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Fu L, Wu Q, Fu J. Exploring the biological roles of DHX36, a DNA/RNA G-quadruplex helicase, highlights functions in male infertility: A comprehensive review. Int J Biol Macromol 2024; 268:131811. [PMID: 38677694 DOI: 10.1016/j.ijbiomac.2024.131811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/29/2024]
Abstract
It is estimated that 15 % of couples at reproductive age worldwide suffer from infertility, approximately 50 % of cases are caused by male factors. Significant progress has been made in the diagnosis and treatment of male infertility through assisted reproductive technology and molecular genetics methods. However, there is still inadequate research on the underlying mechanisms of gene regulation in the process of spermatogenesis. Guanine-quadruplexes (G4s) are a class of non-canonical secondary structures of nucleic acid commonly found in genomes and RNAs that play important roles in various biological processes. Interestingly, the DEAH-box helicase 36 (DHX36) displays high specificity for the G4s which can unwind both DNA G4s and RNA G4s enzymatically and is highly expressed in testis, thereby regulating multiple cellular functions including transcription, pre-mRNA splicing, translation, telomere maintenance, genomic stability, and RNA metabolism in development and male infertility. This review provides an overview of the roles of G4s and DHX36 in reproduction and development. We mainly focus on the potential role of DHX36 in male infertility. We also discuss possible future research directions regarding the mechanism of spermatogenesis mediated by DHX36 through G4s in spermatogenesis-related genes and provide new targets for gene therapy of male infertility.
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Affiliation(s)
- Li Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China; Department of Reproductive Medicine, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China; Faculty of Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Qiang Wu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Junjiang Fu
- The State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, China.
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2
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Ambrosio MR, Migliaccio T, Napolitano F, Di Somma S, Maneli G, Amato J, Pagano B, Randazzo A, Portella G, Formisano P, Malfitano AM. Targeting G-quadruplex motifs interferes with differentiation of adipose-derived mesenchymal stem cells. Stem Cell Res Ther 2023; 14:98. [PMID: 37076894 PMCID: PMC10116735 DOI: 10.1186/s13287-023-03320-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/29/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND G-quadruplex (G4) motifs are nucleic acid secondary structures observed in mammalian genomes and transcriptomes able to regulate various cellular processes. Several small molecules have been developed so far to modulate G4 stability, frequently associated with anticancer activity. However, how G4 structures are regulated over homeostatic conditions is mostly unexplored. Here, we used human adipose-derived mesenchymal stem cells (ASCs) to address the role of G4 motifs during adipogenic differentiation. METHODS Adipocyte differentiation of ASCs was investigated in the presence or absence of a well-known G4 ligand, Braco-19. Cell viability was determined by sulforhodamine B assay. Cell dimension and granularity, DNA G4 motifs and cell cycle were detected by flow cytometry. Lipid droplet accumulation was assessed by Oil Red O staining. Cell senescence was evaluated by β-galactosidase staining. Gene expression was measured by qPCR. Protein release in the extracellular medium was quantified by ELISA. RESULTS Braco-19 used at non-cytotoxic concentrations induced morphological changes in mature adipocytes partially restoring an undifferentiated-like status. Braco-19 reduced lipid vacuolization and PPARG, AP2, LEP and TNFA mRNA levels in terminally differentiated cells. No effect was observed in cell senescence, fibrotic markers, IL-6 and IL-8 production, while the secretion of VEGF was dose-dependently reduced. Interestingly, G4 structures were increased in differentiated adipocytes compared to their precursors. Braco-19 treatment reduced G4 content in mature adipocytes. CONCLUSIONS Our data highlight a new role of G4 motifs as genomic structural elements related to human ASC differentiation into mature adipocytes, with potential implications in physio-pathological processes.
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Affiliation(s)
- Maria Rosaria Ambrosio
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - Teresa Migliaccio
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
| | - Fabiana Napolitano
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
| | - Sarah Di Somma
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
| | - Giovanni Maneli
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, 80131, Naples, Italy
| | - Giuseppe Portella
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy
| | - Pietro Formisano
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy.
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, 80131, Naples, Italy.
| | - Anna Maria Malfitano
- Department of Translational Medical Sciences, University "Federico II", 80131, Naples, Italy.
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Yang C, Yao J, Yi H, Huang X, Zhao W, Yang Z. To unwind the biological knots: The DNA/RNA G-quadruplex resolvase RHAU (DHX36) in development and disease. Animal Model Exp Med 2022; 5:542-549. [PMID: 35789129 PMCID: PMC9773310 DOI: 10.1002/ame2.12251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/21/2022] [Indexed: 12/30/2022] Open
Abstract
The G-quadruplex (G4) sequences are short fragments of 4-interval triple guanine (G) with frequent and ubiquitous distribution in the genome and RNA transcripts. The G4 sequences are usually folded into secondary "knot" structure via Hoogsteen hydrogen bond to exert negative regulation on a variety of biological processes, including DNA replication and transcription, mRNA translation, and telomere maintenance. Recent structural biological and mouse genetics studies have demonstrated that RHAU (DHX36) can bind and unwind the G4 "knots" to modulate embryonic development and postnatal organ function. Deficiency of RHAU gives rise to embryonic lethality, impaired organogenesis, and organ dysfunction. These studies uncovered the pivotal G4 resolvase function of RHAU to release the G4 barrier, which plays fundamental roles in development and physiological homeostasis. This review discusses the latest advancements and findings in deciphering RHAU functions using animal models.
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Affiliation(s)
- Chensi Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Jie Yao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Huijuan Yi
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Xinyi Huang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Wukui Zhao
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Key Laboratory of Molecular MedicineNanjing University Medical SchoolNanjingChina
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4
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Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX with Its Interacting Nucleoid Proteins, and of mtDNA. Cells 2021; 10:cells10123354. [PMID: 34943861 PMCID: PMC8699119 DOI: 10.3390/cells10123354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/20/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022] Open
Abstract
Biallelic pathogenic variants in CLPP, encoding mitochondrial matrix peptidase ClpP, cause a rare autosomal recessive condition, Perrault syndrome type 3 (PRLTS3). It is characterized by primary ovarian insufficiency and early sensorineural hearing loss, often associated with progressive neurological deficits. Mouse models showed that accumulations of (i) its main protein interactor, the substrate-selecting AAA+ ATPase ClpX, (ii) mitoribosomes, and (iii) mtDNA nucleoids are the main cellular consequences of ClpP absence. However, the sequence of these events and their validity in human remain unclear. Here, we studied global proteome profiles to define ClpP substrates among mitochondrial ClpX interactors, which accumulated consistently in ClpP-null mouse embryonal fibroblasts and brains. Validation work included novel ClpP-mutant patient fibroblast proteomics. ClpX co-accumulated in mitochondria with the nucleoid component POLDIP2, the mitochondrial poly(A) mRNA granule element LRPPRC, and tRNA processing factor GFM1 (in mouse, also GRSF1). Only in mouse did accumulated ClpX, GFM1, and GRSF1 appear in nuclear fractions. Mitoribosomal accumulation was minor. Consistent accumulations in murine and human fibroblasts also affected multimerizing factors not known as ClpX interactors, namely, OAT, ASS1, ACADVL, STOM, PRDX3, PC, MUT, ALDH2, PMPCB, UQCRC2, and ACADSB, but the impact on downstream metabolites was marginal. Our data demonstrate the primary impact of ClpXP on the assembly of proteins with nucleic acids and show nucleoid enlargement in human as a key consequence.
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5
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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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6
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Translational control by DHX36 binding to 5'UTR G-quadruplex is essential for muscle stem-cell regenerative functions. Nat Commun 2021; 12:5043. [PMID: 34413292 PMCID: PMC8377060 DOI: 10.1038/s41467-021-25170-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 06/06/2021] [Indexed: 12/30/2022] Open
Abstract
Skeletal muscle has a remarkable ability to regenerate owing to its resident stem cells (also called satellite cells, SCs). SCs are normally quiescent; when stimulated by damage, they activate and expand to form new fibers. The mechanisms underlying SC proliferative progression remain poorly understood. Here we show that DHX36, a helicase that unwinds RNA G-quadruplex (rG4) structures, is essential for muscle regeneration by regulating SC expansion. DHX36 (initially named RHAU) is barely expressed at quiescence but is highly induced during SC activation and proliferation. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration after damage. System-wide mapping in proliferating SCs reveals DHX36 binding predominantly to rG4 structures at various regions of mRNAs, while integrated polysome profiling shows that DHX36 promotes mRNA translation via 5′-untranslated region (UTR) rG4 binding. Furthermore, we demonstrate that DHX36 specifically regulates the translation of Gnai2 mRNA by unwinding its 5′ UTR rG4 structures and identify GNAI2 as a downstream effector of DHX36 for SC expansion. Altogether, our findings uncover DHX36 as an indispensable post-transcriptional regulator of SC function and muscle regeneration acting through binding and unwinding rG4 structures at 5′ UTR of target mRNAs. Skeletal muscle stem cells (or satellite cells, SCs) are normally quiescent but activate and expand in response to injury. Here the authors show that induction of DHX36 helicase during SC activation promotes mRNA translation by binding to 5′UTR mRNA G-quadruplexes (rG4) in targets including Gnai2 and unwinding them.
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7
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Hossain KA, Jurkowski M, Czub J, Kogut M. Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations. Comput Struct Biotechnol J 2021; 19:2526-2536. [PMID: 34025941 PMCID: PMC8114077 DOI: 10.1016/j.csbj.2021.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Because of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type G4s using all-atom molecular dynamics simulations. By computing binding free energies, we found that the two main G4-interacting subdomains of DHX36, DSM and OB, separately exhibit high G4 affinity but they act cooperatively to recognize two distinctive features of parallel G4s: the exposed planar face of a guanine tetrad and the unique backbone conformation of a continuous guanine tract, respectively. Our results also show that DSM-mediated interactions are the main contributor to the binding free energy and rely on making extensive van der Waals contacts between the GXXXG motifs and hydrophobic residues of DSM and a flat guanine plane. Accordingly, the sterically more accessible 5'-G-tetrad allows for more favorable van der Waals and hydrophobic interactions which leads to the preferential binding of DSM to the 5'-side. In contrast to DSM, OB binds to G4 mostly through polar interactions by flexibly adapting to the 5'-terminal guanine tract to form a number of strong hydrogen bonds with the backbone phosphate groups. We also identified a third DHX36/G4 interaction site formed by the flexible loop missing in the crystal structure.
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Affiliation(s)
- Kazi Amirul Hossain
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Michal Jurkowski
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Mateusz Kogut
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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8
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Jiang M, Hu H, Zhao K, Di R, Huang X, Shi Y, Yue Y, Nie J, Yu S, Wang W, Yang Z. The G4 resolvase RHAU modulates mRNA translation and stability to sustain postnatal heart function and regeneration. J Biol Chem 2021; 296:100080. [PMID: 33199370 PMCID: PMC7948451 DOI: 10.1074/jbc.ra120.014948] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/07/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional regulation of mRNA translation and stability is primarily achieved by RNA-binding proteins, which are of increasing importance for heart function. Furthermore, G-quadruplex (G4) and G4 resolvase activity are involved in a variety of biological processes. However, the role of G4 resolvase activity in heart function remains unknown. The present study aims to investigate the role of RNA helicase associated with adenylate- and uridylate-rich element (RHAU), an RNA-binding protein with G4 resolvase activity in postnatal heart function through deletion of Rhau in the cardiomyocytes of postnatal mice. RHAU-deficient mice displayed progressive pathological remodeling leading to heart failure and mortality and impaired neonatal heart regeneration. RHAU ablation reduced the protein levels but enhanced mRNA levels of Yap1 and Hexim1 that are important regulators for heart development and postnatal heart function. Furthermore, RHAU was found to associate with both the 5' and 3' UTRs of these genes to destabilize mRNA and enhance translation. Thus, we have demonstrated the important functions of RHAU in the dual regulation of mRNA translation and stability, which is vital for heart physiology.
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Affiliation(s)
- Mingyang Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Han Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ke Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Ruomin Di
- Department of Cardiology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Xinyi Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yingchao Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Yunyun Yue
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Junwei Nie
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Shan Yu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Wengong Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.
| | - Zhongzhou Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School and MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China.
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9
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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: 13] [Impact Index Per Article: 3.3] [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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10
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Yaneva MY, Cheong VV, Cheng JK, Lim KW, Phan AT. Stapling a G-quadruplex specific peptide. Biochem Biophys Res Commun 2020; 531:62-66. [DOI: 10.1016/j.bbrc.2020.02.144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/22/2020] [Indexed: 12/12/2022]
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11
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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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12
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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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13
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Sauer M, Juranek SA, Marks J, De Magis A, Kazemier HG, Hilbig D, Benhalevy D, Wang X, Hafner M, Paeschke K. DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions. Nat Commun 2019; 10:2421. [PMID: 31160600 PMCID: PMC6547686 DOI: 10.1038/s41467-019-10432-5] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/07/2019] [Indexed: 11/08/2022] Open
Abstract
Translation efficiency can be affected by mRNA stability and secondary structures, including G-quadruplex structures (G4s). The highly conserved DEAH-box helicase DHX36/RHAU resolves G4s on DNA and RNA in vitro, however a systems-wide analysis of DHX36 targets and function is lacking. We map globally DHX36 binding to RNA in human cell lines and find it preferentially interacting with G-rich and G4-forming sequences on more than 4500 mRNAs. While DHX36 knockout (KO) results in a significant increase in target mRNA abundance, ribosome occupancy and protein output from these targets decrease, suggesting that they were rendered translationally incompetent. Considering that DHX36 targets, harboring G4s, preferentially localize in stress granules, and that DHX36 KO results in increased SG formation and protein kinase R (PKR/EIF2AK2) phosphorylation, we speculate that DHX36 is involved in resolution of rG4 induced cellular stress.
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Affiliation(s)
- Markus Sauer
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Stefan A Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - James Marks
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Alessio De Magis
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Daniel Hilbig
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany
| | - Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Xiantao Wang
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Katrin Paeschke
- Department of Biochemistry, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands.
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127, Bonn, Germany.
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14
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Armas P, Calcaterra NB. G-quadruplex in animal development: Contribution to gene expression and genomic heterogeneity. Mech Dev 2018; 154:64-72. [DOI: 10.1016/j.mod.2018.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/18/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022]
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15
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Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG. Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model. Structure 2018; 26:403-415.e4. [PMID: 29429875 DOI: 10.1016/j.str.2018.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/13/2017] [Accepted: 01/12/2018] [Indexed: 11/29/2022]
Abstract
Helicase DHX36 plays essential roles in cell development and differentiation at least partially by resolving G-quadruplex (G4) structures. Here we report crystal structures of the Drosophila homolog of DHX36 (DmDHX36) in complex with RNA and a series of DNAs. By combining structural, small-angle X-ray scattering, molecular dynamics simulation, and single-molecule fluorescence studies, we revealed that positively charged amino acids in RecA2 and OB-like domains constitute an elaborate structural pocket at the nucleic acid entrance, in which negatively charged G4 DNA is tightly bound and partially destabilized. The G4 DNA is then completely unfolded through the 3'-5' translocation activity of the helicase. Furthermore, crystal structures and DNA binding assays show that G-rich DNA is preferentially recognized and in the presence of ATP, specifically bound by DmDHX36, which may cooperatively enhance the G-rich DNA translocation and G4 unfolding. On the basis of these results, a conceptual G4 DNA-resolving mechanism is proposed.
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Affiliation(s)
- Wei-Fei Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Stephane Rety
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, 69007, Lyon, France
| | - Hai-Lei Guo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang-Xue Dai
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Qiang Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d'Orléans, UPRES EA 1207, INRA-USC1328, 45067 Orléans, France
| | - Qian-Wen Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, 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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16
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Yangyuoru PM, Bradburn DA, Liu Z, Xiao TS, Russell R. The G-quadruplex (G4) resolvase DHX36 efficiently and specifically disrupts DNA G4s via a translocation-based helicase mechanism. J Biol Chem 2017; 293:1924-1932. [PMID: 29269411 DOI: 10.1074/jbc.m117.815076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/18/2017] [Indexed: 12/22/2022] Open
Abstract
Single-stranded DNA (ssDNA) and RNA regions that include at least four closely spaced runs of three or more consecutive guanosines strongly tend to fold into stable G-quadruplexes (G4s). G4s play key roles as DNA regulatory sites and as kinetic traps that can inhibit biological processes, but how G4s are regulated in cells remains largely unknown. Here, we developed a kinetic framework for G4 disruption by DEAH-box helicase 36 (DHX36), the dominant G4 resolvase in human cells. Using tetramolecular DNA and RNA G4s with four to six G-quartets, we found that DHX36-mediated disruption is highly efficient, with rates that depend on G4 length under saturating conditions (kcat) but not under subsaturating conditions (kcat/Km ). These results suggest that a step during G4 disruption limits the kcat value and that DHX36 binding limits kcat/Km Similar results were obtained for unimolecular DNA G4s. DHX36 activity depended on a 3' ssDNA extension and was blocked by a polyethylene glycol linker, indicating that DHX36 loads onto the extension and translocates 3'-5' toward the G4. DHX36 unwound dsDNA poorly compared with G4s of comparable intrinsic lifetime. Interestingly, we observed that DHX36 has striking 3'-extension sequence preferences that differ for G4 disruption and dsDNA unwinding, most likely arising from differences in the rate-limiting step for the two activities. Our results indicate that DHX36 disrupts G4s with a conventional helicase mechanism that is tuned for great efficiency and specificity for G4s. The dependence of DHX36 on the 3'-extension sequence suggests that the extent of formation of genomic G4s may not track directly with G4 stability.
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Affiliation(s)
- Philip M Yangyuoru
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
| | - Devin A Bradburn
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
| | - Zhonghua Liu
- the Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Tsan Sam Xiao
- the Department of Pathology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Rick Russell
- From the Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712 and
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17
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Bae HS, Yoon WJ, Cho YD, Islam R, Shin HR, Kim BS, Lim JM, Seo MS, Cho SA, Choi KY, Baek SH, Kim HG, Woo KM, Baek JH, Lee YS, Ryoo HM. An HDAC Inhibitor, Entinostat/MS-275, Partially Prevents Delayed Cranial Suture Closure in Heterozygous Runx2 Null Mice. J Bone Miner Res 2017; 32:951-961. [PMID: 28052439 DOI: 10.1002/jbmr.3076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/23/2016] [Accepted: 01/03/2017] [Indexed: 12/21/2022]
Abstract
Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal disorder caused by mutations in RUNX2, coding a key transcription factor of early osteogenesis. CCD patients suffer from developmental defects in cranial bones. Despite numerous investigations and clinical approaches, no therapeutic strategy has been suggested to prevent CCD. Here, we show that fetal administration of Entinostat/MS-275, a class I histone deacetylase (HDAC)-specific inhibitor, partially prevents delayed closure of cranial sutures in Runx2+/- mice strain of C57BL/6J by two mechanisms: 1) posttranslational acetylation of Runx2 protein, which stabilized the protein and activated its transcriptional activity; and 2) epigenetic regulation of Runx2 and other bone marker genes. Moreover, we show that MS-275 stimulates osteoblast proliferation effectively both in vivo and in vitro, suggesting that delayed skeletal development in CCD is closely related to the decreased number of progenitor cells as well as the delayed osteogenic differentiation. These findings provide the potential benefits of the therapeutic strategy using MS-275 to prevent CCD. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Han-Sol Bae
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Won-Joon Yoon
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Young-Dan Cho
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea.,Department of Periodontology, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Rabia Islam
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Hye-Rim Shin
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Bong-Soo Kim
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Jin-Muk Lim
- Biomedical Knowledge Engineering Laboratory, Institute of Human-Environment Interface Biology, Seoul National University, Republic of Korea
| | - Min-Seok Seo
- Interdisciplinary Program in Bioinformatics and CHO&KIM Genomics, Seoul National University, Seoul, Republic of Korea
| | - Seo-Ae Cho
- Interdisciplinary Program in Bioinformatics and CHO&KIM Genomics, Seoul National University, Seoul, Republic of Korea
| | - Kang-Young Choi
- Department of Plastic and Reconstructive Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Seung-Hak Baek
- Department of Orthodontics, School of Dentistry and Dental Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Hong-Gee Kim
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea.,Biomedical Knowledge Engineering Laboratory, Institute of Human-Environment Interface Biology, Seoul National University, Republic of Korea
| | - Kyung-Mi Woo
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Hwa Baek
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Yun-Sil Lee
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Mo Ryoo
- Department of Molecular Genetics, School of Dentistry and Dental Research Institute, BK21 Program, Seoul National University, Seoul, Republic of Korea
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18
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Gueddouda NM, Mendoza O, Gomez D, Bourdoncle A, Mergny JL. G-quadruplexes unfolding by RHAU helicase. Biochim Biophys Acta Gen Subj 2017; 1861:1382-1388. [PMID: 28065761 DOI: 10.1016/j.bbagen.2017.01.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/02/2017] [Accepted: 01/04/2017] [Indexed: 11/17/2022]
Abstract
G-quadruplexes (G4) are RNA and DNA secondary structures formed by the stacking of guanine quartets in guanine rich sequences. Quadruplex-prone motifs may be found in key genomic regions such as telomeres, ribosomal DNA, transcriptional activators and regulators or oncogene promoters. A number of proteins involved in various biological processes are able to interact with G4s. Among them, proteins dedicated to nucleic acids unwinding such as WRN, BLM, FANCJ or PIF1, can unfold G4 structures. Mutations of these helicases are linked to genome instability and to increases in cancer risks. Here, we present a high-throughput fluorescence-based reliable, inexpensive and fast assay to study G4/RHAU interaction. RHAU is an RNA helicase known as the major source of G4 resolution in HeLa cells. Our assay allows to monitor the unfolding properties of RHAU towards DNA and RNA quadruplexes in parallel and to screen for the optimal conditions for its activity. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
| | - Oscar Mendoza
- Univ. Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33607 Pessac, France
| | - Dennis Gomez
- Univ. Toulouse, IPBS, CNRS UMR 5089, 205 route de Narbonne, 31077 Toulouse, France
| | - Anne Bourdoncle
- Univ. Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33607 Pessac, France.
| | - Jean-Louis Mergny
- Univ. Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33607 Pessac, France.
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19
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You H, Lattmann S, Rhodes D, Yan J. RHAU helicase stabilizes G4 in its nucleotide-free state and destabilizes G4 upon ATP hydrolysis. Nucleic Acids Res 2016; 45:206-214. [PMID: 28069994 PMCID: PMC5224510 DOI: 10.1093/nar/gkw881] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 09/20/2016] [Accepted: 09/24/2016] [Indexed: 12/02/2022] Open
Abstract
The DEAH-box ATP-dependent RHAU helicases specifically unfold RNA and DNA G-quadruplexes (G4s). However, it remains unclear how the RHAU's G4 unfolding activity is coupled to different stages of the ATPase cycle. Here, using a single-molecule manipulation approach, we show that binding of Drosophila RHAU stabilizes an intramolecularly folded parallel DNA G4 against mechanical unfolding in its nucleotide-free and in its AMP-PNP or ADP bound states, while it destabilizes the G4 when coupled to ATP hydrolysis. Importantly, our results show that the ADP·AlF\documentclass[12pt]{minimal}
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}{}$_4^-$\end{document}-bound RHAU does not stabilize the G4. We also found that both a single-stranded 3′ DNA tail and the RSM domain of RHAU that binds specifically to the G4 structure, are dispensable for the stabilization of the G4, but both are required for G4 destabilization. Our study provides the first evidence that the unfolding kinetics of a G-quadruplex can be modulated by different nucleotide-bound states of the helicase.
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Affiliation(s)
- Huijuan You
- Mechanobiology Institute, National University of Singapore, 117411, Singapore
| | - Simon Lattmann
- NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
| | - Daniela Rhodes
- NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, 117411, Singapore .,Department of Physics, National University of Singapore, 117542, Singapore
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20
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Single-molecule imaging reveals a common mechanism shared by G-quadruplex-resolving helicases. Proc Natl Acad Sci U S A 2016; 113:8448-53. [PMID: 27407146 DOI: 10.1073/pnas.1603724113] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
G-quadruplex (GQ) is a four stranded DNA secondary structure that arises from a guanine rich sequence. Stable formation of GQ in genomic DNA can be counteracted by the resolving activity of specialized helicases including RNA helicase AU (associated with AU rich elements) (RHAU) (G4 resolvase 1), Bloom helicase (BLM), and Werner helicase (WRN). However, their substrate specificity and the mechanism involved in GQ unfolding remain uncertain. Here, we report that RHAU, BLM, and WRN exhibit distinct GQ conformation specificity, but use a common mechanism of repetitive unfolding that leads to disrupting GQ structure multiple times in succession. Such unfolding activity of RHAU leads to efficient annealing exclusively within the same DNA molecule. The same resolving activity is sufficient to dislodge a stably bound GQ ligand, including BRACO-19, NMM, and Phen-DC3. Our study demonstrates a plausible biological scheme where different helicases are delegated to resolve specific GQ structures by using a common repetitive unfolding mechanism that provides a robust resolving power.
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21
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RNA Secondary Structure Modulates FMRP's Bi-Functional Role in the MicroRNA Pathway. Int J Mol Sci 2016; 17:ijms17060985. [PMID: 27338369 PMCID: PMC4926514 DOI: 10.3390/ijms17060985] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/23/2016] [Accepted: 06/14/2016] [Indexed: 11/28/2022] Open
Abstract
MicroRNAs act by post-transcriptionally regulating the gene expression of 30%–60% of mammalian genomes. MicroRNAs are key regulators in all cellular processes, though the mechanism by which the cell activates or represses microRNA-mediated translational regulation is poorly understood. In this review, we discuss the RNA binding protein Fragile X Mental Retardation Protein (FMRP) and its role in microRNA-mediated translational regulation. Historically, FMRP is known to function as a translational suppressor. However, emerging data suggests that FMRP has both an agonistic and antagonistic role in regulating microRNA-mediated translational suppression. This bi-functional role is dependent on FMRP’s interaction with the RNA helicase Moloney leukemia virus 10 (MOV10), which modifies the structural landscape of bound mRNA, therefore facilitating or inhibiting its association with the RNA-Induced Silencing Complex.
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22
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Different fixative methods influence histological morphology and TUNEL staining in mouse testes. Reprod Toxicol 2016; 60:53-61. [PMID: 26820454 DOI: 10.1016/j.reprotox.2016.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/11/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
Abstract
Society of Toxicologic Pathology has recommended mDF to fix testes since 2002. However, subsequent studies showed that false TUNEL-positive cells were observed in mDF-fixed testes. This study compared the effects of different fixation methods on histology and TUNEL staining in mouse testes. Results showed that fixation for 24 or 36h in mDF provided better morphologic details in untreated testes, but markedly enhanced false TUNEL-positive staining. To optimize the fixation, testes were fixed using mDF for 6h and then PFA for 18h. Interestingly, fixation using mDF/PFA manifested better morphologic details, and rarely caused false TUNEL-positive cells in testes. Finally, we examined germ cell apoptosis in testes using mDF/PFA fixation in cadmium-treated mice. As expected, cadmium triggered germ cell apoptosis which was well visualized in the mDF/PFA fixed testes. Taken together, mDF plus PFA fixation not only minimizes false TUNEL-positive cells, but also provides integrated morphologic details in testes.
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23
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Booy EP, McRae EKS, Howard R, Deo SR, Ariyo EO, Dzananovic E, Meier M, Stetefeld J, McKenna SA. RNA Helicase Associated with AU-rich Element (RHAU/DHX36) Interacts with the 3'-Tail of the Long Non-coding RNA BC200 (BCYRN1). J Biol Chem 2016; 291:5355-72. [PMID: 26740632 DOI: 10.1074/jbc.m115.711499] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/14/2022] Open
Abstract
RNA helicase associated with AU-rich element (RHAU) is an ATP-dependent RNA helicase that demonstrates high affinity for quadruplex structures in DNA and RNA. To elucidate the significance of these quadruplex-RHAU interactions, we have performed RNA co-immunoprecipitation screens to identify novel RNAs bound to RHAU and characterize their function. In the course of this study, we have identified the non-coding RNA BC200 (BCYRN1) as specifically enriched upon RHAU immunoprecipitation. Although BC200 does not adopt a quadruplex structure and does not bind the quadruplex-interacting motif of RHAU, it has direct affinity for RHAU in vitro. Specifically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an adenosine-rich region near the 3'-end of the RNA. RHAU truncations support binding that is dependent upon a region within the C terminus and is specific to RHAU isoform 1. Tests performed to assess whether BC200 interferes with RHAU helicase activity have demonstrated the ability of BC200 to act as an acceptor of unwound quadruplexes via a cytosine-rich region near the 3'-end of the RNA. Furthermore, an interaction between BC200 and the quadruplex-containing telomerase RNA was confirmed by pull-down assays of the endogenous RNAs. This leads to the possibility that RHAU may direct BC200 to bind and exert regulatory functions at quadruplex-containing RNA or DNA sequences.
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Affiliation(s)
| | | | | | | | | | | | | | - Jörg Stetefeld
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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24
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Ariyo EO, Booy EP, Patel TR, Dzananovic E, McRae EK, Meier M, McEleney K, Stetefeld J, McKenna SA. Biophysical Characterization of G-Quadruplex Recognition in the PITX1 mRNA by the Specificity Domain of the Helicase RHAU. PLoS One 2015; 10:e0144510. [PMID: 26649896 PMCID: PMC4674103 DOI: 10.1371/journal.pone.0144510] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/19/2015] [Indexed: 11/28/2022] Open
Abstract
Nucleic acids rich in guanine are able to fold into unique structures known as G-quadruplexes. G-quadruplexes consist of four tracts of guanylates arranged in parallel or antiparallel strands that are aligned in stacked G-quartet planes. The structure is further stabilized by Hoogsteen hydrogen bonds and monovalent cations centered between the planes. RHAU (RNA helicase associated with AU-rich element) is a member of the ATP-dependent DExH/D family of RNA helicases and can bind and resolve G-quadruplexes. RHAU contains a core helicase domain with an N-terminal extension that enables recognition and full binding affinity to RNA and DNA G-quadruplexes. PITX1, a member of the bicoid class of homeobox proteins, is a transcriptional activator active during development of vertebrates, chiefly in the anterior pituitary gland and several other organs. We have previously demonstrated that RHAU regulates PITX1 levels through interaction with G-quadruplexes at the 3’-end of the PITX1 mRNA. To understand the structural basis of G-quadruplex recognition by RHAU, we characterize a purified minimal PITX1 G-quadruplex using a variety of biophysical techniques including electrophoretic mobility shift assays, UV-VIS spectroscopy, circular dichroism, dynamic light scattering, small angle X-ray scattering and nuclear magnetic resonance spectroscopy. Our biophysical analysis provides evidence that the RNA G-quadruplex, but not its DNA counterpart, can adopt a parallel orientation, and that only the RNA can interact with N-terminal domain of RHAU via the tetrad face of the G-quadruplex. This work extends our insight into how the N-terminal region of RHAU recognizes parallel G-quadruplexes.
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Affiliation(s)
- Emmanuel O. Ariyo
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Evan P. Booy
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Trushar R. Patel
- School of Biosciences, University of Birmingham, Birmingham B152TT, United Kingdom
| | - Edis Dzananovic
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ewan K. McRae
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Markus Meier
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Kevin McEleney
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
- Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jorg Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
- Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A. McKenna
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
- Manitoba Institute for Materials, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba R3T 2N2, Canada
- * E-mail:
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25
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Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2015; 16:1006. [PMID: 26607692 PMCID: PMC4659196 DOI: 10.1186/s12864-015-2219-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/16/2015] [Indexed: 01/15/2023] Open
Abstract
Background The Pacific white shrimp (Litopenaeus vannamei) is the world’s most prevalent cultured crustacean species. However, the supply of high-quality broodstocks is limited and baseline information related to its reproductive activity and molecular issues related to gonad development are scarce. In this study, we performed transcriptome sequencing on the gonads of adult male and female L. vannamei to identify sex-related genes. Results A total of 25.16 gigabases (Gb) of sequences were generated from four L. vannamei gonadal tissue libraries. After quality control, 24.11 Gb of clean reads were selected from the gonadal libraries. De-novo assembly of all the clean reads generated a total of 65,218 unigenes with a mean size of 1021 bp and a N50 of 2000 bp. A search of all-unigene against Nr, SwissProt, KEGG, COG and NT databases resulted in 26,482, 23,062, 20,659, 11,935 and 14,626 annotations, respectively, providing a total of 30,304 annotated unigenes. Among annotated unigenes, 12,320 unigenes were assigned to gene ontology categories and 20,659 unigenes were mapped to 258 KEGG pathways. By comparing the ovary and testis libraries, 19,279 testicular up-regulated and 3,529 ovarian up-regulated unigenes were identified. Enrichment analysis of differentially expressed unigenes resulted in 1060 significantly enriched GO terms and 34 significantly enriched KEGG pathways. Nine ovary-specific, 6 testis-specific, 45 testicular up-regulated and 39 ovarian up-regulated unigenes were then confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, using all-unigenes as a reference, a total of 13,233 simple sequence repeats (SSRs) were identified in 10,411 unigene sequences. Conclusions The present study depicts the first large-scale RNA sequencing of shrimp gonads. We have identified many important sex-related functional genes, GO terms and pathways, all of which will facilitate future research into the reproductive biology of shrimp. We expect that the SSRs detected in this study can then be used as genetic markers for germplasm evaluation of breeding and imported populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2219-4) contains supplementary material, which is available to authorized users.
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