1
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Yang JL, Sun X, Shi JX, Cui QX, Cao XY, Wang KT, An MX, Wu SJ, Yang YL, Sun HZ, Zhao WD. Calmodulin Triggers Activity-Dependent rRNA Biogenesis via Interaction with DDX21. J Neurosci 2024; 44:e1841232024. [PMID: 39060175 PMCID: PMC11358605 DOI: 10.1523/jneurosci.1841-23.2024] [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: 09/26/2023] [Revised: 07/11/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Protein synthesis in response to neuronal activity, known as activity-dependent translation, is critical for synaptic plasticity and memory formation. However, the signaling cascades that couple neuronal activity to the translational events remain elusive. In this study, we identified the role of calmodulin (CaM), a conserved Ca2+-binding protein, in ribosomal RNA (rRNA) biogenesis in neurons. We found the CaM-regulated rRNA synthesis is Ca2+-dependent and necessary for nascent protein synthesis and axon growth in hippocampal neurons. Mechanistically, CaM interacts with nucleolar DEAD (Asp-Glu-Ala-Asp) box RNA helicase (DDX21) in a Ca2+-dependent manner to regulate nascent rRNA transcription within nucleoli. We further found CaM alters the conformation of DDX21 to liberate the DDX21-sequestered RPA194, the catalytic subunit of RNA polymerase I, to facilitate transcription of ribosomal DNA. Using high-throughput screening, we identified the small molecules batefenterol and indacaterol that attenuate the CaM-DDX21 interaction and suppress nascent rRNA synthesis and axon growth in hippocampal neurons. These results unveiled the previously unrecognized role of CaM as a messenger to link the activity-induced Ca2+ influx to the nucleolar events essential for protein synthesis. We thus identified the ability of CaM to transmit information to the nucleoli of neurons in response to stimulation.
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Affiliation(s)
- Jia-Lin Yang
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Xue Sun
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Jun-Xiu Shi
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Qing-Xu Cui
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Xin-Yu Cao
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Kai-Tuo Wang
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Ming-Xin An
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
| | - Si-Jin Wu
- Academy of Pharmacy, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Yong-Liang Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Hong-Zan Sun
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Wei-Dong Zhao
- Department of Developmental Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China
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2
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Wang S, Yang R, Song M, Li J, Zhou Y, Dai C, Song T. Current understanding of the role of DDX21 in orchestrating gene expression in health and diseases. Life Sci 2024; 349:122716. [PMID: 38762067 DOI: 10.1016/j.lfs.2024.122716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/30/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
RNA helicases are involved in almost all biological events, and the DDXs family is one of the largest subfamilies of RNA helicases. Recently, studies have reported that RNA helicase DDX21 is involved in several biological events, specifically in orchestrating gene expression. Hence, in this review, we provide a comprehensive overview of the function of DDX21 in health and diseases. In the genome, DDX21 contributes to genome stability by promoting DNA damage repair and resolving R-loops. It also facilitates transcriptional regulation by directly binding to promoter regions, interacting with transcription factors, and enhancing transcription through non-coding RNA. Moreover, DDX21 is involved in various RNA metabolism such as RNA processing, translation, and decay. Interestingly, the activity and function of DDX21 are regulated by post-translational modifications, which affect the localization and degradation of DDX21. Except for its role of RNA helicase, DDX21 also acts as a non-enzymatic function in unwinding RNA, regulating transcriptional modifications and promoting transcription. Next, we discuss the potential application of DDX21 as a clinical predictor for diseases, which may facilitate providing novel pharmacological targets for molecular therapy.
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Affiliation(s)
- Shaoshuai Wang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqi Yang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengzhen Song
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia Li
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; City of Hope Medical Center, Duarte, CA 91010, USA; Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - Yanrong Zhou
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chen Dai
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan 430030, China.
| | - Tongxing Song
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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3
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Jiang Y, Sun S, Liu X, Su K, Zhang C, Zhang P, Zhao Z, Su Y, Wang C, Du X. U3 snoRNA inter-regulates with DDX21 in the perichromosomal region to control mitosis. Cell Death Dis 2024; 15:342. [PMID: 38760378 PMCID: PMC11101645 DOI: 10.1038/s41419-024-06725-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
U3 snoRNA is essential for ribosome biogenesis during interphase. Upon mitotic onset, the nucleolus disassembles and U3 snoRNA relocates to the perichromosomal region (PR) to be considered as a chromosome passenger. Whether U3 controls mitosis remains unknown. Here, we demonstrate that U3 snoRNA is required for mitotic progression. We identified DDX21 as the predominant U3-binding protein during mitosis and confirmed that U3 snoRNA colocalizes with DDX21 in the PR. DDX21 knockdown induces mitotic catastrophe and similar mitotic defects caused by U3 snoRNA depletion. Interestingly, the uniform PR distribution of U3 snoRNA and DDX21 is interdependent. DDX21 functions in mitosis depending on its PR localization. Mechanistically, U3 snoRNA regulates DDX21 PR localization through maintaining its mobility. Moreover, Cy5-U3 snoRNA downsizes the fibrous condensates of His-DDX21 at proper molecular ratios in vitro. This work highlights the importance of the equilibrium between U3 snoRNA and DDX21 in PR formation and reveals the potential relationship between the PR assembly and mitotic regulation.
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Affiliation(s)
- Yang Jiang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Shiqi Sun
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Xiaofeng Liu
- Hepatopancreatobiliary Surgery Department I, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Cancer Hospital & Institute, Peking University, Beijing, 100142, China
| | - Kunqi Su
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Chunfeng Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Peipei Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Zhuochen Zhao
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Ya Su
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Chang Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China
| | - Xiaojuan Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing, 100083, China.
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4
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Kanwal N, Krogh N, Memet I, Lemus-Diaz N, Thomé C, Welp L, Mizi A, Hackert P, Papantonis A, Urlaub H, Nielsen H, Bohnsack K, Bohnsack M. GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners. Nucleic Acids Res 2024; 52:1953-1974. [PMID: 38113271 PMCID: PMC10939407 DOI: 10.1093/nar/gkad1202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Regulation of RNA helicase activity, often accomplished by protein cofactors, is essential to ensure target specificity within the complex cellular environment. The largest family of RNA helicase cofactors are the G-patch proteins, but the cognate RNA helicases and cellular functions of numerous human G-patch proteins remain elusive. Here, we discover that GPATCH4 is a stimulatory cofactor of DHX15 that interacts with the DEAH box helicase in the nucleolus via residues in its G-patch domain. We reveal that GPATCH4 associates with pre-ribosomal particles, and crosslinks to the transcribed ribosomal DNA locus and precursor ribosomal RNAs as well as binding to small nucleolar- and small Cajal body-associated RNAs that guide rRNA and snRNA modifications. Loss of GPATCH4 impairs 2'-O-methylation at various rRNA and snRNA sites leading to decreased protein synthesis and cell growth. We demonstrate that the regulation of 2'-O-methylation by GPATCH4 is both dependent on, and independent of, its interaction with DHX15. Intriguingly, the ATPase activity of DHX15 is necessary for efficient methylation of DHX15-dependent sites, suggesting a function of DHX15 in regulating snoRNA-guided 2'-O-methylation of rRNA that requires activation by GPATCH4. Overall, our findings extend knowledge on RNA helicase regulation by G-patch proteins and also provide important new insights into the mechanisms regulating installation of rRNA and snRNA modifications, which are essential for ribosome function and pre-mRNA splicing.
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Affiliation(s)
- Nidhi Kanwal
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark
| | - Indira Memet
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Nicolas Lemus-Diaz
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Chairini C Thomé
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Luisa M Welp
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany
- Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Am Fassberg 11, 37077 Göttingen, Germany
- Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 35075 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells’ (MBExC), University of Göttingen, Göttingen
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
- Cluster of Excellence ‘Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells’ (MBExC), University of Göttingen, Göttingen
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
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5
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Eliseeva IA, Buyan AI, Smolin EA, Kaliadzenka KS, Popov S, Kulakovskiy IV, Lyabin DN. Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation. Int J Mol Sci 2024; 25:1736. [PMID: 38339016 PMCID: PMC10855678 DOI: 10.3390/ijms25031736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Y-box-binding proteins (YB proteins) are multifunctional DNA- and RNA-binding proteins that play an important role in the regulation of gene expression. The high homology of their cold shock domains and the similarity between their long, unstructured C-terminal domains suggest that Y-box-binding proteins may have similar functions in a cell. Here, we consider the functional interchangeability of the somatic YB proteins YB-1 and YB-3. RNA-seq and Ribo-seq are used to track changes in the mRNA abundance or mRNA translation in HEK293T cells solely expressing YB-1, YB-3, or neither of them. We show that YB proteins have a dual effect on translation. Although the expression of YB proteins stimulates global translation, YB-1 and YB-3 inhibit the translation of their direct CLIP-identified mRNA targets. The impact of YB-1 and YB-3 on the translation of their mRNA targets is similar, which suggests that they can substitute each other in inhibiting the translation of their mRNA targets in HEK293T cells.
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Affiliation(s)
- Irina A. Eliseeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; (I.A.E.); (A.I.B.); (E.A.S.); (K.S.K.); (I.V.K.)
| | - Andrey I. Buyan
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; (I.A.E.); (A.I.B.); (E.A.S.); (K.S.K.); (I.V.K.)
| | - Egor A. Smolin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; (I.A.E.); (A.I.B.); (E.A.S.); (K.S.K.); (I.V.K.)
| | - Karina S. Kaliadzenka
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; (I.A.E.); (A.I.B.); (E.A.S.); (K.S.K.); (I.V.K.)
| | - Sergey Popov
- Endocrinology Research Center, Moscow 117036, Russia;
| | - Ivan V. Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; (I.A.E.); (A.I.B.); (E.A.S.); (K.S.K.); (I.V.K.)
| | - Dmitry N. Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia; (I.A.E.); (A.I.B.); (E.A.S.); (K.S.K.); (I.V.K.)
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6
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Aryan F, Detrés D, Luo CC, Kim SX, Shah AN, Bartusel M, Flynn RA, Calo E. Nucleolus activity-dependent recruitment and biomolecular condensation by pH sensing. Mol Cell 2023; 83:4413-4423.e10. [PMID: 37979585 PMCID: PMC10803072 DOI: 10.1016/j.molcel.2023.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/20/2023] [Accepted: 10/23/2023] [Indexed: 11/20/2023]
Abstract
DEAD-box ATPases are major regulators of biomolecular condensates and orchestrate diverse biochemical processes that are critical for the functioning of cells. How DEAD-box proteins are selectively recruited to their respective biomolecular condensates is unknown. We explored this in the context of the nucleolus and DEAD-box protein DDX21. We find that the pH of the nucleolus is intricately linked to the transcriptional activity of the organelle and facilitates the recruitment and condensation of DDX21. We identify an evolutionarily conserved feature of the C terminus of DDX21 responsible for nucleolar localization. This domain is essential for zebrafish development, and its intrinsically disordered and isoelectric properties are necessary and sufficient for the ability of DDX21 to respond to changes in pH and form condensates. Molecularly, the enzymatic activities of poly(ADP-ribose) polymerases contribute to maintaining the nucleolar pH and, consequently, DDX21 recruitment and nucleolar partitioning. These observations reveal an activity-dependent physicochemical mechanism for the selective recruitment of biochemical activities to biomolecular condensates.
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Affiliation(s)
- Fardin Aryan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Diego Detrés
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Claire C Luo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Skylar X Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arish N Shah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michaela Bartusel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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7
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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8
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Lafontaine DLJ. In phase with the nucleolus. Cell Res 2023; 33:579-580. [PMID: 37055593 PMCID: PMC10397221 DOI: 10.1038/s41422-023-00801-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023] Open
Affiliation(s)
- Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université libre de Bruxelles (ULB), Biopark Campus, B-6041, Gosselies, Belgium.
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9
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Schuhmacher JS, Tom Dieck S, Christoforidis S, Landerer C, Davila Gallesio J, Hersemann L, Seifert S, Schäfer R, Giner A, Toth-Petroczy A, Kalaidzidis Y, Bohnsack KE, Bohnsack MT, Schuman EM, Zerial M. The Rab5 effector FERRY links early endosomes with mRNA localization. Mol Cell 2023; 83:1839-1855.e13. [PMID: 37267905 DOI: 10.1016/j.molcel.2023.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/06/2022] [Accepted: 05/08/2023] [Indexed: 06/04/2023]
Abstract
Localized translation is vital to polarized cells and requires precise and robust distribution of different mRNAs and ribosomes across the cell. However, the underlying molecular mechanisms are poorly understood and important players are lacking. Here, we discovered a Rab5 effector, the five-subunit endosomal Rab5 and RNA/ribosome intermediary (FERRY) complex, that recruits mRNAs and ribosomes to early endosomes through direct mRNA-interaction. FERRY displays preferential binding to certain groups of transcripts, including mRNAs encoding mitochondrial proteins. Deletion of FERRY subunits reduces the endosomal localization of transcripts in cells and has a significant impact on mRNA levels. Clinical studies show that genetic disruption of FERRY causes severe brain damage. We found that, in neurons, FERRY co-localizes with mRNA on early endosomes, and mRNA loaded FERRY-positive endosomes are in close proximity of mitochondria. FERRY thus transforms endosomes into mRNA carriers and plays a key role in regulating mRNA distribution and transport.
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Affiliation(s)
- Jan S Schuhmacher
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Susanne Tom Dieck
- Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438 Frankfurt am Main, Germany
| | - Savvas Christoforidis
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece; Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Cedric Landerer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Sarah Seifert
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Ramona Schäfer
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Angelika Giner
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Agnes Toth-Petroczy
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany; Göttingen Centre for Molecular Biosciences, University of Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Max-von-Laue-Str. 4, 60438 Frankfurt am Main, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01307 Dresden, Germany.
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10
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Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
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Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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11
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Liao H, Gaur A, McConie H, Shekar A, Wang K, Chang JT, Breton G, Denicourt C. Human NOP2/NSUN1 regulates ribosome biogenesis through non-catalytic complex formation with box C/D snoRNPs. Nucleic Acids Res 2022; 50:10695-10716. [PMID: 36161484 PMCID: PMC9561284 DOI: 10.1093/nar/gkac817] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
5-Methylcytosine (m5C) is a base modification broadly found on various RNAs in the human transcriptome. In eukaryotes, m5C is catalyzed by enzymes of the NSUN family composed of seven human members (NSUN1-7). NOP2/NSUN1 has been primarily characterized in budding yeast as an essential ribosome biogenesis factor required for the deposition of m5C on the 25S ribosomal RNA (rRNA). Although human NOP2/NSUN1 has been known to be an oncogene overexpressed in several types of cancer, its functions and substrates remain poorly characterized. Here, we used a miCLIP-seq approach to identify human NOP2/NSUN1 RNA substrates. Our analysis revealed that NOP2/NSUN1 catalyzes the deposition of m5C at position 4447 on the 28S rRNA. We also find that NOP2/NSUN1 binds to the 5′ETS region of the pre-rRNA transcript and regulates pre-rRNA processing through non-catalytic complex formation with box C/D snoRNAs. We provide evidence that NOP2/NSUN1 facilitates the recruitment of U3 and U8 snoRNAs to pre-90S ribosomal particles and their stable assembly into snoRNP complexes. Remarkably, expression of both WT and catalytically inactive NOP2/NSUN1 in knockdown background rescues the rRNA processing defects and the stable assembly of box C/D snoRNP complexes, suggesting that NOP2/NSUN1-mediated deposition of m5C on rRNA is not required for ribosome synthesis.
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Affiliation(s)
- Han Liao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Anushri Gaur
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Hunter McConie
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Amirtha Shekar
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Karen Wang
- Wiess College, Rice University, Houston, TX 77251, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ghislain Breton
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Catherine Denicourt
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA
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12
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Moraleva AA, Deryabin AS, Rubtsov YP, Rubtsova MP, Dontsova OA. Eukaryotic Ribosome Biogenesis: The 60S Subunit. Acta Naturae 2022; 14:39-49. [PMID: 35925480 PMCID: PMC9307984 DOI: 10.32607/actanaturae.11541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
Ribosome biogenesis is consecutive coordinated maturation of ribosomal precursors in the nucleolus, nucleoplasm, and cytoplasm. The formation of mature ribosomal subunits involves hundreds of ribosomal biogenesis factors that ensure ribosomal RNA processing, tertiary structure, and interaction with ribosomal proteins. Although the main features and stages of ribosome biogenesis are conservative among different groups of eukaryotes, this process in human cells has become more complicated due to the larger size of the ribosomes and pre-ribosomes and intricate regulatory pathways affecting their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. A previous part of this review summarized recent data on the processing of the primary rRNA transcript and compared the maturation of the small 40S subunit in yeast and human cells. This part of the review focuses on the biogenesis of the large 60S subunit of eukaryotic ribosomes.
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Affiliation(s)
- A. A. Moraleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - Yu. P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. P. Rubtsova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
| | - O. A. Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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13
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Rao S, Mahmoudi T. DEAD-ly Affairs: The Roles of DEAD-Box Proteins on HIV-1 Viral RNA Metabolism. Front Cell Dev Biol 2022; 10:917599. [PMID: 35769258 PMCID: PMC9234453 DOI: 10.3389/fcell.2022.917599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
In order to ensure viral gene expression, Human Immunodeficiency virus type-1 (HIV-1) recruits numerous host proteins that promote optimal RNA metabolism of the HIV-1 viral RNAs (vRNAs), such as the proteins of the DEAD-box family. The DEAD-box family of RNA helicases regulates multiple steps of RNA metabolism and processing, including transcription, splicing, nucleocytoplasmic export, trafficking, translation and turnover, mediated by their ATP-dependent RNA unwinding ability. In this review, we provide an overview of the functions and role of all DEAD-box family protein members thus far described to influence various aspects of HIV-1 vRNA metabolism. We describe the molecular mechanisms by which HIV-1 hijacks these host proteins to promote its gene expression and we discuss the implications of these interactions during viral infection, their possible roles in the maintenance of viral latency and in inducing cell death. We also speculate on the emerging potential of pharmacological inhibitors of DEAD-box proteins as novel therapeutics to control the HIV-1 pandemic.
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Affiliation(s)
- Shringar Rao
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Centre, Rotterdam, Netherlands
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14
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Pinard M, Cloutier P, Poitras C, Gauthier MS, Coulombe B. Unphosphorylated Form of the PAQosome Core Subunit RPAP3 Binds Ribosomal Preassembly Complexes to Modulate Ribosome Biogenesis. J Proteome Res 2022; 21:1073-1082. [PMID: 35129352 DOI: 10.1021/acs.jproteome.1c00938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The PAQosome (particle for arrangement of quaternary structure) is a 12-subunit HSP90 co-chaperone involved in the biogenesis of several human protein complexes. Two mechanisms of client selection have previously been identified, namely, the selective recruitment of specific adaptors and the differential use of homologous core subunits. Here, we describe a third client selection mechanism by showing that RPAP3, one of the core PAQosome subunits, is phosphorylated at several Ser residues in HEK293 cells. Affinity purification coupled with mass spectrometry (AP-MS) using the expression of tagged RPAP3 with single phospho-null mutations at Ser116, Ser119, or Ser121 reveals binding of the unphosphorylated form to several proteins involved in ribosome biogenesis. In vitro phosphorylation assays indicate that the kinase CK2 phosphorylates these RPAP3 residues. This finding is supported by data showing that pharmacological inhibition of CK2 enhances the binding of RPAP3 to ribosome preassembly factors in AP-MS experiments. Moreover, the silencing of PAQosome subunits interferes with ribosomal assembly factors' interactome. Altogether, these results indicate that RPAP3 phosphate group addition/removal at specific residues modulates binding to subunits of preribosomal complexes and allows speculating that PAQosome posttranslational modification is a mechanism of client selection.
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Affiliation(s)
- Maxime Pinard
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Philippe Cloutier
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Christian Poitras
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Marie-Soleil Gauthier
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, Québec H2W 1R7, Canada.,Département de Biochimie et Médecine Moléculaire, Faculté de Médecine, Université de Montréal, 2900 Boulevard Édouart-Montpetit, Montréal,QuébecH3T 1J4, Canada
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15
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Kleiber N, Lemus-Diaz N, Stiller C, Heinrichs M, Mai MMQ, Hackert P, Richter-Dennerlein R, Höbartner C, Bohnsack KE, Bohnsack MT. The RNA methyltransferase METTL8 installs m 3C 32 in mitochondrial tRNAs Thr/Ser(UCN) to optimise tRNA structure and mitochondrial translation. Nat Commun 2022; 13:209. [PMID: 35017528 PMCID: PMC8752778 DOI: 10.1038/s41467-021-27905-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 12/30/2022] Open
Abstract
Modified nucleotides in tRNAs are important determinants of folding, structure and function. Here we identify METTL8 as a mitochondrial matrix protein and active RNA methyltransferase responsible for installing m3C32 in the human mitochondrial (mt-)tRNAThr and mt-tRNASer(UCN). METTL8 crosslinks to the anticodon stem loop (ASL) of many mt-tRNAs in cells, raising the question of how methylation target specificity is achieved. Dissection of mt-tRNA recognition elements revealed U34G35 and t6A37/(ms2)i6A37, present concomitantly only in the ASLs of the two substrate mt-tRNAs, as key determinants for METTL8-mediated methylation of C32. Several lines of evidence demonstrate the influence of U34, G35, and the m3C32 and t6A37/(ms2)i6A37 modifications in mt-tRNAThr/Ser(UCN) on the structure of these mt-tRNAs. Although mt-tRNAThr/Ser(UCN) lacking METTL8-mediated m3C32 are efficiently aminoacylated and associate with mitochondrial ribosomes, mitochondrial translation is mildly impaired by lack of METTL8. Together these results define the cellular targets of METTL8 and shed new light on the role of m3C32 within mt-tRNAs.
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MESH Headings
- Anticodon/chemistry
- Anticodon/metabolism
- Base Pairing
- Cytosine/metabolism
- Gene Expression Regulation
- HEK293 Cells
- Humans
- Methylation
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mitochondria/genetics
- Mitochondria/metabolism
- Nucleic Acid Conformation
- Protein Binding
- Protein Biosynthesis
- RNA, Mitochondrial/chemistry
- RNA, Mitochondrial/genetics
- RNA, Mitochondrial/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- RNA, Transfer, Thr/chemistry
- RNA, Transfer, Thr/genetics
- RNA, Transfer, Thr/metabolism
- Signal Transduction
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Affiliation(s)
- Nicole Kleiber
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nicolas Lemus-Diaz
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Carina Stiller
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Marleen Heinrichs
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Mandy Mong-Quyen Mai
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Ricarda Richter-Dennerlein
- Department of Cellular Biochemistry, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, Göttingen, 37077, Germany.
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16
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Aquino GRR, Hackert P, Krogh N, Pan KT, Jaafar M, Henras AK, Nielsen H, Urlaub H, Bohnsack KE, Bohnsack MT. The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly. Nat Commun 2021; 12:6152. [PMID: 34686661 PMCID: PMC8536713 DOI: 10.1038/s41467-021-26208-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Early pre-60S ribosomal particles are poorly characterized, highly dynamic complexes that undergo extensive rRNA folding and compaction concomitant with assembly of ribosomal proteins and exchange of assembly factors. Pre-60S particles contain numerous RNA helicases, which are likely regulators of accurate and efficient formation of appropriate rRNA structures. Here we reveal binding of the RNA helicase Dbp7 to domain V/VI of early pre-60S particles in yeast and show that in the absence of this protein, dissociation of the Npa1 scaffolding complex, release of the snR190 folding chaperone, recruitment of the A3 cluster factors and binding of the ribosomal protein uL3 are impaired. uL3 is critical for formation of the peptidyltransferase center (PTC) and is responsible for stabilizing interactions between the 5′ and 3′ ends of the 25S, an essential pre-requisite for subsequent pre-60S maturation events. Highlighting the importance of pre-ribosome remodeling by Dbp7, our data suggest that in the absence of Dbp7 or its catalytic activity, early pre-ribosomal particles are targeted for degradation. Early steps of large 60S ribosomal subunit biogenesis are not well understood. Here, the authors combine biochemical experiments with protein-RNA crosslinking and mass spectrometry to show that the RNA helicase Dbp7 is key player during early 60S ribosomal assembly. Dbp7 regulates a series of events driving compaction of domain V/VI in early pre60S ribosomal particles.
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Affiliation(s)
- Gerald Ryan R Aquino
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N, Copenhagen, Denmark
| | - Kuan-Ting Pan
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, 37077, Göttingen, Germany.,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590, Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60596, Frankfurt am Main, Germany
| | - Mariam Jaafar
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N, Copenhagen, Denmark.,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, 37077, Göttingen, Germany.,Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany. .,Göttingen Centre for Molecular Biosciences, Georg-August-University, Justus-von-Liebig Weg 11, 37077, Göttingen, Germany.
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17
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Caterino M, Paeschke K. Action and function of helicases on RNA G-quadruplexes. Methods 2021; 204:110-125. [PMID: 34509630 PMCID: PMC9236196 DOI: 10.1016/j.ymeth.2021.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/02/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022] Open
Abstract
Methodological progresses and piling evidence prove the rG4 biology in vivo. rG4s step in virtually every aspect of RNA biology. Helicases unwinding of rG4s is a fine regulatory layer to the downstream processes and general cell homeostasis. The current knowledge is however limited to a few cell lines. The regulation of helicases themselves is delineating as a important question. Non-helicase rG4-processing proteins likely play a role.
The nucleic acid structure called G-quadruplex (G4) is currently discussed to function in nucleic acid-based mechanisms that influence several cellular processes. They can modulate the cellular machinery either positively or negatively, both at the DNA and RNA level. The majority of what we know about G4 biology comes from DNA G4 (dG4) research. RNA G4s (rG4), on the other hand, are gaining interest as researchers become more aware of their role in several aspects of cellular homeostasis. In either case, the correct regulation of G4 structures within cells is essential and demands specialized proteins able to resolve them. Small changes in the formation and unfolding of G4 structures can have severe consequences for the cells that could even stimulate genome instability, apoptosis or proliferation. Helicases are the most relevant negative G4 regulators, which prevent and unfold G4 formation within cells during different pathways. Yet, and despite their importance only a handful of rG4 unwinding helicases have been identified and characterized thus far. This review addresses the current knowledge on rG4s-processing helicases with a focus on methodological approaches. An example of a non-helicase rG4s-unwinding protein is also briefly described.
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Affiliation(s)
- Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, 53127 Bonn, Germany.
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18
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Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far. Noncoding RNA 2021; 7:ncrna7030042. [PMID: 34287370 PMCID: PMC8293466 DOI: 10.3390/ncrna7030042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/09/2021] [Accepted: 07/11/2021] [Indexed: 12/26/2022] Open
Abstract
Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. The nucleolus is a prime example of how different lncRNA species concomitantly regulate gene expression by facilitating the production and processing of ribosomal (r)RNA for ribosome biogenesis. Here, we summarise the current findings on how RNAPII influences nucleolar structure and function. We describe how RNAPII-dependent lncRNA can both promote nucleolar integrity and inhibit ribosomal (r)RNA synthesis by modulating the availability of rRNA synthesis factors in trans. Surprisingly, some lncRNA transcripts can directly originate from nucleolar loci and function in cis. The nucleolar intergenic spacer (IGS), for example, encodes nucleolar transcripts that counteract spurious rRNA synthesis in unperturbed cells. In response to DNA damage, RNAPII-dependent lncRNA originates directly at broken ribosomal (r)DNA loci and is processed into small ncRNA, possibly to modulate DNA repair. Thus, lncRNA-mediated regulation of nucleolar biology occurs by several modes of action and is more direct than anticipated, pointing to an intimate crosstalk of RNA metabolic events.
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19
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Aquino GRR, Krogh N, Hackert P, Martin R, Gallesio JD, van Nues RW, Schneider C, Watkins NJ, Nielsen H, Bohnsack KE, Bohnsack MT. RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2'-O-methylation. Nucleic Acids Res 2021; 49:4066-4084. [PMID: 33721027 PMCID: PMC8053091 DOI: 10.1093/nar/gkab159] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
RNA helicases play important roles in diverse aspects of RNA metabolism through their functions in remodelling ribonucleoprotein complexes (RNPs), such as pre-ribosomes. Here, we show that the DEAD box helicase Dbp3 is required for efficient processing of the U18 and U24 intron-encoded snoRNAs and 2′-O-methylation of various sites within the 25S ribosomal RNA (rRNA) sequence. Furthermore, numerous box C/D snoRNPs accumulate on pre-ribosomes in the absence of Dbp3. Many snoRNAs guiding Dbp3-dependent rRNA modifications have overlapping pre-rRNA basepairing sites and therefore form mutually exclusive interactions with pre-ribosomes. Analysis of the distribution of these snoRNAs between pre-ribosome-associated and ‘free’ pools demonstrated that many are almost exclusively associated with pre-ribosomal complexes. Our data suggest that retention of such snoRNPs on pre-ribosomes when Dbp3 is lacking may impede rRNA 2′-O-methylation by reducing the recycling efficiency of snoRNPs and by inhibiting snoRNP access to proximal target sites. The observation of substoichiometric rRNA modification at adjacent sites suggests that the snoRNPs guiding such modifications likely interact stochastically rather than hierarchically with their pre-rRNA target sites. Together, our data provide new insights into the dynamics of snoRNPs on pre-ribosomal complexes and the remodelling events occurring during the early stages of ribosome assembly.
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Affiliation(s)
- Gerald Ryan R Aquino
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Roman Martin
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Robert W van Nues
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Claudia Schneider
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicholas J Watkins
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark.,Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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20
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McRae EKS, Dupas SJ, Atefi N, McKenna SA. Monitoring Enzymatic RNA G-Quadruplex Unwinding Activities by Nuclease Sensitivity and Reverse Transcription Stop Assays. Methods Mol Biol 2021; 2209:163-173. [PMID: 33201469 DOI: 10.1007/978-1-0716-0935-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Multiple different methods have been employed to investigate the unwinding of RNA G-quadruplexes by various helicase proteins. Each has their own pitfalls, namely, looking at non-native or chemically modified RNA sequences, biasing the unwinding process with competing trap nucleotides, and a lack of context sequence to the 5' and 3' of the RNA G-quadruplex structure. Herein we present two straightforward methods that allow for quadruplex unwinding to be monitored on native RNA sequences without the use of fluorescent modifications, specialized equipment, or trap nucleotides to be employed.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Steven J Dupas
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Negar Atefi
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada. .,Manitoba Institute for Materials, University of Manitoba, Winnipeg, MB, Canada.
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21
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Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
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22
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RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 2021; 11:biom11010076. [PMID: 33430019 PMCID: PMC7826747 DOI: 10.3390/biom11010076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.
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23
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Kaliatsi EG, Giarimoglou N, Stathopoulos C, Stamatopoulou V. Non-Coding RNA-Driven Regulation of rRNA Biogenesis. Int J Mol Sci 2020; 21:E9738. [PMID: 33419375 PMCID: PMC7766524 DOI: 10.3390/ijms21249738] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/30/2022] Open
Abstract
Ribosomal RNA (rRNA) biogenesis takes place in the nucleolus, the most prominent condensate of the eukaryotic nucleus. The proper assembly and integrity of the nucleolus reflects the accurate synthesis and processing of rRNAs which in turn, as major components of ribosomes, ensure the uninterrupted flow of the genetic information during translation. Therefore, the abundant production of rRNAs in a precisely functional nucleolus is of outmost importance for the cell viability and requires the concerted action of essential enzymes, associated factors and epigenetic marks. The coordination and regulation of such an elaborate process depends on not only protein factors, but also on numerous regulatory non-coding RNAs (ncRNAs). Herein, we focus on RNA-mediated mechanisms that control the synthesis, processing and modification of rRNAs in mammals. We highlight the significance of regulatory ncRNAs in rRNA biogenesis and the maintenance of the nucleolar morphology, as well as their role in human diseases and as novel druggable molecular targets.
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Affiliation(s)
| | | | - Constantinos Stathopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
| | - Vassiliki Stamatopoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece; (E.G.K.); (N.G.)
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24
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Marcaida MJ, Kauzlaric A, Duperrex A, Sülzle J, Moncrieffe MC, Adebajo D, Manley S, Trono D, Dal Peraro M. The Human RNA Helicase DDX21 Presents a Dimerization Interface Necessary for Helicase Activity. iScience 2020; 23:101811. [PMID: 33313488 PMCID: PMC7721647 DOI: 10.1016/j.isci.2020.101811] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Members of the DEAD-box helicase family are involved in all fundamental processes of RNA metabolism, and as such, their malfunction is associated with various diseases. Currently, whether and how oligomerization impacts their biochemical and biological functions is not well understood. In this work, we show that DDX21, a human DEAD-box helicase with RNA G-quadruplex resolving activity, is dimeric and that its oligomerization state influences its helicase activity. Solution small-angle X-ray scattering (SAXS) analysis uncovers a flexible multi-domain protein with a central dimerization domain. While the Arg/Gly rich C termini, rather than dimerization, are key to maintaining high affinity for RNA substrates, in vitro helicase assays indicate that an intact dimer is essential for both DDX21 ATP-dependent double-stranded RNA unwinding and ATP-independent G-quadruplex remodeling activities. Our results suggest that oligomerization plays a key role in regulating RNA DEAD-box helicase activity. The human RNA DEAD-box helicase DDX21 is dimeric DDX21 dimerization is mediated by a hydrophobic central core domain SAXS-based modeling reveals that DDX21 is intrinsically flexible Dimerization and C-terminal domains mediate G-quadruplex and dsRNA unwinding
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Affiliation(s)
- Maria J Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Annamaria Kauzlaric
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Alice Duperrex
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Jenny Sülzle
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Martin C Moncrieffe
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Damilola Adebajo
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Suliana Manley
- Laboratory for Experimental Biophysics, Institute of Physics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Didier Trono
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, 1015 Switzerland
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25
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Wang X, Wu Z, Qin W, Sun T, Lu S, Li Y, Wang Y, Hu X, Xu D, Wu Y, Chen Q, Yao W, Liu M, Wei M, Wu H. Long non-coding RNA ZFAS1 promotes colorectal cancer tumorigenesis and development through DDX21-POLR1B regulatory axis. Aging (Albany NY) 2020; 12:22656-22687. [PMID: 33202381 PMCID: PMC7746388 DOI: 10.18632/aging.103875] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/25/2020] [Indexed: 12/19/2022]
Abstract
Increasing evidence supports long non-coding RNA-ZFAS1 as master protein regulators involved in a variety of human cancers. However, the molecular mechanism is not fully understood in colorectal cancer (CRC) and remains to be elucidated. Here, we uncovered a previously unreported mechanism linking RNA helicase DDX21 regulated by lncRNA ZFAS1 in control of POLR1B expression in CRC initiation and progression. Specifically, ZFAS1 exerted its oncogenic functions and was significantly up-regulated accompanied by elevated DDX21, POLR1B expression in CRC cells and tissues, which further closely associated with poor clinical outcomes. Notably, ZFAS1 knockdown dramatically suppressed CRC cell proliferation, invasion, migration, and increased cell apoptosis, which were contrary to the effect caused by ZFAS1 up-regulation. We further revealed that the inhibitory effect caused by ZFAS1 knockdown could be reversed by DDX21 overexpression in vitro and in vivo. Mechanistically, our research found that ZFAS1 could directly recruit DDX21 protein by harboring the specific motif (AAGA or CAGA). Finally, POLR1B was identified as the downstream target of DDX21 regulated by ZFAS1, which was also up-regulated in CRC cells and tissues and closely related to poor prognosis. The unrecognized ZFAS1/DDX21/POLR1B signaling regulation axis may provide new biomarkers and targets for CRC treatment and prognostic evaluation.
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Affiliation(s)
- Xiufang Wang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Zhikun Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Wenyan Qin
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Tong Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Senxu Lu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Yalun Li
- Department of Anorectal Surgery, First Hospital of China Medical University, Shenyang 110001, P. R. China
| | - Yuanhe Wang
- Department of Medical Oncology, Cancer Hospital of China Medical University, Department of Medical Oncology, Liaoning Cancer Hospital and Institute, Shenyang 110042, P. R. China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Dongping Xu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Yutong Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Qiuchen Chen
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Weifan Yao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Mingyan Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang 110122, P. R. China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang 110122, P. R. China
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26
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Nait Slimane S, Marcel V, Fenouil T, Catez F, Saurin JC, Bouvet P, Diaz JJ, Mertani HC. Ribosome Biogenesis Alterations in Colorectal Cancer. Cells 2020; 9:E2361. [PMID: 33120992 PMCID: PMC7693311 DOI: 10.3390/cells9112361] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/24/2022] Open
Abstract
Many studies have focused on understanding the regulation and functions of aberrant protein synthesis in colorectal cancer (CRC), leaving the ribosome, its main effector, relatively underappreciated in CRC. The production of functional ribosomes is initiated in the nucleolus, requires coordinated ribosomal RNA (rRNA) processing and ribosomal protein (RP) assembly, and is frequently hyperactivated to support the needs in protein synthesis essential to withstand unremitting cancer cell growth. This elevated ribosome production in cancer cells includes a strong alteration of ribosome biogenesis homeostasis that represents one of the hallmarks of cancer cells. None of the ribosome production steps escape this cancer-specific dysregulation. This review summarizes the early and late steps of ribosome biogenesis dysregulations described in CRC cell lines, intestinal organoids, CRC stem cells and mouse models, and their possible clinical implications. We highlight how this cancer-related ribosome biogenesis, both at quantitative and qualitative levels, can lead to the synthesis of ribosomes favoring the translation of mRNAs encoding hyperproliferative and survival factors. We also discuss whether cancer-related ribosome biogenesis is a mere consequence of cancer progression or is a causal factor in CRC, and how altered ribosome biogenesis pathways can represent effective targets to kill CRC cells. The association between exacerbated CRC cell growth and alteration of specific steps of ribosome biogenesis is highlighted as a key driver of tumorigenesis, providing promising perspectives for the implementation of predictive biomarkers and the development of new therapeutic drugs.
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Affiliation(s)
- Sophie Nait Slimane
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Virginie Marcel
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Tanguy Fenouil
- Institute of Pathology EST, Hospices Civils de Lyon, Site-Est Groupement Hospitalier- Est, 69677 Bron, France;
| | - Frédéric Catez
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Christophe Saurin
- Gastroenterology and Genetic Department, Edouard Herriot Hospital, Hospices Civils de Lyon, 69008 Lyon, France;
| | - Philippe Bouvet
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
| | - Hichem C. Mertani
- Cancer Initiation and Tumor Cell Identity, Cancer Research Center of Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Inserm U1052, CNRS UMR5286 Centre Léon Bérard, 69008 Lyon, France; (S.N.S.); (V.M.); (F.C.); (P.B.)
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27
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Choudhury P, Kretschmer J, Hackert P, Bohnsack KE, Bohnsack MT. The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region. RNA Biol 2020; 18:1124-1135. [PMID: 33048000 PMCID: PMC8244758 DOI: 10.1080/15476286.2020.1829366] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
RNA helicases contribute to diverse aspects of RNA metabolism through their functions in re-arranging RNA structures. Identification of the remodelling targets of RNA helicases is a critical step in elucidating their cellular functions. Here, we show that, in contrast to many other ribosome biogenesis factors, the DExD box ATPase DDX55 predominantly localizes to the nucleoplasm and we identify a nuclear localization signal within the C-terminal region of the protein. DDX55 associates with pre-ribosomal subunits in human cells and is required for maturation of large subunit pre-rRNAs. Interestingly, in vitro analyses show that DDX55 selectively associates with double-stranded RNA substrates, which also stimulate its ATPase activity, and our data suggest that the C-terminal region of DDX55 contributes to this substrate specificity. The C-terminal region of DDX55 is also necessary for recruitment of the helicase to pre-ribosomes and, using in vivo crosslinking, we reveal a binding site for DDX55 in helix H62 of the 28S ribosomal RNA. Taken together, these data highlight the importance of the C-terminal region of DDX55 in substrate specificity and recruitment, and identify domain IV as a potential remodelling target of DDX55 during LSU biogenesis.
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Affiliation(s)
- Priyanka Choudhury
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Jens Kretschmer
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
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28
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Chen Z, Li Z, Hu X, Xie F, Kuang S, Zhan B, Gao W, Chen X, Gao S, Li Y, Wang Y, Qian F, Ding C, Gan J, Ji C, Xu X, Zhou Z, Huang J, He HH, Li J. Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000532. [PMID: 32714761 PMCID: PMC7375243 DOI: 10.1002/advs.202000532] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/19/2020] [Indexed: 05/20/2023]
Abstract
RNA helicase DDX21 plays vital roles in ribosomal RNA biogenesis, transcription, and the regulation of host innate immunity during virus infection. How DDX21 recognizes and unwinds RNA and how DDX21 interacts with virus remain poorly understood. Here, crystal structures of human DDX21 determined in three distinct states are reported, including the apo-state, the AMPPNP plus single-stranded RNA (ssRNA) bound pre-hydrolysis state, and the ADP-bound post-hydrolysis state, revealing an open to closed conformational change upon RNA binding and unwinding. The core of the RNA unwinding machinery of DDX21 includes one wedge helix, one sensor motif V and the DEVD box, which links the binding pockets of ATP and ssRNA. The mutant D339H/E340G dramatically increases RNA binding activity. Moreover, Hill coefficient analysis reveals that DDX21 unwinds double-stranded RNA (dsRNA) in a cooperative manner. Besides, the nonstructural (NS1) protein of influenza A inhibits the ATPase and unwinding activity of DDX21 via small RNAs, which cooperatively assemble with DDX21 and NS1. The structures illustrate the dynamic process of ATP hydrolysis and RNA unwinding for RNA helicases, and the RNA modulated interaction between NS1 and DDX21 generates a fresh perspective toward the virus-host interface. It would benefit in developing therapeutics to combat the influenza virus infection.
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Affiliation(s)
- Zijun Chen
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
| | - Zhengyang Li
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
| | - Xiaojian Hu
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
| | - Feiyan Xie
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
| | - Siyun Kuang
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
| | - Bowen Zhan
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
| | - Wenqing Gao
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
| | - Xiangjun Chen
- Department of NeurologyHuashan HospitalFudan UniversityShanghai200040China
| | - Siqi Gao
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Yang Li
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Yongming Wang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Feng Qian
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Chen Ding
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Jianhua Gan
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Chaoneng Ji
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesFudan UniversityShanghai200438China
| | - Xue‐Wei Xu
- Key Laboratory of Marine Ecosystem DynamicsMinistry of Natural Resources & Second Institute of OceanographyMinistry of Natural ResourcesHangzhou310012China
| | - Zheng Zhou
- China Novartis Institutes for Biomedical Research Co. LtdShanghai201203China
| | - Jinqing Huang
- Department of ChemistryThe Hong Kong University of Science and TechnologyHong KongChina
| | - Housheng Hansen He
- Department of Medical BiophysicsUniversity of Toronto, and Princess Margaret Cancer CenterUniversity Health NetworkTorontoM5G 1L7, OntarioCanada
| | - Jixi Li
- State Key Laboratory of Genetic EngineeringDepartment of NeurologySchool of Life Sciences and Huashan HospitalCollaborative Innovation Center of Genetics and DevelopmentEngineering Research Center of Gene Technology of MOEShanghai Engineering Research Center of Industrial MicroorganismsFudan UniversityShanghai200438China
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29
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Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Nat Cell Biol 2020; 22:372-379. [PMID: 32231306 PMCID: PMC7185069 DOI: 10.1038/s41556-020-0493-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 02/24/2020] [Indexed: 12/25/2022]
Abstract
The availability of nucleotides has a direct impact on transcription. The inhibition of dihydroorotate dehydrogenase (DHODH) with leflunomide impacts nucleotide pools by reducing pyrimidine levels. Leflunomide abrogates the effective transcription elongation of genes required for neural crest development and melanoma growth in vivo1. To define the mechanism of action, we undertook an in vivo chemical suppressor screen for restoration of neural crest after leflunomide treatment. Surprisingly, we found that alterations in progesterone and progesterone receptor (Pgr) signalling strongly suppressed leflunomide-mediated neural crest effects in zebrafish. In addition, progesterone bypasses the transcriptional elongation block resulting from Paf complex deficiency, rescuing neural crest defects in ctr9 morphant and paf1(alnz24) mutant embryos. Using proteomics, we found that Pgr binds the RNA helicase protein Ddx21. ddx21-deficient zebrafish show resistance to leflunomide-induced stress. At a molecular level, nucleotide depletion reduced the chromatin occupancy of DDX21 in human A375 melanoma cells. Nucleotide supplementation reversed the gene expression signature and DDX21 occupancy changes prompted by leflunomide. Together, our results show that DDX21 acts as a sensor and mediator of transcription during nucleotide stress.
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Affiliation(s)
- Cristina Santoriello
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Audrey Sporrij
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Song Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bilguujin Dorjsuren
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Eugenia Custo Greig
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Wyatt McCall
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Meredith E Stanhope
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Maurizio Fazio
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Michael Superdock
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Asher Lichtig
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Isaac Adatto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Michael Jurynec
- Department of Orthopedics, University of Utah, Salt Lake City, UT, USA
| | - Yi Zhou
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eliezer Calo
- Department of Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonard I Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA.
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30
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Braun CM, Hackert P, Schmid CE, Bohnsack MT, Bohnsack KE, Perez-Fernandez J. Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit. Nucleic Acids Res 2020; 48:405-420. [PMID: 31745560 PMCID: PMC7145529 DOI: 10.1093/nar/gkz1079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/24/2023] Open
Abstract
More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of research have provided a wealth of insights into the functions of many AFs, others remain poorly characterized. Pol5 was initially classified with B-type DNA polymerases, however, several lines of evidence indicate the involvement of this protein in ribosome assembly. Here, we show that depletion of Pol5 affects the processing of pre-rRNAs destined for the both the large and small subunits. Furthermore, we identify binding sites for Pol5 in the 5' external transcribed spacer and within domain III of the 25S rRNA sequence. Consistent with this, we reveal that Pol5 is required for recruitment of ribosomal proteins that form the polypeptide exit tunnel in the LSU and that depletion of Pol5 impairs the release of 5' ETS fragments from early pre-40S particles. The dual functions of Pol5 in 60S assembly and recycling of pre-40S AFs suggest that this factor could contribute to ensuring the stoichiometric production of ribosomal subunits.
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Affiliation(s)
- Christina M Braun
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Catharina E Schmid
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jorge Perez-Fernandez
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
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31
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Yao RW, Liu CX, Chen LL. Linking RNA Processing and Function. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:67-82. [PMID: 32019863 DOI: 10.1101/sqb.2019.84.039495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA processing is critical for eukaryotic mRNA maturation and function. It appears there is no exception for other types of RNAs. Long noncoding RNAs (lncRNAs) represent a subclass of noncoding RNAs, have sizes of >200 nucleotides (nt), and participate in various aspects of gene regulation. Although many lncRNAs are capped, polyadenylated, and spliced just like mRNAs, others are derived from primary transcripts of RNA polymerase II and stabilized by forming circular structures or by ending with small nucleolar RNA-protein complexes. Here we summarize the recent progress in linking the processing and function of these unconventionally processed lncRNAs; we also discuss how directional RNA movement is achieved using the radial flux movement of nascent precursor ribosomal RNA (pre-rRNA) in the human nucleolus as an example.
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Affiliation(s)
- Run-Wen Yao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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32
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Davila Gallesio J, Hackert P, Bohnsack KE, Bohnsack MT. Sgd1 is an MIF4G domain-containing cofactor of the RNA helicase Fal1 and associates with the 5' domain of the 18S rRNA sequence. RNA Biol 2020; 17:539-553. [PMID: 31994962 PMCID: PMC7237134 DOI: 10.1080/15476286.2020.1716540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Assembly of eukaryotic ribosomal subunits is a complex and dynamic process involving the action of more than 200 trans-acting assembly factors. Although recent cryo-electron microscopy structures have provided information on architecture of several pre-ribosomal particles and the binding sites of many AFs, the RNA and protein interactions of many other AFs not captured in these snapshots still remain elusive. RNA helicases are key regulators of structural rearrangements within pre-ribosomal complexes and here we have analysed the eIF4A-like RNA helicase Fal1 and its putative cofactor Sgd1. Our data show that these proteins interact directly via the MIF4G domain of Sgd1 and that the MIF4G domain of Sgd1 stimulates the catalytic activity of Fal1 in vitro. The catalytic activity of Fal1, and the interaction between Fal1 and Sgd1, are required for efficient pre-rRNA processing at the A0, A1 and A2 sites. Furthermore, Sgd1 co-purifies the early small subunit biogenesis factors Lcp5 and Rok1, suggesting that the Fal1-Sgd1 complex likely functions within the SSU processome. In vivo crosslinking data reveal that Sgd1 binds to helix H12 of the 18S rRNA sequence and we further demonstrate that this interaction is formed by the C-terminal region of the protein, which is essential for its function in ribosome biogenesis.
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Affiliation(s)
- Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
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33
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McRae EKS, Dupas SJ, Booy EP, Piragasam RS, Fahlman RP, McKenna SA. An RNA guanine quadruplex regulated pathway to TRAIL-sensitization by DDX21. RNA (NEW YORK, N.Y.) 2020; 26:44-57. [PMID: 31653714 PMCID: PMC6913123 DOI: 10.1261/rna.072199.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
DDX21 is a newly discovered RNA G-quadruplex (rG4) binding protein with no known biological rG4 targets. In this study we used label-free proteomic MS/MS to identify 26 proteins that are expressed at significantly different levels in cells expressing an rG4-binding deficient DDX21 (M4). MS data are available via ProteomeXchange with identifier PXD013501. From this list we validate MAGED2 as a protein that is regulated by DDX21 through rG4 in its 5'-UTR. MAGED2 protein levels, but not mRNA levels, are reduced by half in cells expressing DDX21 M4. MAGED2 has a repressive effect on TRAIL-R2 expression that is relieved under these conditions, resulting in elevated TRAIL-R2 mRNA and protein in MCF-7 cells, rendering them sensitive to TRAIL-mediated apoptosis. Our work identifies the role of DDX21 in regulation at the translational level through biologically relevant rG4 and shows that MAGED2 protein levels are regulated, at least in part, by the potential to form rG4 in their 5'-UTRs.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Steven J Dupas
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | | | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada T6G 2R7
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
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34
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Argaud D, Boulanger MC, Chignon A, Mkannez G, Mathieu P. Enhancer-mediated enrichment of interacting JMJD3-DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription. Nucleic Acids Res 2019; 47:8424-8438. [PMID: 31251802 PMCID: PMC6895255 DOI: 10.1093/nar/gkz560] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 06/17/2019] [Accepted: 06/25/2019] [Indexed: 12/11/2022] Open
Abstract
ENPP2, which encodes for the enzyme autotaxin (ATX), is overexpressed during chronic inflammatory diseases and various cancers. However, the molecular mechanism involved in the ENPP2 transcription remains elusive. Here, in HEK 293T cells, we demonstrated that lipopolysaccharide (LPS) increased the transcription process at ENPP2 locus through a NF-кB pathway and a reduction of H3K27me3 level, a histone repressive mark, by the demethylase UTX. Simultaneously, the H3K27me3 demethylase JMJD3/KDM6B was recruited to the transcription start site (TSS), within the gene body and controlled the expression of ENPP2 in a non-enzymatic manner. Mass spectrometry data revealed a novel interaction for JMJD3 with DDX21, a RNA helicase that unwinds R-loops created by nascent transcript and DNA template. Upon LPS treatment, JMJD3 is necessary for DDX21 recruitment at ENPP2 locus allowing the resolution of aberrant R-loops. CRISPR-Cas9-mediated deletion of a distant-acting enhancer decreased the expression of ENPP2 and lowered the recruitment of JMJD3–DDX21 complex at TSS and its progression through the gene body. Taken together, these findings revealed that enhancer-mediated enrichment of novel JMJD3–DDX21 interaction at ENPP2 locus is necessary for nascent transcript synthesis via the resolution of aberrant R-loops formation in response to inflammatory stimulus.
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Affiliation(s)
- Deborah Argaud
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec G1V-4G5, Canada
| | - Marie-Chloé Boulanger
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec G1V-4G5, Canada
| | - Arnaud Chignon
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec G1V-4G5, Canada
| | - Ghada Mkannez
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec G1V-4G5, Canada
| | - Patrick Mathieu
- Laboratory of Cardiovascular Pathobiology, Quebec Heart and Lung Institute/Research Center, Department of Surgery, Laval University, Quebec G1V-4G5, Canada
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35
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Iost I, Jain C. A DEAD-box protein regulates ribosome assembly through control of ribosomal protein synthesis. Nucleic Acids Res 2019; 47:8193-8206. [PMID: 31188443 PMCID: PMC6736130 DOI: 10.1093/nar/gkz502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023] Open
Abstract
DEAD-box proteins (DBPs) comprise a large family of proteins that most commonly have been identified as regulators of ribosome assembly. The Escherichia coli DBP, SrmB, represents a model bacterial DBP whose absence impairs formation of the large ribosomal subunit (LSU). To define the basis for SrmB function, suppressors of the ribosomal defect of ΔsrmB strains were isolated. The major class of suppressors was found to map to the 5′ untranslated region (UTR) of the rplM-rpsI operon, which encodes the ribosomal proteins (r-proteins) L13 and S9. An analysis of protein abundance indicated that both r-proteins are under-produced in the ΔsrmB strain, but are increased in these suppressors, implicating r-protein underproduction as the molecular basis for the observed ribosomal defects. Reduced r-protein synthesis was determined to be caused by intrinsic transcription termination within the rplM 5′ UTR that is abrogated by SrmB. These results reveal a specific mechanism for DBP regulation of ribosomal assembly, indirectly mediated through its effects on r-protein expression.
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Affiliation(s)
- Isabelle Iost
- ARNA Laboratory, INSERM U1212, CNRS UMR 5320, Université de Bordeaux, France
| | - Chaitanya Jain
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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36
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Bohnsack KE, Bohnsack MT. Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J 2019; 38:e100278. [PMID: 31268599 PMCID: PMC6600647 DOI: 10.15252/embj.2018100278] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/18/2019] [Accepted: 04/26/2019] [Indexed: 12/12/2022] Open
Abstract
The essential cellular process of ribosome biogenesis is at the nexus of various signalling pathways that coordinate protein synthesis with cellular growth and proliferation. The fact that numerous diseases are caused by defects in ribosome assembly underscores the importance of obtaining a detailed understanding of this pathway. Studies in yeast have provided a wealth of information about the fundamental principles of ribosome assembly, and although many features are conserved throughout eukaryotes, the larger size of human (pre-)ribosomes, as well as the evolution of additional regulatory networks that can modulate ribosome assembly and function, have resulted in a more complex assembly pathway in humans. Notably, many ribosome biogenesis factors conserved from yeast appear to have subtly different or additional functions in humans. In addition, recent genome-wide, RNAi-based screens have identified a plethora of novel factors required for human ribosome biogenesis. In this review, we discuss key aspects of human ribosome production, highlighting differences to yeast, links to disease, as well as emerging concepts such as extra-ribosomal functions of ribosomal proteins and ribosome heterogeneity.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
| | - Markus T Bohnsack
- Department of Molecular BiologyUniversity Medical Center GöttingenGöttingenGermany
- Göttingen Center for Molecular BiosciencesGeorg‐August UniversityGöttingenGermany
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37
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Sergiev PV, Aleksashin NA, Chugunova AA, Polikanov YS, Dontsova OA. Structural and evolutionary insights into ribosomal RNA methylation. Nat Chem Biol 2019; 14:226-235. [PMID: 29443970 DOI: 10.1038/nchembio.2569] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/02/2018] [Indexed: 01/24/2023]
Abstract
Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. Identification of all enzymes responsible for rRNA methylation, as well as mapping of all modified rRNA residues, is now complete for a number of model species, such as Escherichia coli and Saccharomyces cerevisiae. Recent high-resolution structures of bacterial ribosomes provided the first direct visualization of methylated nucleotides. The structures of ribosomes from various organisms and organelles have also lately become available, enabling comparative structure-based analysis of rRNA methylation sites in various taxonomic groups. In addition to the conserved core of modified residues in ribosomes from the majority of studied organisms, structural analysis points to the functional roles of some of the rRNA methylations, which are discussed in this Review in an evolutionary context.
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Affiliation(s)
- Petr V Sergiev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Anastasia A Chugunova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Yury S Polikanov
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Olga A Dontsova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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38
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Yan Q, Zhu C, Guang S, Feng X. The Functions of Non-coding RNAs in rRNA Regulation. Front Genet 2019; 10:290. [PMID: 31024617 PMCID: PMC6463246 DOI: 10.3389/fgene.2019.00290] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 03/18/2019] [Indexed: 02/04/2023] Open
Abstract
Ribosomes are ribonucleoprotein machines that decode the genetic information embedded in mRNAs into polypeptides. Ribosome biogenesis is tightly coordinated and controlled from the transcription of pre-rRNAs to the assembly of ribosomes. Defects or disorders in rRNA production result in a number of human ribosomopathy diseases. During the processes of rRNA synthesis, non-coding RNAs, especially snoRNAs, play important roles in pre-rRNA transcription, processing, and maturation. Recent research has started to reveal that other long and short non-coding RNAs, including risiRNA, LoNA, and SLERT (among others), are also involved in pre-rRNA transcription and rRNA production. Here, we summarize the current understanding of the mechanisms of non-coding RNA-mediated rRNA generation and regulation and their biological roles.
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Affiliation(s)
- Qi Yan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chengming Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Hefei, China
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
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39
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Choudhury P, Hackert P, Memet I, Sloan KE, Bohnsack MT. The human RNA helicase DHX37 is required for release of the U3 snoRNP from pre-ribosomal particles. RNA Biol 2018; 16:54-68. [PMID: 30582406 PMCID: PMC6380342 DOI: 10.1080/15476286.2018.1556149] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ribosome synthesis is an essential cellular process, and perturbation of human ribosome production is linked to cancer and genetic diseases termed ribosomopathies. During their assembly, pre-ribosomal particles undergo numerous structural rearrangements, which establish the architecture present in mature complexes and serve as key checkpoints, ensuring the fidelity of ribosome biogenesis. RNA helicases are essential mediators of such remodelling events and here, we demonstrate that the DEAH-box RNA helicase DHX37 is required for maturation of the small ribosomal subunit in human cells. Our data reveal that the presence of DHX37 in early pre-ribosomal particles is monitored by a quality control pathway and that failure to recruit DHX37 leads to pre-rRNA degradation. Using an in vivo crosslinking approach, we show that DHX37 binds directly to the U3 small nucleolar RNA (snoRNA) and demonstrate that the catalytic activity of the helicase is required for dissociation of the U3 snoRNA from pre-ribosomal complexes. This is an important event during ribosome assembly as it enables formation of the central pseudoknot structure of the small ribosomal subunit. We identify UTP14A as a direct interaction partner of DHX37 and our data suggest that UTP14A can act as a cofactor that stimulates the activity of the helicase in the context of U3 snoRNA release.
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Affiliation(s)
- Priyanka Choudhury
- a Department of Molecular Biology , University Medical Centre Göttingen , Göttingen , Germany
| | - Philipp Hackert
- a Department of Molecular Biology , University Medical Centre Göttingen , Göttingen , Germany
| | - Indira Memet
- a Department of Molecular Biology , University Medical Centre Göttingen , Göttingen , Germany
| | - Katherine E Sloan
- a Department of Molecular Biology , University Medical Centre Göttingen , Göttingen , Germany
| | - Markus T Bohnsack
- a Department of Molecular Biology , University Medical Centre Göttingen , Göttingen , Germany.,b Göttingen Center for Molecular Biosciences , Georg-August University , Göttingen , Germany
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40
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Yu G, Zhao Y, Li H. The multistructural forms of box C/D ribonucleoprotein particles. RNA (NEW YORK, N.Y.) 2018; 24:1625-1633. [PMID: 30254138 PMCID: PMC6239191 DOI: 10.1261/rna.068312.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Structural biology studies of archaeal and yeast box C/D ribonucleoprotein particles (RNPs) reveal a surprisingly wide range of forms. If form ever follows function, the different structures of box C/D small ribonucleoprotein particles (snoRNPs) may reflect their versatile functional roles beyond what has been recognized. A large majority of box C/D RNPs serve to site-specifically methylate the ribosomal RNA, typically as independent complexes. Select members of the box C/D snoRNPs also are essential components of the megadalton RNP enzyme, the small subunit processome that is responsible for processing ribosomal RNA. Other box C/D RNPs continue to be uncovered with either unexpected or unknown functions. We summarize currently known box C/D RNP structures in this review and identify the Nop56/58 and box C/D RNA subunits as the key elements underlying the observed structural diversity, and likely, the diverse functional roles of box C/D RNPs.
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Affiliation(s)
- Ge Yu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Yu Zhao
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | - Hong Li
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
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41
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Toczydlowska-Socha D, Zielinska MM, Kurkowska M, Astha, Almeida CF, Stefaniak F, Purta E, Bujnicki JM. Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5' termini. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0161. [PMID: 30397098 PMCID: PMC6232587 DOI: 10.1098/rstb.2018.0161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 11/23/2022] Open
Abstract
The 5′-cap structure, characteristic for RNA polymerase II-transcribed RNAs, plays important roles in RNA metabolism. In humans, RNA cap formation includes post-transcriptional modification of the first transcribed nucleotide by RNA cap1 methyltransferase (CMTr1). Here, we report that CMTr1 activity is hindered towards RNA substrates with highly structured 5′ termini. We found that CMTr1 binds ATP-dependent RNA DHX15 helicase and that this interaction, mediated by the G-patch domain of CMTr1, has an advantageous effect on CMTr1 activity towards highly structured RNA substrates. The effect of DHX15 helicase activity is consistent with the strength of the secondary structure that has to be removed for CMTr1 to access the 5′-terminal residues in a single-stranded conformation. This is, to our knowledge, the first demonstration of the involvement of DHX15 in post-transcriptional RNA modification, and the first example of a molecular process in which DHX15 directly affects the activity of another enzyme. Our findings suggest a new mechanism underlying the regulatory role of DHX15 in the RNA capping process. RNAs with highly structured 5′ termini constitute a significant fraction of the human transcriptome. Hence, CMTr1–DHX15 cooperation is likely to be important for the metabolism of RNA polymerase II-transcribed RNAs. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Diana Toczydlowska-Socha
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Magdalena M Zielinska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Malgorzata Kurkowska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Astha
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Catarina F Almeida
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. ks. Trojdena 4, 02-109 Warsaw, Poland .,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland
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42
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Kretschmer J, Rao H, Hackert P, Sloan KE, Höbartner C, Bohnsack MT. The m 6A reader protein YTHDC2 interacts with the small ribosomal subunit and the 5'-3' exoribonuclease XRN1. RNA (NEW YORK, N.Y.) 2018; 24:1339-1350. [PMID: 29970596 PMCID: PMC6140455 DOI: 10.1261/rna.064238.117] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 06/26/2018] [Indexed: 05/20/2023]
Abstract
N6-methyladenosine (m6A) modifications in RNAs play important roles in regulating many different aspects of gene expression. While m6As can have direct effects on the structure, maturation, or translation of mRNAs, such modifications can also influence the fate of RNAs via proteins termed "readers" that specifically recognize and bind modified nucleotides. Several YTH domain-containing proteins have been identified as m6A readers that regulate the splicing, translation, or stability of specific mRNAs. In contrast to the other YTH domain-containing proteins, YTHDC2 has several defined domains and here, we have analyzed the contribution of these domains to the RNA and protein interactions of YTHDC2. The YTH domain of YTHDC2 preferentially binds m6A-containing RNAs via a conserved hydrophobic pocket, whereas the ankyrin repeats mediate an RNA-independent interaction with the 5'-3' exoribonuclease XRN1. We show that the YTH and R3H domains contribute to the binding of YTHDC2 to cellular RNAs, and using crosslinking and analysis of cDNA (CRAC), we reveal that YTHDC2 interacts with the small ribosomal subunit in close proximity to the mRNA entry/exit sites. YTHDC2 was recently found to promote a "fast-track" expression program for specific mRNAs, and our data suggest that YTHDC2 accomplishes this by recruitment of the RNA degradation machinery to regulate the stability of m6A-containing mRNAs and by utilizing its distinct RNA-binding domains to bridge interactions between m6A-containing mRNAs and the ribosomes to facilitate their efficient translation.
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Affiliation(s)
- Jens Kretschmer
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Harita Rao
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, 37077 Göttingen, Germany
- Institute for Organic Chemistry, University Würzburg, 97074 Würzburg, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, 37073 Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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43
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Abstract
Small nucleolar RNAs (snoRNAs) are a family of conserved nuclear RNAs that function in the modification of small nuclear RNAs (snRNAs) or ribosomal RNAs (rRNAs), or participate in the processing of rRNAs during ribosome subunit maturation. Eukaryotic DNA transcription and RNA processing produce many long noncoding RNA (lncRNA) species. Although most lncRNAs are processed like typical mRNAs to be 5' capped and 3' polyadenylated, other types of lncRNAs are stabilized from primary Pol II transcripts by alternative mechanisms. One way to generate stable lncRNAs is to co-operate with snoRNA processing to produce snoRNA-ended lncRNAs (sno-lncRNAs) and 5' snoRNA-ended and 3'-polyadenylated lncRNAs (SPAs). Rather than silently accumulating in the nucleus, some sno-lncRNAs and SPAs are involved in the regulation of pre-rRNA transcription and alternative splicing of pre-mRNAs. Here we provide a mini-review to discuss the biogenesis and functions of these unusually processed lncRNAs.
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Affiliation(s)
- Yu-Hang Xing
- a State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai , China
| | - Ling-Ling Chen
- a State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology , Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai , China.,b School of Life Science and Technology , ShanghaiTech University , Shanghai , China
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44
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Chuang TD, Xie Y, Yan W, Khorram O. Next-generation sequencing reveals differentially expressed small noncoding RNAs in uterine leiomyoma. Fertil Steril 2018; 109:919-929. [PMID: 29778390 PMCID: PMC6445395 DOI: 10.1016/j.fertnstert.2018.01.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/20/2018] [Accepted: 01/24/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date. DESIGN Laboratory-based investigation. SETTING Academic center. PATIENT(S) Women undergoing hysterectomy for benign indications. INTERVENTION(S) Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). MAIN OUTCOME MEASURE(S) Expression profile of sncRNAs in leiomyoma and matched myometrium. RESULT(S) Screening our previously determined RNA sequencing data with the sncRNA database resulted in identification of 15 small nuclear (sn) RNAs, 284 small nucleolar (sno) RNAs, 98 Piwi-interacting (pi) RNAs, 152 transfer (t) RNAs, and 45 ribosomal (r) RNAs, of which 15 snoRNAs, 24 piRNAs, 7 tRNAs, and 6 rRNAs were differentially expressed at a 1.5-fold change cutoff in leiomyoma compared with myometrium. We selected 5 snoRNAs, 4 piRNAs, 1 tRNA, and 1 rRNA that were differentially expressed and confirmed their expression in paired tissues (n = 20) from both phases of the menstrual cycle with the use of qRT-PCR. The results indicated up-regulation of the snoRNAs (SNORD30, SNORD27, SNORA16A, SNORD46, and SNORD56) and down-regulation of the piRNAs (piR-1311, piR-16677, piR-20365, piR-4153), tRNA (TRG-GCC5-1), and rRNA (RNA5SP202) expression in leiomyoma compared with myometrium (P<.05). The pattern of expression of these sncRNAs was similar to RNA sequencing analysis, with no menstrual cycle-dependent differences detected except for SNORD30. Because Argonaute 2 (AGO2) is required for sncRNA-mediated gene silencing, we determined its expression and found greater abundance in leiomyoma. CONCLUSION(S) Our results provide the first evidence for the differential expression of additional classes of sncRNAs and AGO2 in leiomyoma, implicating their roles as a gene regulatory mechanism.
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Affiliation(s)
- Tsai-Der Chuang
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and LA-Biomed Research Institute, Torrance, California
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | - Omid Khorram
- Department of Obstetrics and Gynecology, Harbor-UCLA Medical Center and LA-Biomed Research Institute, Torrance, California.
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45
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Bryzgalov LO, Korbolina EE, Brusentsov II, Leberfarb EY, Bondar NP, Merkulova TI. Novel functional variants at the GWAS-implicated loci might confer risk to major depressive disorder, bipolar affective disorder and schizophrenia. BMC Neurosci 2018; 19:22. [PMID: 29745862 PMCID: PMC5998904 DOI: 10.1186/s12868-018-0414-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND A challenge of understanding the mechanisms underlying cognition including neurodevelopmental and neuropsychiatric disorders is mainly given by the potential severity of cognitive disorders for the quality of life and their prevalence. However, the field has been focused predominantly on protein coding variation until recently. Given the importance of tightly controlled gene expression for normal brain function, the goal of the study was to assess the functional variation including non-coding variation in human genome that is likely to play an important role in cognitive functions. To this end, we organized and utilized available genome-wide datasets from genomic, transcriptomic and association studies into a comprehensive data corpus. We focused on genomic regions that are enriched in regulatory activity-overlapping transcriptional factor binding regions and repurpose our data collection especially for identification of the regulatory SNPs (rSNPs) that showed associations both with allele-specific binding and allele-specific expression. We matched these rSNPs to the nearby and distant targeted genes and then selected the variants that could implicate the etiology of cognitive disorders according to Genome-Wide Association Studies (GWAS). Next, we use DeSeq 2.0 package to test the differences in the expression of the certain targeted genes between the controls and the patients that were diagnosed bipolar affective disorder and schizophrenia. Finally, we assess the potential biological role for identified drivers of cognition using DAVID and GeneMANIA. RESULTS As a result, we selected fourteen regulatory SNPs locating within the loci, implicated from GWAS for cognitive disorders with six of the variants unreported previously. Grouping of the targeted genes according to biological functions revealed the involvement of processes such as 'posttranscriptional regulation of gene expression', 'neuron differentiation', 'neuron projection development', 'regulation of cell cycle process' and 'protein catabolic processes'. We identified four rSNP-targeted genes that showed differential expression between patient and control groups depending on brain region: NRAS-in schizophrenia cohort, CDC25B, DDX21 and NUCKS1-in bipolar disorder cohort. CONCLUSIONS Overall, our findings are likely to provide the keys for unraveling the mechanisms that underlie cognitive functions including major depressive disorder, bipolar disorder and schizophrenia etiopathogenesis.
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Affiliation(s)
- Leonid O. Bryzgalov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Elena E. Korbolina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
| | - Ilja I. Brusentsov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Elena Y. Leberfarb
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Natalia P. Bondar
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
| | - Tatiana I. Merkulova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
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46
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Abstract
Ribosome biogenesis is a complex and highly energy-demanding process that requires the concerted action of all three nuclear RNA polymerases (Pol I-III) in eukaryotes. The three largest ribosomal RNAs (rRNAs) originate from a precursor transcript (pre-rRNA) that is encoded by multicopy genes located in the nucleolus. Transcription of these rRNA genes (rDNA) by Pol I is the key regulation step in ribosome production and is tightly controlled by an intricate network of signaling pathways and epigenetic mechanisms. In this article, we give an overview of the composition of the basal Pol I machinery and rDNA chromatin. We discuss rRNA gene regulation in response to environmental signals and developmental cues and focus on perturbations occurring in diseases linked to either excessive or limited rRNA levels. Finally, we discuss the emerging view that rDNA integrity and activity may be involved in the aging process.
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Affiliation(s)
- Samim Sharifi
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University, 07745 Jena, Germany; , .,Leibniz-Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
| | - Holger Bierhoff
- Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich Schiller University, 07745 Jena, Germany; , .,Leibniz-Institute on Aging-Fritz Lipmann Institute, 07745 Jena, Germany
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47
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Hammond JA, Zhou L, Lamichhane R, Chu HY, Millar DP, Gerace L, Williamson JR. A Survey of DDX21 Activity During Rev/RRE Complex Formation. J Mol Biol 2018; 430:537-553. [PMID: 28705764 PMCID: PMC5762417 DOI: 10.1016/j.jmb.2017.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 01/17/2023]
Abstract
HIV-1 requires a specialized nuclear export pathway to transport unspliced and partially spliced viral transcripts to the cytoplasm. Central to this pathway is the viral protein Rev, which binds to the Rev response element in stem IIB located on unspliced viral transcripts and subsequently oligomerizes in a cooperative manner. Previous work identified a number of cellular DEAD-box helicases as in vivo binding partners of Rev, and siRNA experiments indicated a functional role for many in the HIV replication cycle. Two DEAD-box proteins, DDX1 and DDX3, had previously been shown to play a role in HIV pathogenesis. In this study, another protein identified in that screen, DDX21, is tested for protein and RNA binding and subsequent enzymatic activities in the context of the Rev/RRE pathway. We found that DDX21 can bind to the RRE with high affinity, and this binding stimulates ATPase activity with an enzymatic efficiency similar to DDX1. Furthermore, DDX21 is both an ATP-dependent and ATP-independent helicase, and both ATPase and ATP-dependent helicase activities are inhibited by Rev in a dose-dependent manner, although ATP-independent helicase activity is not. A conserved binding interaction between DDX protein's DEAD domain and Rev was identified, with Rev's nuclear diffusion inhibitory signal motif playing a significant role in binding. Finally, DDX21 was shown to enhance Rev binding to the RRE in a manner similar to that previously described for DDX1, although DDX3 does not. These data indicate that DDX1 and DDX21 have similar biochemical activities with regard to the Rev/RRE system, while DDX3 differs.
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Affiliation(s)
- John A Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Li Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rajan Lamichhane
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hui-Yi Chu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Larry Gerace
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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48
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Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders. Nature 2018; 554:112-117. [PMID: 29364875 DOI: 10.1038/nature25449] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/11/2017] [Indexed: 02/06/2023]
Abstract
Many craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as transcription or ribosome biogenesis. Although it is understood that many of these malformations are a consequence of defects in cranial neural crest cells, a cell type that gives rise to most of the facial structures during embryogenesis, the mechanism underlying cell-type selectivity of these defects remains largely unknown. By exploring molecular functions of DDX21, a DEAD-box RNA helicase involved in control of both RNA polymerase (Pol) I- and II-dependent transcriptional arms of ribosome biogenesis, we uncovered a previously unappreciated mechanism linking nucleolar dysfunction, ribosomal DNA (rDNA) damage, and craniofacial malformations. Here we demonstrate that genetic perturbations associated with Treacher Collins syndrome, a craniofacial disorder caused by heterozygous mutations in components of the Pol I transcriptional machinery or its cofactor TCOF1 (ref. 1), lead to relocalization of DDX21 from the nucleolus to the nucleoplasm, its loss from the chromatin targets, as well as inhibition of rRNA processing and downregulation of ribosomal protein gene transcription. These effects are cell-type-selective, cell-autonomous, and involve activation of p53 tumour-suppressor protein. We further show that cranial neural crest cells are sensitized to p53-mediated apoptosis, but blocking DDX21 loss from the nucleolus and chromatin rescues both the susceptibility to apoptosis and the craniofacial phenotypes associated with Treacher Collins syndrome. This mechanism is not restricted to cranial neural crest cells, as blood formation is also hypersensitive to loss of DDX21 functions. Accordingly, ribosomal gene perturbations associated with Diamond-Blackfan anaemia disrupt DDX21 localization. At the molecular level, we demonstrate that impaired rRNA synthesis elicits a DNA damage response, and that rDNA damage results in tissue-selective and dosage-dependent effects on craniofacial development. Taken together, our findings illustrate how disruption in general regulators that compromise nucleolar homeostasis can result in tissue-selective malformations.
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49
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McRae EKS, Booy EP, Moya-Torres A, Ezzati P, Stetefeld J, McKenna SA. Human DDX21 binds and unwinds RNA guanine quadruplexes. Nucleic Acids Res 2017; 45:6656-6668. [PMID: 28472472 PMCID: PMC5499804 DOI: 10.1093/nar/gkx380] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/24/2017] [Indexed: 12/24/2022] Open
Abstract
Guanine quadruplexes (G4s) are an important structure of nucleic acids (DNA and RNA) with roles in several cellular processes. RNA G4s require specialized unwinding enzymes, of which only two have been previously identified. We describe the results of a simple and specific mass spectrometry guided method used to screen HEK293T cell lysate for G4 binding proteins. From these results, we validated the RNA helicase protein DDX21. DDX21 is an established RNA helicase, but has not yet been validated as a G4 binding protein. Through biochemical techniques, we confirm that DDX21-quadruplex RNA interactions are direct and mediated via a site of interaction at the C-terminus of the protein. Furthermore, through monitoring changes in nuclease sensitivity we show that DDX21 can unwind RNA G4. Finally, as proof of principle, we demonstrate the ability of DDX21 to suppress the expression of a protein with G4s in the 3΄ UTR of its mRNA.
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Affiliation(s)
- Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aniel Moya-Torres
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Peyman Ezzati
- Manitoba Centre for Proteomics and Systems Biology, Section of Biomedical Proteomics, Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba and Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Manitoba Institute for Materials, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Manitoba Institute for Materials, University of Manitoba, Winnipeg, Manitoba, Canada
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50
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Warda AS, Kretschmer J, Hackert P, Lenz C, Urlaub H, Höbartner C, Sloan KE, Bohnsack MT. Human METTL16 is a N6-methyladenosine (m 6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep 2017; 18:2004-2014. [PMID: 29051200 DOI: 10.15252/embr.201744940] [Citation(s) in RCA: 460] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/17/2017] [Accepted: 09/28/2017] [Indexed: 01/05/2023] Open
Abstract
N6-methyladenosine (m6A) is a highly dynamic RNA modification that has recently emerged as a key regulator of gene expression. While many m6A modifications are installed by the METTL3-METTL14 complex, others appear to be introduced independently, implying that additional human m6A methyltransferases remain to be identified. Using crosslinking and analysis of cDNA (CRAC), we reveal that the putative human m6A "writer" protein METTL16 binds to the U6 snRNA and other ncRNAs as well as numerous lncRNAs and pre-mRNAs. We demonstrate that METTL16 is responsible for N6-methylation of A43 of the U6 snRNA and identify the early U6 biogenesis factors La, LARP7 and the methylphosphate capping enzyme MEPCE as METTL16 interaction partners. Interestingly, A43 lies within an essential ACAGAGA box of U6 that base pairs with 5' splice sites of pre-mRNAs during splicing, suggesting that METTL16-mediated modification of this site plays an important role in splicing regulation. The identification of METTL16 as an active m6A methyltransferase in human cells expands our understanding of the mechanisms by which the m6A landscape is installed on cellular RNAs.
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Affiliation(s)
- Ahmed S Warda
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Jens Kretschmer
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.,Department of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Claudia Höbartner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August-University, Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany .,Göttingen Center for Molecular Biosciences, Georg-August-University, Göttingen, Germany
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