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Dulic M, Godinic-Mikulcic V, Kekez M, Evic V, Rokov-Plavec J. Protein-Protein Interactions of Seryl-tRNA Synthetases with Emphasis on Human Counterparts and Their Connection to Health and Disease. Life (Basel) 2024; 14:124. [PMID: 38255739 PMCID: PMC10817482 DOI: 10.3390/life14010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Seryl-tRNA synthetases (SerRSs), members of the aminoacyl-tRNA synthetase family, interact with diverse proteins, enabling SerRSs to enhance their role in the translation of the genetic message or to perform alternative functions in cellular processes beyond translation. Atypical archaeal SerRS interacts with arginyl-tRNA synthetase and proteins of the ribosomal P-stalk to optimize translation through tRNA channeling. The complex between yeast SerRS and peroxin Pex21p provides a connection between translation and peroxisome function. The partnership between Arabidopsis SerRS and BEN1 indicates a link between translation and brassinosteroid metabolism and may be relevant in plant stress response mechanisms. In Drosophila, the unusual heterodimeric mitochondrial SerRS coordinates mitochondrial translation and replication via interaction with LON protease. Evolutionarily conserved interactions of yeast and human SerRSs with m3C32 tRNA methyltransferases indicate coordination between tRNA modification and aminoacylation in the cytosol and mitochondria. Human cytosolic SerRS is a cellular hub protein connecting translation to vascular development, angiogenesis, lipogenesis, and telomere maintenance. When translocated to the nucleus, SerRS acts as a master negative regulator of VEGFA gene expression. SerRS alone or in complex with YY1 and SIRT2 competes with activating transcription factors NFκB1 and c-Myc, resulting in balanced VEGFA expression important for proper vascular development and angiogenesis. In hypoxia, SerRS phosphorylation diminishes its binding to the VEGFA promoter, while the lack of nutrients triggers SerRS glycosylation, reducing its nuclear localization. Additionally, SerRS binds telomeric DNA and cooperates with the shelterin protein POT1 to regulate telomere length and cellular senescence. As an antitumor and antiangiogenic factor, human cytosolic SerRS appears to be a promising drug target and therapeutic agent for treating cancer, cardiovascular diseases, and possibly obesity and aging.
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Affiliation(s)
| | | | | | | | - Jasmina Rokov-Plavec
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia; (M.D.); (V.G.-M.); (M.K.); (V.E.)
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2
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Jaramillo Ponce JR, Frugier M. Plasmodium, the Apicomplexa Outlier When It Comes to Protein Synthesis. Biomolecules 2023; 14:46. [PMID: 38254646 PMCID: PMC10813123 DOI: 10.3390/biom14010046] [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: 11/23/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Plasmodium is an obligate intracellular parasite that has numerous interactions with different hosts during its elaborate life cycle. This is also the case for the other parasites belonging to the same phylum Apicomplexa. In this study, we bioinformatically identified the components of the multi-synthetase complexes (MSCs) of several Apicomplexa parasites and modelled their assembly using AlphaFold2. It appears that none of these MSCs resemble the two MSCs that we have identified and characterized in Plasmodium. Indeed, tRip, the central protein involved in the association of the two Plasmodium MSCs is different from its homologues, suggesting also that the tRip-dependent import of exogenous tRNAs is not conserved in other apicomplexan parasites. Based on this observation, we searched for obvious differences that could explain the singularity of Plasmodium protein synthesis by comparing tRNA genes and amino acid usage in the different genomes. We noted a contradiction between the large number of asparagine residues used in Plasmodium proteomes and the single gene encoding the tRNA that inserts them into proteins. This observation remains true for all the Plasmodia strains studied, even those that do not contain long asparagine homorepeats.
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Affiliation(s)
| | - Magali Frugier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, F-67084 Strasbourg, France;
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3
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Tijaro-Bulla S, Nyandwi SP, Cui H. Physiological and engineered tRNA aminoacylation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1789. [PMID: 37042417 DOI: 10.1002/wrna.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Aminoacyl-tRNA synthetases form the protein family that controls the interpretation of the genetic code, with tRNA aminoacylation being the key chemical step during which an amino acid is assigned to a corresponding sequence of nucleic acids. In consequence, aminoacyl-tRNA synthetases have been studied in their physiological context, in disease states, and as tools for synthetic biology to enable the expansion of the genetic code. Here, we review the fundamentals of aminoacyl-tRNA synthetase biology and classification, with a focus on mammalian cytoplasmic enzymes. We compile evidence that the localization of aminoacyl-tRNA synthetases can be critical in health and disease. In addition, we discuss evidence from synthetic biology which made use of the importance of subcellular localization for efficient manipulation of the protein synthesis machinery. This article is categorized under: RNA Processing Translation > Translation Regulation RNA Processing > tRNA Processing RNA Export and Localization > RNA Localization.
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Affiliation(s)
| | | | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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4
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Zeng QY, Zhang F, Zhang JH, Hei Z, Li ZH, Huang MH, Fang P, Wang ED, Sun XJ, Zhou XL. Loss of threonyl-tRNA synthetase-like protein Tarsl2 has little impact on protein synthesis but affects mouse development. J Biol Chem 2023; 299:104704. [PMID: 37059185 DOI: 10.1016/j.jbc.2023.104704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 04/16/2023] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential components for mRNA translation. Two sets of aaRSs are required for cytoplasmic and mitochondrial translation in vertebrates. Interestingly, TARSL2 is a recently evolved duplicated gene of TARS1 (encoding cytoplasmic threonyl-tRNA synthetase) and represents the only duplicated aaRS gene in vertebrates. Although TARSL2 retains the canonical aminoacylation and editing activities in vitro, whether it is a true tRNA synthetase for mRNA translation in vivo is unclear. In this study, we showed that Tars1 is an essential gene since homozygous Tars1 knockout mice were lethal. In contrast, when Tarsl2 was deleted in mice and zebrafish, neither the abundance nor the charging levels of tRNAThrs were changed, indicating that cells relied on Tars1 but not on Tarsl2 for mRNA translation. Furthermore, Tarsl2 deletion did not influence the integrity of the multiple tRNA synthetase complex (MSC), suggesting that Tarsl2 is a peripheral member of the MSC. Finally, we observed that Tarsl2-deleted mice exhibited severe developmental retardation, elevated metabolic capacity, and abnormal bone and muscle development after 3 weeks. Collectively, these data suggest that, despite its intrinsic activity, loss of Tarsl2 has little influence on protein synthesis but does affect mouse development.
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Affiliation(s)
- Qi-Yu Zeng
- 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
| | - Fan Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200010
| | - Jian-Hui Zhang
- 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; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024
| | - Zhoufei Hei
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Zi-Han Li
- 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
| | - Meng-Han Huang
- 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
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, 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.
| | - Xiao-Jian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200010.
| | - 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; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024.
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5
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Zhen J, Pan J, Zhou X, Yu Z, Jiang Y, Gong Y, Ding Y, Liu Y, Guo L. FARSB serves as a novel hypomethylated and immune cell infiltration related prognostic biomarker in hepatocellular carcinoma. Aging (Albany NY) 2023; 15:2937-2969. [PMID: 37074800 DOI: 10.18632/aging.204619] [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: 12/28/2022] [Accepted: 03/09/2023] [Indexed: 04/20/2023]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is a prevalent tumor with high morbidity, and an unfavourable prognosis. FARSB is an aminoacyl tRNA synthase, and plays a key role in protein synthesis in cells. Furthermore, previous reports have indicated that FARSB is overexpressed in gastric tumor tissues and is associated with a poor prognosis and tumorigenesis. However, the function of FARSB in HCC has not been studied. RESULTS The results showed that FARSB mRNA and protein levels were upregulated in HCC and were closely related to many clinicopathological characteristics. Besides, according to multivariate Cox analysis, high FARSB expression was linked with a shorter survival time in HCC and may be an independent prognostic factor. In addition, the FARSB promoter methylation level was negatively associated with the expression of FARSB. Furthermore, enrichment analysis showed that FARSB was related to the cell cycle. And TIMER analysis revealed that the FARSB expression was closely linked to tumor purity and immune cell infiltration. The TCGA and ICGC data analysis suggested that FARSB expression is greatly related to m6A modifier related genes. Potential FARSB-related ceRNA regulatory networks were also constructed. What's more, based on the FARSB-protein interaction network, molecular docking models of FARSB and RPLP1 were constructed. Finally, drug susceptibility testing revealed that FARSB was susceptible to 38 different drugs or small molecules. CONCLUSIONS FARSB can serve as a prognostic biomarker for HCC and provide clues about immune infiltration, and m6A modification.
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Affiliation(s)
- Jing Zhen
- Second Affiliated Hospital of Nanchang University, Nanchang, China
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Zichuan Yu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yiyang Gong
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yongqi Ding
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Yue Liu
- Second College of Clinical Medicine, Nanchang University, Nanchang, China
| | - Liangyun Guo
- Department of Ultrasonography, Second Affiliated Hospital of Nanchang University, Nanchang, China
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6
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Jaramillo Ponce JR, Théobald‐Dietrich A, Bénas P, Paulus C, Sauter C, Frugier M. Solution X-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes. Protein Sci 2023; 32:e4564. [PMID: 36606712 PMCID: PMC9878616 DOI: 10.1002/pro.4564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/20/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
tRip is a tRNA import protein specific to Plasmodium, the causative agent of malaria. In addition to its membrane localization and tRNA trafficking properties, tRip has the capacity to associate with three aminoacyl-tRNA synthetases (aaRS), the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases. In eukaryotes, such multi-aaRSs complexes (MSC) regulate the moonlighting activities of aaRSs. In Plasmodium, tRip and the three aaRSs all contain an N-terminal GST-like domain involved in the assembly of two independent complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS) with a 2:2:2 stoichiometry and in which the association of the GST-like domains of tRip and ERS (tRip-N:ERS-N) is central. In this study, the crystal structure of the N-terminal GST-like domain of ERS was solved and made possible further investigation of the solution architecture of the Q- and M-complexes by small-angle x-ray scattering (SAXS). This strategy relied on the engineering of a tRip-N-ERS-N chimeric protein to study the structural scaffold of both Plasmodium MSCs and confirm the unique homodimerization pattern of tRip in solution. The biological impact of these structural arrangements is discussed.
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Affiliation(s)
- José R. Jaramillo Ponce
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002StrasbourgFrance
| | - Anne Théobald‐Dietrich
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002StrasbourgFrance
| | - Philippe Bénas
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002StrasbourgFrance
| | - Caroline Paulus
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002StrasbourgFrance
| | - Claude Sauter
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002StrasbourgFrance
| | - Magali Frugier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002StrasbourgFrance
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7
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Turvey AK, Horvath GA, Cavalcanti ARO. Aminoacyl-tRNA synthetases in human health and disease. Front Physiol 2022; 13:1029218. [PMID: 36330207 PMCID: PMC9623071 DOI: 10.3389/fphys.2022.1029218] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/04/2022] [Indexed: 11/29/2022] Open
Abstract
The Aminoacyl-tRNA Synthetases (aaRSs) are an evolutionarily ancient family of enzymes that catalyze the esterification reaction linking a transfer RNA (tRNA) with its cognate amino acid matching the anticodon triplet of the tRNA. Proper functioning of the aaRSs to create aminoacylated (or “charged”) tRNAs is required for efficient and accurate protein synthesis. Beyond their basic canonical function in protein biosynthesis, aaRSs have a surprisingly diverse array of non-canonical functions that are actively being defined. The human genome contains 37 genes that encode unique aaRS proteins. To date, 56 human genetic diseases caused by damaging variants in aaRS genes have been described: 46 are autosomal recessive biallelic disorders and 10 are autosomal dominant monoallelic disorders. Our appreciation of human diseases caused by damaging genetic variants in the aaRSs has been greatly accelerated by the advent of next-generation sequencing, with 89% of these gene discoveries made since 2010. In addition to these genetic disorders of the aaRSs, anti-synthetase syndrome (ASSD) is a rare autoimmune inflammatory myopathy that involves the production of autoantibodies that disrupt aaRS proteins. This review provides an overview of the basic biology of aaRS proteins and describes the rapidly growing list of human diseases known to be caused by genetic variants or autoimmune targeting that affect both the canonical and non-canonical functions of these essential proteins.
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Affiliation(s)
- Alexandra K. Turvey
- Department of Biology, Pomona College, Claremont, CA, United States
- *Correspondence: Alexandra K. Turvey,
| | - Gabriella A. Horvath
- Division of Biochemical Genetics, Department of Pediatrics, University of British Columbia, BC Children’s Hospital, Vancouver, BC, Canada
- Adult Metabolic Diseases Clinic, Vancouver General Hospital, Vancouver, BC, Canada
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8
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Multimodal cotranslational interactions direct assembly of the human multi-tRNA synthetase complex. Proc Natl Acad Sci U S A 2022; 119:e2205669119. [PMID: 36037331 PMCID: PMC9457175 DOI: 10.1073/pnas.2205669119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amino acid ligation to cognate transfer RNAs (tRNAs) is catalyzed by aminoacyl-tRNA synthetases (aaRSs)-essential interpreters of the genetic code during translation. Mammalian cells harbor 20 cytoplasmic aaRSs, out of which 9 (in 8 proteins), with 3 non-aaRS proteins, AIMPs 1 to 3, form the ∼1.25-MDa multi-tRNA synthetase complex (MSC). The function of MSC remains uncertain, as does its mechanism of assembly. Constituents of multiprotein complexes encounter obstacles during assembly, including inappropriate interactions, topological constraints, premature degradation of unassembled subunits, and suboptimal stoichiometry. To facilitate orderly and efficient complex formation, some complexes are assembled cotranslationally by a mechanism in which a fully formed, mature protein binds a nascent partner as it emerges from the translating ribosome. Here, we show out of the 121 possible interaction events between the 11 MSC constituents, 15 are cotranslational. AIMPs are involved in the majority of these cotranslational interactions, suggesting they are not only critical for MSC structure but also for assembly. Unexpectedly, several cotranslational events involve more than the usual dyad of interacting proteins. We show two modes of cotranslational interaction, namely a "multisite" mechanism in which two or more mature proteins bind the same nascent peptide at distinct sites and a second "piggy-back" mechanism in which a mature protein carries a second fully formed protein and binds to a single site on an emerging peptide. Multimodal mechanisms of cotranslational interaction offer a diversity of pathways for ordered, piecewise assembly of small subcomplexes into larger heteromultimeric complexes such as the mammalian MSC.
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9
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Jaramillo Ponce JR, Kapps D, Paulus C, Chicher J, Frugier M. Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein. J Biol Chem 2022; 298:101987. [PMID: 35487244 PMCID: PMC9136112 DOI: 10.1016/j.jbc.2022.101987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) attach amino acids to their cognate transfer RNAs. In eukaryotes, a subset of cytosolic aaRSs is organized into a multisynthetase complex (MSC), along with specialized scaffolding proteins referred to as aaRS-interacting multifunctional proteins (AIMPs). In Plasmodium, the causative agent of malaria, the tRNA import protein (tRip), is a membrane protein that participates in tRNA trafficking; we show that tRip also functions as an AIMP. We identified three aaRSs, the glutamyl-tRNA synthetase (ERS), glutaminyl-tRNA synthetase (QRS), and methionyl-tRNA synthetase (MRS), which were specifically coimmunoprecipitated with tRip in Plasmodium berghei blood stage parasites. All four proteins contain an N-terminal glutathione-S-transferase (GST)-like domain that was demonstrated to be involved in MSC assembly. In contrast to previous studies, further dissection of GST-like interactions identified two exclusive heterotrimeric complexes: the Q-complex (tRip-ERS-QRS) and the M-complex (tRip-ERS-MRS). Gel filtration and light scattering suggest a 2:2:2 stoichiometry for both complexes but with distinct biophysical properties and mutational analysis further revealed that the GST-like domains of QRS and MRS use different strategies to bind ERS. Taken together, our results demonstrate that neither the singular homodimerization of tRip nor its localization in the parasite plasma membrane prevents the formation of MSCs in Plasmodium. Besides, the extracellular localization of the tRNA-binding module of tRip is compensated by the presence of additional tRNA-binding modules fused to MRS and QRS, providing each MSC with two spatially distinct functions: aminoacylation of intraparasitic tRNAs and binding of extracellular tRNAs. This unique host-pathogen interaction is discussed.
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Affiliation(s)
- José R Jaramillo Ponce
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Delphine Kapps
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Caroline Paulus
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France
| | - Johana Chicher
- Strasbourg-Esplanade Proteomics Facility, Université de Strasbourg, Strasbourg, France
| | - Magali Frugier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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10
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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: 35] [Impact Index Per Article: 17.5] [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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11
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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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12
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Wu S, Zheng L, Hei Z, Zhou JB, Li G, Li P, Wang J, Ali H, Zhou XL, Wang J, Fang P. Human lysyl-tRNA synthetase evolves a dynamic structure that can be stabilized by forming complex. Cell Mol Life Sci 2022; 79:128. [PMID: 35133502 PMCID: PMC11072160 DOI: 10.1007/s00018-022-04158-9] [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: 07/05/2021] [Revised: 01/04/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
The evolutionary necessity of aminoacyl-tRNA synthetases being associated into complex is unknown. Human lysyl-tRNA synthetase (LysRS) is one component of the multi-tRNA synthetase complex (MSC), which is not only critical for protein translation but also involved in multiple cellular pathways such as immune response, cell migration, etc. Here, combined with crystallography, CRISPR/Cas9-based genome editing, biochemistry, and cell biology analyses, we show that the structures of LysRSs from metazoan are more dynamic than those from single-celled organisms. Without the presence of MSC scaffold proteins, such as aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2), human LysRS is free from the MSC. The interaction with AIMP2 stabilizes the closed conformation of LysRS, thereby protects the essential aminoacylation activity under stressed conditions. Deleting AIMP2 from the human embryonic kidney 293 cells leads to retardation in cell growth in nutrient deficient mediums. Together, these results suggest that the evolutionary emergence of the MSC in metazoan might be to protect the aminoacyl-tRNA synthetase components from being modified or recruited for use in other cellular pathways.
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Affiliation(s)
- Siqi Wu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Li Zheng
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Zhoufei Hei
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jing-Bo Zhou
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Guang Li
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Peifeng Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jiayuan Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Hamid Ali
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
- Department of Biosciences, COMSATS University Islamabad, Islamabad, 44000, Pakistan
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Jing Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.
| | - Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.
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13
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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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14
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Kim DK, Lee HJ, Kong J, Cho HY, Kim S, Kang BS. Structural basis for the dynamics of human methionyl-tRNA synthetase in multi-tRNA synthetase complexes. Nucleic Acids Res 2021; 49:6549-6568. [PMID: 34086935 PMCID: PMC8216282 DOI: 10.1093/nar/gkab453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 11/14/2022] Open
Abstract
In mammals, eight aminoacyl-tRNA synthetases (AARSs) and three AARS-interacting multifunctional proteins (AIMPs) form a multi-tRNA synthetase complex (MSC). MSC components possess extension peptides for MSC assembly and specific functions. Human cytosolic methionyl-tRNA synthetase (MRS) has appended peptides at both termini of the catalytic main body. The N-terminal extension includes a glutathione transferase (GST) domain responsible for interacting with AIMP3, and a long linker peptide between the GST and catalytic domains. Herein, we determined crystal structures of the human MRS catalytic main body, and the complex of the GST domain and AIMP3. The structures reveal human-specific structural details of the MRS, and provide a dynamic model for MRS at the level of domain orientation. A movement of zinc knuckles inserted in the catalytic domain is required for MRS catalytic activity. Depending on the position of the GST domain relative to the catalytic main body, MRS can either block or present its tRNA binding site. Since MRS is part of a huge MSC, we propose a dynamic switching between two possible MRS conformations; a closed conformation in which the catalytic domain is compactly attached to the MSC, and an open conformation with a free catalytic domain dissociated from other MSC components.
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Affiliation(s)
- Dong Kyu Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Korea
| | - Hyun Joo Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Korea
| | - Jiwon Kong
- Medicinal Bioconvergence Research Center, College of Pharmacy & School of Medicine, Yonsei University, Incheon 21983, Korea
| | - Ha Yeon Cho
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, College of Pharmacy & School of Medicine, Yonsei University, Incheon 21983, Korea
| | - Beom Sik Kang
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Korea
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15
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Cui H, Kapur M, Diedrich JK, Yates JR, Ackerman SL, Schimmel P. Regulation of ex-translational activities is the primary function of the multi-tRNA synthetase complex. Nucleic Acids Res 2021; 49:3603-3616. [PMID: 33341895 PMCID: PMC8053116 DOI: 10.1093/nar/gkaa1183] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
During mRNA translation, tRNAs are charged by aminoacyl-tRNA synthetases and subsequently used by ribosomes. A multi-enzyme aminoacyl-tRNA synthetase complex (MSC) has been proposed to increase protein synthesis efficiency by passing charged tRNAs to ribosomes. An alternative function is that the MSC repurposes specific synthetases that are released from the MSC upon cues for functions independent of translation. To explore this, we generated mammalian cells in which arginyl-tRNA synthetase and/or glutaminyl-tRNA synthetase were absent from the MSC. Protein synthesis, under a variety of stress conditions, was unchanged. Most strikingly, levels of charged tRNAArg and tRNAGln remained unchanged and no ribosome pausing was observed at codons for arginine and glutamine. Thus, increasing or regulating protein synthesis efficiency is not dependent on arginyl-tRNA synthetase and glutaminyl-tRNA synthetase in the MSC. Alternatively, and consistent with previously reported ex-translational roles requiring changes in synthetase cellular localizations, our manipulations of the MSC visibly changed localization.
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Affiliation(s)
- Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mridu Kapur
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Susan L Ackerman
- Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
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16
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Vasu K, Ramachandiran I, Terenzi F, Khan D, China A, Khan K, Chechi A, Baleanu-Gogonea C, Gogonea V, Fox PL. The zinc-binding domain of mammalian prolyl-tRNA synthetase is indispensable for catalytic activity and organism viability. iScience 2021; 24:102215. [PMID: 33748704 PMCID: PMC7960942 DOI: 10.1016/j.isci.2021.102215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/26/2021] [Accepted: 02/17/2021] [Indexed: 01/10/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) participate in decoding the genome by catalyzing conjugation of amino acids to their cognate tRNAs. During evolution, biochemical and environmental conditions markedly influenced the sequence and structure of the 20 AARSs, revealing adaptations dictating canonical and orthogonal activities. Here, we investigate the function of the appended Zn2+-binding domain (ZBD) in the bifunctional AARS, glutamyl-prolyl-tRNA synthetase (GluProRS). We developed GluProRS mutant mice by CRISPR-Cas9 with a deletion of 29 C-terminal amino acids, including two of four Zn2+-coordinating cysteines. Homozygous ZBD mutant mice die before embryonic day 12.5, but heterozygous mice are healthy. ZBD disruption profoundly reduces GluProRS canonical function by dual mechanisms: it induces rapid proteasomal degradation of the protein and inhibits ProRS aminoacylation activity, likely by sub-optimal positioning of ATP in the spatially adjacent catalytic domain. Collectively, our studies reveal the ZBD as a critical determinant of ProRS activity and GluProRS stability in vitro and in vivo. Conserved zinc-binding domain (ZBD) of GluProRS is required for Pro-tRNA charging ZBD stabilizes GluProRS and positions C-terminal carboxylate in the catalytic site Embryonic lethality in mice with defective GluProRS ZBD reveals in vivo essentiality Locked nucleic acid qPCR assay for CRISPR-mediated screening of chimeric mutant mice
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Affiliation(s)
- Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Aayushi Chechi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | - Valentin Gogonea
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.,Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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17
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Wang J, Yang XL. Novel functions of cytoplasmic aminoacyl-tRNA synthetases shaping the hallmarks of cancer. Enzymes 2020; 48:397-423. [PMID: 33837711 DOI: 10.1016/bs.enz.2020.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
With the intense protein synthesis demands of cancer, the classical enzymatic role of aminoacyl-tRNA synthetases (aaRSs) is required to sustain tumor growth. However, many if not all aaRSs also possess regulatory functions outside of the domain of catalytic tRNA aminoacylation, which can further contribute to or even antagonize cancers in non-translational ways. These regulatory functions of aaRS are likely to be manipulated in cancer to ensure uncontrolled growth and survival. This review will largely focus on the unique capacities of individual and sometimes collaborating synthetases to influence the hallmarks of cancer, which represent the principles and characteristics of tumorigenesis. An interesting feature of cytoplasmic aaRSs in higher eukaryotes is the formation of a large multi-synthetase complex (MSC) with nine aaRSs held together by three non-enzymatic scaffolding proteins (AIMPs). The MSC-associated aaRSs, when released from the complex in response to certain stimulations, often participate in pathways that promote tumorigenesis. In contrast, the freestanding aaRSs are associated with activities in both directions-some promoting while others inhibiting cancer. The AIMPs have emerged as potent tumor suppressors through their own distinct mechanisms. We propose that the tumor-suppressive roles of AIMPs may also be a consequence of keeping the cancer-promoting aaRSs within the MSC. The rich connections between cancer and the synthetases have inspired the development of innovative cancer treatments that target or take advantage of these novel functions of aaRSs.
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Affiliation(s)
- Justin Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States.
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18
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A Almuqbil M, Vernon HJ, Ferguson M, Kline AD. PARS2-associated mitochondrial disease: A case report of a patient with prolonged survival and literature review. Mol Genet Metab Rep 2020; 24:100613. [PMID: 32514400 PMCID: PMC7267727 DOI: 10.1016/j.ymgmr.2020.100613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 10/24/2022] Open
Abstract
Biallelic pathogenic variants in mitochondrial aminoacyl-tRNA synthetase (mt-aaRS) PARS2 are associated with mitochondrial cytopathy. Here, we report the tenth case of an individual with biallelic PARS2 pathogenic variants, detected by exome sequencing (ES), and a literature review of ten cases of PARS2 mutations. Our patient displayed symptoms and clinical and laboratory findings similar to those reported previously with normal lactate levels. These symptoms included seizure disorder (which was managed with antiepileptics), developmental delay, and progressive cardiomyopathy which manifested at 19 years of age. The patient received a vitamin regimen including antioxidants as part of his treatment regimen. While further studies are required to conclusively establish the beneficial role of vitamin and cofactor administration on the mitochondria in PARS2-associated mitochondrial disease, these factors may have delayed the onset of cardiomyopathy.
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Affiliation(s)
- Mohammed A Almuqbil
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.,Division of Pediatric Neurology, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,King Abdullah International Medical Research Center, King Abdullah Specialist Children's Hospital - Ministry of National Guard, Riyadh, Saudi Arabia
| | - Hilary J Vernon
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Marcia Ferguson
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
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19
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Kitagawa M, Balkunde R, Bui H, Jackson D. An Aminoacyl tRNA Synthetase, OKI1, Is Required for Proper Shoot Meristem Size in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:2597-2608. [PMID: 31393575 DOI: 10.1093/pcp/pcz153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
In plants, the stem cells that form the shoot system reside within the shoot apical meristem (SAM), which is regulated by feedback signaling between the WUSCHEL (WUS) homeobox protein and CLAVATA (CLV) peptides and receptors. WUS-CLV feedback signaling can be modulated by various endogenous or exogenous factors, such as chromatin state, hormone signaling, reactive oxygen species (ROS) signaling and nutrition, leading to a dynamic control of SAM size corresponding to meristem activity. Despite these insights, however, the knowledge of genes that control SAM size is still limited, and in particular, the regulation by ROS signaling is only beginning to be comprehended. In this study, we report a new function in maintenance of SAM size, encoded by the OKINA KUKI1 (OKI1) gene. OKI1 is expressed in the SAM and encodes a mitochondrial aspartyl tRNA synthetase (AspRS). oki1 mutants display enlarged SAMs with abnormal expression of WUS and CLV3 and overaccumulation of ROS in the meristem. Our findings support the importance of normal AspRS function in the maintenance of the WUS-CLV3 feedback loop and SAM size.
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Affiliation(s)
- Munenori Kitagawa
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
| | - Rachappa Balkunde
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO, USA
| | - Huyen Bui
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
- Center of Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT, USA
| | - David Jackson
- Cold Spring Harbor Laboratory, 1 Bungtown road, Cold Spring Harbor, NY, USA
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20
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Scheidecker S, Bär S, Stoetzel C, Geoffroy V, Lannes B, Rinaldi B, Fischer F, Becker HD, Pelletier V, Pagan C, Acquaviva-Bourdain C, Kremer S, Mirande M, Tranchant C, Muller J, Friant S, Dollfus H. Mutations in KARS cause a severe neurological and neurosensory disease with optic neuropathy. Hum Mutat 2019; 40:1826-1840. [PMID: 31116475 DOI: 10.1002/humu.23799] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/25/2019] [Accepted: 05/15/2019] [Indexed: 11/09/2022]
Abstract
Mutations in genes encoding aminoacyl-tRNA synthetases have been reported in several neurological disorders. KARS is a dual localized lysyl-tRNA synthetase and its cytosolic isoform belongs to the multiple aminoacyl-tRNA synthetase complex (MSC). Biallelic mutations in the KARS gene were described in a wide phenotypic spectrum ranging from nonsyndromic deafness to complex impairments. Here, we report on a patient with severe neurological and neurosensory disease investigated by whole-exome sequencing and found to carry biallelic mutations c.683C>T (p.Pro228Leu) and c.871T>G (p.Phe291Val), the second one being novel, in the KARS gene. The patient presented with an atypical clinical presentation with an optic neuropathy not previously reported. At the cellular level, we show that cytoplasmic KARS was expressed at a lower level in patient cells and displayed decreased interaction with MSC. In vitro, these two KARS variants have a decreased aminoacylation activity compared with wild-type KARS, the p.Pro228Leu being the most affected. Our data suggest that dysfunction of cytoplasmic KARS resulted in a decreased level of translation of the nuclear-encoded lysine-rich proteins belonging to the respiratory chain complex, thus impairing mitochondria functions.
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Affiliation(s)
- Sophie Scheidecker
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Séverine Bär
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Corinne Stoetzel
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France
| | - Béatrice Lannes
- Service d'Anatomo-pathologie, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Bruno Rinaldi
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Frédéric Fischer
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Hubert D Becker
- Laboratoire de Génétique Moléculaire, Génomique, Microbiologie (GMGM), UMR7156, Université de Strasbourg, CNRS, Strasbourg, France
| | - Valérie Pelletier
- Centre de Référence pour les affections rares en génétique ophtalmologique, CARGO, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Cécile Pagan
- Service de Biochimie et Biologie Moléculaire, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Cécile Acquaviva-Bourdain
- Service de Biochimie et Biologie Moléculaire, Centre de Biologie et de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Stéphane Kremer
- Service de Neuroradiologie/Imagerie 2, CHU de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Marc Mirande
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Christine Tranchant
- Service de Neurologie Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sylvie Friant
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, INSERM U1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, Strasbourg, France.,Centre de Référence pour les affections rares en génétique ophtalmologique, CARGO, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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21
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Hei Z, Wu S, Liu Z, Wang J, Fang P. Retractile lysyl-tRNA synthetase-AIMP2 assembly in the human multi-aminoacyl-tRNA synthetase complex. J Biol Chem 2019; 294:4775-4783. [PMID: 30733335 DOI: 10.1074/jbc.ra118.006356] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/05/2019] [Indexed: 11/06/2022] Open
Abstract
Multi-aminoacyl-tRNA synthetase complex (MSC) is the second largest machinery for protein synthesis in human cells and also regulates multiple nontranslational functions through its components. Previous studies have shown that the MSC can respond to external signals by releasing its components to function outside it. The internal assembly is fundamental to MSC regulation. Here, using crystal structural analyses (at 1.88 Å resolution) along with molecular modeling, gel-filtration chromatography, and co-immunoprecipitation, we report that human lysyl-tRNA synthetase (LysRS) forms a tighter assembly with the scaffold protein aminoacyl-tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2) than previously observed. We found that two AIMP2 N-terminal peptides form an antiparallel scaffold and hold two LysRS dimers through four binding motifs and additional interactions. Of note, the four catalytic subunits of LysRS in the tightly assembled complex were all accessible for tRNA recognition. We further noted that two recently reported human disease-associated mutations conflict with this tighter assembly, cause LysRS release from the MSC, and inactivate the enzyme. These findings reveal a previously unknown dimension of MSC subcomplex assembly and suggest that the retractility of this complex may be critical for its physiological functions.
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Affiliation(s)
- Zhoufei Hei
- From the State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Siqi Wu
- From the State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zaizhou Liu
- From the State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jing Wang
- From the State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Pengfei Fang
- From the State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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22
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Kekez M, Zanki V, Kekez I, Baranasic J, Hodnik V, Duchêne A, Anderluh G, Gruic‐Sovulj I, Matković‐Čalogović D, Weygand‐Durasevic I, Rokov‐Plavec J. Arabidopsis
seryl‐
tRNA
synthetase: the first crystal structure and novel protein interactor of plant aminoacyl‐
tRNA
synthetase. FEBS J 2019; 286:536-554. [DOI: 10.1111/febs.14735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/01/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Mario Kekez
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Vladimir Zanki
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Ivana Kekez
- Division of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Jurica Baranasic
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Vesna Hodnik
- National Institute of Chemistry Ljubljana Slovenia
- Biotechnical faculty University of Ljubljana Slovenia
| | - Anne‐Marie Duchêne
- Institut de biologie moléculaire des plantes CNRS, Université de Strasbourg Strasbourg Cedex France
| | | | - Ita Gruic‐Sovulj
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Dubravka Matković‐Čalogović
- Division of General and Inorganic Chemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Ivana Weygand‐Durasevic
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
| | - Jasmina Rokov‐Plavec
- Division of Biochemistry Department of Chemistry Faculty of Science University of Zagreb Croatia
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23
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Eswarappa SM, Potdar AA, Sahoo S, Sankar S, Fox PL. Metabolic origin of the fused aminoacyl-tRNA synthetase, glutamyl-prolyl-tRNA synthetase. J Biol Chem 2018; 293:19148-19156. [PMID: 30309984 DOI: 10.1074/jbc.ra118.004276] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/03/2018] [Indexed: 11/06/2022] Open
Abstract
About 1 billion years ago, in a single-celled holozoan ancestor of all animals, a gene fusion of two tRNA synthetases formed the bifunctional enzyme, glutamyl-prolyl-tRNA synthetase (EPRS). We propose here that a confluence of metabolic, biochemical, and environmental factors contributed to the specific fusion of glutamyl- (ERS) and prolyl- (PRS) tRNA synthetases. To test this idea, we developed a mathematical model that centers on the precursor-product relationship of glutamic acid and proline, as well as metabolic constraints on free glutamic acid availability near the time of the fusion event. Our findings indicate that proline content increased in the proteome during the emergence of animals, thereby increasing demand for free proline. Together, these constraints contributed to a marked cellular depletion of glutamic acid and its products, with potentially catastrophic consequences. In response, an ancient organism invented an elegant solution in which genes encoding ERS and PRS fused to form EPRS, forcing coexpression of the two enzymes and preventing lethal dysregulation. The substantial evolutionary advantage of this coregulatory mechanism is evidenced by the persistence of EPRS in nearly all extant animals.
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Affiliation(s)
- Sandeep M Eswarappa
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India,
| | - Alka A Potdar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, and
| | - Sarthak Sahoo
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Santhosh Sankar
- From the Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195
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24
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The genotypic and phenotypic spectrum of PARS2-related infantile-onset encephalopathy. J Hum Genet 2018; 63:971-980. [PMID: 29915213 DOI: 10.1038/s10038-018-0478-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 05/24/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022]
Abstract
Mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are a family of enzymes that play critical roles in protein biosynthesis. Mutations in mt-aaRSs are associated with various diseases. As a member of the mt-aaRS family, PARS2 encoding prolyl-tRNA synthetase 2 was recently shown to be associated with Alpers syndrome and certain infantile-onset neurodegenerative disorders in four patients. Here, we present two patients in a pedigree with early developmental delay, epileptic spasms, delayed myelination combined with cerebellar white matter abnormalities, and progressive cortical atrophy. Whole-exome sequencing revealed pathogenic compound heterozygous variants [c.283 G > A (p.95 V > I)] and [c.604 G > C (p.202 R > G)] in PARS2. Nearly all patients had epileptic spasms with early response to treatment, early developmental delay and/or regression followed by generalized hypotonia, postnatal microcephaly, elevated lactate levels, and progressive cerebral atrophy. Our study provides further evidence for validating the role of PARS2 in the pathology of related infantile-onset encephalopathy, contributing to the phenotypic features of this condition, and providing clinical and molecular insight for the diagnosis of this disease entity.
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25
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Stephen J, Nampoothiri S, Banerjee A, Tolman NJ, Penninger JM, Elling U, Agu CA, Burke JD, Devadathan K, Kannan R, Huang Y, Steinbach PJ, Martinis SA, Gahl WA, Malicdan MCV. Loss of function mutations in VARS encoding cytoplasmic valyl-tRNA synthetase cause microcephaly, seizures, and progressive cerebral atrophy. Hum Genet 2018; 137:293-303. [PMID: 29691655 DOI: 10.1007/s00439-018-1882-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/23/2022]
Abstract
Progressive microcephaly and neurodegeneration are genetically heterogenous conditions, largely associated with genes that are essential for the survival of neurons. In this study, we interrogate the genetic etiology of two siblings from a non-consanguineous family with severe early onset of neurological manifestations. Whole exome sequencing identified novel compound heterozygous mutations in VARS that segregated with the proband: a missense (c.3192G>A; p.Met1064Ile) and a splice site mutation (c.1577-2A>G). The VARS gene encodes cytoplasmic valyl-tRNA synthetase (ValRS), an enzyme that is essential during eukaryotic translation. cDNA analysis on patient derived fibroblasts revealed that the splice site acceptor variant allele led to nonsense mediated decay, thus resulting in a null allele. Three-dimensional modeling of ValRS predicts that the missense mutation lies in a highly conserved region and could alter side chain packing, thus affecting tRNA binding or destabilizing the interface between the catalytic and tRNA binding domains. Further quantitation of the expression of VARS showed remarkably reduced levels of mRNA and protein in skin derived fibroblasts. Aminoacylation experiments on patient derived cells showed markedly reduced enzyme activity of ValRS suggesting the mutations to be loss of function. Bi-allelic mutations in cytoplasmic amino acyl tRNA synthetases are well-known for their role in neurodegenerative disorders, yet human disorders associated with VARS mutations have not yet been clinically well characterized. Our study describes the phenotype associated with recessive VARS mutations and further functional delineation of the pathogenicity of novel variants identified, which widens the clinical and genetic spectrum of patients with progressive microcephaly.
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Affiliation(s)
- Joshi Stephen
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala, India
| | - Aditi Banerjee
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nathanial J Tolman
- Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Josef Martin Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria
| | - Ullrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria
| | - Chukwuma A Agu
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Dr. Bohr Gasse 3, Vienna, Austria
| | - John D Burke
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kalpana Devadathan
- Department of Pediatric Neurology, KIMS Hospital, Thiruvananthapuram, Kerala, India
| | - Rajesh Kannan
- Department of Radiology, Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala, India
| | - Yan Huang
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI) and the Common Fund, National Institutes of Health, Bethesda, MD, USA
| | - Peter J Steinbach
- Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, MD, USA
| | - Susan A Martinis
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - William A Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.,Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA.,NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI) and the Common Fund, National Institutes of Health, Bethesda, MD, USA
| | - May Christine V Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. .,Office of the Clinical Director, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA. .,NIH Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI) and the Common Fund, National Institutes of Health, Bethesda, MD, USA.
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26
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Schwarz MA, Lee DD, Bartlett S. Aminoacyl tRNA synthetase complex interacting multifunctional protein 1 simultaneously binds Glutamyl-Prolyl-tRNA synthetase and scaffold protein aminoacyl tRNA synthetase complex interacting multifunctional protein 3 of the multi-tRNA synthetase complex. Int J Biochem Cell Biol 2018; 99:197-202. [PMID: 29679766 DOI: 10.1016/j.biocel.2018.04.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 12/15/2022]
Abstract
Higher eukaryotes have developed extensive compartmentalization of amino acid (aa) - tRNA coupling through the formation of a multi-synthetase complex (MSC) that is composed of eight aa-tRNA synthetases (ARS) and three scaffold proteins: aminoacyl tRNA synthetase complex interacting multifunctional proteins (AIMP1, 2 and 3). Lower eukaryotes have a much smaller complex while yeast MSC consists of only two ARS (MetRS and GluRS) and one ARS cofactor 1 protein, Arc1p (Simos et al., 1996), the homolog of the mammalian AIMP1. Arc1p is reported to form a tripartite complex with GluRS and MetRS through association of the N-terminus GST-like domains (GST-L) of the three proteins (Koehler et al., 2013). Mammalian AIMP1 has no GST-L domain corresponding to Arc1p N-terminus. Instead, AIMP3, another scaffold protein of 18 kDa composed entirely of a GST-L domain, interacts with Methionyl-tRNA synthetase (MARS) (Quevillon et al., 1999) and Glutamyl-Prolyl-tRNA Synthetase (EPRS) (Cho et al., 2015). Here we report two new interactions between MSC members: AIMP1 binds to EPRS and AIMP1 binds to AIMP3. Interestingly, the interaction between AIMP1 and AIMP3 complex makes it the functional equivalent of a single Arc1p polypeptide in yeast. This interaction is not mapped to AIMP1 N-terminal coiled-coil domain, but rather requires an intact tertiary structure of the entire protein. Since AIMP1 also interacts with AIMP2, all three proteins appear to compose a core docking structure for the eight ARS in the MSC complex.
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Affiliation(s)
- Margaret A Schwarz
- Indiana University School of Medicine South Bend, IN, 46617, United States.
| | - Daniel D Lee
- Indiana University School of Medicine South Bend, IN, 46617, United States
| | - Seamus Bartlett
- University of Notre Dame Notre Dame, IN, 46556, United States
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27
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Halawani D, Gogonea V, DiDonato JA, Pipich V, Yao P, China A, Topbas C, Vasu K, Arif A, Hazen SL, Fox PL. Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains. J Biol Chem 2018; 293:8843-8860. [PMID: 29643180 DOI: 10.1074/jbc.m117.807503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/26/2018] [Indexed: 02/02/2023] Open
Abstract
Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH-S-transferase-C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST-C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems.
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Affiliation(s)
- Dalia Halawani
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Valentin Gogonea
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and .,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Joseph A DiDonato
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Vitaliy Pipich
- the Jülich Center for Neutron Science, Outstation at Maier-Leibnitz Zentrum, Forschungszentrum Jülich, GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany, and
| | - Peng Yao
- the Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, New York 14642
| | - Arnab China
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Celalettin Topbas
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Kommireddy Vasu
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Abul Arif
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Stanley L Hazen
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,Center for Cardiovascular Diagnostics and Prevention, and Department of Cardiovascular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Paul L Fox
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
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28
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Perez-Pepe M, Fernández-Alvarez AJ, Boccaccio GL. Life and Work of Stress Granules and Processing Bodies: New Insights into Their Formation and Function. Biochemistry 2018; 57:2488-2498. [PMID: 29595960 DOI: 10.1021/acs.biochem.8b00025] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The dynamic formation of stress granules (SGs), processing bodies (PBs), and related RNA organelles regulates diverse cellular processes, including the coordination of functionally connected messengers, the translational regulation at the synapse, and the control of viruses and retrotransposons. Recent studies have shown that pyruvate kinase and other enzymes localize in SGs and PBs, where they become protected from stress insults. These observations may have implications for enzyme regulation and metabolic control exerted by RNA-based organelles. The formation of these cellular bodies is governed by liquid-liquid phase separation (LLPS) processes, and it needs to be strictly controlled to prevent pathogenic aggregation. The intracellular concentration of key metabolites, such as ATP and sterol derivatives, may influence protein solubility, thus affecting the dynamics of liquid organelles. LLPS in vitro depends on the thermal diffusion of macromolecules, which is limited inside cells, where the condensation and dissolution of membrane-less organelles are helped by energy-driven processes. The active transport by the retrograde motor dynein helps SG assembly, whereas the anterograde motor kinesin mediates SG dissolution; a tug of war between these two molecular motors allows transient SG formation. There is evidence that the efficiency of dynein-mediated transport increases with the number of motor molecules associated with the cargo. The dynein-dependent transport may be influenced by cargo size as larger cargos can load a larger number of motors. We propose a model based on this emergent property of dynein motors, which would be collectively stronger during SG condensation and weaker during SG breakdown, thus allowing kinesin-mediated dispersion.
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Affiliation(s)
- Marcelo Perez-Pepe
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Ana J Fernández-Alvarez
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
| | - Graciela L Boccaccio
- Instituto Leloir and Instituto de Investigaciones Bioquı́micas de Buenos Aires (IIBBA)-CONICET , Buenos Aires , Argentina
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29
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Drew K, Müller CL, Bonneau R, Marcotte EM. Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. PLoS Comput Biol 2017; 13:e1005625. [PMID: 29023445 PMCID: PMC5638211 DOI: 10.1371/journal.pcbi.1005625] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/06/2017] [Indexed: 12/21/2022] Open
Abstract
Determining the three dimensional arrangement of proteins in a complex is highly beneficial for uncovering mechanistic function and interpreting genetic variation in coding genes comprising protein complexes. There are several methods for determining co-complex interactions between proteins, among them co-fractionation / mass spectrometry (CF-MS), but it remains difficult to identify directly contacting subunits within a multi-protein complex. Correlation analysis of CF-MS profiles shows promise in detecting protein complexes as a whole but is limited in its ability to infer direct physical contacts among proteins in sub-complexes. To identify direct protein-protein contacts within human protein complexes we learn a sparse conditional dependency graph from approximately 3,000 CF-MS experiments on human cell lines. We show substantial performance gains in estimating direct interactions compared to correlation analysis on a benchmark of large protein complexes with solved three-dimensional structures. We demonstrate the method’s value in determining the three dimensional arrangement of proteins by making predictions for complexes without known structure (the exocyst and tRNA multi-synthetase complex) and by establishing evidence for the structural position of a recently discovered component of the core human EKC/KEOPS complex, GON7/C14ORF142, providing a more complete 3D model of the complex. Direct contact prediction provides easily calculable additional structural information for large-scale protein complex mapping studies and should be broadly applicable across organisms as more CF-MS datasets become available. Proteins physically associate into complexes in order to carry out the essential functions of life. Knowing how proteins are physically arranged three dimensionally in these complexes provides clues towards how they work. In principle, the associations between proteins in large-scale proteomics datasets should often reflect direct physical contacts between proteins in each complex. Here, we describe a statistical method to discover which subunits within complexes directly contact each other based on their co-purification behavior in published co-fractionation mass spectrometry datasets. Within our predictions, we recover many known protein-protein contacts, serving to validate our method, as well as unknown contacts that can inform future studies of these complexes. Specifically, we observe confident contacts between subunits within the exocyst and tRNA multi-synthetase complexes, two complexes that have incomplete structural information. Using our method, we further provide structural information for a previously missing subunit of the EKC/KEOPS complex. We anticipate that this method and the associated predictions will help to better inform our understanding of the functions and structures of diverse protein complexes.
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Affiliation(s)
- Kevin Drew
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America
- * E-mail: (KD); (CLM); (EMM)
| | - Christian L. Müller
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY, United States of America
- * E-mail: (KD); (CLM); (EMM)
| | - Richard Bonneau
- Flatiron Institute, Center for Computational Biology, Simons Foundation, New York, NY, United States of America
- New York University Center for Genomics and Systems Biology, New York University, New York, NY, United States of America
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America
- * E-mail: (KD); (CLM); (EMM)
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30
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Mutations in RARS cause a hypomyelination disorder akin to Pelizaeus-Merzbacher disease. Eur J Hum Genet 2017; 25:1134-1141. [PMID: 28905880 DOI: 10.1038/ejhg.2017.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 06/18/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
Pelizaeus-Merzbacher disease (PMD) is a rare Mendelian disorder characterised by central nervous system hypomyelination. PMD typically manifests in infancy or early childhood and is caused by mutations in proteolipid protein-1 (PLP1). However, variants in several other genes including gap junction protein gamma 2 (GJC2) can also cause a similar phenotype and are referred to PMD-like disease (PMLD). Whole-exome sequencing in two siblings presenting with clinical symptoms of PMD revealed a homozygous variant in the arginyl-tRNA synthetase (RARS) gene: NM_002887.3: c.[5A>G] p.(Asp2Gly). Subsequent screening of a PMD cohort without a genetic diagnosis identified an unrelated individual with novel compound heterozygous variants including a missense variant c.[1367C>T] p.(Ser456Leu) and a de novo deletion c.[1846_1847delTA] p.(Tyr616Leufs*6). Protein levels of RARS and the multi-tRNA synthetase complex into which it assembles were found to be significantly reduced by 80 and 90% by western blotting and Blue native-PAGE respectively using patient fibroblast extracts. As RARS is involved in protein synthesis whereby it attaches arginine to its cognate tRNA, patient cells were studied to determine their ability to proliferate with limiting amounts of this essential amino acid. Patient fibroblasts cultured in medium with limited arginine at 30 °C and 40 °C, showed a significant decrease in fibroblast proliferation (P<0.001) compared to control cells, suggestive of inefficiency of protein synthesis in the patient cells. Our functional studies provide further evidence that RARS is a PMD-causing gene.
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31
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Moulinier L, Ripp R, Castillo G, Poch O, Sissler M. MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease-causing mutations in human mitochondrial aminoacyl-tRNA synthetases. Hum Mutat 2017; 38:1316-1324. [PMID: 28608363 PMCID: PMC5638098 DOI: 10.1002/humu.23277] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 11/25/2022]
Abstract
Numerous mutations in each of the mitochondrial aminoacyl‐tRNA synthetases (aaRSs) have been implicated in human diseases. The mutations are autosomal and recessive and lead mainly to neurological disorders, although with pleiotropic effects. The processes and interactions that drive the etiology of the disorders associated with mitochondrial aaRSs (mt‐aaRSs) are far from understood. The complexity of the clinical, genetic, and structural data requires concerted, interdisciplinary efforts to understand the molecular biology of these disorders. Toward this goal, we designed MiSynPat, a comprehensive knowledge base together with an ergonomic Web server designed to organize and access all pertinent information (sequences, multiple sequence alignments, structures, disease descriptions, mutation characteristics, original literature) on the disease‐linked human mt‐aaRSs. With MiSynPat, a user can also evaluate the impact of a possible mutation on sequence‐conservation‐structure in order to foster the links between basic and clinical researchers and to facilitate future diagnosis. The proposed integrated view, coupled with research on disease‐related mt‐aaRSs, will help to reveal new functions for these enzymes and to open new vistas in the molecular biology of the cell. The purpose of MiSynPat, freely available at http://misynpat.org, is to constitute a reference and a converging resource for scientists and clinicians.
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Affiliation(s)
- Luc Moulinier
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Raymond Ripp
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Gaston Castillo
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France.,Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, Strasbourg, France
| | - Olivier Poch
- CSTB Complex Systems and Translational Bioinformatics, ICube Laboratory and Strasbourg Federation of Translational Medicine (FMTS), CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie Sissler
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, Strasbourg, France
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32
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part V. {[Fe4S4](SCysγ)4} proteins. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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33
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Abstract
Aminoacyl-tRNA synthetases (AARSs) are essential enzymes that specifically aminoacylate one tRNA molecule by the cognate amino acid. They are a family of twenty enzymes, one for each amino acid. By coupling an amino acid to a specific RNA triplet, the anticodon, they are responsible for interpretation of the genetic code. In addition to this translational, canonical role, several aminoacyl-tRNA synthetases also fulfill nontranslational, moonlighting functions. In mammals, nine synthetases, those specific for amino acids Arg, Asp, Gln, Glu, Ile, Leu, Lys, Met and Pro, associate into a multi-aminoacyl-tRNA synthetase complex, an association which is believed to play a key role in the cellular organization of translation, but also in the regulation of the translational and nontranslational functions of these enzymes. Because the balance between their alternative functions rests on the assembly and disassembly of this supramolecular entity, it is essential to get precise insight into the structural organization of this complex. The high-resolution 3D-structure of the native particle, with a molecular weight of about 1.5 MDa, is not yet known. Low-resolution structures of the multi-aminoacyl-tRNA synthetase complex, as determined by cryo-EM or SAXS, have been reported. High-resolution data have been reported for individual enzymes of the complex, or for small subcomplexes. This review aims to present a critical view of our present knowledge of the aminoacyl-tRNA synthetase complex in 3D. These preliminary data shed some light on the mechanisms responsible for the balance between the translational and nontranslational functions of some of its components.
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Affiliation(s)
- Marc Mirande
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 1 avenue de la Terrasse, 91190, Gif-sur-Yvette, Paris, France.
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Kapps D, Cela M, Théobald-Dietrich A, Hendrickson T, Frugier M. OB or Not OB: Idiosyncratic utilization of the tRNA-binding OB-fold domain in unicellular, pathogenic eukaryotes. FEBS Lett 2016; 590:4180-4191. [PMID: 27714804 DOI: 10.1002/1873-3468.12441] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 11/11/2022]
Abstract
In this review, we examine the so-called OB-fold, a tRNA-binding domain homologous to the bacterial tRNA-binding protein Trbp111. We highlight the ability of OB-fold homologs to bind tRNA species and summarize their distribution in evolution. Nature has capitalized on the advantageous effects acquired when an OB-fold domain binds to tRNA by evolutionarily selecting this domain for fusion to different enzymes. Here, we review our current understanding of how the complexity of OB-fold-containing proteins and enzymes developed to expand their functions, especially in unicellular, pathogenic eukaryotes.
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Affiliation(s)
- Delphine Kapps
- RNA Architecture and Reactivity, Strasbourg University, CNRS, IBMC, France
| | - Marta Cela
- RNA Architecture and Reactivity, Strasbourg University, CNRS, IBMC, France
| | | | | | - Magali Frugier
- RNA Architecture and Reactivity, Strasbourg University, CNRS, IBMC, France
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35
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Arif A, Jia J, Halawani D, Fox PL. Experimental approaches for investigation of aminoacyl tRNA synthetase phosphorylation. Methods 2016; 113:72-82. [PMID: 27729295 DOI: 10.1016/j.ymeth.2016.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/04/2016] [Accepted: 10/06/2016] [Indexed: 02/04/2023] Open
Abstract
Phosphorylation of many aminoacyl tRNA synthetases (AARSs) has been recognized for decades, but the contribution of post-translational modification to their primary role in tRNA charging and decryption of genetic code remains unclear. In contrast, phosphorylation is essential for performance of diverse noncanonical functions of AARSs unrelated to protein synthesis. Phosphorylation of glutamyl-prolyl tRNA synthetase (EPRS) has been investigated extensively in our laboratory for more than a decade, and has served as an archetype for studies of other AARSs. EPRS is a constituent of the IFN-γ-activated inhibitor of translation (GAIT) complex that directs transcript-selective translational control in myeloid cells. Stimulus-dependent phosphorylation of EPRS is essential for its release from the parental multi-aminoacyl tRNA synthetase complex (MSC), for binding to other GAIT complex proteins, and for regulating the binding to target mRNAs. Importantly, phosphorylation is the common driving force for the context- and stimulus-dependent release, and non-canonical activity, of other AARSs residing in the MSC, for example, lysyl tRNA synthetase (KARS). Here, we describe the concepts and experimental methodologies we have used to investigate the influence of phosphorylation on the structure and function of EPRS. We suggest that application of these approaches will help to identify new functional phosphorylation event(s) in other AARSs and elucidate their possible roles in noncanonical activities.
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Affiliation(s)
- Abul Arif
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jie Jia
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dalia Halawani
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul L Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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36
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Gómez Ramos LM, Smeekens JM, Kovacs NA, Bowman JC, Wartell RM, Wu R, Williams LD. Yeast rRNA Expansion Segments: Folding and Function. J Mol Biol 2016; 428:4048-4059. [PMID: 27521697 DOI: 10.1016/j.jmb.2016.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 12/22/2022]
Abstract
Divergence between prokaryotic and eukaryotic ribosomal RNA (rRNA) and among eukaryotic ribosomal RNAs is focused in expansion segments (ESs). Eukaryotic ribosomes are significantly larger than prokaryotic ribosomes partly because of their ESs. We hypothesize that larger rRNAs of complex organisms could confer increased functionality to the ribosome. Here, we characterize the binding partners of Saccharomyces cerevisiae expansion segment 7 (ES7), which is the largest and most variable ES of the eukaryotic large ribosomal subunit and is located at the surface of the ribosome. In vitro RNA-protein pull-down experiments using ES7 as a bait indicate that ES7 is a binding hub for a variety of non-ribosomal proteins essential to ribosomal function in eukaryotes. ES7-associated proteins observed here cluster into four groups based on biological process, (i) response to abiotic stimulus (e.g., response to external changes in temperature, pH, oxygen level, etc.), (ii) ribosomal large subunit biogenesis, (iii) protein transport and localization, and (iv) transcription elongation. Seven synthetases, Ala-, Arg-, Asp-, Asn-, Leu-, Lys- and TyrRS, appear to associate with ES7. Affinities of AspRS, TyrRS and LysRS for ES7 were confirmed by in vitro binding assays. The results suggest that ES7 in S. cerevisiae could play a role analogous to the multi-synthetase complex present in higher order organisms and could be important for the appropriate function of the ribosome. Thermal denaturation studies and footprinting experiments confirm that isolated ES7 is stable and maintains a near-native secondary and tertiary structure.
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Affiliation(s)
- Lizzette M Gómez Ramos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA
| | - Johanna M Smeekens
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA
| | - Nicholas A Kovacs
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA
| | - Jessica C Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA
| | - Roger M Wartell
- School of Biology, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332-0363, USA.
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37
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Monteferrante CG, Jirgensons A, Varik V, Hauryliuk V, Goessens WHF, Hays JP. Evaluation of the characteristics of leucyl-tRNA synthetase (LeuRS) inhibitor AN3365 in combination with different antibiotic classes. Eur J Clin Microbiol Infect Dis 2016; 35:1857-1864. [PMID: 27506217 PMCID: PMC5059401 DOI: 10.1007/s10096-016-2738-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/18/2016] [Indexed: 12/04/2022]
Abstract
Aminoacyl tRNA synthetases are enzymes involved in the key process of coupling an amino acid to its cognate tRNA. AN3365 is a novel antibiotic that specifically targets leucyl-tRNA synthetase, whose development was halted after evaluation in phase II clinical trials owing to the rapid selection of resistance. In an attempt to bring AN3365 back into the developmental pipeline we have evaluated the efficacy of AN3365 in combination with different classes of antibiotic and characterized its mechanism of action. Although we detect no synergy or antagonism in combination with a range of antibiotic classes, a combination of AN3365 with colistin reduces the accumulation of AN3365-resistant and colistin resistance mutations. We also demonstrate that treatment with AN3365 results in the dramatic accumulation of the alarmone (p)ppGpp, the effector of the stringent response—a key player in antibiotic tolerance.
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Affiliation(s)
- C G Monteferrante
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - A Jirgensons
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - V Varik
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 901 87, Umeå, Sweden
| | - V Hauryliuk
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 901 87, Umeå, Sweden
| | - W H F Goessens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center Rotterdam (Erasmus MC), Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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38
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Li M, Wen F, Zhao S, Wang P, Li S, Zhang Y, Zheng N, Wang J. Exploring the Molecular Basis for Binding of Inhibitors by Threonyl-tRNA Synthetase from Brucella abortus: A Virtual Screening Study. Int J Mol Sci 2016; 17:E1078. [PMID: 27447614 PMCID: PMC4964454 DOI: 10.3390/ijms17071078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/19/2016] [Accepted: 06/29/2016] [Indexed: 01/18/2023] Open
Abstract
Targeting threonyl-tRNA synthetase (ThrRS) of Brucella abortus is a promising approach to developing small-molecule drugs against bovine brucellosis. Using the BLASTp algorithm, we identified ThrRS from Escherichia coli (EThrRS, PDB ID 1QF6), which is 51% identical to ThrRS from Brucella abortus (BaThrRS) at the amino acid sequence level. EThrRS was used as the template to construct a BaThrRS homology model which was optimized using molecular dynamics simulations. To determine the residues important for substrate ATP binding, we identified the ATP-binding regions of BaThrRS, docked ATP to the protein, and identified the residues whose side chains surrounded bound ATP. We then used the binding site of ATP to virtually screen for BaThrRS inhibitors and got seven leads. We further characterized the BaThrRS-binding site of the compound with the highest predicted inhibitory activity. Our results should facilitate future experimental effects to find novel drugs for use against bovine brucellosis.
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Affiliation(s)
- Ming Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Fang Wen
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Shengguo Zhao
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Pengpeng Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Songli Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Yangdong Zhang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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39
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Rémion A, Khoder-Agha F, Cornu D, Argentini M, Redeker V, Mirande M. Identification of protein interfaces within the multi-aminoacyl-tRNA synthetase complex: the case of lysyl-tRNA synthetase and the scaffold protein p38. FEBS Open Bio 2016; 6:696-706. [PMID: 27398309 PMCID: PMC4932449 DOI: 10.1002/2211-5463.12074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/23/2016] [Accepted: 04/19/2016] [Indexed: 11/06/2022] Open
Abstract
Human cytoplasmic lysyl-tRNA synthetase (LysRS) is associated within a multi-aminoacyl-tRNA synthetase complex (MSC). Within this complex, the p38 component is the scaffold protein that binds the catalytic domain of LysRS via its N-terminal region. In addition to its translational function when associated to the MSC, LysRS is also recruited in nontranslational roles after dissociation from the MSC. The balance between its MSC-associated and MSC-dissociated states is essential to regulate the functions of LysRS in cellular homeostasis. With the aim of understanding the rules that govern association of LysRS in the MSC, we analyzed the protein interfaces between LysRS and the full-length version of p38, the scaffold protein of the MSC. In a previous study, the cocrystal structure of LysRS with a N-terminal peptide of p38 was reported [Ofir-Birin Y et al. (2013) Mol Cell 49, 30-42]. In order to identify amino acid residues involved in interaction of the two proteins, the non-natural, photo-cross-linkable amino acid p-benzoyl-l-phenylalanine (Bpa) was incorporated at 27 discrete positions within the catalytic domain of LysRS. Among the 27 distinct LysRS mutants, only those with Bpa inserted in place of Lys356 or His364 were cross-linked with p38. Using mass spectrometry, we unambiguously identified the protein interface of the cross-linked complex and showed that Lys356 and His364 of LysRS interact with the peptide from Pro8 to Arg26 in native p38, in agreement with the published cocrystal structure. This interface, which in LysRS is located on the opposite side of the dimer to the site of interaction with its tRNA substrate, defines the core region of the MSC. The residues identified herein in human LysRS are not conserved in yeast LysRS, an enzyme that does not associate within the MSC, and contrast with the residues proposed to be essential for LysRS:p38 association in the earlier work.
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Affiliation(s)
- Azaria Rémion
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS) CNRS Gif-sur-Yvette France
| | - Fawzi Khoder-Agha
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS) CNRS Gif-sur-Yvette France; Institute for Integrative Biology of the Cell (I2BC) CEACNRS Univ. Paris-Sud, Université Paris-Saclay Gif-sur-Yvette France
| | - David Cornu
- Service d'identification et de Caractérisation des Protéines par Spectrométrie de Masse (SICaPS) CEA CNRS Univ. Paris-Sud, Université Paris-Saclay Gif-sur-Yvette France
| | - Manuela Argentini
- Service d'identification et de Caractérisation des Protéines par Spectrométrie de Masse (SICaPS) CEA CNRS Univ. Paris-Sud, Université Paris-Saclay Gif-sur-Yvette France
| | - Virginie Redeker
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS) CNRSGif-sur-Yvette France; Service d'identification et de Caractérisation des Protéines par Spectrométrie de Masse (SICaPS) CEACNRS Univ. Paris-Sud, Université Paris-Saclay Gif-sur-Yvette France; Present address: Paris-Saclay Institute of Neuroscience (Neuro-PSI) CNRS 1 avenue de la Terrasse 91190 Gif-sur-Yvette France
| | - Marc Mirande
- Laboratoire d'Enzymologie et Biochimie Structurales (LEBS) CNRS Gif-sur-Yvette France; Institute for Integrative Biology of the Cell (I2BC) CEACNRS Univ. Paris-Sud, Université Paris-Saclay Gif-sur-Yvette France
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40
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Sharma S, Lafontaine DLJ. 'View From A Bridge': A New Perspective on Eukaryotic rRNA Base Modification. Trends Biochem Sci 2016; 40:560-575. [PMID: 26410597 DOI: 10.1016/j.tibs.2015.07.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 01/23/2023]
Abstract
Eukaryotic rRNA are modified frequently, although the diversity of modifications is low: in yeast rRNA, there are only 12 different types out of a possible natural repertoire exceeding 112. All nine rRNA base methyltransferases (MTases) and one acetyltransferase have recently been identified in budding yeast, and several instances of crosstalk between rRNA, tRNA, and mRNA modifications are emerging. Although the machinery has largely been identified, the functions of most rRNA modifications remain to be established. Remarkably, a eukaryote-specific bridge, comprising a single ribosomal protein (RP) from the large subunit (LSU), contacts four rRNA base modifications across the ribosomal subunit interface, potentially probing for their presence. We hypothesize in this article that long-range allosteric communication involving rRNA modifications is taking place between the two subunits during translation or, perhaps, the late stages of ribosome assembly.
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Affiliation(s)
- Sunny Sharma
- RNA Molecular Biology, FRS/FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, FRS/FNRS, Université Libre de Bruxelles, B-6041 Charleroi-Gosselies, Belgium; Center for Microscopy and Molecular Imaging, BioPark campus, B-6041 Charleroi-Gosselies, Belgium.
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41
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Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? Life (Basel) 2016; 6:life6010009. [PMID: 26901226 PMCID: PMC4810240 DOI: 10.3390/life6010009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 01/18/2023] Open
Abstract
Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process.
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42
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Berezovsky IN, Zheng Z, Kurotani A, Tokmakov AA, Kurochkin IV. Organization of the multiaminoacyl-tRNA synthetase complex and the cotranslational protein folding. Protein Sci 2015; 24:1475-85. [PMID: 26131561 DOI: 10.1002/pro.2735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 11/09/2022]
Abstract
Aminoacyl-tRNA synthetases (ARSs) play an essential role in the protein synthesis by catalyzing an attachment of their cognate amino acids to tRNAs. Unlike their prokaryotic counterparts, ARSs in higher eukaryotes form a multiaminoacyl-tRNA synthetase complex (MARS), consisting of the subset of ARS polypeptides and three auxiliary proteins. The intriguing feature of MARS complex is the presence of only nine out of twenty ARSs, specific for Arg, Asp, Gln, Glu, Ile, Leu, Lys, Met, and Pro, regardless of the organism, cell, or tissue types. Although existence of MARSs complex in higher eukaryotes has been already known for more than four decades, its functional significance remains elusive. We found that seven of the nine corresponding amino acids (Arg, Gln, Glu, Ile, Leu, Lys, and Met) together with Ala form a predictor of the protein α-helicity. Remarkably, all amino acids (besides Ala) in the predictor have the highest possible number of side-chain rotamers. Therefore, compositional bias of a typical α-helix can contribute to the helix's stability by increasing the entropy of the folded state. It also appears that position-specific α-helical propensity, specifically periodic alternation of charged and hydrophobic residues in the helices, may well be provided by the structural organization of the complex. Considering characteristics of MARS complex from the perspective of the α-helicity, we hypothesize that specific composition and structure of the complex represents a functional mechanism for coordination of translation with the fast and correct folding of amphiphilic α-helices.
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Affiliation(s)
- Igor N Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (a*STAR), Singapore, 138671.,Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore, 117579
| | - Zejun Zheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (a*STAR), Singapore, 138671
| | - Atsushi Kurotani
- RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, 230-0045, Japan
| | | | - Igor V Kurochkin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (a*STAR), Singapore, 138671
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