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Liu X, Qi Q, Xiong W, Shen W, Zhang K, Fan R, Zhang Y, Zhao Y, Xu X, Li M, Zhou E, Tian T, Zhou X. Unveiling a Potent Small Molecule Disruptor for RNA G-Quadruplexes Tougher Than DNA G-Quadruplex Disruption. ACS Chem Biol 2024. [PMID: 39225324 DOI: 10.1021/acschembio.4c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
This research presents a unique small molecule characterized by its ability to effectively disrupt RNA G-quadruplexes (G4s), which are notably more stable than their DNA counterparts. We conducted a comprehensive series of in vitro experiments to thoroughly assess the disruptive capabilities of this molecule on RNA G4s. These experiments included comparisons with established G4 stabilizers and DNA G4 disruptors, providing a multifaceted evaluation of the molecule's efficacy. Our extensive in vitro analyses demonstrated that this molecule effectively alters G4 structures and interactions with the BG4 protein, a well-recognized G4-specific antibody. These findings underscore the molecule's potential to modulate G4-protein interactions, indicating promising applications for manipulating cellular functions associated with G4 dynamics in future research.
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Affiliation(s)
- Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Xiong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Shen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Kaisong Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Ruochen Fan
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Yuanyuan Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Yunting Zhao
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Xinyan Xu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Ming Li
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Enyi Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, The Institute of Molecular Medicine, Wuhan University People's Hospital, Wuhan University, Wuhan 430072, Hubei, China
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2
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Dilweg IW, Peer J, Olsthoorn RCL. Xrn1-resistant RNA motifs are disseminated throughout the RNA virome and are able to block scanning ribosomes. Sci Rep 2023; 13:15987. [PMID: 37749116 PMCID: PMC10520033 DOI: 10.1038/s41598-023-43001-4] [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: 06/26/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
RNAs that are able to prevent degradation by the 5'-3' exoribonuclease Xrn1 have emerged as crucial structures during infection by an increasing number of RNA viruses. Several plant viruses employ the so-called coremin motif, an Xrn1-resistant RNA that is usually located in 3' untranslated regions. Investigation of its structural and sequence requirements has led to its identification in plant virus families beyond those in which the coremin motif was initially discovered. In this study, we identified coremin-like motifs that deviate from the original in the number of nucleotides present in the loop region of the 5' proximal hairpin. They are present in a number of viral families that previously did not have an Xrn1-resistant RNA identified yet, including the double-stranded RNA virus families Hypoviridae and Chrysoviridae. Through systematic mutational analysis, we demonstrated that a coremin motif carrying a 6-nucleotide loop in the 5' proximal hairpin generally requires a YGNNAD consensus for stalling Xrn1, similar to the previously determined YGAD consensus required for Xrn1 resistance of the original coremin motif. Furthermore, we determined the minimal requirements for the 3' proximal hairpin. Since some putative coremin motifs were found in intergenic regions or coding sequences, we demonstrated their capacity for inhibiting translation through an in vitro ribosomal scanning inhibition assay. Consequently, this study provides a further expansion on the number of viral families with known Xrn1-resistant elements, while adding a novel, potentially regulatory function for this structure.
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Affiliation(s)
- Ivar W Dilweg
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - Jasper Peer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | - René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC, Leiden, The Netherlands.
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3
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Endoh T, Takahashi S, Sugimoto N. Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase. Chem Commun (Camb) 2023; 59:872-875. [PMID: 36594508 DOI: 10.1039/d2cc05858h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Replication of RNA viruses is catalysed by virus-specific polymerases, which can be targets of therapeutic strategies. In this study, we used a selection strategy to identify endogenous RNAs from a transcriptome library derived from lung cells that interact with the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Some of the selected RNAs weakened the activity of RdRp by forming G-quadruplexes. These results suggest that certain endogenous RNAs, which potentially form G-quadruplexes, can reduce the replication of viral RNAs.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
| | - Shuntaro Takahashi
- 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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4
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Lockd promotes myoblast proliferation and muscle regeneration via binding with DHX36 to facilitate 5' UTR rG4 unwinding and Anp32e translation. Cell Rep 2022; 39:110927. [PMID: 35675771 DOI: 10.1016/j.celrep.2022.110927] [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: 09/21/2020] [Revised: 02/10/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022] Open
Abstract
Adult muscle stem cells, also known as satellite cells (SCs), play pivotal roles in muscle regeneration, and long non-coding RNA (lncRNA) functions in SCs remain largely unknown. Here, we identify a lncRNA, Lockd, which is induced in activated SCs upon acute muscle injury. We demonstrate that Lockd promotes SC proliferation; deletion of Lockd leads to cell-cycle arrest, and in vivo repression of Lockd in mouse muscles hinders regeneration process. Mechanistically, we show that Lockd directly interacts with RNA helicase DHX36 and the 5'end of Lockd possesses the strongest binding with DHX36. Furthermore, we demonstrate that Lockd stabilizes the interaction between DHX36 and EIF3B proteins; synergistically, this complex unwinds the RNA G-quadruplex (rG4) structure formed at Anp32e mRNA 5' UTR and promotes the translation of ANP32E protein, which is required for myoblast proliferation. Altogether, our findings identify a regulatory Lockd/DHX36/Anp32e axis that promotes myoblast proliferation and acute-injury-induced muscle regeneration.
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5
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Characterization of G-Quadruplexes in Enterovirus A71 Genome and Their Interaction with G-Quadruplex Ligands. Microbiol Spectr 2022; 10:e0046022. [PMID: 35446122 PMCID: PMC9241713 DOI: 10.1128/spectrum.00460-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human enteroviruses cause many diseases; however, there is no specific therapeutic drug. G-quadruplex is an atypical secondary structure formed in the guanine rich region of DNA or RNA, which can exist in the viral genome. The different positions of G-quadruplex play an important role in the regulation of virus replication and infection. Whether G-quadruplexes are present in human enteroviruses is unknown. In current study, we analyzed the potential quadruplex forming sequences of human enteroviruses, especially EV-A71 virus, which causes hand, foot, and mouth disease. The results showed that there were a certain number of potential quadruplex-forming sequences in human enteroviruses. Through a variety of experimental methods, we evaluated the formation potential of EV-A71 encoded G-quadruplex and analyzed the binding ability of G-quadruplex ligands, including BRACO-19, pyridostatin and TMPyP4 to virus encoded G-quadruplexes. G-quadruplex ligands BRACO-19, PDS and TMPyP4 could inhibit the transcription of constructs containing EV-A71 G-quadruplex sequences. Moreover, we found that BRACO-19 was able to inhibit the replication of EV-A71, suggesting that targeting G-quadruplexes in EV-A71 genome by G-quadruplex ligands could be a novel antiviral way against EV-A71. Our finding not only uncovered the G-quadruplexes in human enteroviruses, but also would provide a new strategy for human enteroviruses therapy. IMPORTANCE G-quadruplex is a stable nucleic acid secondary structure formed by the folding of guanine rich nucleic acid. The important regulatory function of G-quadruplex makes it an attractive target of antiviral effect. Human enteroviruses cause a variety of human diseases, including common cold, nervous system diseases, cardiovascular damage, and diabetes. Enterovirus A71 (EV-A71) is one of pathogens causing hand, foot, and mouth disease; however, whether G-quadruplexes are present in the genomes of human enteroviruses is unknown. The function of G-quadruplexes in the EV-A71 genomes is not clear. We predicted and characterized G-quadruplex sequences in EV-A71. G-quadruplex ligands were identified to stabilize EV-A71 G-quadruplexes with high affinities. We also demonstrated G-quadruplex ligand BRACO-19 inhibited EV-A71 replication. Our studies provide a framework for targeting G-quadruplexes in the enteroviruses genome, which will be a new way to develop antiviral agents against human enteroviruses.
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6
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Lv L, Cui H, Chen Z, Zhou Y, Zhang L. G‐quadruplex ligands inhibit chikungunya virus replication. J Med Virol 2022; 94:2519-2527. [PMID: 35075669 DOI: 10.1002/jmv.27622] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/27/2021] [Accepted: 01/21/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Lu Lv
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Haoran Cui
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Zhiyang Chen
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Yixuan Zhou
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Leiliang Zhang
- Department of Clinical Laboratory MedicineThe First Affifiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan HospitalJinanShandongChina
- Department of Pathogen BiologySchool of Basic Medical SciencesShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
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7
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Zheng AJL, Thermou A, Guixens Gallardo P, Malbert-Colas L, Daskalogianni C, Vaudiau N, Brohagen P, Granzhan A, Blondel M, Teulade-Fichou MP, Martins RP, Fahraeus R. The different activities of RNA G-quadruplex structures are controlled by flanking sequences. Life Sci Alliance 2021; 5:5/2/e202101232. [PMID: 34785537 PMCID: PMC8605322 DOI: 10.26508/lsa.202101232] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022] Open
Abstract
The role of G-quadruplex (G4) RNA structures is multifaceted and controversial. Here, we have used as a model the EBV-encoded EBNA1 and the Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded LANA1 mRNAs. We have compared the G4s in these two messages in terms of nucleolin binding, nuclear mRNA retention, and mRNA translation inhibition and their effects on immune evasion. The G4s in the EBNA1 message are clustered in one repeat sequence and the G4 ligand PhenDH2 prevents all G4-associated activities. The RNA G4s in the LANA1 message take part in similar multiple mRNA functions but are spread throughout the message. The different G4 activities depend on flanking coding and non-coding sequences and, interestingly, can be separated individually. Together, the results illustrate the multifunctional, dynamic and context-dependent nature of G4 RNAs and highlight the possibility to develop ligands targeting specific RNA G4 functions. The data also suggest a common multifunctional repertoire of viral G4 RNA activities for immune evasion.
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Affiliation(s)
- Alice J-L Zheng
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Aikaterini Thermou
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France.,ICCVS, University of Gdańsk, Science, Gdańsk, Poland
| | - Pedro Guixens Gallardo
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Laurence Malbert-Colas
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Chrysoula Daskalogianni
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France.,ICCVS, University of Gdańsk, Science, Gdańsk, Poland
| | - Nathan Vaudiau
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Petter Brohagen
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Marc Blondel
- Inserm UMR1078, Université de Bretagne Occidentale (UBO), Etablissement Français du Sang (EFS) Bretagne, CHRU Brest, Brest, France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | | | - Robin Fahraeus
- Inserm UMRS1131, Institut de Génétique Moléculaire, Université Paris 7, Hôpital St. Louis, Paris, France .,RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic.,Department of Medical Biosciences, Umeå University, Umeå, Sweden.,ICCVS, University of Gdańsk, Science, Gdańsk, Poland
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8
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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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9
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Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
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10
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Lyu K, Chow EYC, Mou X, Chan TF, Kwok CK. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res 2021; 49:5426-5450. [PMID: 33772593 PMCID: PMC8191793 DOI: 10.1093/nar/gkab187] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are non-classical DNA or RNA secondary structures that have been first observed decades ago. Over the years, these four-stranded structural motifs have been demonstrated to have significant regulatory roles in diverse biological processes, but challenges remain in detecting them globally and reliably. Compared to DNA G4s (dG4s), the study of RNA G4s (rG4s) has received less attention until recently. In this review, we will summarize the innovative high-throughput methods recently developed to detect rG4s on a transcriptome-wide scale, highlight the many novel and important functions of rG4 being discovered in vivo across the tree of life, and discuss the key biological questions to be addressed in the near future.
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Affiliation(s)
- Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Eugene Yui-Ching Chow
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xi Mou
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Ting-Fung Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - 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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11
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Guiblet WM, DeGiorgio M, Cheng X, Chiaromonte F, Eckert KA, Huang YF, Makova KD. Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome. Genome Res 2021; 31:1136-1149. [PMID: 34187812 PMCID: PMC8256861 DOI: 10.1101/gr.269589.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/24/2021] [Indexed: 12/11/2022]
Abstract
Approximately 1% of the human genome has the ability to fold into G-quadruplexes (G4s)-noncanonical strand-specific DNA structures forming at G-rich motifs. G4s regulate several key cellular processes (e.g., transcription) and have been hypothesized to participate in others (e.g., firing of replication origins). Moreover, G4s differ in their thermostability, and this may affect their function. Yet, G4s may also hinder replication, transcription, and translation and may increase genome instability and mutation rates. Therefore, depending on their genomic location, thermostability, and functionality, G4 loci might evolve under different selective pressures, which has never been investigated. Here we conducted the first genome-wide analysis of G4 distribution, thermostability, and selection. We found an overrepresentation, high thermostability, and purifying selection for G4s within genic components in which they are expected to be functional-promoters, CpG islands, and 5' and 3' UTRs. A similar pattern was observed for G4s within replication origins, enhancers, eQTLs, and TAD boundary regions, strongly suggesting their functionality. In contrast, G4s on the nontranscribed strand of exons were underrepresented, were unstable, and evolved neutrally. In general, G4s on the nontranscribed strand of genic components had lower density and were less stable than those on the transcribed strand, suggesting that the former are avoided at the RNA level. Across the genome, purifying selection was stronger at stable G4s. Our results suggest that purifying selection preserves the sequences of functional G4s, whereas nonfunctional G4s are too costly to be tolerated in the genome. Thus, G4s are emerging as fundamental, functional genomic elements.
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Affiliation(s)
- Wilfried M Guiblet
- Bioinformatics and Genomics Graduate Program, Penn State University, University Park, Pennsylvania 16802, USA
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431, USA
| | - Xiaoheng Cheng
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Sant'Anna School of Advanced Studies, 56127 Pisa, Italy
| | - Kristin A Eckert
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
- Department of Pathology, Penn State University, College of Medicine, Hershey, Pennsylvania 17033, USA
| | - Yi-Fei Huang
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
| | - Kateryna D Makova
- Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA
- Center for Medical Genomics, Penn State University, University Park and Hershey, Pennsylvania 16802, USA
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12
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Liu H, Lu YN, Paul T, Periz G, Banco MT, Ferré-D'Amaré AR, Rothstein JD, Hayes LR, Myong S, Wang J. A Helicase Unwinds Hexanucleotide Repeat RNA G-Quadruplexes and Facilitates Repeat-Associated Non-AUG Translation. J Am Chem Soc 2021; 143:7368-7379. [PMID: 33855846 DOI: 10.1021/jacs.1c00131] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of a hexanucleotide repeat GGGGCC (G4C2) in the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The G4C2 expansion leads to repeat-associated non-AUG (RAN) translation and the production of toxic dipeptide repeat (DPR) proteins, but the mechanisms of RAN translation remain enigmatic. Here, we report that the RNA helicase DHX36 is a robust positive regulator of C9orf72 RAN translation. DHX36 has a high affinity for the G4C2 repeat RNA, preferentially binds to the repeat RNA's G-quadruplex conformation, and efficiently unwinds the G4C2 G-quadruplex structures. Native DHX36 interacts with the G4C2 repeat RNA and is essential for effective RAN translation in the cell. In induced pluripotent stem cells and differentiated motor neurons derived from C9orf72-linked ALS patients, reducing DHX36 significantly decreased the levels of endogenous DPR proteins. DHX36 is also aberrantly upregulated in tissues of C9orf72-linked ALS patients. These results indicate that DHX36 facilitates C9orf72 RAN translation by resolving repeat RNA G-quadruplex structures and may be a potential target for therapeutic intervention.
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Affiliation(s)
- Honghe Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Yu-Ning Lu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Goran Periz
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Michael T Banco
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Jeffrey D Rothstein
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Lindsey R Hayes
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
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13
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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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14
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Harkness RW, Hennecker C, Grün JT, Blümler A, Heckel A, Schwalbe H, Mittermaier AK. Parallel reaction pathways accelerate folding of a guanine quadruplex. Nucleic Acids Res 2021; 49:1247-1262. [PMID: 33469659 PMCID: PMC7897495 DOI: 10.1093/nar/gkaa1286] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/21/2020] [Accepted: 12/27/2020] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded, guanine-rich nucleic acid structures that can influence a variety of biological processes such as the transcription and translation of genes and DNA replication. In many cases, a single G4-forming nucleic acid sequence can adopt multiple different folded conformations that interconvert on biologically relevant timescales, entropically stabilizing the folded state. The coexistence of different folded conformations also suggests that there are multiple pathways leading from the unfolded to the folded state ensembles, potentially modulating the folding rate and biological activity. We have developed an experimental method for quantifying the contributions of individual pathways to the folding of conformationally heterogeneous G4s that is based on mutagenesis, thermal hysteresis kinetic experiments and global analysis, and validated our results using photocaged kinetic NMR experiments. We studied the regulatory Pu22 G4 from the c-myc oncogene promoter, which adopts at least four distinct folded isomers. We found that the presence of four parallel pathways leads to a 2.5-fold acceleration in folding; that is, the effective folding rate from the unfolded to folded ensembles is 2.5 times as large as the rate constant for the fastest individual pathway. Since many G4 sequences can adopt many more than four isomers, folding accelerations of more than an order of magnitude are possible via this mechanism.
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Affiliation(s)
- Robert W Harkness
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main 60438, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main 60438, Germany
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15
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Yasuda M, Ma Y, Okabe S, Wakabayashi Y, Su D, Chang YT, Seimiya H, Tera M, Nagasawa K. Target identification of a macrocyclic hexaoxazole G-quadruplex ligand using post-target-binding visualization. Chem Commun (Camb) 2020; 56:12905-12908. [PMID: 33030187 DOI: 10.1039/d0cc04957c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Macrocyclic hexaoxazoles (6OTDs) are G-quadruplex (G4) ligands, and some derivatives, such as L2H2-6OTD (1a) bearing two aminobutyl side chains, show cytotoxicity towards cancer cells. To identify the cellular target of 1a, we employed a post-target-binding strategy utilizing click reaction (Huisgen cyclization) between the azide-conjugated ligand L2H2-6OTD-Az (1b) and the cell-permeable dye CO-1 bearing a strained alkyne moiety and the BODIPY fluorophore under Cu-free conditions. We confirmed that introduction of the small azide group did not alter the physical or biological properties, including anti-cancer activity, of 1a, and we also demonstrated bias-free localization of CO-1. The post-binding visualization strategy suggested that L2H2-6OTD (1a) colocalized with RNA G4 in living cells.
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Affiliation(s)
- Mizuho Yasuda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan.
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16
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Shankar U, Jain N, Majee P, Kodgire P, Sharma TK, Kumar A. Exploring Computational and Biophysical Tools to Study the Presence of G-Quadruplex Structures: A Promising Therapeutic Solution for Drug-Resistant Vibrio cholerae. Front Genet 2020; 11:935. [PMID: 33101360 PMCID: PMC7545536 DOI: 10.3389/fgene.2020.00935] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022] Open
Abstract
Vibrio cholerae, a gram-negative bacterium that causes cholera, has already caused seven major pandemics across the world and infects roughly 1.3–4 million people every year. Cholera treatment primarily involves oral rehydration therapy supplemented with antibiotics. But recently, multidrug-resistant strains of V. cholerae have emerged. High genomic plasticity further enhances the pathogenesis of this human pathogen. Guanines in DNA or RNA assemble to form G-quadruplex (GQ) structures which have begun to be seen as potential drug targeting sites for different pathogenic bacteria and viruses. In this perspective, we carried out a genome-wide hunt in V. cholerae using a bio-informatics approach and observed ∼85 G-quadruplex forming motifs (VC-PGQs) in chromosome I and ∼45 putative G-quadruplexs (PGQs) in chromosome II. Ten putative G-quadruplex forming motifs (VC-PGQs) were selected on the basis of conservation throughout the genus and functional analysis displayed their location in the essential genes encoding bacterial proteins, for example, methyl-accepting chemotaxis protein, orotate phosphoribosyl transferase protein, amidase proteins, etc. The predicted VC-PGQs were validated using different bio-physical techniques, including Nuclear Magnetic Resonance spectroscopy, Circular Dichroism spectroscopy, and electrophoretic mobility shift assay, which demonstrated the formation of highly stable GQ structures in the bacteria. The interaction of these VC-PGQs with the known specific GQ ligand, TMPyP4, was analyzed using ITC and molecular dynamics studies that displayed the stabilization of the VC-PGQs by the GQ ligands and thus represents a potential therapeutic strategy against this enteric pathogen by inhibiting the PGQ harboring gene expression, thereby inhibiting the bacterial growth and virulence. In summary, this study reveals the presence of conserved GQ forming motifs in the V. cholerae genome that has the potential to be used to treat the multi-drug resistance problem of the notorious enteric pathogen.
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Affiliation(s)
- Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Prativa Majee
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | | | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
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17
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Jain N, Mishra SK, Shankar U, Jaiswal A, Sharma TK, Kodgire P, Kumar A. G-quadruplex stabilization in the ions and maltose transporters gene inhibit Salmonella enterica growth and virulence. Genomics 2020; 112:4863-4874. [PMID: 32898642 PMCID: PMC7474834 DOI: 10.1016/j.ygeno.2020.09.010] [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: 11/20/2019] [Revised: 07/15/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
The G-quadruplex structure is a highly conserved drug target for preventing infection of several human pathogens. We tried to explore G-quadruplex forming motifs as promising drug targets in the genome of Salmonella enterica that causes enteric fever in humans. Herein, we report three highly conserved G-quadruplex motifs (SE-PGQ-1, 2, and 3) in the genome of Salmonella enterica. Bioinformatics analysis inferred the presence of SE-PGQ-1 in the regulatory region of mgtA, SE-PGQ-2 in ORF of entA, and SE-PGQ-3 in the promoter region of malE and malK genes. The G-quadruplex forming sequences were confirmed by biophysical and biomolecular techniques. Cellular studies affirm the inhibitory effect of G-quadruplex specific ligands on Salmonella enterica growth. Further, PCR inhibition, reporter based assay, and RT-qPCR assays emphasize the biological relevance of G-quadruplexes in these genes. Thus, this study confirmed the presence of G-quadruplex motifs in Salmonella enterica and characterized them as a promising drug target.
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Affiliation(s)
- Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Ankit Jaiswal
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India.
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18
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Das P, Verma SP. Dual role of G-quadruplex in translocation renal cell carcinoma: Exploring plausible Cancer therapeutic innovation. Biochim Biophys Acta Gen Subj 2020; 1864:129719. [PMID: 32882363 DOI: 10.1016/j.bbagen.2020.129719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND Renal Cell Carcinoma (RCC) is the ninth leading cause of death among kidney cancer. Xp11.2 translocation harboring TFE3 fusion proteins, act as an oncogene in translocation cancers that constitute the hallmark of translocation renal cell carcinoma (tRCC). G-quadruplex (G4), an alternative nucleic acid structure is an emerging and promising factor in cancer. The presence of G4 within the genome plays a pioneering role in cancer as it contributes to genomic aberration as well as inhibition in cell proliferation. SCOPE OF REVIEW Here we discuss the link between G4 and tRCC. We compile the available information of G-quadruplex & propose their dual role in tRCC, suggesting both stabilization and destabilization of G-quadruplex could be considered targets for tRCC. MAJOR CONCLUSIONS Our in Silico analysis of TFE3 and their three fusions partner's PRCC, SFPQ, and ASPSCR1 discloses a few putative G4 forming sequences (PQS) in their corresponding fusion gene or fusion transcript. Stabilization of G4 structure within fusion gene/transcript can be of great use towards potential therapeutics targeting fusion protein derived oncogenesis, as G4 is a serious menace for DNA polymerization, transcription & translation. G-quadruplex at intron-2 of the TFE3 has been reported to mediate its translocation also. Both stabilization and destabilization of the G4 structure would be a promising approach in the suppression of cancerous cell proliferation. GENERAL SIGNIFICANCE Pioneering studies discovered the relevance of G4 in cancer therapy and explore our approaches towards therapeutic innovation against oncogenic fusion protein and tRCC. Selectively targeting G4 in oncogenic fusion transcript will emerge as potential druggable structures.
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Affiliation(s)
- Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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19
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Matsumoto S, Tateishi-Karimata H, Takahashi S, Ohyama T, Sugimoto N. Effect of Molecular Crowding on the Stability of RNA G-Quadruplexes with Various Numbers of Quartets and Lengths of Loops. Biochemistry 2020; 59:2640-2649. [PMID: 32578417 DOI: 10.1021/acs.biochem.0c00346] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
G-Quadruplexes are noncanonical structures formed by guanine-rich regions of not only DNA but also RNA. RNA G-quadruplexes are widely present in the transcriptome as mRNAs and noncoding RNAs and take part in various essential functions in cells. Furthermore, stable RNA G-quadruplexes control the extent of biological functions, such as mRNA translation and antigen presentation. To understand and regulate the functions controlled by RNA G-quadruplexes in cellular environments, which are molecularly crowded, we would be required to investigate the stability of G-quadruplexes in molecular crowding. Here, we systematically investigated the thermodynamic stability of RNA G-quadruplexes with different numbers of G-quartets and lengths of loops. The molecular crowding conditions of polyethylene glycol with an average molecular weight of 200 (PEG200) were found to stabilize RNA G-quadruplexes with three and four G-quartets, while G-quadruplexes with two G-quartets did not exhibit any stabilization upon addition of PEG200. On the other hand, no difference in stabilization by PEG200 was observed among the G-quadruplexes with different loop lengths. Thermodynamic analysis of the RNA G-quadruplexes revealed more appropriate motifs for identifying G-quadruplex-forming sequences. The informatics analysis with new motifs demonstrated that the distributions of G-quadruplexes in human noncoding RNAs differed depending on the number of G-quartets. Therefore, RNA G-quadruplexes with different numbers of G-quartets may play different roles in response to environmental changes in cells.
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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
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Tatsuya Ohyama
- 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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20
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Identification and characterization of two conserved G-quadruplex forming motifs in the Nipah virus genome and their interaction with G-quadruplex specific ligands. Sci Rep 2020; 10:1477. [PMID: 32001794 PMCID: PMC6992748 DOI: 10.1038/s41598-020-58406-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 01/03/2020] [Indexed: 11/09/2022] Open
Abstract
The G-quadruplex (GQ) motifs are considered as potential drug-target sites for several human pathogenic viruses such as Zika, Hepatitis, Ebola, and Human Herpesviruses. The recent outbreaks of Nipah virus (NiV) in India, the highly fatal emerging zoonotic virus is a potential threat to global health security as no anti-viral drug or vaccine in currently available. Therefore, here in the present study, we sought to assess the ability of the putative G-quadruplex forming sequences in the NiV genome to form G-quadruplex structures and act as targets for anti-viral compounds. Bioinformatics analysis underpinned by various biophysical and biochemical techniques (such as NMR, CD, EMSA, DMS footprinting assay) confirmed the presence of two highly conserved G-quadruplex forming sequences (HGQs) in the G and L genes of NiV. These genes encode the cell attachment glycoprotein and RNA-dependent RNA polymerase, respectively and are essential for the virus entry and replication within the host cell. It remains possible that stabilization of these HGQs by the known G-quadruplex binding ligands like TMPyP4 and Braco-19 represents a promising strategy to inhibit the expression of the HGQ harboring genes and thereby stop the viral entry and replication inside the host cell. Accordingly, we report for the first time, that HGQs in Nipah virus genome are targets for G-quadruplex specific ligands; therefore, could serve as potential targets for anti-viral therapy.
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21
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Kharel P, Balaratnam S, Beals N, Basu S. The role of RNA G-quadruplexes in human diseases and therapeutic strategies. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1568. [PMID: 31514263 DOI: 10.1002/wrna.1568] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 08/09/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022]
Abstract
G-quadruplexes (GQs) are four-stranded secondary structures formed by G-rich nucleic acid sequence(s). DNA GQs are present abundantly in the genome and affect a wide range of processes associated with DNA. Recent studies show that RNA GQs are present in different transcripts, including coding and noncoding areas of mRNA, telomeric RNA as well as in other premature and mature noncoding RNAs. When present at specific locations within the RNAs, GQs play important roles in key biological functions, including the regulation of gene expression and telomere homeostasis. RNA GQs regulate pre-mRNA processing, such as splicing and polyadenylation. Evidently, among other processes, RNA GQs also control mRNA translation, miRNA and piRNA biogenesis, and RNA localization. The regulatory mechanisms controlled by RNA GQs mainly involve binding to RNA binding protein that modulate GQ conformation or serve as an entity in recruiting additional protein regulators to act as a block element to the processing machinery. Here we provide an overview of the ever-increasing number of discoveries revealing the role of RNA GQs in biology and their relevance in human diseases and therapeutics. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Prakash Kharel
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Division of Rheumatology, Immunology, and Allergy, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sumirtha Balaratnam
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland
| | - Nathan Beals
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio
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22
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Sauer M, Juranek SA, Marks J, De Magis A, Kazemier HG, Hilbig D, Benhalevy D, Wang X, Hafner M, Paeschke K. DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions. Nat Commun 2019; 10:2421. [PMID: 31160600 PMCID: PMC6547686 DOI: 10.1038/s41467-019-10432-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/07/2019] [Indexed: 11/08/2022] Open
Abstract
Translation efficiency can be affected by mRNA stability and secondary structures, including G-quadruplex structures (G4s). The highly conserved DEAH-box helicase DHX36/RHAU resolves G4s on DNA and RNA in vitro, however a systems-wide analysis of DHX36 targets and function is lacking. We map globally DHX36 binding to RNA in human cell lines and find it preferentially interacting with G-rich and G4-forming sequences on more than 4500 mRNAs. While DHX36 knockout (KO) results in a significant increase in target mRNA abundance, ribosome occupancy and protein output from these targets decrease, suggesting that they were rendered translationally incompetent. Considering that DHX36 targets, harboring G4s, preferentially localize in stress granules, and that DHX36 KO results in increased SG formation and protein kinase R (PKR/EIF2AK2) phosphorylation, we speculate that DHX36 is involved in resolution of rG4 induced cellular stress.
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Affiliation(s)
- Markus Sauer
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - James Marks
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Alessio De Magis
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Daniel Hilbig
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Xiantao Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Katrin Paeschke
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands.
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany.
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23
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Bartas M, Čutová M, Brázda V, Kaura P, Šťastný J, Kolomazník J, Coufal J, Goswami P, Červeň J, Pečinka P. The Presence and Localization of G-Quadruplex Forming Sequences in the Domain of Bacteria. Molecules 2019; 24:molecules24091711. [PMID: 31052562 PMCID: PMC6539912 DOI: 10.3390/molecules24091711] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/09/2023] Open
Abstract
The role of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, the significance of G-quadruplexes was demonstrated in the last decade, and their presence and functional relevance has been demonstrated in many genomes, including humans. In this study, we analyzed the presence and locations of G-quadruplex-forming sequences by G4Hunter in all complete bacterial genomes available in the NCBI database. G-quadruplex-forming sequences were identified in all species, however the frequency differed significantly across evolutionary groups. The highest frequency of G-quadruplex forming sequences was detected in the subgroup Deinococcus-Thermus, and the lowest frequency in Thermotogae. G-quadruplex forming sequences are non-randomly distributed and are favored in various evolutionary groups. G-quadruplex-forming sequences are enriched in ncRNA segments followed by mRNAs. Analyses of surrounding sequences showed G-quadruplex-forming sequences around tRNA and regulatory sequences. These data point to the unique and non-random localization of G-quadruplex-forming sequences in bacterial genomes.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Michaela Čutová
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
| | - Václav Brázda
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Patrik Kaura
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
| | - Jiří Šťastný
- Faculty of Mechanical Engineering, Brno University of Technology, Technicka 2896/2, 616 69 Brno, Czech Republic.
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Kolomazník
- Department of Informatics, Mendel University in Brno, Zemedelska 1665/1, 61300 Brno, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Pratik Goswami
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jiří Červeň
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
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Mishra SK, Shankar U, Jain N, Sikri K, Tyagi JS, Sharma TK, Mergny JL, Kumar A. Characterization of G-Quadruplex Motifs in espB, espK, and cyp51 Genes of Mycobacterium tuberculosis as Potential Drug Targets. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 16:698-706. [PMID: 31128421 PMCID: PMC6531831 DOI: 10.1016/j.omtn.2019.04.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 01/31/2023]
Abstract
G-quadruplex structure forming motifs are among the most studied evolutionarily conserved drug targets that are present throughout the genome of different organisms and susceptible to influencing various biological processes. Here we report highly conserved potential G-quadruplex motifs (PGQs) in three essential genes (espK, espB, and cyp51) among 160 strains of the Mycobacterium tuberculosis genome. Products of these genes are involved in pathways that are responsible for virulence determination of bacteria inside the host cell and its survival by maintaining membrane fluidity. The espK and espB genes are essential players that prevent the formation of mature phagolysosome and antigen presentation by host macrophages. The cyp51 is another PGQ-possessing gene involved in sterol biosynthesis pathway and membrane formation. In the present study, we revealed the formation of stable intramolecular parallel G-quadruplex structures by Mycobacterium PGQs using a combination of techniques (NMR, circular dichroism [CD], and gel electrophoresis). Next, isothermal titration calorimetry (ITC) and CD melting analysis demonstrated that a well-known G-quadruplex ligand, TMPyP4, binds to and stabilizes these PGQ motifs. Finally, polymerase inhibition and qRT-PCR assays highlight the biological relevance of PGQ-possessing genes in this pathogen and demonstrate that G-quadruplexes are potential drug targets for the development of effective anti-tuberculosis therapeutics.
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Affiliation(s)
- Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India
| | - Kriti Sikri
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tarun Kumar Sharma
- Centre for Bio-design and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India
| | - Jean-Louis Mergny
- ARNA Laboratory, INSERM U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France; Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, Indore 453552, India.
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25
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Endoh T, Sugimoto N. Conformational Dynamics of the RNA G-Quadruplex and its Effect on Translation Efficiency. Molecules 2019; 24:molecules24081613. [PMID: 31022854 PMCID: PMC6514569 DOI: 10.3390/molecules24081613] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/22/2019] [Accepted: 04/22/2019] [Indexed: 11/16/2022] Open
Abstract
During translation, intracellular mRNA folds co-transcriptionally and must refold following the passage of ribosome. The mRNAs can be entrapped in metastable structures during these folding events. In the present study, we evaluated the conformational dynamics of the kinetically favored, metastable, and hairpin-like structure, which disturbs the thermodynamically favored G-quadruplex structure, and its effect on co-transcriptional translation in prokaryotic cells. We found that nascent mRNA forms a metastable hairpin-like structure during co-transcriptional folding instead of the G-quadruplex structure. When the translation progressed co-transcriptionally before the metastable hairpin-like structure transition to the G-quadruplex, function of the G-quadruplex as a roadblock of the ribosome was sequestered. This suggested that kinetically formed RNA structures had a dominant effect on gene expression in prokaryotes. The results of this study indicate that it is critical to consider the conformational dynamics of RNA-folding to understand the contributions of the mRNA structures in controlling gene expression.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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26
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Mirihana Arachchilage G, Hetti Arachchilage M, Venkataraman A, Piontkivska H, Basu S. Stable G-quadruplex enabling sequences are selected against by the context-dependent codon bias. Gene 2019; 696:149-161. [PMID: 30753890 DOI: 10.1016/j.gene.2019.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/14/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022]
Abstract
The distributions of secondary structural elements appear to differ between coding regions (CDS) of mRNAs compared to the untranslated regions (UTRs), presumably as a mechanism to fine-tune gene expression, including efficiency of translation. However, a systematic and comprehensive analysis of secondary structure avoidance because of potential bias in codon usage is difficult as some of the common secondary structures, such as, hairpins can be formed by numerous sequence combinations. Using G-quadruplex (GQ) as the model secondary structure we studied the impact of codon bias on GQs within the CDS. Because GQs can be predicted using specific consensus sequence motifs, they provide an excellent platform for investigation of the selectivity of such putative structures at the codon level. Using a bioinformatics approach, we calculated the frequencies of putative GQs within the CDS of a variety of species. Our results suggest that the most stable GQs appear to be significantly underrepresented within the CDS, through the use of specific synonymous codon combinations. Furthermore, we identified many peptide sequence motifs in which silent mutations can potentially alter translation via stable GQ formation. This work not only provides a comprehensive analysis on how stable secondary structures appear to be avoided within the CDS of mRNA, but also broadens the current understanding of synonymous codon usage as they relate to the structure-function relationship of RNA.
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Affiliation(s)
| | | | - Aparna Venkataraman
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States of America
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, United States of America.
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27
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Zarudnaya MI, Kolomiets IM, Potyahaylo AL, Hovorun DM. Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles. J Biomol Struct Dyn 2018; 37:2837-2866. [PMID: 30052138 DOI: 10.1080/07391102.2018.1503972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The homopolynucleotide (homo-oligonucleotide) tracts function as regulatory elements at various stages of mRNAs life cycle. Numerous cellular proteins specifically bind to these tracts. Among them are the different poly(A)-binding proteins, poly(C)-binding proteins, multifunctional fragile X mental retardation protein which binds specifically both to poly(G) and poly(U) and others. Molecular mechanisms of regulation of gene expression mediated by homopolynucleotide tracts in RNAs are not fully understood and the structural diversity of these tracts can contribute substantially to this regulation. This review summarizes current knowledge on different forms of homoribopolynucleotides, in particular, neutral and acidic forms of poly(A) and poly(C), and also biological relevance of homoribopolynucleotide (homoribo-oligonucleotide) tracts is discussed. Under physiological conditions, the acidic forms of poly(A) and poly(C) can be induced by proton transfer from acidic amino acids of proteins to adenine and cytosine bases. Finally, we present potential mechanisms for the regulation of some biological processes through the formation of intramolecular poly(A) duplexes.
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Affiliation(s)
- Margarita I Zarudnaya
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Iryna M Kolomiets
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Andriy L Potyahaylo
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine
| | - Dmytro M Hovorun
- a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , Kyiv , Ukraine.,b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , Kyiv , Ukraine
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28
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Auboeuf D. Genome evolution is driven by gene expression-generated biophysical constraints through RNA-directed genetic variation: A hypothesis. Bioessays 2017; 39. [DOI: 10.1002/bies.201700069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210; Laboratory of Biology and Modelling of the Cell; Site Jacques Monod; Lyon France
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29
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Harkness RW, Mittermaier AK. G-quadruplex dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28642152 DOI: 10.1016/j.bbapap.2017.06.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations. The impact of these dynamics on biological function is currently not well understood. Recently, structural dynamics have been demonstrated to entropically stabilize GQ ensembles, potentially modulating gene expression. Transient, low-populated states in GQ ensembles may additionally regulate nucleic acid interactions and function. This review will underscore the interplay of GQ dynamics and biological function, focusing on several dynamic processes for biological GQs and the characterization of GQ dynamics by nuclear magnetic resonance (NMR) spectroscopy in conjunction with other biophysical techniques. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Robert W Harkness
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada
| | - Anthony K Mittermaier
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada.
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30
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Endoh T, Sugimoto N. Conformational Dynamics of mRNA in Gene Expression as New Pharmaceutical Target. CHEM REC 2017; 17:817-832. [DOI: 10.1002/tcr.201700016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
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31
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Rouleau S, Jodoin R, Garant JM, Perreault JP. RNA G-Quadruplexes as Key Motifs of the Transcriptome. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 170:1-20. [PMID: 28382477 DOI: 10.1007/10_2017_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
G-Quadruplexes are non-canonical secondary structures that can be adopted under physiological conditions by guanine-rich DNA and RNA molecules. They have been reported to occur, and to perform multiple biological functions, in the genomes and transcriptomes of many species, including humans. This chapter focuses specifically on RNA G-quadruplexes and reviews the most recent discoveries in the field, as well as addresses the upcoming challenges researchers studying these structures face.
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Affiliation(s)
- Samuel Rouleau
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Rachel Jodoin
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Jean-Michel Garant
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine des sciences de la santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 rue Jean-Mignault, Sherbrooke, QC, Canada, J1E 4K8.
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32
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Takahashi S, Bhowmik S, Sugimoto N. Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure. J Inorg Biochem 2017; 166:199-207. [DOI: 10.1016/j.jinorgbio.2016.08.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 12/28/2022]
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Effects of metal ions and cosolutes on G-quadruplex topology. J Inorg Biochem 2016; 166:190-198. [PMID: 27665315 DOI: 10.1016/j.jinorgbio.2016.09.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/31/2016] [Accepted: 09/13/2016] [Indexed: 12/11/2022]
Abstract
Topologies of G-quadruplexes depend on oligonucleotide sequences and on environmental factors, and the diversity of G-quadruplex topologies complicates investigation of functions of these nucleic acid structures. To investigate how metal ions and cosolutes regulate topologies of G-quadruplexes, we stabilized the antiparallel conformation by insertion of 2'-deoxyxanthosine and 8-oxo-2'-deoxyguanosine into selected positions of an oligonucleotide. Thermodynamic analyses of the oligonucleotide revealed that Na+ stabilized the antiparallel G-quadruplex, whereas K+ destabilized this topology. This result suggests that metal ions selectively stabilize G-quadruplex topologies with cavities between G-quartet planes of certain sizes. In the presence of KCl in 20wt% poly(ethylene glycol) with average molecular weight of 200, the antiparallel basket-type G-quadruplex conformation was not stabilized compared with the dilute condition. In the presence of NaCl, the cosolute did stabilize the G-quadruplex with respect to the dilute condition. The presented data show that metal ions and cosolutes regulate topologies of G-quadruplexes through mechanisms that depend on sizes of metal ion cavities and hydration states.
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 381] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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35
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Harkness RW, Mittermaier AK. G-register exchange dynamics in guanine quadruplexes. Nucleic Acids Res 2016; 44:3481-94. [PMID: 27060139 PMCID: PMC4856995 DOI: 10.1093/nar/gkw190] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/09/2016] [Indexed: 11/23/2022] Open
Abstract
G-quadruplexes (GQs) are 4-stranded DNA structures formed by tracts of stacked, Hoogsteen-hydrogen bonded guanosines. GQs are found in gene promoters and telomeres where they regulate gene transcription and telomere elongation. Though GQ structures are well-characterized, many aspects of their conformational dynamics are poorly understood. For example, when there are surplus guanosines in some of the tracts, they can slide with respect to one another, a process we term G-register (GR) exchange. These motions could in principle entropically stabilize the folded state, crucially benefitting GQs as their stabilities are closely tied to biological function. We have developed a method for characterizing GR exchange where each isomer in the wild-type conformational ensemble is trapped by mutation and thermal denaturation data for the set of trapped mutants and wild-type are analyzed simultaneously. This yields GR isomer populations as a function of temperature, quantifies conformational entropy and sheds light on correlated sliding motions of the G-tracts. We measured entropic stabilizations from GR exchange up to 14.3 ± 1.6 J mol−1 K−1, with melting temperature increases up to 7.3 ± 1.6°C. Furthermore, bioinformatic analysis suggests a majority of putative human GQ sequences are capable of GR exchange, pointing to the generality of this phenomenon.
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Affiliation(s)
- Robert W Harkness
- McGill University, Department of Chemistry, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Anthony K Mittermaier
- McGill University, Department of Chemistry, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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36
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Fujii T, Sugimoto N. Loop nucleotides impact the stability of intrastrand i-motif structures at neutral pH. Phys Chem Chem Phys 2016; 17:16719-22. [PMID: 26058487 DOI: 10.1039/c5cp02794b] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The stability of i-motif structures at neutral pH is of interest due to the potential of these structures to impact gene expression. A systematic investigation of loop sequence and length revealed that certain loop nucleobases stabilize i-motif quadruplexes.
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Affiliation(s)
- Taiga Fujii
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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37
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Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells. Sci Rep 2016; 6:22719. [PMID: 26948955 PMCID: PMC4780275 DOI: 10.1038/srep22719] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 02/18/2016] [Indexed: 01/10/2023] Open
Abstract
G-quadruplexes formed on DNA and RNA can be roadblocks to movement of polymerases and ribosome on template nucleotides. Although folding and unfolding processes of the G-quadruplexes are deliberately studied in vitro, how the mechanical and physical properties of the G-quadruplexes affect intracellular biological systems is still unclear. In this study, mRNAs with G-quadruplex forming sequences located either in the 5′ untranslated region (UTR) or in the open reading frame (ORF) were constructed to evaluate positional effects of the G-quadruplex on translation suppression in cells. Periodic fluctuation of translation suppression was observed at every three nucleotides within the ORF but not within the 5′ UTR. The results suggested that difference in motion of ribosome at the 5′ UTR and the ORF determined the ability of the G-quadruplex structure to act as a roadblock to translation in cells and provided mechanical insights into ribosomal progression to overcome the roadblock.
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38
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Abstract
G-quadruplexes are non-canonical secondary structures found in guanine rich regions of DNA and RNA. Reports have indicated the wide occurrence of RNA G-quadruplexes across the transcriptome in various regions of mRNAs and non-coding RNAs. RNA G-quadruplexes have been implicated in playing an important role in translational regulation, mRNA processing events and maintenance of chromosomal end integrity. In this review, we summarize the structural and functional aspects of RNA G-quadruplexes with emphasis on recent progress to understand the protein/trans factors binding these motifs. With the revelation of the importance of these secondary structures as regulatory modules in biology, we have also evaluated the various advancements towards targeting these structures and the challenges associated with them. Apart from this, numerous potential applications of this secondary motif have also been discussed.
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Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
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39
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Endoh T, Rode AB, Takahashi S, Kataoka Y, Kuwahara M, Sugimoto N. Real-Time Monitoring of G-Quadruplex Formation during Transcription. Anal Chem 2016; 88:1984-9. [PMID: 26810457 DOI: 10.1021/acs.analchem.5b04396] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cotranscriptional folding of an RNA transcript enables formation of metastable RNA structures. Thermodynamic and kinetic properties of RNA G-quadruplex formation have previously been investigated using purified guanine-rich oligonucleotides. Here, we describe a method for analysis of cotranscriptional dynamics of the G-quadruplex formation based on real-time monitoring of the fluorescence of G-quadruplex ligands. For RNA sequences with the potential to form mutually exclusive hairpin or G-quadruplex structures, the efficiency of G-quadruplex formation during transcription depended on position of the hairpin forming sequence. The real-time monitoring enabled evaluation of environmental effects on RNA dynamics, as we demonstrated facilitation of post-transcriptional G-quadruplex formation under molecular crowding conditions. The strategy demonstrated here provides folding insights into the G-quadruplex during transcription that should be involved in gene regulation.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Ambadas B Rode
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-Minamimachi, Kobe, 650-0047, Japan
| | - Yuka Kataoka
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University , 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, 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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Crenshaw E, Leung BP, Kwok CK, Sharoni M, Olson K, Sebastian NP, Ansaloni S, Schweitzer-Stenner R, Akins MR, Bevilacqua PC, Saunders AJ. Amyloid Precursor Protein Translation Is Regulated by a 3'UTR Guanine Quadruplex. PLoS One 2015; 10:e0143160. [PMID: 26618502 PMCID: PMC4664259 DOI: 10.1371/journal.pone.0143160] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 11/02/2015] [Indexed: 12/13/2022] Open
Abstract
A central event in Alzheimer’s disease is the accumulation of amyloid β (Aβ) peptides generated by the proteolytic cleavage of the amyloid precursor protein (APP). APP overexpression leads to increased Aβ generation and Alzheimer’s disease in humans and altered neuronal migration and increased long term depression in mice. Conversely, reduction of APP expression results in decreased Aβ levels in mice as well as impaired learning and memory and decreased numbers of dendritic spines. Together these findings indicate that therapeutic interventions that aim to restore APP and Aβ levels must do so within an ideal range. To better understand the effects of modulating APP levels, we explored the mechanisms regulating APP expression focusing on post-transcriptional regulation. Such regulation can be mediated by RNA regulatory elements such as guanine quadruplexes (G-quadruplexes), non-canonical structured RNA motifs that affect RNA stability and translation. Via a bioinformatics approach, we identified a candidate G-quadruplex within the APP mRNA in its 3’UTR (untranslated region) at residues 3008–3027 (NM_201414.2). This sequence exhibited characteristics of a parallel G-quadruplex structure as revealed by circular dichroism spectrophotometry. Further, as with other G-quadruplexes, the formation of this structure was dependent on the presence of potassium ions. This G-quadruplex has no apparent role in regulating transcription or mRNA stability as wild type and mutant constructs exhibited equivalent mRNA levels as determined by real time PCR. Instead, we demonstrate that this G-quadruplex negatively regulates APP protein expression using dual luciferase reporter and Western blot analysis. Taken together, our studies reveal post-transcriptional regulation by a 3’UTR G-quadruplex as a novel mechanism regulating APP expression.
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Affiliation(s)
- Ezekiel Crenshaw
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Brian P. Leung
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Chemistry, Drexel University, Philadelphia, PA, United States of America
| | - Chun Kit Kwok
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
- Department of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michal Sharoni
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Kalee Olson
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
| | - Neeraj P. Sebastian
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | - Sara Ansaloni
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
| | | | - Michael R. Akins
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States of America
- Department of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States of America
| | - Aleister J. Saunders
- Department of Biology, Drexel University, Philadelphia, PA, United States of America
- Department of Biochemistry & Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, United States of America
- Department of Neurobiology & Anatomy, Drexel University College of Medicine, Philadelphia, PA, United States of America
- * E-mail:
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Identification of RNA Oligonucleotides Binding to Several Proteins from Potential G-Quadruplex Forming Regions in Transcribed Pre-mRNA. Molecules 2015; 20:20832-40. [PMID: 26610452 PMCID: PMC6332122 DOI: 10.3390/molecules201119733] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/06/2015] [Accepted: 11/12/2015] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical DNA/RNA structures formed by guanine-rich sequences. Recently, G4s have been found not only in aptamers but also in the genomic DNA and transcribed RNA. In this study, we identified new RNA oligonucleotides working as aptamers by focusing on G4-forming RNAs located within the pre-mRNA. We showed that the G4 in the 5′ UTR and first intron of VEGFA bound to the protein encoded in VEGFA gene, VEGF165, with high affinity. Moreover, G4-forming RNAs located within the PDGFA and the PDGFB introns bound to PDGF-AA and PDGF-BB, respectively, indicating that G4 in the pre-mRNA could be an aptamer. It had been reported that the putative G4-forming RNA sequences are located in some parts of most genes, thus our strategy for aptamer identification could be applicable to other proteins. It has been reported that some G4-forming RNAs in 5′ UTRs are involved in translation control; however, G4-forming excised intronic RNA function has not been revealed previously. Therefore, these findings could not only contribute to the identification of RNA aptamers but also provide new insights into the biological functioning of G4-forming RNAs located within intronic RNA sequences.
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Endoh T, Hnedzko D, Rozners E, Sugimoto N. Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; Japan
| | - Dziyana Hnedzko
- Department of Chemistry; Binghamton University; The State University of New York; Binghamton NY 13902 USA
| | - Eriks Rozners
- Department of Chemistry; Binghamton University; The State University of New York; Binghamton NY 13902 USA
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 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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Endoh T, Hnedzko D, Rozners E, Sugimoto N. Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells. Angew Chem Int Ed Engl 2015; 55:899-903. [PMID: 26473504 DOI: 10.1002/anie.201505938] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/08/2015] [Indexed: 11/11/2022]
Abstract
Compounds that bind specifically to double-stranded regions of RNA have potential as regulators of structure-based RNA function; however, sequence-selective recognition of double-stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA-RNA triplexes. Herein, we demonstrate that a 9-mer PNA forms a sequence-specific PNA-RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5' untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex-forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double-stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein-RNA interactions.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan
| | - Dziyana Hnedzko
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 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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Holder IT, Hartig JS. A matter of location: influence of G-quadruplexes on Escherichia coli gene expression. ACTA ACUST UNITED AC 2015; 21:1511-21. [PMID: 25459072 DOI: 10.1016/j.chembiol.2014.09.014] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/13/2014] [Accepted: 09/17/2014] [Indexed: 01/01/2023]
Abstract
We provide important insights into secondary-structure-mediated regulation of gene expression in Escherichia coli. In a comprehensive survey, we show that the strand orientation and the exact position of a G-quadruplex sequence strongly influence its effect on transcription and translation. We generated a series of reporter gene constructs that contained systematically varied positions of quadruplexes and respective control sequences inserted into several positions within the promoter, 50-UTR, and 30-UTR regions. G-rich sequences at specific locations in the promoter and also in proximity to the ribosome-binding site (RBS) showed pronounced inhibitory effects. Additionally, we rationally designed a system where quadruplex formation showed a gene-activating behavior. Moreover, we characterized quadruplexes in proximity to the RBS that occur naturally in E. coli genes, demonstrating that some of these quadruplexes exert significant modulation of gene expression. Taken together, our data show strong position-dependent effects of quadruplex secondary structures on bacterial gene expression.
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Bhattacharyya D, Diamond P, Basu S. An Independently folding RNA G-quadruplex domain directly recruits the 40S ribosomal subunit. Biochemistry 2015; 54:1879-85. [PMID: 25730526 DOI: 10.1021/acs.biochem.5b00091] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we report that a 17-nucleotide independently folding RNA G-quadruplex (GQ) domain within the 294-nucleotide human VEGF IRES A interacts with the 40S ribosomal subunit. Footprinting and structure mapping analyses indicate that the RNA GQ forms independently and interacts directly with the 40S ribosomal subunit in the absence of other protein factors. Moreover, a filter binding assay in conjunction with enzymatic footprinting clearly established that the GQ-forming domain singularly dictates the binding affinity and also the function of internal ribosomal entry site (IRES) A. The deletion of the GQ domain abrogates the binding of the 40S ribosomal subunit to the IRES, which impairs cap-independent translation initiation. The findings provide a unique and defined role for a noncanonical RNA structure in cap-independent translation initiation by cellular IRESs. The GQ structure when present in an IRES acts as an essential element in contrast to their generally accepted inhibitory role in translation. The results of this study explain the hitherto unknown mechanistic necessity of the GQ structure in IRES function.
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Affiliation(s)
| | - Paige Diamond
- ‡Department of Biochemistry, Cell and Molecular Biology, Drake University, Des Moines, Iowa 50311, United States
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Bhattacharyya D, Nguyen K, Basu S. Rationally induced RNA:DNA G-quadruplex structures elicit an anticancer effect by inhibiting endogenous eIF-4E expression. Biochemistry 2014; 53:5461-70. [PMID: 25072107 DOI: 10.1021/bi5008904] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA G-quadruplex (GQ) structures act as regulators of a diverse array of cellular processes including translation, pre-mRNA processing, and mRNA targeting. We report here a strategy of harnessing the natural ability of RNA GQs to inhibit translation by rationally inducing a GQ on a targeted mRNA to knockdown endogenous gene expression. We chose to target eIF-4E because of its key role in translation initiation and overexpression in multiple cancers and with the expectation that downregulation of eIF-4E would result in antiproliferation of cancer cells. Targeted hybrid (RNA:DNA) GQ structures were induced at the 5'-untranslated region (UTR) and the protein coding region of the eIF-4E mRNA by rationally designed and partially modified extraneous DNA sequences and their effect on eIF-4E expression was determined. The formation of a stable induced G-quadruplex was established by biophysical and biochemical methods. Thermodynamic parameters calculated from CD melting indicate formation of a stable induced GQ at a physiologically relevant salt concentration. We established the specificity and efficacy of the induced GQ formation by monitoring the targeted repression of a reporter gene. Most importantly we have demonstrated that inducing GQ in the 5'-UTR and the protein coding region of eIF-4E mRNA in human cancer cells results in 30% and 60% inhibition of the endogenous protein expression, respectively. Treating with the GQ inducing oligonucleotide sequences resulted in a decrease in the viability of human cancer cells in a dose-dependent manner. The above concept opens up a new strategy for targeted modulation of endogenous gene expression.
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Affiliation(s)
- Debmalya Bhattacharyya
- Department of Chemistry & Biochemistry, Kent State University , Kent, Ohio 44242, United States
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Olsthoorn RCL. G-quadruplexes within prion mRNA: the missing link in prion disease? Nucleic Acids Res 2014; 42:9327-33. [PMID: 25030900 PMCID: PMC4132711 DOI: 10.1093/nar/gku559] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Cellular ribonucleic acid (RNA) plays a crucial role in the initial conversion of cellular prion protein PrP(C) to infectious PrP(Sc) or scrapie. The nature of this RNA remains elusive. Previously, RNA aptamers against PrP(C) have been isolated and found to form G-quadruplexes (G4s). PrP(C) binding to G4 RNAs destabilizes its structure and is thought to trigger its conversion to PrP(Sc). Here it is shown that PrP messenger RNA (mRNA) itself contains several G4 motifs, located in the octarepeat region. Investigation of the RNA structure in one of these repeats by circular dichroism, nuclear magnetic resonance and ultraviolet melting studies shows evidence of G4 formation. In vitro translation of full-length PrP mRNA, naturally harboring five consecutive G4 motifs, was specifically affected by G4-binding ligands, lending support to G4 formation in PrP mRNA. A possible role of PrP binding to its own mRNA and the role of anti-prion drugs, many of which are G4-binding ligands, in prion disease are discussed.
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Affiliation(s)
- René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Einsteinweg 55, 2333CC Leiden, The Netherlands
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48
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Small-molecule quadruplex-targeted drug discovery. Bioorg Med Chem Lett 2014; 24:2602-12. [DOI: 10.1016/j.bmcl.2014.04.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 01/24/2023]
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Frees S, Menendez C, Crum M, Bagga PS. QGRS-Conserve: a computational method for discovering evolutionarily conserved G-quadruplex motifs. Hum Genomics 2014; 8:8. [PMID: 24885782 PMCID: PMC4017754 DOI: 10.1186/1479-7364-8-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 04/21/2014] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Nucleic acids containing guanine tracts can form quadruplex structures via non-Watson-Crick base pairing. Formation of G-quadruplexes is associated with the regulation of important biological functions such as transcription, genetic instability, DNA repair, DNA replication, epigenetic mechanisms, regulation of translation, and alternative splicing. G-quadruplexes play important roles in human diseases and are being considered as targets for a variety of therapies. Identification of functional G-quadruplexes and the study of their overall distribution in genomes and transcriptomes is an important pursuit. Traditional computational methods map sequence motifs capable of forming G-quadruplexes but have difficulty in distinguishing motifs that occur by chance from ones which fold into G-quadruplexes. RESULTS We present Quadruplex forming 'G'-rich sequences (QGRS)-Conserve, a computational method for calculating motif conservation across exomes and supports filtering to provide researchers with more precise methods of studying G-quadruplex distribution patterns. Our method quantitatively evaluates conservation between quadruplexes found in homologous nucleotide sequences based on several motif structural characteristics. QGRS-Conserve also efficiently manages overlapping G-quadruplex sequences such that the resulting datasets can be analyzed effectively. CONCLUSIONS We have applied QGRS-Conserve to identify a large number of G-quadruplex motifs in the human exome conserved across several mammalian and non-mammalian species. We have successfully identified multiple homologs of many previously published G-quadruplexes that play post-transcriptional regulatory roles in human genes. Preliminary large-scale analysis identified many homologous G-quadruplexes in the 5'- and 3'-untranslated regions of mammalian species. An expectedly smaller set of G-quadruplex motifs was found to be conserved across larger phylogenetic distances. QGRS-Conserve provides means to build datasets that can be filtered and categorized in a variety of biological dimensions for more targeted studies in order to better understand the roles that G-quadruplexes play.
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Affiliation(s)
- Scott Frees
- Department of Computer Science, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
| | - Camille Menendez
- Department of Bioinformatics, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
| | - Matt Crum
- Department of Bioinformatics, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
| | - Paramjeet S Bagga
- Department of Bioinformatics, Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, NJ 08807, USA
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Endoh T, Sugimoto N. Unusual -1 ribosomal frameshift caused by stable RNA G-quadruplex in open reading frame. Anal Chem 2013; 85:11435-9. [PMID: 24191683 DOI: 10.1021/ac402497x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Tertiary structures formed by mRNAs impact the efficiency of the translation reaction. Ribosomal frameshift is a well-characterized recoding process that occurs during translation elongation. Pseudoknot and stem-loop structures may stimulate frameshifting by causing a translational halt at a slippery sequence. In this study, we evaluated the efficiency of an unusual -1 frameshift caused by a noncanonical RNA G-quadruplex structure in mammalian cells. The reporter gene construct consisting of a fluorescent protein and Luciferase enabled evaluation of apparent and absolute values of the -1 frameshift efficiency and revealed significant increase of the efficiency by G-quadrupex forming potential sequence. In addition, berberine, a small molecule that binds to and stabilizes G-quadruplex structures, further increased the frameshift efficiency. These results indicate that the stable G-quadruplex structure stimulates the unusual -1 frameshift and has a potential to regulate the frameshift with its ligand.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Kobe 650-0047, Japan
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