351
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Sirri V, Grob A, Berthelet J, Jourdan N, Roussel P. Sirtuin 7 promotes 45S pre-rRNA cleavage at site 2 and determines the processing pathway. J Cell Sci 2019; 132:jcs228601. [PMID: 31331964 PMCID: PMC6771141 DOI: 10.1242/jcs.228601] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/10/2019] [Indexed: 01/06/2023] Open
Abstract
In humans, ribosome biogenesis mainly occurs in nucleoli following two alternative pre-rRNA processing pathways differing in the order in which cleavages take place but not by the sites of cleavage. To uncover the role of the nucleolar NAD+-dependent deacetylase sirtuin 7 in the synthesis of ribosomal subunits, pre-rRNA processing was analyzed after sirtinol-mediated inhibition of sirtuin 7 activity or depletion of sirtuin 7 protein. We thus reveal that sirtuin 7 activity is a critical regulator of processing of 45S, 32S and 30S pre-rRNAs. Sirtuin 7 protein is primarily essential to 45S pre-rRNA cleavage at site 2, which is the first step of processing pathway 2. Furthermore, we demonstrate that sirtuin 7 physically interacts with Nop56 and the GAR domain of fibrillarin, and propose that this could interfere with fibrillarin-dependent cleavage. Sirtuin 7 depletion results in the accumulation of 5' extended forms of 32S pre-rRNA, and also influences the localization of fibrillarin. Thus, we establish a close relationship between sirtuin 7 and fibrillarin, which might determine the processing pathway used for ribosome biogenesis.
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Affiliation(s)
- Valentina Sirri
- Université de Paris, Unité de Biologie Fonctionnelle et Adaptative (BFA), UMR 8251, CNRS, 4 rue Marie-Andrée Lagroua Weill-Hallé, F-75013 Paris, France
| | - Alice Grob
- Department of Life Sciences, Imperial College London, London SW7 2AZ, England, UK
| | - Jérémy Berthelet
- Université de Paris, Unité de Biologie Fonctionnelle et Adaptative (BFA), UMR 8251, CNRS, 4 rue Marie-Andrée Lagroua Weill-Hallé, F-75013 Paris, France
| | - Nathalie Jourdan
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), UMR 8256, CNRS, 9 quai St Bernard, F-75005 Paris, France
| | - Pascal Roussel
- Université de Paris, Unité de Biologie Fonctionnelle et Adaptative (BFA), UMR 8251, CNRS, 4 rue Marie-Andrée Lagroua Weill-Hallé, F-75013 Paris, France
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352
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Abel Y, Rederstorff M. SnoRNAs and the emerging class of sdRNAs: Multifaceted players in oncogenesis. Biochimie 2019; 164:17-21. [DOI: 10.1016/j.biochi.2019.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023]
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353
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Sáez-Vásquez J, Delseny M. Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors. THE PLANT CELL 2019; 31:1945-1967. [PMID: 31239391 PMCID: PMC6751116 DOI: 10.1105/tpc.18.00874] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 05/28/2019] [Accepted: 06/25/2019] [Indexed: 05/11/2023]
Abstract
The transcription of 18S, 5.8S, and 18S rRNA genes (45S rDNA), cotranscriptional processing of pre-rRNA, and assembly of mature rRNA with ribosomal proteins are the linchpins of ribosome biogenesis. In yeast (Saccharomyces cerevisiae) and animal cells, hundreds of pre-rRNA processing factors have been identified and their involvement in ribosome assembly determined. These studies, together with structural analyses, have yielded comprehensive models of the pre-40S and pre-60S ribosome subunits as well as the largest cotranscriptionally assembled preribosome particle: the 90S/small subunit processome. Here, we present the current knowledge of the functional organization of 45S rDNA, pre-rRNA transcription, rRNA processing activities, and ribosome assembly factors in plants, focusing on data from Arabidopsis (Arabidopsis thaliana). Based on yeast and mammalian cell studies, we describe the ribonucleoprotein complexes and RNA-associated activities and discuss how they might specifically affect the production of 40S and 60S subunits. Finally, we review recent findings concerning pre-rRNA processing pathways and a novel mechanism involved in a ribosome stress response in plants.
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Affiliation(s)
- Julio Sáez-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
| | - Michel Delseny
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France, and Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, F-66860 Perpignan, France
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354
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Palm D, Streit D, Shanmugam T, Weis BL, Ruprecht M, Simm S, Schleiff E. Plant-specific ribosome biogenesis factors in Arabidopsis thaliana with essential function in rRNA processing. Nucleic Acids Res 2019; 47:1880-1895. [PMID: 30576513 PMCID: PMC6393314 DOI: 10.1093/nar/gky1261] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 12/04/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
rRNA processing and assembly of ribosomal proteins during maturation of ribosomes involve many ribosome biogenesis factors (RBFs). Recent studies identified differences in the set of RBFs in humans and yeast, and the existence of plant-specific RBFs has been proposed as well. To identify such plant-specific RBFs, we characterized T-DNA insertion mutants of 15 Arabidopsis thaliana genes encoding nuclear proteins with nucleotide binding properties that are not orthologues to yeast or human RBFs. Mutants of nine genes show an altered rRNA processing ranging from inhibition of initial 35S pre-rRNA cleavage to final maturation events like the 6S pre-rRNA processing. These phenotypes led to their annotation as 'involved in rRNA processing' - IRP. The irp mutants are either lethal or show developmental and stress related phenotypes. We identified IRPs for maturation of the plant-specific precursor 5'-5.8S and one affecting the pathway with ITS2 first cleavage of the 35S pre-rRNA transcript. Moreover, we realized that 5'-5.8S processing is essential, while a mutant causing 6S accumulation shows only a weak phenotype. Thus, we demonstrate the importance of the maturation of the plant-specific precursor 5'-5.8S for plant development as well as the occurrence of an ITS2 first cleavage pathway in fast dividing tissues.
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Affiliation(s)
- Denise Palm
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Deniz Streit
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Thiruvenkadam Shanmugam
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Benjamin L Weis
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Maike Ruprecht
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
| | - Stefan Simm
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, D-60438 Frankfurt, Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max von Laue Str. 9, D-60438 Frankfurt, Germany
- Frankfurt Institute for Advanced Studies, D-60438 Frankfurt, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, D-60438 Frankfurt, Germany
- To whom correspondence should be addressed. Tel: +49 69 798 29285; Fax: +49 69 798 29286;
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355
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Abstract
Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.
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356
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Taoka M, Nobe Y, Yamaki Y, Sato K, Ishikawa H, Izumikawa K, Yamauchi Y, Hirota K, Nakayama H, Takahashi N, Isobe T. Landscape of the complete RNA chemical modifications in the human 80S ribosome. Nucleic Acids Res 2019; 46:9289-9298. [PMID: 30202881 PMCID: PMC6182160 DOI: 10.1093/nar/gky811] [Citation(s) in RCA: 214] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 09/06/2018] [Indexed: 01/08/2023] Open
Abstract
During ribosome biogenesis, ribosomal RNAs acquire various chemical modifications that ensure the fidelity of translation, and dysregulation of the modification processes can cause proteome changes as observed in cancer and inherited human disorders. Here, we report the complete chemical modifications of all RNAs of the human 80S ribosome as determined with quantitative mass spectrometry. We assigned 228 sites with 14 different post-transcriptional modifications, most of which are located in functional regions of the ribosome. All modifications detected are typical of eukaryotic ribosomal RNAs, and no human-specific modifications were observed, in contrast to a recently reported cryo-electron microscopy analysis. While human ribosomal RNAs appeared to have little polymorphism regarding the post-transcriptional modifications, we found that pseudouridylation at two specific sites in 28S ribosomal RNA are significantly reduced in ribosomes of patients with familial dyskeratosis congenita, a genetic disease caused by a point mutation in the pseudouridine synthase gene DKC1. The landscape of the entire epitranscriptomic ribosomal RNA modifications provides a firm basis for understanding ribosome function and dysfunction associated with human disease.
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Affiliation(s)
- Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Yuka Yamaki
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ko Sato
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hideaki Ishikawa
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Keiichi Izumikawa
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Nakayama
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwai-cho 3-5-8, Fuchu-shi, Tokyo 183-8509, Japan
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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357
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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: 133] [Impact Index Per Article: 26.6] [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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358
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Chen HH, Tarn WY. uORF-mediated translational control: recently elucidated mechanisms and implications in cancer. RNA Biol 2019; 16:1327-1338. [PMID: 31234713 DOI: 10.1080/15476286.2019.1632634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein synthesis is tightly regulated, and its dysregulation can contribute to the pathology of various diseases, including cancer. Increased or selective translation of mRNAs can promote cancer cell proliferation, metastasis and tumor expansion. Translational control is one of the most important means for cells to quickly adapt to environmental stresses. Adaptive translation involves various alternative mechanisms of translation initiation. Upstream open reading frames (uORFs) serve as a major regulator of stress-responsive translational control. Since recent advances in omics technologies including ribo-seq have expanded our knowledge of translation, we discuss emerging mechanisms for uORF-mediated translation regulation and its impact on cancer cell biology. A better understanding of dysregulated translational control of uORFs in cancer would facilitate the development of new strategies for cancer therapy.
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Affiliation(s)
- Hung-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
| | - Woan-Yuh Tarn
- Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan
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359
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Bohnsack MT, Sloan KE. Modifications in small nuclear RNAs and their roles in spliceosome assembly and function. Biol Chem 2019; 399:1265-1276. [PMID: 29908124 DOI: 10.1515/hsz-2018-0205] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/28/2018] [Indexed: 01/27/2023]
Abstract
Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific ribonucleoproteins (scaRNPs). Modified nucleotides typically cluster in functionally important regions of the snRNAs, suggesting that their presence could optimise the interactions of snRNAs with each other or with pre-mRNAs, or may affect the binding of spliceosomal proteins. snRNA modifications appear to play important roles in snRNP biogenesis and spliceosome assembly, and have also been proposed to influence the efficiency and fidelity of pre-mRNA splicing. Interestingly, alterations in the modification status of snRNAs have recently been observed in different cellular conditions, implying that some snRNA modifications are dynamic and raising the possibility that these modifications may fine-tune the spliceosome for particular functions. Here, we review the current knowledge on the snRNA modification machinery and discuss the timing, functions and dynamics of modifications in snRNAs.
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Affiliation(s)
- Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg August University, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
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360
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Delaunay S, Frye M. RNA modifications regulating cell fate in cancer. Nat Cell Biol 2019; 21:552-559. [PMID: 31048770 DOI: 10.1038/s41556-019-0319-0] [Citation(s) in RCA: 217] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/26/2019] [Indexed: 02/02/2023]
Abstract
The deposition of chemical modifications into RNA is a crucial regulator of temporal and spatial gene expression programs during development. Accordingly, altered RNA modification patterns are widely linked to developmental diseases. Recently, the dysregulation of RNA modification pathways also emerged as a contributor to cancer. By modulating cell survival, differentiation, migration and drug resistance, RNA modifications add another regulatory layer of complexity to most aspects of tumourigenesis.
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Affiliation(s)
- Sylvain Delaunay
- Department of Genetics, University of Cambridge, Cambridge, UK
- German Cancer Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany
| | - Michaela Frye
- Department of Genetics, University of Cambridge, Cambridge, UK.
- German Cancer Center (DKFZ), Im Neuenheimer Feld, Heidelberg, Germany.
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361
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Ferretti MB, Karbstein K. Does functional specialization of ribosomes really exist? RNA (NEW YORK, N.Y.) 2019; 25:521-538. [PMID: 30733326 PMCID: PMC6467006 DOI: 10.1261/rna.069823.118] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gain-of-function assays and the demonstration of inducibility under physiological conditions.
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Affiliation(s)
- Max B Ferretti
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Molecular Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, Florida 33458, USA
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362
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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: 116] [Impact Index Per Article: 23.2] [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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363
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Zhang LS, Liu C, Ma H, Dai Q, Sun HL, Luo G, Zhang Z, Zhang L, Hu L, Dong X, He C. Transcriptome-wide Mapping of Internal N 7-Methylguanosine Methylome in Mammalian mRNA. Mol Cell 2019; 74:1304-1316.e8. [PMID: 31031084 DOI: 10.1016/j.molcel.2019.03.036] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 02/26/2019] [Accepted: 03/27/2019] [Indexed: 01/05/2023]
Abstract
N7-methylguanosine (m7G) is a positively charged, essential modification at the 5' cap of eukaryotic mRNA, regulating mRNA export, translation, and splicing. m7G also occurs internally within tRNA and rRNA, but its existence and distribution within eukaryotic mRNA remain to be investigated. Here, we show the presence of internal m7G sites within mammalian mRNA. We then performed transcriptome-wide profiling of internal m7G methylome using m7G-MeRIP sequencing (MeRIP-seq). To map this modification at base resolution, we developed a chemical-assisted sequencing approach that selectively converts internal m7G sites into abasic sites, inducing misincorporation at these sites during reverse transcription. This base-resolution m7G-seq enabled transcriptome-wide mapping of m7G in human tRNA and mRNA, revealing distribution features of the internal m7G methylome in human cells. We also identified METTL1 as a methyltransferase that installs a subset of m7G within mRNA and showed that internal m7G methylation could affect mRNA translation.
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Affiliation(s)
- Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Honghui Ma
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Institute of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Hui-Lung Sun
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Guanzheng Luo
- The State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510060, China
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Linda Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Lulu Hu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xueyang Dong
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.
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364
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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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365
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Correia S, Alhinho AT, Casimiro B, Miguel CM, Oliveira M, Veríssimo P, Canhoto J. NEP-TC a rRNA Methyltransferase Involved on Somatic Embryogenesis of Tamarillo ( Solanum betaceum Cav.). FRONTIERS IN PLANT SCIENCE 2019; 10:438. [PMID: 31024602 PMCID: PMC6459958 DOI: 10.3389/fpls.2019.00438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/22/2019] [Indexed: 05/23/2023]
Abstract
Somatic embryogenesis (SE) is an important biotechnological tool for large-scale clonal propagation and for embryogenesis research. Moreover, genetic transformation and cryopreservation procedures in many species rely on efficient SE protocols. We have been studying different aspects related to SE induction and somatic embryo development in tamarillo (Solanum betaceum Cav.), a small tree from the Solanaceae family. Previous proteomic analyses identified a protein (NEP-TC, 26.5 kDa) consistently present in non-embryogenic calluses of tamarillo, but absent in the embryogenic ones. In this work, the role of NEP-TC during SE was assessed by gene expression analysis and immunolocalization. The results obtained demonstrated that NEP-TC is a putative member of the SpoU rRNA methylase family. This protein, present in the cytoplasm and nucleus, is expressed in non-embryogenic cells and not expressed in embryogenic cells. Slightly enhanced SE induction levels in tamarillo plants with NEP-TC down-regulated levels also supports the role of this protein on SE induction. Heterologous expression was used to confirm NEP-TC rRNA methyltransferase activity, with enhanced activity levels when rRNA was used as a substrate. These data relate a putative member of the SpoU methylase family with plant morphogenesis, in particular with SE induction.
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Affiliation(s)
- Sandra Correia
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ana T. Alhinho
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Bruno Casimiro
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Célia M. Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | - Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-UNL), Oeiras, Portugal
| | - Paula Veríssimo
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Centro de Neurociências e Biologia Celular (CNBC/UC), Edifiício da Faculdade de Medicina, Universidade de Coimbra, Coimbra, Portugal
| | - Jorge Canhoto
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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366
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Sabi R, Tuller T. Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics. NPJ Syst Biol Appl 2019; 5:12. [PMID: 30962948 PMCID: PMC6449359 DOI: 10.1038/s41540-019-0089-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 03/20/2019] [Indexed: 01/14/2023] Open
Abstract
The ability to dynamically control mRNA translation has a great impact on many intracellular processes. Whereas it is believed that translational control in eukaryotes occurs mainly at initiation, the condition-specific changes at the elongation level and their potential regulatory role remain unclear. Using computational approaches applied to ribosome profiling data, we show that elongation rate is dynamic and can change considerably during the yeast meiosis to facilitate the selective translation of stage-specific transcripts. We observed unique elongation changes during meiosis II, including a global inhibition of translation elongation at the onset of anaphase II accompanied by a sharp shift toward increased elongation for genes required at this meiotic stage. We also show that ribosomal proteins counteract the global decreased elongation by maintaining high initiation rates. Our findings provide new insights into gene expression regulation during meiosis and demonstrate that codon usage evolved, among others, to optimize timely translation.
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Affiliation(s)
- Renana Sabi
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
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367
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Åsman AKM, Curtis BA, Archibald JM. Nucleomorph Small RNAs in Cryptophyte and Chlorarachniophyte Algae. Genome Biol Evol 2019; 11:1117-1134. [PMID: 30949682 PMCID: PMC6461891 DOI: 10.1093/gbe/evz064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2019] [Indexed: 12/27/2022] Open
Abstract
The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development, and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically derived “nucleomorph” genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. A total of 32.3 and 35.3 million reads were generated from G. theta and B. natans, respectively. In G. theta, we identified nucleomorph U1, U2, and U4 spliceosomal small nuclear RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform 2′-O methylation of rRNA (but not snRNA). In B. natans, we found the previously undetected 5S rRNA as well as six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of the miniature 18–21 nt introns found in B. natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte G. theta. Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a distinct possibility.
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Affiliation(s)
- Anna K M Åsman
- Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada.,Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Bruce A Curtis
- Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Nova Scotia, Canada
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368
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Burke MF, McLaurin DM, Logan MK, Hebert MD. Alteration of 28S rRNA 2'- O-methylation by etoposide correlates with decreased SMN phosphorylation and reduced Drosha levels. Biol Open 2019; 8:bio041848. [PMID: 30858166 PMCID: PMC6451326 DOI: 10.1242/bio.041848] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
The most common types of modification in human rRNA are pseudouridylation and 2'-O ribose methylation. These modifications are performed by small nucleolar ribonucleoproteins (snoRNPs) which contain a guide RNA (snoRNA) that base pairs at specific sites within the rRNA to direct the modification. rRNA modifications can vary, generating ribosome heterogeneity. One possible method that can be used to regulate rRNA modifications is by controlling snoRNP activity. RNA fragments derived from some small Cajal body-specific RNAs (scaRNA 2, 9 and 17) may influence snoRNP activity. Most scaRNAs accumulate in the Cajal body - a subnuclear domain - where they participate in the biogenesis of small nuclear RNPs, but scaRNA 2, 9 and 17 generate nucleolus-enriched fragments of unclear function, and we hypothesize that these fragments form regulatory RNPs that impact snoRNP activity and modulate rRNA modifications. Our previous work has shown that SMN, Drosha and various stresses, including etoposide treatment, may alter regulatory RNP formation. Here we demonstrate that etoposide treatment decreases the phosphorylation of SMN, reduces Drosha levels and increases the 2'-O-methylation of two sites within 28S rRNA. These findings further support a role for SMN and Drosha in regulating rRNA modification, possibly by affecting snoRNP or regulatory RNP activity.
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Affiliation(s)
- Marilyn F Burke
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Douglas M McLaurin
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Madelyn K Logan
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
| | - Michael D Hebert
- Department of Cell and Molecular Biology, The University of Mississippi Medical Center, Jackson, MS 39216-4505, USA
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369
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Abstract
An emergent theme in cancer biology is that dysregulated energy metabolism may directly influence oncogenic gene expression. This is due to the fact that many enzymes involved in gene regulation use cofactors derived from primary metabolism, including acetyl-CoA, S-adenosylmethionine, and 2-ketoglutarate. While this phenomenon was first studied through the prism of histone and DNA modifications (the epigenome), recent work indicates metabolism can also impact gene regulation by disrupting the balance of RNA post-transcriptional modifications (the epitranscriptome). Here we review recent studies that explore how metabolic regulation of writers and erasers of the epitranscriptome (FTO, TET2, NAT10, MTO1, and METTL16) helps shape gene expression through three distinct mechanisms: cofactor inhibition, cofactor depletion, and writer localization. Our brief survey underscores similarities and differences between the metabolic regulation of the epigenome and epitranscriptome, and highlights fertile ground for future investigation.
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Affiliation(s)
- Justin M. Thomas
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Pedro J. Batista
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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370
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Tuorto F, Parlato R. rRNA and tRNA Bridges to Neuronal Homeostasis in Health and Disease. J Mol Biol 2019; 431:1763-1779. [PMID: 30876917 DOI: 10.1016/j.jmb.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/11/2022]
Abstract
Dysregulation of protein translation is emerging as a unifying mechanism in the pathogenesis of many neuronal disorders. Ribosomal RNA (rRNA) and transfer RNA (tRNA) are structural molecules that have complementary and coordinated functions in protein synthesis. Defects in both rRNAs and tRNAs have been described in mammalian brain development, neurological syndromes, and neurodegeneration. In this review, we present the molecular mechanisms that link aberrant rRNA and tRNA transcription, processing and modifications to translation deficits, and neuropathogenesis. We also discuss the interdependence of rRNA and tRNA biosynthesis and how their metabolism brings together proteotoxic stress and impaired neuronal homeostasis.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | - Rosanna Parlato
- Institute of Applied Physiology, University of Ulm, Albert Einstein Allee 11, 89081 Ulm, Germany; Institute of Anatomy and Cell Biology, Medical Cell Biology, University of Heidelberg, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany.
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371
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Abstract
Posttranscriptional modifications of RNA represent an emerging class of regulatory elements in human biology. Improved methods for studying how these elements are controlled and where they occur has the potential to transform our understanding of gene expression in development and disease. Here we describe a chemical method for nucleotide resolution sequencing of N4-acetylcytidine (ac4C), a highly conserved modified nucleobase whose formation is catalyzed by the essential cytidine acetyltransferase enzyme NAT10. This approach enables the sensitive, PCR-amplifiable detection of individual ac4C sites from nanograms of unfractionated cellular RNA. The sensitive and quantitative nature of this assay provides a powerful tool to understand how cytidine acetylation is targeted, profile RNA acetyltransferase dynamics, and validate the sites and stoichiometry of ac4C in novel RNA species.
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372
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Waduge P, Sakakibara Y, Chow CS. Chemical probing for examining the structure of modified RNAs and ligand binding to RNA. Methods 2019; 156:110-120. [DOI: 10.1016/j.ymeth.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/04/2018] [Accepted: 10/22/2018] [Indexed: 12/15/2022] Open
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373
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Dimitrova DG, Teysset L, Carré C. RNA 2'-O-Methylation (Nm) Modification in Human Diseases. Genes (Basel) 2019; 10:E117. [PMID: 30764532 PMCID: PMC6409641 DOI: 10.3390/genes10020117] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 12/24/2022] Open
Abstract
Nm (2'-O-methylation) is one of the most common modifications in the RNA world. It has the potential to influence the RNA molecules in multiple ways, such as structure, stability, and interactions, and to play a role in various cellular processes from epigenetic gene regulation, through translation to self versus non-self recognition. Yet, building scientific knowledge on the Nm matter has been hampered for a long time by the challenges in detecting and mapping this modification. Today, with the latest advancements in the area, more and more Nm sites are discovered on RNAs (tRNA, rRNA, mRNA, and small non-coding RNA) and linked to normal or pathological conditions. This review aims to synthesize the Nm-associated human diseases known to date and to tackle potential indirect links to some other biological defects.
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Affiliation(s)
- Dilyana G Dimitrova
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Laure Teysset
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
| | - Clément Carré
- Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France.
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374
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Small Non-Coding RNAs Derived From Eukaryotic Ribosomal RNA. Noncoding RNA 2019; 5:ncrna5010016. [PMID: 30720712 PMCID: PMC6468398 DOI: 10.3390/ncrna5010016] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/24/2019] [Accepted: 01/27/2019] [Indexed: 12/13/2022] Open
Abstract
The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will present a nonexhaustive list of referenced small non-coding RNAs (ncRNAs) derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs). We will focus on the rRFs that are experimentally verified, and discuss their origin, length, structure, biogenesis, association with known regulatory proteins, and potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences-because of their overabundance-from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because no one could believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.
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375
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Bohnsack KE, Höbartner C, Bohnsack MT. Eukaryotic 5-methylcytosine (m⁵C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease. Genes (Basel) 2019; 10:genes10020102. [PMID: 30704115 PMCID: PMC6409601 DOI: 10.3390/genes10020102] [Citation(s) in RCA: 274] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/04/2023] Open
Abstract
5-methylcytosine (m⁵C) is an abundant RNA modification that's presence is reported in a wide variety of RNA species, including cytoplasmic and mitochondrial ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as messenger RNAs (mRNAs), enhancer RNAs (eRNAs) and a number of non-coding RNAs. In eukaryotes, C5 methylation of RNA cytosines is catalyzed by enzymes of the NOL1/NOP2/SUN domain (NSUN) family, as well as the DNA methyltransferase homologue DNMT2. In recent years, substrate RNAs and modification target nucleotides for each of these methyltransferases have been identified, and structural and biochemical analyses have provided the first insights into how each of these enzymes achieves target specificity. Functional characterizations of these proteins and the modifications they install have revealed important roles in diverse aspects of both mitochondrial and nuclear gene expression. Importantly, this knowledge has enabled a better understanding of the molecular basis of a number of diseases caused by mutations in the genes encoding m⁵C methyltransferases or changes in the expression level of these enzymes.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, 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, Göttingen, Justus-von-Liebig-Weg 11, 37077 Germany.
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376
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Sloan KE, Knox AA, Wells GR, Schneider C, Watkins NJ. Interactions and activities of factors involved in the late stages of human 18S rRNA maturation. RNA Biol 2019; 16:196-210. [PMID: 30638116 PMCID: PMC6380343 DOI: 10.1080/15476286.2018.1564467] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Ribosome production is an essential cellular process involving a plethora of trans-acting factors, such as nucleases, methyltransferases, RNA helicases and kinases that catalyse key maturation steps. Precise temporal and spatial regulation of such enzymes is essential to ensure accurate and efficient subunit assembly. Here, we focus on the maturation of the 3ʹ end of the 18S rRNA in human cells. We reveal that human RIO2 is an active kinase that phosphorylates both itself and the rRNA methyltransferase DIM1 in vitro. In contrast to yeast, our data confirm that human DIM1 predominantly acts in the nucleus and we further demonstrate that the 21S pre-rRNA is the main target for DIM1-catalysed methylation. We show that the PIN domain of the endonuclease NOB1 is required for site 3 cleavage, while the zinc ribbon domain is essential for pre-40S recruitment. Furthermore, we also demonstrate that NOB1, PNO1 and DIM1 bind to a region of the pre-rRNA encompassing the 3ʹ end of 18S and the start of ITS1, in vitro. Interestingly, NOB1 is present in the cell at higher levels than other pre-40S factors. We provide evidence that NOB1 is multimeric within the cell and show that NOB1 multimerisation is lost when ribosome biogenesis is blocked. Taken together, our data indicate a dynamic interplay of key factors associated with the 3ʹ end of the 18S rRNA during human pre-40S biogenesis and highlight potential mechanisms by which this process can be regulated.
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Affiliation(s)
- Katherine Elizabeth Sloan
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK.,b Department of Molecular Biology , University Medical Centre, Goettingen , Goettingen , Germany
| | - Andrew Alexander Knox
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| | - Graeme Raymond Wells
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| | - Claudia Schneider
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
| | - Nicholas James Watkins
- a Institute for Cell and Molecular Biosciences, The Medical School , Newcastle University , Newcastle upon Tyne , UK
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377
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Hartstock K, Rentmeister A. MappingN6‐Methyladenosine (m6A) in RNA: Established Methods, Remaining Challenges, and Emerging Approaches. Chemistry 2019; 25:3455-3464. [DOI: 10.1002/chem.201804043] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Katja Hartstock
- Institute of BiochemistryDepartment of ChemistryUniversity of Münster Wilhelm-Klemm-Straße 2 48149 Münster Germany
| | - Andrea Rentmeister
- Institute of BiochemistryDepartment of ChemistryUniversity of Münster Wilhelm-Klemm-Straße 2 48149 Münster Germany
- Cells-in-Motion Cluster of Excellence Germany
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378
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Hu J, Manduzio S, Kang H. Epitranscriptomic RNA Methylation in Plant Development and Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2019; 10:500. [PMID: 31110512 PMCID: PMC6499213 DOI: 10.3389/fpls.2019.00500] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/01/2019] [Indexed: 05/19/2023]
Abstract
Recent advances in methylated RNA immunoprecipitation followed by sequencing and mass spectrometry have revealed widespread chemical modifications on mRNAs. Methylation of RNA bases such as N 6-methyladenosine (m6A) and 5-methylcytidine (m5C) is the most prevalent mRNA modifications found in eukaryotes. In recent years, cellular factors introducing, interpreting, and deleting specific methylation marks on mRNAs, designated as "writers (methyltransferase)," "readers (RNA-binding protein)," and "erasers (demethylase)," respectively, have been identified in plants and animals. An emerging body of evidence shows that methylation on mRNAs affects diverse aspects of RNA metabolism, including stability, splicing, nucleus-to-cytoplasm export, alternative polyadenylation, and translation. Although our understanding for roles of writers, readers, and erasers in plants is far behind that for their animal counterparts, accumulating reports clearly demonstrate that these factors are essential for plant growth and abiotic stress responses. This review emphasizes the crucial roles of epitranscriptomic modifications of RNAs in new layer of gene expression regulation during the growth and response of plants to abiotic stresses.
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379
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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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380
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RNA helicases mediate structural transitions and compositional changes in pre-ribosomal complexes. Nat Commun 2018; 9:5383. [PMID: 30568249 PMCID: PMC6300602 DOI: 10.1038/s41467-018-07783-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 11/28/2018] [Indexed: 01/31/2023] Open
Abstract
Production of eukaryotic ribosomal subunits is a highly dynamic process; pre-ribosomes undergo numerous structural rearrangements that establish the architecture present in mature complexes and serve as key checkpoints, ensuring the fidelity of ribosome assembly. Using in vivo crosslinking, we here identify the pre-ribosomal binding sites of three RNA helicases. Our data support roles for Has1 in triggering release of the U14 snoRNP, a critical event during early 40S maturation, and in driving assembly of domain I of pre-60S complexes. Binding of Mak5 to domain II of pre-60S complexes promotes recruitment of the ribosomal protein Rpl10, which is necessary for subunit joining and ribosome function. Spb4 binds to a molecular hinge at the base of ES27 facilitating binding of the export factor Arx1, thereby promoting pre-60S export competence. Our data provide important insights into the driving forces behind key structural remodelling events during ribosomal subunit assembly.
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381
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Grafanaki K, Anastasakis D, Kyriakopoulos G, Skeparnias I, Georgiou S, Stathopoulos C. Translation regulation in skin cancer from a tRNA point of view. Epigenomics 2018; 11:215-245. [PMID: 30565492 DOI: 10.2217/epi-2018-0176] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein synthesis is a central and dynamic process, frequently deregulated in cancer through aberrant activation or expression of translation initiation factors and tRNAs. The discovery of tRNA-derived fragments, a new class of abundant and, in some cases stress-induced, small Noncoding RNAs has perplexed the epigenomics landscape and highlights the emerging regulatory role of tRNAs in translation and beyond. Skin is the biggest organ in human body, which maintains homeostasis of its multilayers through regulatory networks that induce translational reprogramming, and modulate tRNA transcription, modification and fragmentation, in response to various stress signals, like UV irradiation. In this review, we summarize recent knowledge on the role of translation regulation and tRNA biology in the alarming prevalence of skin cancer.
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Affiliation(s)
- Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece.,Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Dimitrios Anastasakis
- National Institute of Musculoskeletal & Arthritis & Skin, NIH, 50 South Drive, Room 1152, Bethesda, MD 20892, USA
| | - George Kyriakopoulos
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Sophia Georgiou
- Department of Dermatology, School of Medicine, University of Patras, 26504 Patras, Greece
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382
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Kumar S, Chinnusamy V, Mohapatra T. Epigenetics of Modified DNA Bases: 5-Methylcytosine and Beyond. Front Genet 2018; 9:640. [PMID: 30619465 PMCID: PMC6305559 DOI: 10.3389/fgene.2018.00640] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
Modification of DNA bases plays vital roles in the epigenetic control of gene expression in both animals and plants. Though much attention is given to the conventional epigenetic signature 5-methylcytosine (5-mC), the field of epigenetics is attracting increased scientific interest through the discovery of additional modifications of DNA bases and their roles in controlling gene expression. Theoretically, each of the DNA bases can be modified; however, modifications of cytosine and adenine only are known so far. This review focuses on the recent findings of the well-studied cytosine modifications and yet poorly characterized adenine modification which serve as an additional layer of epigenetic regulation in animals and discuss their potential roles in plants. Cytosine modification at symmetric (CG, CHG) and asymmetric (CHH) contexts is a key epigenetic feature. In addition to the ROS1 family mediated demethylation, Ten-Eleven Translocation family proteins-mediated hydroxylation of 5-mC to 5-hydroxymethylcytosine as additional active demethylation pathway are also discussed. The epigenetic marks are known to be associated with the regulation of several cellular and developmental processes, pluripotency of stem cells, neuron cell development, and tumor development in animals. Therefore, the most recently discovered N6-methyladenine, an additional epigenetic mark with regulatory potential, is also described. Interestingly, these newly discovered modifications are also found in the genomes which lack canonical 5-mC, signifying their independent epigenetic functions. These modified DNA bases are considered to be important players in epigenomics. The potential for combinatorial interaction among the known modified DNA bases suggests that epigenetic codon is likely to be substantially more complicated than it is thought today.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute (ICAR), New Delhi, India
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383
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Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018; 42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Yves Quentin
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
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384
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Ayadi L, Galvanin A, Pichot F, Marchand V, Motorin Y. RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:253-269. [PMID: 30572123 DOI: 10.1016/j.bbagrm.2018.11.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 01/01/2023]
Abstract
Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.
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Affiliation(s)
- Lilia Ayadi
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Adeline Galvanin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Florian Pichot
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Virginie Marchand
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Yuri Motorin
- UMR7365 IMoPA CNRS-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France.
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385
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Kufel J, Grzechnik P. Small Nucleolar RNAs Tell a Different Tale. Trends Genet 2018; 35:104-117. [PMID: 30563726 DOI: 10.1016/j.tig.2018.11.005] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5' and 3' ends undergo processing to release mature, functional molecules. The maturation strategies of these noncoding RNAs in various organisms follow a similar pattern but employ different factors and are strictly correlated with genomic organisation of their genes.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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386
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Coker H, Wei G, Brockdorff N. m6A modification of non-coding RNA and the control of mammalian gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:310-318. [PMID: 30550772 DOI: 10.1016/j.bbagrm.2018.12.002] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/27/2018] [Accepted: 12/07/2018] [Indexed: 12/27/2022]
Abstract
The biology of non-coding RNA (ncRNA) and the regulation of mammalian gene expression is a rapidly expanding field. In this review, we consider how recent advances in technology, enabling the precise mapping of modifications to RNA transcripts, has provided new opportunities to dissect post-transcriptional gene regulation. With this has come the realisation that in the absence of translation, the modification of ncRNAs may play a fundamental role in their regulation, protein interactome and subsequent downstream effector functions. We focus upon modification of RNA by N6-methyladenosine (m6A); its readers, writers and erasers, before considering the differing role of m6A modified lncRNAs MALAT1 and Xist. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Heather Coker
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Guifeng Wei
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil Brockdorff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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387
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Ma H, Wang X, Cai J, Dai Q, Natchiar SK, Lv R, Chen K, Lu Z, Chen H, Shi YG, Lan F, Fan J, Klaholz BP, Pan T, Shi Y, He C. N 6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Nat Chem Biol 2018; 15:88-94. [PMID: 30531910 DOI: 10.1038/s41589-018-0184-3] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/30/2018] [Indexed: 01/09/2023]
Abstract
N6-Methyladenosine (m6A) RNA modification is present in messenger RNAs (mRNA), ribosomal RNAs (rRNA), and spliceosomal RNAs (snRNA) in humans. Although mRNA m6A modifications have been extensively studied and shown to play critical roles in many cellular processes, the identity of m6A methyltransferases for rRNAs and the function of rRNA m6A modifications are unknown. Here we report a new m6A methyltransferase, ZCCHC4, which primarily methylates human 28S rRNA and also interacts with a subset of mRNAs. ZCCHC4 knockout eliminates m6A4220 modification in 28S rRNA, reduces global translation, and inhibits cell proliferation. We also find that ZCCHC4 protein is overexpressed in hepatocellular carcinoma tumors, and ZCCHC4 knockout significantly reduces tumor size in a xenograft mouse model. Our results highlight the functional significance of an rRNA m6A modification in translation and in tumor biology.
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Affiliation(s)
- Honghui Ma
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Xiaoyun Wang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jiabin Cai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Qing Dai
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - S Kundhavai Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Ruitu Lv
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Kai Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Zhike Lu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Hao Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yujiang Geno Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Endocrinology Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fei Lan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology (IGBMC), CNRS, Inserm, Université de Strasbourg, Illkirch, France
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
| | - Yang Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, and Institute of Biomedical Sciences, Fudan University, Shanghai, China. .,Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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388
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The emerging impact of tRNA modifications in the brain and nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:412-428. [PMID: 30529455 DOI: 10.1016/j.bbagrm.2018.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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389
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Fenwick MK, Ealick SE. Towards the structural characterization of the human methyltransferome. Curr Opin Struct Biol 2018; 53:12-21. [DOI: 10.1016/j.sbi.2018.03.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/06/2018] [Indexed: 10/17/2022]
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390
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Deciphering the Role of the Non-Coding Genome in Regulating Gene-Diet Interactions. Nutrients 2018; 10:nu10121831. [PMID: 30486341 PMCID: PMC6316136 DOI: 10.3390/nu10121831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Protein encoding genes constitute a small fraction of mammalian genomes. In addition to the protein coding genes, there are other functional units within the genome that are transcribed, but not translated into protein, the so called non-coding RNAs. There are many types of non-coding RNAs that have been identified and shown to have important roles in regulating gene expression either at the transcriptional or post-transcriptional level. A number of recent studies have highlighted that dietary manipulation in mammals can influence the expression or function of a number of classes of non-coding RNAs that contribute to the protein translation machinery. The identification of protein translation as a common target for nutritional regulation underscores the need to investigate how this may mechanistically contribute to phenotypes and diseases that are modified by nutritional intervention. Finally, we describe the state of the art and the application of emerging ‘-omics’ technologies to address the regulation of protein translation in response to diet.
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391
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Dudnakova T, Dunn-Davies H, Peters R, Tollervey D. Mapping targets for small nucleolar RNAs in yeast. Wellcome Open Res 2018; 3:120. [PMID: 30345388 PMCID: PMC6171561 DOI: 10.12688/wellcomeopenres.14735.2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2018] [Indexed: 12/15/2022] Open
Abstract
Background: Recent analyses implicate changes in the expression of the box C/D class of small nucleolar RNAs (snoRNAs) in several human diseases. Methods: Here we report the identification of potential novel RNA targets for box C/D snoRNAs in budding yeast, using the approach of UV crosslinking and sequencing of hybrids (CLASH) with the snoRNP proteins Nop1, Nop56 and Nop58. We also developed a bioinformatics approach to filter snoRNA-target interactions for bona fide methylation guide interactions. Results: We recovered 241,420 hybrids, out of which 190,597 were classed as reproducible, high energy hybrids. As expected, the majority of snoRNA interactions were with the ribosomal RNAs (rRNAs). Following filtering, 117,047 reproducible hybrids included 51 of the 55 reported rRNA methylation sites. The majority of interactions at methylation sites were predicted to guide methylation. However, competing, potentially regulatory, binding was also identified. In marked contrast, following CLASH performed with the RNA helicase Mtr4 only 7% of snoRNA-rRNA interactions recovered were predicted to guide methylation. We propose that Mtr4 functions in dissociating inappropriate snoRNA-target interactions. Numerous snoRNA-snoRNA interactions were recovered, indicating potential cross regulation. The snoRNAs snR4 and snR45 were recently implicated in site-directed rRNA acetylation, and hybrids were identified adjacent to the acetylation sites. We also identified 1,368 reproducible snoRNA-mRNA interactions, representing 448 sites of interaction involving 39 snoRNAs and 382 mRNAs. Depletion of the snoRNAs U3, U14 or snR4 each altered the levels of numerous mRNAs. Targets identified by CLASH were over-represented among these species, but causality has yet to be established. Conclusions: Systematic mapping of snoRNA-target binding provides a catalogue of high-confidence binding sites and indicates numerous potential regulatory interactions.
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Affiliation(s)
- Tatiana Dudnakova
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Hywel Dunn-Davies
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Rosie Peters
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
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392
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Ribosome biogenesis: An emerging druggable pathway for cancer therapeutics. Biochem Pharmacol 2018; 159:74-81. [PMID: 30468711 DOI: 10.1016/j.bcp.2018.11.014] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/16/2018] [Indexed: 01/05/2023]
Abstract
Ribosomes are nanomachines essential for protein production in all living cells. Ribosome synthesis increases in cancer cells to cope with a rise in protein synthesis and sustain unrestricted growth. This increase in ribosome biogenesis is reflected by severe morphological alterations of the nucleolus, the cell compartment where the initial steps of ribosome biogenesis take place. Ribosome biogenesis has recently emerged as an effective target in cancer therapy, and several compounds that inhibit ribosome production or function, killing preferentially cancer cells, have entered clinical trials. Recent research indicates that cells express heterogeneous populations of ribosomes and that the composition of ribosomes may play a key role in tumorigenesis, exposing novel therapeutic opportunities. Here, we review recent data demonstrating that ribosome biogenesis is a promising druggable pathway in cancer therapy, and discuss future research perspectives.
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393
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Hoernes TP, Faserl K, Juen MA, Kremser J, Gasser C, Fuchs E, Shi X, Siewert A, Lindner H, Kreutz C, Micura R, Joseph S, Höbartner C, Westhof E, Hüttenhofer A, Erlacher MD. Translation of non-standard codon nucleotides reveals minimal requirements for codon-anticodon interactions. Nat Commun 2018; 9:4865. [PMID: 30451861 PMCID: PMC6242847 DOI: 10.1038/s41467-018-07321-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/25/2018] [Indexed: 01/16/2023] Open
Abstract
The precise interplay between the mRNA codon and the tRNA anticodon is crucial for ensuring efficient and accurate translation by the ribosome. The insertion of RNA nucleobase derivatives in the mRNA allowed us to modulate the stability of the codon-anticodon interaction in the decoding site of bacterial and eukaryotic ribosomes, allowing an in-depth analysis of codon recognition. We found the hydrogen bond between the N1 of purines and the N3 of pyrimidines to be sufficient for decoding of the first two codon nucleotides, whereas adequate stacking between the RNA bases is critical at the wobble position. Inosine, found in eukaryotic mRNAs, is an important example of destabilization of the codon-anticodon interaction. Whereas single inosines are efficiently translated, multiple inosines, e.g., in the serotonin receptor 5-HT2C mRNA, inhibit translation. Thus, our results indicate that despite the robustness of the decoding process, its tolerance toward the weakening of codon-anticodon interactions is limited.
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Affiliation(s)
- Thomas Philipp Hoernes
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Klaus Faserl
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Michael Andreas Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Johannes Kremser
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Catherina Gasser
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Elisabeth Fuchs
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Xinying Shi
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA
| | - Aaron Siewert
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020, Innsbruck, Austria
| | - Simpson Joseph
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0314, USA
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Eric Westhof
- Architecture and Reactivity of RNA, Institute of Molecular and Cellular Biology of the CNRS UPR9002/University of Strasbourg, Strasbourg, 67084, France
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Matthias David Erlacher
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020, Innsbruck, Austria.
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394
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Structural modules of the stress-induced protein HflX: an outlook on its evolution and biological role. Curr Genet 2018; 65:363-370. [PMID: 30448945 DOI: 10.1007/s00294-018-0905-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 12/23/2022]
Abstract
Multifunctional proteins often show modular structures. A functional domain and the structural modules within the domain show evolutionary conservation of their spatial arrangement since that gives the protein its functionality. However, the question remains as to how members of different domains of life (Archaea, Bacteria, Eukarya), polish and perfect these modules within conserved multidomain proteins, to tailor functional proteins according to their specific requirements. In the quest for plausible answers to this question, we studied the bacterial protein HflX. HflX is a universally conserved member of the Obg-GTPase superfamily but its functional role in Archaea and Eukarya is barely known. It is a multidomain protein and possesses, in addition to its conserved GTPase domain, an ATP-binding N-terminal domain. It is involved in heat stress response in Escherichia coli and our laboratory recently identified an ATP-dependent RNA helicase activity of E. coli HflX, which is likely instrumental in rescuing ribosomes during heat stress. Because perception and response to stress is expected to be different in different life forms, the question is whether this activity is preserved in higher organisms or not. Thus, we explored the evolution pattern of different structural modules of HflX, with particular emphasis on the ATP-binding domain, to understand plausible biological role of HflX in other forms of life. Our analyses indicate that, while the evolutionary pattern of the GTPase domain follows a conserved phylogeny, conservation of the ATP-binding domain shows a complicated pattern. The limited analysis described here hints towards possible evolutionary adaptations and modifications of the domain, something which needs to be investigated in more depth in homologs from other life forms. Deciphering how nature 'tweaks' such modules, both structurally and functionally, may help in understanding the evolution of such proteins, and, on a large-scale, of stress-related proteins in general as well.
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395
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Ribosomal flavours: an acquired taste for specific mRNAs? Biochem Soc Trans 2018; 46:1529-1539. [PMID: 30420413 DOI: 10.1042/bst20180160] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 12/20/2022]
Abstract
The regulation of translation is critical in almost every aspect of gene expression. Nonetheless, the ribosome is historically viewed as a passive player in this process. However, evidence is accumulating to suggest that variations in the ribosome can have an important influence on which mRNAs are translated. Scope for variation is provided via multiple avenues, including heterogeneity at the level of both ribosomal proteins and ribosomal RNAs and their covalent modifications. Together, these variations provide the potential for hundreds, if not thousands, of flavours of ribosome, each of which could have idiosyncratic preferences for the translation of certain messenger RNAs. Indeed, perturbations to this heterogeneity appear to affect specific subsets of transcripts and manifest as cell-type-specific diseases. This review provides a historical perspective of the ribosomal code hypothesis, before outlining the various sources of heterogeneity, their regulation and functional consequences for the cell.
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396
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Aučynaitė A, Rutkienė R, Tauraitė D, Meškys R, Urbonavičius J. Identification of a 2'- O-Methyluridine Nucleoside Hydrolase Using the Metagenomic Libraries. Molecules 2018; 23:molecules23112904. [PMID: 30405065 PMCID: PMC6278475 DOI: 10.3390/molecules23112904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 11/16/2022] Open
Abstract
Ribose methylation is among the most ubiquitous modifications found in RNA. 2'-O-methyluridine is found in rRNA, snRNA, snoRNA and tRNA of Archaea, Bacteria, and Eukaryota. Moreover, 2'-O-methylribonucleosides are promising starting materials for the production of nucleic acid-based drugs. Despite the countless possibilities of practical use for the metabolic enzymes associated with methylated nucleosides, there are very few reports regarding the metabolic fate and enzymes involved in the metabolism of 2'-O-alkyl nucleosides. The presented work focuses on the cellular degradation of 2'-O-methyluridine. A novel enzyme was found using a screening strategy that employs Escherichia coli uracil auxotroph and the metagenomic libraries. A 2'-O-methyluridine hydrolase (RK9NH) has been identified together with an aldolase (RK9DPA)-forming a part of a probable gene cluster that is involved in the degradation of 2'-O-methylated nucleosides. The RK9NH is functional in E. coli uracil auxotroph and in vitro. The RK9NH nucleoside hydrolase could be engineered to enzymatically produce 2'-O-methylated nucleosides that are of great demand as raw materials for production of nucleic acid-based drugs. Moreover, RK9NH nucleoside hydrolase converts 5-fluorouridine, 5-fluoro-2'-deoxyuridine and 5-fluoro-2'-O-methyluridine into 5-fluorouracil, which suggests it could be employed in cancer therapy.
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Affiliation(s)
- Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
| | - Daiva Tauraitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania.
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, LT-10223 Vilnius, Lithuania.
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397
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Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry 2018; 58:312-329. [PMID: 30346748 DOI: 10.1021/acs.biochem.8b00949] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Clement Oyeniran
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Joshua R Brickner
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Naga Babu Chinnam
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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398
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Andersen KL, Nielsen H. Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment. Biomolecules 2018; 8:E128. [PMID: 30380771 PMCID: PMC6315972 DOI: 10.3390/biom8040128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/30/2022] Open
Abstract
In eukaryotes, 18S, 5.8S, and 28S rRNAs are transcribed as precursor molecules that undergo extensive modification and nucleolytic processing to form the mature rRNA species. Central in the process are the small nucleolar RNAs (snoRNAs). The majority of snoRNAs guide site specific chemical modifications but a few are involved in defining pre-rRNA cleavages. Here, we describe an unusual snoRNA (TtnuCD32) belonging to the box C/D subgroup from the ciliate Tetrahymena thermophila. We show that TtnuCD32 is unlikely to function as a modification guide snoRNA and that it is critical for cell viability. Cell lines with genetic knock-down of TtnuCD32 were impaired in growth and displayed two novel and apparently unrelated phenotypes. The most prominent phenotype is the accumulation of processing intermediates of 5.8S rRNA. The second phenotype is the decrease in abundance of a ~100 nt 26S rRNA fragment of unknown function. Sequence analysis demonstrated that TtnuCD32 share features with the essential snoRNA U14 but an alternative candidate (TtnuCD25) was more closely related to other U14 sequences. This, together with the fact that the observed rRNA processing phenotypes were not similar to what has been observed in U14 depleted cells, suggests that TtnuCD32 is a U14 homolog that has gained novel functions.
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MESH Headings
- Base Sequence
- Cell Survival
- Conserved Sequence
- Gene Expression Regulation
- Gene Knockdown Techniques
- Genome
- Methylation
- Nucleic Acid Conformation
- Protozoan Proteins/chemistry
- Protozoan Proteins/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- Tetrahymena/genetics
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Kasper L Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200N Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
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399
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Visualizing the Role of 2'-OH rRNA Methylations in the Human Ribosome Structure. Biomolecules 2018; 8:biom8040125. [PMID: 30366442 PMCID: PMC6316459 DOI: 10.3390/biom8040125] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/10/2018] [Accepted: 10/18/2018] [Indexed: 01/17/2023] Open
Abstract
Chemical modifications of RNA have recently gained new attention in biological sciences. They occur notably on messenger RNA (mRNA) and ribosomal RNA (rRNA) and are important for various cellular functions, but their molecular mechanism of action is yet to be understood in detail. Ribosomes are large ribonucleoprotein assemblies, which synthesize proteins in all organisms. Human ribosomes, for example, carry more than 200 modified nucleotides, which are introduced during biogenesis. Chemically modified nucleotides may appear to be only scarcely different from canonical nucleotides, but modifications such as methylations can in fact modulate their chemical and topological properties in the RNA and alter or modulate the overall translation efficiency of the ribosomes resulting in dysfunction of the translation machinery. Recent functional analysis and high-resolution ribosome structures have revealed a large repertoire of modification sites comprising different modification types. In this review, we focus on 2′-O-methylations (2′-O-Me) and discuss the structural insights gained through our recent cryo electron microscopy (cryo-EM) high-resolution structural analysis of the human ribosome, such as their locations and their influence on the secondary and tertiary structures of human rRNAs. The detailed analysis presented here reveals that ribose conformations of the rRNA backbone differ when the 2′-OH hydroxyl position is methylated, with 3′-endo conformations being the default and the 2′-endo conformations being characteristic in that the associated base is flipped-out. We compare currently known 2′-O-Me sites in human rRNAs evaluated using RiboMethSeq and cryo-EM structural analysis and discuss their involvement in several human diseases.
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400
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Aubert M, O'Donohue MF, Lebaron S, Gleizes PE. Pre-Ribosomal RNA Processing in Human Cells: From Mechanisms to Congenital Diseases. Biomolecules 2018; 8:biom8040123. [PMID: 30356013 PMCID: PMC6315592 DOI: 10.3390/biom8040123] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Ribosomal RNAs, the most abundant cellular RNA species, have evolved as the structural scaffold and the catalytic center of protein synthesis in every living organism. In eukaryotes, they are produced from a long primary transcript through an intricate sequence of processing steps that include RNA cleavage and folding and nucleotide modification. The mechanisms underlying this process in human cells have long been investigated, but technological advances have accelerated their study in the past decade. In addition, the association of congenital diseases to defects in ribosome synthesis has highlighted the central place of ribosomal RNA maturation in cell physiology regulation and broadened the interest in these mechanisms. Here, we give an overview of the current knowledge of pre-ribosomal RNA processing in human cells in light of recent progress and discuss how dysfunction of this pathway may contribute to the physiopathology of congenital diseases.
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Affiliation(s)
- Maxime Aubert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Marie-Françoise O'Donohue
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France.
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