1
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Feng Q, Wang D, Xue T, Lin C, Gao Y, Sun L, Jin Y, Liu D. The role of RNA modification in hepatocellular carcinoma. Front Pharmacol 2022; 13:984453. [PMID: 36120301 PMCID: PMC9479111 DOI: 10.3389/fphar.2022.984453] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/11/2022] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly mortal type of primary liver cancer. Abnormal epigenetic modifications are present in HCC, and RNA modification is dynamic and reversible and is a key post-transcriptional regulator. With the in-depth study of post-transcriptional modifications, RNA modifications are aberrantly expressed in human cancers. Moreover, the regulators of RNA modifications can be used as potential targets for cancer therapy. In RNA modifications, N6-methyladenosine (m6A), N7-methylguanosine (m7G), and 5-methylcytosine (m5C) and their regulators have important regulatory roles in HCC progression and represent potential novel biomarkers for the confirmation of diagnosis and treatment of HCC. This review focuses on RNA modifications in HCC and the roles and mechanisms of m6A, m7G, m5C, N1-methyladenosine (m1A), N3-methylcytosine (m3C), and pseudouridine (ψ) on its development and maintenance. The potential therapeutic strategies of RNA modifications are elaborated for HCC.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Dongxu Wang
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Tianyi Xue
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Chao Lin
- School of Grain Science and Technology, Jilin Business and Technology College, Changchun, China
| | - Yongjian Gao
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Liqun Sun
- Department of Pediatrics, First Hospital of Jilin University, Changchun, China
| | - Ye Jin
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Dianfeng Liu
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Dianfeng Liu,
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2
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Vangaveti S, Ranganathan SV, Agris PF. Physical Chemistry of a Single tRNA-Modified Nucleoside Regulates Decoding of the Synonymous Lysine Wobble Codon and Affects Type 2 Diabetes. J Phys Chem B 2022; 126:1168-1177. [PMID: 35119848 DOI: 10.1021/acs.jpcb.1c09053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The 2-methylthio-modification (ms2-) of N6-threonylcarbonyladenosine (t6A37) at position-37 (ms2t6A37) in tRNAUUULys3 provides the needed stability between the tRNA anticodon and the human insulin mRNA codon AAG during translation, as determined by molecular dynamics simulation. Single-nucleoside polymorphisms of the human gene for the enzyme, Cdkal1 that post-transcriptionally modifies t6A37 to ms2t6A37 in tRNAUUULys3, correlate with type 2 diabetes mellitus. Without the ms2-modification, tRNAUUULys3 is incapable of correctly translating the insulin mRNA AAG codon for lysine at the site of protease cleavage between the A-chain and the C-peptide. By enhancing anticodon/codon cross-strand stacking, the ms2-modification adds stability through van der Waals interactions and dehydration of the ASL loop and cavity of the anticodon/codon minihelix but does not add hydrogen bonding of any consequence. Thus, the modifying enzyme Cdkal1, by adding a crucial ms2-group to tRNAUUULys3-t6A37, facilitates the decoding of the AAG codon and enables human pancreatic islets to correctly translate insulin mRNA.
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Affiliation(s)
- Sweta Vangaveti
- The RNA Institute, University at Albany, Albany, New York 12222, United States
| | - Srivathsan V Ranganathan
- Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon 97210 United States
| | - Paul F Agris
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina 27710 United States
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3
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Díaz-Rullo J, Rodríguez-Valdecantos G, Torres-Rojas F, Cid L, Vargas IT, González B, González-Pastor JE. Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile. Front Microbiol 2021; 12:723874. [PMID: 34367123 PMCID: PMC8343002 DOI: 10.3389/fmicb.2021.723874] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 11/15/2022] Open
Abstract
Perchlorate is an oxidative pollutant toxic to most of terrestrial life by promoting denaturation of macromolecules, oxidative stress, and DNA damage. However, several microorganisms, especially hyperhalophiles, are able to tolerate high levels of this compound. Furthermore, relatively high quantities of perchlorate salts were detected on the Martian surface, and due to its strong hygroscopicity and its ability to substantially decrease the freezing point of water, perchlorate is thought to increase the availability of liquid brine water in hyper-arid and cold environments, such as the Martian regolith. Therefore, perchlorate has been proposed as a compound worth studying to better understanding the habitability of the Martian surface. In the present work, to study the molecular mechanisms of perchlorate resistance, a functional metagenomic approach was used, and for that, a small-insert library was constructed with DNA isolated from microorganisms exposed to perchlorate in sediments of a hypersaline pond in the Atacama Desert, Chile (Salar de Maricunga), one of the regions with the highest levels of perchlorate on Earth. The metagenomic library was hosted in Escherichia coli DH10B strain and exposed to sodium perchlorate. This technique allowed the identification of nine perchlorate-resistant clones and their environmental DNA fragments were sequenced. A total of seventeen ORFs were predicted, individually cloned, and nine of them increased perchlorate resistance when expressed in E. coli DH10B cells. These genes encoded hypothetical conserved proteins of unknown functions and proteins similar to other not previously reported to be involved in perchlorate resistance that were related to different cellular processes such as RNA processing, tRNA modification, DNA protection and repair, metabolism, and protein degradation. Furthermore, these genes also conferred resistance to UV-radiation, 4-nitroquinoline-N-oxide (4-NQO) and/or hydrogen peroxide (H2O2), other stress conditions that induce oxidative stress, and damage in proteins and nucleic acids. Therefore, the novel genes identified will help us to better understand the molecular strategies of microorganisms to survive in the presence of perchlorate and may be used in Mars exploration for creating perchlorate-resistance strains interesting for developing Bioregenerative Life Support Systems (BLSS) based on in situ resource utilization (ISRU).
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Affiliation(s)
- Jorge Díaz-Rullo
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Polytechnic School, University of Alcalá, Alcalá de Henares, Spain
| | - Gustavo Rodríguez-Valdecantos
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
| | - Felipe Torres-Rojas
- Department of Hydraulic and Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis Cid
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
| | - Ignacio T. Vargas
- Department of Hydraulic and Environmental Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Centro de Desarrollo Urbano Sustentable (CEDEUS), Santiago, Chile
| | - Bernardo González
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
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4
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Tagel M, Ilves H, Leppik M, Jürgenstein K, Remme J, Kivisaar M. Pseudouridines of tRNA Anticodon Stem-Loop Have Unexpected Role in Mutagenesis in Pseudomonas sp. Microorganisms 2020; 9:microorganisms9010025. [PMID: 33374637 PMCID: PMC7822408 DOI: 10.3390/microorganisms9010025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudouridines are known to be important for optimal translation. In this study we demonstrate an unexpected link between pseudouridylation of tRNA and mutation frequency in Pseudomonas species. We observed that the lack of pseudouridylation activity of pseudouridine synthases TruA or RluA elevates the mutation frequency in Pseudomonas putida 3 to 5-fold. The absence of TruA but not RluA elevates mutation frequency also in Pseudomonas aeruginosa. Based on the results of genetic studies and analysis of proteome data, the mutagenic effect of the pseudouridylation deficiency cannot be ascribed to the involvement of error-prone DNA polymerases or malfunctioning of DNA repair pathways. In addition, although the deficiency in TruA-dependent pseudouridylation made P. putida cells more sensitive to antimicrobial compounds that may cause oxidative stress and DNA damage, cultivation of bacteria in the presence of reactive oxygen species (ROS)-scavenging compounds did not eliminate the mutator phenotype. Thus, the elevated mutation frequency in the absence of tRNA pseudouridylation could be the result of a more specific response or, alternatively, of a cumulative effect of several small effects disturbing distinct cellular functions, which remain undetected when studied independently. This work suggests that pseudouridines link the translation machinery to mutation frequency.
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Affiliation(s)
- Mari Tagel
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | | | | | | | - Jaanus Remme
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
| | - Maia Kivisaar
- Correspondence: (M.T.); (J.R.); (M.K.); Tel.: +372-737-5036 (M.K.)
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5
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Carpentier P, Leprêtre C, Basset C, Douki T, Torelli S, Duarte V, Hamdane D, Fontecave M, Atta M. Structural, biochemical and functional analyses of tRNA-monooxygenase enzyme MiaE from Pseudomonas putida provide insights into tRNA/MiaE interaction. Nucleic Acids Res 2020; 48:9918-9930. [PMID: 32785618 PMCID: PMC7515727 DOI: 10.1093/nar/gkaa667] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022] Open
Abstract
MiaE (2-methylthio-N6-isopentenyl-adenosine37-tRNA monooxygenase) is a unique non-heme diiron enzyme that catalyzes the O2-dependent post-transcriptional allylic hydroxylation of a hypermodified nucleotide 2-methylthio-N6-isopentenyl-adenosine (ms2i6A37) at position 37 of selected tRNA molecules to produce 2-methylthio-N6-4-hydroxyisopentenyl-adenosine (ms2io6A37). Here, we report the in vivo activity, biochemical, spectroscopic characterization and X-ray crystal structure of MiaE from Pseudomonas putida. The investigation demonstrates that the putative pp-2188 gene encodes a MiaE enzyme. The structure shows that Pp-MiaE consists of a catalytic diiron(III) domain with a four alpha-helix bundle fold. A docking model of Pp-MiaE in complex with tRNA, combined with site directed mutagenesis and in vivo activity shed light on the importance of an additional linker region for substrate tRNA recognition. Finally, krypton-pressurized Pp-MiaE experiments, revealed the presence of defined O2 site along a conserved hydrophobic tunnel leading to the diiron active center.
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Affiliation(s)
- Philippe Carpentier
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Chloé Leprêtre
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Christian Basset
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Thierry Douki
- Univ. Grenoble Alpes, CEA, CNRS, SyMMES, F-38000, 17 avenue des martyrs Grenoble, France
| | - Stéphane Torelli
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Victor Duarte
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, UMR CNRS 8229, Collège de France-CNRS-Sorbonne Université, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR CNRS 8229, Collège de France-CNRS-Sorbonne Université, PSL Research University, 11 Place Marcelin Berthelot, 75005 Paris, France
| | - Mohamed Atta
- Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR 5249, 17 avenue des martyrs, Grenoble, France
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6
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A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine. J Mol Biol 2020; 432:913-929. [PMID: 31945376 DOI: 10.1016/j.jmb.2019.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 11/25/2019] [Accepted: 12/05/2019] [Indexed: 11/20/2022]
Abstract
Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNAArg isoacceptors. The anticodon stem and loop (ASL) domains of tRNAArg1 and tRNAArg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I34) and 37 (m2A37). tRNAArg1 is also modified from cytidine to 2-thiocytidine at position 32 (s2C32). The s2C32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s2C32 for C32 in the Saccharomyces cerevisiae tRNAIleIAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s2C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASLArg1ICG and ASLArg2ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C32-A38 cross-loop interaction but failed to fully explain the means by which s2C32 restricts I34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C32-A38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.
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7
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Computational and NMR studies of RNA duplexes with an internal pseudouridine-adenosine base pair. Sci Rep 2019; 9:16278. [PMID: 31700156 PMCID: PMC6838189 DOI: 10.1038/s41598-019-52637-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/03/2019] [Indexed: 01/28/2023] Open
Abstract
Pseudouridine (Ψ) is the most common chemical modification present in RNA. In general, Ψ increases the thermodynamic stability of RNA. However, the degree of stabilization depends on the sequence and structural context. To explain experimentally observed sequence dependence of the effect of Ψ on the thermodynamic stability of RNA duplexes, we investigated the structure, dynamics and hydration of RNA duplexes with an internal Ψ-A base pair in different nearest-neighbor sequence contexts. The structures of two RNA duplexes containing 5′-GΨC/3′-CAG and 5′-CΨG/3′-GAC motifs were determined using NMR spectroscopy. To gain insight into the effect of Ψ on duplex dynamics and hydration, we performed molecular dynamics (MD) simulations of RNA duplexes with 5′-GΨC/3′-CAG, 5′-CΨG/3′-GAC, 5′-AΨU/3′-UAA and 5′-UΨA/3′-AAU motifs and their unmodified counterparts. Our results showed a subtle impact from Ψ modification on the structure and dynamics of the RNA duplexes studied. The MD simulations confirmed the change in hydration pattern when U is replaced with Ψ. Quantum chemical calculations showed that the replacement of U with Ψ affected the intrinsic stacking energies at the base pair steps depending on the sequence context. The calculated intrinsic stacking energies help to explain the experimentally observed sequence dependent changes in the duplex stability from Ψ modification.
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8
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Castillo H, Li X, Schilkey F, Smith GB. Transcriptome analysis reveals a stress response of Shewanella oneidensis deprived of background levels of ionizing radiation. PLoS One 2018; 13:e0196472. [PMID: 29768440 PMCID: PMC5955497 DOI: 10.1371/journal.pone.0196472] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/13/2018] [Indexed: 11/21/2022] Open
Abstract
Natural ionizing background radiation has exerted a constant pressure on organisms since the first forms of life appeared on Earth, so that cells have developed molecular mechanisms to avoid or repair damages caused directly by radiation or indirectly by radiation-induced reactive oxygen species (ROS). In the present study, we investigated the transcriptional effect of depriving Shewanella oneidensis cultures of background levels of radiation by growing the cells in a mine 655 m underground, thus reducing the dose rate from 72.1 to 0.9 nGy h-1 from control to treatment, respectively. RNASeq transcriptome analysis showed the differential expression of 4.6 and 7.6% of the S. oneidensis genome during early- and late-exponential phases of growth, respectively. The greatest change observed in the treatment was the downregulation of ribosomal proteins (21% of all annotated ribosomal protein genes during early- and 14% during late-exponential) and tRNA genes (14% of all annotated tRNA genes in early-exponential), indicating a marked decrease in protein translation. Other significant changes were the upregulation of membrane transporters, implying an increase in the traffic of substrates across the cell membrane, as well as the up and downregulation of genes related to respiration, which could be interpreted as a response to insufficient oxidants in the cells. In other reports, there is evidence in multiple species that some ROS not just lead to oxidative stress, but act as signaling molecules to control cellular metabolism at the transcriptional level. Consistent with these reports, several genes involved in the metabolism of carbon and biosynthesis of amino acids were also regulated, lending support to the idea of a wide metabolic response. Our results indicate that S. oneidensis is sensitive to the withdrawal of background levels of ionizing radiation and suggest that a transcriptional response is required to maintain homeostasis and retain normal growth.
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Affiliation(s)
- Hugo Castillo
- Department of Biology, New Mexico State University, Las Cruces, NM, United States of America
| | - Xiaoping Li
- Department of Botany and Plant Pathology, Oregon State University, Hermiston, OR, United States of America
| | - Faye Schilkey
- National Center for Genome Resources, Santa Fe, NM, United States of America
| | - Geoffrey B Smith
- Department of Biology, New Mexico State University, Las Cruces, NM, United States of America
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9
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Nakamoto MA, Lovejoy AF, Cygan AM, Boothroyd JC. mRNA pseudouridylation affects RNA metabolism in the parasite Toxoplasma gondii. RNA (NEW YORK, N.Y.) 2017; 23:1834-1849. [PMID: 28851751 PMCID: PMC5689004 DOI: 10.1261/rna.062794.117] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/18/2017] [Indexed: 05/09/2023]
Abstract
RNA contains over 100 modified nucleotides that are created post-transcriptionally, among which pseudouridine (Ψ) is one of the most abundant. Although it was one of the first modifications discovered, the biological role of this modification is still not fully understood. Recently, we reported that a pseudouridine synthase (TgPUS1) is necessary for differentiation of the single-celled eukaryotic parasite Toxoplasma gondii from active to chronic infection. To better understand the biological role of pseudouridylation, we report here gel-based and deep-sequencing methods to identify TgPUS1-dependent Ψ's in Toxoplasma RNA, and the use of TgPUS1 mutants to examine the effect of this modification on mRNAs. In addition to identifying conserved sites of pseudouridylation in Toxoplasma rRNA, tRNA, and snRNA, we also report extensive pseudouridylation of Toxoplasma mRNAs, with the Ψ's being relatively depleted in the 3'-UTR but enriched at position 1 of codons. We show that many Ψ's in tRNA and mRNA are dependent on the action of TgPUS1 and that TgPUS1-dependent mRNA Ψ's are enriched in developmentally regulated transcripts. RNA-seq data obtained from wild-type and TgPUS1-mutant parasites shows that genes containing a TgPUS1-dependent Ψ are relatively more abundant in mutant parasites, while pulse/chase labeling of RNA with 4-thiouracil shows that mRNAs containing TgPUS1-dependent Ψ have a modest but statistically significant increase in half-life in the mutant parasites. These data are some of the first evidence suggesting that mRNA Ψ's play an important biological role.
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Affiliation(s)
- Margaret A Nakamoto
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexander F Lovejoy
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alicja M Cygan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John C Boothroyd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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10
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Agris PF, Eruysal ER, Narendran A, Väre VYP, Vangaveti S, Ranganathan SV. Celebrating wobble decoding: Half a century and still much is new. RNA Biol 2017; 15:537-553. [PMID: 28812932 PMCID: PMC6103715 DOI: 10.1080/15476286.2017.1356562] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022] Open
Abstract
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.
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Affiliation(s)
- Paul F. Agris
- The RNA Institute, State University of New York, Albany, NY, USA
- Department of Biology, State University of New York, Albany, NY, USA
- Department of Chemistry, State University of New York, Albany, NY, USA
| | - Emily R. Eruysal
- Department of Biology, State University of New York, Albany, NY, USA
| | - Amithi Narendran
- Department of Biology, State University of New York, Albany, NY, USA
| | - Ville Y. P. Väre
- Department of Biology, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, State University of New York, Albany, NY, USA
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11
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Abstract
All types of nucleic acids in cells undergo naturally occurring chemical modifications, including DNA, rRNA, mRNA, snRNA, and most prominently tRNA. Over 100 different modifications have been described and every position in the purine and pyrimidine bases can be modified; often the sugar is also modified [1]. In tRNA, the function of modifications varies; some modulate global and/or local RNA structure, and others directly impact decoding and may be essential for viability. Whichever the case, the overall importance of modifications is highlighted by both their evolutionary conservation and the fact that organisms use a substantial portion of their genomes to encode modification enzymes, far exceeding what is needed for the de novo synthesis of the canonical nucleotides themselves [2]. Although some modifications occur at exactly the same nucleotide position in tRNAs from the three domains of life, many can be found at various positions in a particular tRNA and their location may vary between and within different tRNAs. With this wild array of chemical diversity and substrate specificities, one of the big challenges in the tRNA modification field has been to better understand at a molecular level the modes of substrate recognition by the different modification enzymes; in this realm RNA binding rests at the heart of the problem. This chapter will focus on several examples of modification enzymes where their mode of RNA binding is well understood; from these, we will try to draw general conclusions and highlight growing themes that may be applicable to the RNA modification field at large.
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12
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Igloi GL, Leisinger AK. Identity elements for the aminoacylation of metazoan mitochondrial tRNA(Arg) have been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment. RNA Biol 2015; 11:1313-23. [PMID: 25603118 PMCID: PMC4615739 DOI: 10.1080/15476286.2014.996094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Eumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNA(Ser)UCU. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNAArg in which the major identity elements permit the arginylation of all 5 encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNAArgUCG structural variants. The established identity elements are sufficient to maintain the fidelity of tRNASerUCU reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNAArgUCG by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the 2 encoded tRNAArgUCG/UCU isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.
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Affiliation(s)
- Gabor L Igloi
- a Institute of Biology III ; University of Freiburg ; Freiburg , Germany
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13
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Spenkuch F, Motorin Y, Helm M. Pseudouridine: still mysterious, but never a fake (uridine)! RNA Biol 2014; 11:1540-54. [PMID: 25616362 PMCID: PMC4615568 DOI: 10.4161/15476286.2014.992278] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 01/15/2023] Open
Abstract
Pseudouridine (Ψ) is the most abundant of >150 nucleoside modifications in RNA. Although Ψ was discovered as the first modified nucleoside more than half a century ago, neither the enzymatic mechanism of its formation, nor the function of this modification are fully elucidated. We present the consistent picture of Ψ synthases, their substrates and their substrate positions in model organisms of all domains of life as it has emerged to date and point out the challenges that remain concerning higher eukaryotes and the elucidation of the enzymatic mechanism.
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MESH Headings
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Humans
- Intramolecular Transferases/genetics
- Intramolecular Transferases/metabolism
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Nucleic Acid Conformation
- Pseudouridine/metabolism
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Uridine/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Felix Spenkuch
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University of Mainz; Mainz, Germany
| | - Yuri Motorin
- Laboratoire IMoPA; Ingénierie Moléculaire et Physiopathologie Articulaire; BioPôle de l'Université de Lorraine; Campus Biologie-Santé; Faculté de Médecine; Vandoeuvre-les-Nancy Cedex, France
| | - Mark Helm
- Institute of Pharmacy and Biochemistry; Johannes Gutenberg-University of Mainz; Mainz, Germany
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14
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Jiang J, Aduri R, Chow CS, SantaLucia J. Structure modulation of helix 69 from Escherichia coli 23S ribosomal RNA by pseudouridylations. Nucleic Acids Res 2013; 42:3971-81. [PMID: 24371282 PMCID: PMC3973299 DOI: 10.1093/nar/gkt1329] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Helix 69 (H69) is a 19-nt stem-loop region from the large subunit ribosomal RNA. Three pseudouridine (Ψ) modifications clustered in H69 are conserved across phylogeny and known to affect ribosome function. To explore the effects of Ψ on the conformations of Escherichia coli H69 in solution, nuclear magnetic resonance spectroscopy was used to reveal the structural differences between H69 with (ΨΨΨ) and without (UUU) Ψ modifications. Comparison of the two structures shows that H69 ΨΨΨ has the following unique features: (i) the loop region is closed by a Watson-Crick base pair between Ψ1911 and A1919, which is potentially reinforced by interactions involving Ψ1911N1H and (ii) Ψ modifications at loop residues 1915 and 1917 promote base stacking from Ψ1915 to A1918. In contrast, the H69 UUU loop region, which lacks Ψ modifications, is less organized. Structure modulation by Ψ leads to alteration in conformational behavior of the 5' half of the H69 loop region, observed as broadening of C1914 non-exchangeable base proton resonances in the H69 ΨΨΨ nuclear magnetic resonance spectra, and plays an important biological role in establishing the ribosomal intersubunit bridge B2a and mediating translational fidelity.
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Affiliation(s)
- Jun Jiang
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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15
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Chang AT, Nikonowicz EP. Solution nuclear magnetic resonance analyses of the anticodon arms of proteinogenic and nonproteinogenic tRNA(Gly). Biochemistry 2012; 51:3662-74. [PMID: 22468768 DOI: 10.1021/bi201900j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Although the fate of most tRNA molecules in the cell is aminoacylation and delivery to the ribosome, some tRNAs are destined to fulfill other functional roles. In addition to their central role in translation, tRNA molecules participate in processes such as regulation of gene expression, bacterial cell wall biosynthesis, viral replication, antibiotic biosynthesis, and suppression of alternative splicing. In bacteria, glycyl-tRNA molecules with anticodon sequences GCC and UCC exhibit multiple extratranslational functions, including transcriptional regulation and cell wall biosynthesis. We have determined the high-resolution structures of three glycyl-tRNA anticodon arms with anticodon sequences GCC and UCC. Two of the tRNA molecules are proteinogenic (tRNA(Gly,GCC) and tRNA(Gly,UCC)), and the third is nonproteinogenic (np-tRNA(Gly,UCC)) and participates in cell wall biosynthesis. The UV-monitored thermal melting curves show that the anticodon arm of tRNA(Gly,UCC) with a loop-closing C-A(+) base pair melts at a temperature 10 °C lower than those of tRNA(Gly,GCC) and np-tRNA(Gly,UCC). U-A and C-G pairs close the loops of the latter two molecules and enhance stem stability. Mg(2+) stabilizes the tRNA(Gly,UCC) anticodon arm and reduces the T(m) differential. The structures of the three tRNA(Gly) anticodon arms exhibit small differences among one another, but none of them form the classical U-turn motif. The anticodon loop of tRNA(Gly,GCC) becomes more dynamic and disordered in the presence of multivalent cations, whereas metal ion coordination in the anticodon loops of tRNA(Gly,UCC) and np-tRNA(Gly,UCC) establishes conformational homogeneity. The conformational similarity of the molecules is greater than their functional differences might suggest. Because aminoacylation of full-length tRNA molecules is accomplished by one tRNA synthetase, the similar structural context of the loop may facilitate efficient recognition of each of the anticodon sequences.
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Affiliation(s)
- Andrew T Chang
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251-1892, United States
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16
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Cantara WA, Bilbille Y, Kim J, Kaiser R, Leszczyńska G, Malkiewicz A, Agris PF. Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2. J Mol Biol 2012; 416:579-97. [DOI: 10.1016/j.jmb.2011.12.054] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 12/13/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
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17
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Denmon AP, Wang J, Nikonowicz EP. Conformation effects of base modification on the anticodon stem-loop of Bacillus subtilis tRNA(Tyr). J Mol Biol 2011; 412:285-303. [PMID: 21782828 DOI: 10.1016/j.jmb.2011.07.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 07/05/2011] [Accepted: 07/08/2011] [Indexed: 10/17/2022]
Abstract
tRNA molecules contain 93 chemically unique nucleotide base modifications that expand the chemical and biophysical diversity of RNA and contribute to the overall fitness of the cell. Nucleotide modifications of tRNA confer fidelity and efficiency to translation and are important in tRNA-dependent RNA-mediated regulatory processes. The three-dimensional structure of the anticodon is crucial to tRNA-mRNA specificity, and the diverse modifications of nucleotide bases in the anticodon region modulate this specificity. We have determined the solution structures and thermodynamic properties of Bacillus subtilis tRNA(Tyr) anticodon arms containing the natural base modifications N(6)-dimethylallyl adenine (i(6)A(37)) and pseudouridine (ψ(39)). UV melting and differential scanning calorimetry indicate that the modifications stabilize the stem and may enhance base stacking in the loop. The i(6)A(37) modification disrupts the hydrogen bond network of the unmodified anticodon loop including a C(32)-A(38)(+) base pair and an A(37)-U(33) base-base interaction. Although the i(6)A(37) modification increases the dynamic nature of the loop nucleotides, metal ion coordination reestablishes conformational homogeneity. Interestingly, the i(6)A(37) modification and Mg(2+) are sufficient to promote the U-turn fold of the anticodon loop of Escherichia coli tRNA(Phe), but these elements do not result in this signature feature of the anticodon loop in tRNA(Tyr).
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Affiliation(s)
- Andria P Denmon
- Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA
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18
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Kim NK, Theimer CA, Mitchell JR, Collins K, Feigon J. Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA. Nucleic Acids Res 2010; 38:6746-56. [PMID: 20554853 PMCID: PMC2965242 DOI: 10.1093/nar/gkq525] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Telomerase extends the 3'-ends of linear chromosomes by adding conserved telomeric DNA repeats and is essential for cell proliferation and genomic stability. Telomerases from all organisms contain a telomerase reverse transcriptase and a telomerase RNA (TER), which together provide the minimal functional elements for catalytic activity in vitro. The RNA component of many functional ribonucleoproteins contains modified nucleotides, including conserved pseudouridines (Ψs) that can have subtle effects on structure and activity. We have identified potential Ψ modification sites in human TER. Two of the predicted Ψs are located in the loop of the essential P6.1 hairpin from the CR4-CR5 domain that is critical for telomerase catalytic activity. We investigated the effect of P6.1 pseudouridylation on its solution NMR structure, thermodynamic stability of folding and telomerase activation in vitro. The pseudouridylated P6.1 has a significantly different loop structure and increase in stability compared to the unmodified P6.1. The extent of loop nucleotide interaction with adjacent residues more closely parallels the extent of loop nucleotide evolutionary sequence conservation in the Ψ-modified P6.1 structure. Pseudouridine-modification of P6.1 slightly attenuates telomerase activity but slightly increases processivity in vitro. Our results suggest that Ψs could have a subtle influence on human telomerase activity via impact on TER-TERT or TER-TER interactions.
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Affiliation(s)
- Nak-Kyoon Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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19
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Byrne RT, Konevega AL, Rodnina MV, Antson AA. The crystal structure of unmodified tRNAPhe from Escherichia coli. Nucleic Acids Res 2010; 38:4154-62. [PMID: 20203084 PMCID: PMC2896525 DOI: 10.1093/nar/gkq133] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report the crystal structure of unmodified tRNAPhe from Escherichia coli at a resolution of 3 Å. We show that in the absence of modifications the overall fold of the tRNA is essentially the same as that of mature tRNA. However, there are a number of significant structural differences, such as rearrangements in a triplet base pair and a widened angle between the acceptor and anticodon stems. Contrary to previous observations, the anticodon adopts the same conformation as seen in mature tRNA.
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Affiliation(s)
- Robert T Byrne
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, North Yorkshire, YO10 5YW, UK
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20
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Baudin-Baillieu A, Fabret C, Liang XH, Piekna-Przybylska D, Fournier MJ, Rousset JP. Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy. Nucleic Acids Res 2010; 37:7665-77. [PMID: 19820108 PMCID: PMC2794176 DOI: 10.1093/nar/gkp816] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Important regions of rRNA are rich in nucleotide modifications that can have strong effects on ribosome biogenesis and translation efficiency. Here, we examine the influence of pseudouridylation and 2′-O-methylation on translation accuracy in yeast, by deleting the corresponding guide snoRNAs. The regions analyzed were: the decoding centre (eight modifications), and two intersubunit bridge domains—the A-site finger and Helix 69 (six and five modifications). Results show that a number of modifications influence accuracy with effects ranging from 0.3- to 2.4-fold of wild-type activity. Blocking subsets of modifications, especially from the decoding region, impairs stop codon termination and reading frame maintenance. Unexpectedly, several Helix 69 mutants possess ribosomes with increased fidelity. Consistent with strong positional and synergistic effects is the finding that single deletions can have a more pronounced phenotype than multiple deficiencies in the same region. Altogether, the results demonstrate that rRNA modifications have significant roles in translation accuracy.
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21
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Liang XH, Liu Q, Fournier MJ. rRNA modifications in an intersubunit bridge of the ribosome strongly affect both ribosome biogenesis and activity. Mol Cell 2008; 28:965-77. [PMID: 18158895 DOI: 10.1016/j.molcel.2007.10.012] [Citation(s) in RCA: 169] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 07/28/2007] [Accepted: 10/09/2007] [Indexed: 10/21/2022]
Abstract
The presence of nucleotide modifications in rRNA has been known for nearly 40 years; however, information about their roles is sparse. Here, we describe the consequences of depleting modifications from an intersubunit bridge (helix 69) of the ribosomal large subunit in yeast. Helix 69 interacts with both A and P site tRNAs and contains five modifications. Blocking one to two modifications has no apparent effect on cell growth, whereas loss of three to five modifications impairs growth and causes the broadest defects observed thus far for modification loss in any ribosome region. Major effects include the following: (1) reduced amino acid incorporation rates in vivo (25%-60%); (2) increased stop codon readthrough activity; (3) increased sensitivity to ribosome-based antibiotics; (4) reduced rRNA levels (20%-50%), due mainly to faster turnover; and (5) altered rRNA structure in the ribosome. Taken together, the results indicate that this subset of rRNA modifications can influence both ribosome synthesis and function and in synergistic ways.
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Affiliation(s)
- Xue-hai Liang
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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22
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Vaidyanathan PP, Deutscher MP, Malhotra A. RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA. RNA (NEW YORK, N.Y.) 2007; 13:1868-76. [PMID: 17872507 PMCID: PMC2040082 DOI: 10.1261/rna.711207] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Pseudouridine modifications in helix 69 (H69) of 23S ribosomal RNA are highly conserved among all organisms. H69 associates with helix 44 of 16S rRNA to form bridge B2a, which plays a vital role in bridging the two ribosomal subunits and stabilizing the ribosome. The three pseudouridines in H69 were shown earlier to play an important role in 50S subunit assembly and in its association with the 30S subunit. In Escherichia coli, these three modifications are made by the pseudouridine synthase, RluD. Previous work showed that RluD is required for normal ribosomal assembly and function, and that it is the only pseudouridine synthase required for normal growth in E. coli. Here, we show that RluD is far more efficient in modifying H69 in structured 50S subunits, compared to free or synthetic 23S rRNA. Based on this observation, we suggest that pseudouridine modifications in H69 are made late in the assembly of 23S rRNA into mature 50S subunits. This is the first reported observation of a pseudouridine synthase being able to modify a highly structured ribonucleoprotein particle, and it may be an important late step in the maturation of 50S ribosomal subunits.
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Affiliation(s)
- Pavanapuresan P Vaidyanathan
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33101-6129, USA
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23
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Tworowska I, Nikonowicz EP. Base pairing within the psi32,psi39-modified anticodon arm of Escherichia coli tRNA(Phe). J Am Chem Soc 2007; 128:15570-1. [PMID: 17147349 DOI: 10.1021/ja0659368] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The base-base hydrogen bond interactions of the psi32,psi39-modified anticodon arm of Escherichia coli tRNAPhe have been investigated using heteronuclear NMR spectroscopy. psi32 and psi39 were enzymatically introduced into a [13C,15N]-isotopically enriched RNA sequence corresponding to the tRNAPhe anticodon arm. Both the psi32-A38 and A31-psi39 nucleotide pairs form Watson-Crick base pairing schemes and the anticodon nucleotides adopt a triloop conformation. Similar effects were observed previously with D2-isopentenyl modification of the A37 N6 that also is native to the tRNAPhe anticodon arm. These results demonstrate that the individual modifications are not sufficient to produce the 32-38 bifurcated hydrogen bond or the U-turn motifs that are observed in crystal structures of tRNAs and tRNA-protein complexes. Thus the formation of these conserved structural features in solution likely require the synergistic interaction of multiple modifications.
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Affiliation(s)
- Izabela Tworowska
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251, USA
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24
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Hoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferré-D'Amaré AR. Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure. Mol Cell 2007; 24:535-45. [PMID: 17188032 DOI: 10.1016/j.molcel.2006.09.017] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2006] [Revised: 09/04/2006] [Accepted: 09/22/2006] [Indexed: 11/25/2022]
Abstract
RluA is a dual-specificity enzyme responsible for pseudouridylating 23S rRNA and several tRNAs. The 2.05 A resolution structure of RluA bound to a substrate RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic reorganization of the RNA. Instead of adopting its canonical U turn conformation, the anticodon loop folds into a new structure with a reverse-Hoogsteen base pair and three flipped-out nucleotides. Sequence conservation, the cocrystal structure, and the results of structure-guided mutagenesis suggest that RluA recognizes its substrates indirectly by probing RNA loops for their ability to adopt the reorganized fold. The planar, cationic side chain of an arginine intercalates between the reverse-Hoogsteen base pair and the bottom pair of the anticodon stem, flipping the nucleotide to be modified into the active site of RluA. Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping.
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Affiliation(s)
- Charmaine Hoang
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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25
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Jones C, Spencer AC, Hsu JL, Spremulli L, Martinis SA, DeRider M, Agris PF. A counterintuitive Mg2+-dependent and modification-assisted functional folding of mitochondrial tRNAs. J Mol Biol 2006; 362:771-86. [PMID: 16949614 PMCID: PMC1781928 DOI: 10.1016/j.jmb.2006.07.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 07/05/2006] [Accepted: 07/19/2006] [Indexed: 10/24/2022]
Abstract
Mitochondrial tRNAs (mtRNAs) often lack domains and posttranscriptional modifications that are found in cytoplasmic tRNAs. These structural and chemical elements normally stabilize the folding of cytoplasmic tRNAs into canonical structures that are competent for aminoacylation and translation. For example, the dihydrouridine (D) stem and loop domain is involved in the tertiary structure of cytoplasmic tRNAs through hydrogen bonds and a Mg2+ bridge to the ribothymidine (T) stem and loop domain. These interactions are often absent in mtRNA because the D-domain is truncated or missing. Using gel mobility shift analyses, UV, circular dichroism and NMR spectroscopies and aminoacylation assays, we have investigated the functional folding interactions of chemically synthesized and site-specifically modified mitochondrial and cytoplasmic tRNAs. We found that Mg2+ is critical for folding of the truncated D-domain of bovine mtRNAMet with the tRNA's T-domain. Contrary to the expectation that Mg2+ stabilizes RNA folding, the mtRNAMet D-domain structure was unfolded and relaxed, rather than stabilized in the presence of Mg2+. Because the D-domain is transcribed prior to the T-domain, we conclude that Mg2+ prevents misfolding of the 5'-half of bovine mtRNAMet facilitating its correct interaction with the T-domain. The interaction of the mtRNAMet D-domain with the T-domain was enhanced by a pseudouridine located in either the D or T-domains compared to that of the unmodified RNAs (Kd=25.3, 24.6 and 44.4 microM, respectively). Mg2+ also affected the folding interaction of a yeast mtRNALeu1, but had minimal effect on the folding of an Escherichia coli cytoplasmic tRNALeu. The D-domain modification, dihydrouridine, facilitated mtRNALeu folding. These data indicate that conserved modifications assist and stabilize the formation of the functional mtRNA tertiary structure.
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Affiliation(s)
- Christopher Jones
- Department of Structural and Molecular Biology, 128 Polk Hall, Campus Box 7622, North Carolina State University, Raleigh, NC 27695-7622
| | - Angela C. Spencer
- Department of Chemistry, Campus Box 3290, Venable and Kenan Laboratories, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290
| | - Jennifer L. Hsu
- Department of Biochemistry, 419 Roger Adams Laboratory, Box B-4, 600 S. Mathews Ave., University of Illinois at Urbana-Champaign, Urbana, Il 61801
| | - Linda Spremulli
- Department of Chemistry, Campus Box 3290, Venable and Kenan Laboratories, University of North Carolina-Chapel Hill, Chapel Hill, NC 27599-3290
| | - Susan A. Martinis
- Department of Biochemistry, 419 Roger Adams Laboratory, Box B-4, 600 S. Mathews Ave., University of Illinois at Urbana-Champaign, Urbana, Il 61801
| | - Michele DeRider
- Department of Structural and Molecular Biology, 128 Polk Hall, Campus Box 7622, North Carolina State University, Raleigh, NC 27695-7622
| | - Paul F. Agris
- Department of Structural and Molecular Biology, 128 Polk Hall, Campus Box 7622, North Carolina State University, Raleigh, NC 27695-7622
- Corresponding author; E-mail address of corresponding author:
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