1
|
Mao XL, Eriani G, Zhou XL. ADATs: roles in tRNA editing and relevance to disease. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39034823 DOI: 10.3724/abbs.2024125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024] Open
Abstract
Transfer RNAs (tRNAs) play central roles in protein biosynthesis. Post-transcriptional RNA modifications affect tRNA function and stability. Among these modifications, RNA editing is a widespread RNA modification in three domains of life. Proteins of the adenosine deaminase acting on tRNA (ADAT) family were discovered more than 20 years ago. They catalyze the deamination of adenosine to inosine (A-to-I) or cytidine to uridine (C-to-U) during tRNA maturation. The most studied example is the TadA- or ADAT2/3-mediated A-to-I conversion of the tRNA wobble position in the anticodon of prokaryotic or eukaryotic tRNAs, respectively. This review provides detailed information on A-to-I and C-to-U editing of tRNAs in different domains of life, presents recent new findings on ADATs for DNA editing, and finally comments on the association of mutations in the ADAT3 gene with intellectual disability.
Collapse
Affiliation(s)
- Xue-Ling Mao
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 2 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Xiao-Long Zhou
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| |
Collapse
|
2
|
Del-Pozo-Rodriguez J, Tilly P, Lecat R, Vaca HR, Mosser L, Balla T, Gomes MV, Ramos-Morales E, Brivio E, Salinas-Giégé T, VanNoy G, England EM, Lovgren AK, O'Leary M, Chopra M, Gable D, Alnuzha A, Kamel M, Almenabawy N, O'Donnell-Luria A, Neil JE, Gleeson JG, Walsh CA, Elkhateeb N, Selim L, Srivastava S, Nedialkova DD, Drouard L, Romier C, Bayam E, Godin JD. Neurodevelopmental disorders associated variants in ADAT3 disrupt the activity of the ADAT2/ADAT3 tRNA deaminase complex and impair neuronal migration. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.01.24303485. [PMID: 38496416 PMCID: PMC10942499 DOI: 10.1101/2024.03.01.24303485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The ADAT2/ADAT3 complex catalyzes the adenosine to inosine modification at the wobble position of eukaryotic tRNAs. Mutations in ADAT3 , the catalytically inactive subunit of the ADAT2/ADAT3 complex, have been identified in patients presenting with severe neurodevelopmental disorders (NDDs). Yet, the physiological function of ADAT2/ADAT3 complex during brain development remains totally unknown. Here we showed that maintaining a proper level of ADAT2/ADAT3 catalytic activity is required for correct radial migration of projection neurons in the developing mouse cortex. In addition, we not only reported 7 new NDD patients carrying biallelic variants in ADAT3 but also deeply characterize the impact of those variants on ADAT2/ADAT3 structure, biochemical properties, enzymatic activity and tRNAs editing and abundance. We demonstrated that all the identified variants alter both the expression and the activity of the complex leading to a significant decrease of I 34 with direct consequence on their steady-state. Using in vivo complementation assays, we correlated the severity of the migration phenotype with the degree of the loss of function caused by the variants. Altogether, our results indicate a critical role of ADAT2/ADAT3 during cortical development and provide cellular and molecular insights into the pathogenicity of ADAT3-related neurodevelopmental disorder.
Collapse
|
3
|
Zhang F, Ignatova VV, Ming GL, Song H. Advances in brain epitranscriptomics research and translational opportunities. Mol Psychiatry 2024; 29:449-463. [PMID: 38123727 PMCID: PMC11116067 DOI: 10.1038/s41380-023-02339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Various chemical modifications of all RNA transcripts, or epitranscriptomics, have emerged as crucial regulators of RNA metabolism, attracting significant interest from both basic and clinical researchers due to their diverse functions in biological processes and immense clinical potential as highlighted by the recent profound success of RNA modifications in improving COVID-19 mRNA vaccines. Rapid accumulation of evidence underscores the critical involvement of various RNA modifications in governing normal neural development and brain functions as well as pathogenesis of brain disorders. Here we provide an overview of RNA modifications and recent advancements in epitranscriptomic studies utilizing animal models to elucidate important roles of RNA modifications in regulating mammalian neurogenesis, gliogenesis, synaptic formation, and brain function. Moreover, we emphasize the pivotal involvement of RNA modifications and their regulators in the pathogenesis of various human brain disorders, encompassing neurodevelopmental disorders, brain tumors, psychiatric and neurodegenerative disorders. Furthermore, we discuss potential translational opportunities afforded by RNA modifications in combatting brain disorders, including their use as biomarkers, in the development of drugs or gene therapies targeting epitranscriptomic pathways, and in applications for mRNA-based vaccines and therapies. We also address current limitations and challenges hindering the widespread clinical application of epitranscriptomic research, along with the improvements necessary for future progress.
Collapse
Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valentina V Ignatova
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
4
|
Dolce LG, Zimmer AA, Tengo L, Weis F, Rubio MAT, Alfonzo JD, Kowalinski E. Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3. Nat Commun 2022; 13:6737. [PMID: 36347890 PMCID: PMC9643335 DOI: 10.1038/s41467-022-34441-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
The essential deamination of adenosine A34 to inosine at the wobble base is the individual tRNA modification with the greatest effects on mRNA decoding, empowering a single tRNA to translate three different codons. To date, many aspects of how eukaryotic deaminases specifically select their multiple substrates remain unclear. Here, using cryo-EM, we present the structure of a eukaryotic ADAT2/3 deaminase bound to a full-length tRNA, revealing that the enzyme distorts the anticodon loop, but in contrast to the bacterial enzymes, selects its substrate via sequence-independent contacts of eukaryote-acquired flexible or intrinsically unfolded motifs distal from the conserved catalytic core. A gating mechanism for substrate entry to the active site is identified. Our multi-step tRNA recognition model yields insights into how RNA editing by A34 deamination evolved, shaped the genetic code, and directly impacts the eukaryotic proteome.
Collapse
Affiliation(s)
- Luciano G Dolce
- EMBL Grenoble, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Aubree A Zimmer
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Laura Tengo
- EMBL Grenoble, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Félix Weis
- EMBL Heidelberg, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Mary Anne T Rubio
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Juan D Alfonzo
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Eva Kowalinski
- EMBL Grenoble, 71 Avenue des Martyrs, 38042, Grenoble, France.
| |
Collapse
|
5
|
Scott CH, Amarillo IE. Identification of Small Regions of Overlap from Copy Number Variable Regions in Patients with Hypospadias. Int J Mol Sci 2022; 23:4246. [PMID: 35457073 PMCID: PMC9027593 DOI: 10.3390/ijms23084246] [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: 02/10/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
Hypospadias is a common form of congenital atypical sex development that is often associated with other congenital comorbidities. Many genes have been associated with the condition, most commonly single sequence variations. Further investigations of recurrent and overlapping copy number variations (CNVs) have resulted in the identification of genes and chromosome regions associated with various conditions, including differences of sex development (DSD). In this retrospective study, we investigated the DECIPHER database, as well as an internal institutional database, to identify small recurrent CNVs among individuals with isolated and syndromic hypospadias. We further investigated these overlapping recurrent CNVs to identify 75 smallest regions of overlap (SROs) on 18 chromosomes. Some of the genes within these SROs may be considered potential candidate genes for the etiology of hypospadias and, occasionally, additional comorbid phenotypes. This study also investigates for the first time additional common phenotypes among individuals with hypospadias and overlapping CNVs. This study provides data that may aid genetic counseling and management of individuals with hypospadias, as well as improve understanding of its underlying genetic etiology and human genital development overall.
Collapse
Affiliation(s)
- Carter H. Scott
- Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Ina E. Amarillo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
6
|
Scott TM, Campbell IM, Hernandez-Garcia A, Lalani SR, Liu P, Shaw CA, Rosenfeld JA, Scott DA. Clinical exome sequencing data reveal high diagnostic yields for congenital diaphragmatic hernia plus (CDH+) and new phenotypic expansions involving CDH. J Med Genet 2022; 59:270-278. [PMID: 33461977 PMCID: PMC8286264 DOI: 10.1136/jmedgenet-2020-107317] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/17/2020] [Accepted: 12/26/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Congenital diaphragmatic hernia (CDH) is a life-threatening birth defect that often co-occurs with non-hernia-related anomalies (CDH+). While copy number variant (CNV) analysis is often employed as a diagnostic test for CDH+, clinical exome sequencing (ES) has not been universally adopted. METHODS We analysed a clinical database of ~12 000 test results to determine the diagnostic yields of ES in CDH+ and to identify new phenotypic expansions. RESULTS Among the 76 cases with an indication of CDH+, a molecular diagnosis was made in 28 cases for a diagnostic yield of 37% (28/76). A provisional diagnosis was made in seven other cases (9%; 7/76). Four individuals had a diagnosis of Kabuki syndrome caused by frameshift variants in KMT2D. Putatively deleterious variants in ALG12 and EP300 were each found in two individuals, supporting their role in CDH development. We also identified individuals with de novo pathogenic variants in FOXP1 and SMARCA4, and compound heterozygous pathogenic variants in BRCA2. The role of these genes in CDH development is supported by the expression of their mouse homologs in the developing diaphragm, their high CDH-specific pathogenicity scores generated using a previously validated algorithm for genome-scale knowledge synthesis and previously published case reports. CONCLUSION We conclude that ES should be ordered in cases of CDH+ when a specific diagnosis is not suspected and CNV analyses are negative. Our results also provide evidence in favour of phenotypic expansions involving CDH for genes associated with ALG12-congenital disorder of glycosylation, Rubinstein-Taybi syndrome, Fanconi anaemia, Coffin-Siris syndrome and FOXP1-related disorders.
Collapse
Affiliation(s)
- Tiana M. Scott
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, 84602, USA,Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Andres Hernandez-Garcia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Seema R. Lalani
- Texas Children’s Hospital, Houston, TX, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Daryl A. Scott
- Texas Children’s Hospital, Houston, TX, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA,Correspondence Daryl A. Scott, R813, One Baylor Plaza. BCM225, Houston, TX 77030, USA, , Phone: +1 713-203-7242
| |
Collapse
|
7
|
Yahia A, Ayed IB, Hamed AA, Mohammed IN, Elseed MA, Bakhiet AM, Guillot-Noel L, Abozar F, Adil R, Emad S, Abubaker R, Musallam MA, Eltazi IZM, Omer Z, Maaroof OM, Soussi A, Bouzid A, Kmiha S, Kamoun H, Salih MA, Ahmed AE, Elsayed L, Masmoudi S, Stevanin G. Genetic diagnosis in Sudanese and Tunisian families with syndromic intellectual disability through exome sequencing. Ann Hum Genet 2022; 86:181-194. [PMID: 35118659 DOI: 10.1111/ahg.12460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Intellectual disability is a form of neurodevelopmental disorders that begin in childhood and is characterized by substantial intellectual difficulties as well as difficulties in conceptual, social, and practical areas of living. Several genetic and nongenetic factors contribute to its development; however, its most severe forms are generally attributed to single-gene defects. High-throughput technologies and data sharing contributed to the diagnosis of hundreds of single-gene intellectual disability subtypes. METHOD We applied exome sequencing to identify potential variants causing syndromic intellectual disability in six Sudanese patients from four unrelated families. Data sharing through the Varsome portal corroborated the diagnosis of one of these patients and a Tunisian patient investigated through exome sequencing. Sanger sequencing validated the identified variants and their segregation with the phenotypes in the five studied families. RESULT We identified three pathogenic/likely pathogenic variants in CCDC82, ADAT3, and HUWE1 and variants of uncertain significance in HERC2 and ATP2B3. The patients with the CCDC82 variants had microcephaly and spasticity, two signs absent in the two previously reported families with CCDC82-related intellectual disability. CONCLUSION In conclusion, we report new patients with pathogenic mutations in the genes CCDC82, ADAT3, and HUWE1. We also highlight the possibility of extending the CCDC82-linked phenotype to include spastic paraplegia and microcephaly.
Collapse
Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan.,Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Ahlam A Hamed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohammed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Aisha M Bakhiet
- Department of Psychiatry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Lena Guillot-Noel
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.,National University Biomedical Research Institute (NUBRI), National University, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Omer M Maaroof
- Council of Diagnostic Radiology, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Amal Soussi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Sana Kmiha
- Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia.,Department of pediatrics, Hedi Chaker Hospital, Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | - Ammar E Ahmed
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena Elsayed
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Giovanni Stevanin
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| |
Collapse
|
8
|
Ramos J, Fu D. Detection of tRNA-specific adenosine deaminase activity and wobble inosine modification in human cell lysates. Methods Enzymol 2021; 658:311-334. [PMID: 34517952 DOI: 10.1016/bs.mie.2021.06.008] [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] [Indexed: 01/04/2023]
Abstract
The wobble inosine modification plays a central role in translation by enabling a single tRNA to decode multiple synonymous codons. In eukaryotes, the formation of wobble inosine is catalyzed by a heterodimeric adenosine deaminase complex comprised of the ADAT2 and ADAT3 subunits. Notably, pathogenic variants in the ADAT3 subunit have been identified as the cause of autosomal recessive intellectual disability in the human population by impacting wobble inosine levels. Here, we describe approaches for monitoring adenosine deaminase activity and inosine modification status at the wobble position of cellular tRNAs. To detect adenosine deaminase activity, we provide protocols for preparing extracts from human cells followed by enzymatic assays with in vitro transcribed tRNA substrates. Furthermore, we describe a method to monitor wobble inosine status of individual tRNAs using cDNA sequencing. These assays can be used to decipher the molecular basis for neurodevelopmental disorders linked to wobble inosine deficiency and disease-associated ADAT2/3 variants.
Collapse
Affiliation(s)
- Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, United States
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, United States.
| |
Collapse
|
9
|
Torres AG, Rodríguez-Escribà M, Marcet-Houben M, Santos Vieira H, Camacho N, Catena H, Murillo Recio M, Rafels-Ybern À, Reina O, Torres F, Pardo-Saganta A, Gabaldón T, Novoa E, Ribas de Pouplana L. Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins. Nucleic Acids Res 2021; 49:7011-7034. [PMID: 34125917 PMCID: PMC8266599 DOI: 10.1093/nar/gkab461] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the transformation of the homodimeric bacterial enzyme TadA, which generates I34 in tRNAArg and tRNALeu, into the heterodimeric eukaryotic enzyme ADAT, which modifies up to eight different tRNAs. The emergence of ADAT and its larger set of substrates, strongly influenced the tRNA composition and codon usage of eukaryotic genomes. However, the selective advantages that drove the expansion of I34-tRNAs remain unknown. Here we investigate the functional relevance of I34-tRNAs in human cells and show that a full complement of these tRNAs is necessary for the translation of low-complexity protein domains enriched in amino acids cognate for I34-tRNAs. The coding sequences for these domains require codons translated by I34-tRNAs, in detriment of synonymous codons that use other tRNAs. I34-tRNA-dependent low-complexity proteins are enriched in functional categories related to cell adhesion, and depletion in I34-tRNAs leads to cellular phenotypes consistent with these roles. We show that the distribution of these low-complexity proteins mirrors the distribution of I34-tRNAs in the phylogenetic tree.
Collapse
Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Marcet-Houben
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
| | | | - Noelia Camacho
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Helena Catena
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Marina Murillo Recio
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Àlbert Rafels-Ybern
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Francisco Miguel Torres
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
| | - Ana Pardo-Saganta
- Centre for Applied Medical Research (CIMA Universidad de Navarra), Pamplona 31008, Spain
| | - Toni Gabaldón
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Catalonia 08034, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| | - Eva Maria Novoa
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain
- University Pompeu Fabra, Barcelona, Catalonia 08003, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08028, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia 08010, Spain
| |
Collapse
|
10
|
Srinivasan S, Torres AG, Ribas de Pouplana L. Inosine in Biology and Disease. Genes (Basel) 2021; 12:600. [PMID: 33921764 PMCID: PMC8072771 DOI: 10.3390/genes12040600] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.
Collapse
Affiliation(s)
- Sundaramoorthy Srinivasan
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Catalonia, Spain
| |
Collapse
|
11
|
Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
Collapse
Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
| | | |
Collapse
|
12
|
Ramos J, Proven M, Halvardson J, Hagelskamp F, Kuchinskaya E, Phelan B, Bell R, Kellner SM, Feuk L, Thuresson AC, Fu D. Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder. RNA (NEW YORK, N.Y.) 2020; 26:1654-1666. [PMID: 32763916 PMCID: PMC7566568 DOI: 10.1261/rna.076380.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The deamination of adenosine to inosine at the wobble position of tRNA is an essential post-transcriptional RNA modification required for wobble decoding in bacteria and eukaryotes. In humans, the wobble inosine modification is catalyzed by the heterodimeric ADAT2/3 complex. Here, we describe novel pathogenic ADAT3 variants impairing adenosine deaminase activity through a distinct mechanism that can be corrected through expression of the heterodimeric ADAT2 subunit. The variants were identified in a family in which all three siblings exhibit intellectual disability linked to biallelic variants in the ADAT3 locus. The biallelic ADAT3 variants result in a missense variant converting alanine to valine at a conserved residue or the introduction of a premature stop codon in the deaminase domain. Fibroblast cells derived from two ID-affected individuals exhibit a reduction in tRNA wobble inosine levels and severely diminished adenosine tRNA deaminase activity. Notably, the ADAT3 variants exhibit impaired interaction with the ADAT2 subunit and alterations in ADAT2-dependent nuclear localization. Based upon these findings, we find that tRNA adenosine deaminase activity and wobble inosine modification can be rescued in patient cells by overexpression of the ADAT2 catalytic subunit. These results uncover a key role for the inactive ADAT3 deaminase domain in proper assembly with ADAT2 and demonstrate that ADAT2/3 nuclear import is required for maintaining proper levels of the wobble inosine modification in tRNA.
Collapse
Affiliation(s)
- Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Melissa Proven
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | | | - Ekaterina Kuchinskaya
- Department of Clinical Genetics, and Department of Clinical Medicine, Linköping University, 581 83 Linköping, Sweden
| | - Benjamin Phelan
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Ryan Bell
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | | | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | - Ann-Charlotte Thuresson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 08 Uppsala, Sweden
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| |
Collapse
|