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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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Lin Y, Wu K, Jia F, Chen L, Wang Z, Zhang Y, Luo Q, Liu S, Qi L, Li N, Dong P, Gao F, Zheng W, Fang X, Zhao Y, Wang F. Single cell imaging reveals cisplatin regulating interactions between transcription (co)factors and DNA. Chem Sci 2021; 12:5419-5429. [PMID: 34163767 PMCID: PMC8179581 DOI: 10.1039/d0sc06760a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 12/21/2022] Open
Abstract
Cisplatin is an extremely successful anticancer drug, and is commonly thought to target DNA. However, the way in which cisplatin-induced DNA lesions regulate interactions between transcription factors/cofactors and genomic DNA remains unclear. Herein, we developed a dual-modal microscopy imaging strategy to investigate, in situ, the formation of ternary binding complexes of the transcription cofactor HMGB1 and transcription factor Smad3 with cisplatin crosslinked DNA in single cells. We utilized confocal microscopy imaging to map EYFP-fused HMGB1 and fluorescent dye-stained DNA in single cells, followed by the visualization of cisplatin using high spatial resolution (200-350 nm) time of flight secondary ion mass spectrometry (ToF-SIMS) imaging of the same cells. The superposition of the fluorescence and the mass spectrometry (MS) signals indicate the formation of HMGB1-Pt-DNA ternary complexes in the cells. More significantly, for the first time, similar integrated imaging revealed that the cisplatin lesions at Smad-binding elements, for example GGC(GC)/(CG) and AGAC, disrupted the interactions of Smad3 with DNA, which was evidenced by the remarkable reduction in the expression of Smad-specific luciferase reporters subjected to cisplatin treatment. This finding suggests that Smad3 and its related signalling pathway are most likely involved in the intracellular response to cisplatin induced DNA damage.
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Affiliation(s)
- Yu Lin
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Kui Wu
- Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology Wuhan 430081 People's Republic of China
| | - Feifei Jia
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Ling Chen
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Zhaoying Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Yanyan Zhang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Qun Luo
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Suyan Liu
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Luyu Qi
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
| | - Nan Li
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Key Laboratory of Molecular Nanostructures and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Pu Dong
- China Telecom Corporation Limited Beijing Research Institute Beijing 100035 People's Republic of China
| | - Fei Gao
- China Telecom Corporation Limited Beijing Research Institute Beijing 100035 People's Republic of China
| | - Wei Zheng
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Xiaohong Fang
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, Key Laboratory of Molecular Nanostructures and Nanotechnology, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 P. R. China
| | - Yao Zhao
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
| | - Fuyi Wang
- Beijing National Laboratory for Molecular Sciences, CAS Research/Education Center for Excellence in Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 People's Republic of China
- University of Chinese Academy of Sciences Beijing 100049 People's Republic of China
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine Jinan 250355 People's Republic of China
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