151
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Abstract
RNA helicases exert mechanical force that changes RNA configurations in many essential cellular pathways, e.g., during mRNA maturation or assembly of ribosomes. DEAH helicases work by translocating along RNA and thereby unwind RNA duplexes or dissociate bound proteins. Because DEAH proteins are poor enzymes without intrinsic selectivity for target RNAs, they require adapter proteins that recruit them to functional sites and enhance their catalytic activity. One essential class of DEAH activators is formed by G-patch proteins, which bind helicases via their eponymous glycine-rich motif. We solved the structure of a G-patch bound to helicase DHX15. Our analysis suggests that G-patches tether mobile sections of DEAH helicases together and activate them by stabilizing a functional conformation with high RNA affinity. RNA helicases of the DEAH/RHA family are involved in many essential cellular processes, such as splicing or ribosome biogenesis, where they remodel large RNA–protein complexes to facilitate transitions to the next intermediate. DEAH helicases couple adenosine triphosphate (ATP) hydrolysis to conformational changes of their catalytic core. This movement results in translocation along RNA, which is held in place by auxiliary C-terminal domains. The activity of DEAH proteins is strongly enhanced by the large and diverse class of G-patch activators. Despite their central roles in RNA metabolism, insight into the molecular basis of G-patch–mediated helicase activation is missing. Here, we have solved the structure of human helicase DHX15/Prp43, which has a dual role in splicing and ribosome assembly, in complex with the G-patch motif of the ribosome biogenesis factor NKRF. The G-patch motif binds in an extended conformation across the helicase surface. It tethers the catalytic core to the flexibly attached C-terminal domains, thereby fixing a conformation that is compatible with RNA binding. Structures in the presence or absence of adenosine diphosphate (ADP) suggest that motions of the catalytic core, which are required for ATP binding, are still permitted. Concomitantly, RNA affinity, helicase, and ATPase activity of DHX15 are increased when G-patch is bound. Mutations that detach one end of the tether but maintain overall binding severely impair this enhancement. Collectively, our data suggest that the G-patch motif acts like a flexible brace between dynamic portions of DHX15 that restricts excessive domain motions but maintains sufficient flexibility for catalysis.
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152
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Zhang Y, Liu S, Jiang H, Deng H, Dong C, Shen W, Chen H, Gao C, Xiao S, Liu ZF, Wei D. G 2-quadruplex in the 3'UTR of IE180 regulates Pseudorabies virus replication by enhancing gene expression. RNA Biol 2020; 17:816-827. [PMID: 32070191 DOI: 10.1080/15476286.2020.1731664] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA secondary structure elements in the mRNA 3'-untranslated regions (3'UTR) play important roles in post-transcriptional regulation. RNA structure elements in the viral RNA provide valuable model for studying diverse regulation mechanisms. Herpesvirus genomes are double-stranded DNA with GC-rich sequences, which can be transcribed into abundant GC-rich RNAs. It is valuable to explore the structures and function of those GC-rich RNAs. We identified a G2-quadruplex-forming sequence named PQS18-1 in the 3'UTR of the unique immediate early gene of Pseudorabies virus (PRV), an important member of Alphaherpesvirinae subfamily. The RNA PQS18-1 was folded into parallel G-quadruplex structure, enhancing gene expression. Both non-G-quadruplex mutant and G3-quadruplex mutant in the 3'UTR showed lower gene expression level than the wildtype G2-quadruplex. TMPyP4 destroyed PQS18-1 G2-quadruplex and suppressed gene expression, accordingly reducing PRV replication by one titre in the PK15 cells at 24 h post infection. Our findings indicated that the RNA G2-quadruplex in 3'UTR was essential for high expression of IE180 gene, and it could be a specific post-transcription regulation element in response to small molecules or other macromolecules. This study discovers a novel RNA G2-quadruplex in the 3'UTR of an immediate early gene of alphaherpesvirus and provides a new nucleic acid target for anti-virus drug design.
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Affiliation(s)
- Yashu Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University , Wuhan, China
| | - Sisi Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China
| | - Hui Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University , Wuhan, China
| | - Hui Deng
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Chen Dong
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Wei Shen
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Haifeng Chen
- College of Science, Huazhong Agricultural University , Wuhan, China
| | - Chao Gao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China.,College of Plant Science and Technology, Huazhong Agricultural University , Wuhan, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University , Wuhan, China
| | - Zheng-Fei Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University , Wuhan, China
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University , Wuhan, China.,College of Science, Huazhong Agricultural University , Wuhan, China
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153
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Wang KB, Dickerhoff J, Wu G, Yang D. PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs. J Am Chem Soc 2020; 142:5204-5211. [PMID: 32101424 DOI: 10.1021/jacs.9b12770] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aberrant expression of PDGFR-β is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-β gene promoter are transcriptional modulators and amenable to small molecule targeting. The major G4 formed in the PDGFR-β gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-β gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiologically relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-β vG4 in K+ solution. This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic analysis elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3'- and 5'-end vG4s is present in the PDGFR-β promoter sequence, and dGMP favors the 5'-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5'-vacancy, except for cGMP. cGMP binds both the 3'- and 5'-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiological and pathological processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-β vG4.
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154
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Srinivasan S, Liu Z, Chuenchor W, Xiao TS, Jankowsky E. Function of Auxiliary Domains of the DEAH/RHA Helicase DHX36 in RNA Remodeling. J Mol Biol 2020; 432:2217-2231. [PMID: 32087197 DOI: 10.1016/j.jmb.2020.02.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 01/06/2023]
Abstract
The DEAH/RHA helicase DHX36 has been linked to cellular RNA and DNA quadruplex structures and to AU-rich RNA elements. In vitro, DHX36 remodels DNA and RNA quadruplex structures and unwinds DNA duplexes in an ATP-dependent manner. DHX36 contains the superfamily 2 helicase core and several auxiliary domains that are conserved in orthologs of the enzyme. The role of these auxiliary domains for the enzymatic function of DHX36 is not well understood. Here, we combine structural and biochemical studies to define the function of three auxiliary domains that contact nucleic acid. We first report the crystal structure of mouse DHX36 bound to ADP. The structure reveals an overall architecture of mouse DHX36 that is similar to previously reported architectures of fly and bovine DHX36. In addition, our structure shows conformational changes that accompany stages of the ATP-binding and hydrolysis cycle. We then examine the roles of the DHX36-specific motif (DSM), the OB-fold, and a conserved β-hairpin (β-HP) in mouse DHX36 in the remodeling of RNA structures. We demonstrate and characterize RNA duplex unwinding for DHX36 and examine the remodeling of inter- and intramolecular RNA quadruplex structures. We find that the DSM not only functions as a quadruplex binding adaptor but also promotes the remodeling of RNA duplex and quadruplex structures. The OB-fold and the β-HP contribute to RNA binding. Both domains are also essential for remodeling RNA quadruplex and duplex structures. Our data reveal roles of auxiliary domains for multiple steps of the nucleic acid remodeling reactions.
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Affiliation(s)
| | - Zhonghua Liu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - Tsan Sam Xiao
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, USA; Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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155
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Abstract
Guanine-rich DNA sequences can fold into four-stranded, noncanonical secondary structures called G-quadruplexes (G4s). G4s were initially considered a structural curiosity, but recent evidence suggests their involvement in key genome functions such as transcription, replication, genome stability, and epigenetic regulation, together with numerous connections to cancer biology. Collectively, these advances have stimulated research probing G4 mechanisms and consequent opportunities for therapeutic intervention. Here, we provide a perspective on the structure and function of G4s with an emphasis on key molecules and methodological advances that enable the study of G4 structures in human cells. We also critically examine recent mechanistic insights into G4 biology and protein interaction partners and highlight opportunities for drug discovery.
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Affiliation(s)
- Jochen Spiegel
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Santosh Adhikari
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Shankar Balasubramanian
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, UK
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156
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Solier S, Müller S, Rodriguez R. Whole-genome mapping of small-molecule targets for cancer medicine. Curr Opin Chem Biol 2020; 56:42-50. [PMID: 31978625 DOI: 10.1016/j.cbpa.2019.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 12/18/2022]
Abstract
Cancers display intratumoral and intertumoral heterogeneity, which poses challenges to small-molecule intervention. Studying drug responses on a whole-genome and transcriptome level using next-generation sequencing has revolutionized our understanding of how small molecules intervene in cells, which helps us to study and potentially predict treatment outcomes. Some small molecules act directly at the genomic level by targeting DNA or chromatin proteins. Here, we review recent advances in establishing whole-genome and transcriptome maps of small-molecule targets, comprising chromatin components or downstream events. We also describe recent advances in studying drug responses using single-cell RNA and DNA sequencing. Furthermore, we discuss how this fundamental research can be taken forward to devise innovative personalized treatment modalities.
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Affiliation(s)
- Stéphanie Solier
- Institut Curie, 26 rue d'Ulm, 75248, Paris, Cedex 05, France; PSL Université Paris, France; Chemical Biology of Cancer Laboratory, CNRS UMR 3666, INSERM U1143, France
| | - Sebastian Müller
- Institut Curie, 26 rue d'Ulm, 75248, Paris, Cedex 05, France; PSL Université Paris, France; Chemical Biology of Cancer Laboratory, CNRS UMR 3666, INSERM U1143, France.
| | - Raphaël Rodriguez
- Institut Curie, 26 rue d'Ulm, 75248, Paris, Cedex 05, France; PSL Université Paris, France; Chemical Biology of Cancer Laboratory, CNRS UMR 3666, INSERM U1143, France.
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157
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Tauber D, Tauber G, Khong A, Van Treeck B, Pelletier J, Parker R. Modulation of RNA Condensation by the DEAD-Box Protein eIF4A. Cell 2020; 180:411-426.e16. [PMID: 31928844 DOI: 10.1016/j.cell.2019.12.031] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 11/04/2019] [Accepted: 12/20/2019] [Indexed: 01/12/2023]
Abstract
Stress granules are condensates of non-translating mRNAs and proteins involved in the stress response and neurodegenerative diseases. Stress granules form in part through intermolecular RNA-RNA interactions, and to better understand how RNA-based condensation occurs, we demonstrate that RNA is effectively recruited to the surfaces of RNA or RNP condensates in vitro. We demonstrate that, through ATP-dependent RNA binding, the DEAD-box protein eIF4A reduces RNA condensation in vitro and limits stress granule formation in cells. This defines a function for eIF4A to limit intermolecular RNA-RNA interactions in cells. These results establish an important role for eIF4A, and potentially other DEAD-box proteins, as ATP-dependent RNA chaperones that limit the condensation of RNA, analogous to the function of proteins like HSP70 in combatting protein aggregates.
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Affiliation(s)
- Devin Tauber
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Gabriel Tauber
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Anthony Khong
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Briana Van Treeck
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; The Rosalind and Morris Goodman Cancer Research Center and the Department of Oncology, McGill University, Montreal, QC, Canada
| | - Roy Parker
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA; Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80309, USA.
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158
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Ngo KH, Yang R, Das P, Nguyen GKT, Lim KW, Tam JP, Wu B, Phan AT. Cyclization of a G4-specific peptide enhances its stability and G-quadruplex binding affinity. Chem Commun (Camb) 2020; 56:1082-1084. [DOI: 10.1039/c9cc06748e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Head-to-tail cyclization of a G-quadruplex-specific peptide was shown to enhance its stability and G-quadruplex binding affinity.
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Affiliation(s)
- Khac Huy Ngo
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - Renliang Yang
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Poulomi Das
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | | | - Kah Wai Lim
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
| | - James P. Tam
- School of Biological Sciences
- Nanyang Technological University
- Singapore
- NTU Institute of Structural Biology
- Nanyang Technological University
| | - Bin Wu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
- NTU Institute of Structural Biology
- Nanyang Technological University
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences
- Nanyang Technological University
- Singapore
- NTU Institute of Structural Biology
- Nanyang Technological University
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159
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Heddi B, Cheong VV, Schmitt E, Mechulam Y, Phan AT. Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3′-end tetrad of a DNA G-quadruplex. J Struct Biol 2020; 209:107399. [DOI: 10.1016/j.jsb.2019.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022]
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160
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McRae EKS, Dupas SJ, Booy EP, Piragasam RS, Fahlman RP, McKenna SA. An RNA guanine quadruplex regulated pathway to TRAIL-sensitization by DDX21. RNA (NEW YORK, N.Y.) 2020; 26:44-57. [PMID: 31653714 PMCID: PMC6913123 DOI: 10.1261/rna.072199.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
DDX21 is a newly discovered RNA G-quadruplex (rG4) binding protein with no known biological rG4 targets. In this study we used label-free proteomic MS/MS to identify 26 proteins that are expressed at significantly different levels in cells expressing an rG4-binding deficient DDX21 (M4). MS data are available via ProteomeXchange with identifier PXD013501. From this list we validate MAGED2 as a protein that is regulated by DDX21 through rG4 in its 5'-UTR. MAGED2 protein levels, but not mRNA levels, are reduced by half in cells expressing DDX21 M4. MAGED2 has a repressive effect on TRAIL-R2 expression that is relieved under these conditions, resulting in elevated TRAIL-R2 mRNA and protein in MCF-7 cells, rendering them sensitive to TRAIL-mediated apoptosis. Our work identifies the role of DDX21 in regulation at the translational level through biologically relevant rG4 and shows that MAGED2 protein levels are regulated, at least in part, by the potential to form rG4 in their 5'-UTRs.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Steven J Dupas
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | | | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 2R7
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
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161
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Butovskaya E, Soldà P, Scalabrin M, Nadai M, Richter SN. HIV-1 Nucleocapsid Protein Unfolds Stable RNA G-Quadruplexes in the Viral Genome and Is Inhibited by G-Quadruplex Ligands. ACS Infect Dis 2019; 5:2127-2135. [PMID: 31646863 PMCID: PMC6909241 DOI: 10.1021/acsinfecdis.9b00272] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
The G-quadruplexes that form in the
HIV-1 RNA genome hinder progression
of reverse transcriptase
in vitro, but not in infected cells. We investigated the possibility
that the HIV-1 nucleocapsid protein NCp7, which remains associated
with the viral RNA during reverse transcription, modulated HIV-1 RNA
G-quadruplex stability. By electrophoresis, circular dichroism, mass
spectrometry, and reverse transcriptase stop assays, we demonstrated
that NCp7 binds and unfolds the HIV-1 RNA G-quadruplexes and promotes
DNA/RNA duplex formation, allowing reverse transcription to proceed.
The G-quadruplex ligand BRACO-19 was able to partially counteract
this effect. These results indicate NCp7 as the first known viral
protein able to unfold RNA G-quadruplexes, and they explain how the
extra-stable HIV-1 RNA G-quadruplexes are processed; they also point
out that the reverse transcription process is hindered by G-quadruplex
ligands at both reverse transcriptase and NCp7 level. This information
can lead to the development of more effective anti-HIV-1 drugs with
a new mechanism of action.
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Affiliation(s)
- Elena Butovskaya
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Paola Soldà
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, via Aristide Gabelli 63, 35121 Padua, Italy
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162
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Roychowdhury A, Joret C, Bourgeois G, Heurgué-Hamard V, Lafontaine DLJ, Graille M. The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis. Nucleic Acids Res 2019; 47:7548-7563. [PMID: 31188444 PMCID: PMC6698733 DOI: 10.1093/nar/gkz529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/28/2019] [Accepted: 06/03/2019] [Indexed: 01/02/2023] Open
Abstract
Ribosome biogenesis is an essential process in all living cells, which entails countless highly sequential and dynamic structural reorganization events. These include formation of dozens RNA helices through Watson-Crick base-pairing within ribosomal RNAs (rRNAs) and between rRNAs and small nucleolar RNAs (snoRNAs), transient association of hundreds of proteinaceous assembly factors to nascent precursor (pre-)ribosomes, and stable assembly of ribosomal proteins. Unsurprisingly, the largest group of ribosome assembly factors are energy-consuming proteins (NTPases) including 25 RNA helicases in budding yeast. Among these, the DEAH-box Dhr1 is essential to displace the box C/D snoRNA U3 from the pre-rRNAs where it is bound in order to prevent premature formation of the central pseudoknot, a dramatic irreversible long-range interaction essential to the overall folding of the small ribosomal subunit. Here, we report the crystal structure of the Dhr1 helicase module, revealing the presence of a remarkable carboxyl-terminal domain essential for Dhr1 function in ribosome biogenesis in vivo and important for its interaction with its coactivator Utp14 in vitro. Furthermore, we report the functional consequences on ribosome biogenesis of DHX37 (human Dhr1) mutations found in patients suffering from microcephaly and other neurological diseases.
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Affiliation(s)
| | - Clément Joret
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), B-6041 Charleroi-Gosselies, Belgium
| | | | | | - Denis L J Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), B-6041 Charleroi-Gosselies, Belgium
| | - Marc Graille
- BIOC, CNRS, Ecole polytechnique, IP Paris, F-91128 Palaiseau, France
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163
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Hamann F, Enders M, Ficner R. Structural basis for RNA translocation by DEAH-box ATPases. Nucleic Acids Res 2019; 47:4349-4362. [PMID: 30828714 PMCID: PMC6486627 DOI: 10.1093/nar/gkz150] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/28/2019] [Accepted: 02/22/2019] [Indexed: 12/15/2022] Open
Abstract
DEAH-box adenosine triphosphatases (ATPases) play a crucial role in the spliceosome-mediated excision of pre-mRNA introns. Recent spliceosomal cryo-EM structures suggest that these proteins utilize translocation to apply forces on ssRNAs rather than direct RNA duplex unwinding to ensure global rearrangements. By solving the crystal structure of Prp22 in different adenosine nucleotide-free states, we identified two missing conformational snapshots of genuine DEAH-box ATPases that help to unravel the molecular mechanism of translocation for this protein family. The intrinsic mobility of the RecA2 domain in the absence of adenosine di- or triphosphate (ADP/ATP) and RNA enables DEAH-box ATPases to adopt different open conformations of the helicase core. The presence of RNA suppresses this mobility and stabilizes one defined open conformation when no adenosine nucleotide is bound. A comparison of this novel conformation with the ATP-bound state of Prp43 reveals that these ATPases cycle between closed and open conformations of the helicase core, which accommodate either a four- or five-nucleotide stack in the RNA-binding tunnel, respectively. The continuous repetition of these states enables these proteins to translocate in 3′-5′ direction along an ssRNA with a step-size of one RNA nucleotide per hydrolyzed ATP. This ATP-driven motor function is maintained by a serine in the conserved motif V that senses the catalytic state and accordingly positions the RecA2 domain.
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Affiliation(s)
- Florian Hamann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Marieke Enders
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Goettingen, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany
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164
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Wang S, Zhang G, Chen Q, Zhou J, Wu Z. Sensing of cocaine using polarized optical microscopy by exploiting the conformational changes of an aptamer at the water/liquid crystal interface. Mikrochim Acta 2019; 186:724. [DOI: 10.1007/s00604-019-3855-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/19/2019] [Indexed: 11/29/2022]
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165
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DDX5 helicase resolves G-quadruplex and is involved in MYC gene transcriptional activation. Proc Natl Acad Sci U S A 2019; 116:20453-20461. [PMID: 31548374 DOI: 10.1073/pnas.1909047116] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (G4) are noncanonical secondary structures formed in guanine-rich DNA and RNA sequences. MYC, one of the most critical oncogenes, forms a DNA G4 in its proximal promoter region (MycG4) that functions as a transcriptional silencer. However, MycG4 is highly stable in vitro and its regulatory role would require active unfolding. Here we report that DDX5, one of the founding members of the DEAD-box RNA helicase family, is extremely proficient at unfolding MycG4-DNA. Our results show that DDX5 is a highly active G4-resolvase that does not require a single-stranded overhang and that ATP hydrolysis is not directly coupled to G4-unfolding of DDX5. The chromatin binding sites of DDX5 are G-rich sequences. In cancer cells, DDX5 is enriched at the MYC promoter and activates MYC transcription. The DDX5 interaction with the MYC promoter and DDX5-mediated MYC activation is inhibited by G4-interactive small molecules. Our results uncover a function of DDX5 in resolving DNA and RNA G4s and suggest a molecular target to suppress MYC for cancer intervention.
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166
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Hou Y, Li F, Zhang R, Li S, Liu H, Qin ZS, Sun X. Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure. Epigenetics 2019; 14:894-911. [PMID: 31177910 PMCID: PMC6691997 DOI: 10.1080/15592294.2019.1621140] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/05/2019] [Accepted: 05/14/2019] [Indexed: 12/14/2022] Open
Abstract
DNA molecules are highly compacted in the eukaryotic nucleus where distal regulatory elements reach their targets through three-dimensional chromosomal interactions. G-quadruplexes, stable four-stranded non-canonical DNA structures, can change local chromatin organization through the exclusion of nucleosomes. However, the relationship between G-quadruplexes and higher-order genome organization remains unknown. Here, we found that G-quadruplexes are significantly enriched at boundaries of topological associated domains (TADs). Architectural protein occupancy, which plays critical roles in the formation of TADs, was highly correlated with the content of G-quadruplexes at TAD boundaries. Moreover, adjacent boundaries containing G-quadruplexes frequently interacted with each other because of the high enrichment of architectural protein binding sites. Similar to CCCTC-binding factor (CTCF) binding sites, G-quadruplexes also showed strong insulation ability in the separation of adjacent regions. Additionally, the insulation ability of CTCF binding sites and TAD boundaries was significantly reinforced by G-quadruplexes. Furthermore, G-quadruplex motifs on different strands were associated with the orientation of CTCF binding sites. These findings suggest a potential role for G-quadruplexes in loop extrusion. The enrichment of transcription factor binding sites (TFBSs) around regulatory elements containing G-quadruplexes led to frequent interactions between regulatory elements containing G-quadruplexes. Intriguingly, more than 99% of G-quadruplexes overlapped with TFBSs. The binding sites of CTCF and cohesin proteins were preferentially located surrounding G-quadruplexes. Accordingly, we proposed a new mechanism of long-distance gene regulation in which G-quadruplexes are involved in distal interactions between enhancers and promoters.
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Affiliation(s)
- Yue Hou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Fuyu Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Rongxin Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Sheng Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Zhaohui S. Qin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
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167
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Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers. Q Rev Biophys 2019; 52:e8. [PMID: 31423956 DOI: 10.1017/s0033583519000064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescence turn-on aptamers, in vitro evolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA-fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.
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168
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Zyner KG, Mulhearn DS, Adhikari S, Martínez Cuesta S, Di Antonio M, Erard N, Hannon GJ, Tannahill D, Balasubramanian S. Genetic interactions of G-quadruplexes in humans. eLife 2019; 8:e46793. [PMID: 31287417 PMCID: PMC6615864 DOI: 10.7554/elife.46793] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/17/2019] [Indexed: 01/20/2023] Open
Abstract
G-quadruplexes (G4) are alternative nucleic acid structures involved in transcription, translation and replication. Aberrant G4 formation and stabilisation is linked to genome instability and cancer. G4 ligand treatment disrupts key biological processes leading to cell death. To discover genes and pathways involved with G4s and gain mechanistic insights into G4 biology, we present the first unbiased genome-wide study to systematically identify human genes that promote cell death when silenced by shRNA in the presence of G4-stabilising small molecules. Many novel genetic vulnerabilities were revealed opening up new therapeutic possibilities in cancer, which we exemplified by an orthogonal pharmacological inhibition approach that phenocopies gene silencing. We find that targeting the WEE1 cell cycle kinase or USP1 deubiquitinase in combination with G4 ligand treatment enhances cell killing. We also identify new genes and pathways regulating or interacting with G4s and demonstrate that the DDX42 DEAD-box helicase is a newly discovered G4-binding protein.
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Affiliation(s)
- Katherine G Zyner
- Cancer Research United Kingdom Cambridge InstituteCambridgeUnited Kingdom
| | - Darcie S Mulhearn
- Cancer Research United Kingdom Cambridge InstituteCambridgeUnited Kingdom
| | - Santosh Adhikari
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Marco Di Antonio
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
| | - Nicolas Erard
- Cancer Research United Kingdom Cambridge InstituteCambridgeUnited Kingdom
| | - Gregory J Hannon
- Cancer Research United Kingdom Cambridge InstituteCambridgeUnited Kingdom
| | - David Tannahill
- Cancer Research United Kingdom Cambridge InstituteCambridgeUnited Kingdom
| | - Shankar Balasubramanian
- Cancer Research United Kingdom Cambridge InstituteCambridgeUnited Kingdom
- Department of ChemistryUniversity of CambridgeCambridgeUnited Kingdom
- School of Clinical MedicineUniversity of CambridgeCambridgeUnited Kingdom
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169
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MOV10L1 Binds RNA G-Quadruplex in a Structure-Specific Manner and Resolves It More Efficiently Than MOV10. iScience 2019; 17:36-48. [PMID: 31252377 PMCID: PMC6600044 DOI: 10.1016/j.isci.2019.06.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/19/2019] [Accepted: 06/11/2019] [Indexed: 12/18/2022] Open
Abstract
MOV10L1 and its paralog MOV10 are evolutionally conserved RNA helicases involved in distinct RNA regulatory pathways. The testis-specific MOV10L1 is essential for spermatogenesis and PIWI-interacting RNAs biogenesis, whereas MOV10 is ubiquitous and multifunctional. Although both proteins have been implied to correlate with RNA G-quadruplex (RG4) in vivo, their capabilities in binding and resolving RG4 and their respective biological significance remain unclear. Herein, we comprehensively characterize and compare the activities of these two helicases on various nucleic acid substrates in vitro, with a focus on RG4 structure. We find that both MOV10L1 and MOV10 are able to resolve RG4, with MOV10L1 being more efficient in that. In contrast to MOV10, MOV10L1 prefers to bind to a junction between single-stranded RNA and RG4, which is mediated by both its N and C termini. Furthermore, we show that RG4 unwinding by MOV10L1 facilitates the cleavage of this specific RNA structure by an endonuclease. Both MOV10L1 and MOV10 can resolve RG4 structure in an ATP-dependent manner MOV10L1 unwinds RG4 more efficiently than MOV10 MOV10L1 preferentially binds to an ssRNA-RG4 junction RG4 unwinding by MOV10L1 facilitates its endonucleolytic cleavage
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170
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Sjekloća L, Ferré-D'Amaré AR. Binding between G Quadruplexes at the Homodimer Interface of the Corn RNA Aptamer Strongly Activates Thioflavin T Fluorescence. Cell Chem Biol 2019; 26:1159-1168.e4. [PMID: 31178406 DOI: 10.1016/j.chembiol.2019.04.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/08/2019] [Accepted: 04/29/2019] [Indexed: 12/21/2022]
Abstract
Thioflavin T (ThT) is widely used for the detection of amyloids. Many unrelated DNAs and RNAs that contain G-quadruplex motifs also bind ThT and strongly activate its fluorescence. To elucidate the structural basis of ThT binding to G quadruplexes and its fluorescence turn-on, we determined its co-crystal structure with the homodimeric RNA Corn, which contains two G quadruplexes. We found that two ThT molecules bind in the dimer interface, constrained by a G quartet from each protomer into a maximally fluorescent planar conformation. The unliganded Corn homodimer crystal structure reveals a collapsed fluorophore-binding site. In solution, Corn must fluctuate between this and an open, binding-competent conformation. A co-crystal structure with another benzothiazole derivate, thiazole orange (TO), also shows binding at the Corn homodimer interface. As the bound ThT and TO make no interactions with the RNA backbone, their Corn co-crystal structures likely explain their fluorescence activation upon sequence-independent DNA and RNA G-quadruplex binding.
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Affiliation(s)
- Ljiljana Sjekloća
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
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171
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Yu Y, Zhou Y, Zhu M, Liu M, Zhu H, Chen Y, Su G, Chen W, Peng H. Programming a split G-quadruplex in a DNA nanocage and its microRNA imaging in live cells. Chem Commun (Camb) 2019; 55:5131-5134. [PMID: 30973555 DOI: 10.1039/c9cc02096a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A novel approach to program target-responsive devices by incorporating the split G4 motifs in a DNA nanocage has been developed. The rigid prism outcompetes the flexible one in reaction kinetics and signal/background ratios, which can be easily internalized by cells and successfully applied in microRNA imaging in live cells.
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Affiliation(s)
- Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, Jiangsu 226001, China.
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172
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Sauer M, Juranek SA, Marks J, De Magis A, Kazemier HG, Hilbig D, Benhalevy D, Wang X, Hafner M, Paeschke K. DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions. Nat Commun 2019; 10:2421. [PMID: 31160600 PMCID: PMC6547686 DOI: 10.1038/s41467-019-10432-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/07/2019] [Indexed: 11/08/2022] Open
Abstract
Translation efficiency can be affected by mRNA stability and secondary structures, including G-quadruplex structures (G4s). The highly conserved DEAH-box helicase DHX36/RHAU resolves G4s on DNA and RNA in vitro, however a systems-wide analysis of DHX36 targets and function is lacking. We map globally DHX36 binding to RNA in human cell lines and find it preferentially interacting with G-rich and G4-forming sequences on more than 4500 mRNAs. While DHX36 knockout (KO) results in a significant increase in target mRNA abundance, ribosome occupancy and protein output from these targets decrease, suggesting that they were rendered translationally incompetent. Considering that DHX36 targets, harboring G4s, preferentially localize in stress granules, and that DHX36 KO results in increased SG formation and protein kinase R (PKR/EIF2AK2) phosphorylation, we speculate that DHX36 is involved in resolution of rG4 induced cellular stress.
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Affiliation(s)
- Markus Sauer
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - James Marks
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Alessio De Magis
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Daniel Hilbig
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Xiantao Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Katrin Paeschke
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands.
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany.
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173
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Boneberg FM, Brandmann T, Kobel L, van den Heuvel J, Bargsten K, Bammert L, Kutay U, Jinek M. Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA (NEW YORK, N.Y.) 2019; 25:685-701. [PMID: 30910870 PMCID: PMC6521606 DOI: 10.1261/rna.069609.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14A to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique carboxy-terminal domain (CTD). Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14A interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the CTD of DHX37 is required, but not sufficient, for interaction with UTP14A in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14A in controlling its recruitment and activity during ribosome biogenesis.
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Affiliation(s)
| | - Tobias Brandmann
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Lena Kobel
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Jasmin van den Heuvel
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Lukas Bammert
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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174
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Novel triazole and morpholine substituted bisnaphthalimide: Synthesis, photophysical and G-quadruplex binding properties. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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175
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Development of a ribonuclease containing a G4-specific binding motif for programmable RNA cleavage. Sci Rep 2019; 9:7432. [PMID: 31092834 PMCID: PMC6520340 DOI: 10.1038/s41598-019-42143-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 03/20/2019] [Indexed: 12/26/2022] Open
Abstract
We developed a ribonuclease for site-specific targeting and cleavage of single-stranded RNA. The engineered RNase protein was constructed by incorporating two independent functional domains, an RNase HI domain that could cleave the RNA strand in a DNA-RNA hybrid, and a domain of the RHAU protein that could selectively recognize a parallel DNA G-quadruplex (G4). The newly designed RNase first recruits a DNA guide oligonucleotide containing both a parallel G4 motif and a template sequence complementary to the target RNA. This RNase:DNA complex targets and efficiently cleaves the single-stranded RNA in a site-specific manner. A major cleavage site occurs at the RNA region that is complementary to the DNA template sequence. The newly designed RNase can serve as a simple tool for RNA manipulation and probing RNA structure.
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176
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Tippana R, Chen MC, Demeshkina NA, Ferré-D'Amaré AR, Myong S. RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36. Nat Commun 2019; 10:1855. [PMID: 31015431 PMCID: PMC6478676 DOI: 10.1038/s41467-019-09802-w] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/18/2019] [Indexed: 12/27/2022] Open
Abstract
DHX36 is a DEAH-box helicase that resolves parallel G-quadruplex structures formed in DNA and RNA. The recent co-crystal structure of DHX36 bound G4-DNA revealed an intimate contact, but did not address the role of ATP hydrolysis in G4 resolving activity. Here, we demonstrate that unlike on G4-DNA, DHX36 displays ATP-independent unfolding of G4-RNA followed by ATP-dependent refolding, generating a highly asymmetric pattern of activity. Interestingly, DHX36 refolds G4-RNA in several steps, reflecting the discrete steps in forming the G4 structure. We show that the ATP-dependent activity of DHX36 arises from the RNA tail rather than the G4. Mutations that perturb G4 contact result in quick dissociation of the protein from RNA upon ATP hydrolysis, while mutations that interfere with binding the RNA tail induce dysregulated activity. We propose that the ATP-dependent activity of DHX36 may be useful for dynamically resolving various G4-RNA structures in cells.
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Affiliation(s)
- Ramreddy Tippana
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Michael C Chen
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1TN, UK.,Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Natalia A Demeshkina
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, Urbana, IL, 61801, USA.
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177
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Trachman RJ, Autour A, Jeng SCY, Abdolahzadeh A, Andreoni A, Cojocaru R, Garipov R, Dolgosheina EV, Knutson JR, Ryckelynck M, Unrau PJ, Ferré-D'Amaré AR. Structure and functional reselection of the Mango-III fluorogenic RNA aptamer. Nat Chem Biol 2019; 15:472-479. [PMID: 30992561 DOI: 10.1038/s41589-019-0267-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the ~30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A10U), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A10U mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A10U) fluoresce ~50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Alexis Autour
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, Strasbourg, France
| | - Sunny C Y Jeng
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Alessio Andreoni
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ramil Garipov
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Elena V Dolgosheina
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jay R Knutson
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, Strasbourg, France
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, MD, USA.
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178
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Gao J, Byrd AK, Zybailov BL, Marecki JC, Guderyon MJ, Edwards AD, Chib S, West KL, Waldrip ZJ, Mackintosh SG, Gao Z, Putnam AA, Jankowsky E, Raney KD. DEAD-box RNA helicases Dbp2, Ded1 and Mss116 bind to G-quadruplex nucleic acids and destabilize G-quadruplex RNA. Chem Commun (Camb) 2019; 55:4467-4470. [PMID: 30855040 PMCID: PMC6459694 DOI: 10.1039/c8cc10091h] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We identified 29 G-quadruplex binding proteins by affinity purification and quantitative LC-MS/MS. We demonstrated that the DEAD-box RNA helicases Dbp2, Ded1 and Mss116 preferentially bind to G-quadruplex nucleic acids in vitro and destabilize RNA quadruplexes, suggesting new potential roles for these helicases in disruption of quadruplex structures in RNA.
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Affiliation(s)
- Jun Gao
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, 4301 West Markham Street (Slot 516), Little Rock, Arkansas 72205, USA.
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179
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Dehghani-Tafti S, Levdikov V, Antson AA, Bax B, Sanders CM. Structural and functional analysis of the nucleotide and DNA binding activities of the human PIF1 helicase. Nucleic Acids Res 2019; 47:3208-3222. [PMID: 30698796 PMCID: PMC6451128 DOI: 10.1093/nar/gkz028] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 12/20/2018] [Accepted: 01/11/2019] [Indexed: 01/06/2023] Open
Abstract
Pif1 is a multifunctional helicase and DNA processing enzyme that has roles in genome stability. The enzyme is conserved in eukaryotes and also found in some prokaryotes. The functions of human PIF1 (hPIF1) are also critical for survival of certain tumour cell lines during replication stress, making it an important target for cancer therapy. Crystal structures of hPIF1 presented here explore structural events along the chemical reaction coordinate of ATP hydrolysis at an unprecedented level of detail. The structures for the apo as well as the ground and transition states reveal conformational adjustments in defined protein segments that can trigger larger domain movements required for helicase action. Comparisons with the structures of yeast and bacterial Pif1 reveal a conserved ssDNA binding channel in hPIF1 that we show is critical for single-stranded DNA binding during unwinding, but not the binding of G quadruplex DNA. Mutational analysis suggests that while the ssDNA-binding channel is important for helicase activity, it is not used in DNA annealing. Structural differences, in particular in the DNA strand separation wedge region, highlight significant evolutionary divergence of the human PIF1 protein from bacterial and yeast orthologues.
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Affiliation(s)
- Saba Dehghani-Tafti
- Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, University of Sheffield, Beech Hill Rd., Sheffield S10 2RX, UK
| | - Vladimir Levdikov
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Ben Bax
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
- Medicines Discovery Institute, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK
| | - Cyril M Sanders
- Department of Oncology and Metabolism, Academic Unit of Molecular Oncology, University of Sheffield, Beech Hill Rd., Sheffield S10 2RX, UK
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180
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Fleming AM, Nguyen NLB, Burrows CJ. Colocalization of m 6A and G-Quadruplex-Forming Sequences in Viral RNA (HIV, Zika, Hepatitis B, and SV40) Suggests Topological Control of Adenosine N 6-Methylation. ACS CENTRAL SCIENCE 2019; 5:218-228. [PMID: 30834310 PMCID: PMC6396389 DOI: 10.1021/acscentsci.8b00963] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Indexed: 05/09/2023]
Abstract
This Outlook calls attention to two seemingly disparate and emerging fields regarding viral genomics that may be correlated in a way previously overlooked. First, we describe identification of conserved potential G-quadruplex-forming sequences (PQSs) in viral genomes relevant to human health. Studies have demonstrated that PQSs are highly conserved and can fold to G-quadruplexes (G4s) to regulate viral processes. Key examples include G4s as a countermeasure to the host's immune system or G4-guided regulation of replication or transcription. Second, emerging data are discussed concerning the epitranscriptomic modification N 6-methyladenosine (m6A) in viral RNA installed by host proteins in a consensus sequence favoring 5'-GG(m6A)C-3'. The proposed pathways by which m6A is written, read, and erased in viral RNA genomes and the impact this has on viral replication are described. The structural reason why certain sites are selected for modification while others are not is still mysterious. Finally, we discuss our new observations regarding these previous sequencing data that identify m6A installation within the loops of two-tetrad PQSs in the RNA genomes of the Zika, HIV, hepatitis B, and SV40 viruses. We hypothesize that conserved viral PQSs can provide a framework (sequence and/or structural) for m6A installation. We also discuss literature sources suggesting that PQSs as sites of RNA modification could be a general phenomenon. We anticipate our observations will provide ample opportunities for exciting discoveries regarding the interplay between G4 structures and epitranscriptomic modifications of RNA.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Ngoc L. B. Nguyen
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University
of Utah, Salt Lake
City, Utah 84112-0850, United States
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181
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Saranathan N, Vivekanandan P. G-Quadruplexes: More Than Just a Kink in Microbial Genomes. Trends Microbiol 2019; 27:148-163. [PMID: 30224157 PMCID: PMC7127049 DOI: 10.1016/j.tim.2018.08.011] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/17/2018] [Accepted: 08/24/2018] [Indexed: 02/06/2023]
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid secondary structures formed by guanine-rich DNA and RNA sequences. In this review we aim to provide an overview of the biological roles of G4s in microbial genomes with emphasis on recent discoveries. G4s are enriched and conserved in the regulatory regions of microbes, including bacteria, fungi, and viruses. Importantly, G4s in hepatitis B virus (HBV) and hepatitis C virus (HCV) genomes modulate genes crucial for virus replication. Recent studies on Epstein-Barr virus (EBV) shed light on the role of G4s within the microbial transcripts as cis-acting regulatory signals that modulate translation and facilitate immune evasion. Furthermore, G4s in microbial genomes have been linked to radioresistance, antigenic variation, recombination, and latency. G4s in microbial genomes represent novel therapeutic targets for antimicrobial therapy.
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Affiliation(s)
- Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India.
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182
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Lerner LK, Sale JE. Replication of G Quadruplex DNA. Genes (Basel) 2019; 10:genes10020095. [PMID: 30700033 PMCID: PMC6409989 DOI: 10.3390/genes10020095] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/03/2023] Open
Abstract
A cursory look at any textbook image of DNA replication might suggest that the complex machine that is the replisome runs smoothly along the chromosomal DNA. However, many DNA sequences can adopt non-B form secondary structures and these have the potential to impede progression of the replisome. A picture is emerging in which the maintenance of processive DNA replication requires the action of a significant number of additional proteins beyond the core replisome to resolve secondary structures in the DNA template. By ensuring that DNA synthesis remains closely coupled to DNA unwinding by the replicative helicase, these factors prevent impediments to the replisome from causing genetic and epigenetic instability. This review considers the circumstances in which DNA forms secondary structures, the potential responses of the eukaryotic replisome to these impediments in the light of recent advances in our understanding of its structure and operation and the mechanisms cells deploy to remove secondary structure from the DNA. To illustrate the principles involved, we focus on one of the best understood DNA secondary structures, G quadruplexes (G4s), and on the helicases that promote their resolution.
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Affiliation(s)
- Leticia Koch Lerner
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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183
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Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid⁻Protein Interaction. Molecules 2019; 24:molecules24030396. [PMID: 30678288 PMCID: PMC6384609 DOI: 10.3390/molecules24030396] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/10/2019] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
G-quadruplex is a special secondary structure of nucleic acids in guanine-rich sequences of genome. G-quadruplexes have been proved to be involved in the regulation of replication, DNA damage repair, and transcription and translation of oncogenes or other cancer-related genes. Therefore, targeting G-quadruplexes has become a novel promising anti-tumor strategy. Different kinds of small molecules targeting the G-quadruplexes have been designed, synthesized, and identified as potential anti-tumor agents, including molecules directly bind to the G-quadruplex and molecules interfering with the binding between the G-quadruplex structures and related binding proteins. This review will explore the feasibility of G-quadruplex ligands acting as anti-tumor drugs, from basis to application. Meanwhile, since helicase is the most well-defined G-quadruplex-related protein, the most extensive research on the relationship between helicase and G-quadruplexes, and its meaning in drug design, is emphasized.
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184
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m⁶A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins. Genes (Basel) 2019; 10:genes10010049. [PMID: 30650668 PMCID: PMC6356822 DOI: 10.3390/genes10010049] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/04/2023] Open
Abstract
The control of gene expression is a multi-layered process occurring at the level of DNA, RNA, and proteins. With the emergence of highly sensitive techniques, new aspects of RNA regulation have been uncovered leading to the emerging field of epitranscriptomics dealing with RNA modifications. Among those post-transcriptional modifications, N6-methyladenosine (m6A) is the most prevalent in messenger RNAs (mRNAs). This mark can either prevent or stimulate the formation of RNA-protein complexes, thereby influencing mRNA-related mechanisms and cellular processes. This review focuses on proteins containing a YTH domain (for YT521-B Homology), a small building block, that selectively detects the m6A nucleotide embedded within a consensus motif. Thereby, it contributes to the recruitment of various effectors involved in the control of mRNA fates through adjacent regions present in the different YTH-containing proteins.
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185
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Huang ZL, Dai J, Luo WH, Wang XG, Tan JH, Chen SB, Huang ZS. Identification of G-Quadruplex-Binding Protein from the Exploration of RGG Motif/G-Quadruplex Interactions. J Am Chem Soc 2018; 140:17945-17955. [PMID: 30517002 DOI: 10.1021/jacs.8b09329] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The arginine/glycine-rich region termed the RGG domain is usually found in G-quadruplex (G4)-binding proteins and is important in G4-protein interactions. Studies on the binding mechanism of RGG domains found that small segments (RGG motif) inside the domain contribute greatly to the G4 binding affinity. However, unlike the entire RGG domains that have been broadly explored, the role of the RGG motif remains obscure, with very limited study. Herein, to clarify the role of the RGG motif in G4-protein interactions, we systematically investigated the binding affinity and mode between RGG-motif peptides and G4s. The internal arrangement of RGG repeats and gap amino acids played a more crucial role in the G4-binding mechanism than a critical number of RGG repeats. Arginines and phenylalanines at the exact position of the RGG motif might enable additional hydrogen bonding and π-stacking interaction with nucleobases and strengthen the binding of G4. Impressively, proceeding from a G4-binding RGG peptide, 12, discovered above, we identified the cold-inducible RNA-binding protein (CIRBP) as a new G4 DNA-binding protein both in vitro and in cells. In addition, we found that the key amino acids for G4 binding in peptide 12 and CIRBP were highly similar, and peptide 12 clearly played a key role in the G4 binding of CIRBP. This report is the first in which a G4-binding protein was identified from exploration of the G4-binding RGG motif. Our findings suggest a novel strategy for discovering new G4-binding proteins by exploring key peptide segments.
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Affiliation(s)
- Zhou-Li Huang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Jing Dai
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Wen-Hua Luo
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Xiang-Gui Wang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
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186
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Lenarčič Živković M, Rozman J, Plavec J. Adenine‐Driven Structural Switch from a Two‐ to Three‐Quartet DNA G‐Quadruplex. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Jan Rozman
- Slovenian NMR CentreNational Institute of Chemistry Hajdrihova 9 Ljubljana Slovenia
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of Chemistry Hajdrihova 9 Ljubljana Slovenia
- EN- FIST Centre of Excellence Trg OF 13 Ljubljana Slovenia
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
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187
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Al-Zeer MA, Kurreck J. Deciphering the Enigmatic Biological Functions of RNA Guanine-Quadruplex Motifs in Human Cells. Biochemistry 2018; 58:305-311. [PMID: 30350579 DOI: 10.1021/acs.biochem.8b00904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanine-rich sequences in nucleic acids can form noncanonical structures known as guanine quadruplexes (G-quadruplexes), which constitute a not yet fully elucidated layer of regulatory function for central cellular processes. RNA G-quadruplexes have been shown to be involved in the modulation of translation, the regulation of (alternative) splicing, and the subcellular transport of mRNAs, among other processes. However, in living cells, an equilibrium between the formation of G-quadruplex structures and their unwinding by RNA helicases is likely. The extent to which G-rich sequences adopt G-quadruplex structures in living eukaryotic cells is currently a matter of debate. Multiple lines of evidence confirm the intracellular formation of G-quadruplex structures, such as their detection by immunochemical approaches, fluorogenic probes, and in vivo nuclear magnetic resonance. However, intracellular chemical probing suggests most if not all are in an unfolded state. It is therefore tempting to speculate that some G-quadruplex structures are only temporarily formed when they are required to contribute to the fine-tuning of the processes mentioned above. Future research should focus on the analysis of G-quadruplex formation under physiological conditions, which will allow the re-evaluation of the biological function of G-quadruplex motifs in regulatory processes in their natural environment and at physiological expression levels. This will help in the elucidation of their significance in the regulation of central processes in molecular biology and the exploitation of their potential as therapeutic targets.
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Affiliation(s)
- Munir A Al-Zeer
- Institute of Biotechnology, Department of Applied Biochemistry , Technische Universität Berlin , 13355 Berlin , Germany
| | - Jens Kurreck
- Institute of Biotechnology, Department of Applied Biochemistry , Technische Universität Berlin , 13355 Berlin , Germany
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188
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Lenarčič Živković M, Rozman J, Plavec J. Adenine-Driven Structural Switch from a Two- to Three-Quartet DNA G-Quadruplex. Angew Chem Int Ed Engl 2018; 57:15395-15399. [PMID: 30222243 PMCID: PMC6563693 DOI: 10.1002/anie.201809328] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Indexed: 12/15/2022]
Abstract
A G‐rich sequence found in the regulatory region of the RANKL gene, which is associated with homeostasis of bone metabolism, folds into a two‐quartet basket‐type G‐quadruplex stabilized by A⋅G⋅A and G⋅G⋅G base‐triads. Perusal of local structural features together with G/A‐to‐T modifications uncovered the critical role of A5 for the formation of a distinct antiparallel two‐quartet topology and not the three‐quartet topology that would be expected based on the sequence with four GGG‐tracts alone. The structural changes induced by the A5‐to‐T5 modification include a switch in orientation and relative positions of G‐strands that together with anti to syn reorientation of G12 provide insights into the complexity of the interactions that influence the folding of G‐rich DNA. Understanding the impact of loop residues on the stability and formation of G‐quadruplexes advances our knowledge and ability to predict structures adopted by G‐rich sequences, which are involved in regulatory mechanisms in the cell, and may also facilitate drug design.
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Affiliation(s)
| | - Jan Rozman
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 9, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 9, Ljubljana, Slovenia.,EN- FIST Centre of Excellence, Trg OF 13, Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
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189
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Stump S, Mou TC, Sprang SR, Natale NR, Beall HD. Crystal structure of the major quadruplex formed in the promoter region of the human c-MYC oncogene. PLoS One 2018; 13:e0205584. [PMID: 30312328 PMCID: PMC6185859 DOI: 10.1371/journal.pone.0205584] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022] Open
Abstract
The c-MYC oncogene mediates multiple tumor cell survival pathways and is dysregulated or overexpressed in the majority of human cancers. The NHE III1 region of the c-MYC promoter forms a DNA quadruplex. Stabilization of this structure with small molecules has been shown to reduce expression of c-MYC, and targeting the c-MYC quadruplex has become an emerging strategy for development of antitumor compounds. Previous solution NMR studies of the c-MYC quadruplex have assigned the major conformer and topology of this important target, however, regions outside the G-quartet core were not as well-defined. Here, we report a high-resolution crystal structure (2.35 Å) of the major quadruplex formed in the NHE III1 region of the c-MYC promoter. The crystal structure is in general agreement with the solution NMR structure, however, key differences are observed in the position of nucleotides outside the G-quartet core. The crystal structure provides an alternative model that, along with comparisons to other reported quadruplex crystal structures, will be important to the rational design of selective compounds. This work will aid in development of ligands to target the c-MYC promoter quadruplex with the goal of creating novel anticancer therapies.
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Affiliation(s)
- Sascha Stump
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, United States of America
| | - Tung-Chung Mou
- Center for Biomolecular Structure and Dynamics, Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Stephen R. Sprang
- Center for Biomolecular Structure and Dynamics, Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Nicholas R. Natale
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, United States of America
| | - Howard D. Beall
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, United States of America
- * E-mail:
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190
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A guanine-flipping and sequestration mechanism for G-quadruplex unwinding by RecQ helicases. Nat Commun 2018; 9:4201. [PMID: 30305632 PMCID: PMC6180126 DOI: 10.1038/s41467-018-06751-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/18/2018] [Indexed: 01/23/2023] Open
Abstract
Homeostatic regulation of G-quadruplexes (G4s), four-stranded structures that can form in guanine-rich nucleic acids, requires G4 unwinding helicases. The mechanisms that mediate G4 unwinding remain unknown. We report the structure of a bacterial RecQ DNA helicase bound to resolved G4 DNA. Unexpectedly, a guanine base from the unwound G4 is sequestered within a guanine-specific binding pocket. Disruption of the pocket in RecQ blocks G4 unwinding, but not G4 binding or duplex DNA unwinding, indicating its essential role in structure-specific G4 resolution. A novel guanine-flipping and sequestration model that may be applicable to other G4-resolving helicases emerges from these studies.
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191
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Byrd AK, Bell MR, Raney KD. Pif1 helicase unfolding of G-quadruplex DNA is highly dependent on sequence and reaction conditions. J Biol Chem 2018; 293:17792-17802. [PMID: 30257865 DOI: 10.1074/jbc.ra118.004499] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/18/2018] [Indexed: 11/06/2022] Open
Abstract
In addition to unwinding double-stranded nucleic acids, helicase activity can also unfold noncanonical structures such as G-quadruplexes. We previously characterized Pif1 helicase catalyzed unfolding of parallel G-quadruplex DNA. Here we characterized unfolding of the telomeric G-quadruplex, which can fold into antiparallel and mixed hybrid structures and found significant differences. Telomeric DNA sequences are unfolded more readily than the parallel quadruplex formed by the c-MYC promoter in K+ Furthermore, we found that under conditions in which the telomeric quadruplex is less stable, such as in Na+, Pif1 traps thermally melted quadruplexes in the absence of ATP, leading to the appearance of increased product formation under conditions in which the enzyme is preincubated with the substrate. Stable telomeric G-quadruplex structures were unfolded in a stepwise manner at a rate slower than that of duplex DNA unwinding; however, the slower dissociation from G-quadruplexes compared with duplexes allowed the helicase to traverse more nucleotides than on duplexes. Consistent with this, the rate of ATP hydrolysis on the telomeric quadruplex DNA was reduced relative to that on single-stranded DNA (ssDNA), but less quadruplex DNA was needed to saturate ATPase activity. Under single-cycle conditions, telomeric quadruplex was unfolded by Pif1, but for the c-MYC quadruplex, unfolding required multiple helicase molecules loaded onto the adjacent ssDNA. Our findings illustrate that Pif1-catalyzed unfolding of G-quadruplex DNA is highly dependent on the specific sequence and the conditions of the reaction, including both the monovalent cation and the order of addition.
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Affiliation(s)
- Alicia K Byrd
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Matthew R Bell
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - Kevin D Raney
- From the Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205.
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192
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Masai H, Kakusho N, Fukatsu R, Ma Y, Iida K, Kanoh Y, Nagasawa K. Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences. J Biol Chem 2018; 293:17033-17049. [PMID: 30217821 DOI: 10.1074/jbc.ra118.005240] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/06/2018] [Indexed: 01/07/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded DNA structures comprising stacks of four guanines, are prevalent in genomes, and have diverse biological functions in various chromosomal structures. A conserved protein, Rap1-interacting factor 1 (Rif1) from fission yeast (Schizosaccharomyces pombe), binds to Rif1-binding sequence (Rif1BS) and regulates DNA replication timing. Rif1BS is characterized by the presence of multiple G-tracts, often on both strands, and their unusual spacing. Although previous studies have suggested generation of G4-like structures on duplex Rif1BS, its precise molecular architecture remains unknown. Using gel-shift DNA binding assays and DNA footprinting with various nuclease probes, we show here that both of the Rif1BS strands adopt specific higher-order structures upon heat denaturation. We observed that the structure generated on the G-strand is consistent with a G4 having unusually long loop segments and that the structure on the complementary C-strand does not have an intercalated motif (i-motif). Instead, we found that the formation of the C-strand structure depends on the G4 formation on the G-strand. Thus, the higher-order structure generated at Rif1BS involved both DNA strands, and in some cases, G4s may form on both of these strands. The presence of multiple G-tracts permitted the formation of alternative structures when some G-tracts were mutated or disrupted by deazaguanine replacement, indicating the robust nature of DNA higher-order structures generated at Rif1BS. Our results provide general insights into DNA structures generated at G4-forming sequences on duplex DNA.
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Affiliation(s)
- Hisao Masai
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan,
| | - Naoko Kakusho
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Rino Fukatsu
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Yue Ma
- the Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan, and
| | - Keisuke Iida
- the Molecular Chirality Research Center, Synthetic Organic Chemistry, Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Yutaka Kanoh
- From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Kazuo Nagasawa
- the Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan, and
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193
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Xin BG, Chen WF, Rety S, Dai YX, Xi XG. Crystal structure of Escherichia coli DEAH/RHA helicase HrpB. Biochem Biophys Res Commun 2018; 504:334-339. [PMID: 30190128 DOI: 10.1016/j.bbrc.2018.08.191] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 11/28/2022]
Abstract
RNA helicases are almost ubiquitous important enzymes that take part in multiple aspects of RNA metabolism. Prokaryotes encode fewer RNA helicases than eukaryotes, suggesting that individual prokaryotic RNA helicases may take on multiple roles. The specific functions and molecular mechanisms of bacterial DEAH/RHA helicases are poorly understood, and no structures are available of these bacterial enzymes. Here, we report the first crystal structure of the DEAH/RHA helicase HrpB of Escherichia coli in a complex with ADP•AlF4. It showed an atypical globular structure, consisting of two RecA domains, an HA2 domain and an OB domain, similar to eukaryotic DEAH/RHA helicases. Notably, it showed a unique C-terminal extension that has never been reported before. Activity assays indicated that EcHrpB binds RNA but not DNA, and does not exhibit unwinding activity in vitro. Thus, within cells, the EcHrpB may function in helicase activity-independent RNA metabolic processes.
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Affiliation(s)
- Ben-Ge Xin
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wei-Fei Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Stephane Rety
- Univ. Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France
| | - Yang-Xue Dai
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; LBPA, ENS de Cachan, Université Paris-Saclay, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235, Cachan, France.
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