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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Garin S, Levi O, Forrest ME, Antonellis A, Arava YS. Comprehensive characterization of mRNAs associated with yeast cytosolic aminoacyl-tRNA synthetases. RNA Biol 2021; 18:2605-2616. [PMID: 34039240 PMCID: PMC8632134 DOI: 10.1080/15476286.2021.1935116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/27/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are a conserved family of enzymes with an essential role in protein synthesis: ligating amino acids to cognate tRNA molecules for translation. In addition to their role in tRNA charging, aaRSs have acquired non-canonical functions, including post-transcriptional regulation of mRNA expression. Yet, the extent and mechanisms of these post-transcriptional functions are largely unknown. Herein, we performed a comprehensive transcriptome analysis to define the mRNAs that are associated with almost all aaRSs present in S. cerevisiae cytosol. Nineteen (out of twenty) isogenic strains of GFP-tagged cytosolic aaRSs were subjected to immunoprecipitation with anti-GFP beads along with an untagged control. mRNAs associated with each aaRS were then identified by RNA-seq. The extent of mRNA association varied significantly between aaRSs, from MetRS in which none appeared to be statistically significant, to PheRS that binds hundreds of different mRNAs. Interestingly, many target mRNAs are bound by multiple aaRSs, suggesting co-regulation by this family of enzymes. Gene Ontology analyses for aaRSs with a considerable number of target mRNAs discovered an enrichment for pathways of amino acid metabolism and of ribosome biosynthesis. Furthermore, sequence and structure motif analysis revealed for some aaRSs an enrichment for motifs that resemble the anticodon stem loop of cognate tRNAs. These data suggest that aaRSs coordinate mRNA expression in response to amino acid availability and may utilize RNA elements that mimic their canonical tRNA binding partners.
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Affiliation(s)
- Shahar Garin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Ofri Levi
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Megan E. Forrest
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yoav S. Arava
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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Okamoto N, Miya F, Tsunoda T, Kanemura Y, Saitoh S, Kato M, Yanagi K, Kaname T, Kosaki K. Four pedigrees with aminoacyl-tRNA synthetase abnormalities. Neurol Sci 2021; 43:2765-2774. [PMID: 34585293 DOI: 10.1007/s10072-021-05626-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 09/23/2021] [Indexed: 01/16/2023]
Abstract
Aminoacyl tRNA synthetases (ARSs) are highly conserved enzymes that link amino acids to their cognate tRNAs. Thirty-seven ARSs are known and their deficiencies cause various genetic disorders. Variants in some ARSs are associated with the autosomal dominant inherited form of axonal neuropathy, including Charcot-Marie-Tooth (CMT) disease. Variants of genes encoding ARSs often cause disorders in an autosomal recessive fashion. The clinical features of cytosolic ARS deficiencies are more variable, including systemic features. Deficiencies of ARSs localized in the mitochondria are often associated with neurological disorders including Leigh and early-onset epileptic syndromes. Whole exome sequencing (WES) is an efficient way to identify the genes causing various symptoms in patients. We identified 4 pedigrees with novel compound heterozygous variants in ARS genes (WARS1, MARS1, AARS2, and PARS2) by WES. Some unique manifestations were noted. The number of patients with ARSs has been increasing since the application of WES. Our findings broaden the known genetic and clinical spectrum associated with ARS variants.
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Affiliation(s)
- Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Osaka, Japan.
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yonehiro Kanemura
- Department of Neurosurgery, National Hospital Organization Osaka National Hospital, Osaka, Japan.,Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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Abstract
BACKGROUND Helminth infections affect ~ 60% of the human population that lives in tropical and subtropical regions worldwide. These infections result in diseases like schistosomiasis, lymphatic filariasis, river blindness and echinococcosis. Here we provide a comprehensive computational analysis of the aminoacyl tRNA synthetase (aaRS) enzyme family from 27 human-infecting helminths. Our analyses support the idea that several helminth aaRSs can be targeted for drug repurposing or for development of new drugs. For experimental validation, we focused on Onchocerciasis (also known as "river blindness"), a filarial vector-borne disease that is prevalent in Africa and Latin America. We show that halofuginone (HF) can act as a potent inhibitor of Onchocerca volvulus prolyl tRNA synthetase (OvPRS). RESULTS The conserved enzyme family of aaRSs has been validated as druggable targets in numerous eukaryotic parasites. We thus embarked on assessing aaRSs from the genomes of 27 helminths that cause infections in humans. In order to delineate the distribution of aaRSs per genome we utilized Hidden Markov Models of aaRS catalytic domains to identify all orthologues. We note that Fasciola hepatica genome encodes the highest number of aaRS-like proteins (69) whereas Taenia asiatica has the lowest count (32). The number of genes for any particular aaRS-like protein varies from 1 to 8 in these 27 studied helminths. Sequence alignments of helminth-encoded lysyl, prolyl, leucyl and threonyl tRNA synthetases suggest that various known aaRS inhibitors like Cladosporin, Halofuginone, Benzoborale and Borrelidin may be of utility against helminths. The recombinantly expressed Onchocerca volvulus PRS was used as proof of concept for targeting aaRS with drug-like molecules like HF. CONCLUSIONS Systematic analysis of unique subdomains within helminth aaRSs reveals the presence of a number of non-canonical domains like PAC3, Utp-14, Pex2_Pex12 fused to catalytic domains in the predicted helminth aaRSs. We have established a platform for biochemical validation of a large number of helminth aaRSs that can be targeted using available inhibitors to jump-start drug repurposing against human helminths.
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Affiliation(s)
- Preeti Goel
- 0000 0004 0498 7682grid.425195.eStructural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India ,0000 0004 0498 8167grid.411816.bDepartment of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110063 India
| | - Suhel Parvez
- 0000 0004 0498 8167grid.411816.bDepartment of Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110063 India
| | - Amit Sharma
- 0000 0004 0498 7682grid.425195.eStructural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067 India
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Abstract
BACKGROUND Treatment of parasitic diseases has been challenging due to evolution of drug resistant parasites, and thus there is need to identify new class of drugs and drug targets. Protein translation is important for survival of malarial parasite, Plasmodium, and the pathway is present in all of its life cycle stages. Aminoacyl tRNA synthetases are primary enzymes in protein translation as they catalyse amino acid addition to the cognate tRNA. This study sought to understand differences between Plasmodium and human aminoacyl tRNA synthetases through bioinformatics analysis. METHODS Plasmodium berghei, Plasmodium falciparum, Plasmodium fragile, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax, Plasmodium yoelii and human aminoacyl tRNA synthetase sequences were retrieved from UniProt database and grouped into 20 families based on amino acid specificity. These families were further divided into two classes. Both families and classes were analysed. Motif discovery was carried out using the MEME software, sequence identity calculation was done using an in-house Python script, multiple sequence alignments were performed using PROMALS3D and TCOFFEE tools, and phylogenetic tree calculations were performed using MEGA vs 7.0 tool. Possible alternative binding sites were predicted using FTMap webserver and SiteMap tool. RESULTS Motif discovery revealed Plasmodium-specific motifs while phylogenetic tree calculations showed that Plasmodium proteins have different evolutionary history to the human homologues. Human aaRSs sequences showed low sequence identity (below 40%) compared to Plasmodium sequences. Prediction of alternative binding sites revealed potential druggable sites in PfArgRS, PfMetRS and PfProRS at regions that are weakly conserved when compared to the human homologues. Multiple sequence analysis, motif discovery, pairwise sequence identity calculations and phylogenetic tree analysis showed significant differences between parasite and human aaRSs proteins despite functional and structural conservation. These differences may provide a basis for further exploration of Plasmodium aminoacyl tRNA synthetases as potential drug targets. CONCLUSION This study showed that, despite, functional and structural conservation, Plasmodium aaRSs have key differences from the human homologues. These differences in Plasmodium aaRSs can be targeted to develop anti-malarial drugs with less toxicity to the host.
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Affiliation(s)
- Dorothy Wavinya Nyamai
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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Di Micco P, Fazzi D'Orsi M, Morea V, Frontali L, Francisci S, Montanari A. The yeast model suggests the use of short peptides derived from mt LeuRS for the therapy of diseases due to mutations in several mt tRNAs. Biochim Biophys Acta 2014; 1843:3065-74. [PMID: 25261707 DOI: 10.1016/j.bbamcr.2014.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 01/23/2023]
Abstract
We have previously established a yeast model of mitochondrial (mt) diseases. We showed that defective respiratory phenotypes due to point-mutations in mt tRNA(Leu(UUR)), tRNA(Ile) and tRNA(Val) could be relieved by overexpression of both cognate and non-cognate nuclearly encoded mt aminoacyl-tRNA synthetases (aaRS) LeuRS, IleRS and ValRS. More recently, we showed that the isolated carboxy-terminal domain (Cterm) of yeast mt LeuRS, and even short peptides derived from the human Cterm, have the same suppressing abilities as the whole enzymes. In this work, we extend these results by investigating the activity of a number of mt aaRS from either class I or II towards a panel of mt tRNAs. The Cterm of both human and yeast mt LeuRS has the same spectrum of activity as mt aaRS belonging to class I and subclass a, which is the most extensive among the whole enzymes. Yeast Cterm is demonstrated to be endowed with mt targeting activity. Importantly, peptide fragments β30_31 and β32_33, derived from the human Cterm, have even higher efficiency as well as wider spectrum of activity, thus opening new avenues for therapeutic intervention. Bind-shifting experiments show that the β30_31 peptide directly interacts with human mt tRNA(Leu(UUR)) and tRNA(Ile), suggesting that the rescuing activity of isolated peptide fragments is mediated by a chaperone-like mechanism. Wide-range suppression appears to be idiosyncratic of LeuRS and its fragments, since it is not shared by Cterminal regions derived from human mt IleRS or ValRS, which are expected to have very different structures and interactions with tRNAs.
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Affiliation(s)
- Patrizio Di Micco
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Mario Fazzi D'Orsi
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Veronica Morea
- National Research Council of Italy (CNR) - Institute of Biology, Molecular Medicine and Nanobiotechnology (IBMN), Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Laura Frontali
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Silvia Francisci
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy; Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, 00185 Rome, Italy.
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