1
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Zhou HX, Kota D, Qin S, Prasad R. Fundamental Aspects of Phase-Separated Biomolecular Condensates. Chem Rev 2024; 124:8550-8595. [PMID: 38885177 PMCID: PMC11260227 DOI: 10.1021/acs.chemrev.4c00138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Biomolecular condensates, formed through phase separation, are upending our understanding in much of molecular, cell, and developmental biology. There is an urgent need to elucidate the physicochemical foundations of the behaviors and properties of biomolecular condensates. Here we aim to fill this need by writing a comprehensive, critical, and accessible review on the fundamental aspects of phase-separated biomolecular condensates. We introduce the relevant theoretical background, present the theoretical basis for the computation and experimental measurement of condensate properties, and give mechanistic interpretations of condensate behaviors and properties in terms of interactions at the molecular and residue levels.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Divya Kota
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
| | - Ramesh Prasad
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, USA
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2
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Liu J, Shen T, Zhang Y, Wei X, Bao Y, Ai R, Gan S, Wang D, Lai X, Zhao L, Zhou W, Fang X. Cell dehydration enables massive production of engineered membrane vesicles with therapeutic functions. J Extracell Vesicles 2024; 13:e12483. [PMID: 39051765 PMCID: PMC11270585 DOI: 10.1002/jev2.12483] [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: 11/03/2023] [Revised: 05/12/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Extracellular vesicles (EVs) have emerged as promising biomaterials for the treatment of different disease. However, only handful types of EVs with clinical transformation potential have been reported to date, and their preparation on a large scale under biosafety-controlled conditions is limited. In this study, we characterize a novel type of EV with promising clinical application potential: dehydration-induced extracellular vesicles (DIMVs). DIMV is a type of micron-diameter cell vesicle that contains more bioactive molecules, such as proteins and RNA, but not DNA, than previously reported cell vesicles. The preparation of DIMV is extraordinarily straightforward, which possesses a high level of biosafety, and the protein utilization ratio is roughly 600 times greater than that of naturally secreted EVs. Additional experiments demonstrate the viability of pre- or post-isolation DIMV modification, including gene editing, nucleic acid encapsulation or surface anchoring, size adjustment. Finally, on animal models, we directly show the biosafety and immunogenicity of DIMV, and investigate its potential application as tumour vaccine or drug carrier in cancer treatment.
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Affiliation(s)
- Jie Liu
- School of Life SciencesFaculty of MedicineTianjin UniversityTianjinPR China
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Tingting Shen
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Yu Zhang
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Xiaojian Wei
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Yuting Bao
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Rui Ai
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
- School of Molecular MedicineHangzhou Institute for Advanced Study, UCASHangzhouPR China
| | - Shaoju Gan
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Dachi Wang
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Xin Lai
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Libo Zhao
- Department of R&DEcho Biotech Co., LtdBeijingPR China
| | - Wei Zhou
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
| | - Xiaohong Fang
- School of Life SciencesFaculty of MedicineTianjin UniversityTianjinPR China
- Hangzhou Institute of Medicine (HIM)University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Chinese Academy of SciencesHangzhouZhejiangPR China
- Beijing National Research Center for Molecular Sciences, Institute of Chemistry, Key Laboratory of Molecular Nanostructure and NanotechnologyChinese Academy of ScienceBeijingPR China
- School of Molecular MedicineHangzhou Institute for Advanced Study, UCASHangzhouPR China
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3
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Zhou Y, Zhang K, Moreno S, Temme A, Voit B, Appelhans D. Continuous Transformation from Membrane-Less Coacervates to Membranized Coacervates and Giant Vesicles: Toward Multicompartmental Protocells with Complex (Membrane) Architectures. Angew Chem Int Ed Engl 2024:e202407472. [PMID: 38847278 DOI: 10.1002/anie.202407472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Indexed: 07/25/2024]
Abstract
The membranization of membrane-less coacervates paves the way for the exploitation of complex protocells with regard to structural and cell-like functional behaviors. However, the controlled transformation from membranized coacervates to vesicles remains a challenge. This can provide stable (multi)phase and (multi)compartmental architectures through the reconfiguration of coacervate droplets in the presence of (bioactive) polymers, bio(macro)molecules and/or nanoobjects. Herein, we present a continuous protocell transformation from membrane-less coacervates to membranized coacervates and, ultimately, to giant hybrid vesicles. This transformation process is orchestrated by altering the balance of non-covalent interactions through varying concentrations of an anionic terpolymer, leading to dynamic processes such as spontaneous membranization of terpolymer nanoparticles at the coacervate surface, disassembly of the coacervate phase mediated by the excess anionic charge, and the redistribution of coacervate components in membrane. The diverse protocells during the transformation course provide distinct structural features and molecular permeability. Notably, the introduction of multiphase coacervates in this continuous transformation process signifies advancements toward the creation of synthetic cells with different diffusible compartments. Our findings emphasize the highly controlled continuous structural reorganization of coacervate protocells and represents a novel step toward the development of advanced and sophisticated synthetic protocells with more precise compositions and complex (membrane) structures.
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Affiliation(s)
- Yang Zhou
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Organic Chemistry of Polymers, TUD Dresden University of Technology, Dresden, 01062, Germany
| | - Kehu Zhang
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Organic Chemistry of Polymers, TUD Dresden University of Technology, Dresden, 01062, Germany
| | - Silvia Moreno
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
| | - Achim Temme
- Department of Neurosurgery, Section Experimental Neurosurgery/Tumor Immunology, University Hospital Carl Gustav Carus, TUD Dresden University of Technology, Dresden, 01307, Germany
- German Cancer Consortium (DKTK), partner site Dresden, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany, National Center for Tumor Diseases (NCT), Fetscherstraße 74, Dresden, 01307, Germany
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
- Organic Chemistry of Polymers, TUD Dresden University of Technology, Dresden, 01062, Germany
| | - Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, Dresden, 01069, Germany
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4
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JCA. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. Nucleic Acids Res 2024; 52:4702-4722. [PMID: 38572746 PMCID: PMC11077067 DOI: 10.1093/nar/gkae229] [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: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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5
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Tanabe K, Miyazaki K, Umeno H, Takemoto M, Nakano S. Basic protein- and peptide-induced stabilization of long-loop DNA G-guadruplexes. Biochimie 2024; 219:110-117. [PMID: 37972915 DOI: 10.1016/j.biochi.2023.11.005] [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: 07/31/2023] [Revised: 10/05/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The human genome contains many G-quadruplex-forming sequences, including sequences containing long single-stranded loops that are believed to be unfavorable for G-quadruplex formation. The intracellular environment of biological cells is crowded with proteins with charged surfaces. Understanding the effects of protein-rich environments is important for understanding the formation of G-quadruplexes in an intracellular environment. In this study, we investigated the structural stability of DNA G-quadruplexes in the presence of several types of globular proteins (lysozyme, cytochrome c, bovine serum albumin, myoglobin, histone proteins, and serum proteins), unstructured polypeptides (protamine and poly-l-lysine), and oligopeptides (RGG/RG-domain peptides and short repeated peptides). Thermal melting studies of G-quadruplex-forming oligonucleotides derived from the human telomeric repeat sequence revealed that environments containing high concentrations of proteins and peptides differently affected the G-quadruplex stability according to their loop lengths. We found that weak electrostatic interactions of G-quadruplex loops with basic proteins and peptides improved the stability of long-loop G-quadruplexes and the interactions were strengthened under crowded conditions simulated by dextran. The comparison of the effects of different types of proteins and peptides indicated that excluded volume interactions and structural flexibility of both DNA and polypeptide chains influenced the efficiency of their interactions. This study provides insights into long-loop G-quadruplex stability in a crowded intracellular environment and the recognition of G-quadruplexes by arginine-rich domains of G-quadruplex-binding proteins.
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Affiliation(s)
- Kazuya Tanabe
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Kouichi Miyazaki
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hikari Umeno
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Marina Takemoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - S Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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6
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Sahoo BR, Kocman V, Clark N, Myers N, Deng X, Wong EL, Yang HJ, Kotar A, Guzman BB, Dominguez D, Plavec J, Bardwell JC. Protein G-quadruplex interactions and their effects on phase transitions and protein aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558871. [PMID: 37790366 PMCID: PMC10542165 DOI: 10.1101/2023.09.21.558871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706's ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.
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Affiliation(s)
- Bikash R. Sahoo
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Vojč Kocman
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Nathan Clark
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Nikhil Myers
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Xiexiong Deng
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ee L. Wong
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Harry J. Yang
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anita Kotar
- National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | - Janez Plavec
- National Institute of Chemistry, Ljubljana, Slovenia
| | - James C.A. Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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7
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Wang W, Li D, Xu Q, Cheng J, Yu Z, Li G, Qiao S, Pan J, Wang H, Shi J, Zheng T, Sui G. G-quadruplexes promote the motility in MAZ phase-separated condensates to activate CCND1 expression and contribute to hepatocarcinogenesis. Nat Commun 2024; 15:1045. [PMID: 38316778 PMCID: PMC10844655 DOI: 10.1038/s41467-024-45353-5] [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: 05/03/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
G-quadruplexes (G4s) can recruit transcription factors to activate gene expression, but detailed mechanisms remain enigmatic. Here, we demonstrate that G4s in the CCND1 promoter propel the motility in MAZ phase-separated condensates and subsequently activate CCND1 transcription. Zinc finger (ZF) 2 of MAZ is a responsible for G4 binding, while ZF3-5, but not a highly disordered region, is critical for MAZ condensation. MAZ nuclear puncta overlaps with signals of G4s and various coactivators including BRD4, MED1, CDK9 and active RNA polymerase II, as well as gene activation histone markers. MAZ mutants lacking either G4 binding or phase separation ability did not form nuclear puncta, and showed deficiencies in promoting hepatocellular carcinoma cell proliferation and xenograft tumor formation. Overall, we unveiled that G4s recruit MAZ to the CCND1 promoter and facilitate the motility in MAZ condensates that compartmentalize coactivators to activate CCND1 expression and subsequently exacerbate hepatocarcinogenesis.
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Affiliation(s)
- Wenmeng Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Dangdang Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
| | - Qingqing Xu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiahui Cheng
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhiwei Yu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Guangyue Li
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shiyao Qiao
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jiasong Pan
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Hao Wang
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Jinming Shi
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tongsen Zheng
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, China
- Key Laboratory of Molecular Oncology of Heilongjiang Province, Harbin, China
| | - Guangchao Sui
- College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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8
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Gemmill DL, Nelson CR, Badmalia MD, Pereira HS, Kerr L, Wolfinger MT, Patel TR. The 3' terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17. Biochem Cell Biol 2024; 102:96-105. [PMID: 37774422 DOI: 10.1139/bcb-2023-0036] [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: 10/01/2023] Open
Abstract
Zika virus (ZIKV) infection remains a worldwide concern, and currently no effective treatments or vaccines are available. Novel therapeutics are an avenue of interest that could probe viral RNA-human protein communication to stop viral replication. One specific RNA structure, G-quadruplexes (G4s), possess various roles in viruses and all domains of life, including transcription and translation regulation and genome stability, and serves as nucleation points for RNA liquid-liquid phase separation. Previous G4 studies on ZIKV using a quadruplex forming G-rich sequences Mapper located a potential G-quadruplex sequence in the 3' terminal region (TR) and was validated structurally using a 25-mer oligo. It is currently unknown if this structure is conserved and maintained in a large ZIKV RNA transcript and its specific roles in viral replication. Using bioinformatic analysis and biochemical assays, we demonstrate that the ZIKV 3' TR G4 is conserved across all ZIKV isolates and maintains its structure in a 3' TR full-length transcript. We further established the G4 formation using pyridostatin and the BG4 G4-recognizing antibody binding assays. Our study also demonstrates that the human DEAD-box helicases, DDX3X132-607 and DDX17135-555, bind to the 3' TR and that DDX17135-555 unfolds the G4 present in the 3' TR. These findings provide a path forward in potential therapeutic targeting of DDX3X or DDX17's binding to the 3' TR G4 region for novel treatments against ZIKV.
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Affiliation(s)
- Dannielle L Gemmill
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Corey R Nelson
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Maulik D Badmalia
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Higor S Pereira
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Liam Kerr
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Michael T Wolfinger
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währinger Strasse 29, 1090, Vienna, Austria
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
- RNA Forecast e.U., 1140 Vienna, Austria
| | - Trushar R Patel
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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9
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Wang Y, Cao K, Zong M, Yuan S, Zhang N, Liu Y. Mutual promotion of co-condensation of KRAS G-quadruplex and a well-folded protein HMGB1. Nucleic Acids Res 2024; 52:288-299. [PMID: 37897365 PMCID: PMC10783520 DOI: 10.1093/nar/gkad938] [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: 06/01/2023] [Revised: 09/09/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) of G-quadruplex (GQ) is involved in many crucial cellular processes, while the quadruplex-folding and their functions are typically modulated by specific DNA-binding proteins. However, the regulatory mechanism of binding proteins, particularly the well-folded proteins, on the LLPS of GQs is largely unknown. Here, we investigated the effect of HMGB1 on the condensation of a G-quadruplex of KRAS promoter (GQKRAS). The results show that these two rigid macro-biomolecules undergo co-condensation through a mutual promotion manner, while neither of them can form LLPS alone. Fluidity measurements confirm that the liquid-like droplets are highly dynamic. HMGB1 facilitates and stabilizes the quadruplex folding of GQKRAS, and this process enhances their co-condensation. The KRAS promoter DNA retains quadruplex folding in the droplets; interference with the GQ-folding disrupts the co-condensation of GQKRAS/HMGB1. Mechanistic studies reveal that electrostatic interaction is a key driving force of the interaction and co-condensation of GQKRAS/HMGB1; meanwhile, the recognition of two macro-biomolecules plays a crucial role in this process. This result indicates that the phase separation of GQs can be modulated by DNA binding proteins, and this process could also be an efficient way to recruit specific DNA binding proteins.
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Affiliation(s)
- Yu Wang
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Kaiming Cao
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Mingxi Zong
- School of Medicine, Xiamen University, Xiamen, Fujian 361102, China
| | - Siming Yuan
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Na Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230031, China
| | - Yangzhong Liu
- Department of Pharmacy, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine; Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230001, China
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10
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Aznauryan M, Birkedal V. Dynamics of G-Quadruplex Formation under Molecular Crowding. J Phys Chem Lett 2023; 14:10354-10360. [PMID: 37948600 DOI: 10.1021/acs.jpclett.3c02453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
G-quadruplex (G4) structures assemble from guanine-rich DNA sequences and are believed to regulate several key cellular processes. G4 formation and conformational interconversions are well-established to occur dynamically in vitro. However, a clear understanding of G4 formation dynamics in cells as well as under conditions mimicking the cellular environment is missing. To fill this gap, we have investigated the G4 dynamics in molecularly crowded solutions, thus replicating the effect of the excluded volume present in cells. The results show that the volume exclusion exerted by large crowding agents accelerates the rate of G4 formation by at least an order of magnitude, leading to significant G4 stabilization. Extrapolation from our experimental data predicts crowding-induced G4 stabilization by more than 3 kcal/mol, under crowding levels found in the cellular environment. Such effects are likely to be important for G4-driven regulatory functions.
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Affiliation(s)
- Mikayel Aznauryan
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
- Univ. Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, Institut Européen de Chimie et Biologie, 33607 Pessac, France
| | - Victoria Birkedal
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus C, Denmark
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11
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Guzman BB, Son A, Litberg TJ, Huang Z, Dominguez D, Horowitz S. Emerging roles for G-quadruplexes in proteostasis. FEBS J 2023; 290:4614-4625. [PMID: 36017725 PMCID: PMC10071977 DOI: 10.1111/febs.16608] [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: 04/05/2022] [Revised: 07/22/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
How nucleic acids interact with proteins, and how they affect protein folding, aggregation, and misfolding is a still-evolving area of research. Considerable effort is now focusing on a particular structure of RNA and DNA, G-quadruplexes, and their role in protein homeostasis and disease. In this state-of-the-art review, we track recent reports on how G-quadruplexes influence protein aggregation, proteolysis, phase separation, and protein misfolding diseases, and pose currently unanswered questions in the advance of this scientific field.
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Affiliation(s)
- Bryan B Guzman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Theodore J Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Zijue Huang
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
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12
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Gao Z, Yuan J, He X, Wang H, Wang Y. Phase Separation Modulates the Formation and Stabilities of DNA Guanine Quadruplex. JACS AU 2023; 3:1650-1657. [PMID: 37388701 PMCID: PMC10301798 DOI: 10.1021/jacsau.3c00106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 07/01/2023]
Abstract
In the presence of monovalent alkali metal ions, G-rich DNA sequences containing four runs of contiguous guanines can fold into G-quadruplex (G4) structures. Recent studies showed that these structures are located in critical regions of the human genome and assume important functions in many essential DNA metabolic processes, including replication, transcription, and repair. However, not all potential G4-forming sequences are actually folded into G4 structures in cells, where G4 structures are known to be dynamic and modulated by G4-binding proteins as well as helicases. It remains unclear whether there are other factors influencing the formation and stability of G4 structures in cells. Herein, we showed that DNA G4s can undergo phase separation in vitro. In addition, immunofluorescence microscopy and ChIP-seq experiments with the use of BG4, a G4 structure-specific antibody, revealed that disruption of phase separation could result in global destabilization of G4 structures in cells. Together, our work revealed phase separation as a new determinant in modulating the formation and stability of G4 structures in human cells.
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Affiliation(s)
- Zi Gao
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Jun Yuan
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California, 92521-0403, United States
| | - Xiaomei He
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Handing Wang
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Yinsheng Wang
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California, 92521-0403, United States
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13
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Pavlova I, Iudin M, Surdina A, Severov V, Varizhuk A. G-Quadruplexes in Nuclear Biomolecular Condensates. Genes (Basel) 2023; 14:genes14051076. [PMID: 37239436 DOI: 10.3390/genes14051076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
G-quadruplexes (G4s) have long been implicated in the regulation of chromatin packaging and gene expression. These processes require or are accelerated by the separation of related proteins into liquid condensates on DNA/RNA matrices. While cytoplasmic G4s are acknowledged scaffolds of potentially pathogenic condensates, the possible contribution of G4s to phase transitions in the nucleus has only recently come to light. In this review, we summarize the growing evidence for the G4-dependent assembly of biomolecular condensates at telomeres and transcription initiation sites, as well as nucleoli, speckles, and paraspeckles. The limitations of the underlying assays and the remaining open questions are outlined. We also discuss the molecular basis for the apparent permissive role of G4s in the in vitro condensate assembly based on the interactome data. To highlight the prospects and risks of G4-targeting therapies with respect to the phase transitions, we also touch upon the reported effects of G4-stabilizing small molecules on nuclear biomolecular condensates.
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Affiliation(s)
- Iuliia Pavlova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Mikhail Iudin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Anastasiya Surdina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Vjacheslav Severov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
| | - Anna Varizhuk
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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14
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Liu W, Lupfer C, Samanta A, Sarkar A, Walther A. Switchable Hydrophobic Pockets in DNA Protocells Enhance Chemical Conversion. J Am Chem Soc 2023; 145:7090-7094. [PMID: 36971596 DOI: 10.1021/jacs.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Synthetic cell models help us understand living cells and the origin of life. Key aspects of living cells are crowded interiors where secondary structures, such as the cytoskeleton and membraneless organelles/condensates, can form. These can form dynamically and serve structural or functional purposes, such as protection from heat shock or as crucibles for various biochemical reactions. Inspired by these phenomena, we introduce a crowded all-DNA protocell and encapsulate a temperature-switchable DNA-b-polymer block copolymer, in which the synthetic polymer phase-segregates at elevated temperatures. We find that thermoreversible phase segregation of the synthetic polymer occurs via bicontinuous phase separation, resulting in artificial organelle structures that can reorient into larger domains depending on the viscoelastic properties of the protocell interior. Fluorescent sensors confirm the formation of hydrophobic compartments, which enhance the reactivity of bimolecular reactions. This study leverages the strengths of biological and synthetic polymers to construct advanced biohybrid artificial cells that provide insights into phase segregation under crowded conditions and the formation of organelles and microreactors in response to environmental stress.
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15
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Li H, Yan Y, Chen J, Shi K, Song C, Ji Y, Jia L, Li J, Qiao Y, Lin Y. Artificial receptor-mediated phototransduction toward protocellular subcompartmentalization and signaling-encoded logic gates. SCIENCE ADVANCES 2023; 9:eade5853. [PMID: 36857444 PMCID: PMC9977178 DOI: 10.1126/sciadv.ade5853] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Engineering artificial cellular systems capable of perceiving and transmitting external signals across membranes to activate downstream targets and coordinate protocellular responses is key to build cell-cell communications and protolife. Here, we report a synthetic photoreceptor-mediated signaling pathway with the integration of light harvesting, photo-to-chemical energy conversion, signal transmission, and amplification in synthetic cells, which ultimately resulted in protocell subcompartmentalization. Key to our design is a ruthenium-bipyridine complex that acts as a membrane-anchored photoreceptor to convert visible light into chemical information and transduce signals across the lipid membrane via flip-flop motion. By coupling receptor-mediated phototransduction with biological recognition and enzymatic cascade reactions, we further develop protocell signaling-encoded Boolean logic gates. Our results illustrate a minimal cell model to mimic the photoreceptor cells that can transduce the energy of light into intracellular responses and pave the way to modular control over the flow of information for complex metabolic and signaling pathways.
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Affiliation(s)
- He Li
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yue Yan
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jing Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Ke Shi
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chuwen Song
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yanglimin Ji
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liyan Jia
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianming Li
- Research Center of New Energy, Research Institute of Petroleum Exploration and Development (RIPED), PetroChina, Beijing 100083, China
| | - Yan Qiao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Laboratory of Polymer Physics and Chemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiyang Lin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
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16
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Guo W, Ji D, Kinghorn AB, Chen F, Pan Y, Li X, Li Q, Huck WTS, Kwok CK, Shum HC. Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condensates. J Am Chem Soc 2023; 145:2375-2385. [PMID: 36689740 DOI: 10.1021/jacs.2c11362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA encodes sequence- and structure-dependent interactions to modulate the assembly and properties of biomolecular condensates. RNA G-quadruplexes (rG4s) formed by guanine-rich sequences can trigger the formation of liquid- or solid-like condensates that are involved in many aberrant phase transitions. However, exactly how rG4 motifs modulate different phase transitions and impart distinct material properties to condensates is unclear. Here, using RNA oligonucleotides and cationic peptides as model systems, we show that RNA-peptide condensates exhibit tunability in material properties over a wide spectrum via interactions arising from rG4 folding/unfolding kinetics. rG4-containing oligonucleotides formed strong pairwise attraction with peptides and tended to form solid-like condensates, while their less-structured non-G4 mutants formed liquid-like droplets. We find that the coupling between rG4 dissociation and RNA-peptide complex coacervation triggers solid-to-liquid transition of condensates prior to the complete unfolding of rG4s. This coupling points to a mechanism that material states of rG4-modulated condensates can be finely tuned from solid-like to liquid-like by the addition of less-structured RNA oligonucleotides, which have weak but dominant binding with peptides. We further show that the tunable material states of condensates can enhance RNA aptamer compartmentalization and RNA cleavage reactions. Our results suggest that condensates with complex properties can emerge from subtle changes in RNA oligonucleotides, contributing ways to treat dysfunctional condensates in diseases and insights into prebiotic compartmentalization.
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Affiliation(s)
- Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Feipeng Chen
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Yi Pan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Xiufeng Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Qingchuan Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
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17
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Signal processing and generation of bioactive nitric oxide in a model prototissue. Nat Commun 2022; 13:5254. [PMID: 36068269 PMCID: PMC9448809 DOI: 10.1038/s41467-022-32941-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/24/2022] [Indexed: 11/08/2022] Open
Abstract
The design and construction of synthetic prototissues from integrated assemblies of artificial protocells is an important challenge for synthetic biology and bioengineering. Here we spatially segregate chemically communicating populations of enzyme-decorated phospholipid-enveloped polymer/DNA coacervate protocells in hydrogel modules to construct a tubular prototissue-like vessel capable of modulating the output of bioactive nitric oxide (NO). By decorating the protocells with glucose oxidase, horseradish peroxidase or catalase and arranging different modules concentrically, a glucose/hydroxyurea dual input leads to logic-gate signal processing under reaction-diffusion conditions, which results in a distinct NO output in the internal lumen of the model prototissue. The NO output is exploited to inhibit platelet activation and blood clot formation in samples of plasma and whole blood located in the internal channel of the device, thereby demonstrating proof-of-concept use of the prototissue-like vessel for anticoagulation applications. Our results highlight opportunities for the development of spatially organized synthetic prototissue modules from assemblages of artificial protocells and provide a step towards the organization of biochemical processes in integrated micro-compartmentalized media, micro-reactor technology and soft functional materials. A challenge for synthetic biology is the design and construction of prototissue. Here, the authors spatially segregate layers of enzyme-decorated coacervate protocells as a model prototissue capable of chemical signal processing and modulating outputs of nitric oxide to inhibit blood clot formation.
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18
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Peng Q, Tan S, Xia L, Wu N, Oyang L, Tang Y, Su M, Luo X, Wang Y, Sheng X, Zhou Y, Liao Q. Phase separation in Cancer: From the Impacts and Mechanisms to Treatment potentials. Int J Biol Sci 2022; 18:5103-5122. [PMID: 35982902 PMCID: PMC9379413 DOI: 10.7150/ijbs.75410] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/16/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer is a public health problem of great concern, and it is also one of the main causes of death in the world. Cancer is a disease characterized by dysregulation of diverse cellular processes, including avoiding growth inhibitory factors, avoiding immune damage and promoting metastasis, etc. However, the precise mechanism of tumorigenesis and tumor progression still needs to be further elucidated. Formations of liquid-liquid phase separation (LLPS) condensates are a common strategy for cells to achieve diverse functions, such as chromatin organization, signal transduction, DNA repair and transcriptional regulation, etc. The biomolecular aggregates formed by LLPS are mainly driven by multivalent weak interactions mediated by intrinsic disordered regions (IDRs) in proteins. In recent years, aberrant phase separations and transition have been reported to be related to the process of various diseases, such as neurodegenerative diseases and cancer. Herein, we discussed recent findings that phase separation regulates tumor-related signaling pathways and thus contributes to tumor progression. We also reviewed some tumor virus-associated proteins to regulate the development of virus-associated tumors via phase separation. Finally, we discussed some possible strategies for treating tumors by targeting phase separation.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China.,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
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19
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Iida K, Suzuki N, Sasaki A, Ishida S, Arai T. Development of a novel light-up probe for detection of G-quadruplexes in stress granules. Sci Rep 2022; 12:12892. [PMID: 35902691 PMCID: PMC9334577 DOI: 10.1038/s41598-022-17230-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
G-quadruplexes (G4s) regulate various biological processes in cells. However, cellular imaging of dynamically forming G4s in biomolecular condensates using small molecules has been poorly investigated. Herein, we present a fluorescent light-up probe with the ability to selectively stabilize G4s and enhance fluorescence upon G4 binding. The foci of the probe were mainly observed in the nucleoli. These were co-localized with anti-fibrillarin antibodies and anti-G4 antibodies (BG4). Moreover, we tested detection of G4 in stress granules using the developed probe. Stress granules were induced through treatment with not only thapsigargin, but also known G4 ligands (pyridostatin, RHPS4, and BRACO-19). In the stress granules, co-localization between the probe, BG4, and stress granule markers (TIA1 and G3BP1) was detected. We present a practical light-up probe for G4s in stress granules, providing potential targets for G4 ligands.
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Affiliation(s)
- Keisuke Iida
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan.
| | - Natsumi Suzuki
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
| | - Ayano Sasaki
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
| | - Shunsuke Ishida
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
| | - Takayoshi Arai
- Soft Molecular Activation Research Center (SMARC), Chiba Iodine Resource Innovation Center (CIRIC), Molecular Chirality Research Center (MCRC), and Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi, Inage, Chiba , 263-8522, Japan
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20
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Ishiguro A, Ishihama A. Essential Roles and Risks of G-Quadruplex Regulation: Recognition Targets of ALS-Linked TDP-43 and FUS. Front Mol Biosci 2022; 9:957502. [PMID: 35898304 PMCID: PMC9309350 DOI: 10.3389/fmolb.2022.957502] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
A non-canonical DNA/RNA structure, G-quadruplex (G4), is a unique structure formed by two or more guanine quartets, which associate through Hoogsteen hydrogen bonding leading to form a square planar arrangement. A set of RNA-binding proteins specifically recognize G4 structures and play certain unique physiological roles. These G4-binding proteins form ribonucleoprotein (RNP) through a physicochemical phenomenon called liquid-liquid phase separation (LLPS). G4-containing RNP granules are identified in both prokaryotes and eukaryotes, but extensive studies have been performed in eukaryotes. We have been involved in analyses of the roles of G4-containing RNAs recognized by two G4-RNA-binding proteins, TDP-43 and FUS, which both are the amyotrophic lateral sclerosis (ALS) causative gene products. These RNA-binding proteins play the essential roles in both G4 recognition and LLPS, but they also carry the risk of agglutination. The biological significance of G4-binding proteins is controlled through unique 3D structure of G4, of which the risk of conformational stability is influenced by environmental conditions such as monovalent metals and guanine oxidation.
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21
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Maccaroni K, La Torre M, Burla R, Saggio I. Phase Separation in the Nucleus and at the Nuclear Periphery during Post-Mitotic Nuclear Envelope Reformation. Cells 2022; 11:cells11111749. [PMID: 35681444 PMCID: PMC9179440 DOI: 10.3390/cells11111749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Membrane-enclosed organelle compartmentalization is not the only way by which cell processes are spatially organized. Phase separation is emerging as a new driver in the organization of membrane-less compartments and biological processes. Liquid–liquid phase separation has been indicated as a new way to control the kinetics of molecular reactions and is based on weak multivalent interactions affecting the stoichiometry of the molecules involved. In the nucleus, liquid–liquid phase separation may represent an ancestral means of controlling genomic activity by forming discrete chromatin regions, regulating transcriptional activity, contributing to the assembly of DNA damage response foci, and controlling the organization of chromosomes. Liquid–liquid phase separation also contributes to chromatin function through its role in the reorganization of the nuclear periphery in the post-mitotic phase. Herein, we describe the basic principles regulating liquid–liquid phase separation, analyze examples of phase separation occurring in the nucleus, and dedicate attention to the implication of liquid–liquid phase separation in the reorganization of the nuclear periphery by the endosomal sorting complexes required for transport (ESCRT) machinery. Although some caution is warranted, current scientific knowledge allows for the hypothesis that many factors and processes in the cell are yet to be discovered which are functionally associated with phase separation.
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Affiliation(s)
- Klizia Maccaroni
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
| | - Mattia La Torre
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
| | - Romina Burla
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
- CNR Institute of Molecular Biology and Pathology, 00185 Rome, Italy
| | - Isabella Saggio
- Department of Biology and Biotechnology, Sapienza University, 00185 Rome, Italy; (K.M.); (M.L.T.); (R.B.)
- CNR Institute of Molecular Biology and Pathology, 00185 Rome, Italy
- Institute of Structural Biology, Nanyang Technological University, Singapore 639798, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- Correspondence:
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22
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Liu Z, Chen J, Bai Q, Lin YN, Liang D. Coacervate Formed by an ATP-Binding Aptamer and Its Dynamic Behavior under Nonequilibrium Conditions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6425-6434. [PMID: 35543367 DOI: 10.1021/acs.langmuir.2c00580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although numerous protocell models have been developed to explore the possible pathway of the origin of life on the early earth, few truly fulfill the roles of the DNA/RNA sequence and ATP molecules, which are keys to cell replication and evolution. The ATP-binding aptamer offers an opportunity to combine sequence and energy molecules. In this work, we choose the coacervate droplet as the protocell model and investigate the interaction of the DNA aptamer, poly(l-lysine)(PLL), and ATP under varying conditions. PLL and aptamers form solid precipitates, which spontaneously transform to coacervate droplets as ATP is introduced. The selective uptake and sequestration of exogenous molecules is achieved by the ATP-containing coacervates. As an electric field is applied to expel ATP, the portion of the droplet deficient in ATP becomes solid. The solid/liquid phase ratio is tunable by varying the electric field strength and excitation time. Together with the vacuolization process, a solid head with a soft mouth periodically opening and closing is created. Moreover, the composite coacervate droplet gradually grows as it is treated with an electric field and cannot recover to the original liquid phase after the power is turned off and replenished with ATP. Our work highlights that the proper integration of the DNA sequence, ATP, and energy input could be a powerful strategy for creating a protocell with certain living features.
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Affiliation(s)
- Zhijun Liu
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiaxin Chen
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qingwen Bai
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ya-Nan Lin
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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23
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Tsuruta M, Torii T, Kohata K, Kawauchi K, Tateishi-Karimata H, Sugimoto N, Miyoshi D. Controlling liquid–liquid phase separation of G-quadruplex-forming RNAs in a sequence-specific manner. Chem Commun (Camb) 2022; 58:12931-12934. [DOI: 10.1039/d2cc04366a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We constructed a minimum liquid–liquid phase separation model system using only G-quadruplex-forming oligonucleotides and cationic oligopeptides. Moreover, droplet redissolution was achieved in a sequence-specific manner.
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Affiliation(s)
- Mitsuki Tsuruta
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Takeru Torii
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Kazuki Kohata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
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24
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Zhu J, Yan Z, Bošković F, Haynes CJE, Kieffer M, Greenfield JL, Wang J, Nitschke JR, Keyser UF. Fe II 4L 4 tetrahedron binds and aggregates DNA G-quadruplexes. Chem Sci 2021; 12:14564-14569. [PMID: 34881008 PMCID: PMC8580047 DOI: 10.1039/d1sc04430c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
Since the discovery of the G-quadruplex (G4) structure in telomeres in 1980s, studies have established the role it plays in various biological processes. Here we report binding between DNA G4 and a self-assembled tetrahedral metal-organic cage 1 and consequent formation of aggregates, whereby the cage protects the DNA G4 from cleavage by S1 nuclease. We monitor DNA–cage interaction using fluorescence spectroscopy, firstly by quenching of a fluorescent label appended to the 5′ end of G4. Secondly, we detect the decrease in fluorescence of the G4-selective dyes thioflavin-T and Zn-PPIX bound to various DNA G4 sequences following the addition of cage 1. Our results demonstrate that 1 interacts with a wide range of G4s. Moreover, gel electrophoresis, circular dichroism and dynamic light scattering measurements establish the binding of 1 to G4 and indicate the formation of aggregate structures. Finally, we find that DNA G4 contained in an aggregate of cage 1 is protected from cleavage by S1 nuclease. We find FeII4L4 binds to G-quadruplex and forms aggregates. G-quadruplex in the aggregates is protected from digestion by S1 nuclease.![]()
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge JJ Thompson Avenue Cambridge CB3 0HE UK
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge JJ Thompson Avenue Cambridge CB3 0HE UK
| | - Cally J E Haynes
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Marion Kieffer
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jake L Greenfield
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Jin Wang
- Department of Chemistry and of Physics, State University of New York at Stony Brook Stony Brook New York 11794-3400 USA
| | - Jonathan R Nitschke
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge JJ Thompson Avenue Cambridge CB3 0HE UK
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