1
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Zhang R, Zhang W, Wang C, Wen CK. Arabidopsis Fhit-like tumor suppressor resumes early terminated constitutive triple response1-10 mRNA translation. PLANT PHYSIOLOGY 2024; 195:2073-2093. [PMID: 38563472 DOI: 10.1093/plphys/kiae192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/09/2024] [Accepted: 02/14/2024] [Indexed: 04/04/2024]
Abstract
The Arabidopsis (Arabidopsis thaliana) constitutive triple response1-10 (ctr1-10) mutant produces a reduced level of CTR1 protein and exhibits a weak ctr1 mutant phenotype. Sequence analysis revealed highly active translation of the upstream open reading frame (uORF) at the extended 5'-UTR of the ctr1-10 mRNA, resulting from T-DNA insertion. Enhancer screening for ctr1-10 isolated the fragile histidine triad-1 (fhit-1) mutation. The fhit-1 ctr1-10 mutant phenotypically resembled strong ctr1 mutants and barely produced CTR1, and the fhit-1 mutation reduced the translation efficiency of ctr1-10 but not that of CTR1 mRNA. The human (Homo sapiens) Fhit that involves tumorigenesis and genome instability has the in vitro dinucleotide 5',5'″-P1, P3-triphosphate hydrolase activity, and expression of the human HsFHIT or the hydrolase-defective HsFHITH96N transgene reversed the fhit-1 ctr1-10 mutant phenotype and restored CTR1 levels. Genetic editing that in situ disrupts individual upstream ATG codons proximal to the ctr1-10 mORF elevated CTR1 levels in ctr1-10 plants independent of FHIT. EUKARYOTIC INITIATION FACTOR3G (eIF3G), which is involved in translation and reinitiation, interacted with FHIT, and both were associated with the polysome. We propose that FHIT resumes early terminated ctr1-10 mORF translation in the face of active and complex uORF translation. Our study unveils a niche that may lead to investigations on the molecular mechanism of Fhit-like proteins in translation reinitiation. The biological significance of FHIT-regulated translation is discussed.
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Affiliation(s)
- Ranran Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chenrunshu Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chi-Kuang Wen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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2
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Firdous Z, Kalra S, Chattopadhyay R, Bari VK. Current insight into the role of mRNA decay pathways in fungal pathogenesis. Microbiol Res 2024; 283:127671. [PMID: 38479232 DOI: 10.1016/j.micres.2024.127671] [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: 12/18/2023] [Revised: 02/19/2024] [Accepted: 02/29/2024] [Indexed: 04/17/2024]
Abstract
Pathogenic fungal species can cause superficial and mucosal infections, to potentially fatal systemic or invasive infections in humans. These infections are more common in immunocompromised or critically ill patients and have a significant morbidity and fatality rate. Fungal pathogens utilize several strategies to adapt the host environment resulting in efficient and comprehensive alterations in their cellular metabolism. Fungal virulence is regulated by several factors and post-transcriptional regulation mechanisms involving mRNA molecules are one of them. Post-transcriptional controls have emerged as critical regulatory mechanisms involved in the pathogenesis of fungal species. The untranslated upstream and downstream regions of the mRNA, as well as RNA-binding proteins, regulate morphogenesis and virulence by controlling mRNA degradation and stability. The limited number of available therapeutic drugs, the emergence of multidrug resistance, and high death rates associated with systemic fungal illnesses pose a serious risk to human health. Therefore, new antifungal treatments that specifically target mRNA pathway components can decrease fungal pathogenicity and when combined increase the effectiveness of currently available antifungal drugs. This review summarizes the mRNA degradation pathways and their role in fungal pathogenesis.
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Affiliation(s)
- Zulikha Firdous
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Sapna Kalra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Rituja Chattopadhyay
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India
| | - Vinay Kumar Bari
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, VPO-Ghudda, Bathinda 151401, India.
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3
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Lukaszewicz M, Ferenc-Mrozek A, Kokosza J, Stefaniuk A, Stepinski J, Bojarska E, Darzynkiewicz E. Mammalian Nudt15 hydrolytic and binding activity on methylated guanosine mononucleotides. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:487-495. [PMID: 37644211 PMCID: PMC10618335 DOI: 10.1007/s00249-023-01678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5'RNA turnover by hydrolyzing m7GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m7GDP, its triphosphate form m7GTP, and the trimethylated counterparts (m32,2,7GDP and m32,2,7GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m7GDP and m32,2,7GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Aleksandra Ferenc-Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Julia Kokosza
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Anna Stefaniuk
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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4
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Katahira J, Ohmae T, Yasugi M, Sasaki R, Itoh Y, Kohda T, Hieda M, Yokota Hirai M, Okamoto T, Miyamoto Y. Nsp14 of SARS-CoV-2 inhibits mRNA processing and nuclear export by targeting the nuclear cap-binding complex. Nucleic Acids Res 2023; 51:7602-7618. [PMID: 37260089 PMCID: PMC10415132 DOI: 10.1093/nar/gkad483] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/12/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
To facilitate selfish replication, viruses halt host gene expression in various ways. The nuclear export of mRNA is one such process targeted by many viruses. SARS-CoV-2, the etiological agent of severe acute respiratory syndrome, also prevents mRNA nuclear export. In this study, Nsp14, a bifunctional viral replicase subunit, was identified as a novel inhibitor of mRNA nuclear export. Nsp14 induces poly(A)+ RNA nuclear accumulation and the dissolution/coalescence of nuclear speckles. Genome-wide gene expression analysis revealed the global dysregulation of splicing and 3'-end processing defects of replication-dependent histone mRNAs by Nsp14. These abnormalities were also observed in SARS-CoV-2-infected cells. A mutation introduced at the guanine-N7-methyltransferase active site of Nsp14 diminished these inhibitory activities. Targeted capillary electrophoresis-mass spectrometry analysis (CE-MS) unveiled the production of N7-methyl-GTP in Nsp14-expressing cells. Association of the nuclear cap-binding complex (NCBC) with the mRNA cap and subsequent recruitment of U1 snRNP and the stem-loop binding protein (SLBP) were impaired by Nsp14. These data suggest that the defects in mRNA processing and export arise from the compromise of NCBC function by N7-methyl-GTP, thus exemplifying a novel viral strategy to block host gene expression.
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Affiliation(s)
- Jun Katahira
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Tatsuya Ohmae
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Mayo Yasugi
- Laboratory of Veterinary Public Health, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoko Kohda
- Laboratory of Veterinary Epidemiology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Miki Hieda
- Department of Medical Technology, Ehime Prefectural University of Health Sciences, 543 Tobe-Cho Takaoda, Iyo, Ehime791-2102, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health, and Nutrition (NIBIOHN), 7-6-8 Saito Asagi, Ibaraki, Osaka 567-0085, Japan
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5
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Swartzel JC, Bond MJ, Pintado-Urbanc AP, Daftary M, Krone MW, Douglas T, Carder EJ, Zimmer JT, Maeda T, Simon MD, Crews CM. Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS Chem Biol 2022; 17:1789-1798. [PMID: 35749470 PMCID: PMC10367122 DOI: 10.1021/acschembio.2c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The RNA decapping scavenger protein, DcpS, has recently been identified as a dependency in acute myeloid leukemia (AML). The potent DcpS inhibitor RG3039 attenuates AML cell viability, and shRNA knockdown of DcpS is also antiproliferative. Importantly, DcpS was found to be non-essential in normal human hematopoietic cells, which opens a therapeutic window for AML treatment by DcpS modulation. Considering this strong DcpS dependence in AML cell lines, we explored PROTAC-mediated degradation as an alternative strategy to modulate DcpS activity. Herein, we report the development of JCS-1, a PROTAC exhibiting effective degradation of DcpS at nanomolar concentrations. JCS-1 non-covalently binds DcpS with a RG3039-based warhead and recruits the E3 ligase VHL, which induces potent, rapid, and sustained DcpS degradation in several AML cell lines. JCS-1 serves as a chemical biology tool to interrogate DcpS degradation and associated changes in RNA processes in different cellular contexts, which may be an attractive strategy for the treatment of AML and other DcpS-dependent genetic disorders.
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Affiliation(s)
- Jake C Swartzel
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Michael J Bond
- Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Andreas P Pintado-Urbanc
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Mehana Daftary
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Mackenzie W Krone
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Todd Douglas
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Evan J Carder
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Joshua T Zimmer
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Matthew D Simon
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M Crews
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States.,Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
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6
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Qin S, Tang X, Chen Y, Chen K, Fan N, Xiao W, Zheng Q, Li G, Teng Y, Wu M, Song X. mRNA-based therapeutics: powerful and versatile tools to combat diseases. Signal Transduct Target Ther 2022; 7:166. [PMID: 35597779 PMCID: PMC9123296 DOI: 10.1038/s41392-022-01007-w] [Citation(s) in RCA: 206] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023] Open
Abstract
The therapeutic use of messenger RNA (mRNA) has fueled great hope to combat a wide range of incurable diseases. Recent rapid advances in biotechnology and molecular medicine have enabled the production of almost any functional protein/peptide in the human body by introducing mRNA as a vaccine or therapeutic agent. This represents a rising precision medicine field with great promise for preventing and treating many intractable or genetic diseases. In addition, in vitro transcribed mRNA has achieved programmed production, which is more effective, faster in design and production, as well as more flexible and cost-effective than conventional approaches that may offer. Based on these extraordinary advantages, mRNA vaccines have the characteristics of the swiftest response to large-scale outbreaks of infectious diseases, such as the currently devastating pandemic COVID-19. It has always been the scientists’ desire to improve the stability, immunogenicity, translation efficiency, and delivery system to achieve efficient and safe delivery of mRNA. Excitingly, these scientific dreams have gradually been realized with the rapid, amazing achievements of molecular biology, RNA technology, vaccinology, and nanotechnology. In this review, we comprehensively describe mRNA-based therapeutics, including their principles, manufacture, application, effects, and shortcomings. We also highlight the importance of mRNA optimization and delivery systems in successful mRNA therapeutics and discuss the key challenges and opportunities in developing these tools into powerful and versatile tools to combat many genetic, infectious, cancer, and other refractory diseases.
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Affiliation(s)
- Shugang Qin
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoshan Tang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuting Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Kepan Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Na Fan
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Xiao
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qian Zheng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Guohong Li
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuqing Teng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA
| | - Xiangrong Song
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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7
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Abstract
The 5'-terminal cap is a fundamental determinant of eukaryotic gene expression which facilitates cap-dependent translation and protects mRNAs from exonucleolytic degradation. Enzyme-directed hydrolysis of the cap (decapping) decisively affects mRNA expression and turnover, and is a heavily regulated event. Following the identification of the decapping holoenzyme (Dcp1/2) over two decades ago, numerous studies revealed the complexity of decapping regulation across species and cell types. A conserved set of Dcp1/2-associated proteins, implicated in decapping activation and molecular scaffolding, were identified through genetic and molecular interaction studies, and yet their exact mechanisms of action are only emerging. In this review, we discuss the prevailing models on the roles and assembly of decapping co-factors, with considerations of conservation across species and comparison across physiological contexts. We next discuss the functional convergences of decapping machineries with other RNA-protein complexes in cytoplasmic P bodies and compare current views on their impact on mRNA stability and translation. Lastly, we review the current models of decapping activation and highlight important gaps in our current understanding.
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Affiliation(s)
- Elva Vidya
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Thomas F. Duchaine
- Goodman Cancer Institute, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
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8
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Nsengimana B, Khan FA, Ngowi EE, Zhou X, Jin Y, Jia Y, Wei W, Ji S. Processing body (P-body) and its mediators in cancer. Mol Cell Biochem 2022; 477:1217-1238. [PMID: 35089528 DOI: 10.1007/s11010-022-04359-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022]
Abstract
In recent years, processing bodies (P-bodies) formed by liquid-liquid phase separation, have attracted growing scientific attention due to their involvement in numerous cellular activities, including the regulation of mRNAs decay or storage. These cytoplasmic dynamic membraneless granules contain mRNA storage and decay components such as deadenylase and decapping factors. In addition, different mRNA metabolic regulators, including m6A readers and gene-mediated miRNA-silencing, are also associated with such P-bodies. Cancerous cells may profit from these mRNA decay shredders by up-regulating the expression level of oncogenes and down-regulating tumor suppressor genes. The main challenges of cancer treatment are drug resistance, metastasis, and cancer relapse likely associated with cancer stem cells, heterogeneity, and plasticity features of different tumors. The mRNA metabolic regulators based on P-bodies play a great role in cancer development and progression. The dysregulation of P-bodies mediators affects mRNA metabolism. However, less is known about the relationship between P-bodies mediators and cancerous behavior. The current review summarizes the recent studies on P-bodies mediators, their contribution to tumor development, and their potential in the clinical setting, particularly highlighting the P-bodies as potential drug-carriers such as exosomes to anticancer in the future.
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Affiliation(s)
- Bernard Nsengimana
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Faiz Ali Khan
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Ebenezeri Erasto Ngowi
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Xuefeng Zhou
- Department of Oncology, Dongtai Affiliated Hospital of Nantong University, Dongtai, 224200, Jiangsu, People's Republic of China
| | - Yu Jin
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Yuting Jia
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China
| | - Wenqiang Wei
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China.
| | - Shaoping Ji
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Henan, 475004, People's Republic of China.
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9
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Borbolis F, Syntichaki P. Biological implications of decapping: beyond bulk mRNA decay. FEBS J 2021; 289:1457-1475. [PMID: 33660392 DOI: 10.1111/febs.15798] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/21/2021] [Accepted: 03/07/2021] [Indexed: 12/12/2022]
Abstract
It is well established that mRNA steady-state levels do not directly correlate with transcription rate. This is attributed to the multiple post-transcriptional mechanisms, which control both mRNA turnover and translation within eukaryotic cells. One such mechanism is the removal of the 5' end cap structure of RNAs (decapping). This 5' cap plays a fundamental role in cellular functions related to mRNA processing, transport, translation, quality control, and decay, while its chemical modifications influence the fate of cytoplasmic mRNAs. Decapping is a highly controlled process, performed by multiple decapping enzymes, and regulated by complex cellular networks. In this review, we provide an updated synopsis of 5' end modifications and functions, and give an overview of mRNA decapping enzymes, presenting their enzymatic properties. Focusing on DCP2 decapping enzyme, a major component on the 5'-3' mRNA decay pathway, we describe cis-elements and trans-acting factors that affect its activity, substrate specificity, and cellular localization. Finally, we discuss current knowledge on the biological functions of mRNA decapping and decay factors, highlighting the major questions that remain to be addressed.
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Affiliation(s)
- Fivos Borbolis
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
| | - Popi Syntichaki
- Biomedical Research Foundation of the Academy of Athens, Center of Basic Research, Athens, Greece
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10
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Chae HJ, Seo JB, Kim SH, Jeon YJ, Suh SS. Fhit induces the reciprocal suppressions between Lin28/Let-7 and miR-17/92miR. Int J Med Sci 2021; 18:706-714. [PMID: 33437205 PMCID: PMC7797533 DOI: 10.7150/ijms.51429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Objective: Fhit gene is known as a genome "caretaker" and frequently inactivated by deletion or hypermethylation on the promoter in several cancers. In spite of several lines of evidence, the exact mechanism underlying Fhit-induced biology is relatively less studied. This study will focus the role of Fhit in regulating Lin28 and microRNAs (miRNAs) loop. Material and Methods: To this end, we employed Fhit overexpressing isogenic cell lines to conduct miRNA nanostring array, and differentially expressed miRNAs were identified. Using real-time PCR and Western blot analysis, expression levels of Lin28b or miRNAs were investigated in response to the overexpression of Fhit gene in H1299 lung cancer cells. Results: A series of in vitro including gene nanostring analyses revealed that Lin28B protein was induced by Fhit gene overexpression, which consequently suppressed Let-7 miRNAs. Also, we found that miRNAs in miR-17/92 clusters are redundantly increased and there is an inverse correlation between Let-7 and miR-17/92 clusters in Fhit-expressing cells. Also, a series of in vitro experiments suggests that ELF-1- and/or STAT1-dependent Lin28b regulation is responsible for Let-7 induction in Fhit-expressing cancer cells. Conclusions: Based on the same experimental system proving that Fhit gene has a robust role in suppressing tumor progression and epithelial-mesenchymal transition, our data show that Fhit mediates the negative feedback between Lin28/Let-7 axis and miR-17/-92 miRNA although the physiological relevance of current interesting observation should be further investigated.
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Affiliation(s)
- Hae-Jung Chae
- Department of Biosciences, Mokpo National University, Joennam 58554, South Korea
| | - Jong Bae Seo
- Department of Biosciences, Mokpo National University, Joennam 58554, South Korea.,Department of Biomedicine, Health & Life Convergence Science, BK21 Four, Mokpo National University, Joennam 58554, South Korea
| | - Sung-Hak Kim
- Lab of Animal Molecular Biochemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Young-Jun Jeon
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, South Korea
| | - Sung-Suk Suh
- Department of Biosciences, Mokpo National University, Joennam 58554, South Korea.,Department of Biomedicine, Health & Life Convergence Science, BK21 Four, Mokpo National University, Joennam 58554, South Korea
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11
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Charenton C, Gaudon-Plesse C, Back R, Ulryck N, Cosson L, Séraphin B, Graille M. Pby1 is a direct partner of the Dcp2 decapping enzyme. Nucleic Acids Res 2020; 48:6353-6366. [PMID: 32396195 PMCID: PMC7293026 DOI: 10.1093/nar/gkaa337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 12/27/2022] Open
Abstract
Most eukaryotic mRNAs harbor a characteristic 5′ m7GpppN cap that promotes pre-mRNA splicing, mRNA nucleocytoplasmic transport and translation while also protecting mRNAs from exonucleolytic attacks. mRNA caps are eliminated by Dcp2 during mRNA decay, allowing 5′-3′ exonucleases to degrade mRNA bodies. However, the Dcp2 decapping enzyme is poorly active on its own and requires binding to stable or transient protein partners to sever the cap of target mRNAs. Here, we analyse the role of one of these partners, the yeast Pby1 factor, which is known to co-localize into P-bodies together with decapping factors. We report that Pby1 uses its C-terminal domain to directly bind to the decapping enzyme. We solved the structure of this Pby1 domain alone and bound to the Dcp1–Dcp2–Edc3 decapping complex. Structure-based mutant analyses reveal that Pby1 binding to the decapping enzyme is required for its recruitment into P-bodies. Moreover, Pby1 binding to the decapping enzyme stimulates growth in conditions in which decapping activation is compromised. Our results point towards a direct connection of Pby1 with decapping and P-body formation, both stemming from its interaction with the Dcp1–Dcp2 holoenzyme.
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Affiliation(s)
- Clément Charenton
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Claudine Gaudon-Plesse
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Régis Back
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Loreline Cosson
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, IP Paris, 91128 Palaiseau, France
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12
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Ferenc-Mrozek A, Bojarska E, Stepinski J, Darzynkiewicz E, Lukaszewicz M. Effect of the His-Tag Location on Decapping Scavenger Enzymes and Their Hydrolytic Activity toward Cap Analogs. ACS OMEGA 2020; 5:10759-10766. [PMID: 32455195 PMCID: PMC7240826 DOI: 10.1021/acsomega.0c00304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/08/2020] [Indexed: 05/11/2023]
Abstract
Decapping scavenger enzymes (DcpSs) are important players in mRNA degradation machinery and conserved in eukaryotes. Importantly, human DcpS is the recognized target for spinal muscular atrophy (SMA) and acute myeloid leukemia (AML) therapy, and has recently been connected to development of intellectual disability. Most recombinant DcpSs used in biochemical and biophysical studies are prepared as tagged proteins, with polyhistidine (His-tag) at the N-terminus or C-terminus. Our work is the first report on the parallel characterization of three versions of DcpSs (native and N- or C-terminally tagged) of three species (humans, Caenorhabditis elegans , and Ascaris suum). The native forms of all three enzymes were prepared by N-(His)10 tag cleavage. Protein thermal stability, measured by differential scanning fluorimetry (DSF), was unaffected in the case of native and tagged versions of human and A. suum DcpS; however, the melting temperature (T m) of C. elagans DcpS of was significantly influenced by the presence of the additional N- or C-tag. To investigate the impact of the tag positioning on the catalytic properties of DcpS, we tested the hydrolytic activity of native DcpS and their His-tagged counterparts toward cap dinucleotides (m7GpppG and m3 2,2,7GpppG) and m7GDP. The kinetic data indicate that dinucleotide substrates are hydrolyzed with comparable efficiency by native human and A. suum DcpS and their His-tagged forms. In contrast, both His-tagged C. elegans DcpSs exhibited higher activity toward m7GpppG than the native enzyme. m7GDP is resistant to enzymatic cleavage by all three forms of human and nematode DcpS.
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Affiliation(s)
- Aleksandra Ferenc-Mrozek
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Elzbieta Bojarska
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Janusz Stepinski
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
- Centre
of New Technologies, University of Warsaw, 02-093 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division
of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-093 Warsaw, Poland
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13
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Pietrow P, Ferenc-Mrozek A, Piecyk K, Bojarska E, Darzynkiewicz E, Jankowska-Anyszka M. Decapping Scavenger Enzyme Activity toward N2-Substituted 5' End mRNA Cap Analogues. ACS OMEGA 2019; 4:17576-17580. [PMID: 31656932 PMCID: PMC6812366 DOI: 10.1021/acsomega.9b02715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/19/2019] [Indexed: 05/03/2023]
Abstract
mRNA degradation is a key mechanism of gene expression regulation. In the 3' → 5' decay pathway, mRNA is degraded by the exosome complex and the resulting cap dinucleotide or short-capped oligonucleotide is hydrolyzed mainly by a decapping scavenger enzyme (DcpS)-a member of the histidine triad family. The decapping mechanism is similar for DcpS from different species; however, their respective substrate specificities differ. In this paper, we describe experiments exploring DcpS activity from human (hDcps), Caenorhabditis elegans (CeDcpS), and Ascaris suum (AsDcpS) toward dinucleotide cap analogues modified at the N2 position of 7-methylguanosine. Various alkyl substituents were tested, and cap analogues with a longer than three-carbon chain were nonhydrolyzable by hDcpS and CeDcpS. Resistance of the modified cap analogues to hDcpS and CeDcpS may be associated with their weaker binding with enzymes.
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Affiliation(s)
- Paulina Pietrow
- Faculty
of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Aleksandra Ferenc-Mrozek
- Division of Biophysics, Institute
of Experimental Physics, Faculty
of Physics and Centre of New Technologies, University
of Warsaw, 02-097 Warsaw, Poland
| | - Karolina Piecyk
- Faculty
of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
| | - Elzbieta Bojarska
- Division of Biophysics, Institute
of Experimental Physics, Faculty
of Physics and Centre of New Technologies, University
of Warsaw, 02-097 Warsaw, Poland
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute
of Experimental Physics, Faculty
of Physics and Centre of New Technologies, University
of Warsaw, 02-097 Warsaw, Poland
| | - Marzena Jankowska-Anyszka
- Faculty
of Chemistry, University of Warsaw, 02-093 Warsaw, Poland
- E-mail: . Phone: (+48) 22 55 26 286
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14
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Sjölander JJ, Sunnerhagen P. The fission yeast FHIT homolog affects checkpoint control of proliferation and is regulated by mitochondrial electron transport. Cell Biol Int 2019; 44:412-423. [PMID: 31538680 PMCID: PMC7003880 DOI: 10.1002/cbin.11241] [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: 06/18/2019] [Accepted: 09/15/2019] [Indexed: 11/08/2022]
Abstract
Genetic analysis has strongly implicated human FHIT (Fragile Histidine Triad) as a tumor suppressor gene, being mutated in a large proportion of early‐stage cancers. The functions of the FHIT protein have, however, remained elusive. Here, we investigated aph1+, the fission yeast homolog of FHIT, for functions related to checkpoint control and oxidative metabolism. In sublethal concentrations of DNA damaging agents, aph1Δ mutants grew with a substantially shorter lag phase. In aph1Δ mutants carrying a hypomorphic allele of cds1 (the fission yeast homolog of Chk2), in addition, increased chromosome fragmentation and missegregation were found. We also found that under hypoxia or impaired electron transport function, the Aph1 protein level was strongly depressed. Previously, FHIT has been linked to regulation of the human 9‐1‐1 checkpoint complex constituted by Hus1, Rad1, and Rad9. In Schizosaccharomyces pombe, the levels of all three 9‐1‐1 proteins are all downregulated by hypoxia in similarity with Aph1. Moreover, deletion of the aph1+ gene reduced the Rad1 protein level, indicating a direct relationship between these two proteins. We conclude that the fission yeast FHIT homolog has a role in modulating DNA damage checkpoint function, possibly through an effect on the 9‐1‐1 complex, and that this effect may be critical under conditions of limiting oxidative metabolism and reoxygenation.
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Affiliation(s)
- Johanna J Sjölander
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, Göteborg, SE-405 30, Sweden
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, Göteborg, SE-405 30, Sweden
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15
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Wulf MG, Buswell J, Chan SH, Dai N, Marks K, Martin ER, Tzertzinis G, Whipple JM, Corrêa IR, Schildkraut I. The yeast scavenger decapping enzyme DcpS and its application for in vitro RNA recapping. Sci Rep 2019; 9:8594. [PMID: 31197197 PMCID: PMC6565619 DOI: 10.1038/s41598-019-45083-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/30/2019] [Indexed: 01/25/2023] Open
Abstract
Eukaryotic mRNAs are modified at their 5′ end early during transcription by the addition of N7-methylguanosine (m7G), which forms the “cap” on the first 5′ nucleotide. Identification of the 5′ nucleotide on mRNA is necessary for determination of the Transcription Start Site (TSS). We explored the effect of various reaction conditions on the activity of the yeast scavenger mRNA decapping enzyme DcpS and examined decapping of 30 chemically distinct cap structures varying the state of methylation, sugar, phosphate linkage, and base composition on 25mer RNA oligonucleotides. Contrary to the generally accepted belief that DcpS enzymes only decap short oligonucleotides, we found that the yeast scavenger decapping enzyme decaps RNA transcripts as long as 1400 nucleotides. Further, we validated the application of yDcpS for enriching capped RNA using a strategy of specifically tagging the 5′ end of capped RNA by first decapping and then recapping it with an affinity-tagged guanosine nucleotide.
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Affiliation(s)
- Madalee G Wulf
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - John Buswell
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Siu-Hong Chan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Nan Dai
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Katherine Marks
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Evan R Martin
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | | | - Joseph M Whipple
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Ivan R Corrêa
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Ira Schildkraut
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA.
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16
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Becker H, Greve G, Kataoka K, Mallm JP, Duque-Afonso J, Ma T, Niemöller C, Pantic M, Duyster J, Cleary ML, Schüler J, Rippe K, Ogawa S, Lübbert M. Identification of enhancer of mRNA decapping 4 as a novel fusion partner of MLL in acute myeloid leukemia. Blood Adv 2019; 3:761-765. [PMID: 30833276 PMCID: PMC6418506 DOI: 10.1182/bloodadvances.2018023879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/23/2019] [Indexed: 01/15/2023] Open
Abstract
mRNA decapping gene EDC4 is a novel fusion partner of MLL in AML. Genes functioning in mRNA decapping may compose a distinct group of MLL fusion partners that links MLL function with mRNA decapping in AML.
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Affiliation(s)
- Heiko Becker
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
| | - Gabriele Greve
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Keisuke Kataoka
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Jan-Philipp Mallm
- Division of Chromatin Networks and
- Single-cell Open Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - Jesús Duque-Afonso
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Pathology, Stanford University, Stanford, CA; and
| | - Tobias Ma
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Niemöller
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Justus Duyster
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
| | | | - Julia Schüler
- Charles River Discovery Research Services Germany GmbH, Freiburg, Germany
| | - Karsten Rippe
- Division of Chromatin Networks and
- Single-cell Open Laboratory, German Cancer Research Center, Heidelberg, Germany
| | - Seishi Ogawa
- German Cancer Consortium partner site, Freiburg, Germany
| | - Michael Lübbert
- Department of Medicine I, Medical Center, and
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium partner site, Freiburg, Germany
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17
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Kramer S, McLennan AG. The complex enzymology of mRNA decapping: Enzymes of four classes cleave pyrophosphate bonds. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1511. [PMID: 30345629 DOI: 10.1002/wrna.1511] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 12/16/2022]
Abstract
The 5' ends of most RNAs are chemically modified to enable protection from nucleases. In bacteria, this is often achieved by keeping the triphosphate terminus originating from transcriptional initiation, while most eukaryotic mRNAs and small nuclear RNAs have a 5'→5' linked N7 -methyl guanosine (m7 G) cap added. Several other chemical modifications have been described at RNA 5' ends. Common to all modifications is the presence of at least one pyrophosphate bond. To enable RNA turnover, these chemical modifications at the RNA 5' end need to be reversible. Dependent on the direction of the RNA decay pathway (5'→3' or 3'→5'), some enzymes cleave the 5'→5' cap linkage of intact RNAs to initiate decay, while others act as scavengers and hydrolyse the cap element of the remnants of the 3'→5' decay pathway. In eukaryotes, there is also a cap quality control pathway. Most enzymes involved in the cleavage of the RNA 5' ends are pyrophosphohydrolases, with only a few having (additional) 5' triphosphonucleotide hydrolase activities. Despite the identity of their enzyme activities, the enzymes belong to four different enzyme classes. Nudix hydrolases decap intact RNAs as part of the 5'→3' decay pathway, DXO family members mainly degrade faulty RNAs, members of the histidine triad (HIT) family are scavenger proteins, while an ApaH-like phosphatase is the major mRNA decay enzyme of trypanosomes, whose RNAs have a unique cap structure. Many novel cap structures and decapping enzymes have only recently been discovered, indicating that we are only beginning to understand the mechanisms of RNA decapping. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Susanne Kramer
- Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alexander G McLennan
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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18
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Saldivar JC, Park D. Mechanisms shaping the mutational landscape of the FRA3B/FHIT-deficient cancer genome. Genes Chromosomes Cancer 2018; 58:317-323. [PMID: 30242938 DOI: 10.1002/gcc.22684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/16/2018] [Indexed: 12/20/2022] Open
Abstract
Genome instability is an enabling characteristic of cancer that facilitates the acquisition of oncogenic mutations that drive tumorigenesis. Underlying much of the instability in cancer is DNA replication stress, which causes both chromosome structural changes and single base-pair mutations. Common fragile sites are some of the earliest and most frequently altered loci in tumors. Notably, the fragile locus, FRA3B, lies within the fragile histidine triad (FHIT) gene, and consequently deletions within FHIT are common in cancer. We review the evidence in support of FHIT as a DNA caretaker and discuss the mechanism by which FHIT promotes genome stability. FHIT increases thymidine kinase 1 (TK1) translation to balance the deoxyribonucleotide triphosphates (dNTPs) for efficient DNA replication. Consequently, FHIT-loss causes replication stress, DNA breaks, aneuploidy, copy-number changes (CNCs), small insertions and deletions, and point mutations. Moreover, FHIT-loss-induced replication stress and DNA breaks cooperate with APOBEC3B overexpression to catalyze DNA hypermutation in cancer, as APOBEC family enzymes prefer single-stranded DNA (ssDNA) as substrates and ssDNA is enriched at sites of both replication stress and DNA breaks. Consistent with the frequent loss of FHIT across a broad spectrum of cancer types, FHIT-deficiency is highly associated with the ubiquitous, clock-like mutation signature 5 occurring in all cancer types thus far examined. The ongoing destabilization of the genome caused by FHIT loss underlies recurrent inactivation of tumor suppressors and activation of oncogenes. Considering that more than 50% of cancers are FHIT-deficient, we propose that FRA3B/FHIT fragility shapes the mutational landscape of cancer genomes.
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Affiliation(s)
- Joshua C Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California
| | - Dongju Park
- Department of Cancer Biology and Genetics, The Ohio State University, Comprehensive Cancer Center, Columbus, Ohio
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19
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Yun JS, Yoon JH, Choi YJ, Son YJ, Kim S, Tong L, Chang JH. Molecular mechanism for the inhibition of DXO by adenosine 3',5'-bisphosphate. Biochem Biophys Res Commun 2018; 504:89-95. [PMID: 30180947 DOI: 10.1016/j.bbrc.2018.08.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 08/22/2018] [Indexed: 10/28/2022]
Abstract
The decapping exoribonuclease DXO functions in pre-mRNA capping quality control, and shows multiple biochemical activities such as decapping, deNADding, pyrophosphohydrolase, and 5'-3' exoribonuclease activities. Previous studies revealed the molecular mechanisms of DXO based on the structures in complexes with a product, substrate mimic, cap analogue, and 3'-NADP+. Despite several reports on the substrate-specific reaction mechanism, the inhibitory mechanism of DXO remains elusive. Here, we demonstrate that adenosine 3', 5'-bisphosphate (pAp), a known inhibitor of the 5'-3' exoribonuclease Xrn1, inhibits the nuclease activity of DXO based on the results of structural and biochemical experiments. We determined the crystal structure of the DXO-pAp-Mg2+ complex at 1.8 Å resolution. In comparison with the DXO-RNA product complex, the position of pAp is well superimposed with the first nucleotide of the product RNA in the vicinity of two magnesium ions. Furthermore, biochemical assays showed that the inhibition by pAp is comparable between Xrn1 and DXO. Collectively, these structural and biochemical studies reveal that pAp inhibits the activities of DXO by occupying the active site to act as a competitive inhibitor.
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Affiliation(s)
- Ji-Sook Yun
- Department of Biology Education, Kyungpook National University, Daegu 41566, South Korea
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Young Jun Choi
- Department of Biology Education, Kyungpook National University, Daegu 41566, South Korea
| | - Young Jin Son
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Sunghwan Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, South Korea; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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20
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Wojtczak BA, Sikorski PJ, Fac-Dabrowska K, Nowicka A, Warminski M, Kubacka D, Nowak E, Nowotny M, Kowalska J, Jemielity J. 5'-Phosphorothiolate Dinucleotide Cap Analogues: Reagents for Messenger RNA Modification and Potent Small-Molecular Inhibitors of Decapping Enzymes. J Am Chem Soc 2018; 140:5987-5999. [PMID: 29676910 DOI: 10.1021/jacs.8b02597] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The 5' cap consists of 7-methylguanosine (m7G) linked by a 5'-5'-triphosphate bridge to messenger RNA (mRNA) and acts as the master regulator of mRNA turnover and translation initiation in eukaryotes. Cap analogues that influence mRNA translation and turnover (either as small molecules or as part of an RNA transcript) are valuable tools for studying gene expression, which is often also of therapeutic relevance. Here, we synthesized a series of 15 dinucleotide cap (m7GpppG) analogues containing a 5'-phosphorothiolate (5'-PSL) moiety (i.e., an O-to-S substitution within the 5'-phosphoester) and studied their biological properties in the context of three major cap-binding proteins: translation initiation factor 4E (eIF4E) and two decapping enzymes, DcpS and Dcp2. While the 5'-PSL moiety was neutral or slightly stabilizing for cap interactions with eIF4E, it significantly influenced susceptibility to decapping. Replacing the γ-phosphoester with the 5'-PSL moiety (γ-PSL) prevented β-γ-pyrophosphate bond cleavage by DcpS and conferred strong inhibitory properties. Combining the γ-PSL moiety with α-PSL and β-phosphorothioate (PS) moiety afforded first cap-derived hDcpS inhibitor with low nanomolar potency. Susceptibility to Dcp2 and translational properties were studied after incorporation of the new analogues into mRNA transcripts by RNA polymerase. Transcripts containing the γ-PSL moiety were resistant to cleavage by Dcp2. Surprisingly, superior translational properties were observed for mRNAs containing the α-PSL moiety, which were Dcp2-susceptible. The overall protein expression measured in HeLa cells for this mRNA was comparable to mRNA capped with the translation augmenting β-PS analogue reported previously. Overall, our study highlights 5'-PSL as a synthetically accessible cap modification, which, depending on the substitution site, can either reduce susceptibility to decapping or confer superior translational properties on the mRNA. The 5'-PSL-analogues may find application as reagents for the preparation of efficiently expressed mRNA or for investigation of the role of decapping enzymes in mRNA processing or neuromuscular disorders associated with decapping.
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Affiliation(s)
- Blazej A Wojtczak
- Centre of New Technologies , University of Warsaw , Banacha 2c Street , 02-097 Warsaw , Poland
| | - Pawel J Sikorski
- Centre of New Technologies , University of Warsaw , Banacha 2c Street , 02-097 Warsaw , Poland
| | - Kaja Fac-Dabrowska
- Centre of New Technologies , University of Warsaw , Banacha 2c Street , 02-097 Warsaw , Poland
| | - Anna Nowicka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , Pasteura 5 Street , 02-093 Warsaw , Poland
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , Pasteura 5 Street , 02-093 Warsaw , Poland
| | - Dorota Kubacka
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , Pasteura 5 Street , 02-093 Warsaw , Poland
| | - Elzbieta Nowak
- International Institute of Molecular and Cell Biology in Warsaw , 4 Ks. Trojdena Street , 02-109 Warsaw , Poland
| | - Marcin Nowotny
- International Institute of Molecular and Cell Biology in Warsaw , 4 Ks. Trojdena Street , 02-109 Warsaw , Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics , University of Warsaw , Pasteura 5 Street , 02-093 Warsaw , Poland
| | - Jacek Jemielity
- Centre of New Technologies , University of Warsaw , Banacha 2c Street , 02-097 Warsaw , Poland
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21
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Heck AM, Wilusz J. The Interplay between the RNA Decay and Translation Machinery in Eukaryotes. Cold Spring Harb Perspect Biol 2018; 10:a032839. [PMID: 29311343 PMCID: PMC5932591 DOI: 10.1101/cshperspect.a032839] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA decay plays a major role in regulating gene expression and is tightly networked with other aspects of gene expression to effectively coordinate post-transcriptional regulation. The goal of this work is to provide an overview of the major factors and pathways of general messenger RNA (mRNA) decay in eukaryotic cells, and then discuss the effective interplay of this cytoplasmic process with the protein synthesis machinery. Given the transcript-specific and fluid nature of mRNA stability in response to changing cellular conditions, understanding the fundamental networking between RNA decay and translation will provide a foundation for a complete mechanistic understanding of this important aspect of cell biology.
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Affiliation(s)
- Adam M Heck
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80525
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado 80525
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22
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Kiss DL, Baez WD, Huebner K, Bundschuh R, Schoenberg DR. Loss of fragile histidine triad (Fhit) protein expression alters the translation of cancer-associated mRNAs. BMC Res Notes 2018. [PMID: 29540221 PMCID: PMC5853088 DOI: 10.1186/s13104-018-3278-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Objectives In > 50% of cancers tumor development involves the early loss of Fhit (fragile histidine triad) protein expression, yet the mechanistic pathway(s) by which Fhit mediates its tumor suppressor functions are not fully understood. Earlier attempts to identify a Fhit-deficient gene expression profile relied on total cellular RNA and microarray analysis. The data here used RNA sequencing (RNA-Seq) of Fhit-negative and Fhit-positive cells as proof of principle for the impact of Fhit on specific mRNAs, and to lay the foundation for a study using ribosome profiling to identify mRNAs whose translation is affected by FHIT loss. Data description RNA-Seq was performed on RNA from lines of Fhit-expressing and Fhit-deficient lung cancer cells. This identified changes in the levels of mRNAs for a number of cell survival and cell cycle progression genes. Polysome profile analysis performed on cytoplasmic extracts from Fhit-negative and Fhit-positive cells showed changes in the sedimentation of select mRNAs consistent with changes in translation efficiency. The impact of differential Fhit expression on the turnover of selected cancer-linked mRNAs was determined by RT-qPCR of cytoplasmic RNA isolated at intervals after treating cells with a transcription inhibitor.
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Affiliation(s)
- Daniel L Kiss
- Center for RNA Biology, The Ohio State University, 484 West 12th Ave., Columbus, OH, 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd., Columbus, OH, 43210, USA
| | - William D Baez
- Center for RNA Biology, The Ohio State University, 484 West 12th Ave., Columbus, OH, 43210, USA.,Department of Physics, The Ohio State University, 191 West Woodruff Ave., Columbus, OH, 43210, USA
| | - Kay Huebner
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH, 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, 484 West 12th Ave., Columbus, OH, 43210, USA.,Department of Physics, The Ohio State University, 191 West Woodruff Ave., Columbus, OH, 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel R Schoenberg
- Center for RNA Biology, The Ohio State University, 484 West 12th Ave., Columbus, OH, 43210, USA. .,Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd., Columbus, OH, 43210, USA.
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23
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Abstract
In this issue of Cancer Cell, Yamauchi et al. identify a dependency of acute myeloid leukemia (AML) on DCPS, which catalyzes the final step of 3'-to-5' mRNA decay and is implicated in numerous aspects of RNA metabolism. DCPS is targetable with a clinical inhibitor, underscoring the translational importance of this discovery.
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Affiliation(s)
- Akihide Yoshimi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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24
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Yamauchi T, Masuda T, Canver MC, Seiler M, Semba Y, Shboul M, Al-Raqad M, Maeda M, Schoonenberg VAC, Cole MA, Macias-Trevino C, Ishikawa Y, Yao Q, Nakano M, Arai F, Orkin SH, Reversade B, Buonamici S, Pinello L, Akashi K, Bauer DE, Maeda T. Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. Cancer Cell 2018; 33:386-400.e5. [PMID: 29478914 PMCID: PMC5849534 DOI: 10.1016/j.ccell.2018.01.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/23/2017] [Accepted: 01/19/2018] [Indexed: 12/26/2022]
Abstract
To identify novel targets for acute myeloid leukemia (AML) therapy, we performed genome-wide CRISPR-Cas9 screening using AML cell lines, followed by a second screen in vivo. Here, we show that the mRNA decapping enzyme scavenger (DCPS) gene is essential for AML cell survival. The DCPS enzyme interacted with components of pre-mRNA metabolic pathways, including spliceosomes, as revealed by mass spectrometry. RG3039, a DCPS inhibitor originally developed to treat spinal muscular atrophy, exhibited anti-leukemic activity via inducing pre-mRNA mis-splicing. Humans harboring germline biallelic DCPS loss-of-function mutations do not exhibit aberrant hematologic phenotypes, indicating that DCPS is dispensable for human hematopoiesis. Our findings shed light on a pre-mRNA metabolic pathway and identify DCPS as a target for AML therapy.
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Affiliation(s)
- Takuji Yamauchi
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Yuichiro Semba
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Mohammad Shboul
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Mohammed Al-Raqad
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore; Al-Balqa Applied University, Faculty of Science, Al-Salt, Salt 19117, Jordan
| | - Manami Maeda
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vivien A C Schoonenberg
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Mitchel A Cole
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Claudio Macias-Trevino
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Yuichi Ishikawa
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Qiuming Yao
- Department of Pathology & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michitaka Nakano
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Bruno Reversade
- Institute of Medical Biology, A∗STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | | | - Luca Pinello
- Department of Pathology & Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Koichi Akashi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan; Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Takahiro Maeda
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Cellular and Molecular Medicine, Kyushu University Hospital, Fukuoka 812-8582, Japan.
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25
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Kiss DL, Baez W, Huebner K, Bundschuh R, Schoenberg DR. Impact of FHIT loss on the translation of cancer-associated mRNAs. Mol Cancer 2017; 16:179. [PMID: 29282095 PMCID: PMC5745650 DOI: 10.1186/s12943-017-0749-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/10/2017] [Indexed: 11/30/2022] Open
Abstract
Background FHIT is a genome caretaker/tumor suppressor that is silenced in >50% of cancers. Although it was identified more than 20 years ago, questions remain as to how FHIT loss contributes to cancer, and conversely, how FHIT acts to maintain genome integrity and suppress malignancy. Fhit belongs to the histidine triad family of enzymes that catalyze the degradation of nucleoside 5′,5′-triphosphates, including the m7GpppN ‘caps’ that are generated when mRNAs undergo 3′-5′ decay. This raised the possibility that Fhit loss might affect changes in the translation of cancer-associated mRNAs, possibly as a consequence of increased intracellular concentrations of these molecules. Results Ribosome profiling identified several hundred mRNAs for which coding region ribosome occupancy changed as a function of Fhit expression. While many of these changes could be explained by changes in mRNA steady-state, a subset of these showed changes in translation efficiency as a function of Fhit expression. The onset of malignancy has been linked to changes in 5’-UTR ribosome occupancy and this analysis also identified ribosome binding to 5′-untranslated regions (UTRs) of a number of cancer-associated mRNAs. 5’-UTR ribosome occupancy of these mRNAs differed between Fhit-negative and Fhit-positive cells, and in some cases these differences correlated with differences in coding region ribosome occupancy. Conclusions In summary, these findings show Fhit expression impacts the translation of a number of cancer associated genes, and they support the hypothesis that Fhit’s genome protective/tumor suppressor function is associated with post-transcriptional changes in expression of genes whose dysregulation contributes to malignancy. Electronic supplementary material The online version of this article (10.1186/s12943-017-0749-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel L Kiss
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.,Biomarker Research Program, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - William Baez
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Kay Huebner
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.,Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.,Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Daniel R Schoenberg
- Center for RNA Biology, The Ohio State University, Columbus, OH, 43210, USA. .,Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA. .,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, 43210, USA.
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26
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Rydzik AM, Warminski M, Sikorski PJ, Baranowski MR, Walczak S, Kowalska J, Zuberek J, Lukaszewicz M, Nowak E, W Claridge TD, Darzynkiewicz E, Nowotny M, Jemielity J. mRNA cap analogues substituted in the tetraphosphate chain with CX2: identification of O-to-CCl2 as the first bridging modification that confers resistance to decapping without impairing translation. Nucleic Acids Res 2017; 45:8661-8675. [PMID: 28666355 PMCID: PMC5587727 DOI: 10.1093/nar/gkx569] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/20/2017] [Indexed: 12/20/2022] Open
Abstract
Analogues of the mRNA 5'-cap are useful tools for studying mRNA translation and degradation, with emerging potential applications in novel therapeutic interventions including gene therapy. We report the synthesis of novel mono- and dinucleotide cap analogues containing dihalogenmethylenebisphosphonate moiety (i.e. one of the bridging O atom substituted with CCl2 or CF2) and their properties in the context of cellular translational and decapping machineries, compared to phosphate-unmodified and previously reported CH2-substituted caps. The analogues were bound tightly to eukaryotic translation initiation factor 4E (eIF4E), with CCl2-substituted analogues having the highest affinity. When incorporated into mRNA, the CCl2-substituted dinucleotide most efficiently promoted cap-dependent translation. Moreover, the CCl2-analogues were potent inhibitors of translation in rabbit reticulocyte lysate. The crystal structure of eIF4E in complex with the CCl2-analogue revealed a significantly different ligand conformation compared to that of the unmodified cap analogue, which likely contributes to the improved binding. Both CCl2- and CF2- analogues showed lower susceptibility to hydrolysis by the decapping scavenger enzyme (DcpS) and, when incorporated into RNA, conferred stability against major cellular decapping enzyme (Dcp2) to transcripts. Furthermore, the use of difluoromethylene cap analogues was exemplified by the development of 19F NMR assays for DcpS activity and eIF4E binding.
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Affiliation(s)
- Anna M Rydzik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Marek R Baranowski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Sylwia Walczak
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Zuberek
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Maciej Lukaszewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Elzbieta Nowak
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Ksiecia Trojdena Street, 02-109 Warsaw, Poland
| | - Timothy D W Claridge
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Edward Darzynkiewicz
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Ksiecia Trojdena Street, 02-109 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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27
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Krakowiak A, Kocoń-Rębowska B, Dolot R, Piotrzkowska D. New interactions between tumor suppressor Fhit protein and a nonhydrolyzable analog of its A P4 A substrate. FEBS Lett 2017; 591:548-559. [PMID: 28094435 DOI: 10.1002/1873-3468.12560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 11/06/2022]
Abstract
Fragile histidine triad protein (Fhit) is a protein which primarily hydrolyses dinucleoside polyphosphates. To investigate possible interactions between the protein and a substrate, we used a nonhydrolyzable phosphorothioate analog of Ap4 A, containing 5-bromo-2'-deoxyuridine instead of one adenosine residue. Photocrosslinking, followed by LC-MS experiments, determined a complex in which the probe was covalently linked to the NDSIYEELQK peptide (residues 110-119). The peptide was located within the 'disordered' region, which is invisible in the known crystal structures of Fhit. This invisible and flexible part seems to play a role in the stabilization of the Fhit-substrate complex, which may be important for its tumor suppressor activity.
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Affiliation(s)
- Agnieszka Krakowiak
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
| | - Beata Kocoń-Rębowska
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
| | - Rafał Dolot
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
| | - Danuta Piotrzkowska
- Department of Bioorganic Chemistry, Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Lodz, Poland
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28
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Warminski M, Sikorski PJ, Kowalska J, Jemielity J. Applications of Phosphate Modification and Labeling to Study (m)RNA Caps. Top Curr Chem (Cham) 2017; 375:16. [PMID: 28116583 PMCID: PMC5396385 DOI: 10.1007/s41061-017-0106-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023]
Abstract
The cap is a natural modification present at the 5' ends of eukaryotic messenger RNA (mRNA), which because of its unique structural features, mediates essential biological functions during the process of gene expression. The core structural feature of the mRNA cap is an N7-methylguanosine moiety linked by a 5'-5' triphosphate chain to the first transcribed nucleotide. Interestingly, other RNA 5' end modifications structurally and functionally resembling the m7G cap have been discovered in different RNA types and in different organisms. All these structures contain the 'inverted' 5'-5' oligophosphate bridge, which is necessary for interaction with specific proteins and also serves as a cleavage site for phosphohydrolases regulating RNA turnover. Therefore, cap analogs containing oligophosphate chain modifications or carrying spectroscopic labels attached to phosphate moieties serve as attractive molecular tools for studies on RNA metabolism and modification of natural RNA properties. Here, we review chemical, enzymatic, and chemoenzymatic approaches that enable preparation of modified cap structures and RNAs carrying such structures, with emphasis on phosphate-modified mRNA cap analogs and their potential applications.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland.
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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29
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Kiss DL, Waters CE, Ouda IM, Saldivar JC, Karras JR, Amin ZA, Mahrous S, Druck T, Bundschuh RA, Schoenberg DR, Huebner K. Identification of Fhit as a post-transcriptional effector of Thymidine Kinase 1 expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:374-382. [PMID: 28093273 DOI: 10.1016/j.bbagrm.2017.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 11/30/2022]
Abstract
FHIT is a genome caretaker gene that is silenced in >50% of cancers. Loss of Fhit protein expression promotes accumulation of DNA damage, affects apoptosis and epithelial-mesenchymal transition, though molecular mechanisms underlying these alterations have not been fully elucidated. Initiation of genome instability directly follows Fhit loss and the associated reduced Thymidine Kinase 1 (TK1) protein expression. The effects on TK1 of Fhit knockdown and Fhit induction in the current study confirmed the role of Fhit in regulating TK1 expression. Changes in Fhit expression did not impact TK1 protein turnover or transcription from the TK1 promoter, nor steady-state levels of TK1 mRNA or turnover. Polysome profile analysis showed that up-regulated Fhit expression resulted in decreased TK1 RNA in non-translating messenger ribonucleoproteins and increased ribosome density on TK1 mRNA. Fhit does not bind RNA but its expression increased luciferase expression from a transgene bearing the TK1 5'-UTR. Fhit has been reported to act as a scavenger decapping enzyme, and a similar result with a mutant (H96) that binds but does not cleave nucleoside 5',5'-triphosphates suggests the impact on TK1 translation is due to its ability to modulate the intracellular level of cap-like molecules. Consistent with this, cells expressing Fhit mutants with reduced activity toward cap-like dinucleotides exhibit DNA damage resulting from TK1 deficiency, whereas cells expressing wild-type Fhit or the H96N mutant do not. The results have implications for the mechanism by which Fhit regulates TK1 mRNA, and more broadly, for its modulation of multiple functions as tumor suppressor/genome caretaker.
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Affiliation(s)
- Daniel L Kiss
- Center for RNA Biology, 484 West 12th Ave., Columbus, OH 43210 USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd., Columbus, OH 43210 USA
| | - Catherine E Waters
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Iman M Ouda
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
- Department of Clinical Pathology, Faculty of Medicine, 2nd floor, Surgery Hospital, Zagazig University, Zagazig 44519, Egypt
| | - Joshua C Saldivar
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Jenna R Karras
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Zaynab A Amin
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Seham Mahrous
- Department of Clinical Pathology, Faculty of Medicine, 2nd floor, Surgery Hospital, Zagazig University, Zagazig 44519, Egypt
| | - Teresa Druck
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
| | - Ralf A Bundschuh
- Center for RNA Biology, 484 West 12th Ave., Columbus, OH 43210 USA
- Department of Physics, Department of Chemistry and Biochemistry, and Division of Hematology, Department of Internal Medicine, The Ohio State University, 191 West Woodruff Ave., Columbus, OH 43210 USA
| | - Daniel R Schoenberg
- Center for RNA Biology, 484 West 12th Ave., Columbus, OH 43210 USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Rd., Columbus, OH 43210 USA
| | - Kay Huebner
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12 Ave., Columbus, OH 43210 USA
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30
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Łabno A, Tomecki R, Dziembowski A. Cytoplasmic RNA decay pathways - Enzymes and mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:3125-3147. [PMID: 27713097 DOI: 10.1016/j.bbamcr.2016.09.023] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/29/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022]
Abstract
RNA decay plays a crucial role in post-transcriptional regulation of gene expression. Work conducted over the last decades has defined the major mRNA decay pathways, as well as enzymes and their cofactors responsible for these processes. In contrast, our knowledge of the mechanisms of degradation of non-protein coding RNA species is more fragmentary. This review is focused on the cytoplasmic pathways of mRNA and ncRNA degradation in eukaryotes. The major 3' to 5' and 5' to 3' mRNA decay pathways are described with emphasis on the mechanisms of their activation by the deprotection of RNA ends. More recently discovered 3'-end modifications such as uridylation, and their relevance to cytoplasmic mRNA decay in various model organisms, are also discussed. Finally, we provide up-to-date findings concerning various pathways of non-coding RNA decay in the cytoplasm.
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Affiliation(s)
- Anna Łabno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland.
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31
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Schrock MS, Karras JR, Guggenbiller MJ, Druck T, Batar B, Huebner K. Fhit and Wwox loss-associated genome instability: A genome caretaker one-two punch. Adv Biol Regul 2016; 63:167-176. [PMID: 27773744 DOI: 10.1016/j.jbior.2016.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 09/21/2016] [Accepted: 09/25/2016] [Indexed: 11/28/2022]
Abstract
Expression of Fhit and Wwox protein is frequently lost or reduced in many human cancers. In this report, we provide data that further characterizes the molecular consequences of Fhit loss in the initiation of DNA double-strand breaks (DSBs), and of Wwox loss in altered repair of DSBs. We show that loss of Fhit initiates mild genome instability in early passage mouse kidney cells, confirming that DNA damage associated with Fhit-deficiency is not limited to cancer cells. We also demonstrate that the cause of Fhit-deficient DSBs: thymidine deficiency-induced replication stress, can be resolved with thymidine supplementation in early passage mouse kidney cells before extensive genome instability occurs. As for consequences of Wwox loss in cancer, we show in a small panel of breast cancer cells and mouse embryonic fibroblasts that Wwox expression predicts response to radiation and mitomycin C, all agents that cause DSBs. In addition, loss of Wwox significantly reduced progression free survival in a cohort of ovarian cancer patients treated with platin-based chemotherapies. Finally, stratification of a cohort of squamous lung cancers by Fhit expression reveals that Wwox expression is significantly reduced in the low Fhit-expressing group, suggesting that loss of Fhit is quickly succeeded by loss of Wwox. We propose that Fhit and Wwox loss work synergistically in cancer progression and that DNA damage caused by Fhit could be targeted early in cancer initiation for prevention, while DNA damage caused by Wwox loss could be targeted later in cancer progression, particularly in cancers that develop resistance to genotoxic therapies.
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Affiliation(s)
- Morgan S Schrock
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jenna R Karras
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Matthew J Guggenbiller
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Teresa Druck
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Bahadir Batar
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Kay Huebner
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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Grudzien-Nogalska E, Kiledjian M. New insights into decapping enzymes and selective mRNA decay. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27425147 DOI: 10.1002/wrna.1379] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/04/2023]
Abstract
Removal of the 5' end cap is a critical determinant controlling mRNA stability and efficient gene expression. Removal of the cap is exquisitely controlled by multiple direct and indirect regulators that influence association with the cap and the catalytic step. A subset of these factors directly stimulate activity of the decapping enzyme, while others influence remodeling of factors bound to mRNA and indirectly stimulate decapping. Furthermore, the components of the general decapping machinery can also be recruited by mRNA-specific regulatory proteins to activate decapping. The Nudix hydrolase, Dcp2, identified as a first decapping enzyme, cleaves capped mRNA and initiates 5'-3' degradation. Extensive studies on Dcp2 led to broad understanding of its activity and the regulation of transcript specific decapping and decay. Interestingly, seven additional Nudix proteins possess intrinsic decapping activity in vitro and at least two, Nudt16 and Nudt3, are decapping enzymes that regulate mRNA stability in cells. Furthermore, a new class of decapping proteins within the DXO family preferentially function on incompletely capped mRNAs. Importantly, it is now evident that each of the characterized decapping enzymes predominantly modulates only a subset of mRNAs, suggesting the existence of multiple decapping enzymes functioning in distinct cellular pathways. WIREs RNA 2017, 8:e1379. doi: 10.1002/wrna.1379 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ewa Grudzien-Nogalska
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
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Ziemniak M, Mugridge JS, Kowalska J, Rhoads RE, Gross JD, Jemielity J. Two-headed tetraphosphate cap analogs are inhibitors of the Dcp1/2 RNA decapping complex. RNA (NEW YORK, N.Y.) 2016; 22:518-29. [PMID: 26826132 PMCID: PMC4793208 DOI: 10.1261/rna.055152.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/10/2015] [Indexed: 05/08/2023]
Abstract
Dcp1/2 is the major eukaryotic RNA decapping complex, comprised of the enzyme Dcp2 and activator Dcp1, which removes the 5' m(7)G cap from mRNA, committing the transcript to degradation. Dcp1/2 activity is crucial for RNA quality control and turnover, and deregulation of these processes may lead to disease development. The molecular details of Dcp1/2 catalysis remain elusive, in part because both cap substrate (m(7)GpppN) and m(7)GDP product are bound by Dcp1/2 with weak (mM) affinity. In order to find inhibitors to use in elucidating the catalytic mechanism of Dcp2, we screened a small library of synthetic m(7)G nucleotides (cap analogs) bearing modifications in the oligophosphate chain. One of the most potent cap analogs, m(7)GpSpppSm(7)G, inhibited Dcp1/2 20 times more efficiently than m(7)GpppN or m(7)GDP. NMR experiments revealed that the compound interacts with specific surfaces of both regulatory and catalytic domains of Dcp2 with submillimolar affinities. Kinetics analysis revealed that m(7)GpSpppSm(7)G is a mixed inhibitor that competes for the Dcp2 active site with micromolar affinity. m(7)GpSpppSm(7)G-capped RNA undergoes rapid decapping, suggesting that the compound may act as a tightly bound cap mimic. Our identification of the first small molecule inhibitor of Dcp2 should be instrumental in future studies aimed at understanding the structural basis of RNA decapping and may provide insight toward the development of novel therapeutically relevant decapping inhibitors.
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Affiliation(s)
- Marcin Ziemniak
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Jeffrey S Mugridge
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089 Warsaw, Poland
| | - Robert E Rhoads
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana 71130-3932, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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Cytoplasmic mRNA turnover and ageing. Mech Ageing Dev 2015; 152:32-42. [PMID: 26432921 PMCID: PMC4710634 DOI: 10.1016/j.mad.2015.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/17/2015] [Accepted: 09/27/2015] [Indexed: 12/12/2022]
Abstract
We address the cytoplasmic mRNA decay processes that determine the mRNAs half-life. We briefly describe the major, evolutionary conserved, ageing pathways and mechanisms. We summarize critical findings that link mRNA turnover and ageing modulators.
Messenger RNA (mRNA) turnover that determines the lifetime of cytoplasmic mRNAs is a means to control gene expression under both normal and stress conditions, whereas its impact on ageing and age-related disorders has just become evident. Gene expression control is achieved at the level of the mRNA clearance as well as mRNA stability and accessibility to other molecules. All these processes are regulated by cis-acting motifs and trans-acting factors that determine the rates of translation and degradation of transcripts. Specific messenger RNA granules that harbor the mRNA decay machinery or various factors, involved in translational repression and transient storage of mRNAs, are also part of the mRNA fate regulation. Their assembly and function can be modulated to promote stress resistance to adverse conditions and over time affect the ageing process and the lifespan of the organism. Here, we provide insights into the complex relationships of ageing modulators and mRNA turnover mechanisms.
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Neu A, Neu U, Fuchs AL, Schlager B, Sprangers R. An excess of catalytically required motions inhibits the scavenger decapping enzyme. Nat Chem Biol 2015; 11:697-704. [PMID: 26258763 PMCID: PMC4544744 DOI: 10.1038/nchembio.1866] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/01/2015] [Indexed: 12/28/2022]
Abstract
The scavenger decapping enzyme hydrolyses the protecting 5′ cap structure from short mRNAs that result from exosomal degradation. Based on static crystal structures and NMR data it is apparent that the dimeric enzyme has to undergo large structural changes to bind substrate in a catalytically competent conformation. Here, we study the yeast enzyme and show that the associated opening-closing motions can be orders of magnitude faster than the catalytic turnover rate. This excess of motion is induced by binding of a second ligand to the enzyme, which occurs under high substrate concentrations. We designed a mutant that disrupts the allosteric pathway that links the second binding event to the dynamics and show that this mutant enzyme is hyperactive. Our data reveals a unique mechanism of substrate inhibition, where motions that are required for catalytic activity also inhibit efficient turnover, when they are present in excess.
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Affiliation(s)
- Ancilla Neu
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ursula Neu
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Anna-Lisa Fuchs
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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Zhou M, Bail S, Plasterer HL, Rusche J, Kiledjian M. DcpS is a transcript-specific modulator of RNA in mammalian cells. RNA (NEW YORK, N.Y.) 2015; 21:1306-1312. [PMID: 26001796 PMCID: PMC4478349 DOI: 10.1261/rna.051573.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/09/2015] [Indexed: 06/04/2023]
Abstract
The scavenger decapping enzyme DcpS is a multifunctional protein initially identified by its property to hydrolyze the resulting cap structure following 3' end mRNA decay. In Saccharomyces cerevisiae, the DcpS homolog Dcs1 is an obligate cofactor for the 5'-3' exoribonuclease Xrn1 while the Caenorhabditis elegans homolog Dcs-1, facilitates Xrn1 mediated microRNA turnover. In both cases, this function is independent of the decapping activity. Whether DcpS and its decapping activity can affect mRNA steady state or stability in mammalian cells remains unknown. We sought to determine DcpS target genes in mammalian cells using a cell-permeable DcpS inhibitor compound, RG3039 initially developed for therapeutic treatment of spinal muscular atrophy. Global mRNA levels were examined following DcpS decapping inhibition with RG3039. The steady-state levels of 222 RNAs were altered upon RG3039 treatment. Of a subset selected for validation, two transcripts that appear to be long noncoding RNAs HS370762 and BC011766, were dependent on DcpS and its scavenger decapping catalytic activity and referred to as DcpS-responsive noncoding transcripts (DRNT) 1 and 2, respectively. Interestingly, only the increase in DRNT1 transcript was accompanied with an increase of its RNA stability and this increase was dependent on both DcpS and Xrn1. Importantly, unlike in yeast where the DcpS homolog is an obligate cofactor for Xrn1, stability of additional Xrn1 dependent RNAs were not altered by a reduction in DcpS levels. Collectively, our data demonstrate that DcpS in conjunction with Xrn1 has the potential to regulate RNA stability in a transcript-selective manner in mammalian cells.
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Affiliation(s)
- Mi Zhou
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sophie Bail
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA
| | | | - James Rusche
- Repligen Corporation, Waltham, Massachusetts 02453, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey 08854, USA
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Wojdyła-Mamoń AM, Guranowski A. Adenylylsulfate-ammonia adenylyltransferase activity is another inherent property of Fhit proteins. Biosci Rep 2015; 35:e00235. [PMID: 26181368 PMCID: PMC4613722 DOI: 10.1042/bsr20150135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 06/02/2015] [Accepted: 06/04/2015] [Indexed: 01/01/2023] Open
Abstract
Fhits (fragile histidine triad proteins) occur in eukaryotes but their function is largely unknown, although human Fhit is believed to act as a tumour suppressor. Fhits also exhibit dinucleoside triphosphatase, adenylylsulfatase and nucleoside phosphoramidase activities that in each case yield nucleoside 5'-monophosphate as a product. Due to the dinucleoside triphosphatase activity, Fhits may also be involved in mRNA decapping. In the present study, we demonstrate Fhit-catalysed ammonolysis of adenosine 5'-phosphosulfate, which results in the formation of adenosine 5'-phosphoramidate. This reaction has previously been associated with adenylylsulfate-ammonia adenylyltransferase (EC 2.7.7.51). Our finding shows that the capacity to catalyse ammonolysis is another inherent property of Fhits. Basic kinetic parameters and substrate specificity of this reaction catalysed by human Fhit are presented.
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Affiliation(s)
- Anna M Wojdyła-Mamoń
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, 60-632 Poznań, Poland
| | - Andrzej Guranowski
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, 60-632 Poznań, Poland
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Ng CKL, Shboul M, Taverniti V, Bonnard C, Lee H, Eskin A, Nelson SF, Al-Raqad M, Altawalbeh S, Séraphin B, Reversade B. Loss of the scavenger mRNA decapping enzyme DCPS causes syndromic intellectual disability with neuromuscular defects. Hum Mol Genet 2015; 24:3163-71. [PMID: 25712129 PMCID: PMC4424953 DOI: 10.1093/hmg/ddv067] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/16/2015] [Indexed: 12/23/2022] Open
Abstract
mRNA decay is an essential and active process that allows cells to continuously adapt gene expression to internal and environmental cues. There are two mRNA degradation pathways: 3′ to 5′ and 5′ to 3′. The DCPS protein is the scavenger mRNA decapping enzyme which functions in the last step of the 3′ end mRNA decay pathway. We have identified a DCPS pathogenic mutation in a large family with three affected individuals presenting with a novel recessive syndrome consisting of craniofacial anomalies, intellectual disability and neuromuscular defects. Using patient's primary cells, we show that this homozygous splice mutation results in a DCPS loss-of-function allele. Diagnostic biochemical analyses using various m7G cap derivatives as substrates reveal no DCPS enzymatic activity in patient's cells. Our results implicate DCPS and more generally RNA catabolism, as a critical cellular process for neurological development, normal cognition and organismal homeostasis in humans.
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Affiliation(s)
- Calista K L Ng
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Mohammad Shboul
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Valerio Taverniti
- IGBMC, CNRS UMR 1704/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Carine Bonnard
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Singapore 138648, Singapore
| | - Hane Lee
- Department of Pathology and Laboratory Medicine
| | - Ascia Eskin
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Mohammed Al-Raqad
- Queen Rania Paediatric Hospital, King Hussein Medical Centre, Royal Medical Services, Amman, Jordan
| | - Samah Altawalbeh
- Queen Rania Paediatric Hospital, King Hussein Medical Centre, Royal Medical Services, Amman, Jordan
| | - Bertrand Séraphin
- IGBMC, CNRS UMR 1704/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Bruno Reversade
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Singapore 138648, Singapore Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
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