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Ghanbar MI, Danoff SK. Review of Pulmonary Manifestations in Antisynthetase Syndrome. Semin Respir Crit Care Med 2024; 45:365-385. [PMID: 38710221 DOI: 10.1055/s-0044-1785536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Antisynthetase syndrome (ASyS) is now a widely recognized entity within the spectrum of idiopathic inflammatory myopathies. Initially described in patients with a triad of myositis, arthritis, and interstitial lung disease (ILD), its presentation can be diverse. Additional common symptoms experienced by patients with ASyS include Raynaud's phenomenon, mechanic's hand, and fever. Although there is a significant overlap with polymyositis and dermatomyositis, the key distinction lies in the presence of antisynthetase antibodies (ASAs). Up to 10 ASAs have been identified to correlate with a presentation of ASyS, each having manifestations that may slightly differ from others. Despite the proposal of three classification criteria to aid diagnosis, the heterogeneous nature of patient presentations poses challenges. ILD confers a significant burden in patients with ASyS, sometimes manifesting in isolation. Notably, ILD is also often the initial presentation of ASyS, requiring pulmonologists to remain vigilant for an accurate diagnosis. This article will comprehensively review the various aspects of ASyS, including disease presentation, diagnosis, management, and clinical course, with a primary focus on its pulmonary manifestations.
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Affiliation(s)
- Mohammad I Ghanbar
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Sonye K Danoff
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland
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2
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Zhang H, Ling J. Serine mistranslation induces the integrated stress response without accumulation of uncharged tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578812. [PMID: 38370842 PMCID: PMC10871240 DOI: 10.1101/2024.02.04.578812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that support robust and accurate protein synthesis. A rapidly expanding number of studies show that mutations in aaRSs lead to multiple human diseases, including neurological disorders and cancer. Much remains unknown about how aaRS mutations impact human health. In particular, how aminoacylation errors affect stress responses and fitness in eukaryotic cells remains poorly understood. The integrated stress response (ISR) is an adaptive mechanism in response to multiple stresses. However, chronic activation of the ISR contributes to the development of multiple diseases (e.g., neuropathies). Here we show that Ser misincorporation into Ala and Thr codons, resulting from aaRS editing defects or mutations in tRNAs, constitutively active the ISR. Such activation does not appear to depend on the accumulation of uncharged tRNAs, implicating that Ser mistranslation may lead to ribosome stalling and collision.
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Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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3
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Zhang H, Murphy P, Yu J, Lee S, Tsai FTF, van Hoof A, Ling J. Coordination between aminoacylation and editing to protect against proteotoxicity. Nucleic Acids Res 2023; 51:10606-10618. [PMID: 37742077 PMCID: PMC10602869 DOI: 10.1093/nar/gkad778] [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: 06/16/2023] [Revised: 08/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that ligate amino acids to tRNAs, and often require editing to ensure accurate protein synthesis. Recessive mutations in aaRSs cause various neurological disorders in humans, yet the underlying mechanism remains poorly understood. Pathogenic aaRS mutations frequently cause protein destabilization and aminoacylation deficiency. In this study, we report that combined aminoacylation and editing defects cause severe proteotoxicity. We show that the ths1-C268A mutation in yeast threonyl-tRNA synthetase (ThrRS) abolishes editing and causes heat sensitivity. Surprisingly, experimental evolution of the mutant results in intragenic mutations that restore heat resistance but not editing. ths1-C268A destabilizes ThrRS and decreases overall Thr-tRNAThr synthesis, while the suppressor mutations in the evolved strains improve aminoacylation. We further show that deficiency in either ThrRS aminoacylation or editing is insufficient to cause heat sensitivity, and that ths1-C268A impairs ribosome-associated quality control. Our results suggest that aminoacylation deficiency predisposes cells to proteotoxic stress.
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Affiliation(s)
- Hong Zhang
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Jason Yu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
| | - Sukyeong Lee
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
| | - Francis T F Tsai
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Advanced Technology Core for Macromolecular X-ray Crystallography, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD 20742, USA
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4
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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: 2] [Impact Index Per Article: 2.0] [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.
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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.
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5
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Jin D, Wek SA, Cordova RA, Wek RC, Lacombe D, Michaud V, Musier-Forsyth K. Aminoacylation-defective bi-allelic mutations in human EPRS1 associated with psychomotor developmental delay, epilepsy, and deafness. Clin Genet 2023; 103:358-363. [PMID: 36411955 PMCID: PMC9898101 DOI: 10.1111/cge.14269] [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: 08/18/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
Aminoacyl-tRNA synthetases are enzymes that ensure accurate protein synthesis. Variants of the dual-functional cytoplasmic human glutamyl-prolyl-tRNA synthetase, EPRS1, have been associated with leukodystrophy, diabetes and bone disease. Here, we report compound heterozygous variants in EPRS1 in a 4-year-old female patient presenting with psychomotor developmental delay, seizures and deafness. Functional studies of these two missense mutations support major defects in enzymatic function in vitro and contributed to confirmation of the diagnosis.
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Affiliation(s)
- Danni Jin
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus OH 43210, USA
| | - Sheree A. Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Ricardo A. Cordova
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Ronald C. Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis IN 46202, USA
| | - Didier Lacombe
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
| | - Vincent Michaud
- Department of Medical Genetics, University Hospital of Bordeaux, Bordeaux, France
- INSERM U1211, Rare Diseases, Genetics and Metabolism, University of Bordeaux, Bordeaux, France
- Co-corresponding authors ,
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus OH 43210, USA
- Co-corresponding authors ,
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6
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Kanaji S, Chen W, Morodomi Y, Shapiro R, Kanaji T, Yang XL. Mechanistic perspectives on anti-aminoacyl-tRNA synthetase syndrome. Trends Biochem Sci 2023; 48:288-302. [PMID: 36280495 PMCID: PMC9974581 DOI: 10.1016/j.tibs.2022.09.011] [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: 06/01/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 02/18/2023]
Abstract
Antisynthetase syndrome (ASSD) is an autoimmune disease characterized by circulating autoantibodies against one of eight aminoacyl-tRNA synthetases (aaRSs). Although these autoantibodies are believed to play critical roles in ASSD pathogenesis, the nature of their roles remains unclear. Here we describe ASSD pathogenesis and discuss ASSD-linked aaRSs - from the WHEP domain that may impart immunogenicity to the role of tRNA in eliciting the innate immune response and the secretion of aaRSs from cells. Through these explorations, we propose that ASSD pathogenesis involves the tissue-specific secretion of aaRSs and that extracellular tRNAs or tRNA fragments and their ability to engage Toll-like receptor signaling may be important disease factors.
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Affiliation(s)
- Sachiko Kanaji
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wenqian Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yosuke Morodomi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan Shapiro
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Taisuke Kanaji
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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7
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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Preger C, Notarnicola A, Hellström C, Wigren E, Fernandes-Cerqueira C, Kvarnström M, Wahren-Herlenius M, Idborg H, Lundberg IE, Persson H, Gräslund S, Jakobsson PJ. Autoantigenic properties of the aminoacyl tRNA synthetase family in idiopathic inflammatory myopathies. J Autoimmun 2023; 134:102951. [PMID: 36470210 DOI: 10.1016/j.jaut.2022.102951] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 12/04/2022]
Abstract
OBJECTIVES Autoantibodies are thought to play a key role in the pathogenesis of idiopathic inflammatory myopathies (IIM). However, up to 40% of IIM patients, even those with clinical manifestations of anti-synthetase syndrome (ASSD), test seronegative to known myositis-specific autoantibodies. We hypothesized the existence of new potential autoantigens among human cytoplasmic aminoacyl tRNA synthetases (aaRS) in patients with IIM. METHODS Plasma samples from 217 patients with IIM according to 2017 EULAR/ACR criteria, including 50 patients with ASSD, 165 without, and two with unknown ASSD status were identified retrospectively, as well as age and gender-matched sera from 156 population controls, and 219 disease controls. Patients with previously documented ASSD had to test positive for at least one of the five most common anti-aaRS autoantibodies (anti-Jo1, -PL7, -PL12, -EJ, and -OJ) and present with one or more of the following clinical manifestations: interstitial lung disease, myositis, arthritis, Raynaud's phenomenon, fever, or mechanic's hands. Demographics, laboratory, and clinical data of the IIM cohort (ASSD and non-ASSD) were compared. Samples were screened using a multiplex bead array assay for presence of autoantibodies against a panel of 117 recombinant protein variants, representing 33 myositis-related proteins, including all nineteen cytoplasmic aaRS. Prospectively collected clinical data for the IIM cohort were retrieved and compared between groups within the IIM cohort and correlated with the results of the autoantibody screening. Principal component analysis was used to analyze clinical manifestations between ASSD, non-ASSD groups, and individuals with novel anti-aaRS autoantibodies. RESULTS We identified reactivity towards 16 aaRS in 72 of the 217 IIM patients. Twelve patients displayed reactivity against nine novel aaRS. The novel autoantibody specificities were detected in four previously seronegative patients for myositis-specific autoantibodies and eight with previously detected myositis-specific autoantibodies. IIM individuals with novel anti-aaRS autoantibodies (n = 12) all had signs of myositis, and they had either muscle weakness and/or muscle enzyme elevation, 2/12 had mechanic's hands, 3/12 had interstitial lung disease, and 2/12 had arthritis. The individuals with novel anti-aaRS and a pathological muscle biopsy all presented widespread up-regulation of major histocompatibility complex class I. The reactivities against novel aaRS could be confirmed in ELISA and western blot. Using the multiplex bead array assay, we could confirm previously known reactivities to four of the most common aaRS (Jo1, PL12, PL7, and EJ (n = 45)) and identified patients positive for anti-Zo, -KS, and -HA (n = 10) that were not previously tested. A low frequency of anti-aaRS autoantibodies was also detected in controls. CONCLUSION Our results suggest that most, if not all, cytoplasmic aaRS may become autoantigenic. Autoantibodies against new aaRS may be found in plasma of patients previously classified as seronegative with potential high clinical relevance.
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Affiliation(s)
- Charlotta Preger
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Antonella Notarnicola
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Hellström
- KTH Royal Institute of Technology, Department of Protein Science, SciLifeLab, Stockholm, Sweden
| | - Edvard Wigren
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | | | - Marika Kvarnström
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Academic Specialist Center, Center for Rheumatology, Stockholm Health Services, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Helena Idborg
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid E Lundberg
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Helena Persson
- KTH Royal Institute of Technology, Department of Protein Science, SciLifeLab, Stockholm, Sweden
| | - Susanne Gräslund
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Karolinska Institutet, Division of Rheumatology, Department of Medicine Solna, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden.
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Lei L, Yuan X, Fu K, Chen Y, Lu Y, Shou N, Wu D, Chen X, Shi J, Zhang M, Chen Z, Shi Z. Pseudotargeted metabolomics revealed the adaptive mechanism of Draba oreades Schrenk at high altitude. FRONTIERS IN PLANT SCIENCE 2022; 13:1052640. [PMID: 36570906 PMCID: PMC9784223 DOI: 10.3389/fpls.2022.1052640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Strong ultraviolet radiation and low temperature environment on Gangshika Mountain, located in the eastern part of the Qilian Mountains in Qinghai Province, can force plants to produce some special secondary metabolites for resisting severe environmental stress. However, the adaptive mechanism of Draba oreades Schrenk at high altitude are still unclear. In the current study, Draba oreades Schrenk from the Gangshika Mountain at altitudes of 3800 m, 4000 m and 4200 m were collected for comprehensive metabolic evaluation using pseudotargeted metabolomics method. Through KEGG pathway enrichment analysis, we found that phenylpropanoid biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis and phenylalanine metabolism related to the biosynthesis of flavonoids were up-regulated in the high-altitude group, which may enhance the environmental adaptability to strong ultraviolet intensity and low temperature stress in high altitude areas. By TopFc20 distribution diagram, the content of flavonoids gradually increased with the elevation of altitude, mainly including apigenin, luteolin, quercetin, hesperidin, kaempferol and their derivatives. Based on the random forest model, 10 important metabolites were identified as potential biomarkers. L-phenylalanine, L-histidine, naringenin-7-O-Rutinoside-4'-O-glucoside and apigenin related to the flavonoids biosynthesis and plant disease resistance were increased with the elevation of altitude. This study provided important insights for the adaptive mechanism of Draba oreades Schrenk at high altitude by pseudotargeted metabolomics.
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Affiliation(s)
- Ling Lei
- Clinical Psychology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Xuefeng Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Keyi Fu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yijun Lu
- Clinical Psychology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Na Shou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Dandan Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xi Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jian Shi
- Metabolomics Detection Department, Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Minjuan Zhang
- Metabolomics Detection Department, Wuhan Metware Biotechnology Co., Ltd, Wuhan, China
| | - Zhe Chen
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, China
| | - Zunji Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Martin S, Allan KC, Pinkard O, Sweet T, Tesar PJ, Coller J. Oligodendrocyte differentiation alters tRNA modifications and codon optimality-mediated mRNA decay. Nat Commun 2022; 13:5003. [PMID: 36008413 PMCID: PMC9411196 DOI: 10.1038/s41467-022-32766-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 08/15/2022] [Indexed: 11/08/2022] Open
Abstract
Oligodendrocytes are specialized cells that confer neuronal myelination in the central nervous system. Leukodystrophies associated with oligodendrocyte deficits and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocyte cell lineage and find that specific tRNAs are hypomodified in oligodendrocytes within or near the anticodon compared to oligodendrocyte progenitor cells (OPCs). This hypomodified state may be the result of differential expression of key modification enzymes during oligodendrocyte differentiation. Moreover, we observe a concomitant relationship between tRNA hypomodification and tRNA decoding potential; observing oligodendrocyte specific alterations in codon optimality-mediated mRNA decay and ribosome transit. Our results reveal that oligodendrocytes naturally maintain a delicate, hypersensitized tRNA/mRNA axis. We suggest this axis is a potential mediator of pathology in leukodystrophies and white matter disease when further insult to tRNA metabolism is introduced.
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Affiliation(s)
- Sophie Martin
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Otis Pinkard
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Thomas Sweet
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jeff Coller
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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11
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Chen W, Lin Y, Jiang M, Wang Q, Shu Q. Identification of LARS as an essential gene for osteosarcoma proliferation through large-Scale CRISPR-Cas9 screening database and experimental verification. Lab Invest 2022; 20:355. [PMID: 35962451 PMCID: PMC9373537 DOI: 10.1186/s12967-022-03571-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/04/2022] [Indexed: 11/12/2022]
Abstract
Background Osteosarcoma is one of the most malignant tumors, and it occurs mostly in children and adolescents. Currently, surgery and chemotherapy are the main treatments. The recurrence rate is high and the prognosis is often poor. Finding an effective target gene therapy for osteosarcoma may effectively improve its prognosis. Method In this study, genes essential for the survival of osteosarcoma cells were identified by genome-wide screening of CRISPR-Cas9 based on the DepMap database. The expression of these essential genes in osteosarcoma patients’ tissues and normal tissues was identified in the GSE19276 database. Functional pathway enrichment analysis, protein interaction network construction, and LASSO were performed to construct a prognostic risk model based on these essential genes. CCK8 assay was used to detect the effect of essential gene-LARS (Leucyl-TRNA Synthetase 1) on the proliferation of osteosarcoma. Results In this study, 785 genes critical for osteosarcoma cell proliferation were identified from the DepMap. Among these 785 essential genes, 59 DEGs were identified in osteosarcoma tissues. In the functional enrichment analysis, these 59 essential genes were mainly enriched in cell cycle-related signaling pathways. Furthermore, we established a risk score module, including LARS and DNAJC17, screened from these 59 genes, and this module could divide osteosarcoma patients into the low-risk and high-risk groups. In addition, knockdown of LARS expression inhibited the proliferative ability of osteosarcoma cells. A significant correlation was found between LARS expression and Monocytic lineage, T cells, and Fibroblasts. Conclusion In conclusion, LARS was identified as an essential gene for survival in osteosarcoma based on the DepMap database. Knockdown of LARS expression significantly inhibited the proliferation of osteosarcoma cells, suggesting that it is involved in the formation and development of osteosarcoma. The results are useful as a foundation for further studies to elucidate a potential osteosarcoma diagnostic index and therapeutic targets. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03571-9.
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Affiliation(s)
- Wenhao Chen
- Department of Orthopedics, The Children's Hospital, Zhejiang University School of Medicine, National Children's Regional Medical Center, National Clinical Research Center for Child Health, 3333 Bingsheng Road, Hangzhou, 310052, Zhejiang Province, China
| | - Yuxiang Lin
- Department of Breast Surgery, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350001, Fujian Province, China.,Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, Fujian Province, China.,Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Meichen Jiang
- Department of Pathology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, 350001, Fujian Province, China
| | - Qingshui Wang
- College of Life Sciences, Fujian Normal University, 8 South Xuefu Road, Fuzhou, 350117, Fujian Province, China.
| | - Qiang Shu
- The Children's Hospital, Zhejiang University School of Medicine, National Children's Regional Medical Center, National Clinical Research Center for Child Health, 3333 Bingsheng Road, Hangzhou, 310052, Zhejiang Province, China.
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Galindo-Feria AS, Notarnicola A, Lundberg IE, Horuluoglu B. Aminoacyl-tRNA Synthetases: On Anti-Synthetase Syndrome and Beyond. Front Immunol 2022; 13:866087. [PMID: 35634293 PMCID: PMC9136399 DOI: 10.3389/fimmu.2022.866087] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/28/2022] [Indexed: 12/20/2022] Open
Abstract
Anti-synthetase syndrome (ASSD) is an autoimmune disease characterized by the presence of autoantibodies targeting one of several aminoacyl t-RNA synthetases (aaRSs) along with clinical features including interstitial lung disease, myositis, Raynaud’s phenomenon, arthritis, mechanic’s hands, and fever. The family of aaRSs consists of highly conserved cytoplasmic and mitochondrial enzymes, one for each amino acid, which are essential for the RNA translation machinery and protein synthesis. Along with their main functions, aaRSs are involved in the development of immune responses, regulation of transcription, and gene-specific silencing of translation. During the last decade, these proteins have been associated with cancer, neurological disorders, infectious responses, and autoimmune diseases including ASSD. To date, several aaRSs have been described to be possible autoantigens in different diseases. The most commonly described are histidyl (HisRS), threonyl (ThrRS), alanyl (AlaRS), glycyl (GlyRS), isoleucyl (IleRS), asparaginyl (AsnRS), phenylalanyl (PheRS), tyrosyl (TyrRS), lysyl (LysRS), glutaminyl (GlnRS), tryptophanyl (TrpRS), and seryl (SerRS) tRNA synthetases. Autoantibodies against the first eight autoantigens listed above have been associated with ASSD while the rest have been associated with other diseases. This review will address what is known about the function of the aaRSs with a focus on their autoantigenic properties. We will also describe the anti-aaRSs autoantibodies and their association to specific clinical manifestations, and discuss their potential contribution to the pathogenesis of ASSD.
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Affiliation(s)
- Angeles S. Galindo-Feria
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Antonella Notarnicola
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Ingrid E. Lundberg
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Begum Horuluoglu
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, and Karolinska University Hospital Solna, Stockholm, Sweden
- *Correspondence: Begum Horuluoglu,
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Giong HK, Lee JS. Systematic expression profiling of neuropathy-related aminoacyl-tRNA synthetases in zebrafish during development. Biochem Biophys Res Commun 2022; 587:92-98. [PMID: 34872004 DOI: 10.1016/j.bbrc.2021.11.098] [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: 10/22/2021] [Accepted: 11/27/2021] [Indexed: 12/01/2022]
Abstract
Aminoacyl tRNA synthetases (ARSs) are a group of proteins, acting as transporters to transfer and attach the appropriate amino acids onto their cognate tRNAs for translation. So far, 18 out of 20 cytoplasmic ARSs are reported to be connected to different neuropathy disorders with multi-organ defects that are often accompanied with developmental delays. Thus, it is important to understand functions and impacts of ARSs at the whole organism level. Here, we systematically analyzed the spatiotemporal expression of 14 ars and 2 aimp genes during development in zebrafish that have not be previously reported. Not only in the brain, their dynamic expression patterns in several tissues such as in the muscles, liver and intestine suggest diverse roles in a wide range of development processes in addition to neuronal function, which is consistent with potential involvement in multiple syndrome diseases associated with ARS mutations. In particular, hinted by its robust expression pattern in the brain, we confirmed that aimp1 is required for the formation of cerebrovasculature by a loss-of-function approach. Overall, our systematic profiling data provides a useful basis for studying roles of ARSs during development and understanding their potential functions in the etiology of related diseases.
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Affiliation(s)
- Hoi-Khoanh Giong
- Disease Target Structure Research Center, KRIBB, Daejeon, South Korea; KRIBB School, University of Science and Technology, Daejeon, South Korea; Dementia DTC R&D Convergence Program, KIST, Seoul, South Korea
| | - Jeong-Soo Lee
- Disease Target Structure Research Center, KRIBB, Daejeon, South Korea; KRIBB School, University of Science and Technology, Daejeon, South Korea; Dementia DTC R&D Convergence Program, KIST, Seoul, South Korea.
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Sissler M. Decoding the impact of disease-causing mutations in an essential aminoacyl-tRNA synthetase. J Biol Chem 2021; 297:101386. [PMID: 34752820 PMCID: PMC8626572 DOI: 10.1016/j.jbc.2021.101386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 11/26/2022] Open
Abstract
Aminoacyl-tRNA synthetases are housekeeping enzymes that catalyze the specific attachment of amino acids onto cognate tRNAs, providing building blocks for ribosomal protein synthesis. Owing to the absolutely essential nature of these enzymes, the possibility that mutations in their sequence could be the underlying cause of diseases had not been foreseen. However, we are learning of patients bearing familial mutations in aminoacyl-tRNA synthetases at an exponential rate. In a recent issue of JBC, Jin et al. analyzed the impact of two such mutations in the very special bifunctional human glutamyl-prolyl-tRNA synthetase and convincingly decode how these mutations elicit the integrated stress response.
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Affiliation(s)
- Marie Sissler
- ARNA - UMR5320 CNRS - U1212 INSERM, Université de Bordeaux, IECB, Pessac, France.
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Jin D, Wek SA, Kudlapur NT, Cantara WA, Bakhtina M, Wek RC, Musier-Forsyth K. Disease-associated mutations in a bifunctional aminoacyl-tRNA synthetase gene elicit the integrated stress response. J Biol Chem 2021; 297:101203. [PMID: 34537243 PMCID: PMC8511952 DOI: 10.1016/j.jbc.2021.101203] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) catalyze the charging of specific amino acids onto cognate tRNAs, an essential process for protein synthesis. Mutations in ARSs are frequently associated with a variety of human diseases. The human EPRS1 gene encodes a bifunctional glutamyl-prolyl-tRNA synthetase (EPRS) with two catalytic cores and appended domains that contribute to nontranslational functions. In this study, we report compound heterozygous mutations in EPRS1, which lead to amino acid substitutions P14R and E205G in two patients with diabetes and bone diseases. While neither mutation affects tRNA binding or association of EPRS with the multisynthetase complex, E205G in the glutamyl-tRNA synthetase (ERS) region of EPRS is defective in amino acid activation and tRNAGlu charging. The P14R mutation induces a conformational change and altered tRNA charging kinetics in vitro. We propose that the altered catalytic activity and conformational changes in the EPRS variants sensitize patient cells to stress, triggering an increased integrated stress response (ISR) that diminishes cell viability. Indeed, patient-derived cells expressing the compound heterozygous EPRS show heightened induction of the ISR, suggestive of disruptions in protein homeostasis. These results have important implications for understanding ARS-associated human disease mechanisms and development of new therapeutics.
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Affiliation(s)
- Danni Jin
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - Sheree A Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis Indiana, USA
| | - Nathan T Kudlapur
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - Marina Bakhtina
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis Indiana, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus Ohio, USA.
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Drosophila Models for Charcot-Marie-Tooth Neuropathy Related to Aminoacyl-tRNA Synthetases. Genes (Basel) 2021; 12:genes12101519. [PMID: 34680913 PMCID: PMC8536177 DOI: 10.3390/genes12101519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/29/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRS) represent the largest cluster of proteins implicated in Charcot–Marie–Tooth neuropathy (CMT), the most common neuromuscular disorder. Dominant mutations in six aaRS cause different axonal CMT subtypes with common clinical characteristics, including progressive distal muscle weakness and wasting, impaired sensory modalities, gait problems and skeletal deformities. These clinical manifestations are caused by “dying back” axonal degeneration of the longest peripheral sensory and motor neurons. Surprisingly, loss of aminoacylation activity is not a prerequisite for CMT to occur, suggesting a gain-of-function disease mechanism. Here, we present the Drosophila melanogaster disease models that have been developed to understand the molecular pathway(s) underlying GARS1- and YARS1-associated CMT etiology. Expression of dominant CMT mutations in these aaRSs induced comparable neurodegenerative phenotypes, both in larvae and adult animals. Interestingly, recent data suggests that shared molecular pathways, such as dysregulation of global protein synthesis, might play a role in disease pathology. In addition, it has been demonstrated that the important function of nuclear YARS1 in transcriptional regulation and the binding properties of mutant GARS1 are also conserved and can be studied in D. melanogaster in the context of CMT. Taken together, the fly has emerged as a faithful companion model for cellular and molecular studies of aaRS-CMT that also enables in vivo investigation of candidate CMT drugs.
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Structural analyses of a human lysyl-tRNA synthetase mutant associated with autosomal recessive nonsyndromic hearing impairment. Biochem Biophys Res Commun 2021; 554:83-88. [PMID: 33784510 DOI: 10.1016/j.bbrc.2021.03.093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) catalyze the ligation of amino acids to their cognate tRNAs and therefore play an essential role in protein biosynthesis in all living cells. The KARS gene in human encodes both cytosolic and mitochondrial lysyl-tRNA synthetase (LysRS). A recent study identified a missense mutation in KARS gene (c.517T > C) that caused autosomal recessive nonsyndromic hearing loss. This mutation led to a tyrosine to histidine (YH) substitution in both cytosolic and mitochondrial LysRS proteins, and decreased their aminoacylation activity to different levels. Here, we report the crystal structure of LysRS YH mutant at a resolution of 2.5 Å. We found that the mutation did not interfere with the active center, nor did it cause any significant conformational changes in the protein. The loops involved in tetramer interface and tRNA anticodon binding site showed relatively bigger variations between the mutant and wild type proteins. Considering the differences between the cytosolic and mitochondrial tRNAlyss, we suggest that the mutation triggered subtle changes in the tRNA anticodon binding region, and the interferences were further amplified by the different D and T loops in mitochondrial tRNAlys, and led to a complete loss of the aminoacylation of mitochondrial tRNAlys.
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