1
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Katsuda Y, Sato SI, Inoue M, Tsugawa H, Kamura T, Kida T, Matsumoto R, Asamitsu S, Shioda N, Shiroto S, Oosawatsu Y, Yatsuzuka K, Kitamura Y, Hagihara M, Ihara T, Uesugi M. Small molecule-based detection of non-canonical RNA G-quadruplex structures that modulate protein translation. Nucleic Acids Res 2022; 50:8143-8153. [PMID: 35801908 PMCID: PMC9371906 DOI: 10.1093/nar/gkac580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/24/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Tandem repeats of guanine-rich sequences in RNA often form thermodynamically stable four-stranded RNA structures. Such RNA G-quadruplexes have long been considered to be linked to essential biological processes, yet their physiological significance in cells remains unclear. Here, we report a approach that permits the detection of RNA G-quadruplex structures that modulate protein translation in mammalian cells. The approach combines antibody arrays and RGB-1, a small molecule that selectively stabilizes RNA G-quadruplex structures. Analysis of the protein and mRNA products of 84 cancer-related human genes identified Nectin-4 and CapG as G-quadruplex-controlled genes whose mRNAs harbor non-canonical G-quadruplex structures on their 5′UTR region. Further investigations revealed that the RNA G-quadruplex of CapG exhibits a structural polymorphism, suggesting a possible mechanism that ensures the translation repression in a KCl concentration range of 25–100 mM. The approach described in the present study sets the stage for further discoveries of RNA G-quadruplexes.
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Affiliation(s)
- Yousuke Katsuda
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Maimi Inoue
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Hisashi Tsugawa
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Takuto Kamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Rio Matsumoto
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Sefan Asamitsu
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Norifumi Shioda
- Department of Genomic Neurology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan.,Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe, Chuo-ku, Kumamoto 862-0973, Japan
| | - Shuhei Shiroto
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Yoshiki Oosawatsu
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yusuke Kitamura
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masaki Hagihara
- Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Toshihiro Ihara
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Motonari Uesugi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.,School of Pharmacy, Fudan University, Shanghai 201203, China
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2
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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3
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Tseng YJ, Sandwith SN, Green KM, Chambers AE, Krans A, Raimer HM, Sharlow ME, Reisinger MA, Richardson AE, Routh ED, Smaldino MA, Wang YH, Vaughn JP, Todd PK, Smaldino PJ. The RNA helicase DHX36-G4R1 modulates C9orf72 GGGGCC hexanucleotide repeat-associated translation. J Biol Chem 2021; 297:100914. [PMID: 34174288 PMCID: PMC8326427 DOI: 10.1016/j.jbc.2021.100914] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022] Open
Abstract
GGGGCC (G4C2) hexanucleotide repeat expansions in the endosomal trafficking gene C9orf72 are the most common genetic cause of ALS and frontotemporal dementia. Repeat-associated non-AUG (RAN) translation of this expansion through near-cognate initiation codon usage and internal ribosomal entry generates toxic proteins that accumulate in patients' brains and contribute to disease pathogenesis. The helicase protein DEAH-box helicase 36 (DHX36–G4R1) plays active roles in RNA and DNA G-quadruplex (G4) resolution in cells. As G4C2 repeats are known to form G4 structures in vitro, we sought to determine the impact of manipulating DHX36 expression on repeat transcription and RAN translation. Using a series of luciferase reporter assays both in cells and in vitro, we found that DHX36 depletion suppresses RAN translation in a repeat length–dependent manner, whereas overexpression of DHX36 enhances RAN translation from G4C2 reporter RNAs. Moreover, upregulation of RAN translation that is typically triggered by integrated stress response activation is prevented by loss of DHX36. These results suggest that DHX36 is active in regulating G4C2 repeat translation, providing potential implications for therapeutic development in nucleotide repeat expansion disorders.
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Affiliation(s)
- Yi-Ju Tseng
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA; Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, USA
| | - Siara N Sandwith
- Department of Biology, Ball State University, Muncie, Indiana, USA
| | - Katelyn M Green
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Amy Krans
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Heather M Raimer
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | | | | | | | - Eric D Routh
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - James P Vaughn
- Division of Cancer Biology, NanoMedica LLC, Winston-Salem, North Carolina, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA; Department of Neurology, Ann Arbor VA Medical Center, Ann Arbor, Michigan, USA.
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4
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Liu H, Lu YN, Paul T, Periz G, Banco MT, Ferré-D'Amaré AR, Rothstein JD, Hayes LR, Myong S, Wang J. A Helicase Unwinds Hexanucleotide Repeat RNA G-Quadruplexes and Facilitates Repeat-Associated Non-AUG Translation. J Am Chem Soc 2021; 143:7368-7379. [PMID: 33855846 DOI: 10.1021/jacs.1c00131] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of a hexanucleotide repeat GGGGCC (G4C2) in the C9orf72 gene is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The G4C2 expansion leads to repeat-associated non-AUG (RAN) translation and the production of toxic dipeptide repeat (DPR) proteins, but the mechanisms of RAN translation remain enigmatic. Here, we report that the RNA helicase DHX36 is a robust positive regulator of C9orf72 RAN translation. DHX36 has a high affinity for the G4C2 repeat RNA, preferentially binds to the repeat RNA's G-quadruplex conformation, and efficiently unwinds the G4C2 G-quadruplex structures. Native DHX36 interacts with the G4C2 repeat RNA and is essential for effective RAN translation in the cell. In induced pluripotent stem cells and differentiated motor neurons derived from C9orf72-linked ALS patients, reducing DHX36 significantly decreased the levels of endogenous DPR proteins. DHX36 is also aberrantly upregulated in tissues of C9orf72-linked ALS patients. These results indicate that DHX36 facilitates C9orf72 RAN translation by resolving repeat RNA G-quadruplex structures and may be a potential target for therapeutic intervention.
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Affiliation(s)
- Honghe Liu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Yu-Ning Lu
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Tapas Paul
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Goran Periz
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Michael T Banco
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892, United States
| | - Jeffrey D Rothstein
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Lindsey R Hayes
- Brain Science Institute and Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
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5
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Russon MP, Westerhouse KM, Tran EJ. Transcription, translation, and DNA repair: new insights from emerging noncanonical substrates of RNA helicases. Biol Chem 2020; 402:637-644. [PMID: 33857360 DOI: 10.1515/hsz-2020-0333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/23/2020] [Indexed: 11/15/2022]
Abstract
RNA helicases are enzymes that exist in all domains of life whose canonical functions include ATP-dependent remodeling of RNA structures and displacement of proteins from ribonucleoprotein complexes (RNPs). These enzymes play roles in virtually all processes of RNA metabolism, including pre-mRNA splicing, rRNA processing, nuclear mRNA export, translation and RNA decay. Here we review emerging noncanonical substrates of RNA helicases including RNA-DNA hybrids (R-loops) and RNA and DNA G-quadruplexes and discuss their biological significance.
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Affiliation(s)
- Matthew P Russon
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Kirsten M Westerhouse
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN, 47907, USA.,Purdue University Center for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN, 47907, USA
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6
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Schult P, Paeschke K. The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes. Biol Chem 2020; 402:581-591. [PMID: 33021960 DOI: 10.1515/hsz-2020-0292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
DHX36 is a member of the DExD/H box helicase family, which comprises a large number of proteins involved in various cellular functions. Recently, the function of DHX36 in the regulation of G-quadruplexes (G4s) was demonstrated. G4s are alternative nucleic acid structures, which influence many cellular pathways on a transcriptional and post-transcriptional level. In this review we provide an overview of the current knowledge about DHX36 structure, substrate specificity, and mechanism of action based on the available models and crystal structures. Moreover, we outline its multiple functions in cellular homeostasis, immunity, and disease. Finally, we discuss the open questions and provide potential directions for future research.
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Affiliation(s)
- Philipp Schult
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
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7
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Richardson A, Zentz ZA, Chambers AE, Sandwith SN, Reisinger MA, Saunders DW, Tompkins JD, Riggs AD, Routh ED, Rubenstein EM, Smaldino MA, Vaughn JP, Haney RA, Smaldino PJ. G-Quadruplex Helicase DHX36/G4R1 Engages Nuclear Lamina Proteins in Quiescent Breast Cancer Cells. ACS OMEGA 2020; 5:24916-24926. [PMID: 33015511 PMCID: PMC7528498 DOI: 10.1021/acsomega.0c03723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
G-quadruplexes (G4s) are nucleic acid structures found enriched within gene regulatory sequences. G4s control fundamental cellular processes, including replication, transcription, and translation. Proto-oncogenes are enriched with G4 sequences, while tumor-suppressor genes are depleted, suggesting roles for G4s in cell survival and proliferation. Specialized helicases participate in G4-mediated gene regulation via enzymatic unwinding activity. One such enzyme, DHX36/G4R1, is the major G4-helicase and is a master regulator of G4-DNAs and mRNAs. G4-resolution promotes the expression of proproliferative genes; as such, DHX36/G4R1 promotes cell proliferation. Little is known about how DHX36/G4R1 itself is regulated in nondividing cells. We hypothesized that DHX36/G4R1 protein binding partners are altered when a cell transitions from a dividing to a quiescent state. We found that DHX36/G4R1 co-purifies with a distinct set of proteins under quiescent conditions, which may represent a novel complex that regulates DHX36/G4R1 during cell cycle transitions and have implications for development and cancer.
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Affiliation(s)
- Adam.
E. Richardson
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Zachary. A. Zentz
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Antonio E. Chambers
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Siara N. Sandwith
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Michael A. Reisinger
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Destinee W. Saunders
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Joshua D. Tompkins
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Arthur D. Riggs
- Department
of Diabetes Complications and Metabolism, City of Hope, Duarte, California 91010, United States
| | - Eric D. Routh
- Lineberger
Comprehensive Cancer Center, University
of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Eric M. Rubenstein
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Melissa A. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - James P. Vaughn
- NanoMedica
LLC, Winston-Salem, North Carolina 27101, United States
| | - Robert A. Haney
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
| | - Philip J. Smaldino
- Department
of Biology, Ball State University, Muncie, Indiana 47306, United States
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8
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General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation. Int J Mol Sci 2020; 21:ijms21124402. [PMID: 32575790 PMCID: PMC7352612 DOI: 10.3390/ijms21124402] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/19/2022] Open
Abstract
DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.
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9
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Al-Zeer MA, Dutkiewicz M, von Hacht A, Kreuzmann D, Röhrs V, Kurreck J. Alternatively spliced variants of the 5'-UTR of the ARPC2 mRNA regulate translation by an internal ribosome entry site (IRES) harboring a guanine-quadruplex motif. RNA Biol 2019; 16:1622-1632. [PMID: 31387452 DOI: 10.1080/15476286.2019.1652524] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The 5'-UTR of the actin-related protein 2/3 complex subunit 2 (ARPC2) mRNA exists in two variants. Using a bicistronic reporter construct, the present study demonstrates that the longer variant of the 5'-UTR harbours an internal ribosome entry site (IRES) which is lacking in the shorter one. Multiple control assays confirmed that only this variant promotes cap-independent translation. Furthermore, it includes a guanine-rich region that is capable of forming a guanine-quadruplex (G-quadruplex) structure which was found to contribute to the IRES activity. To investigate the cellular function of the IRES element, we determined the expression level of ARPC2 at various cell densities. At high cell density, the relative ARPC2 protein level increases, supporting the presumed function of IRES elements in driving the expression of certain genes under stressful conditions that compromise cap-dependent translation. Based on chemical probing experiments and computer-based predictions, we propose a structural model of the IRES element, which includes the G-quadruplex motif exposed from the central stem-loop element. Taken together, our study describes the functional relevance of two alternative 5'-UTR splice variants of the ARPC2 mRNA, one of which contains an IRES element with a G-quadruplex as a central motif, promoting translation under stressful cellular conditions.
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Affiliation(s)
- Munir A Al-Zeer
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
| | - Mariola Dutkiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan , Poland
| | | | - Denise Kreuzmann
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
| | - Viola Röhrs
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
| | - Jens Kurreck
- Institute of Biotechnology, Technische Universität Berlin , Berlin , Germany
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