1
|
Terrell JR, Le TT, Paul A, Brinton MA, Wilson WD, Poon GMK, Germann MW, Siemer JL. Structure of an RNA G-quadruplex from the West Nile virus genome. Nat Commun 2024; 15:5428. [PMID: 38926367 PMCID: PMC11208454 DOI: 10.1038/s41467-024-49761-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Potential G-quadruplex sites have been identified in the genomes of DNA and RNA viruses and proposed as regulatory elements. The genus Orthoflavivirus contains arthropod-transmitted, positive-sense, single-stranded RNA viruses that cause significant human disease globally. Computational studies have identified multiple potential G-quadruplex sites that are conserved across members of this genus. Subsequent biophysical studies established that some G-quadruplexes predicted in Zika and tickborne encephalitis virus genomes can form and known quadruplex binders reduced viral yields from cells infected with these viruses. The susceptibility of RNA to degradation and the variability of loop regions have made structure determination challenging. Despite these difficulties, we report a high-resolution structure of the NS5-B quadruplex from the West Nile virus genome. Analysis reveals two stacked tetrads that are further stabilized by a stacked triad and transient noncanonical base pairing. This structure expands the landscape of solved RNA quadruplex structures and demonstrates the diversity and complexity of biological quadruplexes. We anticipate that the availability of this structure will assist in solving further viral RNA quadruplexes and provides a model for a conserved antiviral target in Orthoflavivirus genomes.
Collapse
Affiliation(s)
- J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Thao T Le
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Margo A Brinton
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jessica L Siemer
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
| |
Collapse
|
2
|
Zhang Z, Mlýnský V, Krepl M, Šponer J, Stadlbauer P. Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. J Chem Inf Model 2024; 64:3896-3911. [PMID: 38630447 PMCID: PMC11094737 DOI: 10.1021/acs.jcim.4c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
Collapse
Affiliation(s)
- Zhengyue Zhang
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
- CEITEC−Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno 625 00, Czech Republic
- National
Center for Biomolecular Research,
Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| |
Collapse
|
3
|
Vannutelli A, Ouangraoua A, Perreault JP. Toward a Better Understanding of G4 Evolution in the 3 Living Kingdoms. Evol Bioinform Online 2023; 19:11769343231212075. [PMID: 38046653 PMCID: PMC10693206 DOI: 10.1177/11769343231212075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/18/2023] [Indexed: 12/05/2023] Open
Abstract
Background G-quadruplexes (G4s) are secondary structures in DNA and RNA that impact various cellular processes, such as transcription, splicing, and translation. Due to their numerous functions, G4s are involved in many diseases, making their study important. Yet, G4s evolution remains largely unknown, due to their low sequence similarity and the poor quality of their sequence alignments across several species. To address this, we designed a strategy that avoids direct G4s alignment to study G4s evolution in the 3 species kingdoms. We also explored the coevolution between RBPs and G4s. Methods We retrieved one-to-one orthologous genes from the Ensembl Compara database and computed groups of one-to-one orthologous genes. For each group, we aligned gene sequences and identified G4 families as groups of overlapping G4s in the alignment. We analyzed these G4 families using Count, a tool to infer feature evolution into a gene or a species tree. Additionally, we utilized these G4 families to predict G4s by homology. To establish a control dataset, we performed mono-, di- and tri-nucleotide shuffling. Results Only a few conserved G4s occur among all living kingdoms. In eukaryotes, G4s exhibit slight conservation among vertebrates, and few are conserved between plants. In archaea and bacteria, at most, only 2 G4s are common. The G4 homology-based prediction increases the number of conserved G4s in common ancestors. The coevolution between RNA-binding proteins and G4s was investigated and revealed a modest impact of RNA-binding proteins evolution on G4 evolution. However, the details of this relationship remain unclear. Conclusion Even if G4 evolution still eludes us, the present study provides key information to compute groups of homologous G4 and to reveal the evolution history of G4 families.
Collapse
Affiliation(s)
- Anaïs Vannutelli
- Département de biochimie et de génomique fonctionnelle, faculté de médecine et des sciences de la santé, pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
- Département d’informatique, faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Aïda Ouangraoua
- Département d’informatique, faculté des sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Jean-Pierre Perreault
- Département de biochimie et de génomique fonctionnelle, faculté de médecine et des sciences de la santé, pavillon de recherche appliquée sur le cancer, Université de Sherbrooke, Sherbrooke, QC, Canada
| |
Collapse
|
4
|
Guo W, Ji D, Kinghorn AB, Chen F, Pan Y, Li X, Li Q, Huck WTS, Kwok CK, Shum HC. Tuning Material States and Functionalities of G-Quadruplex-Modulated RNA-Peptide Condensates. J Am Chem Soc 2023; 145:2375-2385. [PMID: 36689740 DOI: 10.1021/jacs.2c11362] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
RNA encodes sequence- and structure-dependent interactions to modulate the assembly and properties of biomolecular condensates. RNA G-quadruplexes (rG4s) formed by guanine-rich sequences can trigger the formation of liquid- or solid-like condensates that are involved in many aberrant phase transitions. However, exactly how rG4 motifs modulate different phase transitions and impart distinct material properties to condensates is unclear. Here, using RNA oligonucleotides and cationic peptides as model systems, we show that RNA-peptide condensates exhibit tunability in material properties over a wide spectrum via interactions arising from rG4 folding/unfolding kinetics. rG4-containing oligonucleotides formed strong pairwise attraction with peptides and tended to form solid-like condensates, while their less-structured non-G4 mutants formed liquid-like droplets. We find that the coupling between rG4 dissociation and RNA-peptide complex coacervation triggers solid-to-liquid transition of condensates prior to the complete unfolding of rG4s. This coupling points to a mechanism that material states of rG4-modulated condensates can be finely tuned from solid-like to liquid-like by the addition of less-structured RNA oligonucleotides, which have weak but dominant binding with peptides. We further show that the tunable material states of condensates can enhance RNA aptamer compartmentalization and RNA cleavage reactions. Our results suggest that condensates with complex properties can emerge from subtle changes in RNA oligonucleotides, contributing ways to treat dysfunctional condensates in diseases and insights into prebiotic compartmentalization.
Collapse
Affiliation(s)
- Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Feipeng Chen
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Yi Pan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China
| | - Xiufeng Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Qingchuan Li
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong 999077, China.,Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong 999077, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong 999077,China
| |
Collapse
|
5
|
Shi X, Teng H, Sun Z. An updated overview of experimental and computational approaches to identify non-canonical DNA/RNA structures with emphasis on G-quadruplexes and R-loops. Brief Bioinform 2022; 23:6751149. [PMID: 36208174 PMCID: PMC9677470 DOI: 10.1093/bib/bbac441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/22/2022] [Accepted: 09/13/2022] [Indexed: 12/14/2022] Open
Abstract
Multiple types of non-canonical nucleic acid structures play essential roles in DNA recombination and replication, transcription, and genomic instability and have been associated with several human diseases. Thus, an increasing number of experimental and bioinformatics methods have been developed to identify these structures. To date, most reviews have focused on the features of non-canonical DNA/RNA structure formation, experimental approaches to mapping these structures, and the association of these structures with diseases. In addition, two reviews of computational algorithms for the prediction of non-canonical nucleic acid structures have been published. One of these reviews focused only on computational approaches for G4 detection until 2020. The other mainly summarized the computational tools for predicting cruciform, H-DNA and Z-DNA, in which the algorithms discussed were published before 2012. Since then, several experimental and computational methods have been developed. However, a systematic review including the conformation, sequencing mapping methods and computational prediction strategies for these structures has not yet been published. The purpose of this review is to provide an updated overview of conformation, current sequencing technologies and computational identification methods for non-canonical nucleic acid structures, as well as their strengths and weaknesses. We expect that this review will aid in understanding how these structures are characterised and how they contribute to related biological processes and diseases.
Collapse
Affiliation(s)
- Xiaohui Shi
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The first Affiliated Hospital of WMU; Beijing Institutes of Life Science, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Ouhai District, Wenzhou 325000, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) at Peking University Cancer Hospital and Institute, Ouhai District, Wenzhou 325000, China
| | - Zhongsheng Sun
- Corresponding author: Zhongsheng Sun, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The 1st Affiliated Hospital of WMU, Nanbaixiang Wenyi Yiyuan Xinyuan District, Ouhai District, Wenzhou 325000, China. E-mail:
| |
Collapse
|
6
|
Vannutelli A, Schell L, Perreault JP, Ouangraoua A. GAIA: G-quadruplexes in alive creature database. Nucleic Acids Res 2022; 51:D135-D140. [PMID: 35971612 PMCID: PMC9825426 DOI: 10.1093/nar/gkac657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/08/2022] [Accepted: 08/08/2022] [Indexed: 01/29/2023] Open
Abstract
G-quadruplexes (G4) are 3D structures that are found in both DNA and RNA. Interest in this structure has grown over the past few years due to both its implication in diverse biological mechanisms and its potential use as a therapeutic target, to name two examples. G4s in humans have been widely studied; however, the level of their study in other species remains relatively minimal. That said, progress in this field has resulted in the prediction of G4s structures in various species, ranging from bacteria to eukaryotes. These predictions were analysed in a previous study which revealed that G4s are present in all living kingdoms. To date, eleven different databases have grouped the various G4s depending on either their structures, on the proteins that might bind them, or on their location in the various genomes. However, none of these databases contains information on their location in the transcriptome of many of the implicated species. The GAIA database was designed so as to make this data available online in a user-friendly manner. Through its web interface, users can query GAIA to filter G4s, which, we hope, will help the research in this field. GAIA is available at: https://gaia.cobius.usherbrooke.ca.
Collapse
Affiliation(s)
- Anaïs Vannutelli
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada,Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC J1K 2R1, Canada
| | | | - Jean-Pierre Perreault
- Correspondence may also be addressed to Jean-Pierre Perreault. Tel: +1 819 821 8000 (Ext 75310);
| | - Aïda Ouangraoua
- To whom correspondence should be addressed. Tel: +1 819 821 8000 (Ext 62014);
| |
Collapse
|
7
|
Chang-Gu B, Venkatesan S, Russell R. Kinetics measurements of G-quadruplex binding and unfolding by helicases. Methods 2022; 204:1-13. [PMID: 35483547 PMCID: PMC10034854 DOI: 10.1016/j.ymeth.2022.04.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 01/28/2023] Open
Abstract
G-quadruplex structures (G4s) form readily in DNA and RNA and play diverse roles in gene expression and other processes, and their inappropriate formation and stabilization are linked to human diseases. G4s are inherently long-lived, such that their timely unfolding depends on a suite of DNA and RNA helicase proteins. Biochemical analysis of G4 binding and unfolding by individual helicase proteins is important for establishing their levels of activity, affinity, and specificity for G4s, including individual G4s of varying sequence and structure. Here we describe a set of simple, accessible methods in which electrophoretic mobility shift assays (EMSA) are used to measure the kinetics of G4 binding, dissociation, and unfolding by helicase proteins. We focus on practical considerations and the pitfalls that are most likely to arise when these methods are used to study the activities of helicases on G4s.
Collapse
Affiliation(s)
- Bruce Chang-Gu
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, United States
| | - Sneha Venkatesan
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, United States
| | - Rick Russell
- Department of Molecular Biosciences, University of Texas at Austin, Austin TX 78712, United States.
| |
Collapse
|
8
|
Synthesis and evaluation of 2,9-disubstituted-1,10-phenanthroline derivatives as G-quadruplex binders. Bioorg Med Chem 2022; 73:116971. [DOI: 10.1016/j.bmc.2022.116971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022]
|
9
|
Vannutelli A, Perreault JP, Ouangraoua A. G-quadruplex occurrence and conservation: more than just a question of guanine–cytosine content. NAR Genom Bioinform 2022; 4:lqac010. [PMID: 35261973 PMCID: PMC8896161 DOI: 10.1093/nargab/lqac010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/06/2021] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in humans and a few other species. Recently, predictions have been made with bacterial and archaeal genomes. Nevertheless, a global comparison of predicted G4s (pG4s) across and within the three living kingdoms has not been addressed. In this study, we aimed to predict G4s in genes and transcripts of all kingdoms of living organisms and investigated the differences in their distributions. The relation of the predictions with GC content was studied. It appears that GC content is not the only parameter impacting G4 predictions and abundance. The distribution of pG4 densities varies depending on the class of transcripts and the group of species. Indeed, we have observed that, in coding transcripts, there are more predicted G4s than expected for eukaryotes but not for archaea and bacteria, while in noncoding transcripts, there are as many or fewer predicted G4s in all species groups. We even noticed that some species with the same GC content presented different pG4 profiles. For instance, Leishmania major and Chlamydomonas reinhardtii both have 60% of GC content, but the former has a pG4 density of 0.07 and the latter 1.16.
Collapse
Affiliation(s)
- Anaïs Vannutelli
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
| | - Aïda Ouangraoua
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
| |
Collapse
|
10
|
Hoque ME, Mahendran T, Basu S. Reversal of G-Quadruplexes' Role in Translation Control When Present in the Context of an IRES. Biomolecules 2022; 12:314. [PMID: 35204814 PMCID: PMC8869680 DOI: 10.3390/biom12020314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
G-quadruplexes (GQs) are secondary nucleic acid structures that play regulatory roles in various cellular processes. G-quadruplex-forming sequences present within the 5' UTR of mRNAs can function not only as repressors of translation but also as elements required for optimum function. Based upon previous reports, the majority of the 5' UTR GQ structures inhibit translation, presumably by blocking the ribosome scanning process that is essential for detection of the initiation codon. However, there are certain mRNAs containing GQs that have been identified as positive regulators of translation, as they are needed for translation initiation. While most cellular mRNAs utilize the 5' cap structure to undergo cap-dependent translation initiation, many rely on cap-independent translation under certain conditions in which the cap-dependent initiation mechanism is not viable or slowed down, for example, during development, under stress and in many diseases. Cap-independent translation mainly occurs via Internal Ribosomal Entry Sites (IRESs) that are located in the 5' UTR of mRNAs and are equipped with structural features that can recruit the ribosome or other factors to initiate translation without the need for a 5' cap. In this review, we will focus only on the role of RNA GQs present in the 5' UTR of mRNAs, where they play a critical role in translation initiation, and discuss the potential mechanism of this phenomenon, which is yet to be fully delineated.
Collapse
Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA; (M.E.H.); (T.M.)
| |
Collapse
|
11
|
Mukherjee SK, Knop JM, Winter RHA. Modulation of the Conformational Space of SARS-CoV-2 RNA Quadruplex RG-1 by Cellular Components and the Amyloidogenic Peptides α-Synuclein and hIAPP. Chemistry 2021; 28:e202104182. [PMID: 34882862 PMCID: PMC9015630 DOI: 10.1002/chem.202104182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Indexed: 11/10/2022]
Abstract
Given the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), which particularly threatens older people with comorbidities such as diabetes mellitus and dementia, understanding the relationship between Covid-19 and other diseases is an important factor for treatment. Possible targets for medical intervention include G-quadruplexes (G4Qs) and their protein interaction partners. We investigated the stability and conformational space of the RG-1 RNA-G-quadruplex of the SARS-CoV-2 N-gene in the presence of salts, cosolutes, crowders and intrinsically disordered peptides, focusing on α-Synuclein and the human islet amyloid polypeptide, which are involved in Parkinson's disease (PD) and type-II diabetes mellitus (T2DM), respectively. We found that the conformational dynamics of the RG-1 G4Q is strongly affected by the various solution conditions. Further, the amyloidogenic peptides were found to strongly modulate the conformational equilibrium of the RG-1. Considerable changes are observed with respect to their interaction with human telomeric G4Qs, which adopt different topologies. These results may therefore shed more light on the relationship between PD as well as T2DM and the SARS-CoV-2 disease and their molecular underpinnings. Since dysregulation of G4Q formation by rationally designed targeting compounds affects the control of cellular processes, this study should contribute to the development of specific ligands for intervention.
Collapse
Affiliation(s)
- Sanjib K Mukherjee
- TU Dortmund University: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Jim-Marcel Knop
- TU Dortmund University: Technische Universitat Dortmund, Chemistry and Chemical Biology, GERMANY
| | - Roland Hermann Alfons Winter
- TU Dortmund University, Chemistry and Chemical Biology, Otto-Hahn Str. 4a, Physical Chemistry I, 44227, Dortmund, GERMANY
| |
Collapse
|
12
|
Ishiguro A, Lu J, Ozawa D, Nagai Y, Ishihama A. ALS-linked FUS mutations dysregulate G-quadruplex-dependent liquid-liquid phase separation and liquid-to-solid transition. J Biol Chem 2021; 297:101284. [PMID: 34624313 PMCID: PMC8567205 DOI: 10.1016/j.jbc.2021.101284] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 01/15/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by the accumulation of protein aggregates in motor neurons. Recent discoveries of genetic mutations in ALS patients promoted research into the complex molecular mechanisms underlying ALS. FUS (fused in sarcoma) is a representative ALS-linked RNA-binding protein (RBP) that specifically recognizes G-quadruplex (G4)-DNA/RNAs. However, the effects of ALS-linked FUS mutations on the G4-RNA-binding activity and the phase behavior have never been investigated. Using the purified full-length FUS, we analyzed the molecular mechanisms of multidomain structures consisting of multiple functional modules that bind to G4. Here we succeeded to observe the liquid–liquid phase separation (LLPS) of FUS condensate formation and subsequent liquid-to-solid transition (LST) leading to the formation of FUS aggregates. This process was markedly promoted through FUS interaction with G4-RNA. To further investigate, we selected a total of eight representative ALS-linked FUS mutants within multidomain structures and purified these proteins. The regulation of G4-RNA-dependent LLPS and LST pathways was lost for all ALS-linked FUS mutants defective in G4-RNA recognition tested, supporting the essential role of G4-RNA in this process. Noteworthy, the P525L mutation that causes juvenile ALS exhibited the largest effect on both G4-RNA binding and FUS aggregation. The findings described herein could provide a clue to the hitherto undefined connection between protein aggregation and dysfunction of RBPs in the complex pathway of ALS pathogenesis.
Collapse
Affiliation(s)
- Akira Ishiguro
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan.
| | - Jun Lu
- Medical Examination Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Daisaku Ozawa
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan; Department of Neurology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Yoshitaka Nagai
- Department of Neurotherapeutics, Osaka University Graduate School of Medicine, Suita, Osaka, Japan; Department of Neurology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
| |
Collapse
|
13
|
Cadoni E, De Paepe L, Manicardi A, Madder A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res 2021; 49:6638-6659. [PMID: 33978760 PMCID: PMC8266634 DOI: 10.1093/nar/gkab334] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/15/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
G-Quadruplexes (G4s) are widely studied secondary DNA/RNA structures, naturally occurring when G-rich sequences are present. The strategic localization of G4s in genome areas of crucial importance, such as proto-oncogenes and telomeres, entails fundamental implications in terms of gene expression regulation and other important biological processes. Although thousands of small molecules capable to induce G4 stabilization have been reported over the past 20 years, approaches based on the hybridization of a synthetic probe, allowing sequence-specific G4-recognition and targeting are still rather limited. In this review, after introducing important general notions about G4s, we aim to list, explain and critically analyse in more detail the principal approaches available to target G4s by using oligonucleotides and synthetic analogues such as Locked Nucleic Acids (LNAs) and Peptide Nucleic Acids (PNAs), reporting on the most relevant examples described in literature to date.
Collapse
Affiliation(s)
- Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Lessandro De Paepe
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Müller D, Bessi I, Richter C, Schwalbe H. The Folding Landscapes of Human Telomeric RNA and DNA G-Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021; 60:10895-10901. [PMID: 33539622 PMCID: PMC8252441 DOI: 10.1002/anie.202100280] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/04/2021] [Indexed: 01/23/2023]
Abstract
We investigated the folding kinetics of G-quadruplex (G4) structures by comparing the K+ -induced folding of an RNA G4 derived from the human telomeric repeat-containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real-time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off-pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with 19 F bound to C2' in arabino configuration adopt exclusively anti conformations for χ. These fluoro-modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.
Collapse
Affiliation(s)
- Diana Müller
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Irene Bessi
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
- Present address: Julius-Maximilians-University Würzburg, Institute of Organic Chemistry, Am Hubland 16, 97074, Würzburg, Germany
| | - Christian Richter
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Goethe University Frankfurt/Centre for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
| |
Collapse
|
16
|
The Folding Landscapes of Human Telomeric RNA and DNA G‐Quadruplexes are Markedly Different. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
17
|
Tao Y, Zheng Y, Zhai Q, Wei D. Recent advances in the development of small molecules targeting RNA G-quadruplexes for drug discovery. Bioorg Chem 2021; 110:104804. [PMID: 33740677 DOI: 10.1016/j.bioorg.2021.104804] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/12/2022]
Abstract
Extensive evidence indicates that RNA G-quadruplexes have associated with some important cellular events. Investigation of RNA G-quadruplexes is thus vital to revealing their biofunctions. Several small molecules have been developed to target RNA G-quadruplexes to date. Some of the small molecules showed significantly light-up fluorescence signals upon binding to RNA G-quadruplexes, while some of them regulated the biofunctions of RNA G-quadruplexes. In this mini-review, the small molecules divided into four kinds are expounded which focused mainly on their structural features and biological activities. Moreover, we raised the current challenges and promising prospects. This mini-review might contribute to exploiting more sophisticated small molecules targeting RNA G-quadruplexes with high specificity based on the reported chemical structural features.
Collapse
Affiliation(s)
- Yanfei Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingge Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qianqian Zhai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
18
|
Ishiguro A, Katayama A, Ishihama A. Different recognition modes of G-quadruplex RNA between two ALS/FTLD-linked proteins TDP-43 and FUS. FEBS Lett 2020; 595:310-323. [PMID: 33269497 DOI: 10.1002/1873-3468.14013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/15/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis/frontotemporal lobar degeneration-linked proteins, TDP-43 and fused in sarcoma (FUS), bind to G-quadruplex-containing mRNAs and transport them to distal neurites for local translation. The specificity and mechanism of G4-RNA binding, however, remain largely unsolved. Using purified full-length TDP-43 and FUS and a set of seven G4-DNA/RNA, we compared their recognition properties of G4-RNAs. Both TDP-43 and FUS recognized and bound to G4-DNA/RNAs, but the target selectivity differed between two proteins. TDP-43 recognized only parallel-stranded G4-DNA/RNAs, leading to stabilize the G4 conformation. In contrast, FUS bound to all three types, parallel, hybrid, and antiparallel, of G4-DNA/RNAs, resulting in deformation of the G4 structure. We then concluded that the target selectivity and the influence on G4 RNA structure differed between TDP-43 and FUS.
Collapse
Affiliation(s)
- Akira Ishiguro
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
| | - Akira Katayama
- Department of Molecular Analysis Laboratory, Nippon Medical School, Bunkyo-ku, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
| |
Collapse
|
19
|
Asamitsu S, Yabuki Y, Ikenoshita S, Wada T, Shioda N. Pharmacological prospects of G-quadruplexes for neurological diseases using porphyrins. Biochem Biophys Res Commun 2020; 531:51-55. [DOI: 10.1016/j.bbrc.2020.01.054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 12/14/2022]
|
20
|
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.
Collapse
Affiliation(s)
- Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | | |
Collapse
|
21
|
Athar YM, Joseph S. RNA-Binding Specificity of the Human Fragile X Mental Retardation Protein. J Mol Biol 2020; 432:3851-3868. [PMID: 32343993 DOI: 10.1016/j.jmb.2020.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Fragile X syndrome is the most common form of inherited intellectual disability and is caused by a deficiency of the fragile X mental retardation protein (FMRP) in neurons. FMRP regulates the translation of numerous mRNAs within dendritic synapses, but how FMRP recognizes these target mRNAs remains unknown. FMRP has KH0, KH1, KH2, and RGG domains, which are thought to bind to specific RNA recognition elements (RREs). Several studies used high-throughput methods to identify various RREs in mRNAs that FMRP may bind to in vivo. However, there is little overlap in the mRNA targets identified by each study, suggesting that the RNA-binding specificity of FMRP is still unknown. To determine the specificity of FMRP for the RREs, we performed quantitative in vitroRNA binding studies with various constructs of human FMRP. Unexpectedly, our studies show that the KH domains do not bind to the previously identified RREs. To further investigate the RNA-binding specificity of FMRP, we developed a new method called Motif Identification by Analysis of Simple sequences (MIDAS) to identify single-stranded RNA sequences bound by KH domains. We find that the FMRP KH0, KH1, and KH2 domains bind weakly to the single-stranded RNA sequences suggesting that they may have evolved to bind more complex RNA structures. Additionally, we find that the RGG motif of human FMRP binds with a high affinity to an RNAG-quadruplex structure that lacks single-stranded loops, double-stranded stems, or junctions.
Collapse
Affiliation(s)
- Youssi M Athar
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093-0314, USA
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093-0314, USA.
| |
Collapse
|
22
|
Pany SPP, Sapra M, Sharma J, Dhamodharan V, Patankar S, Pradeepkumar PI. Presence of Potential G‐Quadruplex RNA‐Forming Motifs at the 5′‐UTR of
PP2Acα
mRNA Repress Translation. Chembiochem 2019; 20:2955-2960. [DOI: 10.1002/cbic.201900336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Indexed: 01/08/2023]
Affiliation(s)
| | - Mahak Sapra
- Centre for Research in Nanotechnology and ScienceIndian Institute of Technology Bombay Mumbai 400076 India
| | - Jitendar Sharma
- Department of ChemistryIndian Institute of Technology Bombay Mumbai 400076 India
| | - V. Dhamodharan
- Department of ChemistryIndian Institute of Technology Bombay Mumbai 400076 India
| | - Swati Patankar
- Department of Bioscience and BioengineeringIndian Institute of Technology Bombay Mumbai 400076 India
| | - P. I. Pradeepkumar
- Department of ChemistryIndian Institute of Technology Bombay Mumbai 400076 India
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
G-Quadruplexes in Human Ribosomal RNA. J Mol Biol 2019; 431:1940-1955. [PMID: 30885721 DOI: 10.1016/j.jmb.2019.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 11/20/2022]
Abstract
rRNA is the single most abundant polymer in most cells. Mammalian rRNAs are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments, which contain extended tentacles in metazoans. Here we show that the terminus of an rRNA tentacle of Homo sapiens contains 10 tandem G-tracts that form highly stable G-quadruplexes in vitro. We characterized rRNA of the H. sapiens large ribosomal subunit by computation, circular dichroism, UV melting, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts, and blotting. We investigated Expansion Segment 7 (ES7), oligomers derived from ES7, intact 28S rRNA, 80S ribosomes, and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. These proteins include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins. Finally, by multiple sequence alignments, we observe that G-quadruplex-forming sequences are a general feature of LSU rRNA of Chordata but not, as far as we can tell, of other species. Chordata ribosomes present polymorphic tentacles with the potential to switch between inter- and intramolecular G-quadruplexes. To our knowledge, G-quadruplexes have not been reported previously in ribosomes.
Collapse
|
25
|
CNBP Homologues Gis2 and Znf9 Interact with a Putative G-Quadruplex-Forming 3' Untranslated Region, Altering Polysome Association and Stress Tolerance in Cryptococcus neoformans. mSphere 2018; 3:3/4/e00201-18. [PMID: 30089646 PMCID: PMC6083090 DOI: 10.1128/msphere.00201-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Stress adaptation is fundamental to the success of Cryptococcus neoformans as a human pathogen and requires a reprogramming of the translating pool of mRNA. This reprogramming begins with the regulated degradation of mRNAs encoding the translational machinery. The mechanism by which these mRNAs are specified has not been determined. This study has identified a cis element within a G-quadruplex structure that binds two C. neoformans homologues of cellular nucleic acid binding protein (CNBP). These proteins regulate the polysome association of the target mRNA but perform functions related to sterol homeostasis which appear independent of ribosomal protein mRNAs. The presence of two CNBP homologues in C. neoformans suggests a diversification of function of these proteins, one of which appears to regulate sterol biosynthesis and fluconazole sensitivity. In Cryptococcus neoformans, mRNAs encoding ribosomal proteins (RP) are rapidly and specifically repressed during cellular stress, and the bulk of this repression is mediated by deadenylation-dependent mRNA decay. A motif-finding approach was applied to the 3′ untranslated regions (UTRs) of RP transcripts regulated by mRNA decay, and a single, significant motif, GGAUG, was identified. Znf9, a small zinc knuckle RNA binding protein identified by mass spectrometry, was found to interact specifically with the RPL2 3′-UTR probe. A second, homologous protein, Gis2, was identified in the genome of C. neoformans and also bound the 3′-UTR probe, and deletion of both genes resulted in loss of binding in cell extracts. The RPL2 3′ UTR contains four G-triplets (GGG) that have the potential to form a G-quadruplex, and temperature gradient gel electrophoresis revealed a potassium-dependent structure consistent with a G-quadruplex that was abrogated by mutation of G-triplets. However, deletion of G-triplets did not abrogate the binding of either Znf9 or Gis2, suggesting that these proteins either bind irrespective of structure or act to prevent structure formation. Deletion of both GIS2 and ZNF9 resulted in a modest increase in basal stability of the RPL2 mRNA which resulted in an association with higher-molecular-weight polysomes under unstressed conditions. The gis2Δ mutant and gis2Δ znf9Δ double mutant exhibited sensitivity to cobalt chloride, fluconazole, and oxidative stress, and although transcriptional induction of ERG25 was similar to that of the wild type, analysis of sterol content revealed repressed levels of sterols in the gis2Δ and gis2Δ znf9Δ double mutant, suggesting a role in translational regulation of sterol biosynthesis. IMPORTANCE Stress adaptation is fundamental to the success of Cryptococcus neoformans as a human pathogen and requires a reprogramming of the translating pool of mRNA. This reprogramming begins with the regulated degradation of mRNAs encoding the translational machinery. The mechanism by which these mRNAs are specified has not been determined. This study has identified a cis element within a G-quadruplex structure that binds two C. neoformans homologues of cellular nucleic acid binding protein (CNBP). These proteins regulate the polysome association of the target mRNA but perform functions related to sterol homeostasis which appear independent of ribosomal protein mRNAs. The presence of two CNBP homologues in C. neoformans suggests a diversification of function of these proteins, one of which appears to regulate sterol biosynthesis and fluconazole sensitivity.
Collapse
|
26
|
Benner SA. Detecting Darwinism from Molecules in the Enceladus Plumes, Jupiter's Moons, and Other Planetary Water Lagoons. ASTROBIOLOGY 2017; 17:840-851. [PMID: 28665680 PMCID: PMC5610385 DOI: 10.1089/ast.2016.1611] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
To the astrobiologist, Enceladus offers easy access to a potential subsurface biosphere via the intermediacy of a plume of water emerging directly into space. A direct question follows: If we were to collect a sample of this plume, what in that sample, through its presence or its absence, would suggest the presence and/or absence of life in this exotic locale? This question is, of course, relevant for life detection in any aqueous lagoon that we might be able to sample. This manuscript reviews physical chemical constraints that must be met by a genetic polymer for it to support Darwinism, a process believed to be required for a chemical system to generate properties that we value in biology. We propose that the most important of these is a repeating backbone charge; a Darwinian genetic biopolymer must be a "polyelectrolyte." Relevant to mission design, such biopolymers are especially easy to recover and concentrate from aqueous mixtures for detection, simply by washing the aqueous mixtures across a polycharged support. Several device architectures are described to ensure that, once captured, the biopolymer meets two other requirements for Darwinism, homochirality and a small building block "alphabet." This approach is compared and contrasted with alternative biomolecule detection approaches that seek homochirality and constrained alphabets in non-encoded biopolymers. This discussion is set within a model for the history of the terran biosphere, identifying points in that natural history where these alternative approaches would have failed to detect terran life. Key Words: Enceladus-Life detection-Europa-Icy moon-Biosignatures-Polyelectrolyte theory of the gene. Astrobiology 17, 840-851.
Collapse
Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution , Alachua, Florida
| |
Collapse
|
27
|
Kulikov K, Nozinovic S, Kath-Schorr S. The 5'-AG 5 CC-3' Fragment from the Human CPEB3 Ribozyme Forms an Ultrastable Parallel RNA G-Quadruplex. Chembiochem 2017; 18:969-973. [PMID: 28296179 DOI: 10.1002/cbic.201700028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 11/07/2022]
Abstract
An unusually thermostable G-quadruplex is formed by a sequence fragment of a naturally occurring ribozyme, the human CPEB3 ribozyme. Strong evidence is provided for the formation of a uniquely stable intermolecular G-quadruplex structure consisting of five tetrad layers, by using CD spectroscopy, UV melting curves, 2D NMR spectroscopy, and gel shift analysis. The cationic porphyrin TMPyP4 destabilizes the complex.
Collapse
Affiliation(s)
- Katharina Kulikov
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Senada Nozinovic
- Institute for Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| |
Collapse
|
28
|
Liao JY, Anosova I, Bala S, Van Horn WD, Chaput JC. A parallel stranded G-quadruplex composed of threose nucleic acid (TNA). Biopolymers 2017; 107. [PMID: 27718227 DOI: 10.1002/bip.22999] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/26/2016] [Accepted: 10/05/2016] [Indexed: 11/08/2022]
Abstract
G-rich sequences can adopt four-stranded helical structures, called G-quadruplexes, that self-assemble around monovalent cations like sodium (Na+ ) and potassium (K+ ). Whether similar structures can be formed from xeno-nucleic acid (XNA) polymers with a shorter backbone repeat unit is an unanswered question with significant implications on the fold space of functional XNA polymers. Here, we examine the potential for TNA (α-l-threofuranosyl nucleic acid) to adopt a four-stranded helical structure based on a planar G-quartet motif. Using native polyacrylamide gel electrophoresis (PAGE), circular dichroism (CD) and solution-state nuclear magnetic resonance (NMR) spectroscopy, we show that despite a backbone repeat unit that is one atom shorter than the backbone repeat unit found in DNA and RNA, TNA can self-assemble into stable G-quadruplex structures that are similar in thermal stability to equivalent DNA structures. However, unlike DNA, TNA does not appear to discriminate between Na+ and K+ ions, as G-quadruplex structures form equally well in the presence of either ion. Together, these findings demonstrate that despite a shorter backbone repeat unit, TNA is capable of self-assembling into stable G-quadruplex structures.
Collapse
Affiliation(s)
- Jen-Yu Liao
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697
| | - Irina Anosova
- School of Molecular Sciences and the Biodesign Institute, Arizona State University. Tempe, AZ, 85287
| | - Saikat Bala
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697
| | - Wade D Van Horn
- School of Molecular Sciences and the Biodesign Institute, Arizona State University. Tempe, AZ, 85287
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697
| |
Collapse
|
29
|
Pandey S, Agarwala P, Maiti S. Targeting RNA G-Quadruplexes for Potential Therapeutic Applications. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
30
|
Jeng SCY, Chan HHY, Booy EP, McKenna SA, Unrau PJ. Fluorophore ligand binding and complex stabilization of the RNA Mango and RNA Spinach aptamers. RNA (NEW YORK, N.Y.) 2016; 22:1884-1892. [PMID: 27777365 PMCID: PMC5113208 DOI: 10.1261/rna.056226.116] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/23/2016] [Indexed: 05/29/2023]
Abstract
The effective tracking and purification of biological RNAs and RNA protein complexes is currently challenging. One promising strategy to simultaneously address both of these problems is to develop high-affinity RNA aptamers against taggable small molecule fluorophores. RNA Mango is a 39-nucleotide, parallel-stranded G-quadruplex RNA aptamer motif that binds with nanomolar affinity to a set of thiazole orange (TO1) derivatives while simultaneously inducing a 103-fold increase in fluorescence. We find that RNA Mango has a large increase in its thermal stability upon the addition of its TO1-Biotin ligand. Consistent with this thermal stabilization, RNA Mango can effectively discriminate TO1-Biotin from a broad range of small molecule fluorophores. In contrast, RNA Spinach, which is known to have a substantially more rigid G-quadruplex structure, was found to bind to this set of fluorophores, often with higher affinity than to its native ligand, 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), and did not exhibit thermal stabilization in the presence of the TO1-Biotin fluorophore. Our data suggest that RNA Mango is likely to use a concerted ligand-binding mechanism that allows it to simultaneously bind and recognize its TO1-Biotin ligand, whereas RNA Spinach appears to lack such a mechanism. The high binding affinity and fluorescent efficiency of RNA Mango provides a compelling alternative to RNA Spinach as an RNA reporter system and paves the way for the future development of small fluorophore RNA reporter systems.
Collapse
Affiliation(s)
- Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Hedy H Y Chan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
31
|
Nasiri AH, Wurm JP, Immer C, Weickhmann AK, Wöhnert J. An intermolecular G-quadruplex as the basis for GTP recognition in the class V-GTP aptamer. RNA (NEW YORK, N.Y.) 2016; 22:1750-1759. [PMID: 27659052 PMCID: PMC5066627 DOI: 10.1261/rna.058909.116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
Many naturally occurring or artificially created RNAs are capable of binding to guanine or guanine derivatives with high affinity and selectivity. They bind their ligands using very different recognition modes involving a diverse set of hydrogen bonding and stacking interactions. Apparently, the potential structural diversity for guanine, guanosine, and guanine nucleotide binding motifs is far from being fully explored. Szostak and coworkers have derived a large set of different GTP-binding aptamer families differing widely in sequence, secondary structure, and ligand specificity. The so-called class V-GTP aptamer from this set binds GTP with very high affinity and has a complex secondary structure. Here we use solution NMR spectroscopy to demonstrate that the class V aptamer binds GTP through the formation of an intermolecular two-layered G-quadruplex structure that directly incorporates the ligand and folds only upon ligand addition. Ligand binding and G-quadruplex formation depend strongly on the identity of monovalent cations present with a clear preference for potassium ions. GTP binding through direct insertion into an intermolecular G-quadruplex is a previously unobserved structural variation for ligand-binding RNA motifs and rationalizes the previously observed specificity pattern of the class V aptamer for GTP analogs.
Collapse
Affiliation(s)
- Amir H Nasiri
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Jan Philip Wurm
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carina Immer
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Anna Katharina Weickhmann
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, 60438 Frankfurt, Germany
| |
Collapse
|
32
|
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: 377] [Impact Index Per Article: 47.1] [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.
Collapse
Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
| |
Collapse
|
33
|
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.
Collapse
Affiliation(s)
- Prachi Agarwala
- Proteomics and Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India.
| | | | | |
Collapse
|
34
|
Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
Collapse
Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| |
Collapse
|
35
|
Abstract
Recent research has established clear connections between G-quadruplexes and human disease. Features of quadruplex structures that promote genomic instability have been determined. Quadruplexes have been identified as transcriptional, translational and epigenetic regulatory targets of factors associated with human genetic disease. An expandable GGGGCC motif that can adopt a G4 structure, located in the previously obscure C9ORF72 locus, has been shown to contribute to two well-recognized neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). This review focuses on these advances, which further dispel the view that genomic biology is limited to the confines of the canonical B-form DNA duplex, and show how quadruplexes contribute spatial and temporal dimensionalities to linear sequence information. This recent progress also has clear practical ramifications, as prevention, diagnosis, and treatment of disease depend on understanding the underlying mechanisms.
Collapse
|
36
|
Cajigas I, Leib DE, Cochrane J, Luo H, Swyter KR, Chen S, Clark BS, Thompson J, Yates JR, Kingston RE, Kohtz JD. Evf2 lncRNA/BRG1/DLX1 interactions reveal RNA-dependent inhibition of chromatin remodeling. Development 2015; 142:2641-52. [PMID: 26138476 DOI: 10.1242/dev.126318] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/09/2015] [Indexed: 01/12/2023]
Abstract
Transcription-regulating long non-coding RNAs (lncRNAs) have the potential to control the site-specific expression of thousands of target genes. Previously, we showed that Evf2, the first described ultraconserved lncRNA, increases the association of transcriptional activators (DLX homeodomain proteins) with key DNA enhancers but represses gene expression. In this report, mass spectrometry shows that the Evf2-DLX1 ribonucleoprotein (RNP) contains the SWI/SNF-related chromatin remodelers Brahma-related gene 1 (BRG1, SMARCA4) and Brahma-associated factor (BAF170, SMARCC2) in the developing mouse forebrain. Evf2 RNA colocalizes with BRG1 in nuclear clouds and increases BRG1 association with key DNA regulatory enhancers in the developing forebrain. While BRG1 directly interacts with DLX1 and Evf2 through distinct binding sites, Evf2 directly inhibits BRG1 ATPase and chromatin remodeling activities. In vitro studies show that both RNA-BRG1 binding and RNA inhibition of BRG1 ATPase/remodeling activity are promiscuous, suggesting that context is a crucial factor in RNA-dependent chromatin remodeling inhibition. Together, these experiments support a model in which RNAs convert an active enhancer to a repressed enhancer by directly inhibiting chromatin remodeling activity, and address the apparent paradox of RNA-mediated stabilization of transcriptional activators at enhancers with a repressive outcome. The importance of BRG1/RNA and BRG1/homeodomain interactions in neurodevelopmental disorders is underscored by the finding that mutations in Coffin-Siris syndrome, a human intellectual disability disorder, localize to the BRG1 RNA-binding and DLX1-binding domains.
Collapse
Affiliation(s)
- Ivelisse Cajigas
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - David E Leib
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Jesse Cochrane
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Hao Luo
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Kelsey R Swyter
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Sean Chen
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | - Brian S Clark
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| | | | - John R Yates
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert E Kingston
- Department of Molecular Biology, Harvard University, Boston, MA 02114, USA
| | - Jhumku D Kohtz
- Developmental Biology and Department of Pediatrics, Stanley Manne Children's Research Institute and Feinberg School of Medicine, Northwestern University, Box 204, 2430 N. Halsted, Chicago, IL 60614, USA
| |
Collapse
|
37
|
Abstract
RNAs adopt diverse folded structures that are essential for function and thus play critical roles in cellular biology. A striking example of this is the ribosome, a complex, three-dimensionally folded macromolecular machine that orchestrates protein synthesis. Advances in RNA biochemistry, structural and molecular biology, and bioinformatics have revealed other non-coding RNAs whose functions are dictated by their structure. It is not surprising that aberrantly folded RNA structures contribute to disease. In this Review, we provide a brief introduction into RNA structural biology and then describe how RNA structures function in cells and cause or contribute to neurological disease. Finally, we highlight successful applications of rational design principles to provide chemical probes and lead compounds targeting structured RNAs. Based on several examples of well-characterized RNA-driven neurological disorders, we demonstrate how designed small molecules can facilitate the study of RNA dysfunction, elucidating previously unknown roles for RNA in disease, and provide lead therapeutics.
Collapse
Affiliation(s)
- Viachaslau Bernat
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
| |
Collapse
|
38
|
Mirihana Arachchilage G, Dassanayake AC, Basu S. A potassium ion-dependent RNA structural switch regulates human pre-miRNA 92b maturation. ACTA ACUST UNITED AC 2015; 22:262-72. [PMID: 25641166 DOI: 10.1016/j.chembiol.2014.12.013] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/11/2014] [Accepted: 12/29/2014] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are an important set of oligonucleotide sequences with a biogenesis that involves Dicer-mediated cleavage as a critical step. Dicer cleaves the precursor miRNA (pre-miRNA) stem-loop structure to produce the mature miRNA. Using bioinformatics analysis, we discovered the presence of putative G-quadruplex (GQ)-forming sequences in about 16% of pre-miRNAs. We report the existence of a GQ as an alternative to the canonical stem-loop structure in the clinically important human pre-miRNA 92b. GQ formation led to unwinding of the stem-loop structure imparting resistance to Dicer-mediated cleavage both in vitro and in vivo. A potential K(+) ion-dependent equilibrium between GQ and the stem-loop structure has the ability to regulate the Dicer-mediated maturation of pre-miRNA 92b, which consequently affects target gene silencing. These findings unravel a new mechanism of regulation in pre-miRNA maturation, albeit at the RNA structure level.
Collapse
Affiliation(s)
| | - Arosha C Dassanayake
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA.
| |
Collapse
|
39
|
Komatsu R, Sawada R, Umehara T, Tamura K. Proline might have been the first amino acid in the primitive genetic code. J Mol Evol 2014; 78:310-2. [PMID: 24973301 DOI: 10.1007/s00239-014-9629-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/07/2014] [Indexed: 11/25/2022]
Abstract
Stereochemical assignment of amino acids and corresponding codons or anticodons has not been successful so far. Here, we focused on proline and GGG (anticodon of tRNA(Pro)) and investigated their mutual interaction. Circular dichroism spectroscopy revealed that guanosine nucleotides (GG, GGG) formed G-quartet structures. The structures were destroyed by adding high concentrations of proline. We propose that the possibility of the reversible proline/G-quartet interaction could have contributed to the specific assignment of proline on GGG and that this coding could have been the first in the genetic code.
Collapse
Affiliation(s)
- Reina Komatsu
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | | | | | | |
Collapse
|
40
|
Abstract
Recent experiments provide fascinating examples of how G4 DNA and G4 RNA structures—aka quadruplexes—may contribute to normal biology and to genomic pathologies. Quadruplexes are transient and therefore difficult to identify directly in living cells, which initially caused skepticism regarding not only their biological relevance but even their existence. There is now compelling evidence for functions of some G4 motifs and the corresponding quadruplexes in essential processes, including initiation of DNA replication, telomere maintenance, regulated recombination in immune evasion and the immune response, control of gene expression, and genetic and epigenetic instability. Recognition and resolution of quadruplex structures is therefore an essential component of genome biology. We propose that G4 motifs and structures that participate in key processes compose the G4 genome, analogous to the transcriptome, proteome, or metabolome. This is a new view of the genome, which sees DNA as not only a simple alphabet but also a more complex geography. The challenge for the future is to systematically identify the G4 motifs that form quadruplexes in living cells and the features that confer on specific G4 motifs the ability to function as structural elements.
Collapse
|
41
|
Umehara T, Kitagawa T, Nakazawa Y, Yoshino H, Nemoto R, Tamura K. RNA tetraplex as a primordial peptide synthesis scaffold. Biosystems 2012; 109:145-50. [PMID: 22465151 DOI: 10.1016/j.biosystems.2012.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/02/2012] [Accepted: 03/08/2012] [Indexed: 11/29/2022]
Abstract
Peptide bond formation at the peptidyl transferase center on the ribosome is a crucial phenomenon in life systems. In this study, we conceptually propose possible roles of the RNA tetraplex as a scaffold for two aminoacyl minihelices that enable peptide bond formation. The basic rationale of this model is that "parallel" complementary templates composed of only 10-mer nucleotides can position two amino acids in close proximity, which is conceptually and essentially similar to the situation observed in ribosomes. Using supportive experimental data, we discuss the origin and evolution of peptide bond formation in early biological systems.
Collapse
Affiliation(s)
- Takuya Umehara
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | | | | | | | | | | |
Collapse
|
42
|
Lease RA, Arluison V, Lavelle C. Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assembly in vivo.. FRONTIERS IN LIFE SCIENCE 2012; 6:19-32. [PMID: 23914307 PMCID: PMC3725660 DOI: 10.1080/21553769.2012.761163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/18/2012] [Indexed: 11/23/2022]
Abstract
The primacy and power of RNA in governing many processes of life has begun to be more fully appreciated in both the discovery and inventive sciences. A variety of RNA interactions regulate gene expression, and structural self-assembly underlies many of these processes. The understanding sparked by these discoveries has inspired and informed the engineering of novel RNA structures, control elements, and genetic circuits in cells. Many of these engineered systems are built up fundamentally from RNA–RNA interactions, often combining modular, rational design with functional selection and screening. It is therefore useful to review the particular class of RNA-based regulatory mechanisms that rely on RNA self-assembly either through homomeric (self–self) or heteromeric (self–nonself) RNA–RNA interactions. Structures and sequence elements within individual RNAs create a basis for the pairing interactions, and in some instances can even lead to the formation of RNA polymers. Example systems of dimers, multimers, and polymers are reviewed in this article in the context of natural systems, wherein the function and impact of self-assemblies are understood. Following this, a brief overview is presented of specific engineered RNA self-assembly systems implemented in vivo, with lessons learned from both discovery and engineering approaches to RNA–RNA self-assembly.
Collapse
Affiliation(s)
- Richard A Lease
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | | | | |
Collapse
|
43
|
Bugaut A, Balasubramanian S. 5'-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res 2012; 40:4727-41. [PMID: 22351747 PMCID: PMC3367173 DOI: 10.1093/nar/gks068] [Citation(s) in RCA: 469] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
RNA structures in the untranslated regions (UTRs) of mRNAs influence post-transcriptional regulation of gene expression. Much of the knowledge in this area depends on canonical double-stranded RNA elements. There has been considerable recent advancement of our understanding of guanine(G)-rich nucleic acids sequences that form four-stranded structures, called G-quadruplexes. While much of the research has been focused on DNA G-quadruplexes, there has recently been a rapid emergence of interest in RNA G-quadruplexes, particularly in the 5′-UTRs of mRNAs. Collectively, these studies suggest that RNA G-quadruplexes exist in the 5′-UTRs of many genes, including genes of clinical interest, and that such structural elements can influence translation. This review features the progresses in the study of 5′-UTR RNA G-quadruplex-mediated translational control. It covers computational analysis, cell-free, cell-based and chemical biology studies that have sought to elucidate the roles of RNA G-quadruplexes in both cap-dependent and -independent regulation of mRNA translation. We also discuss protein trans-acting factors that have been implicated and the evidence that such RNA motifs have potential as small molecule target. Finally, we close the review with a perspective on the future challenges in the field of 5′-UTR RNA G-quadruplex-mediated translation regulation.
Collapse
Affiliation(s)
- Anthony Bugaut
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | | |
Collapse
|
44
|
Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. Research Progress of RNA Quadruplex. Nucleic Acid Ther 2011; 21:185-200. [DOI: 10.1089/nat.2010.0272] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Xiaohui Ji
- Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Huaxi Zhou
- Department of Systems Science, School of Management, Beijing Normal University, Beijing, China
| | - Junfeng Xiang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Changqi Zhao
- Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
45
|
Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. Research Progress of RNA Quadruplex. Oligonucleotides 2011:121102072334007. [PMID: 21574857 DOI: 10.1089/oli.2010.0272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
RNA/DNA sequences rich in guanine (G) can form a 4-strand structure, G-quadruplex, which has been extensively researched and observed in mammalian, fungi, and plants, with in vivo existence in eukaryotic cells. Compared with DNA quadruplex, the potential existence of RNA quadruplex appears to be generally rare; however, it is believed by some researchers to be more inevitable in vivo and speculated to play an important role where it exists. Recently, researches concerning the function of G-quadruplexes in RNAs commence, making much progress. However, there is no available review particularly focusing on RNA quadruplex till now as we know. Therefore, we decide to give a review to comprehensively summarize research progress on it. This review highlights the diverse topologies for RNA quadruplex structure and its effect factors; outlines the current knowledge of RNA quadruplex's physiological functions in biological systems, especially in gene expression; and presents the prospects of RNA quadruplex.
Collapse
Affiliation(s)
- Xiaohui Ji
- 1 Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology, College of Life Sciences, Beijing Normal University , Beijing, China
| | | | | | | | | | | |
Collapse
|
46
|
Abstract
Opposed to DNA quadruplex sequences, RNA quadruplexes are still less well characterized. On the other hand, RNA quadruplexes are found to be at least as stable as their DNA counterparts. They show the same dependence on metal ions but seem to be much more restricted with respect to the adopted conformations. Other than DNA, which is mostly found to be double-stranded inside cells, RNAs are produced during transcription without its complementary sequence. The absence of a second strand that is able to hybridize and form a duplex makes the folding of RNA quadruplexes a likely event of intramolecular structure formation. Consequently, the formation of RNA quadruplexes in cellular RNAs has recently been suggested and the study of their influence and potential roles in cellular processes has just started. Here we give an overview of the RNA quadruplex field, summarizing issues such as structures, stabilities, and anticipated roles of these interesting four-stranded, guanosine-rich sequences.
Collapse
Affiliation(s)
- Kangkan Halder
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
| | | |
Collapse
|
47
|
Liang R, Kierzek E, Kierzek R, Turner DH. Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain. Biochemistry 2010; 49:8155-68. [PMID: 20557101 PMCID: PMC2938832 DOI: 10.1021/bi100286n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/16/2010] [Indexed: 11/29/2022]
Abstract
Microarrays with isoenergetic pentamer and hexamer 2'-O-methyl oligonucleotide probes with LNA (locked nucleic acid) and 2,6-diaminopurine substitutions were used to probe the binding sites on the RNase P RNA specificity domain of Bacillus subtilis. Unexpected binding patterns were revealed. Because of their enhanced binding free energies, isoenergetic probes can break short duplexes, merge adjacent loops, and/or induce refolding. This suggests new approaches to the rational design of short oligonucleotide therapeutics but limits the utility of microarrays for providing constraints for RNA structure determination. The microarray results are compared to results from chemical mapping experiments, which do provide constraints. Results from both types of experiments indicate that the RNase P RNA folds similarly in 1 M Na(+) and 10 mM Mg(2+).
Collapse
Affiliation(s)
- Ruiting Liang
- Department of Chemistry, University of Rochester, Rochester, New York 14627
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627
| |
Collapse
|
48
|
MATSUMURA TAKUYA, HU ZONGYI, KATO TAKANOBU, DREUX MARLENE, ZHANG YONG, IMAMURA MICHIO, HIRAGA NOBUHIKO, JUTEAU JEAN, COSSET FRANCOIS, CHAYAMA KAZUAKI, VAILLANT ANDREW, LIANG TJAKE. Amphipathic DNA polymers inhibit hepatitis C virus infection by blocking viral entry. Gastroenterology 2009; 137:673-81. [PMID: 19394333 PMCID: PMC2803092 DOI: 10.1053/j.gastro.2009.04.048] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2008] [Revised: 03/26/2009] [Accepted: 04/16/2009] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Hepatitis C virus (HCV) gains entry into susceptible cells by interacting with cell surface receptor(s). Viral entry is an attractive target for antiviral development because of the highly conserved mechanism. METHODS HCV culture systems were used to study the effects of phosphorothioate oligonucleotides (PS-ONs), as amphipathic DNA polymers (APs), on HCV infection. The in vivo effects of APs were tested in urokinase plasminogen activator (uPA)/severe combined immunodeficient (SCID) mice engrafted with human hepatocytes. RESULTS We show the sequence-independent inhibitory effects of APs on HCV infection. APs were shown to potently inhibit HCV infection at submicromolar concentrations. APs exhibited a size-dependent antiviral activity and were equally active against HCV pseudoparticles of various genotypes. Control phosphodiester oligonucleotide (PO-ON) polymer without the amphipathic structure was inactive. APs had no effect on viral replication in the HCV replicon system or binding of HCV to cells but inhibited viral internalization, indicating that the target of inhibition is at the postbinding, cell entry step. In uPA/SCID mice engrafted with human hepatocytes, APs efficiently blocked de novo HCV infection. CONCLUSIONS Our results demonstrate that APs are a novel class of antiviral compounds that hold promise as a drug to inhibit HCV entry.
Collapse
Affiliation(s)
- TAKUYA MATSUMURA
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - ZONGYI HU
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - TAKANOBU KATO
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - MARLENE DREUX
- Universite de Lyon, INSERM U758, and Ecole Normale Superieure de Lyon, Lyon, France
| | - YONG–YUAN ZHANG
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - MICHIO IMAMURA
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - NOBUHIKO HIRAGA
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | | | - FRANCOIS–LOIC COSSET
- Universite de Lyon, INSERM U758, and Ecole Normale Superieure de Lyon, Lyon, France
| | - KAZUAKI CHAYAMA
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | | | - T. JAKE LIANG
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
49
|
Morris MJ, Basu S. An unusually stable G-quadruplex within the 5'-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells. Biochemistry 2009; 48:5313-9. [PMID: 19397366 DOI: 10.1021/bi900498z] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MT3-MMP is a matrix metalloproteinase involved in the regulation of cancer cell invasion and metastasis. The MT3-MMP mRNA contains a 20-nucleotide G-rich region (M3Q) upstream of the initiation codon. Herein, we report that the M3Q purine-only sequence forms an extremely stable intramolecular G-quadruplex structure and has an inhibitory role on translation of a reporter gene in eukaryotic cells. The formation of the G-quadruplex structure was indicated by circular dichroism (CD) spectroscopy and enzymatic footprinting with RNase T1. The unusual stability of the G-quadruplex was evidenced when addition of only 1 mM KCl resulted in about a 30 degrees C increase in the melting temperature (T(m)), as compared to that obtained in the absence of added salt. The T(m) was independent of the RNA concentration, suggesting an intramolecular G-quadruplex structure. Additionally, in a dual luciferase reporter assay performed in eukaryotic cells, the M3Q motif present in the context of the entire 5'-UTR of MT3-MMP repressed activity of its downstream gene by more than half. To the best of our knowledge, the naturally occurring M3Q sequence forms one of the most stable, intramolecular RNA G-quadruplexes reported. This report is the first to establish a functional role of a G-quadruplex forming sequence within the MT3-MMP 5'-UTR in the regulation of translation in eukaryotic cells.
Collapse
Affiliation(s)
- Mark J Morris
- Department of Chemistry, Kent State University, Kent, Ohio 44242, USA
| | | |
Collapse
|
50
|
Iwahashi H. 8-Oxo-7,8-dihydro-2'-deoxyguanosine Forms a Relatively Unstable Tetrameric Structure Compared with 2'-Deoxyguanosine. J Clin Biochem Nutr 2009; 44:57-61. [PMID: 19177189 PMCID: PMC2613500 DOI: 10.3164/jcbn.08-157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 07/25/2008] [Indexed: 11/22/2022] Open
Abstract
The hydrogen-bonded guanine tetrad, or G-quartet has been implicated in a variety of biological roles, including the function of chromosome telomeres. Here effect of the hydroxylation of guanosine at the 8 position on the G-quartet formation was examined. Electrospray inonization mass (ESI-MS) spectra of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 2'-deoxyguanosine (dG) were measured in order to know whether or not 8-oxodG forms a tetrameric structure as 2'-deoxyguanosine forms in teromeres. The ESI-MS spectra of dG shows prominent peaks at m/z 290, m/z 557, and m/z 1092, corresponding to [dG + Na]+, [dG2 + Na]+, and [dG4 + Na]+ in the presence of 0.1 mM NaCl. On the other hand, the ESI-MS spectra of 8-oxodG in the presence of 0.1 mM NaCl shows prominent peaks at m/z 306 and m/z 589, corresponding to [8-oxodG + Na]+ and [8-oxodG2 + Na]+. The results showed that 8-oxodG forms a relatively unstable tetrameric structure compared with dG.
Collapse
Affiliation(s)
- Hideo Iwahashi
- *To whom correspondence should be addressed. Tel: +81-73-441-0772 Fax: +81-73-441-0772 E-mail:
| |
Collapse
|