1
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.31.565030. [PMID: 37961685 PMCID: PMC10635034 DOI: 10.1101/2023.10.31.565030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions - Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueEs secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of one gene, one enzyme, one function, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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2
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. PLoS Genet 2024; 20:e1011287. [PMID: 38768229 PMCID: PMC11142719 DOI: 10.1371/journal.pgen.1011287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/31/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint residues in QueE that contribute distinctly to each of its functions-Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE's secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of "one gene, one enzyme, one function", which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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Affiliation(s)
- Samuel A. Adeleye
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
| | - Srujana S. Yadavalli
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
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3
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Michael FS, Hamouda MB, Stupak J, Li J, Pearson A, Sauvageau J. Identification of glycosylated nucleosides in small synthetic glyco-RNAs. Chembiochem 2024; 25:e202300784. [PMID: 38116890 DOI: 10.1002/cbic.202300784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Recently, the post-transcriptional modification of RNA with N-glycans was reported, changing the paradigm that RNAs are not commonly N-glycosylated. Moreover, glycan modifications of RNA are investigated for therapeutic targeting purposes. But the glyco-RNA field is in its infancy with many challenges to overcome. One question is how to accurately characterize glycosylated RNA constructs. Thus, we generated glycosylated forms of Y5 RNA mimics, a short non-coding RNA. The simple glycans lactose and sialyllactose were attached to the RNA backbone using azide-alkyne cycloadditions. Using nuclease digestion followed by LC-MS, we confirmed the presence of the glycosylated nucleosides, and characterized the chemical linkage. Next, we probed if glycosylation would affect the cellular response to Y5 RNA. We treated human foreskin fibroblasts in culture with the generated compounds. Key transcripts in the innate immune response were quantified by RT-qPCR. We found that under our experimental conditions, exposure of cells to the Y5 RNA did not trigger an interferon response, and glycosylation of this RNA did not have an impact. Thus, we have identified a successful approach to chemically characterize synthetic glyco-RNAs, which will be critical for further studies to elucidate how the presence of complex glycans on RNA affects the cellular response.
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Affiliation(s)
- Frank St Michael
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Maha Ben Hamouda
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531, boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Jacek Stupak
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Jianjun Li
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Angela Pearson
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531, boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Janelle Sauvageau
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
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4
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Zhao X, Ma D, Ishiguro K, Saito H, Akichika S, Matsuzawa I, Mito M, Irie T, Ishibashi K, Wakabayashi K, Sakaguchi Y, Yokoyama T, Mishima Y, Shirouzu M, Iwasaki S, Suzuki T, Suzuki T. Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. Cell 2023; 186:5517-5535.e24. [PMID: 37992713 DOI: 10.1016/j.cell.2023.10.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 08/14/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates.
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Affiliation(s)
- Xuewei Zhao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ding Ma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kensuke Ishiguro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Hironori Saito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Shinichiro Akichika
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Ikuya Matsuzawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Mari Mito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toru Irie
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kota Ishibashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Kimi Wakabayashi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takeshi Yokoyama
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Yuichiro Mishima
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto 603-8555, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan.
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5
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Pichler A, Hillmeier M, Heiss M, Peev E, Xefteris S, Steigenberger B, Thoma I, Müller M, Borsò M, Imhof A, Carell T. Synthesis and Structure Elucidation of Glutamyl-Queuosine. J Am Chem Soc 2023; 145:25528-25532. [PMID: 37967838 PMCID: PMC10690763 DOI: 10.1021/jacs.3c10075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/17/2023]
Abstract
Queuosine is one of the most complex hypermodified RNA nucleosides found in the Wobble position of tRNAs. In addition to Queuosine itself, several further modified derivatives are known, where the cyclopentene ring structure is additionally modified by a galactosyl-, a mannosyl-, or a glutamyl-residue. While sugar-modified Queuosine derivatives are found in the tRNAs of vertebrates, glutamylated Queuosine (gluQ) is only known in bacteria. The exact structure of gluQ, particularly with respect to how and where the glutamyl side chain is connected to the Queuosine cyclopentene side chain, is unknown. Here we report the first synthesis of gluQ and, using UHPLC-MS-coinjection and NMR studies, we show that the isolated natural gluQ is the α-allyl-connected gluQ compound.
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Affiliation(s)
- Alexander Pichler
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Markus Hillmeier
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Matthias Heiss
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Elsa Peev
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Stylianos Xefteris
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Barbara Steigenberger
- Mass
Spectrometry Core Facility, Max Planck Institute
of Biochemistry, Am Klopferspitz 18, Martinsried, 82152, Planegg, Germany
| | - Ines Thoma
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Markus Müller
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Marco Borsò
- Department
of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, Martinsried, 82152 Planegg, Germany
| | - Axel Imhof
- Department
of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, Martinsried, 82152 Planegg, Germany
| | - Thomas Carell
- Department
of Chemistry, Institute of Chemical Epigenetics,
Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany
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6
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Cirzi C, Dyckow J, Legrand C, Schott J, Guo W, Perez Hernandez D, Hisaoka M, Parlato R, Pitzer C, van der Hoeven F, Dittmar G, Helm M, Stoecklin G, Schirmer L, Lyko F, Tuorto F. Queuosine-tRNA promotes sex-dependent learning and memory formation by maintaining codon-biased translation elongation speed. EMBO J 2023; 42:e112507. [PMID: 37609797 PMCID: PMC10548180 DOI: 10.15252/embj.2022112507] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/24/2023] Open
Abstract
Queuosine (Q) is a modified nucleoside at the wobble position of specific tRNAs. In mammals, queuosinylation is facilitated by queuine uptake from the gut microbiota and is introduced into tRNA by the QTRT1-QTRT2 enzyme complex. By establishing a Qtrt1 knockout mouse model, we discovered that the loss of Q-tRNA leads to learning and memory deficits. Ribo-Seq analysis in the hippocampus of Qtrt1-deficient mice revealed not only stalling of ribosomes on Q-decoded codons, but also a global imbalance in translation elongation speed between codons that engage in weak and strong interactions with their cognate anticodons. While Q-dependent molecular and behavioral phenotypes were identified in both sexes, female mice were affected more severely than males. Proteomics analysis confirmed deregulation of synaptogenesis and neuronal morphology. Together, our findings provide a link between tRNA modification and brain functions and reveal an unexpected role of protein synthesis in sex-dependent cognitive performance.
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Affiliation(s)
- Cansu Cirzi
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
| | - Julia Dyckow
- Department of Neurology, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Interdisciplinary Center for NeurosciencesHeidelberg UniversityHeidelbergGermany
| | - Carine Legrand
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Université Paris Cité, Génomes, Biologie Cellulaire et Thérapeutique U944, INSERM, CNRSParisFrance
| | - Johanna Schott
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Wei Guo
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | | | - Miharu Hisaoka
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Rosanna Parlato
- Division of Neurodegenerative Disorders, Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational NeurosciencesHeidelberg UniversityMannheimGermany
| | - Claudia Pitzer
- Interdisciplinary Neurobehavioral Core (INBC), Medical Faculty HeidelbergHeidelberg UniversityHeidelbergGermany
| | | | - Gunnar Dittmar
- Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgLuxembourg
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Science (IPBS)Johannes Gutenberg‐University MainzMainzGermany
| | - Georg Stoecklin
- Faculty of BiosciencesHeidelberg UniversityHeidelbergGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Lucas Schirmer
- Department of Neurology, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Interdisciplinary Center for NeurosciencesHeidelberg UniversityHeidelbergGermany
- Mannheim Center for Translational Neuroscience and Institute for Innate Immunoscience, Medical Faculty MannheimHeidelberg UniversityMannheimGermany
| | - Frank Lyko
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Francesca Tuorto
- Division of Epigenetics, DKFZ‐ZMBH AllianceGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty MannheimHeidelberg UniversityMannheimGermany
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7
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Cotter M, Varghese S, Chevot F, Fergus C, Kelly VP, Connon SJ, Southern JM. Queuine Analogues Incorporating the 7-Aminomethyl-7-deazaguanine Core: Structure-Activity Relationships in the Treatment of Experimental Autoimmune Encephalomyelitis. ChemMedChem 2023; 18:e202300207. [PMID: 37350546 DOI: 10.1002/cmdc.202300207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023]
Abstract
A library of queuine analogues targeting the modification of tRNA isoacceptors for Asp, Asn, His and Tyr catalysed by queuine tRNA ribosyltransferase (QTRT, also known as TGT) was evaluated in the treatment of a chronic multiple sclerosis model: murine experimental autoimmune encephalomyelitis. Several active 7-deazaguanines emerged, together with a structure-activity relationship involving the necessity for a flexible alkyl chain of fixed length.
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Affiliation(s)
- Michelle Cotter
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Sreeja Varghese
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Franciane Chevot
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
| | - J Mike Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College, Dublin, Ireland
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8
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The Repertoire of RNA Modifications Orchestrates a Plethora of Cellular Responses. Int J Mol Sci 2023; 24:ijms24032387. [PMID: 36768716 PMCID: PMC9916637 DOI: 10.3390/ijms24032387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
Although a plethora of DNA modifications have been extensively investigated in the last decade, recent breakthroughs in molecular biology, including high throughput sequencing techniques, have enabled the identification of post-transcriptional marks that decorate RNAs; hence, epitranscriptomics has arisen. This recent scientific field aims to decode the regulatory layer of the transcriptome and set the ground for the detection of modifications in ribose nucleotides. Until now, more than 170 RNA modifications have been reported in diverse types of RNA that contribute to various biological processes, such as RNA biogenesis, stability, and transcriptional and translational accuracy. However, dysfunctions in the RNA-modifying enzymes that regulate their dynamic level can lead to human diseases and cancer. The present review aims to highlight the epitranscriptomic landscape in human RNAs and match the catalytic proteins with the deposition or deletion of a specific mark. In the current review, the most abundant RNA modifications, such as N6-methyladenosine (m6A), N5-methylcytosine (m5C), pseudouridine (Ψ) and inosine (I), are thoroughly described, their functional and regulatory roles are discussed and their contributions to cellular homeostasis are stated. Ultimately, the involvement of the RNA modifications and their writers, erasers, and readers in human diseases and cancer is also discussed.
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9
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Pollo-Oliveira L, Davis NK, Hossain I, Ho P, Yuan Y, Salguero García P, Pereira C, Byrne SR, Leng J, Sze M, Blaby-Haas CE, Sekowska A, Montoya A, Begley T, Danchin A, Aalberts DP, Angerhofer A, Hunt J, Conesa A, Dedon PC, de Crécy-Lagard V. The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12. Metallomics 2022; 14:mfac065. [PMID: 36066904 PMCID: PMC9508795 DOI: 10.1093/mtomcs/mfac065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 09/09/2022] [Indexed: 02/04/2023]
Abstract
Queuosine (Q) is a conserved hypermodification of the wobble base of tRNA containing GUN anticodons but the physiological consequences of Q deficiency are poorly understood in bacteria. This work combines transcriptomic, proteomic and physiological studies to characterize a Q-deficient Escherichia coli K12 MG1655 mutant. The absence of Q led to an increased resistance to nickel and cobalt, and to an increased sensitivity to cadmium, compared to the wild-type (WT) strain. Transcriptomic analysis of the WT and Q-deficient strains, grown in the presence and absence of nickel, revealed that the nickel transporter genes (nikABCDE) are downregulated in the Q- mutant, even when nickel is not added. This mutant is therefore primed to resist to high nickel levels. Downstream analysis of the transcriptomic data suggested that the absence of Q triggers an atypical oxidative stress response, confirmed by the detection of slightly elevated reactive oxygen species (ROS) levels in the mutant, increased sensitivity to hydrogen peroxide and paraquat, and a subtle growth phenotype in a strain prone to accumulation of ROS.
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Affiliation(s)
- Leticia Pollo-Oliveira
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Nick K Davis
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Intekhab Hossain
- Department of Physics, Williams College, Williamstown, MA 01267, USA
| | - Peiying Ho
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Pedro Salguero García
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Valencia 46022, Spain
| | - Cécile Pereira
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Shane R Byrne
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jiapeng Leng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Melody Sze
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Crysten E Blaby-Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | | | - Alvaro Montoya
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Thomas Begley
- The RNA Institute and Department of Biology, University at Albany, Albany, NY 12222, USA
| | - Antoine Danchin
- Kodikos Labs, 23 rue Baldassini, Lyon 69007, France
- School of Biomedical Sciences, Li Kashing Faculty of Medicine, University of Hong Kong, Pokfulam, SAR Hong Kong
| | - Daniel P Aalberts
- Department of Physics, Williams College, Williamstown, MA 01267, USA
| | | | - John Hunt
- Department of Biological Sciences, Columbia University, New York, NY 10024, USA
| | - Ana Conesa
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Institute for Integrative Systems Biology, Spanish National Research Council, Paterna 46980, Spain
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
- Genetic Institute, University of Florida, Gainesville, FL 32611, USA
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10
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Maviza TP, Zarechenskaia AS, Burmistrova NR, Tchoub AS, Dontsova OA, Sergiev PV, Osterman IA. RtcB2-PrfH Operon Protects E. coli ATCC25922 Strain from Colicin E3 Toxin. Int J Mol Sci 2022; 23:6453. [PMID: 35742896 PMCID: PMC9223846 DOI: 10.3390/ijms23126453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/28/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
In the bid to survive and thrive in an environmental setting, bacterial species constantly interact and compete for resources and space in the microbial ecosystem. Thus, they have adapted to use various antibiotics and toxins to fight their rivals. Simultaneously, they have evolved an ability to withstand weapons that are directed against them. Several bacteria harbor colicinogenic plasmids which encode toxins that impair the translational apparatus. One of them, colicin E3 ribotoxin, mediates cleavage of the 16S rRNA in the decoding center of the ribosome. In order to thrive upon deployment of such ribotoxins, competing bacteria may have evolved counter-conflict mechanisms to prevent their demise. A recent study demonstrated the role of PrfH and the RtcB2 module in rescuing a damaged ribosome and the subsequent re-ligation of the cleaved 16S rRNA by colicin E3 in vitro. The rtcB2-prfH genes coexist as gene neighbors in an operon that is sporadically spread among different bacteria. In the current study, we report that the RtcB2-PrfH module confers resistance to colicin E3 toxicity in E. coli ATCC25922 cells in vivo. We demonstrated that the viability of E. coli ATCC25922 strain that is devoid of rtcB2 and prfH genes is impaired upon action of colicin E3, in contrast to the parental strain which has intact rtcB2 and prfH genes. Complementation of the rtcB2 and prfH gene knockout with a high copy number-plasmid (encoding either rtcB2 alone or both rtcB2-prfH operon) restored resistance to colicin E3. These results highlight a counter-conflict system that may have evolved to thwart colicin E3 activity.
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Affiliation(s)
- Tinashe P. Maviza
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
| | - Anastasiia S. Zarechenskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Nadezhda R. Burmistrova
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Andrey S. Tchoub
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Olga A. Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 119992, Russia
| | - Petr V. Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
| | - Ilya A. Osterman
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia; (T.P.M.); (A.S.Z.); (O.A.D.); (P.V.S.)
- Department of Chemistry, Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (N.R.B.); (A.S.T.)
- Genetics and Life Sciences Research Center, Sirius University of Science and Technology, 1 Olympic Ave., Sochi 354340, Russia
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11
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Pushkarev SV, Vinnik VA, Shapovalova IV, Švedas VK, Nilov DK. Modeling the Structure of Human tRNA-Guanine Transglycosylase in Complex with 7-Methylguanine and Revealing the Factors that Determine the Enzyme Interaction with Inhibitors. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:443-449. [PMID: 35790378 DOI: 10.1134/s0006297922050054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
tRNA-guanine transglycosylase, an enzyme catalyzing replacement of guanine with queuine in human tRNA and participating in the translation mechanism, is involved in the development of cancer. However, information on the small-molecule inhibitors that can suppress activity of this enzyme is very limited. Molecular dynamics simulations were used to determine the amino acid residues that provide efficient binding of inhibitors in the active site of tRNA-guanine transglycosylase. It was demonstrated using 7-methylguanine molecule as a probe that the ability of the inhibitor to adopt a charged state in the environment of hydrogen bond acceptors Asp105 and Asp159 plays a key role in complex formation. Formation of the hydrogen bonds and hydrophobic contacts with Gln202, Gly229, Phe109, and Met259 residues are also important. It has been predicted that introduction of the substituents would have a different effect on the ability to inhibit tRNA-guanine transglycosylase, as well as the DNA repair protein poly(ADP-ribose) polymerase 1, which can contribute to the development of more efficient and selective compounds.
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Affiliation(s)
- Sergey V Pushkarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Valeriia A Vinnik
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Irina V Shapovalova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vytas K Švedas
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Dmitry K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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12
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Zhou C, Yang S, Ka W, Gao P, Li Y, Long R, Wang J. Association of Gut Microbiota With Metabolism in Rainbow Trout Under Acute Heat Stress. Front Microbiol 2022; 13:846336. [PMID: 35432278 PMCID: PMC9007319 DOI: 10.3389/fmicb.2022.846336] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/23/2022] [Indexed: 12/25/2022] Open
Abstract
Global warming is one of the most common environmental challenges faced by cold-water fish farming. Heat stress seriously affects the feeding, growth, immunity, and disease resistance of fish. These changes are closely related to the destruction of intestinal barrier function, the change of intestinal microbiota, and metabolic dysfunction. However, the causal relationship between the phenotypic effects of heat stress as well as intestinal and metabolic functions of fish is unknown. In the current study, the optimal growth temperature (16°C) of rainbow trout was used as the control group, while the fish treated at 22.5°C, 23.5°C, and 24.5°C for 24 h, respectively, were the treatment groups. The 16S rRNA gene sequencing analysis showed that with the increase in temperature, the relative abundance and diversity of intestinal microbiota decreased significantly, while the number of Mycoplasma, Firmicutes, and Tenericutes increased significantly. Non-targeted metabolomics analysis by liquid chromatography-mass spectrometry analysis and correlation analysis showed that the changes of metabolites related to amino acids, vitamins, and short-chain fatty acids in serum of rainbow trout under acute heat stress were strongly correlated with the decrease of relative abundance of various intestinal microbiota, especially Morganella, Enterobacter, Lactobacillus, Lawsonia, and Cloacibacterium. In addition, we also found that acute heat stress seriously affected the intestinal structure and barrier function, and also caused the pathological damage of epithelial cells. These results indicate that the gut microbiome of acute heat-stressed rainbow trout could mediate metabolite transfer through the gut barrier by affecting its integrity. Significant changes in gut morphology, permeability, antioxidant capacity, and pro-inflammatory cytokine levels were observed. Therefore, it is necessary to explore the changes of intestinal microbiota under heat stress to help understand the regulatory mechanism of heat stress and protect the intestinal health of rainbow trout from the negative effects of rising water temperature.
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Affiliation(s)
- Changqing Zhou
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Grassland Agriculture Engineering Center, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,College of Ecology, Lanzhou University, Lanzhou, China
| | - Shunwen Yang
- Gansu Fishery Research Institute, Lanzhou, China
| | - Wei Ka
- Gansu Fishery Research Institute, Lanzhou, China
| | - Pan Gao
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Grassland Agriculture Engineering Center, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yalan Li
- Gansu Agriculture Technology College, Lanzhou, China
| | - Ruijun Long
- College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianlin Wang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Grassland Agriculture Engineering Center, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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13
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Kelley M, Uhran M, Herbert C, Yoshida G, Watts ER, Limbach PA, Benoit JB. Abundances of transfer RNA modifications and transcriptional levels of tRNA-modifying enzymes are sex-associated in mosquitoes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103741. [PMID: 35181477 PMCID: PMC9034435 DOI: 10.1016/j.ibmb.2022.103741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 06/03/2023]
Abstract
As carriers of multiple human diseases, understanding the mechanisms behind mosquito reproduction may have implications for remediation strategies. Transfer RNA (tRNA) acts as the adapter molecule of amino acids and are key components in protein synthesis. A critical factor in the function of tRNAs is chemical modifications which contribute to codon-anticodon interactions. Here, we provide an assessment of tRNA modifications between sexes for three mosquito species and examine the correlation of transcript levels underlying key proteins involved in tRNA modification. Thirty-three tRNA modifications were detected among mosquito species and most of these modifications are higher in females compared to males for three mosquito species. Analysis of previous male and female RNA-seq datasets indicated a similar increase in transcript levels of tRNA-modifying enzymes in females among six mosquito species, supporting our observed female enrichment of tRNA modifications. Tissues-specific expressional studies revealed higher transcript levels for tRNA-modifying enzymes in the ovaries for Aedes aegypti, but not male reproductive tissues. These studies suggest that tRNA modifications may be critical to reproduction in mosquitoes, representing a potential novel target for control through suppression of fecundity.
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Affiliation(s)
- Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA.
| | - Melissa Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Cassandra Herbert
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - George Yoshida
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Emmarie R Watts
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, 45211, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45211, USA.
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14
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Greenhalgh ED, Kincannon W, Bandarian V, Brunold TC. Spectroscopic and Computational Investigation of the Epoxyqueuosine Reductase QueG Reveals Intriguing Similarities with the Reductive Dehalogenase PceA. Biochemistry 2022; 61:195-205. [PMID: 35061353 PMCID: PMC8935625 DOI: 10.1021/acs.biochem.1c00644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Queuosine (Q) is a highly modified nucleoside of transfer RNA that is formed from guanosine triphosphate over the course of eight steps. The final step in this process, involving the conversion of epoxyqueuosine (oQ) to Q, is catalyzed by the enzyme QueG. A recent X-ray crystallographic study revealed that QueG possesses the same cofactors as reductive dehalogenases, including a base-off Co(II)cobalamin (Co(II)Cbl) species and two [4Fe-4S] clusters. While the initial step in the catalytic cycle of QueG likely involves the formation of a reduced Co(I)Cbl species, the mechanisms employed by this enzyme to accomplish the thermodynamically challenging reduction of base-off Co(II)Cbl to Co(I)Cbl and to convert oQ to Q remain unknown. In this study, we have used electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) spectroscopies in conjunction with whole-protein quantum mechanics/molecular mechanics (QM/MM) computations to further characterize wild-type QueG and select variants. Our data indicate that the Co(II)Cbl cofactor remains five-coordinate upon substrate binding to QueG. Notably, during a QM/MM optimization of a putative QueG reaction intermediate featuring an alkyl-Co(III) species, the distance between the Co ion and coordinating C atom of oQ increased to >3.3 Å and the C-O bond of the epoxide reformed to regenerate the oQ-bound Co(I)Cbl reactant state of QueG. Thus, our computations indicate that the QueG mechanism likely involves single-electron transfer from the transient Co(I)Cbl species to oQ rather than direct Co-C bond formation, similar to the mechanism that has recently been proposed for the tetrachloroethylene reductive dehalogenase PceA.
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Affiliation(s)
- Elizabeth D. Greenhalgh
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - William Kincannon
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Thomas C. Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States,Corresponding Author:. Phone: (608) 265-9056
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15
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Kesh K, Mendez R, Mateo-Victoriano B, Garrido VT, Durden B, Gupta VK, Oliveras Reyes A, Merchant N, Datta J, Banerjee S, Banerjee S. Obesity enriches for tumor protective microbial metabolites and treatment refractory cells to confer therapy resistance in PDAC. Gut Microbes 2022; 14:2096328. [PMID: 35816618 PMCID: PMC9275504 DOI: 10.1080/19490976.2022.2096328] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Obesity causes chronic inflammation and changes in gut microbiome. However, how this contributes to poor survival and therapy resistance in patients with pancreatic cancer remain undetermined. Our current study shows that high fat diet-fed obese pancreatic tumor bearing mice do not respond to standard of care therapy with gemcitabine and paclitaxel when compared to corresponding control diet-fed mice. C57BL6 mice were put on control and high fat diet for 1 month following with pancreatic tumors were implanted in both groups. Microbiome of lean (control) and obese (high fat diet fed) mice was analyzed. Fecal matter transplant from control mice to obese mice sensitized tumors to chemotherapy and demonstrated extensive cell death. Analysis of gut microbiome showed an enrichment of queuosine (Q) producing bacteria in obese mice and an enrichment of S-adenosyl methionine (SAM) producing bacteria in control diet-fed mice. Further, supplementation of obese animals with SAM sensitized pancreatic tumors to chemotherapy. Treatment of pancreatic cancer cells with Q increased PRDX1 involved in oxidative stress protection. In parallel, tumors in obese mice showed increase in CD133+ treatment refractory tumor populations compared to control animals. These observations indicated that microbial metabolite Q accumulation in high fat diet-fed mice protected tumors from chemotherapy induced oxidative stress by upregulating PRDX1. This protection could be reversed by treatment with SAM. We conclude that relative concentration of SAM and queuosine in fecal samples of pancreatic cancer patients can be developed as a potential biomarker and therapeutic target in chemotherapy refractory pancreatic cancer.
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Affiliation(s)
- Kousik Kesh
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Roberto Mendez
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | | | - Vanessa T Garrido
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Brittany Durden
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Vineet K Gupta
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | | | - Nipun Merchant
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Jashodeep Datta
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Santanu Banerjee
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
- Miami Integrative Metabolomics Research Center, University of Miami, Miami, FL, USA
| | - Sulagna Banerjee
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
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16
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Hillmeier M, Wagner M, Ensfelder T, Korytiakova E, Thumbs P, Müller M, Carell T. Synthesis and structure elucidation of the human tRNA nucleoside mannosyl-queuosine. Nat Commun 2021; 12:7123. [PMID: 34880214 PMCID: PMC8654956 DOI: 10.1038/s41467-021-27371-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 11/11/2021] [Indexed: 11/09/2022] Open
Abstract
Queuosine (Q) is a structurally complex, non-canonical RNA nucleoside. It is present in many eukaryotic and bacterial species, where it is part of the anticodon loop of certain tRNAs. In higher vertebrates, including humans, two further modified queuosine-derivatives exist - galactosyl- (galQ) and mannosyl-queuosine (manQ). The function of these low abundant hypermodified RNA nucleosides remains unknown. While the structure of galQ was elucidated and confirmed by total synthesis, the reported structure of manQ still awaits confirmation. By combining total synthesis and LC-MS-co-injection experiments, together with a metabolic feeding study of labelled hexoses, we show here that the natural compound manQ isolated from mouse liver deviates from the literature-reported structure. Our data show that manQ features an α-allyl connectivity of its sugar moiety. The yet unidentified glycosylases that attach galactose and mannose to the Q-base therefore have a maximally different constitutional connectivity preference. Knowing the correct structure of manQ will now pave the way towards further elucidation of its biological function.
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Affiliation(s)
- Markus Hillmeier
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Mirko Wagner
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Timm Ensfelder
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Eva Korytiakova
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Peter Thumbs
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Markus Müller
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany
| | - Thomas Carell
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, 81377, München, Germany.
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17
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Valadon C, Namy O. The Importance of the Epi-Transcriptome in Translation Fidelity. Noncoding RNA 2021; 7:51. [PMID: 34564313 PMCID: PMC8482273 DOI: 10.3390/ncrna7030051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022] Open
Abstract
RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly complex structures, such as sugars. Their consequences for translation fidelity are not always well documented. Unlike the well-known m6A modification, they are thought to have direct effects on either the folding of the molecule or the ability of tRNAs to bind their codons. Here we describe how modifications found in tRNAs anticodon-loop, rRNA, and mRNA can affect translation fidelity, and how approaches based on direct manipulations of the level of RNA modification could potentially be used to modulate translation for the treatment of human genetic diseases.
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Affiliation(s)
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France;
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18
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Richard P, Kozlowski L, Guillorit H, Garnier P, McKnight NC, Danchin A, Manière X. Queuine, a bacterial-derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration. PLoS One 2021; 16:e0253216. [PMID: 34379627 PMCID: PMC8357117 DOI: 10.1371/journal.pone.0253216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/29/2021] [Indexed: 11/26/2022] Open
Abstract
Growing evidence suggests that human gut bacteria, which comprise the microbiome, are linked to several neurodegenerative disorders. An imbalance in the bacterial population in the gut of Parkinson's disease (PD) and Alzheimer's disease (AD) patients has been detected in several studies. This dysbiosis very likely decreases or increases microbiome-derived molecules that are protective or detrimental, respectively, to the human body and those changes are communicated to the brain through the so-called 'gut-brain-axis'. The microbiome-derived molecule queuine is a hypermodified nucleobase enriched in the brain and is exclusively produced by bacteria and salvaged by humans through their gut epithelium. Queuine replaces guanine at the wobble position (position 34) of tRNAs with GUN anticodons and promotes efficient cytoplasmic and mitochondrial mRNA translation. Queuine depletion leads to protein misfolding and activation of the endoplasmic reticulum stress and unfolded protein response pathways in mice and human cells. Protein aggregation and mitochondrial impairment are often associated with neural dysfunction and neurodegeneration. To elucidate whether queuine could facilitate protein folding and prevent aggregation and mitochondrial defects that lead to proteinopathy, we tested the effect of chemically synthesized queuine, STL-101, in several in vitro models of neurodegeneration. After neurons were pretreated with STL-101 we observed a significant decrease in hyperphosphorylated alpha-synuclein, a marker of alpha-synuclein aggregation in a PD model of synucleinopathy, as well as a decrease in tau hyperphosphorylation in an acute and a chronic model of AD. Additionally, an associated increase in neuronal survival was found in cells pretreated with STL-101 in both AD models as well as in a neurotoxic model of PD. Measurement of queuine in the plasma of 180 neurologically healthy individuals suggests that healthy humans maintain protective levels of queuine. Our work has identified a new role for queuine in neuroprotection uncovering a therapeutic potential for STL-101 in neurological disorders.
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Affiliation(s)
- Patricia Richard
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
| | | | - Hélène Guillorit
- Stellate Therapeutics SAS, Paris, France
- Institut de Génomique Fonctionnelle, Montpellier, France
| | | | - Nicole C. McKnight
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
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19
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The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol 2021; 22:375-392. [PMID: 33658722 DOI: 10.1038/s41580-021-00342-0] [Citation(s) in RCA: 305] [Impact Index Per Article: 101.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2021] [Indexed: 02/08/2023]
Abstract
Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.
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20
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Alqasem MA, Fergus C, Southern JM, Connon SJ, Kelly VP. The eukaryotic tRNA-guanine transglycosylase enzyme inserts queuine into tRNA via a sequential bi-bi mechanism. Chem Commun (Camb) 2020; 56:3915-3918. [PMID: 32149287 DOI: 10.1039/c9cc09887a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Eukaryotic tRNA-guanine transglycosylase (TGT) - an enzyme recently recognised to be of potential therapeutic importance - catalyses base-exchange of guanine for queuine at the wobble position of tRNAs associated with 4 amino acids via a distinct mechanism to that reported for its eubacterial homologue. The presence of queuine is unequivocally required as a trigger for reaction between the enzyme and tRNA and exhibits cooperativity not seen using guanine as a substrate.
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Affiliation(s)
- Mashael A Alqasem
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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21
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Aleksashin NA, Leppik M, Hockenberry AJ, Klepacki D, Vázquez-Laslop N, Jewett MC, Remme J, Mankin AS. Assembly and functionality of the ribosome with tethered subunits. Nat Commun 2019; 10:930. [PMID: 30804338 PMCID: PMC6389949 DOI: 10.1038/s41467-019-08892-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/25/2019] [Indexed: 12/02/2022] Open
Abstract
Ribo-T is an engineered ribosome whose small and large subunits are tethered together by linking 16S rRNA and 23S rRNA in a single molecule. Although Ribo-T can support cell proliferation in the absence of wild type ribosomes, Ribo-T cells grow slower than those with wild type ribosomes. Here, we show that cell growth defect is likely explained primarily by slow Ribo-T assembly rather than its imperfect functionality. Ribo-T maturation is stalled at a late assembly stage. Several post-transcriptional rRNA modifications and some ribosomal proteins are underrepresented in the accumulated assembly intermediates and rRNA ends are incompletely trimmed. Ribosome profiling of Ribo-T cells shows no defects in translation elongation but reveals somewhat higher occupancy by Ribo-T of the start codons and to a lesser extent stop codons, suggesting that subunit tethering mildly affects the initiation and termination stages of translation. Understanding limitations of Ribo-T system offers ways for its future development. The tethered ribosome system Ribo-T supports cell proliferation though at a reduced rate. Here the authors show this is due to slower ribosome assembly instead of reduced functionality.
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Affiliation(s)
- Nikolay A Aleksashin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Margus Leppik
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia
| | - Adam J Hockenberry
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.,Department of Integrative Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, USA
| | - Dorota Klepacki
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering and Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Jaanus Remme
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010, Tartu, Estonia.
| | - Alexander S Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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22
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Abstract
It is proposed that proteins/enzymes be classified into two classes according to their essentiality for immediate survival/reproduction and their function in long-term health: that is, survival proteins versus longevity proteins. As proposed by the triage theory, a modest deficiency of one of the nutrients/cofactors triggers a built-in rationing mechanism that favors the proteins needed for immediate survival and reproduction (survival proteins) while sacrificing those needed to protect against future damage (longevity proteins). Impairment of the function of longevity proteins results in an insidious acceleration of the risk of diseases associated with aging. I also propose that nutrients required for the function of longevity proteins constitute a class of vitamins that are here named "longevity vitamins." I suggest that many such nutrients play a dual role for both survival and longevity. The evidence for classifying taurine as a conditional vitamin, and the following 10 compounds as putative longevity vitamins, is reviewed: the fungal antioxidant ergothioneine; the bacterial metabolites pyrroloquinoline quinone (PQQ) and queuine; and the plant antioxidant carotenoids lutein, zeaxanthin, lycopene, α- and β-carotene, β-cryptoxanthin, and the marine carotenoid astaxanthin. Because nutrient deficiencies are highly prevalent in the United States (and elsewhere), appropriate supplementation and/or an improved diet could reduce much of the consequent risk of chronic disease and premature aging.
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Affiliation(s)
- Bruce N Ames
- Nutrition and Metabolism Center, Children's Hospital Oakland Research Institute (CHORI), Oakland, CA 94609-1809
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23
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Crystal Structure of the Human tRNA Guanine Transglycosylase Catalytic Subunit QTRT1. Biomolecules 2018; 8:biom8030081. [PMID: 30149595 PMCID: PMC6165067 DOI: 10.3390/biom8030081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022] Open
Abstract
RNA modifications have been implicated in diverse and important roles in all kingdoms of life with over 100 of them present on tRNAs. A prominent modification at the wobble base of four tRNAs is the 7-deaza-guanine derivative queuine which substitutes the guanine at position 34. This exchange is catalyzed by members of the enzyme class of tRNA guanine transglycosylases (TGTs). These enzymes incorporate guanine substituents into tRNAAsp, tRNAAsn tRNAHis, and tRNATyr in all kingdoms of life. In contrast to the homodimeric bacterial TGT, the active eukaryotic TGT is a heterodimer in solution, comprised of a catalytic QTRT1 subunit and a noncatalytic QTRT2 subunit. Bacterial TGT enzymes, that incorporate a queuine precursor, have been identified or proposed as virulence factors for infections by pathogens in humans and therefore are valuable targets for drug design. To date no structure of a eukaryotic catalytic subunit is reported, and differences to its bacterial counterpart have to be deducted from sequence analysis and models. Here we report the first crystal structure of a eukaryotic QTRT1 subunit and compare it to known structures of the bacterial TGT and murine QTRT2. Furthermore, we were able to determine the crystal structure of QTRT1 in complex with the queuine substrate.
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24
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Devi M, Chingbiaknem E, Lyngdoh RHD. A molecular mechanics study on GA codon box translation. J Theor Biol 2018; 441:28-43. [PMID: 29305181 DOI: 10.1016/j.jtbi.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/01/2018] [Accepted: 01/02/2018] [Indexed: 11/28/2022]
Abstract
The GA codon box incorporates the two-fold degeneracy of aspartic acid and of glutamic acid. Using the molecular mechanics approach of the AMBER suite, the four codons of the GA box are paired via H-bonding with two aspartic acid anticodons and two glutamic acid anticodons to yield 8 cognate and 11 non-cognate codon-anticodon duplexes. In addition four select non-cognate duplexes between the GA box codons and three alanine anticodons are also studied. These 23 duplexes display a variety of base-pairing possibilities at the wobble position. Cognate duplexes are differentiated from non-cognate duplexes on the grounds of structure and stability (chiefly the former). The results are in line with Crick's wobble hypothesis, and corroborate the observed reading properties of the aspartic acid anticodons GUC and QUC and of the glutamic acid anticodons CUC and SmnUC.
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Affiliation(s)
- Martina Devi
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - Esther Chingbiaknem
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India
| | - R H Duncan Lyngdoh
- Department of Chemistry, North-Eastern Hill University, Shillong 793022, India.
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25
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Jung Y, Goldman D. Role of RNA modifications in brain and behavior. GENES, BRAIN, AND BEHAVIOR 2018; 17:e12444. [PMID: 29244246 PMCID: PMC6233296 DOI: 10.1111/gbb.12444] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/07/2018] [Indexed: 12/23/2022]
Abstract
Much progress in our understanding of RNA metabolism has been made since the first RNA nucleoside modification was identified in 1957. Many of these modifications are found in noncoding RNAs but recent interest has focused on coding RNAs. Here, we summarize current knowledge of cellular consequences of RNA modifications, with a special emphasis on neuropsychiatric disorders. We present evidence for the existence of an "RNA code," similar to the histone code, that fine-tunes gene expression in the nervous system by using combinations of different RNA modifications. Unlike the relatively stable genetic code, this combinatorial RNA epigenetic code, or epitranscriptome, may be dynamically reprogrammed as a cause or consequence of psychiatric disorders. We discuss potential mechanisms linking disregulation of the epitranscriptome with brain disorders and identify potential new avenues of research.
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Affiliation(s)
- Y. Jung
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
| | - D. Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, Maryland
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26
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Varghese S, Cotter M, Chevot F, Fergus C, Cunningham C, Mills KH, Connon SJ, Southern JM, Kelly VP. In vivo modification of tRNA with an artificial nucleobase leads to full disease remission in an animal model of multiple sclerosis. Nucleic Acids Res 2017; 45:2029-2039. [PMID: 28204548 PMCID: PMC5389723 DOI: 10.1093/nar/gkw847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 08/10/2016] [Accepted: 09/03/2016] [Indexed: 01/07/2023] Open
Abstract
Queuine is a modified pyrrolopyrimidine nucleobase derived exclusively from bacteria. It post-transcriptionally replaces guanine 34 in transfer RNA isoacceptors for Asp, Asn, His and Tyr, in almost all eukaryotic organisms, through the activity of the ancient tRNA guanine transglycosylase (TGT) enzyme. tRNA hypomodification with queuine is a characteristic of rapidly-proliferating, non-differentiated cells. Autoimmune diseases, including multiple sclerosis, are characterised by the rapid expansion of T cells directed to self-antigens. Here, we demonstrate the potential medicinal relevance of targeting the modification of tRNA in the treatment of a chronic multiple sclerosis model—murine experimental autoimmune encephalomyelitis. Administration of a de novo designed eukaryotic TGT substrate (NPPDAG) led to an unprecedented complete reversal of clinical symptoms and a dramatic reduction of markers associated with immune hyperactivation and neuronal damage after five daily doses. TGT is essential for the therapeutic effect, since animals deficient in TGT activity were refractory to therapy. The data suggest that exploitation of the eukaryotic TGT enzyme is a promising approach for the treatment of multiple sclerosis.
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Affiliation(s)
- Sreeja Varghese
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - Michelle Cotter
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - Franciane Chevot
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - Colm Cunningham
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - Kingston H Mills
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - John M Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, 152-160 Pearse Street, Trinity College Dublin, Ireland
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27
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Bednářová A, Hanna M, Durham I, VanCleave T, England A, Chaudhuri A, Krishnan N. Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. Front Mol Neurosci 2017; 10:135. [PMID: 28536502 PMCID: PMC5422465 DOI: 10.3389/fnmol.2017.00135] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are key molecules participating in protein synthesis. To augment their functionality they undergo extensive post-transcriptional modifications and, as such, are subject to regulation at multiple levels including transcription, transcript processing, localization and ribonucleoside base modification. Post-transcriptional enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and influences specific anticodon-codon interactions and regulates translation, its efficiency and fidelity. This phenomenon of nucleoside modification is most remarkable and results in a rich structural diversity of tRNA of which over 100 modified nucleosides have been characterized. Most often these hypermodified nucleosides are found in the wobble position of tRNAs, where they play a direct role in codon recognition as well as in maintaining translational efficiency and fidelity, etc. Several recent studies have pointed to a link between defects in tRNA modifications and human diseases including neurological disorders. Therefore, defects in tRNA modifications in humans need intensive characterization at the enzymatic and mechanistic level in order to pave the way to understand how lack of such modifications are associated with neurological disorders with the ultimate goal of gaining insights into therapeutic interventions.
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Affiliation(s)
- Andrea Bednářová
- Department of Biochemistry and Physiology, Institute of Entomology, Biology Centre, Academy of SciencesČeské Budějovice, Czechia.,Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Marley Hanna
- Molecular Biosciences Program, Arkansas State UniversityJonesboro, AR, USA
| | - Isabella Durham
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State UniversityMississippi State, MS, USA
| | - Tara VanCleave
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Alexis England
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | | | - Natraj Krishnan
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
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28
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Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crécy-Lagard V. Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. ACS Chem Biol 2017; 12:844-851. [PMID: 28128549 PMCID: PMC5495094 DOI: 10.1021/acschembio.6b01100] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The reduction of epoxyqueuosine (oQ)
is the last step in the synthesis
of the tRNA modification queuosine (Q). While the epoxyqueuosine reductase
(EC 1.17.99.6) enzymatic activity was first described 30 years ago,
the encoding gene queG was only identified in Escherichia coli in 2011. Interestingly, queG is absent from a large number of sequenced genomes that harbor Q
synthesis or salvage genes, suggesting the existence of an alternative
epoxyqueuosine reductase in these organisms. By analyzing phylogenetic
distributions, physical gene clustering, and fusions, members of the
Domain of Unknown Function 208 (DUF208) family were predicted to encode
for an alternative epoxyqueuosine reductase. This prediction was validated
with genetic methods. The Q modification is present in Lactobacillus
salivarius, an organism missing queG but
harboring the duf208 gene. Acinetobacter
baylyi ADP1 is one of the few organisms that harbor both
QueG and DUF208, and deletion of both corresponding genes was required
to observe the absence of Q and the accumulation of oQ in tRNA. Finally,
the conversion oQ to Q was restored in an E. coli queG mutant by complementation with plasmids harboring duf208 genes from different bacteria. Members of the DUF208 family are
not homologous to QueG enzymes, and thus, duf208 is
a non-orthologous replacement of queG. We propose
to name DUF208 encoding genes as queH. While QueH
contains conserved cysteines that could be involved in the coordination
of a Fe/S center in a similar fashion to what has been identified
in QueG, no cobalamin was identified associated with recombinant QueH
protein.
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Affiliation(s)
- Rémi Zallot
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| | - Robert Ross
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Wei-Hung Chen
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Patrick A. Limbach
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
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29
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Zallot R, Yuan Y, de Crécy-Lagard V. The Escherichia coli COG1738 Member YhhQ Is Involved in 7-Cyanodeazaguanine (preQ₀) Transport. Biomolecules 2017; 7:E12. [PMID: 28208705 PMCID: PMC5372724 DOI: 10.3390/biom7010012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 11/17/2022] Open
Abstract
Queuosine (Q) is a complex modification of the wobble base in tRNAs with GUN anticodons. The full Q biosynthesis pathway has been elucidated in Escherichia coli. FolE, QueD, QueE and QueC are involved in the conversion of guanosine triphosphate (GTP) to 7-cyano-7-deazaguanine (preQ₀), an intermediate of increasing interest for its central role in tRNA and DNA modification and secondary metabolism. QueF then reduces preQ₀ to 7-aminomethyl-7-deazaguanine (preQ₁). PreQ₁ is inserted into tRNAs by tRNA guanine(34) transglycosylase (TGT). The inserted base preQ₁ is finally matured to Q by two additional steps involving QueA and QueG or QueH. Most Eubacteria harbor the full set of Q synthesis genes and are predicted to synthesize Q de novo. However, some bacteria only encode enzymes involved in the second half of the pathway downstream of preQ₀ synthesis, including the signature enzyme TGT. Different patterns of distribution of the queF, tgt, queA and queG or queH genes are observed, suggesting preQ₀, preQ₁ or even the queuine base being salvaged in specific organisms. Such salvage pathways require the existence of specific 7-deazapurine transporters that have yet to be identified. The COG1738 family was identified as a candidate for a missing preQ₀/preQ₁ transporter in prokaryotes, by comparative genomics analyses. The existence of Q precursor salvage was confirmed for the first time in bacteria, in vivo, through an indirect assay. The involvement of the COG1738 in salvage of a Q precursor was experimentally validated in Escherichia coli, where it was shown that the COG1738 family member YhhQ is essential for preQ₀ transport.
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Affiliation(s)
- Rémi Zallot
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Yifeng Yuan
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
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30
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Ogawa T. tRNA-targeting ribonucleases: molecular mechanisms and insights into their physiological roles. Biosci Biotechnol Biochem 2016; 80:1037-45. [PMID: 26967967 DOI: 10.1080/09168451.2016.1148579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Most bacteria produce antibacterial proteins known as bacteriocins, which aid bacterial defence systems to provide a physiological advantage. To date, many kinds of bacteriocins have been characterized. Colicin has long been known as a plasmidborne bacteriocin that kills other Escherichia coli cells lacking the same plasmid. To defeat other cells, colicins exert specific activities such as ion-channel, DNase, and RNase activity. Colicin E5 and colicin D impair protein synthesis in sensitive E. coli cells; however, their physiological targets have not long been identified. This review describes our finding that colicins E5 and D are novel RNases targeting specific E. coli tRNAs and elucidates their enzymatic properties based on biochemical analyses and X-ray crystal structures. Moreover, tRNA cleavage mediates bacteriostasis, which depends on trans-translation. Based on these results and others, cell growth regulation depending on tRNA cleavage is also discussed.
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Affiliation(s)
- Tetsuhiro Ogawa
- a Department of Biotechnology , The University of Tokyo , Tokyo , Japan
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31
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Miles ZD, Myers WK, Kincannon WM, Britt RD, Bandarian V. Biochemical and Spectroscopic Studies of Epoxyqueuosine Reductase: A Novel Iron-Sulfur Cluster- and Cobalamin-Containing Protein Involved in the Biosynthesis of Queuosine. Biochemistry 2015; 54:4927-35. [PMID: 26230193 DOI: 10.1021/acs.biochem.5b00335] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Queuosine is a hypermodified nucleoside present in the wobble position of tRNAs with a 5'-GUN-3' sequence in their anticodon (His, Asp, Asn, and Tyr). The 7-deazapurine core of the base is synthesized de novo in prokaryotes from guanosine 5'-triphosphate in a series of eight sequential enzymatic transformations, the final three occurring on tRNA. Epoxyqueuosine reductase (QueG) catalyzes the final step in the pathway, which entails the two-electron reduction of epoxyqueuosine to form queuosine. Biochemical analyses reveal that this enzyme requires cobalamin and two [4Fe-4S] clusters for catalysis. Spectroscopic studies show that the cobalamin appears to bind in a base-off conformation, whereby the dimethylbenzimidazole moiety of the cofactor is removed from the coordination sphere of the cobalt but not replaced by an imidazole side chain, which is a hallmark of many cobalamin-dependent enzymes. The bioinformatically identified residues are shown to have a role in modulating the primary coordination sphere of cobalamin. These studies provide the first demonstration of the cofactor requirements for QueG.
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Affiliation(s)
- Zachary D Miles
- †Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - William K Myers
- ‡Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - William M Kincannon
- †Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - R David Britt
- ‡Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Vahe Bandarian
- †Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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32
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Fergus C, Barnes D, Alqasem MA, Kelly VP. The queuine micronutrient: charting a course from microbe to man. Nutrients 2015; 7:2897-929. [PMID: 25884661 PMCID: PMC4425180 DOI: 10.3390/nu7042897] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/25/2015] [Indexed: 12/24/2022] Open
Abstract
Micronutrients from the diet and gut microbiota are essential to human health and wellbeing. Arguably, among the most intriguing and enigmatic of these micronutrients is queuine, an elaborate 7-deazaguanine derivative made exclusively by eubacteria and salvaged by animal, plant and fungal species. In eubacteria and eukaryotes, queuine is found as the sugar nucleotide queuosine within the anticodon loop of transfer RNA isoacceptors for the amino acids tyrosine, asparagine, aspartic acid and histidine. The physiological requirement for the ancient queuine molecule and queuosine modified transfer RNA has been the subject of varied scientific interrogations for over four decades, establishing relationships to development, proliferation, metabolism, cancer, and tyrosine biosynthesis in eukaryotes and to invasion and proliferation in pathogenic bacteria, in addition to ribosomal frameshifting in viruses. These varied effects may be rationalized by an important, if ill-defined, contribution to protein translation or may manifest from other presently unidentified mechanisms. This article will examine the current understanding of queuine uptake, tRNA incorporation and salvage by eukaryotic organisms and consider some of the physiological consequence arising from deficiency in this elusive and lesser-recognized micronutrient.
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Affiliation(s)
- Claire Fergus
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Dominic Barnes
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Mashael A Alqasem
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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33
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Iron-sulfur proteins responsible for RNA modifications. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1272-83. [PMID: 25533083 DOI: 10.1016/j.bbamcr.2014.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/22/2022]
Abstract
RNA molecules are decorated with various chemical modifications, which are introduced post-transcriptionally by RNA-modifying enzymes. These modifications are required for proper RNA function. Among more than 100 known species of RNA modifications, several modified bases in tRNAs and rRNAs are introduced by RNA-modifying enzymes containing iron-sulfur (Fe/S) clusters. Most Fe/S-containing RNA-modifying enzymes contain radical SAM domains that catalyze a variety of chemical reactions, including methylation, methylthiolation, carboxymethylation, tricyclic purine formation, and deazaguanine formation. Lack of these modifications can cause pathological consequences. Here, we review recent studies on the biogenesis and function of RNA modifications mediated by Fe/S proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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34
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Zallot R, Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de Crécy-Lagard V. Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. ACS Chem Biol 2014; 9:1812-25. [PMID: 24911101 PMCID: PMC4136680 DOI: 10.1021/cb500278k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Queuosine (Q) is a modification found
at the wobble position of
tRNAs with GUN anticodons. Although Q is present in most eukaryotes
and bacteria, only bacteria can synthesize Q de novo. Eukaryotes acquire queuine (q), the free base of Q, from diet and/or
microflora, making q an important but under-recognized micronutrient
for plants, animals, and fungi. Eukaryotic type tRNA-guanine transglycosylases
(eTGTs) are composed of a catalytic subunit (QTRT1) and a homologous
accessory subunit (QTRTD1) forming a complex that catalyzes q insertion
into target tRNAs. Phylogenetic analysis of eTGT subunits revealed
a patchy distribution pattern in which gene losses occurred independently
in different clades. Searches for genes co-distributing with eTGT
family members identified DUF2419 as a potential Q salvage protein
family. This prediction was experimentally validated in Schizosaccharomyces
pombe by confirming that Q was present by analyzing tRNAAsp with anticodon GUC purified from wild-type cells and by
showing that Q was absent from strains carrying deletions in the QTRT1
or DUF2419 encoding genes. DUF2419 proteins occur in most Eukarya
with a few possible cases of horizontal gene transfer to bacteria.
The universality of the DUF2419 function was confirmed by complementing
the S. pombe mutant with the Zea mays (maize), human, and Sphaerobacter thermophilus homologues.
The enzymatic function of this family is yet to be determined, but
structural similarity with DNA glycosidases suggests a ribonucleoside
hydrolase activity.
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Affiliation(s)
- Rémi Zallot
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| | - Céline Brochier-Armanet
- Université
Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie
Evolutive, Université de Lyon, 69622 Villeurbanne, France
| | - Kirk W. Gaston
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Farhad Forouhar
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Patrick A. Limbach
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - John F. Hunt
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Genetics Institute, Gainesville, Florida 32611, United States
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35
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El Yacoubi B, Bailly M, de Crécy-Lagard V. Biosynthesis and Function of Posttranscriptional Modifications of Transfer RNAs. Annu Rev Genet 2012; 46:69-95. [DOI: 10.1146/annurev-genet-110711-155641] [Citation(s) in RCA: 380] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Marc Bailly
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700;
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36
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Nomura Y, Onda Y, Ohno S, Taniguchi H, Ando K, Oka N, Nishikawa K, Yokogawa T. Purification and comparison of native and recombinant tRNA-guanine transglycosylases from Methanosarcina acetivorans. Protein Expr Purif 2012. [PMID: 23201278 DOI: 10.1016/j.pep.2012.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Many archaeal tRNAs have archaeosine (G(+)) at position 15 in the D-loop and this is thought to strengthen the tertiary interaction with C48 in the V-loop. In the first step of G(+) biosynthesis, archaeosine tRNA-guanine transglycosylase (ArcTGT)(1) catalyzes the base exchange reaction from guanine to 7-cyano-7-deazaguanine (preQ(0)). ArcTGT is classified into full-size or split types, according to databases of genomic information. Although the full-size type forms a homodimeric structure, the split type has been assumed to form a heterotetrameric structure, consisting of two kinds of peptide. However, there has been no definitive evidence for this presented to date. Here, we show that native ArcTGT could be isolated from Methanosarcina acetivorans and two peptides formed a robust complex in cells. Consequently, the two peptides function as actual subunits of ArcTGT. We also overexpressed recombinant ArcTGT in Escherichia coli cells. Product was successfully obtained by co-overexpression of the two subunits but one subunit alone was not adequately expressed in soluble fractions. This result suggests that interaction between the two subunits may contribute to the conformational stability of split ArcTGT. The values of the kinetic parameters for the recombinant and native ArcTGT were closely similar. Moreover, tRNA transcript with preQ(0) at position 15 was successfully prepared using the recombinant ArcTGT. This tRNA transcript is expected to be useful as a substrate for studies seeking the enzymes responsible for G(+) biosynthesis.
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Affiliation(s)
- Yuichiro Nomura
- Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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37
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Das G, Lyngdoh RHD. Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position. J Mol Model 2012; 18:3805-20. [PMID: 22399149 DOI: 10.1007/s00894-012-1385-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 02/15/2012] [Indexed: 02/07/2023]
Abstract
Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases.
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Affiliation(s)
- Gunajyoti Das
- Department of Chemistry, North-Eastern Hill University, Shillong, 793022, India
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38
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39
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Rakovich T, Boland C, Bernstein I, Chikwana VM, Iwata-Reuyl D, Kelly VP. Queuosine deficiency in eukaryotes compromises tyrosine production through increased tetrahydrobiopterin oxidation. J Biol Chem 2011; 286:19354-63. [PMID: 21487017 DOI: 10.1074/jbc.m111.219576] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Queuosine is a modified pyrrolopyrimidine nucleoside found in the anticodon loop of transfer RNA acceptors for the amino acids tyrosine, asparagine, aspartic acid, and histidine. Because it is exclusively synthesized by bacteria, higher eukaryotes must salvage queuosine or its nucleobase queuine from food and the gut microflora. Previously, animals made deficient in queuine died within 18 days of withdrawing tyrosine, a nonessential amino acid, from the diet (Marks, T., and Farkas, W. R. (1997) Biochem. Biophys. Res. Commun. 230, 233-237). Here, we show that human HepG2 cells deficient in queuine and mice made deficient in queuosine-modified transfer RNA, by disruption of the tRNA guanine transglycosylase enzyme, are compromised in their ability to produce tyrosine from phenylalanine. This has similarities to the disease phenylketonuria, which arises from mutation in the enzyme phenylalanine hydroxylase or from a decrease in the supply of its cofactor tetrahydrobiopterin (BH4). Immunoblot and kinetic analysis of liver from tRNA guanine transglycosylase-deficient animals indicates normal expression and activity of phenylalanine hydroxylase. By contrast, BH4 levels are significantly decreased in the plasma, and both plasma and urine show a clear elevation in dihydrobiopterin, an oxidation product of BH4, despite normal activity of the salvage enzyme dihydrofolate reductase. Our data suggest that queuosine modification limits BH4 oxidation in vivo and thereby potentially impacts on numerous physiological processes in eukaryotes.
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Affiliation(s)
- Tatsiana Rakovich
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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40
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Brückl T, Thoma I, Wagner AJ, Knochel P, Carell T. Efficient Synthesis of Deazaguanosine-Derived tRNA Nucleosides PreQ0, PreQ1, and Archaeosine Using the Turbo-Grignard Method. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000987] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Watanabe K. Unique features of animal mitochondrial translation systems. The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2010; 86:11-39. [PMID: 20075606 PMCID: PMC3417567 DOI: 10.2183/pjab.86.11] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 11/17/2009] [Indexed: 05/17/2023]
Abstract
In animal mitochondria, several codons are non-universal and their meanings differ depending on the species. In addition, the tRNA structures that decipher codons are sometimes unusually truncated. These features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. These organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. It is plausible that these events brought about the various characteristic features of animal mt translation systems, such as genetic code variations, unusually truncated tRNA and rRNA structures, unilateral tRNA recognition mechanisms by aminoacyl-tRNA synthetases, elongation factors and ribosomes, and compensation for RNA deficits by enlarged proteins. In this article, we discuss molecular mechanisms for these phenomena. Finally, we describe human mt diseases that are caused by modification defects in mt tRNAs.
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Affiliation(s)
- Kimitsuna Watanabe
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan.
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42
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Boland C, Hayes P, Santa-Maria I, Nishimura S, Kelly VP. Queuosine formation in eukaryotic tRNA occurs via a mitochondria-localized heteromeric transglycosylase. J Biol Chem 2009; 284:18218-27. [PMID: 19414587 DOI: 10.1074/jbc.m109.002477] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
tRNA guanine transglycosylase (TGT) enzymes are responsible for the formation of queuosine in the anticodon loop (position 34) of tRNA(Asp), tRNA(Asn), tRNA(His), and tRNA(Tyr); an almost universal event in eubacterial and eukaryotic species. Despite extensive characterization of the eubacterial TGT the eukaryotic activity has remained undefined. Our search of mouse EST and cDNA data bases identified a homologue of the Escherichia coli TGT and three spliced variants of the queuine tRNA guanine transglycosylase domain containing 1 (QTRTD1) gene. QTRTD1 variant_1 (Qv1) was found to be the predominant adult form. Functional cooperativity of TGT and Qv1 was suggested by their coordinate mRNA expression in Northern blots and from their association in vivo by immunoprecipitation. Neither TGT nor Qv1 alone could complement a tgt mutation in E. coli. However, transglycosylase activity could be obtained when the proteins were combined in vitro. Confocal and immunoblot analysis suggest that TGT weakly interacts with the outer mitochondrial membrane possibly through association with Qv1, which was found to be stably associated with the organelle.
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Affiliation(s)
- Coilin Boland
- School of Biochemistry & Immunology, Trinity College Dublin, Dublin 2, Ireland
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43
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Ogawa T, Hidaka M, Kohno K, Masaki H. Colicin E5 Ribonuclease Domain Cleaves Saccharomyces cerevisiae tRNAs Leading to Impairment of the Cell Growth. J Biochem 2009; 145:461-6. [DOI: 10.1093/jb/mvp004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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44
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Queuine promotes antioxidant defence system by activating cellular antioxidant enzyme activities in cancer. Biosci Rep 2008; 28:73-81. [DOI: 10.1042/bsr20070011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 02/06/2008] [Accepted: 02/22/2008] [Indexed: 11/17/2022] Open
Abstract
Constant generation of ROS (reactive oxygen species) during normal cellular metabolism of an organism is generally balanced by a similar rate of consumption by antioxidants. Imbalance between ROS production and antioxidant defence results in an increased level of ROS, causing oxidative stress, which leads to promotion of malignancy. Queuine is a hyper-modified base analogue of guanine, found at the first anticodon position of the Q-family of tRNAs. These tRNAs are completely modified with respect to queuosine in terminally differentiated somatic cells; however, hypo-modification of Q-tRNAs is closely associated with cell proliferation. Q-tRNA modification is essential for normal development, differentiation and cellular function. Queuine is a nutrient factor for eukaryotes. It is found to promote the cellular antioxidant defence system and inhibit tumorigenesis. The activities of antioxidant enzymes such as catalase, superoxide dismutase, glutathione peroxidase and glutathione reductase are found to be low in the DLAT (Dalton's lymphoma ascites transplanted) mouse liver compared with normal mouse liver. However, exogenous administration of queuine to the DLAT cancerous mouse improves the activities of antioxidant enzymes. These results suggest that queuine promotes the antioxidant defence system by increasing antioxidant enzyme activities and in turn inhibits oxidative stress and tumorigenesis.
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45
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Pathak C, Jaiswal YK, Vinayak M. Queuine mediated inhibition in phosphorylation of tyrosine phosphoproteins in cancer. Mol Biol Rep 2007; 35:369-74. [PMID: 17514433 DOI: 10.1007/s11033-007-9095-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 04/30/2007] [Indexed: 10/23/2022]
Abstract
Protein phosphorylation or dephosphorylation is the most important regulatory switch of signal transduction contributing to control of cell proliferation. The reversibility of phosphorylation and dephosphorylation is due to the activities of kinases and phosphatase, which determine protein phosphorylation level of cell under different physiological and pathological conditions. Receptor tyrosine kinase (RTK) mediated cellular signaling is precisely coordinated and tightly controlled in normal cells which ensures regulated mitosis. Deregulation of RTK signaling resulting in aberrant activation in RTKs leads to malignant transformation. Queuine is one of the modified base of tRNA which participates in down regulation of tyrosine kinase activity. The guanine analogue queuine is a nutrient factor to eukaryotes and occurs as free base or modified nucleoside queuosine into the first anticodon position of specific tRNAs. The tRNAs are often queuine deficient in cancer and fast proliferating tissues. The present study is aimed to investigate queuine mediated inhibition in phosphorylation of tyrosine phosphorylated proteins in lymphoma bearing mouse. The result shows high level of cytosolic and membrane associated tyrosine phosphoprotein in DLAT cancerous mouse liver compared to normal. Queuine treatments down regulate the level of tyrosine phosphoproteins, which suggests that queuine is involved in regulation of mitotic signaling pathways.
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Affiliation(s)
- Chandramani Pathak
- Biochemistry & Molecular Biology Laboratory, Center of Advanced Study in Zoology, Banaras Hindu University, Varanasi, India
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46
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Abstract
An increase in cell number is one of the most prominent characteristics of cancer cells. This may be caused by an increase in cell proliferation or decrease in cell death. Queuine is one of the modified base which is found at first anticodon position of specific tRNAs. It is ubiquitously present throughout the living system except mycoplasma and yeast. The tRNAs of Q-family are completely modified to Q-tRNAs in terminally differentiated somatic cells, however hypomodification of Q-tRNA is closely associated with cell proliferation and malignancy. Queuine participates at various cellular functions such as regulation of cell proliferation, cell signaling and alteration in the expression of growth associated proto-oncogenes. Like other proto-oncogenes bcl2 is known to involve in cell survival by inhibiting apoptosis. Queuine or Q-tRNA is suggested to inhibit cell proliferation but the mechanism of regulation of cell proliferation by queuine or Q-tRNA is not well understood. Therefore, in the present study regulation in cell proliferation by queuine in vivo and in vitro as well as the expression of cell death regulatory protein Bcl2 are investigated. For this DLAT cancerous mouse, U87 cell line and HepG2 cell line are treated with different concentrations of queuine and the effect of queuine on cell proliferation and apoptosis are studied. The results indicate that queuine down regulates cell proliferation and expression of Bcl2 protein, suggesting that queuine promotes cell death and participates in the regulation of cell proliferation.
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47
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Flatt PM, Mahmud T. Biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds. Nat Prod Rep 2006; 24:358-92. [PMID: 17390001 DOI: 10.1039/b603816f] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review covers the biosynthesis of aminocyclitol-aminoglycoside antibiotics and related compounds, particularly from the molecular genetic perspectives. 195 references are cited.
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Affiliation(s)
- Patricia M Flatt
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR 97331-3507, USA
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48
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Takai K. Classification of the possible pairs between the first anticodon and the third codon positions based on a simple model assuming two geometries with which the pairing effectively potentiates the decoding complex. J Theor Biol 2006; 242:564-80. [PMID: 16764891 DOI: 10.1016/j.jtbi.2006.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 02/11/2006] [Accepted: 04/11/2006] [Indexed: 11/24/2022]
Abstract
Crick's wobble theory states that some specific pairs between the bases at the first position of the anticodon (position 34) and the third position of the codon (position III) are allowed and the others are disallowed during the correct codon recognition. However, later researches have shown that the pairing rule, or the wobble rule, is different from the supposed one. Despite the continuing efforts including computer-aided model building studies and analyses of three-dimensional structures in the crystals of the ribosomes, the structural backgrounds of the wobble rule are still unclear. Here, I classify the possible pairs into 6 classes according to the increases accompanying the formation of the pairs in the potential productivity of the decoding complex on the basis of a simple model that was originally proposed previously and is refined here. In the model, the conformation with the base at position 34 displaced toward the minor groove side from the position for the Watson-Crick pairs is supposed to be equivalent to the conformation with the Watson-Crick pairs. It is also reasoned and supposed that some weak pairs may sometimes be allowed depending on the structural context. It is demonstrated that most of the experimental results reported so far are consistent with the model. I discuss on which experimental facts can be reasoned with the model and which need further explanations. I expect that the model will be a good basis for further understanding of the wobble rule and its structural backgrounds.
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Affiliation(s)
- Kazuyuki Takai
- Cell-free Science and Technology Research Center, Ehime University, 3, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan.
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49
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Nishimura S, Watanabe K. The discovery of modified nucleosides from the early days to the present: A personal perspective. J Biosci 2006; 31:465-75. [PMID: 17206067 DOI: 10.1007/bf02705186] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Susumu Nishimura
- Center for TARA, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki, 305-8577, Japan.
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50
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Ogawa T, Inoue S, Yajima S, Hidaka M, Masaki H. Sequence-specific recognition of colicin E5, a tRNA-targeting ribonuclease. Nucleic Acids Res 2006; 34:6065-73. [PMID: 16963495 PMCID: PMC1635277 DOI: 10.1093/nar/gkl629] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Colicin E5 is a novel Escherichia coli ribonuclease that specifically cleaves the anticodons of tRNA(Tyr), tRNA(His), tRNA(Asn) and tRNA(Asp). Since this activity is confined to its 115 amino acid long C-terminal domain (CRD), the recognition mechanism of E5-CRD is of great interest. The four tRNA substrates share the unique sequence UQU within their anticodon loops, and are cleaved between Q (modified base of G) and 3' U. Synthetic minihelix RNAs corresponding to the substrate tRNAs were completely susceptible to E5-CRD and were cleaved in the same manner as the authentic tRNAs. The specificity determinant for E5-CRD was YGUN at -1 to +3 of the 'anticodon'. The YGU is absolutely required and the extent of susceptibility of minihelices depends on N (third letter of the anticodon) in the order A > C > G > U accounting for the order of susceptibility tRNA(Tyr) > tRNA(Asp) > tRNA(His), tRNA(Asn). Contrastingly, we showed that GpUp is the minimal substrate strictly retaining specificity to E5-CRD. The effect of contiguous nucleotides is inconsistent between the loop and linear RNAs, suggesting that nucleotide extension on each side of GpUp introduces a structural constraint, which is reduced by a specific loop structure formation that includes a 5' pyrimidine and 3' A.
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Affiliation(s)
- Tetsuhiro Ogawa
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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