1
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Wei G, Russo S, Tuorto F. Lost in translation: How neurons cope with tRNA decoding. Bioessays 2024:e2400107. [PMID: 38990077 DOI: 10.1002/bies.202400107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Post-transcriptional tRNA modifications contribute to the decoding efficiency of tRNAs by supporting codon recognition and tRNA stability. Recent work shows that the molecular and cellular functions of tRNA modifications and tRNA-modifying-enzymes are linked to brain development and neurological disorders. Lack of these modifications affects codon recognition and decoding rate, promoting protein aggregation and translational stress response pathways with toxic consequences to the cell. In this review, we discuss the peculiarity of local translation in neurons, suggesting a role for fine-tuning of translation performed by tRNA modifications. We provide several examples of tRNA modifications involved in physiology and pathology of the nervous system, highlighting their effects on protein translation and discussing underlying mechanisms, like the unfolded protein response (UPR), ribosome quality control (RQC), and no-go mRNA decay (NGD), which could affect neuronal functions. We aim to deepen the understanding of the roles of tRNA modifications and the coordination of these modifications with the protein translation machinery in the nervous system.
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Affiliation(s)
- Guo Wei
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Stefano Russo
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Francesca Tuorto
- Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3), Mannheim Cancer Center (MCC), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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2
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Cotter M, Quinn SM, Fearon U, Ansboro S, Rakovic T, Southern JM, Kelly VP, Connon SJ. A new class of 7-deazaguanine agents targeting autoimmune diseases: dramatic reduction of synovial fibroblast IL-6 production from human rheumatoid arthritis patients and improved performance against murine experimental autoimmune encephalomyelitis. RSC Med Chem 2024; 15:1556-1564. [PMID: 38784475 PMCID: PMC11110761 DOI: 10.1039/d4md00028e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/17/2024] [Indexed: 05/25/2024] Open
Abstract
A simple in vitro assay involving the measurement of IL-6 production in human synovial fibroblasts from rheumatoid arthritis patients has been utilised to select candidates from a targeted library of queuine tRNA ribosyltransferase (QTRT) substrates for subsequent in vivo screening in murine experimental autoimmune encephalomyelitis (EAE - a model of multiple sclerosis). The in vitro activity assay discriminated between poor and excellent 7-deazaguanine QTRT substrates and allowed the identification of several structures which subsequently outperformed the previous lead in EAE. Two molecules were of significant promise: one rigidified analogue of the lead, and another considerably simpler structure incorporating an oxime motif which differs structurally from the lead to a considerable extent. These studies provide data from human cells for the first time and have expanded both the chemical space and current understanding of the structure-activity relationship underpinning the remarkable potential of 7-deazguanines in a Multiple Sclerosis disease model.
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Affiliation(s)
- Michelle Cotter
- School of Chemistry, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Shauna M Quinn
- School of Biochemistry & Immunology, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Ursula Fearon
- School of Medicine, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Sharon Ansboro
- School of Medicine, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Tatsiana Rakovic
- School of Medicine, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - John M Southern
- School of Chemistry, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Vincent P Kelly
- School of Biochemistry & Immunology, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity College, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin Ireland
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3
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de Crécy-Lagard V, Hutinet G, Cediel-Becerra JDD, Yuan Y, Zallot R, Chevrette MG, Ratnayake RMMN, Jaroch M, Quaiyum S, Bruner S. Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages. Microbiol Mol Biol Rev 2024; 88:e0019923. [PMID: 38421302 PMCID: PMC10966956 DOI: 10.1128/mmbr.00199-23] [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] [Indexed: 03/02/2024] Open
Abstract
SUMMARYDeazaguanine modifications play multifaceted roles in the molecular biology of DNA and tRNA, shaping diverse yet essential biological processes, including the nuanced fine-tuning of translation efficiency and the intricate modulation of codon-anticodon interactions. Beyond their roles in translation, deazaguanine modifications contribute to cellular stress resistance, self-nonself discrimination mechanisms, and host evasion defenses, directly modulating the adaptability of living organisms. Deazaguanine moieties extend beyond nucleic acid modifications, manifesting in the structural diversity of biologically active natural products. Their roles in fundamental cellular processes and their presence in biologically active natural products underscore their versatility and pivotal contributions to the intricate web of molecular interactions within living organisms. Here, we discuss the current understanding of the biosynthesis and multifaceted functions of deazaguanines, shedding light on their diverse and dynamic roles in the molecular landscape of life.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
- University of Florida Genetics Institute, Gainesville, Florida, USA
| | - Geoffrey Hutinet
- Department of Biology, Haverford College, Haverford, Pennsylvania, USA
| | | | - Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Rémi Zallot
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - Marc G. Chevrette
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | | | - Marshall Jaroch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, USA
| | - Steven Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
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4
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Sebastiani M, Behrens C, Dörr S, Gerber HD, Benazza R, Hernandez-Alba O, Cianférani S, Klebe G, Heine A, Reuter K. Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase. ACS Chem Biol 2022; 17:2229-2247. [PMID: 35815944 DOI: 10.1021/acschembio.2c00368] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In tRNAAsp, tRNAAsn, tRNATyr, and tRNAHis of most bacteria and eukaryotes, the anticodon wobble position may be occupied by the modified nucleoside queuosine, which affects the speed and the accuracy of translation. Since eukaryotes are not able to synthesize queuosine de novo, they have to salvage queuine (the queuosine base) as a micronutrient from food and/or the gut microbiome. The heterodimeric Zn2+ containing enzyme tRNA-guanine transglycosylase (TGT) catalyzes the insertion of queuine into the above-named tRNAs in exchange for the genetically encoded guanine. This enzyme has attracted medical interest since it was shown to be potentially useful for the treatment of multiple sclerosis. In addition, TGT inactivation via gene knockout leads to the suppressed cell proliferation and migration of certain breast cancer cells, which may render this enzyme a potential target for the design of compounds supporting breast cancer therapy. As a prerequisite to fully exploit the medical potential of eukaryotic TGT, we have determined and analyzed a number of crystal structures of the functional murine TGT with and without bound queuine. In addition, we have investigated the importance of two residues of its non-catalytic subunit on dimer stability and determined the Michaelis-Menten parameters of murine TGT with respect to tRNA and several natural and artificial nucleobase substrates. Ultimately, on the basis of available TGT crystal structures, we provide an entirely conclusive reaction mechanism for this enzyme, which in detail explains why the TGT-catalyzed insertion of some nucleobases into tRNA occurs reversibly while that of others is irreversible.
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Affiliation(s)
- Maurice Sebastiani
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Christina Behrens
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Stefanie Dörr
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
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5
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Shaukat AN, Kaliatsi EG, Stamatopoulou V, Stathopoulos C. Mitochondrial tRNA-Derived Fragments and Their Contribution to Gene Expression Regulation. Front Physiol 2021; 12:729452. [PMID: 34539450 PMCID: PMC8446549 DOI: 10.3389/fphys.2021.729452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/09/2021] [Indexed: 01/14/2023] Open
Abstract
Mutations in human mitochondrial tRNAs (mt-tRNAs) are responsible for several and sometimes severe clinical phenotypes, classified among mitochondrial diseases. In addition, post-transcriptional modifications of mt-tRNAs in correlation with several stress signals can affect their stability similarly to what has been described for their nuclear-encoded counterparts. Many of the perturbations related to either point mutations or aberrant modifications of mt-tRNAs can lead to specific cleavage and the production of mitochondrial tRNA-derived fragments (mt-tRFs). Although mt-tRFs have been detected in several studies, the exact biogenesis steps and biological role remain, to a great extent, unexplored. Several mt-tRFs are produced because of the excessive oxidative stress which predominantly affects mitochondrial DNA integrity. In addition, mt-tRFs have been detected in various diseases with possible detrimental consequences, but also their production may represent a response mechanism to external stimuli, including infections from pathogens. Finally, specific point mutations on mt-tRNAs have been reported to impact the pool of the produced mt-tRFs and there is growing evidence suggesting that mt-tRFs can be exported and act in the cytoplasm. In this review, we summarize current knowledge on mitochondrial tRNA-deriving fragments and their possible contribution to gene expression regulation.
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Affiliation(s)
| | - Eleni G Kaliatsi
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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6
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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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7
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Fergus C, Al-Qasem M, Cotter M, McDonnell CM, Sorrentino E, Chevot F, Hokamp K, Senge MO, Southern JM, Connon SJ, Kelly VP. The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity. Nucleic Acids Res 2021; 49:4877-4890. [PMID: 34009357 PMCID: PMC8136771 DOI: 10.1093/nar/gkab289] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/12/2022] Open
Abstract
Base-modification can occur throughout a transfer RNA molecule; however, elaboration is particularly prevalent at position 34 of the anticodon loop (the wobble position), where it functions to influence protein translation. Previously, we demonstrated that the queuosine modification at position 34 can be substituted with an artificial analogue via the queuine tRNA ribosyltransferase enzyme to induce disease recovery in an animal model of multiple sclerosis. Here, we demonstrate that the human enzyme can recognize a very broad range of artificial 7-deazaguanine derivatives for transfer RNA incorporation. By contrast, the enzyme displays strict specificity for transfer RNA species decoding the dual synonymous NAU/C codons, determined using a novel enzyme-RNA capture-release method. Our data highlight the broad scope and therapeutic potential of exploiting the queuosine incorporation pathway to intentionally engineer chemical diversity into the transfer RNA anticodon.
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Affiliation(s)
- Claire Fergus
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Mashael Al-Qasem
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Michelle Cotter
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Ciara M McDonnell
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Emiliano Sorrentino
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Franciane Chevot
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Karsten Hokamp
- School of Genetics and Microbiology, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Mathias O Senge
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - John M Southern
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Stephen J Connon
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, The University of Dublin, 152-160 Pearse Street, Dublin 2, Ireland
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8
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Yuan Y, Zallot R, Grove TL, Payan DJ, Martin-Verstraete I, Šepić S, Balamkundu S, Neelakandan R, Gadi VK, Liu CF, Swairjo MA, Dedon PC, Almo SC, Gerlt JA, de Crécy-Lagard V. Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. Proc Natl Acad Sci U S A 2019; 116:19126-19135. [PMID: 31481610 PMCID: PMC6754566 DOI: 10.1073/pnas.1909604116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Queuosine (Q) is a complex tRNA modification widespread in eukaryotes and bacteria that contributes to the efficiency and accuracy of protein synthesis. Eukaryotes are not capable of Q synthesis and rely on salvage of the queuine base (q) as a Q precursor. While many bacteria are capable of Q de novo synthesis, salvage of the prokaryotic Q precursors preQ0 and preQ1 also occurs. With the exception of Escherichia coli YhhQ, shown to transport preQ0 and preQ1, the enzymes and transporters involved in Q salvage and recycling have not been well described. We discovered and characterized 2 Q salvage pathways present in many pathogenic and commensal bacteria. The first, found in the intracellular pathogen Chlamydia trachomatis, uses YhhQ and tRNA guanine transglycosylase (TGT) homologs that have changed substrate specificities to directly salvage q, mimicking the eukaryotic pathway. The second, found in bacteria from the gut flora such as Clostridioides difficile, salvages preQ1 from q through an unprecedented reaction catalyzed by a newly defined subgroup of the radical-SAM enzyme family. The source of q can be external through transport by members of the energy-coupling factor (ECF) family or internal through hydrolysis of Q by a dedicated nucleosidase. This work reinforces the concept that hosts and members of their associated microbiota compete for the salvage of Q precursors micronutrients.
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Affiliation(s)
- Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Rémi Zallot
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Daniel J Payan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Isabelle Martin-Verstraete
- Laboratoire de Pathogénèse des Bactéries Anaérobies, Institut Pasteur et Université de Paris, F-75015 Paris, France
| | - Sara Šepić
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Vinod K Gadi
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Chuan-Fa Liu
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182
- The Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
- Department of Biological Engineering and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611;
- University of Florida Genetics Institute, Gainesville, FL 32610
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9
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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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10
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Behrens C, Biela I, Petiot-Bécard S, Botzanowski T, Cianférani S, Sager CP, Klebe G, Heine A, Reuter K. Homodimer Architecture of QTRT2, the Noncatalytic Subunit of the Eukaryotic tRNA-Guanine Transglycosylase. Biochemistry 2018; 57:3953-3965. [DOI: 10.1021/acs.biochem.8b00294] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Christina Behrens
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Inna Biela
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Stéphanie Petiot-Bécard
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Christoph P. Sager
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
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11
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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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12
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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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Cross-Talk between Dnmt2-Dependent tRNA Methylation and Queuosine Modification. Biomolecules 2017; 7:biom7010014. [PMID: 28208632 PMCID: PMC5372726 DOI: 10.3390/biom7010014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 12/22/2022] Open
Abstract
Enzymes of the Dnmt2 family of methyltransferases have yielded a number of unexpected discoveries. The first surprise came more than ten years ago when it was realized that, rather than being DNA methyltransferases, Dnmt2 enzymes actually are transfer RNA (tRNA) methyltransferases for cytosine-5 methylation, foremost C38 (m5C38) of tRNAAsp. The second unanticipated finding was our recent discovery of a nutritional regulation of Dnmt2 in the fission yeast Schizosaccharomyces pombe. Significantly, the presence of the nucleotide queuosine in tRNAAsp strongly stimulates Dnmt2 activity both in vivo and in vitro in S. pombe. Queuine, the respective base, is a hypermodified guanine analog that is synthesized from guanosine-5’-triphosphate (GTP) by bacteria. Interestingly, most eukaryotes have queuosine in their tRNA. However, they cannot synthesize it themselves, but rather salvage it from food or from gut microbes. The queuine obtained from these sources comes from the breakdown of tRNAs, where the queuine ultimately was synthesized by bacteria. Queuine thus has been termed a micronutrient. This review summarizes the current knowledge of Dnmt2 methylation and queuosine modification with respect to translation as well as the organismal consequences of the absence of these modifications. Models for the functional cooperation between these modifications and its wider implications are discussed.
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