1
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Wang S, Yang R, Song M, Li J, Zhou Y, Dai C, Song T. Current understanding of the role of DDX21 in orchestrating gene expression in health and diseases. Life Sci 2024; 349:122716. [PMID: 38762067 DOI: 10.1016/j.lfs.2024.122716] [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: 01/30/2024] [Revised: 04/30/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
RNA helicases are involved in almost all biological events, and the DDXs family is one of the largest subfamilies of RNA helicases. Recently, studies have reported that RNA helicase DDX21 is involved in several biological events, specifically in orchestrating gene expression. Hence, in this review, we provide a comprehensive overview of the function of DDX21 in health and diseases. In the genome, DDX21 contributes to genome stability by promoting DNA damage repair and resolving R-loops. It also facilitates transcriptional regulation by directly binding to promoter regions, interacting with transcription factors, and enhancing transcription through non-coding RNA. Moreover, DDX21 is involved in various RNA metabolism such as RNA processing, translation, and decay. Interestingly, the activity and function of DDX21 are regulated by post-translational modifications, which affect the localization and degradation of DDX21. Except for its role of RNA helicase, DDX21 also acts as a non-enzymatic function in unwinding RNA, regulating transcriptional modifications and promoting transcription. Next, we discuss the potential application of DDX21 as a clinical predictor for diseases, which may facilitate providing novel pharmacological targets for molecular therapy.
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Affiliation(s)
- Shaoshuai Wang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqi Yang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengzhen Song
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia Li
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; City of Hope Medical Center, Duarte, CA 91010, USA; Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - Yanrong Zhou
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chen Dai
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan 430030, China.
| | - Tongxing Song
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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2
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Kankia N, Lomidze L, Stevenson S, Musier-Forsyth K, Kankia B. Defined folding pattern of poly(rG) supports inherent ability to encode biological information. Biopolymers 2024:e23615. [PMID: 39004945 DOI: 10.1002/bip.23615] [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: 04/15/2024] [Revised: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
The RNA World hypothesis posits that RNA can represent a primitive life form by reproducing itself and demonstrating catalytic activity. However, this hypothesis is incapable of addressing several major origin-of-life (OoL) questions. A recently described paradox-free alternative OoL hypothesis, the Quadruplex (G4) World, is based on the ability of poly(dG) to fold into a stable architecture with an unambiguous folding pattern using G-tetrads as building elements. Because of the folding pattern of three G-tetrads and single-G loops, dG15 is programmable and has the capability to encode biological information. Here, we address two open questions of the G4 World hypothesis: (1) Does RNA follow the same folding pattern as DNA? (2) How do stable quadruplexes evolve into the present-day system of information transfer, which is based on Watson-Crick base pair complementarity? To address these questions, we systematically studied the thermodynamic and optical properties of both DNA and RNA G15- and G3T (GGGTGGGTGGGTGGG)-derived sequences. Our study revealed that similar to DNA sequences, RNAs adopt quadruplexes with only three G-tetrads. Thus, both poly(dG) and poly(rG) possess inherent ability to fold into 3D quadruplex architecture with strictly defined folding pattern. The study also revealed that despite high stability of both DNA and RNA quadruplexes, they are vulnerable to single-nucleotide substitutions, which drop the thermal stability by ~40°C and can facilitate introduction of the complementarity principle into the G4 World.
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Affiliation(s)
- Nickolas Kankia
- Department of Chemistry and Biochemistry, Center for RNA biology, The Ohio State University, Columbus, Ohio, USA
| | - Levan Lomidze
- Institute of Biophysics, Ilia State University, Tbilisi, Georgia
| | - Skylar Stevenson
- Department of Chemistry and Biochemistry, Center for RNA biology, The Ohio State University, Columbus, Ohio, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA biology, The Ohio State University, Columbus, Ohio, USA
| | - Besik Kankia
- Department of Chemistry and Biochemistry, Center for RNA biology, The Ohio State University, Columbus, Ohio, USA
- Institute of Biophysics, Ilia State University, Tbilisi, Georgia
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3
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Liu W, He X, Zhu Y, Li Y, Wang Z, Li P, Pan J, Wang J, Chu B, Yang G, Zhang M, He Q, Li Y, Li W, Zhang C. Identification of a conserved G-quadruplex within the E165R of African swine fever virus (ASFV) as a potential antiviral target. J Biol Chem 2024; 300:107453. [PMID: 38852886 PMCID: PMC11261444 DOI: 10.1016/j.jbc.2024.107453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/11/2024] Open
Abstract
Identification of a conserved G-quadruplex in E165R of ASFVAfrican swine fever virus (ASFV) is a double-stranded DNA arbovirus with high transmissibility and mortality rates. It has caused immense economic losses to the global pig industry. Currently, no effective vaccines or medications are to combat ASFV infection. G-quadruplex (G4) structures have attracted increasing interest because of their regulatory role in vital biological processes. In this study, we identified a conserved G-rich sequence within the E165R gene of ASFV. Subsequently, using various methods, we verified that this sequence could fold into a parallel G4. In addition, the G4-stabilizers pyridostatin and 5,10,15,20-tetrakis-(N-methyl-4-pyridyl) porphin (TMPyP4) can bind and stabilize this G4 structure, thereby inhibiting E165R gene expression, and the inhibitory effect is associated with G4 formation. Moreover, the G4 ligand pyridostatin substantially impeded ASFV proliferation in Vero cells by reducing gene copy number and viral protein expression. These compelling findings suggest that G4 structures may represent a promising and novel antiviral target against ASFV.
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Affiliation(s)
- Wenhao Liu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Xinglin He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Yance Zhu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Yaqin Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Zhihao Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Pengfei Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Jiajia Pan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Jiang Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Beibei Chu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Guoyu Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China
| | - Mengjia Zhang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Qigai He
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.
| | - Wentao Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
| | - Chao Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China; Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture and Rural Affairs, Zhengzhou, China; Key Laboratory of Animal Growth and Development of Henan Province, Henan Agricultural University, Zhengzhou, China.
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4
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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5
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Ugrina M, Burkhart I, Müller D, Schwalbe H, Schwierz N. RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy. Nucleic Acids Res 2024; 52:87-100. [PMID: 37986217 PMCID: PMC10783511 DOI: 10.1093/nar/gkad1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023] Open
Abstract
The kinetics of folding is crucial for the function of many regulatory RNAs including RNA G-quadruplexes (rG4s). Here, we characterize the folding pathways of a G-quadruplex from the telomeric repeat-containing RNA by combining all-atom molecular dynamics and coarse-grained simulations with circular dichroism experiments. The quadruplex fold is stabilized by cations and thus, the ion atmosphere forming a double layer surrounding the highly charged quadruplex guides the folding process. To capture the ionic double layer in implicit solvent coarse-grained simulations correctly, we develop a matching procedure based on all-atom simulations in explicit water. The procedure yields quantitative agreement between simulations and experiments as judged by the populations of folded and unfolded states at different salt concentrations and temperatures. Subsequently, we show that coarse-grained simulations with a resolution of three interaction sites per nucleotide are well suited to resolve the folding pathways and their intermediate states. The results reveal that the folding progresses from unpaired chain via hairpin, triplex and double-hairpin constellations to the final folded structure. The two- and three-strand intermediates are stabilized by transient Hoogsteen interactions. Each pathway passes through two on-pathway intermediates. We hypothesize that conformational entropy is a hallmark of rG4 folding. Conformational entropy leads to the observed branched multi-pathway folding process for TERRA25. We corroborate this hypothesis by presenting the free energy landscapes and folding pathways of four rG4 systems with varying loop length.
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Affiliation(s)
- Marijana Ugrina
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
- Department of Theoretical Biophysics, Max-Planck-Institute of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Ines Burkhart
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Diana Müller
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Nadine Schwierz
- Institute of Physics, University of Augsburg, Universitätsstraße 1, 86159 Augsburg, Germany
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6
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Nassour J, Przetocka S, Karlseder J. Telomeres as hotspots for innate immunity and inflammation. DNA Repair (Amst) 2024; 133:103591. [PMID: 37951043 PMCID: PMC10842095 DOI: 10.1016/j.dnarep.2023.103591] [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: 07/24/2023] [Revised: 10/05/2023] [Accepted: 10/24/2023] [Indexed: 11/13/2023]
Abstract
Aging is marked by the gradual accumulation of deleterious changes that disrupt organ function, creating an altered physiological state that is permissive for the onset of prevalent human diseases. While the exact mechanisms governing aging remain a subject of ongoing research, there are several cellular and molecular hallmarks that contribute to this biological process. This review focuses on two factors, namely telomere dysfunction and inflammation, which have emerged as crucial contributors to the aging process. We aim to discuss the mechanistic connections between these two distinct hallmarks and provide compelling evidence highlighting the loss of telomere protection as a driver of pro-inflammatory states associated with aging. By reevaluating the interplay between telomeres, innate immunity, and inflammation, we present novel perspectives on the etiology of aging and its associated diseases.
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Affiliation(s)
- Joe Nassour
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, 12801 E. 17th Ave, Aurora, CO 80045, USA; The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Sara Przetocka
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jan Karlseder
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd, La Jolla, CA 92037, USA.
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7
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Xu Y, Komiyama M. G-Quadruplexes in Human Telomere: Structures, Properties, and Applications. Molecules 2023; 29:174. [PMID: 38202757 PMCID: PMC10780218 DOI: 10.3390/molecules29010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing the latest developments in chemical approaches designed to probe these G-quadruplex structures. Furthermore, this review explores the applications of G-quadruplex structures in targeting human telomeres. Finally, the manuscript outlines the imminent challenges in this evolving field, setting the stage for future investigations.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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8
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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [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: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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9
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Ghosh A, Pandey S, Joshi D, Rana P, Ansari A, Sundar J, Singh P, Khan Y, Ekka M, Chakraborty D, Maiti S. Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin. Nucleic Acids Res 2023; 51:9415-9431. [PMID: 37558241 PMCID: PMC11314421 DOI: 10.1093/nar/gkad639] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 07/13/2023] [Indexed: 08/11/2023] Open
Abstract
Nuclear-retained long non-coding RNAs (lncRNAs) including MALAT1 have emerged as critical regulators of many molecular processes including transcription, alternative splicing and chromatin organization. Here, we report the presence of three conserved and thermodynamically stable RNA G-quadruplexes (rG4s) located in the 3' region of MALAT1. Using rG4 domain-specific RNA pull-down followed by mass spectrometry and RNA immunoprecipitation, we demonstrated that the MALAT1 rG4 structures are specifically bound by two nucleolar proteins, Nucleolin (NCL) and Nucleophosmin (NPM). Using imaging, we found that the MALAT1 rG4s facilitate the localization of both NCL and NPM to nuclear speckles, and specific G-to-A mutations that disrupt the rG4 structures compromised the localization of both NCL and NPM in speckles. In vitro biophysical studies established that a truncated version of NCL (ΔNCL) binds tightly to all three rG4s. Overall, our study revealed new rG4s within MALAT1, established that they are specifically recognized by NCL and NPM, and showed that disrupting the rG4s abolished localization of these proteins to nuclear speckles.
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Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Satya Prakash Pandey
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Dheeraj Chandra Joshi
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Priya Rana
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | | | - Praveen Singh
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura
Road, Delhi 110025, India
- Academy of Scientific & Innovative Research (AcSIR),
Ghaziabad 201 002, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune
411 008, India
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10
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Porubiaková O, Havlík J, Indu, Šedý M, Přepechalová V, Bartas M, Bidula S, Šťastný J, Fojta M, Brázda V. Variability of Inverted Repeats in All Available Genomes of Bacteria. Microbiol Spectr 2023; 11:e0164823. [PMID: 37358458 PMCID: PMC10434271 DOI: 10.1128/spectrum.01648-23] [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: 04/21/2023] [Accepted: 06/03/2023] [Indexed: 06/27/2023] Open
Abstract
Noncanonical secondary structures in nucleic acids have been studied intensively in recent years. Important biological roles of cruciform structures formed by inverted repeats (IRs) have been demonstrated in diverse organisms, including humans. Using Palindrome analyser, we analyzed IRs in all accessible bacterial genome sequences to determine their frequencies, lengths, and localizations. IR sequences were identified in all species, but their frequencies differed significantly across various evolutionary groups. We detected 242,373,717 IRs in all 1,565 bacterial genomes. The highest mean IR frequency was detected in the Tenericutes (61.89 IRs/kbp) and the lowest mean frequency was found in the Alphaproteobacteria (27.08 IRs/kbp). IRs were abundant near genes and around regulatory, tRNA, transfer-messenger RNA (tmRNA), and rRNA regions, pointing to the importance of IRs in such basic cellular processes as genome maintenance, DNA replication, and transcription. Moreover, we found that organisms with high IR frequencies were more likely to be endosymbiotic, antibiotic producing, or pathogenic. On the other hand, those with low IR frequencies were far more likely to be thermophilic. This first comprehensive analysis of IRs in all available bacterial genomes demonstrates their genomic ubiquity, nonrandom distribution, and enrichment in genomic regulatory regions. IMPORTANCE Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence and localization of these important regulatory sequences in bacterial genomes. This work revealed a strong abundance of these sequences in regulatory regions and provides researchers with a valuable tool for their manipulation.
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Affiliation(s)
- Otília Porubiaková
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Havlík
- Mendel University in Brno, Brno, Czech Republic
| | - Indu
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Šedý
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Veronika Přepechalová
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Stefan Bidula
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jiří Šťastný
- Mendel University in Brno, Brno, Czech Republic
- Brno University of Technology, Faculty of Mechanical Engineering, Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Brno University of Technology, Faculty of Chemistry, Brno, Czech Republic
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11
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Taghavi A, Baisden JT, Childs-Disney JL, Yildirim I, Disney M. Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies. Nucleic Acids Res 2023; 51:5325-5340. [PMID: 37216594 PMCID: PMC10287959 DOI: 10.1093/nar/gkad403] [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: 01/08/2023] [Revised: 04/15/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
G4C2 and G2C4 repeat expansions in chromosome 9 open reading frame 72 (C9orf72) are the most common cause of genetically defined amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), or c9ALS/FTD. The gene is bidirectionally transcribed, producing G4C2 repeats [r(G4C2)exp] and G2C4 repeats [r(G2C4)exp]. The c9ALS/FTD repeat expansions are highly structured, and structural studies showed that r(G4C2)exp predominantly folds into a hairpin with a periodic array of 1 × 1 G/G internal loops and a G-quadruplex. A small molecule probe revealed that r(G4C2)exp also adopts a hairpin structure with 2 × 2 GG/GG internal loops. We studied the conformational dynamics adopted by 2 × 2 GG/GG loops using temperature replica exchange molecular dynamics (T-REMD) and further characterized the structure and underlying dynamics using traditional 2D NMR techniques. These studies showed that the loop's closing base pairs influence both structure and dynamics, particularly the configuration adopted around the glycosidic bond. Interestingly, r(G2C4) repeats, which fold into an array of 2 × 2 CC/CC internal loops, are not as dynamic. Collectively, these studies emphasize the unique sensitivity of r(G4C2)exp to small changes in stacking interactions, which is not observed in r(G2C4)exp, providing important considerations for further principles in structure-based drug design.
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Affiliation(s)
- Amirhossein Taghavi
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jared T Baisden
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
| | - Ilyas Yildirim
- Department of Chemistry and Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, Scripps Research and The Herbert Wertheim UF-Scripps Institute for Biomedical Research & Innovation, 130 Scripps Way, 3A1 Jupiter, FL 33458, USA
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12
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Patidar RK, Tiwari K, Tiwari R, Ranjan N. Promoter G-Quadruplex Binding Styryl Benzothiazolium Derivative for Applications in Ligand Affinity Ranking and as Ethidium Bromide Substitute in Gel Staining. ACS APPLIED BIO MATERIALS 2023. [PMID: 37229607 DOI: 10.1021/acsabm.3c00060] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Fluorescent compounds that can preferentially interact with certain nucleic acids are of great importance in new drug discovery in a multitude of functions including fluorescence-based displacement assays and gel staining. Here, we report the discovery of an orange emissive styryl-benzothiazolium derivative (compound 4) which interacts preferentially with Pu22 G-quadruplex DNA among a pool of nucleic acid structures containing G-quadruplex, duplex, and single-stranded DNA structures as well as RNA structures. Fluorescence-based binding analysis revealed that compound 4 interacts with Pu22 G-quadruplex DNA in a 1:1 DNA to ligand binding stoichiometry. The association constant (Ka) for this interaction was found to be 1.12 (±0.15) × 106 M-1. Circular dichroism studies showed that the binding of the probe does not cause changes in the overall parallel G-quadruplex conformation; however, signs of higher-order complex formation were seen in the form of exciton splitting in the chromophore absorption region. UV-visible spectroscopy studies confirmed the stacking nature of the interaction of the fluorescent probe with the G-quadruplex which was further complemented by heat capacity measurement studies. Finally, we have shown that this fluorescent probe can be used toward G-quadruplex-based fluorescence displacement assays for ligand affinity ranking and as a substitute for ethidium bromide in gel staining.
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Affiliation(s)
- Rajesh Kumar Patidar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
| | - Khushboo Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
| | - Ratnesh Tiwari
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, India 226002
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13
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Advances in
G
‐quadruplexes‐based fluorescent imaging. Biopolymers 2022; 113:e23528. [DOI: 10.1002/bip.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
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14
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Jose D, Michael MM, Bentsen C, Rosenblum B, Zelaya A. A Spectroscopic Approach to Unravel the Local Conformations of a G-Quadruplex Using CD-Active Fluorescent Base Analogues. Biochemistry 2022; 61:2720-2732. [DOI: 10.1021/acs.biochem.2c00461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Davis Jose
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey07764, United States
| | - Miya Mary Michael
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey07764, United States
| | - Christopher Bentsen
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey07764, United States
| | - Brandon Rosenblum
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey07764, United States
| | - Adriana Zelaya
- Department of Chemistry and Physics, Monmouth University, West Long Branch, New Jersey07764, United States
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15
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Falanga AP, Terracciano M, Oliviero G, Roviello GN, Borbone N. Exploring the Relationship between G-Quadruplex Nucleic Acids and Plants: From Plant G-Quadruplex Function to Phytochemical G4 Ligands with Pharmaceutic Potential. Pharmaceutics 2022; 14:2377. [PMID: 36365194 PMCID: PMC9698481 DOI: 10.3390/pharmaceutics14112377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 10/31/2023] Open
Abstract
G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.
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Affiliation(s)
- Andrea P. Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Applied Sciences and Intelligent Systems, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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16
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Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
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17
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Zhai LY, Liu JF, Zhao JJ, Su AM, Xi XG, Hou XM. Targeting the RNA G-Quadruplex and Protein Interactome for Antiviral Therapy. J Med Chem 2022; 65:10161-10182. [PMID: 35862260 DOI: 10.1021/acs.jmedchem.2c00649] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, G-quadruplexes (G4s), types of noncanonical four-stranded nucleic acid structures, have been identified in many viruses that threaten human health, such as HIV and Epstein-Barr virus. In this context, G4 ligands were designed to target the G4 structures, among which some have shown promising antiviral effects. In this Perspective, we first summarize the diversified roles of RNA G4s in different viruses. Next, we introduce small-molecule ligands developed as G4 modulators and highlight their applications in antiviral studies. In addition to G4s, we comprehensively review the medical intervention of G4-interacting proteins from both the virus (N protein, viral-encoded helicases, severe acute respiratory syndrome-unique domain, and Epstein-Barr nuclear antigen 1) and the host (heterogeneous nuclear ribonucleoproteins, RNA helicases, zinc-finger cellular nucelic acid-binding protein, and nucleolin) by inhibitors as an alternative way to disturb the normal functions of G4s. Finally, we discuss the challenges and opportunities in G4-based antiviral therapy.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China.,Laboratory of Biology and Applied Pharmacology, CNRS UMR 8113, IDA FR3242, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette 91190, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Xianyang, Shaanxi 712100, China
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18
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Zhao H, Wong HY, Ji D, Lyu K, Kwok CK. Novel L-RNA Aptamer Controls APP Gene Expression in Cells by Targeting RNA G-Quadruplex Structure. ACS APPLIED MATERIALS & INTERFACES 2022; 14:30582-30594. [PMID: 35762921 DOI: 10.1021/acsami.2c06390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Guanine quadruplex (G4) structure is a four-stranded nucleic acid secondary structure motif with unique chemical properties and important biological roles. Amyloid precursor protein (APP) is an Alzheimer's disease (AD)-related gene, and recently, we reported the formation of RNA G4 (rG4) at the 3'UTR of APP mRNA and demonstrated its repressive role in translation. Herein, we apply rG4-SELEX to develop a novel L-RNA aptamer, L-Apt.8f, which binds to APP 3'UTR D-rG4 strongly with subnanomolar affinity. We structurally characterize the aptamer and find that it contains a thermostable and parallel G4 motif, and mutagenesis analysis identifies the key nucleotides that are involved in the target recognition. We also reveal that the L-Apt.8f-APP D-rG4 interaction is enantiomeric-, magnesium ion-, and potassium ion-dependent. Notably, L-Apt.8f preferentially recognizes APP rG4 over other structural motifs, and it can control the APP reporter gene and native transcript translation in cells. Our work introduces a novel strategy and reports a new L-aptamer candidate to target APP 3'UTR rG4 structure, which laid the foundation for further applying L-RNA as an important class of biomolecule for practical L-aptamer-based targeting and controlling of gene expression in cells.
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Affiliation(s)
- Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Hei Yuen Wong
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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19
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Luo Y, Verga D, Mergny JL. Iso-FRET: an isothermal competition assay to analyze quadruplex formation in vitro. Nucleic Acids Res 2022; 50:e93. [PMID: 35670668 PMCID: PMC9458428 DOI: 10.1093/nar/gkac465] [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: 10/26/2021] [Revised: 04/26/2022] [Accepted: 05/16/2022] [Indexed: 11/23/2022] Open
Abstract
Algorithms have been widely used to predict G-quadruplexes (G4s)-prone sequences. However, an experimental validation of these predictions is generally required. We previously reported a high-throughput technique to evidence G4 formation in vitro called FRET-MC. This method, while convenient and reproducible, has one known weakness: its inability to pin point G4 motifs of low thermal stability. As such quadruplexes may still be biologically relevant if formed at physiological temperature, we wanted to develop an independent assay to overcome this limitation. To this aim, we introduced an isothermal version of the competition assay, called iso-FRET, based on a duplex-quadruplex competition and a well-characterized bis-quinolinium G4 ligand, PhenDC3. G4-forming competitors act as decoys for PhenDC3, lowering its ability to stabilize the G4-forming motif reporter oligonucleotide conjugated to a fluorescence quencher (37Q). The decrease in available G4 ligand concentration restores the ability of 37Q to hybridize to its FAM-labeled short complementary C-rich strand (F22), leading to a decrease in fluorescence signal. In contrast, when no G4-forming competitor is present, PhenDC3 remains available to stabilize the 37Q quadruplex, preventing the formation of the F22 + 37Q complex. Iso-FRET was first applied to a reference panel of 70 sequences, and then used to investigate 23 different viral sequences.
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Affiliation(s)
- Yu Luo
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France.,CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405 Orsay, France.,CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405 Orsay, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91128 Palaiseau, France
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20
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Shu H, Zhang R, Xiao K, Yang J, Sun X. G-Quadruplex-Binding Proteins: Promising Targets for Drug Design. Biomolecules 2022; 12:biom12050648. [PMID: 35625576 PMCID: PMC9138358 DOI: 10.3390/biom12050648] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
G-quadruplexes (G4s) are non-canonical secondary nucleic acid structures. Sequences with the potential to form G4s are abundant in regulatory regions of the genome including telomeres, promoters and 5′ non-coding regions, indicating they fulfill important genome regulatory functions. Generally, G4s perform various biological functions by interacting with proteins. In recent years, an increasing number of G-quadruplex-binding proteins have been identified with biochemical experiments. G4-binding proteins are involved in vital cellular processes such as telomere maintenance, DNA replication, gene transcription, mRNA processing. Therefore, G4-binding proteins are also associated with various human diseases. An intensive study of G4-protein interactions provides an attractive approach for potential therapeutics and these proteins can be considered as drug targets for novel medical treatment. In this review, we present biological functions and structural properties of G4-binding proteins, and discuss how to exploit G4-protein interactions to develop new therapeutic targets.
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21
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Gupta P, Ojha D, Nadimetla DN, Bhosale SV, Rode AB. Tetraphenylethene Derivatives Modulate the RNA Hairpin-G-quadruplex Conformational Equilibria in Proto-Oncogenes. Chembiochem 2022; 23:e202200131. [PMID: 35467068 DOI: 10.1002/cbic.202200131] [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: 03/04/2022] [Revised: 04/05/2022] [Indexed: 11/10/2022]
Abstract
RNA G-quadruplexes (GQs) sequence in 5' UTRs of certain proto-oncogenes colocalize with hairpin (Hp) forming sequence resulting in intramolecular Hp-GQ conformational equilibria which is suggested to regulate cancer development and progression. Thus, regulation of Hp-GQ equilibria with small molecules is an attractive but less explored therapeutic approach. Herein, two tetraphenylethenes (TPE) derivatives TPE-Py and TPE-MePy were synthesized and their effect on Hp-GQ equilibrium was explored. The FRET, CD and molecular docking experiments suggested that cationic TPE-MePy shifts the Hp-GQ equilibrium significantly towards the GQ conformer mainly through π-π stacking and van der waals interaction. In presence of TPE-MePy the observed rate constant values for first and second folding step was increased up to 14.6 and 2.6-fold respectively. The FRET melting assay showed a strong stabilizing ability of TPE-MePy (ΔTm = 4.36 °C). Notably, the unmethylated derivative TPE-Py did not alter the Hp-GQ equilibrium. Subsequently, the luciferase assay demonstrated that the TPE-MePy derivatives suppressed the translation efficiency by ∼5.7-fold by shifting the Hp-GQ equilibrium toward GQ conformers in 5' UTR of TRF2. Our data suggest that HpGQ equilibria could be selectively targeted with small molecules to modulate translation for therapy.
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Affiliation(s)
- Payal Gupta
- Regional Centre for Biotechnology, RCB, INDIA
| | - Divya Ojha
- Regional Centre for Biotechnology, RCB, INDIA
| | | | | | - Ambadas B Rode
- Regional Centre for Biotechnology, RCB, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway P.O. Box, 121001, Faridabad, INDIA
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22
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues to have devastating consequences worldwide. Recently, great efforts have been made to identify SARS-CoV-2 host factors, but the regulatory mechanisms of these host molecules, as well as the virus per se, remain elusive. Here we report a role of RNA G-quadruplex (RG4) in SARS-CoV-2 infection. Combining bioinformatics, biochemical and biophysical assays, we demonstrate the presence of RG4s in both SARS-CoV-2 genome and host factors. The biological and pathological importance of these RG4s is then exemplified by a canonical 3-quartet RG4 within Tmprss2, which can inhibit Tmprss2 translation and prevent SARS-CoV-2 entry. Intriguingly, G-quadruplex (G4)-specific stabilizers attenuate SARS-CoV-2 infection in pseudovirus cell systems and mouse models. Consistently, the protein level of TMPRSS2 is increased in lungs of COVID-19 patients. Our findings reveal a previously unknown mechanism underlying SARS-CoV-2 infection and suggest RG4 as a potential target for COVID-19 prevention and treatment. Understanding the mechanisms of SARS-CoV-2 infection is important to control the pandemic. Here the authors show the biological and pathological role of RNA G-quadruplex structure in both SARS-CoV-2 genome and host factors, particularly TMPRSS2.
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23
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Boyle EP, Lomidze L, Musier‐Forsyth K, Kankia B. A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability. ChemistryOpen 2022; 11:e202100276. [PMID: 35103415 PMCID: PMC8805387 DOI: 10.1002/open.202100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/13/2021] [Indexed: 11/22/2022] Open
Abstract
Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K+ or Sr2+ . TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines.
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Affiliation(s)
- Elaina P. Boyle
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOH 43210USA
- Center for RNA BiologyThe Ohio State UniversityColumbusOH 43210USA
| | - Levan Lomidze
- Institute of BiophysicsIlia State UniversityTbilisi0162Republic of Georgia
| | - Karin Musier‐Forsyth
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOH 43210USA
- Center for RNA BiologyThe Ohio State UniversityColumbusOH 43210USA
| | - Besik Kankia
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOH 43210USA
- Center for RNA BiologyThe Ohio State UniversityColumbusOH 43210USA
- Institute of BiophysicsIlia State UniversityTbilisi0162Republic of Georgia
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24
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Ghosh A, Pandey SP, Ansari AH, Sundar J, Singh P, Khan Y, Ekka MK, Chakraborty D, Maiti S. Alternative splicing modulation mediated by G-quadruplex structures in MALAT1 lncRNA. Nucleic Acids Res 2022; 50:378-396. [PMID: 34761272 PMCID: PMC8754661 DOI: 10.1093/nar/gkab1066] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
MALAT1, an abundant lncRNA specifically localized to nuclear speckles, regulates alternative-splicing (AS). The molecular basis of its role in AS remains poorly understood. Here, we report three conserved, thermodynamically stable, parallel RNA-G-quadruplexes (rG4s) present in the 3' region of MALAT1 which regulates this function. Using rG4 domain-specific RNA-pull-down followed by mass-spectrometry, RNA-immuno-precipitation, and imaging, we demonstrate the rG4 dependent localization of Nucleolin (NCL) and Nucleophosmin (NPM) to nuclear speckles. Specific G-to-A mutations that abolish rG4 structures, result in the localization loss of both the proteins from speckles. Functionally, disruption of rG4 in MALAT1 phenocopies NCL knockdown resulting in altered pre-mRNA splicing of endogenous genes. These results reveal a central role of rG4s within the 3' region of MALAT1 orchestrating AS.
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Affiliation(s)
- Arpita Ghosh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Satya Prakash Pandey
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | | | - Praveen Singh
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Yasmeen Khan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Mary Krishna Ekka
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110025, India
- Academy of Scientific & Innovative Research, CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar, Ghaziabad 201 002, Uttar Pradesh, India
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
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25
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Yoshida A, Oyoshi T, Suda A, Futaki S, Imanishi M. Recognition of G-quadruplex RNA by a crucial RNA methyltransferase component, METTL14. Nucleic Acids Res 2021; 50:449-457. [PMID: 34908152 PMCID: PMC8755082 DOI: 10.1093/nar/gkab1211] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/29/2021] [Accepted: 11/26/2021] [Indexed: 01/04/2023] Open
Abstract
N6-methyladenosine (m6A) is an important epitranscriptomic chemical modification that is mainly catalyzed by the METTL3/METTL14 RNA methyltransferase heterodimer. Although m6A is found at the consensus sequence of 5′-DRACH-3′ in various transcripts, the mechanism by which METTL3/METTL14 determines its target is unclear. This study aimed to clarify the RNA binding property of METTL3/METTL14. We found that the methyltransferase heterodimer itself has a binding preference for RNA G-quadruplex (rG4) structures, which are non-canonical four-stranded structures formed by G-rich sequences, via the METTL14 RGG repeats. Additionally, the methyltransferase heterodimer selectively methylated adenosines close to the rG4 sequences. These results suggest a possible process for direct recruitment of METTL3/METTL14 to specific methylation sites, especially near the G4-forming regions. This study is the first to report the RNA binding preference of the m6A writer complex for the rG4 structure and provides insights into the role of rG4 in epitranscriptomic regulation.
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Affiliation(s)
- Atsuhiro Yoshida
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takanori Oyoshi
- Graduate School of Integrated Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Akiyo Suda
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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26
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Dumetz F, Chow EYC, Harris LM, Liew SW, Jensen A, Umar MI, Chung B, Chan TF, Merrick CJ, Kwok CK. G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Res 2021; 49:12486-12501. [PMID: 34792144 PMCID: PMC8643661 DOI: 10.1093/nar/gkab1095] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/15/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
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Affiliation(s)
- Franck Dumetz
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Eugene Yui-Ching Chow
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Lynne M Harris
- Centre for Applied Entomology and Parasitology, Faculty of Natural Sciences, Keele University, Keele, Staffordshire, ST5 5BG, UK
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Anders Jensen
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Betty Chung
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Ting Fung Chan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Catherine J Merrick
- Department of Pathology, Cambridge University, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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Liu Y, Zhu X, Wang K, Zhang B, Qiu S. The Cellular Functions and Molecular Mechanisms of G-Quadruplex Unwinding Helicases in Humans. Front Mol Biosci 2021; 8:783889. [PMID: 34912850 PMCID: PMC8667583 DOI: 10.3389/fmolb.2021.783889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/02/2021] [Indexed: 01/19/2023] Open
Abstract
G-quadruplexes (G4s) are stable non-canonical secondary structures formed by G-rich DNA or RNA sequences. They play various regulatory roles in many biological processes. It is commonly agreed that G4 unwinding helicases play key roles in G4 metabolism and function, and these processes are closely related to physiological and pathological processes. In recent years, more and more functional and mechanistic details of G4 helicases have been discovered; therefore, it is necessary to carefully sort out the current research efforts. Here, we provide a systematic summary of G4 unwinding helicases from the perspective of functions and molecular mechanisms. First, we provide a general introduction about helicases and G4s. Next, we comprehensively summarize G4 unfolding helicases in humans and their proposed cellular functions. Then, we review their study methods and molecular mechanisms. Finally, we share our perspective on further prospects. We believe this review will provide opportunities for researchers to reach the frontiers in the functions and molecular mechanisms of human G4 unwinding helicases.
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Affiliation(s)
- Yang Liu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Xinting Zhu
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Kejia Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
| | - Bo Zhang
- College of Basic Medicine, Zunyi Medical University, Zunyi, China
| | - Shuyi Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology and Agro-Bioengineering (CICMEAB), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, China
- The Key Laboratory of Fermentation Engineering and Biological Pharmacy of Guizhou Province, Guizhou University, Guiyang, China
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China
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28
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Ligands as Stabilizers of G-Quadruplexes in Non-Coding RNAs. Molecules 2021; 26:molecules26206164. [PMID: 34684745 PMCID: PMC8540333 DOI: 10.3390/molecules26206164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
The non-coding RNAs (ncRNA) are RNA transcripts with different sizes, structures and biological functions that do not encode functional proteins. RNA G-quadruplexes (rG4s) have been found in small and long ncRNAs. The existence of an equilibrium between rG4 and stem-loop structures in ncRNAs and its effect on biological processes remains unexplored. For example, deviation from the stem-loop leads to deregulated mature miRNA levels, demonstrating that miRNA biogenesis can be modulated by ions or small molecules. In light of this, we report several examples of rG4s in certain types of ncRNAs, and the implications of G4 stabilization using small molecules, also known as G4 ligands, in the regulation of gene expression, miRNA biogenesis, and miRNA-mRNA interactions. Until now, different G4 ligands scaffolds were synthesized for these targets. The regulatory role of the above-mentioned rG4s in ncRNAs can be used as novel therapeutic approaches for adjusting miRNA levels.
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29
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Kundu S. ProTG4: A Web Server to Approximate the Sequence of a Generic Protein From an in Silico Library of Translatable G-Quadruplex ( TG4)-Mapped Peptides. Bioinform Biol Insights 2021; 15:11779322211045878. [PMID: 34602814 PMCID: PMC8482721 DOI: 10.1177/11779322211045878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/13/2021] [Indexed: 11/25/2022] Open
Abstract
An RNA G-quadruplex in the protein coding segment of mRNA is translatable (TG4) and may potentially impact protein translation. This can be consequent to staggered ribosomal synthesis and/or result in an increased frequency of missense translational events. A mathematical model of the peptides that encompass the substituted amino acids, ie, the TG4-mapped peptidome, has been previously studied. However, the significance and relevance to disease biology of this model remains to be established. ProTG4 computes a confidence-of-sequence-identity (γ)-score, which is the average weighted length of every matched TG4-mapped peptide in a generic protein sequence. The weighted length is the product of the length of the peptide and the probability of its non-random occurrence in a library of randomly generated sequences of equivalent lengths. This is then averaged over the entire length of the protein sequence. ProTG4 is simple to operate, has clear instructions, and is accompanied by a set of ready-to-use examples. The rationale of the study, algorithms deployed, and the computational pipeline deployed are also part of the web page. Analyses by ProTG4 of taxonomically diverse protein sequences suggest that there is significant homology to TG4-mapped peptides. These findings, especially in potentially infectious and infesting agents, offer plausible explanations into the aetiology and pathogenesis of certain proteopathies. ProTG4 can also provide a quantitative measure to identify and annotate the canonical form of a generic protein sequence from its known isoforms. The article presents several case studies and discusses the relevance of ProTG4-assisted peptide analysis in gaining insights into various mechanisms of disease biology (mistranslation, alternate splicing, amino acid substitutions).
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Affiliation(s)
- Siddhartha Kundu
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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30
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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31
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Gudanis D, Zielińska K, Baranowski D, Kierzek R, Kozłowski P, Gdaniec Z. Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex-Duplex Hybrid Formation. Biomolecules 2021; 11:biom11081236. [PMID: 34439902 PMCID: PMC8392043 DOI: 10.3390/biom11081236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 12/02/2022] Open
Abstract
In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ or 5′–GGGCGGG–3′ fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.
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Affiliation(s)
- Dorota Gudanis
- Correspondence: (D.G.); (Z.G.); Tel.: +48-61-852-85-03 (ext. 1286) (D.G.)
| | | | | | | | | | - Zofia Gdaniec
- Correspondence: (D.G.); (Z.G.); Tel.: +48-61-852-85-03 (ext. 1286) (D.G.)
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32
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Nawaz A, Shilikbay T, Skariah G, Ceman S. Unwinding the roles of RNA helicase MOV10. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1682. [PMID: 34327836 PMCID: PMC8799784 DOI: 10.1002/wrna.1682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022]
Abstract
MOV10 is an RNA helicase that associates with the RNA‐induced silencing complex component Argonaute (AGO), likely resolving RNA secondary structures. MOV10 also binds the Fragile X mental retardation protein to block AGO2 binding at some sites and associates with UPF1, a principal component of the nonsense‐mediated RNA decay pathway. MOV10 is widely expressed and has a key role in the cellular response to viral infection and in suppressing retrotransposition. Posttranslational modifications of MOV10 include ubiquitination, which leads to stimulation‐dependent degradation, and phosphorylation, which has an unknown function. MOV10 localizes to the nucleus and/or cytoplasm in a cell type‐specific and developmental stage‐specific manner. Knockout of Mov10 leads to embryonic lethality, underscoring an important role in development where it is required for the completion of gastrulation. MOV10 is expressed throughout the organism; however, most studies have focused on germline cells and neurons. In the testes, the knockdown of Mov10 disrupts proliferation of spermatogonial progenitor cells. In brain, MOV10 is significantly elevated postnatally and binds mRNAs encoding cytoskeleton and neuron projection proteins, suggesting an important role in neuronal architecture. Heterozygous Mov10 mutant mice are hyperactive and anxious and their cultured hippocampal neurons have reduced dendritic arborization. Zygotic knockdown of Mov10 in Xenopus laevis causes abnormal head and eye development and mislocalization of neuronal precursors in the brain. Thus, MOV10 plays a vital role during development, defense against viral infection and in neuronal development and function: its many roles and regulation are only beginning to be unraveled. This article is categorized under:RNA Interactions with Proteins and Other Molecules > RNA‐Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications
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Affiliation(s)
- Aatiqa Nawaz
- Department of Cell and Developmental Biology, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
| | - Temirlan Shilikbay
- Department of Cell and Developmental Biology, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
| | - Geena Skariah
- Neuroscience Program, University of Illinois-Urbana Champaign, Champaign, Illinois, USA.,Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie Ceman
- Department of Cell and Developmental Biology, Neuroscience Program, University of Illinois-Urbana Champaign, Champaign, Illinois, USA
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33
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Cadoni E, De Paepe L, Manicardi A, Madder A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res 2021; 49:6638-6659. [PMID: 33978760 PMCID: PMC8266634 DOI: 10.1093/nar/gkab334] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.
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Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
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34
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Abstract
RNAs are involved in an enormous range of cellular processes, including gene regulation, protein synthesis, and cell differentiation, and dysfunctional RNAs are associated with disorders such as cancers, neurodegenerative diseases, and viral infections. Thus, the identification of compounds with the ability to bind RNAs and modulate their functions is an exciting approach for developing next-generation therapies. Numerous RNA-binding agents have been reported over the past decade, but the design of synthetic molecules with selectivity for specific RNA sequences is still in its infancy. In this perspective, we highlight recent advances in targeting RNAs with synthetic molecules, and we discuss the potential value of this approach for the development of innovative therapeutic agents.
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Affiliation(s)
- Farzad Zamani
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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35
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Ye S, Chen Z, Zhang X, Li F, Guo L, Hou XM, Wu WQ, Wang J, Liu C, Zheng K, Sun B. Proximal Single-Stranded RNA Destabilizes Human Telomerase RNA G-Quadruplex and Induces Its Distinct Conformers. J Phys Chem Lett 2021; 12:3361-3366. [PMID: 33783224 DOI: 10.1021/acs.jpclett.1c00250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Single-stranded guanine-rich RNA sequences have a propensity to fold into compact G-quadruplexes (RG4s). The conformational transitions of these molecules provide an important way to regulate their biological functions. Here, we examined the stability and conformation of an RG4-forming sequence identified near the end of human telomerase RNA. We found that a proximal single-stranded (ss) RNA significantly impairs RG4 stability at physiological K+ concentrations, resulting in a reduced RG4 rupture force of ∼ 24.4 pN and easier accessibility of the G-rich sequence. The destabilizing effect requires a minimum of six nucleotides of ssRNA and is effective at either end of RG4. Remarkably, this RG4-forming sequence, under the influence of such a proximal ssRNA, exhibits interconversions between at least three less stable RG4 conformers that might represent potential intermediates along its folding/unfolding pathway. This work provides insights into the stability and folding dynamics of RG4 that are essential for understanding its biological functions.
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Affiliation(s)
- Shasha Ye
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziting Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Fangfang Li
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Lijuan Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Wen-Qiang Wu
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jian Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Cong Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Center for Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Bo Sun
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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36
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Banco MT, Ferré-D'Amaré AR. The emerging structural complexity of G-quadruplex RNAs. RNA (NEW YORK, N.Y.) 2021; 27:390-402. [PMID: 33483368 PMCID: PMC7962482 DOI: 10.1261/rna.078238.120] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base-pairing. Until recently, most RNA G4 structures were thought to conform to a sequence pattern in which guanines stacking within the G4 would also be contiguous in sequence (e.g., four successive guanine trinucleotide tracts separated by loop nucleotides). Such a sequence restriction, and the stereochemical constraints inherent to RNA (arising, in particular, from the presence of the 2'-OH), dictate relatively simple RNA G4 structures. Recent crystallographic and solution NMR structure determinations of a number of in vitro selected RNA aptamers have revealed RNA G4 structures of unprecedented complexity. Structures of the Sc1 aptamer that binds an RGG peptide from the Fragile-X mental retardation protein, various fluorescence turn-on aptamers (Corn, Mango, and Spinach), and the spiegelmer that binds the complement protein C5a, in particular, reveal complexity hitherto unsuspected in RNA G4s, including nucleotides in syn conformation, locally inverted strand polarity, and nucleotide quartets that are not all-G. Common to these new structures, the sequences folding into G4s do not conform to the requirement that guanine stacks arise from consecutive (contiguous in sequence) nucleotides. This review highlights how emancipation from this constraint drastically expands the structural possibilities of RNA G-quadruplexes.
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Affiliation(s)
- Michael T Banco
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-8012, USA
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37
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Exploration of head-to-tail and head-to-head isomers of a guanine quadruplex platinum-based binder. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Matsumoto S, Sugimoto N. New Insights into the Functions of Nucleic Acids Controlled by Cellular Microenvironments. Top Curr Chem (Cham) 2021; 379:17. [PMID: 33782792 DOI: 10.1007/s41061-021-00329-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
The right-handed double-helical B-form structure (B-form duplex) has been widely recognized as the canonical structure of nucleic acids since it was first proposed by James Watson and Francis Crick in 1953. This B-form duplex model has a monochronic and static structure and codes genetic information within a sequence. Interestingly, DNA and RNA can form various non-canonical structures, such as hairpin loops, left-handed helices, triplexes, tetraplexes of G-quadruplex and i-motif, and branched junctions, in addition to the canonical structure. The formation of non-canonical structures depends not only on sequence but also on the surrounding environment. Importantly, these non-canonical structures may exhibit a wide variety of biological roles by changing their structures and stabilities in response to the surrounding environments, which undergo vast changes at specific locations and at specific times in cells. Here, we review recent progress regarding the interesting behaviors and functions of nucleic acids controlled by molecularly crowded cellular conditions. New insights gained from recent studies suggest that nucleic acids not only code genetic information in sequences but also have unknown functions regarding their structures and stabilities through drastic structural changes in cellular environments.
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Affiliation(s)
- Saki Matsumoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan.
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39
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Tao Y, Zheng Y, Zhai Q, Wei D. Recent advances in the development of small molecules targeting RNA G-quadruplexes for drug discovery. Bioorg Chem 2021; 110:104804. [PMID: 33740677 DOI: 10.1016/j.bioorg.2021.104804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Extensive evidence indicates that RNA G-quadruplexes have associated with some important cellular events. Investigation of RNA G-quadruplexes is thus vital to revealing their biofunctions. Several small molecules have been developed to target RNA G-quadruplexes to date. Some of the small molecules showed significantly light-up fluorescence signals upon binding to RNA G-quadruplexes, while some of them regulated the biofunctions of RNA G-quadruplexes. In this mini-review, the small molecules divided into four kinds are expounded which focused mainly on their structural features and biological activities. Moreover, we raised the current challenges and promising prospects. This mini-review might contribute to exploiting more sophisticated small molecules targeting RNA G-quadruplexes with high specificity based on the reported chemical structural features.
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Affiliation(s)
- Yanfei Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingge Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
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40
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TERRA G-quadruplex RNA interaction with TRF2 GAR domain is required for telomere integrity. Sci Rep 2021; 11:3509. [PMID: 33568696 PMCID: PMC7876106 DOI: 10.1038/s41598-021-82406-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/13/2021] [Indexed: 12/15/2022] Open
Abstract
Telomere dysfunction causes chromosomal instability which is associated with many cancers and age-related diseases. The non-coding telomeric repeat-containing RNA (TERRA) forms a structural and regulatory component of the telomere that is implicated in telomere maintenance and chromosomal end protection. The basic N-terminal Gly/Arg-rich (GAR) domain of telomeric repeat-binding factor 2 (TRF2) can bind TERRA but the structural basis and significance of this interaction remains poorly understood. Here, we show that TRF2 GAR recognizes G-quadruplex features of TERRA. We show that small molecules that disrupt the TERRA-TRF2 GAR complex, such as N-methyl mesoporphyrin IX (NMM) or genetic deletion of TRF2 GAR domain, result in the loss of TERRA, and the induction of γH2AX-associated telomeric DNA damage associated with decreased telomere length, and increased telomere aberrations, including telomere fragility. Taken together, our data indicates that the G-quadruplex structure of TERRA is an important recognition element for TRF2 GAR domain and this interaction between TRF2 GAR and TERRA is essential to maintain telomere stability.
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41
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Miron CE, Staalduinen L, Rangaswamy AM, Chen M, Liang Y, Jia Z, Mergny J, Petitjean A. Going Platinum to the Tune of a Remarkable Guanine Quadruplex Binder: Solution‐ and Solid‐State Investigations. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Caitlin E. Miron
- Department of Chemistry Queen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Laura Staalduinen
- Department of Biomedical and Molecular Sciences Queen's University Kingston ON K7L 3N6 Canada
| | - Alana M. Rangaswamy
- Department of Chemistry Queen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Mickey Chen
- Department of Chemistry Queen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Yushi Liang
- Department of Chemistry Queen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences Queen's University Kingston ON K7L 3N6 Canada
| | - Jean‐Louis Mergny
- Inserm U1212/CNRS UMR5320/Université de Bordeaux Institut Européen de Chimie et Biologie 2 rue Escarpit 33607 Pessac France
- Laboratoire d'Optique et Biosciences École Polytechnique CNRS INSERM Institut Polytechnique de Paris 91128 Palaiseau cedex France
| | - Anne Petitjean
- Department of Chemistry Queen's University 90 Bader Lane Kingston ON K7L 3N6 Canada
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42
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Su H, Xu J, Chen Y, Wang Q, Lu Z, Chen Y, Chen K, Han S, Fang Z, Wang P, Yuan BF, Zhou X. Photoactive G-Quadruplex Ligand Identifies Multiple G-Quadruplex-Related Proteins with Extensive Sequence Tolerance in the Cellular Environment. J Am Chem Soc 2021; 143:1917-1923. [DOI: 10.1021/jacs.0c10792] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | | | | | | | | | - Yage Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics−Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | | | | | | | - Ping Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics−Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
- MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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43
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Marcaida MJ, Kauzlaric A, Duperrex A, Sülzle J, Moncrieffe MC, Adebajo D, Manley S, Trono D, Dal Peraro M. The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity. iScience 2020; 23:101811. [PMID: 33313488 PMCID: PMC7721647 DOI: 10.1016/j.isci.2020.101811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Members of the DEAD-box helicase family are involved in all fundamental processes of RNA metabolism, and as such, their malfunction is associated with various diseases. Currently, whether and how oligomerization impacts their biochemical and biological functions is not well understood. In this work, we show that DDX21, a human DEAD-box helicase with RNA G-quadruplex resolving activity, is dimeric and that its oligomerization state influences its helicase activity. Solution small-angle X-ray scattering (SAXS) analysis uncovers a flexible multi-domain protein with a central dimerization domain. While the Arg/Gly rich C termini, rather than dimerization, are key to maintaining high affinity for RNA substrates, in vitro helicase assays indicate that an intact dimer is essential for both DDX21 ATP-dependent double-stranded RNA unwinding and ATP-independent G-quadruplex remodeling activities. Our results suggest that oligomerization plays a key role in regulating RNA DEAD-box helicase activity. The human RNA DEAD-box helicase DDX21 is dimeric DDX21 dimerization is mediated by a hydrophobic central core domain SAXS-based modeling reveals that DDX21 is intrinsically flexible Dimerization and C-terminal domains mediate G-quadruplex and dsRNA unwinding
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Affiliation(s)
- Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Annamaria Kauzlaric
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Alice Duperrex
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Jenny Sülzle
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Martin C Moncrieffe
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Damilola Adebajo
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Suliana Manley
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
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44
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Ghashghaeinia M, Dreischer P, Wieder T, Köberle M. Coronavirus disease 2019 (COVID-19), human erythrocytes and the PKC-alpha/-beta inhibitor chelerythrine -possible therapeutic implication. Cell Cycle 2020; 19:3399-3405. [PMID: 33305655 PMCID: PMC7781621 DOI: 10.1080/15384101.2020.1859197] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19. Until now, diverse drugs have been used for the treatment of COVID-19. These drugs are associated with severe side effects, e.g. induction of erythrocyte death, named eryptosis. This massively affects the oxygen (O2) supply of the organism. Therefore, three elementary aspects should be considered simultaneously: (1) a potential drug should directly attack the virus, (2) eliminate virus-infected host cells and (3) preserve erythrocyte survival and functionality. It is known that PKC-α inhibition enhances the vitality of human erythrocytes, while it dose-dependently activates the apoptosis machinery in nucleated cells. Thus, the use of chelerythrine as a specific PKC-alpha and -beta (PKC-α/-β) inhibitor should be a promising approach to treat people infected with SARS-CoV-2.
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Affiliation(s)
- Mehrdad Ghashghaeinia
- Psoriasis-Center, Department of Dermatology, University Medical Center Schleswig-Holstein , Kiel, Germany.,Physiologisches Institut, Abteilung für Vegetative und Klinische Physiologie, Eberhard Karls University of Tübingen , Tübingen, Germany
| | - Peter Dreischer
- Physiologisches Institut, Abteilung für Vegetative und Klinische Physiologie, Eberhard Karls University of Tübingen , Tübingen, Germany
| | - Thomas Wieder
- Physiologisches Institut, Abteilung für Vegetative und Klinische Physiologie, Eberhard Karls University of Tübingen , Tübingen, Germany
| | - Martin Köberle
- Department of Dermatology and Allergology, School of Medicine, Technical University of Munich , München, Germany
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45
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Miron CE, van Staalduinen L, Rangaswamy AM, Chen M, Liang Y, Jia Z, Mergny JL, Petitjean A. Going Platinum to the Tune of a Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations. Angew Chem Int Ed Engl 2020; 60:2500-2507. [PMID: 33090592 DOI: 10.1002/anie.202012520] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Indexed: 12/17/2022]
Abstract
Guanine quadruplex recognition has gained increasing attention, inspired by the growing awareness of the key roles played by these non-canonical nucleic acid architectures in cellular regulatory processes. We report here the solution and solid-state studies of a novel planar platinum(II) complex that is easily assembled from a simple ligand, and exhibits notable binding affinity for guanine quadruplex structures, while maintaining good selectivity for guanine quadruplex over duplex structures. A crystal structure of this ligand complexed with a telomeric quadruplex confirms double end-capping, with dimerization at the 5' interface.
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Affiliation(s)
- Caitlin E Miron
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L 3N6, Canada
| | - Laura van Staalduinen
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Alana M Rangaswamy
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L 3N6, Canada
| | - Mickey Chen
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L 3N6, Canada
| | - Yushi Liang
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L 3N6, Canada
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Jean-Louis Mergny
- Inserm U1212/CNRS UMR5320/Université de Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33607, Pessac, France.,Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau cedex, France
| | - Anne Petitjean
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L 3N6, Canada
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46
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Powers-Riggs NE, Zuo X, Young RM, Wasielewski MR. Solvent independent symmetry-breaking charge separation in terrylenediimide guanine-quadruplex nanoparticles. J Chem Phys 2020; 153:204302. [DOI: 10.1063/5.0027471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Natalia E. Powers-Riggs
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Ryan M. Young
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, USA
| | - Michael R. Wasielewski
- Department of Chemistry and Institute for Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, USA
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47
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Ding D, Wei C, Dong K, Liu J, Stanton A, Xu C, Min J, Hu J, Chen C. LOTUS domain is a novel class of G-rich and G-quadruplex RNA binding domain. Nucleic Acids Res 2020; 48:9262-9272. [PMID: 32766792 PMCID: PMC7498356 DOI: 10.1093/nar/gkaa652] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/24/2020] [Accepted: 08/05/2020] [Indexed: 02/06/2023] Open
Abstract
LOTUS domains are helix-turn-helix protein folds identified in essential germline proteins and are conserved in prokaryotes and eukaryotes. Despite originally predicted as an RNA binding domain, its molecular binding activity towards RNA and protein is controversial. In particular, the most conserved binding property for the LOTUS domain family remains unknown. Here, we uncovered an unexpected specific interaction of LOTUS domains with G-rich RNA sequences. Intriguingly, LOTUS domains exhibit high affinity to RNA G-quadruplex tertiary structures implicated in diverse cellular processes including piRNA biogenesis. This novel LOTUS domain-RNA interaction is conserved in bacteria, plants and animals, comprising the most ancient binding feature of the LOTUS domain family. By contrast, LOTUS domains do not preferentially interact with DNA G-quadruplexes. We further show that a subset of LOTUS domains display both RNA and protein binding activities. These findings identify the LOTUS domain as a specialized RNA binding domain across phyla and underscore the molecular mechanism underlying the function of LOTUS domain-containing proteins in RNA metabolism and regulation.
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Affiliation(s)
- Deqiang Ding
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chao Wei
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Kunzhe Dong
- USDA Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Jiali Liu
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Alexander Stanton
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Chao Xu
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jian Hu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI 49503, USA
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48
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Recent advances in fluorescent probes for G-quadruplex nucleic acids. Biochem Biophys Res Commun 2020; 531:18-24. [DOI: 10.1016/j.bbrc.2020.02.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/07/2019] [Accepted: 02/18/2020] [Indexed: 01/31/2023]
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49
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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50
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Malina J, Scott P, Brabec V. Stabilization of human telomeric RNA G-quadruplex by the water-compatible optically pure and biologically-active metallohelices. Sci Rep 2020; 10:14543. [PMID: 32884069 PMCID: PMC7471899 DOI: 10.1038/s41598-020-71429-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
RNA G-quadruplexes have been suggested to play key roles in fundamental biological processes and are linked to human diseases. Thus, they also represent good potential therapeutic targets. Here, we describe, using the methods of molecular biophysics, interactions of a series of biologically-active supramolecular cationic metallohelices with human telomeric RNA G-quadruplex. We demonstrate that the investigated metallohelices bind with a high affinity to human telomeric RNA G-quadruplex and that their binding selectivity considerably differs depending on the dimensions and overall shape of the metallohelices. Additionally, the investigated metallohelices inhibit DNA synthesis on the RNA template containing four repeats of the human telomeric sequence by stabilizing the RNA G-quadruplex structure. Collectively, the results of this study suggest that stabilization of RNA sequences capable of G-quadruplex formation by metallohelices investigated in this work might contribute to the mechanism of their biological activity.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic.
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