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Walukiewicz HE, Farris Y, Burnet MC, Feid SC, You Y, Kim H, Bank T, Christensen D, Payne SH, Wolfe AJ, Rao CV, Nakayasu ES. Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation. mBio 2024:e0177324. [PMID: 39189746 DOI: 10.1128/mbio.01773-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024] Open
Abstract
Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics data set from 48 bacterial strains representing six phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. Comparative proteomics analysis combined with inorganic polyphosphate and guanosine tetra/pentaphosphate assays of the ΔprmA mutant in Escherichia coli revealed that bL11 methylation is important for stringent response signaling. In the stationary phase, we found that the ΔprmA mutant has impaired guanosine tetra/pentaphosphate production. This leads to a reduction in inorganic polyphosphate levels, accumulation of RNA and ribosomal proteins, and an abnormal polysome profile. Overall, our investigation demonstrates that the evolutionarily conserved bL11 methylation is important for stringent response signaling and ribosomal activity regulation and turnover. IMPORTANCE Protein methylation in bacteria was first identified over 60 years ago. Since then, its functional role has been identified for only a few proteins. To better understand the functional role of methylation in bacteria, we analyzed a large phyloproteomics data set encompassing 48 diverse bacteria. Our analysis revealed that ribosomal proteins are often methylated at conserved residues, suggesting that methylation of these sites may have a functional role in translation. Further analysis revealed that methylation of ribosomal protein L11 is important for stringent response signaling and ribosomal homeostasis.
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Affiliation(s)
- Hanna E Walukiewicz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sarah C Feid
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Hyeyoon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Thomas Bank
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - David Christensen
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, Utah, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Health Sciences Division, Loyola University Chicago, Maywood, Illinois, USA
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
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2
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Xiang Y, Zhang D, Li L, Xue YX, Zhang CY, Meng QF, Wang J, Tan XL, Li YL. Detection, distribution, and functions of RNA N 6-methyladenosine (m 6A) in plant development and environmental signal responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1429011. [PMID: 39081522 PMCID: PMC11286456 DOI: 10.3389/fpls.2024.1429011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
The epitranscriptomic mark N 6-methyladenosine (m6A) is the most common type of messenger RNA (mRNA) post-transcriptional modification in eukaryotes. With the discovery of the demethylase FTO (FAT MASS AND OBESITY-ASSOCIATED PROTEIN) in Homo Sapiens, this modification has been proven to be dynamically reversible. With technological advances, research on m6A modification in plants also rapidly developed. m6A modification is widely distributed in plants, which is usually enriched near the stop codons and 3'-UTRs, and has conserved modification sequences. The related proteins of m6A modification mainly consist of three components: methyltransferases (writers), demethylases (erasers), and reading proteins (readers). m6A modification mainly regulates the growth and development of plants by modulating the RNA metabolic processes and playing an important role in their responses to environmental signals. In this review, we briefly outline the development of m6A modification detection techniques; comparatively analyze the distribution characteristics of m6A in plants; summarize the methyltransferases, demethylases, and binding proteins related to m6A; elaborate on how m6A modification functions in plant growth, development, and response to environmental signals; and provide a summary and outlook on the research of m6A in plants.
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3
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Hudspeth J, Rogge K, Dörner S, Müll M, Hoffmeister D, Rupp B, Werten S. Methyl transfer in psilocybin biosynthesis. Nat Commun 2024; 15:2709. [PMID: 38548735 PMCID: PMC10978996 DOI: 10.1038/s41467-024-46997-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
Psilocybin, the natural hallucinogen produced by Psilocybe ("magic") mushrooms, holds great promise for the treatment of depression and several other mental health conditions. The final step in the psilocybin biosynthetic pathway, dimethylation of the tryptophan-derived intermediate norbaeocystin, is catalysed by PsiM. Here we present atomic resolution (0.9 Å) crystal structures of PsiM trapped at various stages of its reaction cycle, providing detailed insight into the SAM-dependent methylation mechanism. Structural and phylogenetic analyses suggest that PsiM derives from epitranscriptomic N6-methyladenosine writers of the METTL16 family, which is further supported by the observation that bound substrates physicochemically mimic RNA. Inherent limitations of the ancestral monomethyltransferase scaffold hamper the efficiency of psilocybin assembly and leave PsiM incapable of catalysing trimethylation to aeruginascin. The results of our study will support bioengineering efforts aiming to create novel variants of psilocybin with improved therapeutic properties.
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Affiliation(s)
- Jesse Hudspeth
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- Department of Chemistry, Colorado School of Mines, Golden, CO, USA
| | - Kai Rogge
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Sebastian Dörner
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Maximilian Müll
- Research Group Biosynthetic Design of Natural Products, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
- Research Group Pharmaceutical Microbiology, Leibniz Institute of Natural Product Research and Infection Biology, Hans Knöll Institute, Jena, Germany
| | - Bernhard Rupp
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria
- k.-k. Hofkristallamt, San Diego, California, USA
| | - Sebastiaan Werten
- Institute of Genetic Epidemiology, Medical University of Innsbruck, Innsbruck, Austria.
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D’Aquila P, De Rango F, Paparazzo E, Passarino G, Bellizzi D. Epigenetic-Based Regulation of Transcriptome in Escherichia coli Adaptive Antibiotic Resistance. Microbiol Spectr 2023; 11:e0458322. [PMID: 37184386 PMCID: PMC10269836 DOI: 10.1128/spectrum.04583-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
Adaptive antibiotic resistance is a transient metabolic adaptation of bacteria limiting their sensitivity to low, progressively increased, concentrations of antibiotics. Unlike innate and acquired resistance, adaptive resistance is dependent on the presence of antibiotics, and it disappears when the triggering factor is removed. Low concentrations of antibiotics are largely diffused in natural environments, in the food industry or in certain body compartments of humans when used therapeutically, or in animals when used for growth promotion. However, molecular mechanisms underlying this phenomenon are still poorly characterized. Here, we present experiments suggesting that epigenetic modifications, triggered by low concentrations of ampicillin, gentamicin, and ciprofloxacin, may modulate the sensitivity of bacteria to antibiotics. The epigenetic modifications we observed were paralleled by modifications of the expression pattern of many genes, including some of those that have been found mutated in strains with permanent antibiotic resistance. As the use of low concentrations of antibiotics is spreading in different contexts, our findings may suggest new targets and strategies to avoid adaptive antibiotic resistance. This might be very important as, in the long run, this transient adaptation may increase the chance, allowing the survival and the flourishing of bacteria populations, of the onset of mutations leading to stable resistance. IMPORTANCE In this study, we characterized the modifications of epigenetic marks and of the whole transcriptome in the adaptive response of Escherichia coli cells to low concentrations of ampicillin, gentamicin, and ciprofloxacin. As the transient adaptation does increase the chance of permanent resistance, possibly allowing the survival and flourishing of bacteria populations where casual mutations providing resistance may give an immediate advantage, the importance of this study is not only in the identification of possible molecular mechanisms underlying adaptive resistance to antibiotics, but also in suggesting new strategies to avoid adaptation.
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Affiliation(s)
- Patrizia D’Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Francesco De Rango
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
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5
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Jurdzinski KT, Mehrshad M, Delgado LF, Deng Z, Bertilsson S, Andersson AF. Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity. SCIENCE ADVANCES 2023; 9:eadg2059. [PMID: 37235649 PMCID: PMC10219603 DOI: 10.1126/sciadv.adg2059] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.
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Affiliation(s)
- Krzysztof T. Jurdzinski
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luis Fernando Delgado
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Ziling Deng
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F. Andersson
- Department of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden
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6
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Abstract
The chemical modification of ribonucleotides plays an integral role in the biology of diverse viruses and their eukaryotic host cells. Mapping the precise identity, location, and abundance of modified ribonucleotides remains a key goal of many studies aimed at characterizing the function and importance of a given modification. While mapping of specific RNA modifications through short-read sequencing approaches has powered a wealth of new discoveries in the past decade, this approach is limited by inherent biases and an absence of linkage information. Moreover, in viral contexts, the challenge is increased due to the compact nature of viral genomes giving rise to many overlapping transcript isoforms that cannot be adequately resolved using short-read sequencing approaches. The recent emergence of nanopore sequencing, specifically the ability to directly sequence native RNAs from virus-infected host cells, provides not just a new methodology for mapping modified ribonucleotides but also a new conceptual framework for what can be derived from the resulting sequencing data. In this minireview, we provide a detailed overview of how nanopore direct RNA sequencing works, the computational approaches applied to identify modified ribonucleotides, and the core concepts underlying both. We further highlight recent studies that have applied this approach to interrogating viral biology and finish by discussing key experimental considerations and how we predict that these methodologies will continue to evolve.
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Affiliation(s)
- Jonathan S. Abebe
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Ruth Verstraten
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
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7
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Biziaev NS, Shuvalov AV, Alkalaeva EZ. HEMK-Like Methyltransferases in the Regulation of Cellular Processes. Mol Biol 2022. [DOI: 10.1134/s0026893322030025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Sun J, Cheng B, Su Y, Li M, Ma S, Zhang Y, Zhang A, Cai S, Bao Q, Wang S, Zhu P. The Potential Role of m6A RNA Methylation in the Aging Process and Aging-Associated Diseases. Front Genet 2022; 13:869950. [PMID: 35518355 PMCID: PMC9065606 DOI: 10.3389/fgene.2022.869950] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/31/2022] [Indexed: 12/15/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common and conserved internal eukaryotic mRNA modification. m6A modification is a dynamic and reversible post-transcriptional regulatory modification, initiated by methylase and removed by RNA demethylase. m6A-binding proteins recognise the m6A modification to regulate gene expression. Recent studies have shown that altered m6A levels and abnormal regulator expression are crucial in the ageing process and the occurrence of age-related diseases. In this review, we summarise some key findings in the field of m6A modification in the ageing process and age-related diseases, including cell senescence, autophagy, inflammation, oxidative stress, DNA damage, tumours, neurodegenerative diseases, diabetes, and cardiovascular diseases (CVDs). We focused on the biological function and potential molecular mechanisms of m6A RNA methylation in ageing and age-related disease progression. We believe that m6A modification may provide a new target for anti-ageing therapies.
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Affiliation(s)
- Jin Sun
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Bokai Cheng
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Yongkang Su
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Man Li
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Shouyuan Ma
- Department of Geriatric Cardiology, The Second Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yan Zhang
- Department of Outpatient, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Anhang Zhang
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Shuang Cai
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Qiligeer Bao
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Shuxia Wang
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
| | - Ping Zhu
- Department of Geriatrics, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China.,Medical School of Chinese PLA, Beijing, China
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9
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Feng P, Feng L, Tang C. Comparison and Analysis of Computational Methods for Identifying N6-Methyladenosine Sites in Saccharomyces cerevisiae. Curr Pharm Des 2021; 27:1219-1229. [PMID: 33167827 DOI: 10.2174/1381612826666201109110703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/20/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND N6-methyladenosine (m6A) plays critical roles in a broad range of biological processes. Knowledge about the precise location of m6A site in the transcriptome is vital for deciphering its biological functions. Although experimental techniques have made substantial contributions to identify m6A, they are still labor intensive and time consuming. As complement to experimental methods, in the past few years, a series of computational approaches have been proposed to identify m6A sites. METHODS In order to facilitate researchers to select appropriate methods for identifying m6A sites, it is necessary to conduct a comprehensive review and comparison of existing methods. RESULTS Since research works on m6A in Saccharomyces cerevisiae are relatively clear, in this review, we summarized recent progress of computational prediction of m6A sites in S. cerevisiae and assessed the performance of existing computational methods. Finally, future directions of computationally identifying m6A sites are presented. CONCLUSION Taken together, we anticipate that this review will serve as an important guide for computational analysis of m6A modifications.
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Affiliation(s)
- Pengmian Feng
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
| | - Lijing Feng
- School of Sciences, North China University of Science and Technology, Tangshan 063000, China
| | - Chaohui Tang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611730, China
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10
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RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 2021; 11:biom11010076. [PMID: 33430019 PMCID: PMC7826747 DOI: 10.3390/biom11010076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.
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11
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Shetty S, Varshney U. Regulation of translation by one-carbon metabolism in bacteria and eukaryotic organelles. J Biol Chem 2021; 296:100088. [PMID: 33199376 PMCID: PMC7949028 DOI: 10.1074/jbc.rev120.011985] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Protein synthesis is an energetically costly cellular activity. It is therefore important that the process of mRNA translation remains in excellent synchrony with cellular metabolism and its energy reserves. Unregulated translation could lead to the production of incomplete, mistranslated, or misfolded proteins, squandering the energy needed for cellular sustenance and causing cytotoxicity. One-carbon metabolism (OCM), an integral part of cellular intermediary metabolism, produces a number of one-carbon unit intermediates (formyl, methylene, methenyl, methyl). These OCM intermediates are required for the production of amino acids such as methionine and other biomolecules such as purines, thymidylate, and redox regulators. In this review, we discuss how OCM impacts the translation apparatus (composed of ribosome, tRNA, mRNA, and translation factors) and regulates crucial steps in protein synthesis. More specifically, we address how the OCM metabolites regulate the fidelity and rate of translation initiation in bacteria and eukaryotic organelles such as mitochondria. Modulation of the fidelity of translation initiation by OCM opens new avenues to understand alternative translation mechanisms involved in stress tolerance and drug resistance.
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Affiliation(s)
- Sunil Shetty
- Biozentrum, University of Basel, Basel, Switzerland
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India; Jawaharlal Nehru Centre for Advanced Scientific Studies, Jakkur, Bangalore, India.
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12
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Baulin E, Metelev V, Bogdanov A. Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes. Nucleic Acids Res 2020; 48:8675-8685. [PMID: 32687167 PMCID: PMC7470943 DOI: 10.1093/nar/gkaa610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/25/2022] Open
Abstract
Along with nucleobase pairing, base-base stacking interactions are one of the two main types of strong non-covalent interactions that define the unique secondary and tertiary structure of RNA. In this paper we studied two subfamilies of nucleobase-inserted stacking structures: (i) with any base intercalated between neighboring nucleotide residues (base-intercalated element, BIE, i + 1); (ii) with any base wedged into a hydrophobic cavity formed by heterocyclic bases of two nucleotides which are one nucleotide apart in sequence (base-wedged element, BWE, i + 2). We have exploited the growing database of natively folded RNA structures in Protein Data Bank to analyze the distribution and structural role of these motifs in RNA. We found that these structural elements initially found in yeast tRNAPhe are quite widespread among the tertiary structures of various RNAs. These motifs perform diverse roles in RNA 3D structure formation and its maintenance. They contribute to the folding of RNA bulges and loops and participate in long-range interactions of single-stranded stretches within RNA macromolecules. Furthermore, both base-intercalated and base-wedged motifs participate directly or indirectly in the formation of RNA functional centers, which interact with various ligands, antibiotics and proteins.
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Affiliation(s)
- Eugene Baulin
- Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Valeriy Metelev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey Bogdanov
- To whom correspondence should be addressed. Tel: +7 495 9393143; Fax: +7 495 9393181;
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13
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Atdjian C, Coelho D, Iannazzo L, Ethève-Quelquejeu M, Braud E. Synthesis of Triazole-Linked SAM-Adenosine Conjugates: Functionalization of Adenosine at N-1 or N-6 Position without Protecting Groups. Molecules 2020; 25:molecules25143241. [PMID: 32708658 PMCID: PMC7397255 DOI: 10.3390/molecules25143241] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
More than 150 RNA chemical modifications have been identified to date. Among them, methylation of adenosine at the N-6 position (m6A) is crucial for RNA metabolism, stability and other important biological events. In particular, this is the most abundant mark found in mRNA in mammalian cells. The presence of a methyl group at the N-1 position of adenosine (m1A) is mostly found in ncRNA and mRNA and is mainly responsible for stability and translation fidelity. These modifications are installed by m6A and m1A RNA methyltransferases (RNA MTases), respectively. In human, deregulation of m6A RNA MTases activity is associated with many diseases including cancer. To date, the molecular mechanism involved in the methyl transfer, in particular substrate recognition, remains unclear. We report the synthesis of new SAM-adenosine conjugates containing a triazole linker branched at the N-1 or N-6 position of adenosine. Our methodology does not require protecting groups for the functionalization of adenosine at these two positions. The molecules described here were designed as potential bisubstrate analogues for m6A and m1A RNA MTases that could be further employed for structural studies. This is the first report of compounds mimicking the transition state of the methylation reaction catalyzed by m1A RNA MTases.
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14
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Sergeeva O, Sergeev P, Melnikov P, Prikazchikova T, Dontsova O, Zatsepin T. Modification of Adenosine196 by Mettl3 Methyltransferase in the 5'-External Transcribed Spacer of 47S Pre-rRNA Affects rRNA Maturation. Cells 2020; 9:cells9041061. [PMID: 32344536 PMCID: PMC7226171 DOI: 10.3390/cells9041061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023] Open
Abstract
Ribosome biogenesis is among the founding processes in the cell. During the first stages of ribosome biogenesis, polycistronic precursor of ribosomal RNA passes complex multistage maturation after transcription. Quality control of preribosomal RNA (pre-rRNA) processing is precisely regulated by non-ribosomal proteins and structural features of pre-rRNA molecules, including modified nucleotides. However, many participants of rRNA maturation are still unknown or poorly characterized. We report that RNA m6A methyltransferase Mettl3 interacts with the 5' external transcribed spacer (5'ETS) of the 47S rRNA precursor and modifies adenosine 196. We demonstrated that Mettl3 knockdown results in the increase of pre-rRNA processing rates, while intracellular amounts of rRNA processing machinery components (U3, U8, U13, U14, and U17 small nucleolar RNA (snoRNA)and fibrillarin, nucleolin, Xrn2, and rrp9 proteins), rRNA degradation rates, and total amount of mature rRNA in the cell stay unchanged. Increased efficacy of pre-rRNA cleavage at A' and A0 positions led to the decrease of 47S and 45S pre-rRNAs in the cell and increase of mature rRNA amount in the cytoplasm. The newly identified conserved motif DRACH sequence modified by Mettl3 in the 5'-ETS region is found and conserved only in primates, which may suggest participation of m6A196 in quality control of pre-rRNA processing at initial stages demanded by increased complexity of ribosome biogenesis.
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Affiliation(s)
- Olga Sergeeva
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia
- Correspondence: ; Tel.: +79-263-880-865
| | - Philipp Sergeev
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia
| | - Pavel Melnikov
- Serbsky National Medical Research Center for Psychiatry and Narcology, Kropotkinsky Lane 23, 119034 Moscow, Russia
| | | | - Olga Dontsova
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Timofei Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, 121205 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119992 Moscow, Russia
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Qi X, Guan F, Wen Y, Li P, Ma M, Cheng S, Zhang L, Liang C, Cheng B, Zhang F. Integrating genome-wide association study and methylation functional annotation data identified candidate genes and pathways for schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2020; 96:109736. [PMID: 31425724 DOI: 10.1016/j.pnpbp.2019.109736] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 08/07/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Schizophrenia (SCZ) is a severe mental disorder. Both environmental and genetic factors contribute to the development of SCZ. The estimated heritability of SCZ is about 80%. Previous genetic studies of SCZ mainly focused on the genetic variations associated the risk of SCZ. Limited efforts are paid to explore the roles and biological mechanism of nuclear acid methylation implicated in the pathogenesis of SCZ. METHODS A two-stage integrative analysis of SCZ GWAS and nuclear acid methylation functional annotation data (including meQTLs and m6A) was performed in this study. First, the discovery GWAS of SCZ was aligned with genomic meQTLs and m6A annotation data to identify the candidate genes associated with SCZ. Second, another independent replication GWAS dataset of SCZ was applied to validate the discovery results. Furthermore, the functional relevance of identified candidate genes with SCZ were validated by the mRNA expression profiling of SCZ brain tissues. Gene ontology (GO) and pathway enrichment analysis of identified candidate genes was performed by the DAVID tool. RESULTS The two-stage integrative analysis detected 106 meQTLs related candidate genes for SCZ. After comparing with the differentially expressed genes in SCZ brain tissues, 49 overlapped genes were identified for meQTLs, such as ZSCAN12, BTN3A2 and HLA-DQA1. Besides, for meQTLs, 29 SCZ associated pathways and 56 SCZ associated GO terms were detected, such as cell adhesion molecules and asthma. For m6A, 25 candidate genes were detected by the two-stage integrative analysis for SCZ, such as ZSCAN12, HLA-DQA1 and SNX19. Furthermore, 17 of the 25 genes were detected in the mRNA expression profiling of SCZ brain tissues. CONCLUSION This study identified multiple SCZ associated genes and pathways, supporting the implication of nuclear acid methylation in the pathogenesis of SCZ.
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Affiliation(s)
- Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Fanglin Guan
- School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, PR China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, PR China.
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16
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Oerum S, Catala M, Atdjian C, Brachet F, Ponchon L, Barraud P, Iannazzo L, Droogmans L, Braud E, Ethève-Quelquejeu M, Tisné C. Bisubstrate analogues as structural tools to investigate m 6A methyltransferase active sites. RNA Biol 2019; 16:798-808. [PMID: 30879411 PMCID: PMC6546350 DOI: 10.1080/15476286.2019.1589360] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m6A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m6A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m6A RNA MTases. The same analogues cause changes in the melting temperature of the m1A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m6A RNA MTase inhibition should aim to increase selectivity, as well as affinity.
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Affiliation(s)
- Stephanie Oerum
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Marjorie Catala
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Franck Brachet
- Institut de Biologie Physico-Chimique, IBPC, CNRS, Paris, France
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris, France
| | - Pierre Barraud
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), Gosselies, Belgium
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Carine Tisné
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
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17
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Lence T, Paolantoni C, Worpenberg L, Roignant JY. Mechanistic insights into m6A RNA enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:222-229. [DOI: 10.1016/j.bbagrm.2018.10.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/27/2018] [Indexed: 12/09/2022]
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18
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Berlivet S, Scutenaire J, Deragon JM, Bousquet-Antonelli C. Readers of the m 6A epitranscriptomic code. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:329-342. [PMID: 30660758 DOI: 10.1016/j.bbagrm.2018.12.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/20/2018] [Accepted: 12/28/2018] [Indexed: 12/21/2022]
Abstract
N6-methyl adenosine (m6A) is the most prevalent and evolutionarily conserved, modification of polymerase II transcribed RNAs. By post-transcriptionally controlling patterns of gene expression, m6A deposition is crucial for organism reproduction, development and likely stress responses. m6A mostly mediates its effect by recruiting reader proteins that either directly accommodate the modified residue in a hydrophobic pocket formed by their YTH domain, or otherwise have their affinity positively influenced by the presence of m6A. We firstly describe here the evolutionary history, and review known molecular and physiological roles of eukaryote YTH readers. In the second part, we present non YTH-proteins whose roles as m6A readers largely remain to be explored. The diversity and multiplicity of m6A readers together with the possibility to regulate their expression and function in response to various cues, offers a multitude of possible combinations to rapidly and finely tune gene expression patterns and hence cellular plasticity. 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)
- Soizik Berlivet
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jérémy Scutenaire
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France
| | - Jean-Marc Deragon
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France; Institut Universitaire de France (IUF), 1 rue Descartes, 75231 Paris Cedex 05, France
| | - Cécile Bousquet-Antonelli
- LGDP-UMR5096 CNRS, 58 Av Paul Alduy, 66860 Perpignan, France; LGDP-UMR5096, Université de Perpignan, Via Domitia, 58 Av Paul Alduy, 66860 Perpignan, France.
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Abstract
In modern molecular biology, RNA has emerged as a versatile macromolecule capable of mediating an astonishing number of biological functions beyond its role as a transient messenger of genetic information. The recent discovery and functional analyses of new classes of noncoding RNAs (ncRNAs) have revealed their widespread use in many pathways, including several in the nucleus. This Review focuses on the mechanisms by which nuclear ncRNAs directly contribute to the maintenance of genome stability. We discuss how ncRNAs inhibit spurious recombination among repetitive DNA elements, repress mobilization of transposable elements (TEs), template or bridge DNA double-strand breaks (DSBs) during repair, and direct developmentally regulated genome rearrangements in some ciliates. These studies reveal an unexpected repertoire of mechanisms by which ncRNAs contribute to genome stability and even potentially fuel evolution by acting as templates for genome modification.
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20
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Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine. Sci Rep 2017; 7:969. [PMID: 28428565 PMCID: PMC5430550 DOI: 10.1038/s41598-017-01186-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/23/2017] [Indexed: 11/24/2022] Open
Abstract
Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site. One monomer provides the SAM-binding site, whereas the conserved C-terminal tail of the second monomer provides residues essential for catalysis. Our findings elucidate the mechanism by which a small protein dimer assembles a functionally asymmetric architecture.
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Abstract
The recent discovery of reversible mRNA methylation has opened a new realm of post-transcriptional gene regulation in eukaryotes. The identification and functional characterization of proteins that specifically recognize RNA N6-methyladenosine (m6A) unveiled it as a modification that cells utilize to accelerate mRNA metabolism and translation. N6-adenosine methylation directs mRNAs to distinct fates by grouping them for differential processing, translation and decay in processes such as cell differentiation, embryonic development and stress responses. Other mRNA modifications, including N1-methyladenosine (m1A), 5-methylcytosine (m5C) and pseudouridine, together with m6A form the epitranscriptome and collectively code a new layer of information that controls protein synthesis.
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Affiliation(s)
- Boxuan Simen Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Ian A Roundtree
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA
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22
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Jia CZ, Zhang JJ, Gu WZ. RNA-MethylPred: A high-accuracy predictor to identify N6-methyladenosine in RNA. Anal Biochem 2016; 510:72-75. [DOI: 10.1016/j.ab.2016.06.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
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RNAs Containing Modified Nucleotides Fail To Trigger RIG-I Conformational Changes for Innate Immune Signaling. mBio 2016; 7:mBio.00833-16. [PMID: 27651356 PMCID: PMC5030355 DOI: 10.1128/mbio.00833-16] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Invading pathogen nucleic acids are recognized and bound by cytoplasmic (retinoic acid-inducible gene I [RIG-I]-like) and membrane-bound (Toll-like) pattern recognition receptors to activate innate immune signaling. Modified nucleotides, when present in RNA molecules, diminish the magnitude of these signaling responses. However, mechanisms explaining the blunted signaling have not been elucidated. In this study, we used several independent biological assays, including inhibition of virus replication, RIG-I:RNA binding assays, and limited trypsin digestion of RIG-I:RNA complexes, to begin to understand how RNAs containing modified nucleotides avoid or suppress innate immune signaling. The experiments were based on a model innate immune activating RNA molecule, the polyU/UC RNA domain of hepatitis C virus, which was transcribed in vitro with canonical nucleotides or with one of eight modified nucleotides. The approach revealed signature assay responses associated with individual modified nucleotides or classes of modified nucleotides. For example, while both N-6-methyladenosine (m6A) and pseudouridine nucleotides correlate with diminished signaling, RNA containing m6A modifications bound RIG-I poorly, while RNA containing pseudouridine bound RIG-I with high affinity but failed to trigger the canonical RIG-I conformational changes associated with robust signaling. These data advance understanding of RNA-mediated innate immune signaling, with additional relevance for applying nucleotide modifications to RNA therapeutics. The innate immune system provides the first response to virus infections and must distinguish between host and pathogen nucleic acids to mount a protective immune response without activating autoimmune responses. While the presence of nucleotide modifications in RNA is known to correlate with diminished innate immune signaling, the underlying mechanisms have not been explored. The data reported here are important for defining mechanistic details to explain signaling suppression by RNAs containing modified nucleotides. The results suggest that RNAs containing modified nucleotides interrupt signaling at early steps of the RIG-I-like innate immune activation pathway and also that nucleotide modifications with similar chemical structures can be organized into classes that suppress or evade innate immune signaling steps. These data contribute to defining the molecular basis for innate immune signaling suppression by RNAs containing modified nucleotides. The results have important implications for designing therapeutic RNAs that evade innate immune detection.
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