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Khan D, Ramachandiran I, Vasu K, China A, Khan K, Cumbo F, Halawani D, Terenzi F, Zin I, Long B, Costain G, Blaser S, Carnevale A, Gogonea V, Dutta R, Blankenberg D, Yoon G, Fox PL. Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6A site accessibility. Nat Commun 2024; 15:4284. [PMID: 38769304 PMCID: PMC11106242 DOI: 10.1038/s41467-024-48549-x] [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: 10/15/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is an autosomal recessive disorder characterized by defective central nervous system myelination. Exome sequencing of two siblings with severe cognitive and motor impairment and progressive hypomyelination characteristic of HLD revealed homozygosity for a missense single-nucleotide variant (SNV) in EPRS1 (c.4444 C > A; p.Pro1482Thr), encoding glutamyl-prolyl-tRNA synthetase, consistent with HLD15. Patient lymphoblastoid cell lines express markedly reduced EPRS1 protein due to dual defects in nuclear export and cytoplasmic translation of variant EPRS1 mRNA. Variant mRNA exhibits reduced METTL3 methyltransferase-mediated writing of N6-methyladenosine (m6A) and reduced reading by YTHDC1 and YTHDF1/3 required for efficient mRNA nuclear export and translation, respectively. In contrast to current models, the variant does not alter the sequence of m6A target sites, but instead reduces their accessibility for modification. The defect was rescued by antisense morpholinos predicted to expose m6A sites on target EPRS1 mRNA, or by m6A modification of the mRNA by METTL3-dCas13b, a targeted RNA methylation editor. Our bioinformatic analysis predicts widespread occurrence of SNVs associated with human health and disease that similarly alter accessibility of distal mRNA m6A sites. These results reveal a new RNA-dependent etiologic mechanism by which SNVs can influence gene expression and disease, consequently generating opportunities for personalized, RNA-based therapeutics targeting these disorders.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fabio Cumbo
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Dalia Halawani
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Isaac Zin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Briana Long
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Amanda Carnevale
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Grace Yoon
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Department of Paediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA.
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Malone TJ, Kaczmarek LK. The role of altered translation in intellectual disability and epilepsy. Prog Neurobiol 2022; 213:102267. [PMID: 35364140 PMCID: PMC10583652 DOI: 10.1016/j.pneurobio.2022.102267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Abstract
A very high proportion of cases of intellectual disability are genetic in origin and are associated with the occurrence of epileptic seizures during childhood. These two disorders together effect more than 5% of the world's population. One feature linking the two diseases is that learning and memory require the synthesis of new synaptic components and ion channels, while maintenance of overall excitability also requires synthesis of similar proteins in response to altered neuronal stimulation. Many of these disorders result from mutations in proteins that regulate mRNA processing, translation initiation, translation elongation, mRNA stability or upstream translation modulators. One theme that emerges on reviewing this field is that mutations in proteins that regulate changes in translation following neuronal stimulation are more likely to result in epilepsy with intellectual disability than general translation regulators with no known role in activity-dependent changes. This is consistent with the notion that activity-dependent translation in neurons differs from that in other cells types in that the changes in local cellular composition, morphology and connectivity that occur generally in response to stimuli are directly coupled to local synaptic activity and persist for months or years after the original stimulus.
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Affiliation(s)
- Taylor J Malone
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA
| | - Leonard K Kaczmarek
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA.
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Khan K, Gogonea V, Fox PL. Aminoacyl-tRNA synthetases of the multi-tRNA synthetase complex and their role in tumorigenesis. Transl Oncol 2022; 19:101392. [PMID: 35278792 PMCID: PMC8914993 DOI: 10.1016/j.tranon.2022.101392] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, 20 aminoacyl-tRNA synthetases (AARS) catalyze the ligation of amino acids to their cognate tRNAs to generate aminoacylated-tRNAs. In higher eukaryotes, 9 of the 20 AARSs, along with 3 auxiliary proteins, join to form the cytoplasmic multi-tRNA synthetase complex (MSC). The complex is absent in prokaryotes, but evolutionary expansion of MSC constituents, primarily by addition of novel interacting domains, facilitates formation of subcomplexes that join to establish the holo-MSC. In some cases, environmental cues direct the release of constituents from the MSC which enables the execution of non-canonical, i.e., "moonlighting", functions distinct from their essential activities in protein translation. These activities are generally beneficial, but can also be deleterious to the cell. Elucidation of the non-canonical activities of several AARSs residing in the MSC suggest they are potential therapeutic targets for cancer, as well as metabolic and neurologic diseases. Here, we describe the role of MSC-resident AARSs in cancer progression, and the factors that regulate their release from the MSC. Also, we highlight recent developments in therapeutic modalities that target MSC AARSs for cancer prevention and treatment.
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Affiliation(s)
- Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States of America.
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, United States of America
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States of America.
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Nayak P, Kejriwal A, Ratnaparkhi GS. SUMOylation of Arginyl tRNA Synthetase Modulates the Drosophila Innate Immune Response. Front Cell Dev Biol 2021; 9:695630. [PMID: 34660574 PMCID: PMC8514731 DOI: 10.3389/fcell.2021.695630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
SUMO conjugation of a substrate protein can modify its activity, localization, interaction or function. A large number of SUMO targets in cells have been identified by Proteomics, but biological roles for SUMO conjugation for most targets remains elusive. The multi-aminoacyl tRNA synthetase complex (MARS) is a sensor and regulator of immune signaling. The proteins of this 1.2 MDa complex are targets of SUMO conjugation, in response to infection. Arginyl tRNA Synthetase (RRS), a member of the sub-complex II of MARS, is one such SUMO conjugation target. The sites for SUMO conjugation are Lys 147 and 383. Replacement of these residues by Arg (RRS K147R,K383R ), creates a SUMO conjugation resistant variant (RRS SCR ). Transgenic Drosophila lines for RRS WT and RRS SCR were generated by expressing these variants in a RRS loss of function (lof) animal, using the UAS-Gal4 system. The RRS-lof line was itself generated using CRISPR/Cas9 genome editing. Expression of both RRS WT and RRS SCR rescue the RRS-lof lethality. Adult animals expressing RRS WT and RRS SCR are compared and contrasted for their response to bacterial infection by gram positive M. luteus and gram negative Ecc15. We find that RRS SCR , when compared to RRS WT , shows modulation of the transcriptional response, as measured by quantitative 3' mRNA sequencing. Our study uncovers a possible non-canonical role for SUMOylation of RRS, a member of the MARS complex, in host-defense.
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Affiliation(s)
- Prajna Nayak
- Indian Institute of Science Education and Research (IISER), Pune, India
| | - Aarti Kejriwal
- Indian Institute of Science Education and Research (IISER), Pune, India
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Levi O, Arava Y. mRNA association by aminoacyl tRNA synthetase occurs at a putative anticodon mimic and autoregulates translation in response to tRNA levels. PLoS Biol 2019; 17:e3000274. [PMID: 31100060 PMCID: PMC6542539 DOI: 10.1371/journal.pbio.3000274] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 05/30/2019] [Accepted: 05/02/2019] [Indexed: 12/25/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are well studied for their role in binding and charging tRNAs with cognate amino acids. Recent RNA interactome studies had suggested that these enzymes can also bind polyadenylated RNAs. Here, we explored the mRNA repertoire bound by several yeast aaRSs. RNA immunoprecipitation (RIP) followed by deep sequencing revealed unique sets of mRNAs bound by each aaRS. Interestingly, for every tested aaRSs, a preferential association with its own mRNA was observed, suggesting an autoregulatory process. Self-association of histidyl-tRNA synthetase (HisRS) was found to be mediated primarily through binding to a region predicted to fold into a tRNAHis anticodon-like structure. Introducing point mutations that are expected to disassemble this putative anticodon mimic alleviated self-association, concomitant with increased synthesis of the protein. Finally, we found that increased cellular levels of uncharged tRNAHis lead to reduced self-association and increased HisRS translation, in a manner that depends on the anticodon-like element. Together, these results reveal a novel post-transcriptional autoregulatory mechanism that exploits binding mimicry to control mRNA translation according to tRNA demands. Better known for their enzymatic role in charging tRNAs with their cognate amino acids, this study shows that tRNA synthetases also bind mRNAs, regulating translation in order to balance the production of a tRNA synthetase with the level of its cognate tRNA.
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Affiliation(s)
- Ofri Levi
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, Israel
| | - Yoav Arava
- Faculty of Biology, Technion, Israel Institute of Technology, Haifa, Israel
- * E-mail:
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Yu M, Luo C, Huang X, Chen D, Li S, Qi H, Gao X. Amino acids stimulate glycyl‐tRNA synthetase nuclear localization for mammalian target of rapamycin expression in bovine mammary epithelial cells. J Cell Physiol 2018; 234:7608-7621. [DOI: 10.1002/jcp.27523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/10/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Mengmeng Yu
- The Key Laboratory of Dairy Science of Education Ministry, Life College, Northeast Agricultural University Harbin China
| | - Chaochao Luo
- The Key Laboratory of Dairy Science of Education Ministry, Life College, Northeast Agricultural University Harbin China
| | - Xin Huang
- The Key Laboratory of Dairy Science of Education Ministry, Life College, Northeast Agricultural University Harbin China
| | - Dongying Chen
- The Key Laboratory of Dairy Science of Education Ministry, Life College, Northeast Agricultural University Harbin China
| | - Shanshan Li
- The Key Laboratory of Dairy Science of Education Ministry, Life College, Northeast Agricultural University Harbin China
| | - Hao Qi
- The Key Laboratory of Dairy Science of Education Ministry, Life College, Northeast Agricultural University Harbin China
| | - Xuejun Gao
- The Key Laboratory of Dairy Science of Education Ministry, Life College, Northeast Agricultural University Harbin China
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Arif A, Yao P, Terenzi F, Jia J, Ray PS, Fox PL. The GAIT translational control system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 9. [PMID: 29152905 PMCID: PMC5815886 DOI: 10.1002/wrna.1441] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/12/2017] [Accepted: 07/31/2017] [Indexed: 01/19/2023]
Abstract
The interferon (IFN)‐γ‐activated inhibitor of translation (GAIT) system directs transcript‐selective translational control of functionally related genes. In myeloid cells, IFN‐γ induces formation of a multiprotein GAIT complex that binds structural GAIT elements in the 3′‐untranslated regions (UTRs) of multiple inflammation‐related mRNAs, including ceruloplasmin and VEGF‐A, and represses their translation. The human GAIT complex is a heterotetramer containing glutamyl‐prolyl tRNA synthetase (EPRS), NS1‐associated protein 1 (NSAP1), ribosomal protein L13a (L13a), and glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH). A network of IFN‐γ‐stimulated kinases regulates recruitment and assembly of GAIT complex constituents. Activation of cyclin‐dependent kinase 5 (Cdk5), mammalian target of rapamycin complex 1 (mTORC1), and S6K1 kinases induces EPRS release from its parental multiaminoacyl tRNA synthetase complex to join NSAP1 in a ‘pre‐GAIT’ complex. Subsequently, the DAPK‐ZIPK kinase axis phosphorylates L13a, inducing release from the 60S ribosomal subunit and binding to GAPDH. The subcomplexes join to form the functional GAIT complex. Each constituent has a distinct role in the GAIT system. EPRS binds the GAIT element in target mRNAs, NSAP1 negatively regulates mRNA binding, L13a binds eIF4G to block ribosome recruitment, and GAPDH shields L13a from proteasomal degradation. The GAIT system is susceptible to genetic and condition‐specific regulation. An N‐terminus EPRS truncate is a dominant‐negative inhibitor ensuring a ‘translational trickle’ of target transcripts. Also, hypoxia and oxidatively modified lipoproteins regulate GAIT activity. Mouse models exhibiting absent or genetically modified GAIT complex constituents are beginning to elucidate the physiological role of the GAIT system, particularly in the resolution of chronic inflammation. Finally, GAIT‐like systems in proto‐chordates suggests an evolutionarily conserved role of the pathway in innate immunity. WIREs RNA 2018, 9:e1441. doi: 10.1002/wrna.1441 This article is categorized under:
Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes Regulatory RNAs/RNAi/Riboswitches > Riboswitches
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Affiliation(s)
- Abul Arif
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine & Dentistry, Rochester, NY, USA
| | - Fulvia Terenzi
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jie Jia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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