytoplasm. Here, we report the fragile X-related protein 1 (FXR1) network, an mRNA-protein (mRNP) network present throughout the cytoplasm, formed by FXR1-mediated packaging of exceptionally long mRNAs. These mRNAs serve as an underlying condensate scaffold and concentrate FXR1 molecules. The FXR1 network contains multiple protein binding sites and functions as a signaling scaffold for interacting proteins. We show that it is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. Point mutations in FXR1, found in its homolog FMR1, where they cause fragile X syndrome, disrupt the network. FXR1 network disruption prevents actomyosin remodeling-an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. Our findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as an organizer of signaling reactions.
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Affiliation(s)
- Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Urška Janjoš
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; Biosciences PhD Program, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; UK Dementia Research Institute at King's College London, London SE5 9NU, UK
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA.
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4
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Wang L, Li P. Arginine methylation-enabled FUS phase separation with SMN contributes to neuronal granule formation. Cell Rep 2024; 43:114537. [PMID: 39052476 DOI: 10.1016/j.celrep.2024.114537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 05/03/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
Various ribonucleoprotein complexes (RNPs) often function in the form of membraneless organelles derived from multivalence-driven liquid-liquid phase separation (LLPS). Post-translational modifications, such as phosphorylation and arginine methylation, govern the assembly and disassembly of membraneless organelles. This study reveals that asymmetric dimethylation of arginine can create extra binding sites for multivalent Tudor domain-containing proteins like survival of motor neuron (SMN) protein, thereby lowering the threshold for LLPS of RNPs, such as fused in sarcoma (FUS). Accordingly, FUS hypomethylation or knockdown of SMN disrupts the formation and transport of neuronal granules in axons. Wild-type SMN, but not the spinal muscular atrophy-associated form of SMN, SMN-Δ7, rescues neuronal defects due to SMN knockdown. Importantly, a fusion of SMN-Δ7 to an exogenous oligomeric protein is sufficient to rescue axon length defects caused by SMN knockdown. Our findings highlight the significant role of arginine methylation-enabled multivalent interactions in LLPS and suggest their potential impact on various aspects of neuronal activities in neurodegenerative diseases.
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Affiliation(s)
- Lingyao Wang
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Pilong Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
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5
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Lühmann KL, Seemann S, Martinek N, Ostendorp S, Kehr J. The glycine-rich domain of GRP7 plays a crucial role in binding long RNAs and facilitating phase separation. Sci Rep 2024; 14:16018. [PMID: 38992080 PMCID: PMC11239674 DOI: 10.1038/s41598-024-66955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024] Open
Abstract
Microscale thermophoresis (MST) is a well-established method to quantify protein-RNA interactions. In this study, we employed MST to analyze the RNA binding properties of glycine-rich RNA binding protein 7 (GRP7), which is known to have multiple biological functions related to its ability to bind different types of RNA. However, the exact mechanism of GRP7's RNA binding is not fully understood. While the RNA-recognition motif of GRP7 is known to be involved in RNA binding, the glycine-rich region (known as arginine-glycine-glycine-domain or RGG-domain) also influences this interaction. To investigate to which extend the RGG-domain of GRP7 is involved in RNA binding, mutation studies on putative RNA interacting or modulating sites were performed. In addition to MST experiments, we examined liquid-liquid phase separation of GRP7 and its mutants, both with and without RNA. Furthermore, we systemically investigated factors that might affect RNA binding selectivity of GRP7 by testing RNAs of different sizes, structures, and modifications. Consequently, our study revealed that GRP7 exhibits a high affinity for a variety of RNAs, indicating a lack of pronounced selectivity. Moreover, we established that the RGG-domain plays a crucial role in binding longer RNAs and promoting phase separation.
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Affiliation(s)
- Kim Lara Lühmann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Silja Seemann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Nina Martinek
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Steffen Ostendorp
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Julia Kehr
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.
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6
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Hu J, Dong H, Li Y, Gu J, Yang L, Si C, Zhang Y, Li T, Li D, Liu C. Hsp90α forms condensate engaging client proteins with RG motif repeats. Chem Sci 2024; 15:10508-10518. [PMID: 38994413 PMCID: PMC11234873 DOI: 10.1039/d4sc00267a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/28/2024] [Indexed: 07/13/2024] Open
Abstract
Hsp90α, a pivotal canonical chaperone, is renowned for its broad interaction with numerous protein clients to maintain protein homeostasis, chromatin remodeling, and cell growth. Recent studies indicate its role in modifying various components of membraneless organelles (MLOs) such as stress granules and processing bodies, suggesting its participation in the regulation of protein condensates. In this study, we found that Hsp90α possesses an inherent ability to form dynamic condensates in vitro. Utilizing LC-MS/MS, we further pinpointed proteins in cell lysates that preferentially integrate into Hsp90α condensates. Significantly, we observed a prevalence of RG motif repeats in client proteins of Hsp90α condensates, many of which are linked to various MLOs. Moreover, each of the three domains of Hsp90α was found to undergo phase separation, with numerous solvent-exposed negatively charged residues on these domains being crucial for driving Hsp90α condensation through multivalent weak electrostatic interactions. Additionally, various clients like TDP-43 and hnRNPA1, along with poly-GR and PR dipeptide repeats, exhibit varied impacts on the dynamic behavior of Hsp90α condensates. Our study spotlights various client proteins associated with Hsp90α condensates, illustrating its intricate adaptive nature in interacting with diverse clients and its functional adaptability across multiple MLOs.
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Affiliation(s)
- Jiaojiao Hu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
| | - Yichen Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University Shanghai 200240 China
| | - Jinge Gu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
| | - Liang Yang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center Beijing 100191 China
- Key Laboratory for Neuroscience, Ministry of Education, National Health Commission of China, Peking University Beijing 100191 China
| | - Chenfang Si
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center Beijing 100191 China
- Key Laboratory for Neuroscience, Ministry of Education, National Health Commission of China, Peking University Beijing 100191 China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University Shanghai 200240 China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University Shanghai 200240 China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 201210 China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Shanghai 200032 China
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7
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Kletzien OA, Wuttke DS, Batey RT. The RNA-binding Selectivity of the RGG/RG Motifs of hnRNP U is Abolished by Elements Within the C-terminal Intrinsically Disordered Region. J Mol Biol 2024; 436:168702. [PMID: 38996909 DOI: 10.1016/j.jmb.2024.168702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024]
Abstract
The abundant nuclear protein hnRNP U interacts with a broad array of RNAs along with DNA and protein to regulate nuclear chromatin architecture. The RNA-binding activity is achieved via a disordered ∼100 residue C-terminal RNA-binding domain (RBD) containing two distinct RGG/RG motifs. Although the RNA-binding capabilities of RGG/RG motifs have been widely reported, less is known about hnRNP U's RNA-binding selectivity. Furthermore, while it is well established that hnRNP U binds numerous nuclear RNAs, it remains unknown whether it selectively recognizes sequence or structural motifs in target RNAs. To address this question, we performed equilibrium binding assays using fluorescence anisotropy (FA) and electrophoretic mobility shift assays (EMSAs) to quantitatively assess the ability of human hnRNP U RBD to interact with segments of cellular RNAs identified from eCLIP data. These RNAs often, but not exclusively, contain poly-uridine or 5'-AGGGAG sequence motifs. Detailed binding analysis of several target RNAs reveal that the hnRNP U RBD binds RNA in a promiscuous manner with high affinity for a broad range of structured RNAs, but with little preference for any distinct sequence motif. In contrast, the isolated RGG/RG of hnRNP U motif exhibits a strong preference for G-quadruplexes, similar to that observed for other RGG motif bearing peptides. These data reveal that the hnRNP U RBD attenuates the RNA binding selectivity of its core RGG motifs to achieve an extensive RNA interactome. We propose that a critical role of RGG/RG motifs in RNA biology is to alter binding affinity or selectivity of adjacent RNA-binding domains.
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Affiliation(s)
- Otto A Kletzien
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA.
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA.
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA.
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8
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Yang A, Song J, Li J, Li Y, Bai S, Zhou C, Wang M, Zhou Y, Wen K, Luo M, Chen P, Liu B, Yang H, Bai Y, Wong WL, Cai Q, Pu H, Qian Y, Hu W, Huang W, Wan M, Zhang C, Feng X. Ligand-Receptor Interaction-Induced Intracellular Phase Separation: A Global Disruption Strategy for Resistance-Free Lethality of Pathogenic Bacteria. J Am Chem Soc 2024. [PMID: 38980064 DOI: 10.1021/jacs.4c04749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Addressing the global challenge of bacterial resistance demands innovative approaches, among which multitargeting is a widely used strategy. Current strategies of multitargeting, typically achieved through drug combinations or single agents inherently aiming at multiple targets, face challenges such as stringent pharmacokinetic and pharmacodynamic requirements and cytotoxicity concerns. In this report, we propose a bacterial-specific global disruption approach as a vastly expanded multitargeting strategy that effectively disrupts bacterial subcellular organization. This effect is achieved through a pioneering chemical design of ligand-receptor interaction-induced aggregation of small molecules, i.e., DNA-induced aggregation of a diarginine peptidomimetic within bacterial cells. These intracellular aggregates display affinity toward various proteins and thus substantially interfere with essential bacterial functions and rupture bacterial cell membranes in an "inside-out" manner, leading to robust antibacterial activities and suppression of drug resistance. Additionally, biochemical analysis of macromolecule binding affinity, cytoplasmic localization patterns, and bacterial stress responses suggests that this bacterial-specific intracellular aggregation mechanism is fundamentally different from nonselective classic DNA or membrane binding mechanisms. These mechanistic distinctions, along with the peptidomimetic's selective permeation of bacterial membranes, contribute to its favorable biocompatibility and pharmacokinetic properties, enabling its in vivo antimicrobial efficacy in several animal models, including mice-based superficial wound models, subcutaneous abscess models, and septicemia infection models. These results highlight the great promise of ligand-receptor interaction-induced intracellular aggregation in achieving a globally disruptive multitargeting effect, thereby offering potential applications in the treatment of malignant cells, including pathogens, tumor cells, and infected tissues.
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Affiliation(s)
- Anming Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Junfeng Song
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jiaqi Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Youzhi Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Silei Bai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Cailing Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Min Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yu Zhou
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Kang Wen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Miaomiao Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Peiren Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Bo Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
| | - Huan Yang
- School of Medical Technology, Xuzhou Medical University, Xuzhou 221004, China
| | - Yugang Bai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR 999077, China
| | - Qingyun Cai
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Huangsheng Pu
- College of Advanced Interdisciplinary Studies & Hunan Provincial Key Laboratory of Novel NanoOptoelectronic Information Materials and Devices, National University of Defense Technology, Changsha, Hunan 410073, China
- Nanhu Laser Laboratory, National University of Defense Technology, Changsha 410073, China
| | - Yu Qian
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wenhao Hu
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Wei Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, No.555 Zuchongzhi Rd, Pudong, Shanghai 201203, China
| | - Muyang Wan
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Chunhui Zhang
- College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Xinxin Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, and School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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9
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Chew PY, Joseph JA, Collepardo-Guevara R, Reinhardt A. Aromatic and arginine content drives multiphasic condensation of protein-RNA mixtures. Biophys J 2024; 123:1342-1355. [PMID: 37408305 PMCID: PMC11163273 DOI: 10.1016/j.bpj.2023.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
Multiphasic architectures are found ubiquitously in biomolecular condensates and are thought to have important implications for the organization of multiple chemical reactions within the same compartment. Many of these multiphasic condensates contain RNA in addition to proteins. Here, we investigate the importance of different interactions in multiphasic condensates comprising two different proteins and RNA using computer simulations with a residue-resolution coarse-grained model of proteins and RNA. We find that in multilayered condensates containing RNA in both phases, protein-RNA interactions dominate, with aromatic residues and arginine forming the key stabilizing interactions. The total aromatic and arginine content of the two proteins must be appreciably different for distinct phases to form, and we show that this difference increases as the system is driven toward greater multiphasicity. Using the trends observed in the different interaction energies of this system, we demonstrate that we can also construct multilayered condensates with RNA preferentially concentrated in one phase. The "rules" identified can thus enable the design of synthetic multiphasic condensates to facilitate further study of their organization and function.
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Affiliation(s)
- Pin Yu Chew
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jerelle A Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Physics, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Aleks Reinhardt
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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10
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Chen X, Fansler MM, Janjoš U, Ule J, Mayr C. The FXR1 network acts as signaling scaffold for actomyosin remodeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.05.565677. [PMID: 37961296 PMCID: PMC10635158 DOI: 10.1101/2023.11.05.565677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
It is currently not known whether mRNAs fulfill structural roles in the cytoplasm. Here, we report the FXR1 network, an mRNA-protein (mRNP) network present throughout the cytoplasm, formed by FXR1-mediated packaging of exceptionally long mRNAs. These mRNAs serve as underlying condensate scaffold and concentrate FXR1 molecules. The FXR1 network contains multiple protein binding sites and functions as a signaling scaffold for interacting proteins. We show that it is necessary for RhoA signaling-induced actomyosin reorganization to provide spatial proximity between kinases and their substrates. Point mutations in FXR1, found in its homolog FMR1, where they cause Fragile X syndrome, disrupt the network. FXR1 network disruption prevents actomyosin remodeling-an essential and ubiquitous process for the regulation of cell shape, migration, and synaptic function. These findings uncover a structural role for cytoplasmic mRNA and show how the FXR1 RNA-binding protein as part of the FXR1 network acts as organizer of signaling reactions.
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Affiliation(s)
- Xiuzhen Chen
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Mervin M Fansler
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Urška Janjoš
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- Biosciences PhD Program, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jernej Ule
- National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
- UK Dementia Research Institute at King's College London, London, SE5 9NU, UK
| | - Christine Mayr
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY 10065, USA
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11
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Salazar OR, Chen K, Melino VJ, Reddy MP, Hřibová E, Čížková J, Beránková D, Arciniegas Vega JP, Cáceres Leal LM, Aranda M, Jaremko L, Jaremko M, Fedoroff NV, Tester M, Schmöckel SM. SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii. Nat Commun 2024; 15:4279. [PMID: 38769297 PMCID: PMC11106269 DOI: 10.1038/s41467-024-48595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
The identification of genes involved in salinity tolerance has primarily focused on model plants and crops. However, plants naturally adapted to highly saline environments offer valuable insights into tolerance to extreme salinity. Salicornia plants grow in coastal salt marshes, stimulated by NaCl. To understand this tolerance, we generated genome sequences of two Salicornia species and analyzed the transcriptomic and proteomic responses of Salicornia bigelovii to NaCl. Subcellular membrane proteomes reveal that SbiSOS1, a homolog of the well-known SALT-OVERLY-SENSITIVE 1 (SOS1) protein, appears to localize to the tonoplast, consistent with subcellular localization assays in tobacco. This neo-localized protein can pump Na+ into the vacuole, preventing toxicity in the cytosol. We further identify 11 proteins of interest, of which SbiSALTY, substantially improves yeast growth on saline media. Structural characterization using NMR identified it as an intrinsically disordered protein, localizing to the endoplasmic reticulum in planta, where it can interact with ribosomes and RNA, stabilizing or protecting them during salt stress.
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Affiliation(s)
- Octavio R Salazar
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Ke Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Vanessa J Melino
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Muppala P Reddy
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Denisa Beránková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 77900, Olomouc, Czech Republic
| | - Juan Pablo Arciniegas Vega
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lina María Cáceres Leal
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Manuel Aranda
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Lukasz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Nina V Fedoroff
- Department of Biology, Penn State University, University Park, PA, 16801, US
| | - Mark Tester
- Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
- Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| | - Sandra M Schmöckel
- Department Physiology of Yield Stability, Institute of Crop Science, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
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12
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Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Malukhina K, Gu Y, Deep A, Naritomi J, Liang Q, Aigner S, Adler B, Cress B, Doudna J, Chaikeeratisak V, Cleveland D, Ghassemian M, Bintu B, Yeo G, Pogliano J, Corbett K. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. Nucleic Acids Res 2024; 52:4440-4455. [PMID: 38554115 PMCID: PMC11077065 DOI: 10.1093/nar/gkae216] [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: 09/27/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily G Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Sitao Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kseniya Malukhina
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jack T Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Qishan Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Benjamin A Adler
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Bogdan Bintu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
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13
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Cascarina SM, Ross ED. Identification of Low-Complexity Domains by Compositional Signatures Reveals Class-Specific Frequencies and Functions Across the Domains of Life. PLoS Comput Biol 2024; 20:e1011372. [PMID: 38748749 PMCID: PMC11132505 DOI: 10.1371/journal.pcbi.1011372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 05/28/2024] [Accepted: 05/04/2024] [Indexed: 05/29/2024] Open
Abstract
Low-complexity domains (LCDs) in proteins are typically enriched in one or two predominant amino acids. As a result, LCDs often exhibit unusual structural/biophysical tendencies and can occupy functional niches. However, for each organism, protein sequences must be compatible with intracellular biomolecules and physicochemical environment, both of which vary from organism to organism. This raises the possibility that LCDs may occupy sequence spaces in select organisms that are otherwise prohibited in most organisms. Here, we report a comprehensive survey and functional analysis of LCDs in all known reference proteomes (>21k organisms), with added focus on rare and unusual types of LCDs. LCDs were classified according to both the primary amino acid and secondary amino acid in each LCD sequence, facilitating detailed comparisons of LCD class frequencies across organisms. Examination of LCD classes at different depths (i.e., domain of life, organism, protein, and per-residue levels) reveals unique facets of LCD frequencies and functions. To our surprise, all 400 LCD classes occur in nature, although some are exceptionally rare. A number of rare classes can be defined for each domain of life, with many LCD classes appearing to be eukaryote-specific. Certain LCD classes were consistently associated with identical functions across many organisms, particularly in eukaryotes. Our analysis methods enable simultaneous, direct comparison of all LCD classes between individual organisms, resulting in a proteome-scale view of differences in LCD frequencies and functions. Together, these results highlight the remarkable diversity and functional specificity of LCDs across all known life forms.
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Affiliation(s)
- Sean M. Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Eric D. Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
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14
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Steinhauser S, Estoppey D, Buehler DP, Xiong Y, Pizzato N, Rietsch A, Wu F, Leroy N, Wunderlin T, Claerr I, Tropberger P, Müller M, Davison LM, Sheng Q, Bergling S, Wild S, Moulin P, Liang J, English WJ, Williams B, Knehr J, Altorfer M, Reyes A, Mickanin C, Hoepfner D, Nigsch F, Frederiksen M, Flynn CR, Fodor BD, Brown JD, Kolter C. The transcription factor ZNF469 regulates collagen production in liver fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591188. [PMID: 38712281 PMCID: PMC11071482 DOI: 10.1101/2024.04.25.591188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) - characterized by excess accumulation of fat in the liver - now affects one third of the world's population. As NAFLD progresses, extracellular matrix components including collagen accumulate in the liver causing tissue fibrosis, a major determinant of disease severity and mortality. To identify transcriptional regulators of fibrosis, we computationally inferred the activity of transcription factors (TFs) relevant to fibrosis by profiling the matched transcriptomes and epigenomes of 108 human liver biopsies from a deeply-characterized cohort of patients spanning the full histopathologic spectrum of NAFLD. CRISPR-based genetic knockout of the top 100 TFs identified ZNF469 as a regulator of collagen expression in primary human hepatic stellate cells (HSCs). Gain- and loss-of-function studies established that ZNF469 regulates collagen genes and genes involved in matrix homeostasis through direct binding to gene bodies and regulatory elements. By integrating multiomic large-scale profiling of human biopsies with extensive experimental validation we demonstrate that ZNF469 is a transcriptional regulator of collagen in HSCs. Overall, these data nominate ZNF469 as a previously unrecognized determinant of NAFLD-associated liver fibrosis.
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15
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Gupta MN, Uversky VN. Reexamining the diverse functions of arginine in biochemistry. Biochem Biophys Res Commun 2024; 705:149731. [PMID: 38432110 DOI: 10.1016/j.bbrc.2024.149731] [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: 12/24/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Arginine in a free-state and as part of peptides and proteins shows distinct tendency to form clusters. In free-form, it has been found useful in cryoprotection, as a drug excipient for both solid and liquid formulations, as an aggregation suppressor, and an eluent in protein chromatography. In many cases, the mechanisms by which arginine acts in all these applications is either debatable or at least continues to attract interest. It is quite possible that arginine clusters may be involved in many such applications. Furthermore, it is possible that such clusters are likely to behave as intrinsically disordered polypeptides. These considerations may help in understanding the roles of arginine in diverse applications and may even lead to better strategies for using arginine in different situations.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India.
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Institutskaya Str., 7, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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16
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Gu H, Gu C, Locker N, Ewing AG. Amperometry and Electron Microscopy show Stress Granules Induce Homotypic Fusion of Catecholamine Vesicles. Angew Chem Int Ed Engl 2024; 63:e202400422. [PMID: 38380500 DOI: 10.1002/anie.202400422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
An overreactive stress granule (SG) pathway and long-lived, stable SGs formation are thought to participate in the progress of neurodegenerative diseases (NDs). To understand if and how SGs contribute to disorders of neurotransmitter release in NDs, we examined the interaction between extracellular isolated SGs and vesicles. Amperometry shows that the vesicular content increases and dynamics of vesicle opening slow down after vesicles are treated with SGs, suggesting larger vesicles are formed. Data from transmission electron microscopy (TEM) clearly shows that a portion of large dense-core vesicles (LDCVs) with double/multiple cores appear, thus confirming that SGs induce homotypic fusion between LDCVs. This might be a protective step to help cells to survive following high oxidative stress. A hypothetical mechanism is proposed whereby enriched mRNA or protein in the shell of SGs is likely to bind intrinsically disordered protein (IDP) regions of vesicle associated membrane protein (VAMP) driving a disrupted membrane between two closely buddled vesicles to fuse with each other to form double-core vesicles. Our results show that SGs induce homotypic fusion of LDCVs, providing better understanding of how SGs intervene in pathological processes and opening a new direction to investigations of SGs involved neurodegenerative disease.
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Affiliation(s)
- Hui Gu
- Department of Chemistry and Chemical Engineering, Hunan University of Science and Technology, 411201, Xiangtan, China
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Chaoyi Gu
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Nicolas Locker
- Faculty of Health and Medical Sciences School of Biosciences and Medicine, University of Surrey, GU27XH, Guildford Surrey, UK
| | - Andrew G Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390, Gothenburg, Sweden
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17
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Lu Q, Xi P, Xu S, Zhang Z, Gong B, Liu J, Zhu Q, Sun T, Zhu S, Chen R. A novel risk signature based on liquid-liquid phase separation-related genes reveals prognostic and tumour microenvironmental features in clear cell renal cell carcinoma. Aging (Albany NY) 2024; 16:6118-6134. [PMID: 38546385 PMCID: PMC11042959 DOI: 10.18632/aging.205691] [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: 09/13/2023] [Accepted: 02/07/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Clear cell renal cell carcinoma(ccRCC) is one of the most common malignancies. However, there are still many barriers to its underlying causes, early diagnostic techniques and therapeutic approaches. MATERIALS AND METHODS The Cancer Genome Atlas (TCGA)- Kidney renal clear cell (KIRC) cohort differentially analysed liquid-liquid phase separation (LLPS)-related genes from the DrLLPS website. Univariate and multivariate Cox regression analyses and LASSO regression analyses were used to construct prognostic models. The E-MTAB-1980 cohort was used for external validation. Then, potential functions, immune infiltration analysis, and mutational landscapes were analysed for the high-risk and low-risk groups. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) experiments as well as single-cell analyses validated the genes key to the model. RESULTS We screened 174 LLPS-related genes in ccRCC and constructed a risk signature consisting of five genes (CLIC5, MXD3, NUF2, PABPC1L, PLK1). The high-risk group was found to be associated with worse prognosis in different subgroups. A nomogram constructed by combining age and tumour stage had a strong predictive power for the prognosis of ccRCC patients. In addition, there were differences in pathway enrichment, immune cell infiltration, and mutational landscapes between the two groups. The results of qRT-PCR in renal cancer cell lines and renal cancer tissues were consistent with the biosignature prediction. Three single-cell data of GSE159115, GSE139555, and GSE121636 were analysed for differences in the presence of these five genes in different cells. CONCLUSIONS We developed a risk signature constructed based on the five LLPS-related genes and can have a high ability to predict the prognosis of ccRCC patients, further providing a strong support for clinical decision-making.
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Affiliation(s)
- Qing Lu
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, P.R. China
| | - Ping Xi
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Suling Xu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Zhicheng Zhang
- Department of Surgery, Fuzhou First People’s Hospital, Fuzhou 344000, Jiangxi, China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Ji Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Qiqi Zhu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, Jiangxi, China
| | - Shaoxing Zhu
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, P.R. China
| | - Ru Chen
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian, P.R. China
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18
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Sun J, Qu J, Zhao C, Zhang X, Liu X, Wang J, Wei C, Liu X, Wang M, Zeng P, Tang X, Ling X, Qing L, Jiang S, Chen J, Chen TSR, Kuang Y, Gao J, Zeng X, Huang D, Yuan Y, Fan L, Yu H, Ding J. Precise prediction of phase-separation key residues by machine learning. Nat Commun 2024; 15:2662. [PMID: 38531854 DOI: 10.1038/s41467-024-46901-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
Understanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme. In vivo and in vitro validations demonstrate that truncating just 6 key residues in GATA3 disrupts phase separation, enhancing tumor cell migration and inhibiting growth. Glycine and its motifs are enriched in spacer and key residues, as revealed by our comprehensive analysis. PSPHunter identifies nearly 80% of disease-associated phase-separating proteins, with frequent mutated pathological residues like glycine and proline often residing in these key residues. PSPHunter thus emerges as a crucial tool to uncover key residues, facilitating insights into phase separation mechanisms governing transcriptional control, cell fate transitions, and disease development.
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Affiliation(s)
- Jun Sun
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiale Qu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cai Zhao
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyao Zhang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyu Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chao Wei
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xinyi Liu
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Mulan Wang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pengguihang Zeng
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiuxiao Tang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoru Ling
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Li Qing
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shaoshuai Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiahao Chen
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tara S R Chen
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yalan Kuang
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Jinhang Gao
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Xiaoxi Zeng
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China
| | - Dongfeng Huang
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China
| | - Yong Yuan
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Lili Fan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Jinan University, Guangzhou, Guangdong, China.
| | - Haopeng Yu
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
| | - Junjun Ding
- Department of Thoracic Surgery and West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Med-X Center for Informatics, Sichuan University, Chengdu, 610041, China.
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, 518107, China.
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19
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Luige J, Armaos A, Tartaglia GG, Ørom UAV. Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation. Nat Commun 2024; 15:2585. [PMID: 38519458 PMCID: PMC10959947 DOI: 10.1038/s41467-024-46731-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
RNA-binding proteins are central for many biological processes and their characterization has demonstrated a broad range of functions as well as a wide spectrum of target structures. RNA G-quadruplexes are important regulatory elements occurring in both coding and non-coding transcripts, yet our knowledge of their structure-based interactions is at present limited. Here, using theoretical predictions and experimental approaches, we show that many chromatin-binding proteins bind to RNA G-quadruplexes, and we classify them based on their RNA G-quadruplex-binding potential. Combining experimental identification of nuclear RNA G-quadruplex-binding proteins with computational approaches, we build a prediction tool that assigns probability score for a nuclear protein to bind RNA G-quadruplexes. We show that predicted G-quadruplex RNA-binding proteins exhibit a high degree of protein disorder and hydrophilicity and suggest involvement in both transcription and phase-separation into membrane-less organelles. Finally, we present the G4-Folded/UNfolded Nuclear Interaction Explorer System (G4-FUNNIES) for estimating RNA G4-binding propensities at http://service.tartaglialab.com/new_submission/G4FUNNIES .
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Affiliation(s)
- Johanna Luige
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy.
- Catalan Institution for Research and Advanced Studies ICREA Passeig Lluis Companys, 23 08010, Barcelona, Spain.
| | - Ulf Andersson Vang Ørom
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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20
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Fakim H, Vande Velde C. The implications of physiological biomolecular condensates in amyotrophic lateral sclerosis. Semin Cell Dev Biol 2024; 156:176-189. [PMID: 37268555 DOI: 10.1016/j.semcdb.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
In recent years, there has been an emphasis on the role of phase-separated biomolecular condensates, especially stress granules, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). This is largely due to several ALS-associated mutations occurring in genes involved in stress granule assembly and observations that pathological inclusions detected in ALS patient neurons contain stress granule proteins, including the ALS-linked proteins TDP-43 and FUS. However, protein components of stress granules are also found in numerous other phase-separated biomolecular condensates under physiological conditions which are inadequately discussed in the context of ALS. In this review, we look beyond stress granules and describe the roles of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites, such as the nucleolus, Cajal bodies, paraspeckles and neuronal RNA transport granules. We also discuss the consequences of ALS-linked mutations in TDP-43 and FUS on their ability to phase separate into these stress-independent biomolecular condensates and perform their respective functions. Importantly, biomolecular condensates sequester multiple overlapping protein and RNA components, and their dysregulation could contribute to the observed pleiotropic effects of both sporadic and familial ALS on RNA metabolism.
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Affiliation(s)
- Hana Fakim
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada.
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21
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Unarta IC, Cao S, Goonetilleke EC, Niu J, Gellman SH, Huang X. Submillisecond Atomistic Molecular Dynamics Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate. J Phys Chem B 2024; 128:2347-2359. [PMID: 38416758 PMCID: PMC11057999 DOI: 10.1021/acs.jpcb.3c08126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Liquid-liquid phase separation mediated by proteins and/or nucleic acids is believed to underlie the formation of many distinct condensed phases, or membraneless organelles, within living cells. These condensates have been proposed to orchestrate a variety of important processes. Despite recent advances, the interactions that regulate the dynamics of molecules within a condensate remain poorly understood. We performed accumulated 564.7 μs all-atom molecular dynamics (MD) simulations (system size ∼200k atoms) of model condensates formed by a scaffold RNA oligomer and a scaffold peptide rich in arginine (Arg). These model condensates contained one of three possible guest peptides: the scaffold peptide itself or a variant in which six Arg residues were replaced by lysine (Lys) or asymmetric dimethyl arginine (ADMA). We found that the Arg-rich peptide can form the largest number of hydrogen bonds and bind the strongest to the scaffold RNA in the condensate, relative to the Lys- and ADMA-rich peptides. Our MD simulations also showed that the Arg-rich peptide diffused more slowly in the condensate relative to the other two guest peptides, which is consistent with a recent fluorescence microscopy study. There was no significant increase in the number of cation-π interactions between the Arg-rich peptide and the scaffold RNA compared to the Lys-rich and ADMA-rich peptides. Our results indicate that hydrogen bonds between the peptides and the RNA backbone, rather than cation-π interactions, play a major role in regulating peptide diffusion in the condensate.
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Affiliation(s)
- Ilona C. Unarta
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Siqin Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Eshani C. Goonetilleke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, WI, 53706, USA
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22
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Zheng H, Zhang H. More than a bystander: RNAs specify multifaceted behaviors of liquid-liquid phase-separated biomolecular condensates. Bioessays 2024; 46:e2300203. [PMID: 38175843 DOI: 10.1002/bies.202300203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/06/2024]
Abstract
Cells contain a myriad of membraneless ribonucleoprotein (RNP) condensates with distinct compositions of proteins and RNAs. RNP condensates participate in different cellular activities, including RNA storage, mRNA translation or decay, stress response, etc. RNP condensates are assembled via liquid-liquid phase separation (LLPS) driven by multivalent interactions. Transition of RNP condensates into bodies with abnormal material properties, such as solid-like amyloid structures, is associated with the pathogenesis of various diseases. In this review, we focus on how RNAs regulate multiple aspects of RNP condensates, such as dynamic assembly and/or disassembly and biophysical properties. RNA properties - including concentration, sequence, length and structure - also determine the phase behaviors of RNP condensates. RNA is also involved in specifying autophagic degradation of RNP condensates. Unraveling the role of RNA in RNPs provides novel insights into pathological accumulation of RNPs in various diseases. This new understanding can potentially be harnessed to develop therapeutic strategies.
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Affiliation(s)
- Hui Zheng
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, P.R. China
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23
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Yan X, Zhang M, Wang D. Interplay between posttranslational modifications and liquid‒liquid phase separation in tumors. Cancer Lett 2024; 584:216614. [PMID: 38246226 DOI: 10.1016/j.canlet.2024.216614] [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: 11/08/2023] [Revised: 12/22/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Liquid‒liquid phase separation (LLPS) is a general phenomenon recently recognized to be critically involved in the regulation of a variety of cellular biological processes, such as transcriptional regulation, heterochromatin formation and signal transduction, through the compartmentalization of proteins or nucleic acids into droplet-like condensates. These processes are directly or indirectly related to tumor initiation and treatment. Posttranslational modifications (PTMs), which represent a rapid and reversible mechanism involved in the functional regulation of proteins, have emerged as key events in modulating LLPS under physiological or pathophysiological conditions, including tumorigenesis and antitumor therapy. In this review, we introduce the biological functions participated in cancer-associated LLPS, discuss the potential roles of LLPS during tumor onset or therapy, and emphasize the mechanistic characteristics of LLPS regulated by PTMs and its effects on tumor progression. We then provide a perspective on further studies on LLPS and its regulation by PTMs in cancer research. This review aims to broaden the understanding of the functions of LLPS and its regulation by PTMs under normal or aberrant cellular conditions.
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Affiliation(s)
- Xiaojun Yan
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Meng Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Donglai Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases & Department of Medical Genetics, Institute of Basic Medical Sciences & School of Basic Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
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24
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Dumelie JG, Chen Q, Miller D, Attarwala N, Gross SS, Jaffrey SR. Biomolecular condensates create phospholipid-enriched microenvironments. Nat Chem Biol 2024; 20:302-313. [PMID: 37973889 PMCID: PMC10922641 DOI: 10.1038/s41589-023-01474-4] [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: 05/24/2022] [Accepted: 10/08/2023] [Indexed: 11/19/2023]
Abstract
Proteins and RNA can phase separate from the aqueous cellular environment to form subcellular compartments called condensates. This process results in a protein-RNA mixture that is chemically different from the surrounding aqueous phase. Here, we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and extracts of cellular metabolites and identified metabolites enriched in the condensate phase. Among the most condensate-enriched metabolites were phospholipids, due primarily to the hydrophobicity of their fatty acyl moieties. We found that phospholipids can alter the number and size of phase-separated condensates and in some cases alter their morphology. Finally, we found that phospholipids partition into a diverse set of endogenous condensates as well as artificial condensates expressed in cells. Overall, these data show that many condensates are protein-RNA-lipid mixtures with chemical microenvironments that are ideally suited to facilitate phospholipid biology and signaling.
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Affiliation(s)
- Jason G Dumelie
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Dawson Miller
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Nabeel Attarwala
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Steven S Gross
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA.
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25
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Li S, Zhang Y, Chen J. Backbone interactions and secondary structures in phase separation of disordered proteins. Biochem Soc Trans 2024; 52:319-329. [PMID: 38348795 DOI: 10.1042/bst20230618] [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: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/29/2024]
Abstract
Intrinsically disordered proteins (IDPs) are one of the major drivers behind the formation and characteristics of biomolecular condensates. Due to their inherent flexibility, the backbones of IDPs are significantly exposed, rendering them highly influential and susceptible to biomolecular phase separation. In densely packed condensates, exposed backbones have a heightened capacity to interact with neighboring protein chains, which might lead to strong coupling between the secondary structures and phase separation and further modulate the subsequent transitions of the condensates, such as aging and fibrillization. In this mini-review, we provide an overview of backbone-mediated interactions and secondary structures within biomolecular condensates to underscore the importance of protein backbones in phase separation. We further focus on recent advances in experimental techniques and molecular dynamics simulation methods for probing and exploring the roles of backbone interactions and secondary structures in biomolecular phase separation involving IDPs.
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Affiliation(s)
- Shanlong Li
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Yumeng Zhang
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, U.S.A
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26
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Sicoli G, Sieme D, Overkamp K, Khalil M, Backer R, Griesinger C, Willbold D, Rezaei-Ghaleh N. Large dynamics of a phase separating arginine-glycine-rich domain revealed via nuclear and electron spins. Nat Commun 2024; 15:1610. [PMID: 38383529 PMCID: PMC10881997 DOI: 10.1038/s41467-024-45788-w] [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: 03/31/2023] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Liquid-liquid phase separation is the key process underlying formation of membrane-less compartments in cells. A highly dynamic cellular body with rapid component exchange is Cajal body (CB), which supports the extensive compositional dynamics of the RNA splicing machinery, spliceosome. Here, we select an arginine-glycine (RG)-rich segment of coilin, the major component of CB, establish its RNA-induced phase separation, and through combined use of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) probes, interrogate its dynamics within the crowded interior of formed droplets. Taking advantage of glycine-based singlet-states, we show that glycines retain a large level of sub-nanoseconds dynamics inside the coilin droplets. Furthermore, the continuous-wave (CW) and electron-electron dipolar (PELDOR) and electron-nucleus hyperfine coupling EPR data (HYSCORE) support the RNA-induced formation of dynamic coilin droplets with high coilin peptide concentrations. The combined NMR and EPR data reveal the high dynamics of the RG-rich coilin within droplets and suggest its potential role in the large dynamics of CBs.
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Affiliation(s)
- Giuseppe Sicoli
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Daniel Sieme
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Kerstin Overkamp
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Mahdi Khalil
- CNRS UMR 8516, University of Lille, LASIRE, C4 Building, Avenue Paul Langevin, F-59655, Villeneuve d'Ascq, France
| | - Robin Backer
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, D-37077, Göttingen, Germany
| | - Dieter Willbold
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany
| | - Nasrollah Rezaei-Ghaleh
- Heinrich Heine University (HHU) Düsseldorf, Faculty of Mathematics and Natural Sciences, Institute of Physical Biology, Universitätsstrasse 1, D-40225, Düsseldorf, Germany.
- Institute of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, D-52428, Jülich, Germany.
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27
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Doan VS, Alshareedah I, Singh A, Banerjee PR, Shin S. Diffusiophoresis promotes phase separation and transport of biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.03.547532. [PMID: 37461689 PMCID: PMC10350024 DOI: 10.1101/2023.07.03.547532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The internal microenvironment of a living cell is heterogeneous and comprises a multitude of organelles with distinct biochemistry. Amongst them are biomolecular condensates, which are membrane-less, phase-separated compartments enriched in system-specific proteins and nucleic acids. The heterogeneity of the cell engenders the presence of multiple spatiotemporal gradients in chemistry, charge, concentration, temperature, and pressure. Such thermodynamic gradients can lead to non-equilibrium driving forces for the formation and transport of biomolecular condensates. Here, we report how ion gradients impact the transport processes of biomolecular condensates on the mesoscale and biomolecules on the microscale. Utilizing a microfluidic platform, we demonstrate that the presence of ion concentration gradients can accelerate the transport of biomolecules, including nucleic acids and proteins, via diffusiophoresis. This hydrodynamic transport process allows localized enrichment of biomolecules, thereby promoting the location-specific formation of biomolecular condensates via phase separation. The ion gradients further impart active motility of condensates, allowing them to exhibit enhanced diffusion along the gradient. Coupled with a reentrant phase behavior, the gradient-induced active motility leads to a dynamical redistribution of condensates that ultimately extends their lifetime. Together, our results demonstrate diffusiophoresis as a non-equilibrium thermodynamic force that governs the formation and transport of biomolecular condensates.
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Affiliation(s)
- Viet Sang Doan
- Department of Mechanical and Aerospace Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Ibraheem Alshareedah
- Department of Physics, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Anurag Singh
- Department of Physics, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Priya R Banerjee
- Department of Physics, University at Buffalo, The State University of New York, Buffalo, NY 14260
| | - Sangwoo Shin
- Department of Mechanical and Aerospace Engineering, University at Buffalo, The State University of New York, Buffalo, NY 14260
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28
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Wake N, Weng SL, Zheng T, Wang SH, Kirilenko V, Mittal J, Fawzi NL. Expanding the molecular grammar of polar residues and arginine in FUS prion-like domain phase separation and aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580391. [PMID: 38405719 PMCID: PMC10888811 DOI: 10.1101/2024.02.15.580391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A molecular grammar governing low-complexity prion-like domains phase separation (PS) has been proposed based on mutagenesis experiments that identified tyrosine and arginine as primary drivers of phase separation via aromatic-aromatic and aromatic-arginine interactions. Here we show that additional residues make direct favorable contacts that contribute to phase separation, highlighting the need to account for these contributions in PS theories and models. We find that tyrosine and arginine make important contacts beyond only tyrosine-tyrosine and tyrosine-arginine, including arginine-arginine contacts. Among polar residues, glutamine in particular contributes to phase separation with sequence/position-specificity, making contacts with both tyrosine and arginine as well as other residues, both before phase separation and in condensed phases. For glycine, its flexibility, not its small solvation volume, favors phase separation by allowing favorable contacts between other residues and inhibits the liquid-to-solid (LST) transition. Polar residue types also make sequence-specific contributions to aggregation that go beyond simple rules, which for serine positions is linked to formation of an amyloid-core structure by the FUS low-complexity domain. Hence, here we propose a revised molecular grammar expanding the role of arginine and polar residues in prion-like domain protein phase separation and aggregation.
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Affiliation(s)
- Noah Wake
- Therapeutic Sciences Graduate Program, Brown University, Providence, RI 02912
| | - Shuo-Lin Weng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tongyin Zheng
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Valentin Kirilenko
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jeetain Mittal
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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29
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Robinson AO, Lee J, Cameron A, Keating CD, Adamala KP. Cell-Free Expressed Membraneless Organelles Inhibit Translation in Synthetic Cells. ACS Biomater Sci Eng 2024; 10:773-781. [PMID: 38226971 DOI: 10.1021/acsbiomaterials.3c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Compartments within living cells create specialized microenvironments, allowing multiple reactions to be carried out simultaneously and efficiently. While some organelles are bound by a lipid bilayer, others are formed by liquid-liquid phase separation such as P-granules and nucleoli. Synthetic minimal cells are widely used to study many natural processes, including organelle formation. In this work, synthetic cells expressing artificial membrane-less organelles that inhibit translation are described. RGG-GFP-RGG, a phase-separating protein derived from Caenorhabditis elegans P-granules, is expressed by cell-free transcription and translation, forming artificial membraneless organelles that can sequester RNA and reduce protein expression in synthetic cells. The introduction of artificial membrane-less organelles creates complex microenvironments within the synthetic cell cytoplasm and functions as a tool to inhibit protein expression in synthetic cells. The engineering of compartments within synthetic cells furthers the understanding of the evolution and function of natural organelles and facilitates the creation of more complex and multifaceted synthetic lifelike systems.
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Affiliation(s)
- Abbey O Robinson
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
| | - Jessica Lee
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Anders Cameron
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 SE Washington Ave., Minneapolis, Minnesota 55455, United States
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30
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Kletzien OA, Wuttke DS, Batey RT. The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs. Biochemistry 2024. [PMID: 38329035 DOI: 10.1021/acs.biochem.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG motif within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV cross-linking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing 11 of these identified cross-link sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG motif is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG motif with RNA-binding properties comparable to those of the canonical RGG/RG motif. These RGG/RG motifs serve redundant functions, with neither serving as the primary RBD. While in isolation, each RGG/RG motif has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling the binding of most of the designed RNA set with low to midnanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlight the perils of a reductionist approach to defining biochemical activities in this system and pave the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A Kletzien
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
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31
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Corre M, Lebreton A. Regulation of cold-inducible RNA-binding protein (CIRBP) in response to cellular stresses. Biochimie 2024; 217:3-9. [PMID: 37037339 DOI: 10.1016/j.biochi.2023.04.003] [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: 02/27/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/12/2023]
Abstract
Cold-inducible RNA-Binding Protein (CIRBP) is a general stress-response factor in vertebrates harboring two domains: an RNA-recognition motif and a regulatory domain rich in RG/RGG motifs. CIRBP has been described to bind mRNAs upon various stress conditions (cold, infections, UV, hypoxia …) and regulate their stability and translation. The proteins encoded by its targets are involved in key stress-responsive cellular pathways including apoptosis, inflammation, cell proliferation or translation, thus allowing their coordination. Due to its role in regulating central cellular functions, the expression of CIRBP is tightly controlled. We review here current understanding of the multiple mechanistic layers affecting CIRBP expression and function. Beyond transcriptional regulation by cold-responsive elements and the use of alternative promoters and transcription start sites, CIRBP undergoes various alternative splicing (AS) events which, depending on conditions, modulate the stability of CIRBP transcripts and/or impact the sequence of the encoded polypeptide. Typically, whilst CIRBP expression is induced in the context of hypothermia or viral infection, AS events preferentially address alternative isoforms towards mRNA degradation pathways in response to heat stress or to bacterial-secreted pore forming toxins. Post-translational modifications of CIRBP, mostly in its RGG domain, also condition CIRBP subcellular localization and access to its targets, thereby promoting or inhibiting their expression. For instance, phosphorylation and methylation events gate CIRBP nuclear to cytoplasmic translocation and control its recruitment to stress granules. Considering the therapeutic potential of modulating the expression and function of this central player in stress responses, a fine understanding of CIRBP regulation mechanisms deserves further attention.
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Affiliation(s)
- Morgane Corre
- Institut de biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Alice Lebreton
- Institut de biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France; INRAE, Micalis Institute, 78350, Jouy-en-Josas, France.
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32
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Wang F, Zhang Y. Physiology and pharmacological targeting of phase separation. J Biomed Sci 2024; 31:11. [PMID: 38245749 PMCID: PMC10800077 DOI: 10.1186/s12929-024-00993-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) in biology describes a process by which proteins form membraneless condensates within a cellular compartment when conditions are met, including the concentration and posttranslational modifications of the protein components, the condition of the aqueous solution (pH, ionic strength, pressure, and temperature), and the existence of assisting factors (such as RNAs or other proteins). In these supramolecular liquid droplet-like inclusion bodies, molecules are held together through weak intermolecular and/or intramolecular interactions. With the aid of LLPS, cells can assemble functional sub-units within a given cellular compartment by enriching or excluding specific factors, modulating cellular function, and rapidly responding to environmental or physiological cues. Hence, LLPS is emerging as an important means to regulate biology and physiology. Yet, excessive inclusion body formation by, for instance, higher-than-normal concentrations or mutant forms of the protein components could result in the conversion from dynamic liquid condensates into more rigid gel- or solid-like aggregates, leading to the disruption of the organelle's function followed by the development of human disorders like neurodegenerative diseases. In summary, well-controlled formation and de-formation of LLPS is critical for normal biology and physiology from single cells to individual organisms, whereas abnormal LLPS is involved in the pathophysiology of human diseases. In turn, targeting these aggregates or their formation represents a promising approach in treating diseases driven by abnormal LLPS including those neurodegenerative diseases that lack effective therapies.
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Affiliation(s)
- Fangfang Wang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA.
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33
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Zheng LW, Liu CC, Yu KD. Phase separations in oncogenesis, tumor progressions and metastasis: a glance from hallmarks of cancer. J Hematol Oncol 2023; 16:123. [PMID: 38110976 PMCID: PMC10726551 DOI: 10.1186/s13045-023-01522-5] [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: 11/07/2023] [Accepted: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a novel principle for interpreting precise spatiotemporal coordination in living cells through biomolecular condensate (BMC) formation via dynamic aggregation. LLPS changes individual molecules into membrane-free, droplet-like BMCs with specific functions, which coordinate various cellular activities. The formation and regulation of LLPS are closely associated with oncogenesis, tumor progressions and metastasis, the specific roles and mechanisms of LLPS in tumors still need to be further investigated at present. In this review, we comprehensively summarize the conditions of LLPS and identify mechanisms involved in abnormal LLPS in cancer processes, including tumor growth, metastasis, and angiogenesis from the perspective of cancer hallmarks. We have also reviewed the clinical applications of LLPS in oncologic areas. This systematic summary of dysregulated LLPS from the different dimensions of cancer hallmarks will build a bridge for determining its specific functions to further guide basic research, finding strategies to intervene in LLPS, and developing relevant therapeutic approaches.
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Affiliation(s)
- Le-Wei Zheng
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cui-Cui Liu
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Department of Oncology, Key Laboratory of Breast Cancer in Shanghai, Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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34
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Mann R, Notani D. Transcription factor condensates and signaling driven transcription. Nucleus 2023; 14:2205758. [PMID: 37129580 PMCID: PMC10155639 DOI: 10.1080/19491034.2023.2205758] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 05/03/2023] Open
Abstract
Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment of the nucleus. However, the current understanding of how TF-condensates can achieve these feet so quickly and efficiently is still unclear. In this review, we draw parallels with other protein condensates and share our speculations on how the nucleus uses these TF-condensates to achieve high transcriptional specificity and fidelity. We discuss the various constituents of TF-condensates, their properties, and the known and unknown functions of TF-condensates with a particular focus on steroid signaling-induced transcriptional programs.
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Affiliation(s)
- Rajat Mann
- National Centre for Biological Sciences, TIFR, Bangalore, India
| | - Dimple Notani
- National Centre for Biological Sciences, TIFR, Bangalore, India
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35
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Mamontova EM, Clément MJ, Sukhanova MV, Joshi V, Bouhss A, Rengifo-Gonzalez JC, Desforges B, Hamon L, Lavrik OI, Pastré D. FUS RRM regulates poly(ADP-ribose) levels after transcriptional arrest and PARP-1 activation on DNA damage. Cell Rep 2023; 42:113199. [PMID: 37804508 DOI: 10.1016/j.celrep.2023.113199] [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: 03/06/2023] [Revised: 07/08/2023] [Accepted: 09/15/2023] [Indexed: 10/09/2023] Open
Abstract
PARP-1 activation at DNA damage sites leads to the synthesis of long poly(ADP-ribose) (PAR) chains, which serve as a signal for DNA repair. Here we show that FUS, an RNA-binding protein, is specifically directed to PAR through its RNA recognition motif (RRM) to increase PAR synthesis by PARP-1 in HeLa cells after genotoxic stress. Using a structural approach, we also identify specific residues located in the FUS RRM, which can be PARylated by PARP-1 to control the level of PAR synthesis. Based on the results of this work, we propose a model in which, following a transcriptional arrest that releases FUS from nascent mRNA, FUS can be recruited by PARP-1 activated by DNA damage to stimulate PAR synthesis. We anticipate that this model offers new perspectives to understand the role of FET proteins in cancers and in certain neurodegenerative diseases such as amyotrophic lateral sclerosis.
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Affiliation(s)
- Evgeniya M Mamontova
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France; Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Marie-Jeanne Clément
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Maria V Sukhanova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia
| | - Vandana Joshi
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ahmed Bouhss
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | | | - Bénédicte Desforges
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Av. 8, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogov Street, Novosibirsk 630090, Russia.
| | - David Pastré
- SABNP, University Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France.
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36
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Mier P, Andrade-Navarro MA. The nucleotide landscape of polyXY regions. Comput Struct Biotechnol J 2023; 21:5408-5412. [PMID: 38022702 PMCID: PMC10652141 DOI: 10.1016/j.csbj.2023.10.054] [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: 10/02/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/01/2023] Open
Abstract
PolyXY regions are compositionally biased regions composed of two different amino acids. They are classified according to the arrangement of the two amino acid types 'X' and 'Y' into direpeats (composed of alternating amino acids, e.g. 'XYXYXY'), joined (composed of two consecutive stretches of each amino acid, e.g. 'XXXYYY') and shuffled (other arrangements, e.g., 'XYXXYY'). They have been characterized at the amino acid level in all domains of life, and are described as often found within intrinsically disordered regions. Since DNA replication slippage has been proposed as a driver of repeat variation, and given that some polyXY have a repetitive nature, we hypothesized that characterizing the nucleotide coding of various types of polyXY could give hints about their origin and evolution. To test this, we obtained all polyXY regions in the human transcriptome, categorized them, and studied their coding nucleotide sequences. We observed that polyXY exacerbates the codon biases, and that the similarity between the X and Y codons is higher than in the background proteome. Our results support a general mechanism of emergence and evolution of polyXY from single-codon polyX. PolyXY are revealed as hotspots for replication slippage, particularly those composed of repeats: joined and direpeat polyXY. Inter-conversion to shuffled polyXY disrupts nucleotide repeats and restricts further evolution by replication slippage, a mechanism that we previously observed in polyX. Our results shed light on polyXY composition and should simplify the determination of their functions.
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Affiliation(s)
- Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
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37
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Lewis BA, Das SK, Jha RK, Levens D. Self-assembly of promoter DNA and RNA Pol II machinery into transcriptionally active biomolecular condensates. SCIENCE ADVANCES 2023; 9:eadi4565. [PMID: 37851801 PMCID: PMC10584347 DOI: 10.1126/sciadv.adi4565] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/13/2023] [Indexed: 10/20/2023]
Abstract
Transcription in the nucleus occurs in a concentrated, dense environment, and no reasonable biochemical facsimile of this milieu exists. Such a biochemical environment would be important for further understanding transcriptional regulation. We describe here the formation of dense, transcriptionally active bodies in vitro with only nuclear extracts and promoter DNA. These biomolecular condensates (BMCs) are 0.5 to 1 μm in diameter, have a macromolecular density of approximately 100 mg/ml, and are a consequence of a phase transition between promoter DNA and nuclear extract proteins. BMCs are physically associated with transcription as any disruption of one compromised the other. The BMCs contain RNA polymerase II and elongation factors, as well as factors necessary for BMC formation in vivo. We suggest that BMCs are representative of the in vivo nuclear environment and a more physiologically relevant manifestation of the preinitiation complex/elongation machinery.
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Affiliation(s)
- Brian A. Lewis
- Gene Regulation Section, LP/CCR/NCI/NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Subhendu Kumar Das
- Gene Regulation Section, LP/CCR/NCI/NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Rajiv Kumar Jha
- Gene Regulation Section, LP/CCR/NCI/NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - David Levens
- Gene Regulation Section, LP/CCR/NCI/NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
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38
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Ratovitski T, Kamath SV, O'Meally RN, Gosala K, Holland CD, Jiang M, Cole RN, Ross CA. Arginine methylation of RNA-binding proteins is impaired in Huntington's disease. Hum Mol Genet 2023; 32:3006-3025. [PMID: 37535888 PMCID: PMC10549789 DOI: 10.1093/hmg/ddad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion in the HD gene, coding for huntingtin protein (HTT). Mechanisms of HD cellular pathogenesis remain undefined and likely involve disruptions in many cellular processes and functions presumably mediated by abnormal protein interactions of mutant HTT. We previously found HTT interaction with several protein arginine methyl-transferase (PRMT) enzymes. Protein arginine methylation mediated by PRMT enzymes is an important post-translational modification with an emerging role in neurodegeneration. We found that normal (but not mutant) HTT can facilitate the activity of PRMTs in vitro and the formation of arginine methylation complexes. These interactions appear to be disrupted in HD neurons. This suggests an additional functional role for HTT/PRMT interactions, not limited to substrate/enzyme relationship, which may result in global changes in arginine protein methylation in HD. Our quantitative analysis of striatal precursor neuron proteome indicated that arginine protein methylation is significantly altered in HD. We identified a cluster highly enriched in RNA-binding proteins with reduced arginine methylation, which is essential to their function in RNA processing and splicing. We found that several of these proteins interact with HTT, and their RNA-binding and localization are affected in HD cells likely due to a compromised arginine methylation and/or abnormal interactions with mutant HTT. These studies reveal a potential new mechanism for disruption of RNA processing in HD, involving a direct interaction of HTT with methyl-transferase enzymes and modulation of their activity and highlighting methylation of arginine as potential new therapeutic target for HD.
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Affiliation(s)
- Tamara Ratovitski
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Siddhi V Kamath
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Robert N O'Meally
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Keerthana Gosala
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Chloe D Holland
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Mali Jiang
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Robert N Cole
- Department of Biological Chemistry, Mass Spectrometry and Proteomics Facility, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Christopher A Ross
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Johns Hopkins University, Baltimore, MD 21287, USA
- Departments of Neurology, Neuroscience and Pharmacology, Johns Hopkins University, Baltimore, MD 21287, USA
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39
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Triandafillou CG, Pan RW, Dinner AR, Drummond DA. Pervasive, conserved secondary structure in highly charged protein regions. PLoS Comput Biol 2023; 19:e1011565. [PMID: 37844070 PMCID: PMC10602382 DOI: 10.1371/journal.pcbi.1011565] [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: 03/01/2023] [Revised: 10/26/2023] [Accepted: 10/02/2023] [Indexed: 10/18/2023] Open
Abstract
Understanding how protein sequences confer function remains a defining challenge in molecular biology. Two approaches have yielded enormous insight yet are often pursued separately: structure-based, where sequence-encoded structures mediate function, and disorder-based, where sequences dictate physicochemical and dynamical properties which determine function in the absence of stable structure. Here we study highly charged protein regions (>40% charged residues), which are routinely presumed to be disordered. Using recent advances in structure prediction and experimental structures, we show that roughly 40% of these regions form well-structured helices. Features often used to predict disorder-high charge density, low hydrophobicity, low sequence complexity, and evolutionarily varying length-are also compatible with solvated, variable-length helices. We show that a simple composition classifier predicts the existence of structure far better than well-established heuristics based on charge and hydropathy. We show that helical structure is more prevalent than previously appreciated in highly charged regions of diverse proteomes and characterize the conservation of highly charged regions. Our results underscore the importance of integrating, rather than choosing between, structure- and disorder-based approaches.
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Affiliation(s)
- Catherine G. Triandafillou
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rosalind Wenshan Pan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Aaron R. Dinner
- Department of Chemistry, University of Chicago, Chicago, Illinois, United States of America
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, Illinois, United States of America
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40
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Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Gu Y, Deep A, Naritomi JT, Liang Q, Aigner S, Adler BA, Cress BF, Doudna JA, Chaikeeratisak V, Cleveland DW, Ghassemian M, Yeo GW, Pogliano J, Corbett KD. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559000. [PMID: 37790334 PMCID: PMC10542519 DOI: 10.1101/2023.09.22.559000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Large-genome bacteriophages (jumbo phages) of the Chimalliviridae family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d halts infections at an early stage. Taken together, our data suggest that the conserved ChmC protein acts as a chaperone for phage mRNAs, potentially stabilizing these mRNAs and driving their translocation through the nuclear shell to promote translation and infection progression.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Emily G. Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Jina Lee
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Sitao Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jack T. Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qishan Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Benjamin A. Adler
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Brady F. Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A. Doudna
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Don W. Cleveland
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Kevin D. Corbett
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
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Kletzien OA, Wuttke DS, Batey RT. The RNA-binding domain of hnRNP U extends beyond the RGG/RG motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558674. [PMID: 37786719 PMCID: PMC10541603 DOI: 10.1101/2023.09.20.558674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG element within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV crosslinking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing eleven of these identified crosslink sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG element is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG element with RNA-binding properties comparable to the canonical RGG/RG element. These RGG/RG elements serve redundant functions, with neither serving as the primary RBD. While in isolation each RGG/RG element has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling binding of most of the designed RNA set with low to mid-nanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlights the perils of a reductionist approach to defining biochemical activities in this system and paves the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A. Kletzien
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T. Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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Cheng Y, Miwa T, Taguchi H. The mRNA binding-mediated self-regulatory function of small heat shock protein IbpA in γ-proteobacteria is conferred by a conserved arginine. J Biol Chem 2023; 299:105108. [PMID: 37517700 PMCID: PMC10474464 DOI: 10.1016/j.jbc.2023.105108] [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: 04/26/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
Bacterial small heat shock proteins, such as inclusion body-associated protein A (IbpA) and IbpB, coaggregate with denatured proteins and recruit other chaperones for the processing of aggregates thereby assisting in protein refolding. In addition, as a recently revealed uncommon feature, Escherichia coli IbpA self-represses its own translation through interaction with the 5'-untranslated region of the ibpA mRNA, enabling IbpA to act as a mediator of negative feedback regulation. Although IbpA also suppresses the expression of IbpB, IbpB does not have this self-repression activity despite the two Ibps being highly homologous. In this study, we demonstrate that the self-repression function of IbpA is conserved in other γ-proteobacterial IbpAs. Moreover, we show a cationic residue-rich region in the α-crystallin domain of IbpA, which is not conserved in IbpB, is critical for the self-suppression activity. Notably, we found arginine 93 (R93) located within the α-crystallin domain is an essential residue that cannot be replaced by any of the other 19 amino acids including lysine. We observed that IbpA-R93 mutants completely lost the interaction with the 5' untranslated region of the ibpA mRNA, but retained almost all chaperone activity and were able to sequester denatured proteins. Taken together, we propose the conserved Arg93-mediated translational control of IbpA through RNA binding would be beneficial for a rapid and massive supply of the chaperone on demand.
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Affiliation(s)
- Yajie Cheng
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tsukumi Miwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hideki Taguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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Blazquez S, Sanchez‐Burgos I, Ramirez J, Higginbotham T, Conde MM, Collepardo‐Guevara R, Tejedor AR, Espinosa JR. Location and Concentration of Aromatic-Rich Segments Dictates the Percolating Inter-Molecular Network and Viscoelastic Properties of Ageing Condensates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207742. [PMID: 37386790 PMCID: PMC10477902 DOI: 10.1002/advs.202207742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/03/2023] [Indexed: 07/01/2023]
Abstract
Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-binding proteins can promote aggregation by forming inter-protein β-sheet fibrils that accumulate over time and ultimately drive the liquid-to-solid transition of the condensates. Here, atomistic molecular dynamics simulations are combined with sequence-dependent coarse-grained models of various resolutions to investigate the role of LARKS abundance and position within the amino acid sequence in the maturation of condensates. Remarkably, proteins with tail-located LARKS display much higher viscosity over time than those in which the LARKS are placed toward the center. Yet, at very long timescales, proteins with a single LARKS-independently of its location-can still relax and form high viscous liquid condensates. However, phase-separated condensates of proteins containing two or more LARKS become kinetically trapped due to the formation of percolated β-sheet networks that display gel-like behavior. Furthermore, as a work case example, they demonstrate how shifting the location of the LARKS-containing low-complexity domain of FUS protein toward its center effectively precludes the accumulation of β-sheet fibrils in FUS-RNA condensates, maintaining functional liquid-like behavior without ageing.
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Affiliation(s)
- Samuel Blazquez
- Department of Physical‐ChemistryUniversidad Complutense de MadridAv. Complutense s/nMadrid28040Spain
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Ignacio Sanchez‐Burgos
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Jorge Ramirez
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Tim Higginbotham
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
| | - Maria M. Conde
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Rosana Collepardo‐Guevara
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of GeneticsUniversity of CambridgeCambridgeCB2 3EH, UK
| | - Andres R. Tejedor
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
- Department of Chemical EngineeringUniversidad Politécnica de MadridJosé Gutiérrez Abascal 2Madrid28006Spain
| | - Jorge R. Espinosa
- Department of Physical‐ChemistryUniversidad Complutense de MadridAv. Complutense s/nMadrid28040Spain
- Maxwell Centre, Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AvenueCambridgeCB3 0HEUK
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Xu D, Chen X, Kuang Y, Hong M, Xu T, Wang K, Huang X, Fu C, Ruan K, Zhu C, Feng X, Guang S. rRNA intermediates coordinate the formation of nucleolar vacuoles in C. elegans. Cell Rep 2023; 42:112915. [PMID: 37537842 DOI: 10.1016/j.celrep.2023.112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Abstract
The nucleolus is the most prominent membraneless organelle within the nucleus. How the nucleolar structure is regulated is poorly understood. Here, we identified two types of nucleoli in C. elegans. Type I nucleoli are spherical and do not have visible nucleolar vacuoles (NoVs), and rRNA transcription and processing factors are evenly distributed throughout the nucleolus. Type II nucleoli contain vacuoles, and rRNA transcription and processing factors exclusively accumulate in the periphery rim. The NoV contains nucleoplasmic proteins and is capable of exchanging contents with the nucleoplasm. The high-order structure of the nucleolus is dynamically regulated in C. elegans. Faithful rRNA processing is important to prohibit NoVs. The depletion of 27SA2 rRNA processing factors resulted in NoV formation. The inhibition of RNA polymerase I (RNAPI) transcription and depletion of two conserved nucleolar factors, nucleolin and fibrillarin, prohibits the formation of NoVs. This finding provides a mechanism to coordinate structure maintenance and gene expression.
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Affiliation(s)
- Demin Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yan Kuang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Minjie Hong
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ting Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ke Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xinya Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chuanhai Fu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ke Ruan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Xuezhu Feng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, The USTC RNA Institute, Ministry of Education Key Laboratory for Membraneless Organelles & Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, Anhui 230027, China.
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Enders L, Siklos M, Borggräfe J, Gaussmann S, Koren A, Malik M, Tomek T, Schuster M, Reiniš J, Hahn E, Rukavina A, Reicher A, Casteels T, Bock C, Winter GE, Hannich JT, Sattler M, Kubicek S. Pharmacological perturbation of the phase-separating protein SMNDC1. Nat Commun 2023; 14:4504. [PMID: 37587144 PMCID: PMC10432564 DOI: 10.1038/s41467-023-40124-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
SMNDC1 is a Tudor domain protein that recognizes di-methylated arginines and controls gene expression as an essential splicing factor. Here, we study the specific contributions of the SMNDC1 Tudor domain to protein-protein interactions, subcellular localization, and molecular function. To perturb the protein function in cells, we develop small molecule inhibitors targeting the dimethylarginine binding pocket of the SMNDC1 Tudor domain. We find that SMNDC1 localizes to phase-separated membraneless organelles that partially overlap with nuclear speckles. This condensation behavior is driven by the unstructured C-terminal region of SMNDC1, depends on RNA interaction and can be recapitulated in vitro. Inhibitors of the protein's Tudor domain drastically alter protein-protein interactions and subcellular localization, causing splicing changes for SMNDC1-dependent genes. These compounds will enable further pharmacological studies on the role of SMNDC1 in the regulation of nuclear condensates, gene regulation and cell identity.
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Affiliation(s)
- Lennart Enders
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jan Borggräfe
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Gaussmann
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Monika Malik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Andreas Reicher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Tamara Casteels
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Sloan Kettering Institute, 1275 York Avenue, New York, NY, 10065, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Währinger Straße 25a, 1090, Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria
| | - Michael Sattler
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg, 85764, München, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, 85748, München, Germany
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, 1090, Vienna, Austria.
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Miyaji M, Kawano S, Furuta R, Murakami E, Ikeda S, Tsutsui KM, Tsutsui K. Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA. PLoS One 2023; 18:e0289599. [PMID: 37540655 PMCID: PMC10403129 DOI: 10.1371/journal.pone.0289599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/20/2023] [Indexed: 08/06/2023] Open
Abstract
A human protein heterogeneous ribonucleoprotein U (hnRNP U) also known as Scaffold attachment factor A (SAF-A) and its orthologous rat protein SP120 are abundant and multifunctional nuclear protein that directly binds to both DNA and RNA. The C-terminal region of hnRNP U enriched with arginine and glycine is essential for the interaction with RNA and the N-terminal region of SAF-A termed SAP domain has been ascribed to the DNA binding. We have reported that rat hnRNP U specifically and cooperatively binds to AT-rich DNA called nuclear scaffold/matrix-associated region (S/MAR) although its detailed mechanism remained unclear. In the present study analysis of hnRNP U deletion mutants revealed for the first time that a C-terminal domain enriched with Arg-Gly (defined here as 'RG domain') is predominantly important for the S/MAR-selective DNA binding activities. RG domain alone directly bound to S/MAR and coexistence with the SAP domain exerted a synergistic effect. The binding was inhibited by netropsin, a minor groove binder with preference to AT pairs that are enriched in S/MAR, suggesting that RG domain interacts with minor groove of S/MAR DNA. Interestingly, excess amounts of RNA attenuated the RG domain-dependent S/MAR-binding of hnRNP U. Taken together, hnRNP U may be the key element for the RNA-regulated recognition of S/MAR DNA and thus contributing to the dynamic structural changes of chromatin compartments.
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Affiliation(s)
- Mary Miyaji
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Shinji Kawano
- Faculty of Science, Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | - Ryohei Furuta
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Emi Murakami
- Faculty of Science, Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | - Shogo Ikeda
- Faculty of Science, Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | - Kimiko M Tsutsui
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Ken Tsutsui
- Department of Neurogenomics, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Campagnaro GD, Lorenzon LB, Rodrigues MA, Defina TPA, Pinzan CF, Ferreira TR, Cruz AK. Overexpression of Leishmania major protein arginine methyltransferase 6 reduces parasite infectivity in vivo. Acta Trop 2023; 244:106959. [PMID: 37257676 DOI: 10.1016/j.actatropica.2023.106959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/02/2023]
Abstract
Arginine methylation is catalysed by Protein Arginine Methyltransferases (PRMTs) and can affect how a target protein functions and how it interacts with other macromolecules, which in turn impacts on cell metabolism and gene expression control. Leishmania parasites express five different PRMTs, and although the presence of each individual PRMT is not essential per se, the imbalanced activity of these PRMTs can impact the virulence of Leishmania parasites in vitro and in vivo. Here we created a Leishmania major cell line overexpressing PRMT6 and show that similar to what was observed for the T. brucei homologous enzyme, L. major PRMT6 probably has a narrow substrate range. However, its overexpression notably impairs the infection in mice, with a mild reduction in the number of viable parasites in the lymph nodes. Our results indicate that arginine methylation by LmjPRMT6 plays a significant role in the adaptation of the parasite to the environment found in the mammalian host.
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Affiliation(s)
- Gustavo Daniel Campagnaro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas Bigolin Lorenzon
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mateus Augusto Rodrigues
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tânia Paula Aquino Defina
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Camila Figueiredo Pinzan
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tiago Rodrigues Ferreira
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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Li Q, Kang C. Targeting RNA-binding proteins with small molecules: Perspectives, pitfalls and bifunctional molecules. FEBS Lett 2023; 597:2031-2047. [PMID: 37519019 DOI: 10.1002/1873-3468.14710] [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: 03/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
RNA-binding proteins (RBPs) play vital roles in organisms through binding with RNAs to regulate their functions. Small molecules affecting the function of RBPs have been developed, providing new avenues for drug discovery. Herein, we describe the perspectives on developing small molecule regulators of RBPs. The following types of small molecule modulators are of great interest in drug discovery: small molecules binding to RBPs to affect interactions with RNA molecules, bifunctional molecules binding to RNA or RBP to influence their interactions, and other types of molecules that affect the stability of RNA or RBPs. Moreover, we emphasize that the bifunctional molecules may play important roles in small molecule development to overcome the challenges encountered in the process of drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
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Sanchez-Burgos I, Herriott L, Collepardo-Guevara R, Espinosa JR. Surfactants or scaffolds? RNAs of varying lengths control the thermodynamic stability of condensates differently. Biophys J 2023; 122:2973-2987. [PMID: 36883003 PMCID: PMC10398262 DOI: 10.1016/j.bpj.2023.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Biomolecular condensates, thought to form via liquid-liquid phase separation of intracellular mixtures, are multicomponent systems that can include diverse types of proteins and RNAs. RNA is a critical modulator of RNA-protein condensate stability, as it induces an RNA concentration-dependent reentrant phase transition-increasing stability at low RNA concentrations and decreasing it at high concentrations. Beyond concentration, RNAs inside condensates can be heterogeneous in length, sequence, and structure. Here, we use multiscale simulations to understand how different RNA parameters interact with one another to modulate the properties of RNA-protein condensates. To do so, we perform residue/nucleotide resolution coarse-grained molecular dynamics simulations of multicomponent RNA-protein condensates containing RNAs of different lengths and concentrations, and either FUS or PR25 proteins. Our simulations reveal that RNA length regulates the reentrant phase behavior of RNA-protein condensates: increasing RNA length sensitively rises the maximum value that the critical temperature of the mixture reaches, and the maximum concentration of RNA that the condensate can incorporate before beginning to become unstable. Strikingly, RNAs of different lengths are organized heterogeneously inside condensates, which allows them to enhance condensate stability via two distinct mechanisms: shorter RNA chains accumulate at the condensate's surface acting as natural biomolecular surfactants, while longer RNA chains concentrate inside the core to saturate their bonds and enhance the density of molecular connections in the condensate. Using a patchy particle model, we additionally demonstrate that the combined impact of RNA length and concentration on condensate properties is dictated by the valency, binding affinity, and polymer length of the various biomolecules involved. Our results postulate that diversity on RNA parameters within condensates allows RNAs to increase condensate stability by fulfilling two different criteria: maximizing enthalpic gain and minimizing interfacial free energy; hence, RNA diversity should be considered when assessing the impact of RNA on biomolecular condensates regulation.
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Affiliation(s)
- Ignacio Sanchez-Burgos
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Lara Herriott
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Jorge R Espinosa
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom; Departament of Chemical Physics, Faculty of Chemical Sciences, Universidad Complutense de Madrid, Madrid, Spain.
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Mier P, Andrade-Navarro MA. Evolutionary Study of Protein Short Tandem Repeats in Protein Families. Biomolecules 2023; 13:1116. [PMID: 37509152 PMCID: PMC10377733 DOI: 10.3390/biom13071116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Tandem repeats in proteins are patterns of residues repeated directly adjacent to each other. The evolution of these repeats can be assessed by using groups of homologous sequences, which can help pointing to events of unit duplication or deletion. High pressure in a protein family for variation of a given type of repeat might point to their function. Here, we propose the analysis of protein families to calculate protein short tandem repeats (pSTRs) in each protein sequence and assess their variability within the family in terms of number of units. To facilitate this analysis, we developed the pSTR tool, a method to analyze the evolution of protein short tandem repeats in a given protein family by pairwise comparisons between evolutionarily related protein sequences. We evaluated pSTR unit number variation in protein families of 12 complete metazoan proteomes. We hypothesize that families with more dynamic ensembles of repeats could reflect particular roles of these repeats in processes that require more adaptability.
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Affiliation(s)
- Pablo Mier
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany
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