1
|
Yan H, Tang W. Programmed RNA editing with an evolved bacterial adenosine deaminase. Nat Chem Biol 2024; 20:1361-1370. [PMID: 38969862 DOI: 10.1038/s41589-024-01661-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
Programmed RNA editing presents an attractive therapeutic strategy for genetic disease. In this study, we developed bacterial deaminase-enabled recoding of RNA (DECOR), which employs an evolved Escherichia coli transfer RNA adenosine deaminase, TadA8e, to deposit adenosine-to-inosine editing to CRISPR-specified sites in the human transcriptome. DECOR functions in a variety of cell types, including human lung fibroblasts, and delivers on-target activity similar to ADAR-overexpressing RNA-editing platforms with 88% lower off-target effects. High-fidelity DECOR further reduces off-target effects to basal level. We demonstrate the clinical potential of DECOR by targeting Van der Woude syndrome-causing interferon regulatory factor 6 (IRF6) insufficiency. DECOR-mediated RNA editing removes a pathogenic upstream open reading frame (uORF) from the 5' untranslated region of IRF6 and rescues primary ORF expression from 12.3% to 36.5%, relative to healthy transcripts. DECOR expands the current portfolio of effector proteins and opens new territory in programmed RNA editing.
Collapse
Affiliation(s)
- Hao Yan
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Weixin Tang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
2
|
Schultz SK, Kothe U. RNA modifying enzymes shape tRNA biogenesis and function. J Biol Chem 2024; 300:107488. [PMID: 38908752 PMCID: PMC11301382 DOI: 10.1016/j.jbc.2024.107488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning to emerge. tRNAs have two general clusters of modifications. The first cluster is within the anticodon stem-loop including several modifications essential for protein translation. The second cluster of modifications is within the tRNA elbow, and roles for these modifications are less clear. In general, tRNA elbow modifications are typically not essential for cell growth, but nonetheless several tRNA elbow modifications have been highly conserved throughout all domains of life. In addition to forming modifications, many tRNA modifying enzymes have been demonstrated or hypothesized to also play an important role in folding tRNA acting as tRNA chaperones. In this review, we summarize the known functions of tRNA modifying enzymes throughout the lifecycle of a tRNA molecule, from transcription to degradation. Thereby, we describe how tRNA modification and folding by tRNA modifying enzymes enhance tRNA maturation, tRNA aminoacylation, and tRNA function during protein synthesis, ultimately impacting cellular phenotypes and disease.
Collapse
Affiliation(s)
- Sarah K Schultz
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
| | - Ute Kothe
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada; Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
| |
Collapse
|
3
|
Tao WB, Xiong J, Yuan BF. Site-specific quantification of Adenosine-to-Inosine RNA editing by Endonuclease-Mediated qPCR. Bioorg Med Chem 2024; 110:117837. [PMID: 39013280 DOI: 10.1016/j.bmc.2024.117837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024]
Abstract
RNA molecules contain diverse modified nucleobases that play pivotal roles in numerous biological processes. Adenosine-to-inosine (A-to-I) RNA editing, one of the most prevalent RNA modifications in mammalian cells, is linked to a multitude of human diseases. To unveil the functions of A-to-I RNA editing, accurate quantification of inosine at specific sites is essential. In this study, we developed an endonuclease-mediated cleavage and real-time fluorescence quantitative PCR method for A-to-I RNA editing (EM-qPCR) to quantitatively analyze A-to-I RNA editing at a single site. By employing this method, we successfully quantified the levels of A-to-I RNA editing on various transfer RNA (tRNA) molecules at position 34 (I34) in mammalian cells with precision. Subsequently, this method was applied to tissues from sleep-deprived mice, revealing a notable alteration in the levels of I34 between sleep-deprived and control mice. The proposed method sets a precedent for the quantitative analysis of A-to-I RNA editing at specific sites, facilitating a deeper understanding of the biological implications of A-to-I RNA editing.
Collapse
Affiliation(s)
- Wan-Bing Tao
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, PR China
| | - Jun Xiong
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, PR China; Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, PR China
| | - Bi-Feng Yuan
- College of Chemistry and Molecular Sciences, Research Center of Public Health, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430060, PR China; Department of Occupational and Environmental Health, School of Public Health, Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, PR China; Hubei Key Laboratory of Biomass Resource Chemistry and Environmental Biotechnology, Wuhan University, Wuhan 430072, PR China; Cancer Precision Diagnosis and Treatment and Translational Medicine Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan 430071, PR China.
| |
Collapse
|
4
|
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
|
5
|
Lejeune C, Cornu D, Sago L, Redeker V, Virolle MJ. The stringent response is strongly activated in the antibiotic producing strain, Streptomyces coelicolor. Res Microbiol 2024; 175:104177. [PMID: 38159786 DOI: 10.1016/j.resmic.2023.104177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
S. lividans and S. coelicolor are phylogenetically closely related strains with different abilities to produce the same specialized metabolites. Previous studies revealed that the strong antibiotic producer, S. coelicolor, had a lower ability to assimilate nitrogen and phosphate than the weak producer, Streptomyces lividans, and this resulted into a lower growth rate. A comparative proteomic dataset was used to establish the consequences of these nutritional stresses on the abundance of proteins of the translational apparatus of these strains, grown in low and high phosphate availability. Our study revealed that most proteins of the translational apparatus were less abundant in S. coelicolor than in S. lividans whereas it was the opposite for ET-Tu 3 and a TrmA-like methyltransferase. The expression of the latter being known to be under the positive control of the stringent response whereas that of the other ribosomal proteins is under its negative control, this indicated the occurrence of a strong activation of the stringent response in S. coelicolor. Furthermore, in S. lividans, ribosomal proteins were more abundant in phosphate proficiency than in phosphate limitation suggesting that a limitation in phosphate, that was also shown to trigger RelA expression, contributes to the induction of the stringent response.
Collapse
Affiliation(s)
- Clara Lejeune
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - David Cornu
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Laila Sago
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| | - Virginie Redeker
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France; Institut Francois Jacob, Molecular Imaging Center (MIRCen), Laboratory of Neurodegenerative Diseases, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique, Université Paris-Saclay, Fontenay-aux-Roses, France.
| | - Marie-Joelle Virolle
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France.
| |
Collapse
|
6
|
Ashley CN, Broni E, Miller WA. ADAR Family Proteins: A Structural Review. Curr Issues Mol Biol 2024; 46:3919-3945. [PMID: 38785511 PMCID: PMC11120146 DOI: 10.3390/cimb46050243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
This review aims to highlight the structures of ADAR proteins that have been crucial in the discernment of their functions and are relevant to future therapeutic development. ADAR proteins can correct or diversify genetic information, underscoring their pivotal contribution to protein diversity and the sophistication of neuronal networks. ADAR proteins have numerous functions in RNA editing independent roles and through the mechanisms of A-I RNA editing that continue to be revealed. Provided is a detailed examination of the ADAR family members-ADAR1, ADAR2, and ADAR3-each characterized by distinct isoforms that offer both structural diversity and functional variability, significantly affecting RNA editing mechanisms and exhibiting tissue-specific regulatory patterns, highlighting their shared features, such as double-stranded RNA binding domains (dsRBD) and a catalytic deaminase domain (CDD). Moreover, it explores ADARs' extensive roles in immunity, RNA interference, and disease modulation, demonstrating their ambivalent nature in both the advancement and inhibition of diseases. Through this comprehensive analysis, the review seeks to underline the potential of targeting ADAR proteins in therapeutic strategies, urging continued investigation into their biological mechanisms and health implications.
Collapse
Affiliation(s)
- Carolyn N. Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA; (C.N.A.); (E.B.)
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| |
Collapse
|
7
|
Schmitt MA, Tittle JM, Fisk JD. Codon decoding by orthogonal tRNAs interrogates the in vivo preferences of unmodified adenosine in the wobble position. Front Genet 2024; 15:1386299. [PMID: 38706795 PMCID: PMC11066159 DOI: 10.3389/fgene.2024.1386299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/30/2024] [Indexed: 05/07/2024] Open
Abstract
The in vivo codon decoding preferences of tRNAs with an authentic adenosine residue at position 34 of the anticodon, the wobble position, are largely unexplored because very few unmodified A34 tRNA genes exist across the three domains of life. The expanded wobble rules suggest that unmodified adenosine pairs most strongly with uracil, modestly with cytosine, and weakly with guanosine and adenosine. Inosine, a modified adenosine, on the other hand, pairs strongly with both uracil and cytosine and to a lesser extent adenosine. Orthogonal pair directed sense codon reassignment experiments offer a tool with which to interrogate the translational activity of A34 tRNAs because the introduced tRNA can be engineered with any anticodon. Our fluorescence-based screen utilizes the absolute requirement of tyrosine at position 66 of superfolder GFP for autocatalytic fluorophore formation. The introduced orthogonal tRNA competes with the endogenous translation machinery to incorporate tyrosine in response to a codon typically assigned another meaning in the genetic code. We evaluated the codon reassignment efficiencies of 15 of the 16 possible orthogonal tRNAs with A34 anticodons. We examined the Sanger sequencing chromatograms for cDNAs from each of the reverse transcribed tRNAs for evidence of inosine modification. Despite several A34 tRNAs decoding closely-related C-ending codons, partial inosine modification was detected for only three species. These experiments employ a single tRNA body with a single attached amino acid to interrogate the behavior of different anticodons in the background of in vivo E. coli translation and greatly expand the set of experimental measurements of the in vivo function of A34 tRNAs in translation. For the most part, unmodified A34 tRNAs largely pair with only U3 codons as the original wobble rules suggest. In instances with GC pairs in the first two codon positions, unmodified A34 tRNAs decode the C- and G-ending codons as well as the expected U-ending codon. These observations support the "two-out-of-three" and "strong and weak" codon hypotheses.
Collapse
Affiliation(s)
| | | | - John D. Fisk
- Department of Chemistry, University of Colorado Denver, Denver, CO, United States
| |
Collapse
|
8
|
Andac CA, Hornemann U, Noyanalpan N, Stringfellow TC. Synthesis, NMR kinetics and dynamic structure of a 17-mer heptaloop RNA hairpin carrying a 3- N-methyluridine nucleotide residue in the loop region. J Biomol Struct Dyn 2024; 42:3659-3681. [PMID: 37278223 DOI: 10.1080/07391102.2023.2214231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/10/2023] [Indexed: 06/07/2023]
Abstract
A 17-mer RNA hairpin (5'GGGAGUXAGCGGCUCCC3') carrying 3-N-methyluridine (m3U) at position X (m3U7-RNA), designed to represent the anticodon stem-loop (ACSL) region of tRNAs to study an open loop state (O-state), was synthesized, purified by HPLC, and characterized by MALDI-ToF_MS and NMR methods. 1H-NMR data revealed primary (P-state in 56.1%), secondary (S-state in 43.9%) and tertiary (∼5-6%) ACSL conformations. Exchange rate constant (kex) for interconversion between P and S states is 112 sec-1 (<Δω ∼454 rad/sec), confirming a slow exchange regime between the two states. Forward (kPS) and backward (kSP) rate constants are 49.166 sec-1 and 62.792 sec-1, respectively, leading to a longer life-time (20.339 msec) for the P-state and a shorter life-time (15.926 msec) for the S-state. In accordance with conformational populations determined by 1H-NMR, dynamics of the P/S/tertiary states of m3U7-RNA and its wild-type counterpart (wt-RNA) were studied by three independent MD production simulations. Cluster analysis revealed that wt-RNA reflects the structural characteristics of the ACSL region of tRNAs. The P-state of m3U7-RNA was found to be structurally similar to wt-RNA but lacks an intraloop H-bond between m3U7 and C10 (U33 and nt36 in tRNAs). In the S-state of m3U7-RNA, m3U7 flips out of the loop region. O-state loop conformations of m3U7-RNA were also clustered (4.8%), wherein the loop nucleotides m3U7.A8.G9.C10.G11 stack one after another. We propose that the O-state of m3U7-RNA is the most suitable conformation that makes the loop accessible for complementary nucleotides and for non-enzymatic primordial replication of small circular RNAs.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Cenk A Andac
- Department of Medical Pharmacology, School of Medicine, Yeditepe University, Istanbul, Turkiye
| | - Ulfert Hornemann
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Ningur Noyanalpan
- Department of Medicinal Chemistry, School of Pharmacy, Gazi University, Ankara, Turkiye
| | | |
Collapse
|
9
|
Bian Z, Wang Z, Wang D, Xu JR. Sexual stage-specific A-to-I mRNA editing is mediated by tRNA-editing enzymes in fungi. Proc Natl Acad Sci U S A 2024; 121:e2319235121. [PMID: 38466838 PMCID: PMC10962958 DOI: 10.1073/pnas.2319235121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
A-to-I RNA editing catalyzed by adenosine-deaminase-acting-on-RNA (ADARs) was assumed to be unique to metazoans because fungi and plants lack ADAR homologs. However, genome-wide messenger RNA (mRNA) editing was found to occur specifically during sexual reproduction in filamentous ascomycetes. Because systematic characterization of adenosine/cytosine deaminase genes has implicated the involvement of TAD2 and TAD3 orthologs in A-to-I editing, in this study, we used genetic and biochemical approaches to characterize the role of FgTAD2, an essential adenosine-deaminase-acting-on-tRNA (ADAT) gene, in mRNA editing in Fusarium graminearum. FgTAD2 had a sexual-stage-specific isoform and formed heterodimers with enzymatically inactive FgTAD3. Using a repeat-induced point (RIP) mutation approach, we identified 17 mutations in FgTAD2 that affected mRNA editing during sexual reproduction but had no effect on transfer RNA (tRNA) editing and vegetative growth. The functional importance of the H352Y and Q375*(nonsense) mutations in sexual reproduction and mRNA editing were confirmed by introducing specific point mutations into the endogenous FgTAD2 allele in the wild type. An in vitro assay was developed to show that FgTad2-His proteins purified from perithecia, but not from vegetative hyphae, had mRNA editing activities. Moreover, the H352Y mutation affected the enzymatic activity of FgTad2 to edit mRNA but had no effect on its ADAT activity. We also identified proteins co-purified with FgTad2-His by mass spectrometry analysis and found that two of them have the RNA recognition motif. Taken together, genetic and biochemical data from this study demonstrated that FgTad2, an ADAT, catalyzes A-to-I mRNA editing with the stage-specific isoform and cofactors during sexual reproduction in fungi.
Collapse
Affiliation(s)
- Zhuyun Bian
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| | - Zeyi Wang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| | - Diwen Wang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| |
Collapse
|
10
|
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
|
11
|
Smith TJ, Giles RN, Koutmou KS. Anticodon stem-loop tRNA modifications influence codon decoding and frame maintenance during translation. Semin Cell Dev Biol 2024; 154:105-113. [PMID: 37385829 DOI: 10.1016/j.semcdb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/01/2023]
Abstract
RNAs are central to protein synthesis, with ribosomal RNA, transfer RNAs and messenger RNAs comprising the core components of the translation machinery. In addition to the four canonical bases (uracil, cytosine, adenine, and guanine) these RNAs contain an array of enzymatically incorporated chemical modifications. Transfer RNAs (tRNAs) are responsible for ferrying amino acids to the ribosome, and are among the most abundant and highly modified RNAs in the cell across all domains of life. On average, tRNA molecules contain 13 post-transcriptionally modified nucleosides that stabilize their structure and enhance function. There is an extensive chemical diversity of tRNA modifications, with over 90 distinct varieties of modifications reported within tRNA sequences. Some modifications are crucial for tRNAs to adopt their L-shaped tertiary structure, while others promote tRNA interactions with components of the protein synthesis machinery. In particular, modifications in the anticodon stem-loop (ASL), located near the site of tRNA:mRNA interaction, can play key roles in ensuring protein homeostasis and accurate translation. There is an abundance of evidence indicating the importance of ASL modifications for cellular health, and in vitro biochemical and biophysical studies suggest that individual ASL modifications can differentially influence discrete steps in the translation pathway. This review examines the molecular level consequences of tRNA ASL modifications in mRNA codon recognition and reading frame maintenance to ensure the rapid and accurate translation of proteins.
Collapse
Affiliation(s)
- Tyler J Smith
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Rachel N Giles
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA
| | - Kristin S Koutmou
- University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, USA.
| |
Collapse
|
12
|
Giguère S, Wang X, Huber S, Xu L, Warner J, Weldon SR, Hu J, Phan QA, Tumang K, Prum T, Ma D, Kirsch KH, Nair U, Dedon P, Batista FD. Antibody production relies on the tRNA inosine wobble modification to meet biased codon demand. Science 2024; 383:205-211. [PMID: 38207021 PMCID: PMC10954030 DOI: 10.1126/science.adi1763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
Antibodies are produced at high rates to provide immunoprotection, which puts pressure on the B cell translational machinery. Here, we identified a pattern of codon usage conserved across antibody genes. One feature thereof is the hyperutilization of codons that lack genome-encoded Watson-Crick transfer RNAs (tRNAs), instead relying on the posttranscriptional tRNA modification inosine (I34), which expands the decoding capacity of specific tRNAs through wobbling. Antibody-secreting cells had increased I34 levels and were more reliant on I34 for protein production than naïve B cells. Furthermore, antibody I34-dependent codon usage may influence B cell passage through regulatory checkpoints. Our work elucidates the interface between the tRNA pool and protein production in the immune system and has implications for the design and selection of antibodies for vaccines and therapeutics.
Collapse
Affiliation(s)
- Sophie Giguère
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Sabrina Huber
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Liling Xu
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - John Warner
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Stephanie R. Weldon
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Jennifer Hu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Quynh Anh Phan
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Katie Tumang
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Thavaleak Prum
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Duanduan Ma
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kathrin H. Kirsch
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Peter Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Facundo D. Batista
- The Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
13
|
Zhu Y, Peng B, Luo X, Sun W, Liu D, Li N, Qiu P, Long G. High-Resolution Profiling of Head and Neck Squamous Cells Carcinoma Identifies Specific Biomarkers and Expression Subtypes of Clinically Relevant Vulnerabilities. Curr Med Chem 2024; 31:2431-2448. [PMID: 37936459 DOI: 10.2174/0109298673276128231031112655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSC) is the seventh most common cancer worldwide. Although there are several options for the treatment of HNSC, there is still a lack of better biomarkers to accurately predict the response to treatment and thus be more able to correctly treat the therapeutic modality. METHODS First, we typed cases from the TCGA-HNSC cohort into subtypes by a Bayesian non-negative matrix factorization (BayesNMF)-based consensus clustering approach. Subsequently, genomic and proteomic data from HNSC cell lines were integrated to identify biomarkers of response to targeted therapies and immunotherapies. Finally, associations between HNSC subtypes and CD8 T-cell-associated effector molecules, common immune checkpoint genes, were compared to assess the potential of HNSC subtypes as clinically predictive immune checkpoint blockade therapy. RESULTS The 500 HNSC cases from TCGA were put through a consensus clustering approach to identify six HNSC expression subtypes. In addition, subtypes with unique proteomics and dependency profiles were defined based on HNSC cell line histology and proteomics data. Subtype 4 (S4) exhibits hyperproliferative and hyperimmune properties, and S4-associated cell lines show specific vulnerability to ADAT2, EIF5AL1, and PAK2. PD-L1 and CASP1 inhibitors have therapeutic potential in S4, and we have also demonstrated that S4 is more responsive to immune checkpoint blockade therapy. CONCLUSION Overall, our HNSC typing approach identified robust tumor-expressing subtypes, and data from multiple screens also revealed subtype-specific biology and vulnerabilities. These HNSC expression subtypes and their biomarkers will help develop more effective therapeutic strategies.
Collapse
Affiliation(s)
- Yingying Zhu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Bi Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoxiao Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Sun
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Dongbo Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Na Li
- Department of Medical, Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen, 518038, China
| | - Ping Qiu
- Department of Medical, Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, Shenzhen, 518038, China
| | - Guoxian Long
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| |
Collapse
|
14
|
Saleh S, Farabaugh PJ. Posttranscriptional modification to the core of tRNAs modulates translational misreading errors. RNA (NEW YORK, N.Y.) 2023; 30:37-51. [PMID: 37907335 PMCID: PMC10726164 DOI: 10.1261/rna.079797.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023]
Abstract
Protein synthesis on the ribosome involves successive rapid recruitment of cognate aminoacyl-tRNAs and rejection of the much more numerous incorrect near- or non-cognates. The principal feature of translation elongation is that at every step, many incorrect aa-tRNAs unsuccessfully enter the A site for each cognate accepted. Normal levels of translational accuracy require that cognate tRNAs have relatively similar acceptance rates by the ribosome. To achieve that, tRNAs evolved to compensate for differences in amino acid properties and codon-anticodon strength that affect acceptance. Part of that response involved tRNA posttranscriptional modifications, which can affect tRNA decoding efficiency, accuracy, and structural stability. The most intensively modified regions of the tRNA are the anticodon loop and structural core of the tRNA. Anticodon loop modifications directly affect codon-anticodon pairing and therefore modulate accuracy. Core modifications have been thought to ensure consistent decoding rates principally by stabilizing tRNA structure to avoid degradation; however, degradation due to instability appears to only be a significant issue above normal growth temperatures. We suspected that the greater role of modification at normal temperatures might be to tune tRNAs to maintain consistent intrinsic rates of acceptance and peptide transfer and that hypomodification by altering these rates might degrade the process of discrimination, leading to increased translational errors. Here, we present evidence that most tRNA core modifications do modulate the frequency of misreading errors, suggesting that the need to maintain accuracy explains their deep evolutionary conservation.
Collapse
Affiliation(s)
- Sima Saleh
- Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
| | - Philip J Farabaugh
- Department of Biological Sciences and Program in Molecular and Cell Biology, University of Maryland Baltimore County, Baltimore, Maryland 21250, USA
| |
Collapse
|
15
|
Budzko L, Hoffa-Sobiech K, Jackowiak P, Figlerowicz M. Engineered deaminases as a key component of DNA and RNA editing tools. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102062. [PMID: 38028200 PMCID: PMC10661471 DOI: 10.1016/j.omtn.2023.102062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Over recent years, zinc-dependent deaminases have attracted increasing interest as key components of nucleic acid editing tools that can generate point mutations at specific sites in either DNA or RNA by combining a targeting module (such as a catalytically impaired CRISPR-Cas component) and an effector module (most often a deaminase). Deaminase-based molecular tools are already being utilized in a wide spectrum of therapeutic and research applications; however, their medical and biotechnological potential seems to be much greater. Recent reports indicate that the further development of nucleic acid editing systems depends largely on our ability to engineer the substrate specificity and catalytic activity of the editors themselves. In this review, we summarize the current trends and achievements in deaminase engineering. The presented data indicate that the potential of these enzymes has not yet been fully revealed or understood. Several examples show that even relatively minor changes in the structure of deaminases can give them completely new and unique properties.
Collapse
Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Hoffa-Sobiech
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| |
Collapse
|
16
|
Keegan LP, Hajji K, O’Connell MA. Adenosine Deaminase Acting on RNA (ADAR) Enzymes: A Journey from Weird to Wondrous. Acc Chem Res 2023; 56:3165-3174. [PMID: 37906879 PMCID: PMC10666284 DOI: 10.1021/acs.accounts.3c00433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 11/02/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes that catalyze the conversion of adenosine to inosine in double-stranded (ds)RNA are evolutionarily conserved and are essential for many biological functions including nervous system function, hematopoiesis, and innate immunity. Initially it was assumed that the wide-ranging biological roles of ADARs are due to inosine in mRNA being read as guanosine by the translational machinery, allowing incomplete RNA editing in a target codon to generate two different proteins from the same primary transcript. In humans, there are approximately seventy-six positions that undergo site-specific editing in tissues at greater than 20% efficiency that result in recoding. Many of these transcripts are expressed in the central nervous system (CNS) and edited by ADAR2. Exploiting mouse genetic models revealed that transgenic mice lacking the gene encoding Adar2 die within 3 weeks of birth. Therefore, the role of ADAR2 in generating protein diversity in the nervous system is clear, but why is ADAR RNA editing activity essential in other biological processes, particularly editing mainly involving ADAR1? ADAR1 edits human transcripts having embedded Alu element inverted repeats (AluIRs), but the link from this activity to innate immunity activation was elusive. Mice lacking the gene encoding Adar1 are embryonically lethal, and a major breakthrough was the discovery that the role of Adar1 in innate immunity is due to its ability to edit such repetitive element inverted repeats which have the ability to form dsRNA in transcripts. The presence of inosine prevents activation of the dsRNA sensor melanoma differentiation-associated protein 5 (Mda5). Thus, inosine helps the cell discriminate self from non-self RNA, acting like a barcode on mRNA. As innate immunity is key to many different biological processes, the basis for this widespread biological role of the ADAR1 enzyme became evident.Our group has been studying ADARs from the outset of research on these enzymes. In this Account, we give a historical perspective, moving from the initial purification of ADAR1 and ADAR2 and cloning of their encoding genes up to the current research focus in the field and what questions still remain to be addressed. We discuss the characterizations of the proteins, their localizations, posttranslational modifications, and dimerization, and how all of these affect their biological activities. Another aspect we explore is the use of mouse and Drosophila genetic models to study ADAR functions and how these were crucial in determining the biological functions of the ADAR proteins. Finally, we describe the severe consequences of rare mutations found in the human genes encoding ADAR1 and ADAR2.
Collapse
Affiliation(s)
- Liam P. Keegan
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
| | - Khadija Hajji
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
| | - Mary A. O’Connell
- CEITEC, Masaryk
University, Kamenice 735/5, E35, Brno 62500, Czechia
| |
Collapse
|
17
|
Dhingra Y, Gupta S, Gupta V, Agarwal M, Katiyar-Agarwal S. The emerging role of epitranscriptome in shaping stress responses in plants. PLANT CELL REPORTS 2023; 42:1531-1555. [PMID: 37481775 DOI: 10.1007/s00299-023-03046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
KEY MESSAGE RNA modifications and editing changes constitute 'epitranscriptome' and are crucial in regulating the development and stress response in plants. Exploration of the epitranscriptome and associated machinery would facilitate the engineering of stress tolerance in crops. RNA editing and modifications post-transcriptionally decorate almost all classes of cellular RNAs, including tRNAs, rRNAs, snRNAs, lncRNAs and mRNAs, with more than 170 known modifications, among which m6A, Ψ, m5C, 8-OHG and C-to-U editing are the most abundant. Together, these modifications constitute the "epitranscriptome", and contribute to changes in several RNA attributes, thus providing an additional structural and functional diversification to the "cellular messages" and adding another layer of gene regulation in organisms, including plants. Numerous evidences suggest that RNA modifications have a widespread impact on plant development as well as in regulating the response of plants to abiotic and biotic stresses. High-throughput sequencing studies demonstrate that the landscapes of m6A, m5C, Am, Cm, C-to-U, U-to-G, and A-to-I editing are remarkably dynamic during stress conditions in plants. GO analysis of transcripts enriched in Ψ, m6A and m5C modifications have identified bonafide components of stress regulatory pathways. Furthermore, significant alterations in the expression pattern of genes encoding writers, readers, and erasers of certain modifications have been documented when plants are grown in challenging environments. Notably, manipulating the expression levels of a few components of RNA editing machinery markedly influenced the stress tolerance in plants. We provide updated information on the current understanding on the contribution of RNA modifications in shaping the stress responses in plants. Unraveling of the epitranscriptome has opened new avenues for designing crops with enhanced productivity and stress resilience in view of global climate change.
Collapse
Affiliation(s)
- Yashika Dhingra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shitij Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
| | - Vaishali Gupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Manu Agarwal
- Department of Botany, University of Delhi North Campus, Delhi, 110007, India
| | - Surekha Katiyar-Agarwal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
| |
Collapse
|
18
|
Davyt M, Bharti N, Ignatova Z. Effect of mRNA/tRNA mutations on translation speed: Implications for human diseases. J Biol Chem 2023; 299:105089. [PMID: 37495112 PMCID: PMC10470029 DOI: 10.1016/j.jbc.2023.105089] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Recent discoveries establish tRNAs as central regulators of mRNA translation dynamics, and therefore cotranslational folding and function of the encoded protein. The tRNA pool, whose composition and abundance change in a cell- and tissue-dependent manner, is the main factor which determines mRNA translation velocity. In this review, we discuss a group of pathogenic mutations, in the coding sequences of either protein-coding genes or in tRNA genes, that alter mRNA translation dynamics. We also summarize advances in tRNA biology that have uncovered how variations in tRNA levels on account of genetic mutations affect protein folding and function, and thereby contribute to phenotypic diversity in clinical manifestations.
Collapse
Affiliation(s)
- Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| |
Collapse
|
19
|
Soma A, Kubota A, Tomoe D, Ikeuchi Y, Kawamura F, Arimoto H, Shiwa Y, Kanesaki Y, Nanamiya H, Yoshikawa H, Suzuki T, Sekine Y. yaaJ, the tRNA-Specific Adenosine Deaminase, Is Dispensable in Bacillus subtilis. Genes (Basel) 2023; 14:1515. [PMID: 37628567 PMCID: PMC10454642 DOI: 10.3390/genes14081515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
Post-transcriptional modifications of tRNA are crucial for their core function. The inosine (I; 6-deaminated adenosine) at the first position in the anticodon of tRNAArg(ICG) modulates the decoding capability and is generally considered essential for reading CGU, CGC, and CGA codons in eubacteria. We report here that the Bacillus subtilis yaaJ gene encodes tRNA-specific adenosine deaminase and is non-essential for viability. A β-galactosidase reporter assay revealed that the translational activity of CGN codons was not impaired in the yaaJ-deletion mutant. Furthermore, tRNAArg(CCG) responsible for decoding the CGG codon was dispensable, even in the presence or absence of yaaJ. These results strongly suggest that tRNAArg with either the anticodon ICG or ACG has an intrinsic ability to recognize all four CGN codons, providing a fundamental concept of non-canonical wobbling mediated by adenosine and inosine nucleotides in the anticodon. This is the first example of the four-way wobbling by inosine nucleotide in bacterial cells. On the other hand, the absence of inosine modification induced +1 frameshifting, especially at the CGA codon. Additionally, the yaaJ deletion affected growth and competency. Therefore, the inosine modification is beneficial for translational fidelity and proper growth-phase control, and that is why yaaJ has been actually conserved in B. subtilis.
Collapse
Affiliation(s)
- Akiko Soma
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Atsushi Kubota
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Daisuke Tomoe
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yoshiho Ikeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Fujio Kawamura
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hijiri Arimoto
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
- Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yu Kanesaki
- Shizuoka Instrumental Analysis Center, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hideaki Nanamiya
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Fukushima Translational Research Foundation, Capital Front Bldg., 7-4, 1-35, Sakae-machi, Fukushima 960-8031, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| |
Collapse
|
20
|
Gao Z, Jiang W, Zhang Y, Zhang L, Yi M, Wang H, Ma Z, Qu B, Ji X, Long H, Zhang S. Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA. Commun Biol 2023; 6:744. [PMID: 37464027 PMCID: PMC10354150 DOI: 10.1038/s42003-023-05134-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Adenosine-to-inosine tRNA-editing enzyme has been identified for more than two decades, but the study on its DNA editing activity is rather scarce. We show that amphioxus (Branchiostoma japonicum) ADAT2 (BjADAT2) contains the active site 'HxE-PCxxC' and the key residues for target-base-binding, and amphioxus ADAT3 (BjADAT3) harbors both the N-terminal positively charged region and the C-terminal pseudo-catalytic domain important for recognition of substrates. The sequencing of BjADAT2-transformed Escherichia coli genome suggests that BjADAT2 has the potential to target E. coli DNA and can deaminate at TCG and GAA sites in the E. coli genome. Biochemical analyses further demonstrate that BjADAT2, in complex with BjADAT3, can perform A-to-I editing of tRNA and convert C-to-U and A-to-I deamination of DNA. We also show that BjADAT2 preferentially deaminates adenosines and cytidines in the loop of DNA hairpin structures of substrates, and BjADAT3 also affects the type of DNA substrate targeted by BjADAT2. Finally, we find that C89, N113, C148 and Y156 play critical roles in the DNA editing activity of BjADAT2. Collectively, our study indicates that BjADAT2/3 is the sole naturally occurring deaminase with both tRNA and DNA editing capacity identified so far in Metazoa.
Collapse
Affiliation(s)
- Zhan Gao
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China.
| | - Wanyue Jiang
- Institute of Evolution & Marine Biodiversity, KLMME, Ocean University of China, 266003, Qingdao, China
| | - Yu Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Liping Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Mengmeng Yi
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Haitao Wang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Zengyu Ma
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Baozhen Qu
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Xiaohan Ji
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China
| | - Hongan Long
- Institute of Evolution & Marine Biodiversity, KLMME, Ocean University of China, 266003, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, 266237, Qingdao, China
| | - Shicui Zhang
- Institute of Evolution & Marine Biodiversity and Department of Marine Biology, Ocean University of China, 266003, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, 266237, Qingdao, China.
| |
Collapse
|
21
|
Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
Collapse
Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
| |
Collapse
|
22
|
Ponzetti M, Rucci N, Falone S. RNA methylation and cellular response to oxidative stress-promoting anticancer agents. Cell Cycle 2023; 22:870-905. [PMID: 36648057 PMCID: PMC10054233 DOI: 10.1080/15384101.2023.2165632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.
Collapse
Affiliation(s)
- Marco Ponzetti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Nadia Rucci
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L'Aquila, Italy
| | - Stefano Falone
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| |
Collapse
|
23
|
Yamagami R, Hori H. Functional analysis of tRNA modification enzymes using mutational profiling. Methods Enzymol 2023; 692:69-101. [PMID: 37925188 DOI: 10.1016/bs.mie.2023.02.021] [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: 11/06/2023]
Abstract
Transfer RNA (tRNA) delivers amino acids to the ribosome and functions as an essential adapter molecule for decoding codons on the messenger RNA (mRNA) during protein synthesis. Before attaining their proper activity, tRNAs undergo multiple post-transcriptional modifications with highly diversified roles such as stabilization of the tRNA structure, recognition of aminoacyl tRNA synthetases, precise codon-anticodon recognition, support of viral replication and onset of immune responses. The synthesis of the majority of modified nucleosides is catalyzed by a site-specific tRNA modification enzyme. This chapter provides a detailed protocol for using mutational profiling to analyze the enzymatic function of a tRNA methyltransferase in a high-throughput manner. In a previous study, we took tRNA m1A22 methyltransferase TrmK from Geobacillus stearothermophilus as a model tRNA methyltransferase and applied this protocol to gain mechanistic insights into how TrmK recognizes the substrate tRNAs. In theory, this protocol can be used unaltered for studying enzymes that catalyze modifications at the Watson-Crick face such as 1-methyladenosine (m1A), 3-methylcytosine (m3C), 3-methyluridine (m3U), 1-methylguanosine (m1G), and N2,N2-dimethylguanosine (m22G).
Collapse
Affiliation(s)
- Ryota Yamagami
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
| | - Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime, Japan.
| |
Collapse
|
24
|
Longan ER, Ramos J, Fu D. ADATscan - A flexible tool for scanning exomes for wobble inosine-dependent codons reveals a neurological bias for genes enriched in such codons in humans and mice. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000675. [PMID: 36733466 PMCID: PMC9887483 DOI: 10.17912/micropub.biology.000675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/14/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023]
Abstract
The conversion of adenosine to inosine at the wobble position of select tRNAs is essential for decoding specific codons in bacteria and eukarya. In eukarya, wobble inosine modification is catalyzed by the heterodimeric ADAT complex containing ADAT2 and ADAT3. Human individuals homozygous for loss of function variants in ADAT3 exhibit intellectual disability disorders. We created a flexible computational tool to scan the human, mouse, nematode, fruit fly, and yeast exomes for genes either enriched or depleted in ADAT-dependent codons as compared to background models of codon bias derived from the exomes themselves. We find that many genes are enriched or depleted for ADAT-dependent codons as compared to the genomic background in all five species. Among those genes enriched for ADAT-dependent codons in humans, we find there is significant Gene Ontology (GO) enrichment for genes involved in diverse neurological processes. This pattern persists in the mouse exome but not the fruit fly or nematode exome. In the nematode exome, genes enriched in ADAT-dependent codons are GO enriched for translation associated genes, and in yeast there is GO enrichment for genes involved in metabolic functions. There is also GO-term overlap between yeast and fruit flies. Importantly, in its generalized form, ADATscan can also be used to scan any exome for genes enriched in any subset of codons specified by the user.
Collapse
Affiliation(s)
- Emery R. Longan
- University of Rochester, Department of Biology, Rochester, NY 14620
,
Correspondence to: Emery R. Longan (
)
| | - Jillian Ramos
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045
| | - Dragony Fu
- University of Rochester, Department of Biology, Rochester, NY 14620
| |
Collapse
|
25
|
Zhang S, Yuan B, Cao J, Song L, Chen J, Qiu J, Qiu Z, Zhao XM, Chen J, Cheng TL. TadA orthologs enable both cytosine and adenine editing of base editors. Nat Commun 2023; 14:414. [PMID: 36702837 PMCID: PMC9880001 DOI: 10.1038/s41467-023-36003-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Cytidine and adenosine deaminases are required for cytosine and adenine editing of base editors respectively, and no single deaminase could enable concurrent and comparable cytosine and adenine editing. Additionally, distinct properties of cytidine and adenosine deaminases lead to various types of off-target effects, including Cas9-indendepent DNA off-target effects for cytosine base editors (CBEs) and RNA off-target effects particularly severe for adenine base editors (ABEs). Here we demonstrate that 25 TadA orthologs could be engineered to generate functional ABEs, CBEs or ACBEs via single or double mutations, which display minimized Cas9-independent DNA off-target effects and genotoxicity, with orthologs B5ZCW4, Q57LE3, E8WVH3, Q13XZ4 and B3PCY2 as promising candidates for further engineering. Furthermore, RNA off-target effects of TadA ortholog-derived base editors could be further reduced or even eliminated by additional single mutation. Taken together, our work expands the base editing toolkits, and also provides important clues for the potential evolutionary process of deaminases.
Collapse
Affiliation(s)
- Shuqian Zhang
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
- Department of Pediatrics, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Bo Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jixin Cao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Liting Song
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
| | - Jinlong Chen
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
| | - Jiayi Qiu
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China
| | - Zilong Qiu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- National Clinical Research Center for Aging and Medicine, Huashan Hopsital, Fudan University, Shanghai, 200032, China
- Songjiang Hospital, Songjiang Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jingqi Chen
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tian-Lin Cheng
- Institute for Translational Brain Research, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institute of Pediatrics, National Children's Medical Center, Children's Hospital, Fudan University, Shanghai, China.
| |
Collapse
|
26
|
Xie L, Miao X, Luo Q, Zhao H, Qin X. Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep. Genes (Basel) 2023; 14:203. [PMID: 36672944 PMCID: PMC9859159 DOI: 10.3390/genes14010203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/31/2022] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear. METHODS In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue. RESULTS We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2). CONCLUSIONS We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep.
Collapse
Affiliation(s)
| | - Xiangyang Miao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | | | | | | |
Collapse
|
27
|
Avcilar-Kucukgoze I, Gamper H, Hou YM, Kashina AS. Preparation of an Enriched tRNA Arg Fraction for Arginylation by Expression in E. coli. Methods Mol Biol 2023; 2620:101-106. [PMID: 37010754 DOI: 10.1007/978-1-0716-2942-0_13] [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: 04/04/2023]
Abstract
The method described here provides a fast and efficient way to obtain an enriched preparation of tRNA of interest, which is also posttranscriptionally modified by the intracellular machinery of the host cells, E. coli. While this preparation also contains a mixture of total E. coli tRNA, the enriched tRNA of interest is obtained in high yields (milligram) and is highly efficient for biochemical assays in vitro. It is routinely used in our lab for arginylation.
Collapse
Affiliation(s)
- Irem Avcilar-Kucukgoze
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Gamper
- Department of Biochemistry and Molecular Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Ya-Ming Hou
- Department of Biochemistry and Molecular Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna S Kashina
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
28
|
Liao W, Nie W, Ahmad I, Chen G, Zhu B. The occurrence, characteristics, and adaptation of A-to-I RNA editing in bacteria: A review. Front Microbiol 2023; 14:1143929. [PMID: 36960293 PMCID: PMC10027721 DOI: 10.3389/fmicb.2023.1143929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
A-to-I RNA editing is a very important post-transcriptional modification or co-transcriptional modification that creates isoforms and increases the diversity of proteins. In this process, adenosine (A) in RNA molecules is hydrolyzed and deaminated into inosine (I). It is well known that ADAR (adenosine deaminase acting on RNA)-dependent A-to-I mRNA editing is widespread in animals. Next, the discovery of A-to-I mRNA editing was mediated by TadA (tRNA-specific adenosine deaminase) in Escherichia coli which is ADAR-independent event. Previously, the editing event S128P on the flagellar structural protein FliC enhanced the bacterial tolerance to oxidative stress in Xoc. In addition, the editing events T408A on the enterobactin iron receptor protein XfeA act as switches by controlling the uptake of Fe3+ in response to the concentration of iron in the environment. Even though bacteria have fewer editing events, the great majority of those that are currently preserved have adaptive benefits. Interestingly, it was found that a TadA-independent A-to-I RNA editing event T408A occurred on xfeA, indicating that there may be other new enzymes that perform a function like TadA. Here, we review recent advances in the characteristics, functions, and adaptations of editing in bacteria.
Collapse
Affiliation(s)
- Weixue Liao
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhan Nie
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Wenhan Nie,
| | - Iftikhar Ahmad
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Vehari, Pakistan
| | - Gongyou Chen
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Zhu
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Shanghai Cooperative Innovation Center for Modern Seed Industry, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Bo Zhu,
| |
Collapse
|
29
|
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
|
30
|
Abstract
The field of epitranscriptomics has expanded dramatically in recent years, both in the number of identified RNA modifications and the number of researchers studying them. As knowledge of post-transcriptional modifications continues to expand, numerous new methods have been developed to detect these modifications. Additionally, modifications are being extended to therapeutic settings, such as with recent mRNA vaccines. With this increase in knowledge and use, the community is recognizing the necessity for user-friendly databases to (i) store information from both high- and low-throughput studies and (ii) provide prediction software on how RNA modifications contribute to RNA function and disease. This mini-review highlights select RNA modification databases and their key attributes with the aim of providing a resource to researchers in the field of epitranscriptomics.
Collapse
Affiliation(s)
- Jillian Ramos
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, Colorado 80045, USA
| |
Collapse
|
31
|
Çakan E, Gunaydin G. Activation induced cytidine deaminase: An old friend with new faces. Front Immunol 2022; 13:965312. [PMID: 36405752 PMCID: PMC9670734 DOI: 10.3389/fimmu.2022.965312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Activation induced cytidine deaminase (AID) protein is a member of APOBEC family. AID converts cytidine to uracil, which is a key step for somatic hypermutation (SHM) and class switch recombination (CSR). AID also plays critical roles in B cell precursor stages, removing polyreactive B cells from immune repertoire. Since the main function of AID is inducing point mutations, dysregulation can lead to increased mutation load, translocations, disturbed genomic integrity, and lymphomagenesis. As such, expression of AID as well as its function is controlled strictly at various molecular steps. Other members of the APOBEC family also play crucial roles during carcinogenesis. Considering all these functions, AID represents a bridge, linking chronic inflammation to carcinogenesis and immune deficiencies to autoimmune manifestations.
Collapse
Affiliation(s)
- Elif Çakan
- Hacettepe University School of Medicine, Sihhiye, Ankara, Turkey
| | - Gurcan Gunaydin
- Department of Basic Oncology, Hacettepe University Cancer Institute, Sihhiye, Ankara, Turkey
| |
Collapse
|
32
|
Detection technologies for RNA modifications. Exp Mol Med 2022; 54:1601-1616. [PMID: 36266445 PMCID: PMC9636272 DOI: 10.1038/s12276-022-00821-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/21/2022] [Accepted: 05/18/2022] [Indexed: 12/29/2022] Open
Abstract
To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
Collapse
|
33
|
Kimura S, Srisuknimit V, McCarty KL, Dedon PC, Kranzusch PJ, Waldor MK. Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine. Nat Commun 2022; 13:5994. [PMID: 36220828 PMCID: PMC9553926 DOI: 10.1038/s41467-022-33714-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
Post-transcriptional RNA editing modulates gene expression in a condition-dependent fashion. We recently discovered C-to-Ψ editing in Vibrio cholerae tRNA. Here, we characterize the biogenesis, regulation, and functions of this previously undescribed RNA editing process. We show that an enzyme, TrcP, mediates the editing of C-to-U followed by the conversion of U to Ψ, consecutively. AlphaFold-2 predicts that TrcP consists of two globular domains (cytidine deaminase and pseudouridylase) and a long helical domain. The latter domain tethers tRNA substrates during both the C-to-U editing and pseudouridylation, likely enabling a substrate channeling mechanism for efficient catalysis all the way to the terminal product. C-to-Ψ editing both requires and suppresses other modifications, creating an interdependent network of modifications in the tRNA anticodon loop that facilitates coupling of tRNA modification states to iron availability. Our findings provide mechanistic insights into an RNA editing process that likely promotes environmental adaptation.
Collapse
Affiliation(s)
- Satoshi Kimura
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Veerasak Srisuknimit
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Kacie L McCarty
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institution of Technology, Cambridge, MA, USA
- Singapore-MIT Alliance for Research and Technology Antimicrobial Resistance Interdisciplinary Research Group, Singapore, Singapore
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| |
Collapse
|
34
|
Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
Collapse
Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
| |
Collapse
|
35
|
Bertotti S, Fleming I, Cámara MDLM, Centeno Cameán C, Carmona SJ, Agüero F, Balouz V, Zahn A, Di Noia JM, Alfonzo JD, Buscaglia CA. Characterization of ADAT2/3 molecules in Trypanosoma cruzi and regulation of mucin gene expression by tRNA editing. Biochem J 2022; 479:561-580. [PMID: 35136964 DOI: 10.1042/bcj20210850] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/28/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022]
Abstract
Adenosine-to-inosine conversion at position 34 (A34-to-I) of certain tRNAs is essential for expanding their decoding capacity. This reaction is catalyzed by the adenosine deaminase acting on tRNA (ADAT) complex, which in Eukarya is formed by two subunits: ADAT2 and ADAT3. We herein identified and thoroughly characterized the ADAT molecules from the protozoan pathogen Trypanosoma cruzi, the causative agent of Chagas Disease. TcADAT2 and TcADAT3 spontaneously form a catalytically active complex, as shown by expression in engineered bacteria and/or by the increased ex vivo tRNA A-to-I deamination activity of T. cruzi epimastigotes overexpressing TcADAT subunits. Importantly, enhanced TcADAT2/3 activity in transgenic parasites caused a shift in their in vivo tRNAThrAGU signature, which correlated with significant changes in the expression of the Thr-rich TcSMUG proteins. To our knowledge, this is the first evidence indicating that T. cruzi tRNA editing can be modulated in vivo, in turn post-transcriptionally changing the expression of specific genes. Our findings suggest tRNA editing/availability as a forcible step in controlling gene expression and driving codon adaptation in T. cruzi. Moreover, we unveil certain differences between parasite and mammalian host tRNA editing and processing, such as cytosine-to-uridine conversion at position 32 of tRNAThrAGU in T. cruzi, that may be exploited for the identification of novel druggable targets of intervention.
Collapse
Affiliation(s)
- Santiago Bertotti
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Ian Fleming
- Department of Microbiology, The Ohio State University, 318 W 12th Ave. (Aronoff Building), Columbus, U.S.A
| | - María de Los Milagros Cámara
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Camila Centeno Cameán
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Santiago J Carmona
- Trypanosomatics Laboratory, IIBio (UNSAM and CONICET), Buenos Aires, Argentina
| | - Fernán Agüero
- Trypanosomatics Laboratory, IIBio (UNSAM and CONICET), Buenos Aires, Argentina
| | - Virginia Balouz
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montreal (IRCM), Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Juan D Alfonzo
- Department of Microbiology, The Ohio State University, 318 W 12th Ave. (Aronoff Building), Columbus, U.S.A
| | - Carlos A Buscaglia
- Laboratory of Molecular Biology of Protozoa, Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde' (IIBio, Universidad Nacional de San Martín, UNSAM, and Consejo Nacional de Investigaciones Científicas y Técnicas, CONICET), Av. 25 de Mayo y Francia, Campus UNSAM, San Martín (1650), Buenos Aires, Argentina
| |
Collapse
|
36
|
Lateef OM, Akintubosun MO, Olaoba OT, Samson SO, Adamczyk M. Making Sense of "Nonsense" and More: Challenges and Opportunities in the Genetic Code Expansion, in the World of tRNA Modifications. Int J Mol Sci 2022; 23:938. [PMID: 35055121 PMCID: PMC8779196 DOI: 10.3390/ijms23020938] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/09/2023] Open
Abstract
The evolutional development of the RNA translation process that leads to protein synthesis based on naturally occurring amino acids has its continuation via synthetic biology, the so-called rational bioengineering. Genetic code expansion (GCE) explores beyond the natural translational processes to further enhance the structural properties and augment the functionality of a wide range of proteins. Prokaryotic and eukaryotic ribosomal machinery have been proven to accept engineered tRNAs from orthogonal organisms to efficiently incorporate noncanonical amino acids (ncAAs) with rationally designed side chains. These side chains can be reactive or functional groups, which can be extensively utilized in biochemical, biophysical, and cellular studies. Genetic code extension offers the contingency of introducing more than one ncAA into protein through frameshift suppression, multi-site-specific incorporation of ncAAs, thereby increasing the vast number of possible applications. However, different mediating factors reduce the yield and efficiency of ncAA incorporation into synthetic proteins. In this review, we comment on the recent advancements in genetic code expansion to signify the relevance of systems biology in improving ncAA incorporation efficiency. We discuss the emerging impact of tRNA modifications and metabolism in protein design. We also provide examples of the latest successful accomplishments in synthetic protein therapeutics and show how codon expansion has been employed in various scientific and biotechnological applications.
Collapse
Affiliation(s)
- Olubodun Michael Lateef
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | | | - Olamide Tosin Olaoba
- Laboratory of Functional and Structural Biochemistry, Federal University of Sao Carlos, Sao Carlos 13565-905, SP, Brazil;
| | - Sunday Ocholi Samson
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| | - Malgorzata Adamczyk
- Faculty of Chemistry, Warsaw University of Technology, 00-664 Warsaw, Poland; (O.M.L.); (M.O.A.); (S.O.S.)
| |
Collapse
|
37
|
Huang ZX, Li J, Xiong QP, Li H, Wang ED, Liu RJ. Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2. Nucleic Acids Res 2021; 49:13045-13061. [PMID: 34871455 PMCID: PMC8682788 DOI: 10.1093/nar/gkab1148] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/05/2021] [Accepted: 11/03/2021] [Indexed: 12/05/2022] Open
Abstract
Dnmt2, a member of the DNA methyltransferase superfamily, catalyzes the formation of 5-methylcytosine at position 38 in the anticodon loop of tRNAs. Dnmt2 regulates many cellular biological processes, especially the production of tRNA-derived fragments and intergenerational transmission of paternal metabolic disorders to offspring. Moreover, Dnmt2 is closely related to human cancers. The tRNA substrates of mammalian Dnmt2s are mainly detected using bisulfite sequencing; however, we lack supporting biochemical data concerning their substrate specificity or recognition mechanism. Here, we deciphered the tRNA substrates of human DNMT2 (hDNMT2) as tRNAAsp(GUC), tRNAGly(GCC) and tRNAVal(AAC). Intriguingly, for tRNAAsp(GUC) and tRNAGly(GCC), G34 is the discriminator element; whereas for tRNAVal(AAC), the inosine modification at position 34 (I34), which is formed by the ADAT2/3 complex, is the prerequisite for hDNMT2 recognition. We showed that the C32U33(G/I)34N35 (C/U)36A37C38 motif in the anticodon loop, U11:A24 in the D stem, and the correct size of the variable loop are required for Dnmt2 recognition of substrate tRNAs. Furthermore, mammalian Dnmt2s possess a conserved tRNA recognition mechanism.
Collapse
MESH Headings
- 5-Methylcytosine/metabolism
- Adenosine Deaminase/genetics
- Adenosine Deaminase/metabolism
- Animals
- Anticodon/genetics
- Anticodon/metabolism
- Base Sequence
- DNA (Cytosine-5-)-Methyltransferases/chemistry
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- HEK293 Cells
- HeLa Cells
- Humans
- Inosine/metabolism
- Mice
- Models, Molecular
- NIH 3T3 Cells
- Nucleic Acid Conformation
- Protein Binding
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Gly/chemistry
- RNA, Transfer, Gly/genetics
- RNA, Transfer, Gly/metabolism
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Substrate Specificity
Collapse
Affiliation(s)
- Zhi-Xuan Huang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Jing Li
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Qing-Ping Xiong
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Hao Li
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100039, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Hua Xia Road, Shanghai 201210, China
| |
Collapse
|
38
|
Zhou JB, Wang ED, Zhou XL. Modifications of the human tRNA anticodon loop and their associations with genetic diseases. Cell Mol Life Sci 2021; 78:7087-7105. [PMID: 34605973 PMCID: PMC11071707 DOI: 10.1007/s00018-021-03948-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/07/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022]
Abstract
Transfer RNAs (tRNAs) harbor the most diverse posttranscriptional modifications. Among such modifications, those in the anticodon loop, either on nucleosides or base groups, compose over half of the identified posttranscriptional modifications. The derivatives of modified nucleotides and the crosstalk of different chemical modifications further add to the structural and functional complexity of tRNAs. These modifications play critical roles in maintaining anticodon loop conformation, wobble base pairing, efficient aminoacylation, and translation speed and fidelity as well as mediating various responses to different stress conditions. Posttranscriptional modifications of tRNA are catalyzed mainly by enzymes and/or cofactors encoded by nuclear genes, whose mutations are firmly connected with diverse human diseases involving genetic nervous system disorders and/or the onset of multisystem failure. In this review, we summarize recent studies about the mechanisms of tRNA modifications occurring at tRNA anticodon loops. In addition, the pathogenesis of related disease-causing mutations at these genes is briefly described.
Collapse
Affiliation(s)
- Jing-Bo Zhou
- State Key Laboratory of Molecular Biology, 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, 320 Yue Yang Road, Shanghai, 200031, China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, 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, 320 Yue Yang Road, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 93 Middle Huaxia Road, Shanghai, 201210, China.
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, 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, 320 Yue Yang Road, Shanghai, 200031, China.
| |
Collapse
|
39
|
Wang DO. Epitranscriptomic regulation of cognitive development and decline. Semin Cell Dev Biol 2021; 129:3-13. [PMID: 34857470 DOI: 10.1016/j.semcdb.2021.11.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Functional genomics and systems biology have opened new doors to previously inaccessible genomic information and holistic approaches to study complex networks of genes and proteins in the central nervous system. The advances are revolutionizing our understanding of the genetic underpinning of cognitive development and decline by facilitating identifications of novel molecular regulators and physiological pathways underlying brain function, and by associating polymorphism and mutations to cognitive dysfunction and neurological diseases. However, our current understanding of these complex gene regulatory mechanisms has yet lacked sufficient mechanistic resolution for further translational breakthroughs. Here we review recent findings from the burgeoning field of epitranscriptomics in association of cognitive functions with a special focus on the epitranscritomic regulation in subcellular locations such as chromosome, synapse, and mitochondria. Although there are important gaps in knowledge, current evidence is suggesting that this layer of RNA regulation may be of particular interest for the spatiotemporally coordinated regulation of gene networks in developing and maintaining brain function that underlie cognitive changes.
Collapse
Affiliation(s)
- Dan Ohtan Wang
- Center for Biosystems Dynamics Research, RIKEN, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Biostudies, Kyoto University, Yoshida Hon-machi, Kyoto 606-8501, Japan.
| |
Collapse
|
40
|
Owens MC, Zhang C, Liu KF. Recent technical advances in the study of nucleic acid modifications. Mol Cell 2021; 81:4116-4136. [PMID: 34480848 PMCID: PMC9109655 DOI: 10.1016/j.molcel.2021.07.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 12/30/2022]
Abstract
Enzyme-mediated chemical modifications of nucleic acids are indispensable regulators of gene expression. Our understanding of the biochemistry and biological significance of these modifications has largely been driven by an ever-evolving landscape of technologies that enable accurate detection, mapping, and manipulation of these marks. Here we provide a summary of recent technical advances in the study of nucleic acid modifications with a focus on techniques that allow accurate detection and mapping of these modifications. For each modification discussed (N6-methyladenosine, 5-methylcytidine, inosine, pseudouridine, and N4-acetylcytidine), we begin by introducing the "gold standard" technique for its mapping and detection, followed by a discussion of techniques developed to address any shortcomings of the gold standard. By highlighting the commonalities and differences of these techniques, we hope to provide a perspective on the current state of the field and to lay out a guideline for development of future technologies.
Collapse
Affiliation(s)
- Michael C Owens
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Celia Zhang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
41
|
Valadon C, Namy O. The Importance of the Epi-Transcriptome in Translation Fidelity. Noncoding RNA 2021; 7:51. [PMID: 34564313 PMCID: PMC8482273 DOI: 10.3390/ncrna7030051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 12/11/2022] Open
Abstract
RNA modifications play an essential role in determining RNA fate. Recent studies have revealed the effects of such modifications on all steps of RNA metabolism. These modifications range from the addition of simple groups, such as methyl groups, to the addition of highly complex structures, such as sugars. Their consequences for translation fidelity are not always well documented. Unlike the well-known m6A modification, they are thought to have direct effects on either the folding of the molecule or the ability of tRNAs to bind their codons. Here we describe how modifications found in tRNAs anticodon-loop, rRNA, and mRNA can affect translation fidelity, and how approaches based on direct manipulations of the level of RNA modification could potentially be used to modulate translation for the treatment of human genetic diseases.
Collapse
Affiliation(s)
| | - Olivier Namy
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198 Gif-sur-Yvette, France;
| |
Collapse
|
42
|
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
|
43
|
Jiao WB, Patel V, Klasen J, Liu F, Pecinkova P, Ferrand M, Gy I, Camilleri C, Effgen S, Koornneef M, Pecinka A, Loudet O, Schneeberger K. The Evolutionary Dynamics of Genetic Incompatibilities Introduced by Duplicated Genes in Arabidopsis thaliana. Mol Biol Evol 2021; 38:1225-1240. [PMID: 33247726 PMCID: PMC8042742 DOI: 10.1093/molbev/msaa306] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudofunctionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. Although such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here, we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions that included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently coexist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.
Collapse
Affiliation(s)
- Wen-Biao Jiao
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vipul Patel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jonas Klasen
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Fang Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Petra Pecinkova
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Marina Ferrand
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Isabelle Gy
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Christine Camilleri
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Sigi Effgen
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Laboratory of Genetics, Wageningen University & Research, Wageningen, The Netherlands
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Institute of Experimental Botany (IEB), Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research (CRH), Olomouc, Czech Republic
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| |
Collapse
|
44
|
A semi-quantitative pull-down assay to study tRNA substrate specificity of modification enzymes. Methods Enzymol 2021; 658:359-377. [PMID: 34517954 DOI: 10.1016/bs.mie.2021.06.010] [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: 01/04/2023]
Abstract
A tRNA interacts with numerous proteins throughout its biogenesis and during translation, and a significant portion of these interacting proteins are involved in post-transcriptional modifications. While some of the modifying enzymes use relatively simple recognition elements for substrate recognition, many enzymes selectively modify a specific subset of tRNA species without obvious recognition rules. In this chapter we describe a semi-quantitative pull-down assay to study tRNA substrate specificity of modification enzymes, by using the yeast Saccharomyces cerevisiae m3C32 methyltransferase Trm140 as an example. We also discuss some overall considerations for a successful pull-down experiment, with a focus on practical applications of the dissociation constant KD between the protein and the tRNA and the off-rate.
Collapse
|
45
|
Ramos-Morales E, Bayam E, Del-Pozo-Rodríguez J, Salinas-Giegé T, Marek M, Tilly P, Wolff P, Troesch E, Ennifar E, Drouard L, Godin JD, Romier C. The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucleic Acids Res 2021; 49:6529-6548. [PMID: 34057470 PMCID: PMC8216470 DOI: 10.1093/nar/gkab436] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 01/26/2023] Open
Abstract
Post-transcriptional modification of tRNA wobble adenosine into inosine is crucial for decoding multiple mRNA codons by a single tRNA. The eukaryotic wobble adenosine-to-inosine modification is catalysed by the ADAT (ADAT2/ADAT3) complex that modifies up to eight tRNAs, requiring a full tRNA for activity. Yet, ADAT catalytic mechanism and its implication in neurodevelopmental disorders remain poorly understood. Here, we have characterized mouse ADAT and provide the molecular basis for tRNAs deamination by ADAT2 as well as ADAT3 inactivation by loss of catalytic and tRNA-binding determinants. We show that tRNA binding and deamination can vary depending on the cognate tRNA but absolutely rely on the eukaryote-specific ADAT3 N-terminal domain. This domain can rotate with respect to the ADAT catalytic domain to present and position the tRNA anticodon-stem-loop correctly in ADAT2 active site. A founder mutation in the ADAT3 N-terminal domain, which causes intellectual disability, does not affect tRNA binding despite the structural changes it induces but most likely hinders optimal presentation of the tRNA anticodon-stem-loop to ADAT2.
Collapse
Affiliation(s)
- Elizabeth Ramos-Morales
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Efil Bayam
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Jordi Del-Pozo-Rodríguez
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Martin Marek
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Peggy Tilly
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Edouard Troesch
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Eric Ennifar
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - Juliette D Godin
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| | - Christophe Romier
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, U 1258, 1 rue Laurent Fries, B.P. 10142, 67404, Illkirch Cedex, France
| |
Collapse
|
46
|
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: 19] [Impact Index Per Article: 6.3] [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
|
47
|
Paris Z, Svobodová M, Kachale A, Horáková E, Nenarokova A, Lukeš J. A mitochondrial cytidine deaminase is responsible for C to U editing of tRNA Trp to decode the UGA codon in Trypanosoma brucei. RNA Biol 2021; 18:278-286. [PMID: 34224320 PMCID: PMC8677022 DOI: 10.1080/15476286.2021.1940445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In kinetoplastid protists, all mitochondrial tRNAs are encoded in the nucleus and imported from the cytoplasm to maintain organellar translation. This also applies to the tryptophanyl tRNA (tRNATrp) encoded by a single-copy nuclear gene, with a CCA anticodon to read UGG codon used in the cytosolic translation. Yet, in the mitochondrion it is unable to decode the UGA codon specifying tryptophan. Following mitochondrial import of tRNATrp, this problem is solved at the RNA level by a single C34 to U34 editing event that creates the UCA anticodon, recognizing UGA. To identify the enzyme responsible for this critical editing activity, we scrutinized the genome of Trypanosoma brucei for putative cytidine deaminases as the most likely candidates. Using RNAi silencing and poisoned primer extension, we have identified a novel deaminase enzyme, named here TbmCDAT for mitochondrial Cytidine Deaminase Acting on tRNA, which is responsible for this organelle-specific activity in T. brucei. The ablation of TbmCDAT led to the downregulation of mitochondrial protein synthesis, supporting its role in decoding the UGA tryptophan codon.
Collapse
Affiliation(s)
- Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Michaela Svobodová
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Budweis, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| |
Collapse
|
48
|
Liu X, Zhou J, Ge R, Xie W. Functional and structural investigation of N-terminal domain of the SpTad2/3 heterodimeric tRNA deaminase. Comput Struct Biotechnol J 2021; 19:3384-3393. [PMID: 34194665 PMCID: PMC8217354 DOI: 10.1016/j.csbj.2021.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/27/2022] Open
Abstract
N-terminal domain of SpTad2/3 is a putative kinase but not functional. N-SpTad2 does not bind tRNA but its deletion renders the deaminase inactive. Structure of N-SpTad2 was solved, revealing it may bind phosphates. Incapable of binding to DNA, N-SpTad2 may enhance the stability of the holoenzyme.
Editing is a post-transcriptional process that changes the content of nucleic acids occurring on both DNA and RNA levels. Inosine at position 34 in tRNA is one such example, commonly produced via the deamination of A34, catalyzed by adenosine deaminase acting on tRNA (ADAT or Tad). The formation of inosine is essential for cell viability. The eukaryotic deaminases normally consist of the catalytic subunit Tad2 and the structural subunit Tad3, but the catalytic process is poorly understood. Despite the conservation of the (pseudo-) catalytic domains, the heterodimeric enzyme Tad2/3 also possesses additional domains that could exhibit novel functions. Here we present the structure of the N-terminal domain of the Schizosaccharomyces pombe Tad2/3 heterodimeric tRNA(A34) deaminase (N-SpTad2), which shares ~30% sequence identities with uridine-cytidine or pantothenate kinases, but lacks the predicted kinase functions. While biochemical assays indicated that the domain is not a nucleic-acid binder, it is able to significantly influence the A34-tRNA deamination activity of the holoenzyme. Through co-expression and purification analyses, we deduce that N-SpTad2 plays a role in mediating protein-protein contacts and enhancing the stability and solubility of SpTad2/3, without which the deaminase is not functional. Taken together, our structural and biochemical studies highlighted the importance of the additional domains to the intrinsic deaminase functions of heterodimeric Tad2/3 enzymes and promoted our understanding on this essential post-transcriptional tRNA modification.
Collapse
Affiliation(s)
- Xiwen Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancun Erheng Rd, Guangzhou, Guangdong 510655, People's Republic of China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Ruiguang Ge
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
- Corresponding author.
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
- Corresponding author.
| |
Collapse
|
49
|
Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
Collapse
Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M. Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| |
Collapse
|
50
|
Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
Collapse
Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
| |
Collapse
|