tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory

Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability. Significance Statement tRNA modifying enzymes are emerging as important regulators of nervous system development and function due to their growing links to neurological disorders. Yet, their roles in the nervous system remain largely elusive. Through in vivo studies in Drosophila, we link tRNA methyltransferase-regulated selenoprotein synthesis to synapse development and associative memory. These findings demonstrate the key role of tRNA modifiers in redox homeostasis during nervous system development and highlight the potential therapeutic benefit of antioxidant-based therapies for cognitive disorders linked to dysregulation of tRNA modification.

[1]  M. Koutmos,et al.  Selenoproteins and tRNA-Sec: regulators of cancer redox homeostasis. , 2023, Trends in cancer.

[2]  R. Burgess,et al.  tRNA Dysregulation in Neurodevelopmental and Neurodegenerative Diseases. , 2023, Annual review of cell and developmental biology.

[3]  Sunil Q. Mehta,et al.  The role of selenoproteins in neurodevelopment and neurological function: Implications in autism spectrum disorder , 2023, Frontiers in Molecular Neuroscience.

[4]  Chunfang Zhang,et al.  tRNA Modifications and Modifying Enzymes in Disease, the Potential Therapeutic Targets , 2023, International journal of biological sciences.

[5]  Š. Vaňáčová,et al.  HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs , 2022, RNA.

[6]  Thomas J. Begley,et al.  Selenoproteins and the senescence-associated epitranscriptome , 2022, Experimental biology and medicine.

[7]  U. Schweizer,et al.  Selenoproteins in brain development and function. , 2022, Free radical biology & medicine.

[8]  Changsoo Kim,et al.  Dual Oxidase, a Hydrogen-Peroxide-Producing Enzyme, Regulates Neuronal Oxidative Damage and Animal Lifespan in Drosophila melanogaster , 2022, Cells.

[9]  Muhammad Umair,et al.  Case Report: Biallelic Variant in the tRNA Methyltransferase Domain of the AlkB Homolog 8 Causes Syndromic Intellectual Disability , 2022, Frontiers in Genetics.

[10]  P. Sil,et al.  ROS-Influenced Regulatory Cross-Talk With Wnt Signaling Pathway During Perinatal Development , 2022, Frontiers in Molecular Biosciences.

[11]  M. Francis,et al.  Reactive Oxygen Species: Angels and Demons in the Life of a Neuron , 2022, NeuroSci.

[12]  T. Pan,et al.  tRNA modification dynamics from individual organisms to metaepitranscriptomics of microbiomes. , 2022, Molecular cell.

[13]  K. Chatterjee,et al.  Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency , 2021, International journal of molecular sciences.

[14]  F. Alkuraya,et al.  Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant , 2021, Human Genetics.

[15]  E. Wang,et al.  Modifications of the human tRNA anticodon loop and their associations with genetic diseases , 2021, Cellular and Molecular Life Sciences.

[16]  Thomas J. Begley,et al.  Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen , 2021, bioRxiv.

[17]  R. Gillette,et al.  Characterization of Neuronal RNA Modifications during Non-associative Learning in Aplysia Reveals Key Roles for tRNAs in Behavioral Sensitization , 2021, ACS central science.

[18]  A. D. L. de la Cruz,et al.  Local Translation in Nervous System Pathologies , 2021, Frontiers in Integrative Neuroscience.

[19]  J. Lupski,et al.  Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant , 2021, American journal of medical genetics. Part A.

[20]  Tsutomu Suzuki The expanding world of tRNA modifications and their disease relevance , 2021, Nature Reviews Molecular Cell Biology.

[21]  U. Schweizer,et al.  The Neurobiology of Selenium: Looking Back and to the Future , 2021, Frontiers in Neuroscience.

[22]  C. Brandl,et al.  Transfer RNAs: diversity in form and function , 2020, RNA biology.

[23]  Laura Fort-Aznar,et al.  JNK signalling regulates antioxidant responses in neurons , 2020, bioRxiv.

[24]  Y. Ok,et al.  Role of Selenoproteins in Redox Regulation of Signaling and the Antioxidant System: A Review , 2020, Antioxidants.

[25]  Thomas J. Begley,et al.  The epitranscriptomic writer ALKBH8 drives tolerance and protects mouse lungs from the environmental pollutant naphthalene , 2020, Epigenetics.

[26]  F. Alkuraya,et al.  An intellectual disability‐associated missense variant in TRMT1 impairs tRNA modification and reconstitution of enzymatic activity , 2020, Human mutation.

[27]  Thomas J. Begley,et al.  Loss of epitranscriptomic control of selenocysteine utilization engages senescence and mitochondrial reprogramming , 2019, Redox biology.

[28]  Liang-Jun Yan,et al.  Role of Catalase in Oxidative Stress- and Age-Associated Degenerative Diseases , 2019, Oxidative Medicine and Cellular Longevity.

[29]  Thomas J. Begley,et al.  Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. , 2019, Free radical biology & medicine.

[30]  José Antonio Valer,et al.  Interplay between BMPs and Reactive Oxygen Species in Cell Signaling and Pathology , 2019, Biomolecules.

[31]  J. O'donnell,et al.  Innate immune responses to paraquat exposure in a Drosophila model of Parkinson’s disease , 2019, Scientific Reports.

[32]  Chi-Kuang Yao,et al.  A circuit-dependent ROS feedback loop mediates glutamate excitotoxicity to sculpt the Drosophila motor system , 2019, eLife.

[33]  F. Alkuraya,et al.  Recessive Truncating Mutations in ALKBH8 Cause Intellectual Disability and Severe Impairment of Wobble Uridine Modification. , 2019, American journal of human genetics.

[34]  Dragony Fu,et al.  The emerging impact of tRNA modifications in the brain and nervous system. , 2019, Biochimica et biophysica acta. Gene regulatory mechanisms.

[35]  M. Landgraf,et al.  Reactive oxygen species regulate activity-dependent neuronal plasticity in Drosophila , 2018, eLife.

[36]  Manuel A. S. Santos,et al.  Impact of tRNA Modifications and tRNA-Modifying Enzymes on Proteostasis and Human Disease , 2018, International journal of molecular sciences.

[37]  A. Riccio,et al.  Post-transcriptional Processing of mRNA in Neurons: The Vestiges of the RNA World Drive Transcriptome Diversity , 2018, Front. Mol. Neurosci..

[38]  W. Sossin,et al.  Translational Control in the Brain in Health and Disease. , 2018, Cold Spring Harbor perspectives in biology.

[39]  M. Hammell,et al.  Chromatin-mediated translational control is essential for neural cell fate specification , 2018, Life Science Alliance.

[40]  R. Branicky,et al.  Superoxide dismutases: Dual roles in controlling ROS damage and regulating ROS signaling , 2018, The Journal of cell biology.

[41]  D. Söll,et al.  Transfer RNA function and evolution , 2018, RNA biology.

[42]  M. Landgraf,et al.  Regulation of neuronal development and function by ROS , 2018, FEBS letters.

[43]  Jimok Yoon,et al.  The MICALs are a Family of F-actin Dismantling Oxidoreductases Conserved from Drosophila to Humans , 2018, Scientific Reports.

[44]  D. Dickman,et al.  Endogenous tagging reveals differential regulation of Ca2+ channels at single AZs during presynaptic homeostatic potentiation and depression , 2017, bioRxiv.

[45]  C. González-Billault,et al.  From birth to death: A role for reactive oxygen species in neuronal development. , 2017, Seminars in cell & developmental biology.

[46]  R. Fetter,et al.  Retrograde Semaphorin-Plexin Signaling Drives Homeostatic Synaptic Plasticity , 2017, Nature.

[47]  Tao Pan,et al.  Dynamic RNA Modifications in Gene Expression Regulation , 2017, Cell.

[48]  A. Bednářová,et al.  Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders , 2017, Front. Mol. Neurosci..

[49]  Sebastian A. Leidel,et al.  Wobble uridine modifications–a reason to live, a reason to die?! , 2017, RNA biology.

[50]  Sarah M. Carpanini,et al.  Analysis of gene expression in the nervous system identifies key genes and novel candidates for health and disease , 2017, neurogenetics.

[51]  H. Sies Hydrogen peroxide as a central redox signaling molecule in physiological oxidative stress: Oxidative eustress☆ , 2017, Redox biology.

[52]  H. Zhan,et al.  Fife organizes synaptic vesicles and calcium channels for high-probability neurotransmitter release , 2017, The Journal of cell biology.

[53]  U. Schweizer,et al.  Why 21? The significance of selenoproteins for human health revealed by inborn errors of metabolism , 2016, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[54]  Pavel Masek,et al.  Gustatory processing and taste memory in Drosophila , 2016, Journal of neurogenetics.

[55]  Luonan Chen,et al.  Gene expression profiling of selenophosphate synthetase 2 knockdown in Drosophila melanogaster. , 2016, Metallomics : integrated biometal science.

[56]  E. Westhof,et al.  Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code , 2016, Nature Communications.

[57]  Thomas J. Begley,et al.  Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation , 2015, PLoS genetics.

[58]  M. Graille,et al.  Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure , 2015, Nucleic acids research.

[59]  Zesheng Zhang,et al.  Cordyceps sinensis oral liquid prolongs the lifespan of the fruit fly, Drosophila melanogaster, by inhibiting oxidative stress , 2015, International journal of molecular medicine.

[60]  A. Paetau,et al.  Selenoprotein biosynthesis defect causes progressive encephalopathy with elevated lactate , 2015, Neurology.

[61]  Thomas J. Begley,et al.  Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage , 2015, PloS one.

[62]  T. Ziv,et al.  Cell-selective labelling of proteomes in Drosophila melanogaster , 2015, Nature Communications.

[63]  R. Burgess,et al.  Impaired protein translation in Drosophila models for Charcot–Marie–Tooth neuropathy caused by mutant tRNA synthetases , 2015, Nature Communications.

[64]  Gerald M. Rubin,et al.  A Dopamine-Modulated Neural Circuit Regulating Aversive Taste Memory in Drosophila , 2015, Current Biology.

[65]  Kristin Scott,et al.  Gustatory Learning and Processing in the Drosophila Mushroom Bodies , 2015, The Journal of Neuroscience.

[66]  J. Jackman,et al.  Diversity in mechanism and function of tRNA methyltransferases , 2015, RNA biology.

[67]  Z. Ignatova,et al.  Emerging roles of tRNA in adaptive translation, signalling dynamics and disease , 2014, Nature Reviews Genetics.

[68]  Z. Modrušan,et al.  Regulation of Neuronal Gene Expression and Survival by Basal NMDA Receptor Activity: A Role for Histone Deacetylase 4 , 2014, The Journal of Neuroscience.

[69]  V. Gladyshev,et al.  Selenoproteins: molecular pathways and physiological roles. , 2014, Physiological reviews.

[70]  H. Hori Methylated nucleosides in tRNA and tRNA methyltransferases , 2014, Front. Genet..

[71]  I. Mansuy,et al.  Epigenetic regulation in neurodevelopment and neurodegenerative diseases , 2014, Neuroscience.

[72]  Clement T Y Chan,et al.  Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry , 2014, Nature Protocols.

[73]  C. Rubinstein,et al.  Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila , 2014, Genetics.

[74]  C. Holt,et al.  The Central Dogma Decentralized: New Perspectives on RNA Function and Local Translation in Neurons , 2013, Neuron.

[75]  Mikyoung Park,et al.  Growth factors in synaptic function , 2013, Front. Synaptic Neurosci..

[76]  Ravikumar Hosamani Acute exposure of Drosophila melanogaster to paraquat causes oxidative stress and mitochondrial dysfunction. , 2013, Archives of insect biochemistry and physiology.

[77]  V. de Crécy-Lagard,et al.  Biosynthesis and function of posttranscriptional modifications of transfer RNAs. , 2012, Annual review of genetics.

[78]  Pavel Masek,et al.  Optogenetic induction of aversive taste memory , 2012, Neuroscience.

[79]  Ashish Patil,et al.  Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications , 2012, RNA biology.

[80]  P. Salinas Wnt signaling in the vertebrate central nervous system: from axon guidance to synaptic function. , 2012, Cold Spring Harbor perspectives in biology.

[81]  S. Sweeney,et al.  Oxidative stress in synapse development and function , 2012, Developmental neurobiology.

[82]  J. Watterson,et al.  Paraquat administration in Drosophila for use in metabolic studies of oxidative stress. , 2011, Analytical biochemistry.

[83]  S. Sweeney,et al.  Oxidative stress induces overgrowth of the Drosophila neuromuscular junction , 2011, Proceedings of the National Academy of Sciences.

[84]  M. Gallo,et al.  Taste Learning and Memory: A Window on the Study of Brain Aging , 2011, Front. Syst. Neurosci..

[85]  F. Kirpekar,et al.  Roles of Trm9- and ALKBH8-like proteins in the formation of modified wobble uridines in Arabidopsis tRNA , 2011, Nucleic acids research.

[86]  V. Gladyshev,et al.  Analyses of Fruit Flies That Do Not Express Selenoproteins or Express the Mouse Selenoprotein, Methionine Sulfoxide Reductase B1, Reveal a Role of Selenoproteins in Stress Resistance* , 2011, The Journal of Biological Chemistry.

[87]  F. Kirpekar,et al.  ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA. , 2011, Nature communications.

[88]  Clement T Y Chan,et al.  A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress , 2010, PLoS genetics.

[89]  T. Pan,et al.  The AlkB domain of mammalian ABH8 catalyzes hydroxylation of 5-methoxycarbonylmethyluridine at the wobble position of tRNA. , 2010, Angewandte Chemie.

[90]  D. Söll,et al.  Mutations disrupting selenocysteine formation cause progressive cerebello-cerebral atrophy. , 2010, American journal of human genetics.

[91]  Kristin Scott,et al.  Limited taste discrimination in Drosophila , 2010, Proceedings of the National Academy of Sciences.

[92]  Elias S. J. Arnér Selenoproteins-What unique properties can arise with selenocysteine in place of cysteine? , 2010, Experimental cell research.

[93]  Clement T Y Chan,et al.  Human AlkB Homolog ABH8 Is a tRNA Methyltransferase Required for Wobble Uridine Modification and DNA Damage Survival , 2010, Molecular and Cellular Biology.

[94]  F. Kirpekar,et al.  Mammalian ALKBH8 Possesses tRNA Methyltransferase Activity Required for the Biogenesis of Multiple Wobble Uridine Modifications Implicated in Translational Decoding , 2010, Molecular and Cellular Biology.

[95]  Simon Tavaré,et al.  Hydrogen Peroxide Stimulates Activity and Alters Behavior in Drosophila melanogaster , 2009, PloS one.

[96]  Anirvan Ghosh,et al.  A Brief History of Neuronal Gene Expression: Regulatory Mechanisms and Cellular Consequences , 2008, Neuron.

[97]  I. Wood,et al.  Regulation of gene expression in the nervous system. , 2008, The Biochemical journal.

[98]  Steven W. Flavell,et al.  Signaling mechanisms linking neuronal activity to gene expression and plasticity of the nervous system. , 2008, Annual review of neuroscience.

[99]  Thomas J. Begley,et al.  Trm9-catalyzed tRNA modifications link translation to the DNA damage response. , 2007, Molecular cell.

[100]  Barry J Dickson,et al.  Function of the Drosophila CPEB protein Orb2 in long-term courtship memory , 2007, Nature Neuroscience.

[101]  M. Berry,et al.  Selenoprotein H Is a Redox-sensing High Mobility Group Family DNA-binding Protein That Up-regulates Genes Involved in Glutathione Synthesis and Phase II Detoxification* , 2007, Journal of Biological Chemistry.

[102]  A. Diantonio,et al.  Synaptic development: insights from Drosophila , 2007, Current Opinion in Neurobiology.

[103]  V. Villalobos,et al.  Paraquat-induced Oxidative Stress in Drosophila melanogaster: Effects of Melatonin, Glutathione, Serotonin, Minocycline, Lipoic Acid and Ascorbic Acid , 2006, Neurochemical Research.

[104]  G. D. de Polavieja,et al.  Age-Independent Synaptogenesis by Phosphoinositide 3 Kinase , 2006, The Journal of Neuroscience.

[105]  So Yeon Kwon,et al.  A DNA replication-related element downstream from the initiation site of Drosophila selenophosphate synthetase 2 gene is essential for its transcription. , 2004, Nucleic acids research.

[106]  S. Clarke,et al.  Novel Methyltransferase for Modified Uridine Residues at the Wobble Position of tRNA , 2003, Molecular and Cellular Biology.

[107]  R. Guigó,et al.  Characterization of Mammalian Selenoproteomes , 2003, Science.

[108]  V. Budnik,et al.  The Drosophila Wnt, Wingless, Provides an Essential Signal for Pre- and Postsynaptic Differentiation , 2002, Cell.

[109]  M. Ramaswami,et al.  AP-1 functions upstream of CREB to control synaptic plasticity in Drosophila , 2002, Nature.

[110]  Richard D. Fetter,et al.  wishful thinking Encodes a BMP Type II Receptor that Regulates Synaptic Growth in Drosophila , 2002, Neuron.

[111]  M. O’Connor,et al.  The Drosophila BMP Type II Receptor Wishful Thinking Regulates Neuromuscular Synapse Morphology and Function , 2002, Neuron.

[112]  G. Kryukov,et al.  Selenium Metabolism in Drosophila , 2001, The Journal of Biological Chemistry.

[113]  R. Guigó,et al.  In silico identification of novel selenoproteins in the Drosophila melanogaster genome , 2001, EMBO reports.

[114]  V. Ramakrishnan,et al.  Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit , 2001, Science.

[115]  H. Jäckle,et al.  The class 2 selenophosphate synthetase gene of Drosophila contains a functional mammalian‐type SECIS , 2000, EMBO reports.

[116]  D. Hatfield,et al.  Dietary selenium affects methylation of the wobble nucleoside in the anticodon of selenocysteine tRNA([Ser]Sec). , 1993, The Journal of biological chemistry.

[117]  A. Benda,et al.  ALKB-8, a 2-Oxoglutarate-Dependent Dioxygenase and S-Adenosine Methionine-Dependent Methyltransferase Modulates Metabolic Events Linked to Lysosome-Related Organelles and Aging in C. elegans. , 2018, Folia biologica.

[118]  Thomas J. Begley,et al.  A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications. , 2015, Methods in enzymology.

[119]  J. Alfonzo,et al.  Transfer RNA modifications: nature's combinatorial chemistry playground , 2013, Wiley interdisciplinary reviews. RNA.

[120]  V. Gladyshev,et al.  Selenocysteine incorporation machinery and the role of selenoproteins in development and health. , 2006, Progress in nucleic acid research and molecular biology.

[121]  G. Rubin,et al.  The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes , 2004 .

[122]  Vadim N. Gladyshev,et al.  SELENOPROTEINS, SELENOPROTEIN mRNA EXPRESSION, FERTILITY, AND MORTALITY* , 2001 .

[123]  J. Ule,et al.  Opus: University of Bath Online Publication Store Aberrant Methylation of Trnas Links Cellular Stress to Neuro-developmental Disorders , 2022 .