1
|
Eguchi M, Yoshimura H, Ueda Y, Ozawa T. Split Luciferase-Fragment Reconstitution for Unveiling RNA Localization and Dynamics in Live Cells. ACS Sens 2023; 8:4055-4063. [PMID: 37889477 DOI: 10.1021/acssensors.3c01080] [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: 10/28/2023]
Abstract
The intracellular distribution and dynamics of RNAs play pivotal roles in various physiological phenomena. The ability to monitor the amount and localization of endogenous RNAs in living cells allows for elucidating the mechanisms of various intracellular events. Protein-based fluorescent RNA probes are now widely used to visualize and analyze RNAs in living cells. However, continuously monitoring the temporal changes in RNA localization and dynamics in living cells is challenging. In this study, we developed a bioluminescent probe for spatiotemporal monitoring of RNAs in living cells by using a split-luciferase reconstitution technique. The probe consists of split fragments of a bioluminescent protein, NanoLuc, connected with RNA-binding protein domains generated from a custom-made mutation of a PUM-HD. The probe showed rapid luminescence intensity changes in response to an increase or decrease in the amount of a target RNA in vitro. In live-cell imaging, temporal alteration of the intracellular distribution of endogenous β-actin mRNA was visualized in response to extracellular stimulation. Furthermore, the application of the probe to the visualization of the specific localization of β-actin mRNA in primary hippocampal neurons was conducted. These results demonstrate the capability of the bioluminescent RNA probe to monitor the changes in localization, dynamics, and the amount of target RNA in living cells.
Collapse
Affiliation(s)
- Masatoshi Eguchi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshibumi Ueda
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| |
Collapse
|
2
|
Imanishi M. Mechanisms and Strategies for Determining m 6 A RNA Modification Sites by Natural and Engineered m 6 A Effector Proteins. Chem Asian J 2022; 17:e202200367. [PMID: 35750635 DOI: 10.1002/asia.202200367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/17/2022] [Indexed: 12/13/2022]
Abstract
N6 -Methyladenosine (m6 A) is the most common internal RNA modification in the consensus sequence of 5'-RRACH-3'. The methyl mark is added by writer proteins (METTL3/METTL14 metyltransferase complex) and removed by eraser proteins (m6 A demethylases; FTO and ALKBH5). Recognition of this methyl mark by m6 A reader proteins leads to changes in RNA metabolism. How the writer and eraser proteins determine their targets is not well-understood, despite the importance of this information in understanding the regulatory mechanisms and physiological roles of m6 A. However, approaches for targeted manipulation of the methylation state at specific sites are being developed. In this review, I summarize the recent findings on the mechanisms of target identification of m6 A regulatory proteins, as well as recent approaches for targeted m6 A modifications.
Collapse
Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto, 611-0011, Japan
| |
Collapse
|
3
|
Cao H, Wang Y, Zhang N, Xia S, Tian P, Lu L, Du J, Du Y. Progress of CRISPR-Cas13 Mediated Live-Cell RNA Imaging and Detection of RNA-Protein Interactions. Front Cell Dev Biol 2022; 10:866820. [PMID: 35356276 PMCID: PMC8959342 DOI: 10.3389/fcell.2022.866820] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/21/2022] [Indexed: 12/26/2022] Open
Abstract
Ribonucleic acid (RNA) and proteins play critical roles in gene expression and regulation. The relevant study increases the understanding of various life processes and contributes to the diagnosis and treatment of different diseases. RNA imaging and mapping RNA-protein interactions expand the understanding of RNA biology. However, the existing methods have some limitations. Recently, precise RNA targeting of CRISPR-Cas13 in cells has been reported, which is considered a new promising platform for RNA imaging in living cells and recognition of RNA-protein interactions. In this review, we first described the current findings on Cas13. Furthermore, we introduced current tools of RNA real-time imaging and mapping RNA-protein interactions and highlighted the latest advances in Cas13-mediated tools. Finally, we discussed the advantages and disadvantages of Cas13-based methods, providing a set of new ideas for the optimization of Cas13-mediated methods.
Collapse
Affiliation(s)
- Huake Cao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Yuechen Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Ning Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Siyuan Xia
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Second School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Pengfei Tian
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, China
- First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li Lu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Juan Du
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, China
- Longgang District People’s Hospital of Shenzhen & The Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen, China
- *Correspondence: Yinan Du, ; Juan Du,
| | - Yinan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Yinan Du, ; Juan Du,
| |
Collapse
|
4
|
Yoshimura H. Triple-color single-molecule imaging for analysis of the role of receptor oligomers in signal transduction. Biophys Physicobiol 2022; 19:1-9. [PMID: 35435651 PMCID: PMC8968032 DOI: 10.2142/biophysico.bppb-v19.0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 12/01/2022] Open
Abstract
Membrane receptors provide interfaces of various extracellular stimuli to transduce the signal into the cell. Receptors are required to possess such conflicting properties as high sensitivity and noise reduction for the cell to keep its homeostasis and appropriate responses. To understand the mechanisms by which these functions are achieved, single-molecule monitoring of the motilities of receptors and signaling molecules on the plasma membrane is one of the most direct approaches. This review article introduces several recent single-molecule imaging studies of receptors, including the author’s recent work on triple-color single-molecule imaging of G protein-coupled receptors. Based on these researches, advantages and perspectives of the single-molecule imaging approach to solving the mechanisms of receptor functions are illustrated.
Collapse
|
5
|
Vos PD, Leedman PJ, Filipovska A, Rackham O. Modulation of miRNA function by natural and synthetic RNA-binding proteins in cancer. Cell Mol Life Sci 2019; 76:3745-3752. [PMID: 31165201 PMCID: PMC11105495 DOI: 10.1007/s00018-019-03163-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/02/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
RNA-binding proteins (RBPs) and microRNAs (miRNAs) are the most important regulators of mRNA stability and translation in eukaryotic cells; however, the complex interplay between these systems is only now coming to light. RBPs and miRNAs regulate a unique set of targets in either a positive or negative manner and their regulation is mainly opposed to each other on overlapping targets. In some cases, the levels of RBPs or miRNAs regulate the cellular levels of one another and decreased levels of either results in changes in translation of their targets. There is growing evidence that these regulatory circuits are crucial in the development and progression of cancer; however, the rules underlying synergism and antagonism between miRNAs and RNA-binding proteins remain unclear. Synthetic biology seeks to develop artificial systems to better understand their natural counterparts and to develop new, useful technologies for manipulation of gene expression at the RNA level. The recent development of artificial RNA-binding proteins promises to enable a much greater understanding of the importance of the functional interactions between RNA-binding proteins and miRNAs, as well as enabling their manipulation for therapeutic purposes.
Collapse
Affiliation(s)
- Pascal D Vos
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
- School of Molecular and Chemical Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Peter J Leedman
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
- Medical School, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, Nedlands, WA, 6009, Australia
- School of Molecular and Chemical Sciences, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA, 6102, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, 6102, Australia.
| |
Collapse
|
6
|
Yoshimura H, Ozawa T. Real-Time Fluorescence Imaging of Single-Molecule Endogenous Noncoding RNA in Living Cells. Methods Mol Biol 2018; 1649:337-347. [PMID: 29130208 DOI: 10.1007/978-1-4939-7213-5_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Visualizing RNA in living cells is increasingly important to facilitate accumulation of knowledge about the relation between specific RNA dynamics and physiological events. Single-molecule fluorescence imaging of target RNAs is an excellent approach to analyzing intracellular RNA motion, but it requires special techniques for probe design and microscope setup. Herein, we present a principle and protocol of an RNA visualization probe based on an RNA binding protein of the Pumilio homology domain (PUM-HD). We also describe the setup and operation of a microscope, and introduce an application to visualize telomeric repeats-containing RNA with telomeres and a telomere-related protein: hnRNPA1. This imaging technique is applicable to visualization of different RNAs, especially including repetitive sequences, in living cells.
Collapse
Affiliation(s)
- Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| |
Collapse
|
7
|
Wu M, Ye H, Tang Z, Shao C, Lu G, Chen B, Yang Y, Wang G, Hao H. p53 dynamics orchestrates with binding affinity to target genes for cell fate decision. Cell Death Dis 2017; 8:e3130. [PMID: 29048401 PMCID: PMC5682658 DOI: 10.1038/cddis.2017.492] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/27/2017] [Accepted: 08/29/2017] [Indexed: 01/15/2023]
Abstract
Emerging evidence support that temporal dynamics is pivotal for signaling molecules in orchestrating smart responses to diverse stimuli. p53 is such a signaling molecule that employs temporal dynamics for the selective activation of downstream target genes and ultimately for cell fate decision. Yet how this fine-tuned p53 machinery is quantitatively decoded remains largely unclear. Here we report a quantitative mechanism defining how p53 dynamics orchestrates with binding affinity to target genes for cell fate decision. Treating cells with a genotoxic drug doxorubicin at various doses and durations, we found that a mild and prolonged challenge triggered sequential p53 pulses and ultimately resulted in a terminal pulse enacting apoptosis in a comparable rate with that induced by an acute and high-dose treatment. To transactivate proapoptotic genes and thereafter executing apoptosis, p53 must exceed a certain threshold and accumulate for sufficient time at levels above it. Effective cumulative levels above the threshold, defined as E∫p53, but not the total accumulation levels of p53, precisely discriminate survival and apoptotic cells. p53 accumulation below this threshold, even with prolonging time to reach a total level comparable to that from the accumulation over the threshold, could not transactivate proapoptotic genes to which the binding affinity of p53 is lower than that of proarrest genes, and this property is independent of dynamic features. Our findings indicate that the dynamic feature per se does not directly control cell fate, but rather it orchestrates with the binding affinity to target genes to confer an appropriate time window for cell fate choice. Our study provides a quantitative mechanism unifying p53 dynamics and binding affinity to target genes, providing novel insights to understand how p53 can respond quantitatively to chemotherapeutic drugs, and guiding the design of metronomic regimens for chemotherapeutic drugs.
Collapse
Affiliation(s)
- Mengqiu Wu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China.,Department of Nephrology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, China
| | - Hui Ye
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Zhiyuan Tang
- Department of Respiratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Chang Shao
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Gaoyuan Lu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Baoqiang Chen
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Yuyu Yang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Guangji Wang
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| | - Haiping Hao
- Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Tongjiaxiang #24, Nanjing, Jiangsu 210009, China
| |
Collapse
|
8
|
Sato T, Sato Y, Nishizawa S. Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-Stranded RNA. Chemistry 2017; 23:4079-4088. [PMID: 27897343 DOI: 10.1002/chem.201604676] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 12/24/2022]
Abstract
A series of triplex-forming peptide nucleic acid (TFP) probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found that the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base. Isothermal titration calorimetry experiments revealed that the increased binding affinity resulted from the gain in the binding enthalpy, which could be explained by the enhanced π-stacking interaction between the TO base surrogate and the dsRNA part of the triplex. We expect that these results will provide a molecular basis for designing strong binding tFIT probes for fluorescence sensing of various kinds of purine-rich dsRNAs sequences including those carrying a pyrimidine-purine inversion. The obtained data also offers a new insight into further development of the universal bases incorporated in TFP.
Collapse
Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| |
Collapse
|