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Wongkittichote P, Magistrati M, Shimony JS, Smyser CD, Fatemi SA, Fine AS, Bellacchio E, Dallabona C, Shinawi M. Functional analysis of missense DARS2 variants in siblings with leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation. Mol Genet Metab 2022; 136:260-267. [PMID: 35820270 DOI: 10.1016/j.ymgme.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/18/2022]
Abstract
Biallelic pathogenic variants in the nuclear gene DARS2 (MIM# 610956), encoding the mitochondrial enzyme aspartyl-tRNA synthetase (MT-ASPRS) cause leukoencephalopathy with Brain Stem and Spinal Cord Involvement and Lactate Elevation (LBSL) (MIM# 611105), a neurometabolic disorder characterized by progressive ataxia, spasticity, developmental arrest or regression and characteristic brain MRI findings. Most patients exhibit a slowly progressive disease course with motor deterirartion that begins in childhood or adolescence, but can also occasionaly occur in adulthood. More severe LBSL presentations with atypical brain MRI findings have been recently described. Baker's yeast orthologue of DARS2, MSD1, is required for growth on oxidative carbon sources. A yeast with MSD1 knockout (msd1Δ) demonstrated a complete lack of oxidative growth which could be rescued by wild-type MSD1 but not MSD1 with pathogenic variants. Here we reported two siblings who exhibited developmental regression and ataxia with different age of onset and phenotypic severity. Exome sequencing revealed 2 compound heterozygous missense variants in DARS2: c.473A>T (p.Glu158Val) and c.829G>A (p.Glu277Lys); this variant combination has not been previously reported. The msd1Δ yeast transformed with plasmids expressing p.Glu259Lys, equivalent to human p.Glu277Lys, showed complete loss of oxidative growth and oxygen consumption, while the strain carrying p.Gln137Val, equivalent to human p.Glu158Val, showed a significant reduction of oxidative growth, but a residual ability to grow was retained. Structural analysis indicated that p.Glu158Val may interfere with protein binding of tRNAAsp, while p.Glu277Lys may impact both homodimerization and catalysis of MT-ASPRS. Our data illustrate the utility of yeast model and in silico analysis to determine pathogenicity of DARS2 variants, expand the genotypic spectrum and suggest intrafamilial variability in LBSL.
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Affiliation(s)
- Parith Wongkittichote
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Joshua S Shimony
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Christopher D Smyser
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA; Division of Pediatric Neurology, Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | - Seyed Ali Fatemi
- Kennedy Krieger Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Amena S Fine
- Kennedy Krieger Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA.
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Liu M, Xiao W, Yang F, Wang X, Chen C, Jin S, Ran N, Chen W, Yang D. Case Report: DARS Mutations Responsible for Hypomyelination With Brain Stem and Spinal Cord Involvement and Leg Spasticity. Front Genet 2022; 13:845967. [PMID: 35571067 PMCID: PMC9094363 DOI: 10.3389/fgene.2022.845967] [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: 12/30/2021] [Accepted: 04/07/2022] [Indexed: 11/28/2022] Open
Abstract
Objective: Hypomyelination with brain stem and spinal cord involvement and leg spasticity (HBSL) is a rare form of leukodystrophy presenting with varying clinical and imaging features. We report a case of HBSL to investigate the clinical and radiological characteristics of HBSL resulting from cytoplasmic aspartyl-tRNA synthetase gene (DARS) mutations. Subjects: We report a patient of HBSL with compound heterozygous mutations in DARS1. To study the potential genetic variations of the patient, targeted next-generation sequencing, whole-exome sequencing, and Sanger sequencing were used. We reviewed the clinical and radiological features of the patient. The literature was thoroughly evaluated. Results: The patient suffered from developmental regression associated with lower limbs spasticity, developmental delay, and paralysis of the lower limbs since childhood. Decreased T1 and increased T2 signals were observed on the bilateral basal, centrum ovale, frontal lobe, parietal lobe, and ganglia in cervical cord magnetic resonance imaging (MRI). The patient had two compound heterozygous mutations (NM_001349:c.1363T > C and NM_001349:c.821C > G) in the DARS1 gene. Conclusion: Two mutations in DARS1 were found to be associated with HBSL, one of them being reported for the first time. These findings can be valuable for diagnosing and providing genetic counseling to HBSL patients in the future.
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Affiliation(s)
- Meijun Liu
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wen Xiao
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fang Yang
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xueqing Wang
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chao Chen
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuoguo Jin
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ningjing Ran
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Weiyin Chen
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dongdong Yang
- Neurology Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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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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Kim MH, Kang BS. Structure and Dynamics of the Human Multi-tRNA Synthetase Complex. Subcell Biochem 2022; 99:199-233. [PMID: 36151377 DOI: 10.1007/978-3-031-00793-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes that ligate amino acids to their cognate tRNAs during protein synthesis. A growing body of scientific evidence acknowledges that ubiquitously expressed ARSs act as crossover mediators of biological processes, such as immunity and metabolism, beyond translation. In particular, a cytoplasmic multi-tRNA synthetase complex (MSC), which consists of eight ARSs and three ARS-interacting multifunctional proteins in humans, is recognized to be a central player that controls the complexity of biological systems. Although the role of the MSC in biological processes including protein synthesis is still unclear, maintaining the structural integrity of MSC is essential for life. This chapter deals with current knowledge on the structural aspects of the human MSC and its protein components. The main focus is on the regulatory functions of MSC beyond its catalytic activity.
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Affiliation(s)
- Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.
| | - Beom Sik Kang
- School of Life Sciences, Kyungpook National University, Daegu, South Korea.
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Hei Z, Wu S, Zheng L, Zhou J, Liu Z, Wang J, Fang P. Crystal structures reveal a novel dimer of the RWD domain of human general control nonderepressible 2. Biochem Biophys Res Commun 2021; 549:164-170. [PMID: 33676185 DOI: 10.1016/j.bbrc.2021.02.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 02/23/2021] [Indexed: 10/22/2022]
Abstract
General control nonderepressible 2 (GCN2) is a serine/threonine protein kinase, detecting a variety of stresses including amino acid starvation, reactive oxygen species, etc. in eukaryotic cells. Activation of GCN2 requires the interaction of the N-terminal RWD domain with the upstream GCN1 protein and the dimerization by the kinase domain. In this study, we determined two crystal structures of the RWD domain of human GCN2 in two different crystal packing modes. These two different crystal structures reveal a same dimer of the RWD domain, which has not been reported in previous studies. We further confirmed this novel dimer interaction in solution using gel filtration experiments, and in human embryonic kidney (HEK) 293 cells using bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation (co-IP) assays. Together, this study discovers a potential protein-protein interface on the RWD domain of human GCN2, and suggests a possible regulation between the interaction of GCN1 and the formation of GCN2 dimer.
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Affiliation(s)
- 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
| | - 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
| | - Jintong Zhou
- 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
| | - Zaizhou Liu
- 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 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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Muthiah A, Housley GD, Klugmann M, Fröhlich D. The Leukodystrophies HBSL and LBSL-Correlates and Distinctions. Front Cell Neurosci 2021; 14:626610. [PMID: 33574740 PMCID: PMC7870476 DOI: 10.3389/fncel.2020.626610] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) accurately charge tRNAs with their respective amino acids. As such, they are vital for the initiation of cytosolic and mitochondrial protein translation. These enzymes have become increasingly scrutinized in recent years for their role in neurodegenerative disorders caused by the mutations of ARS-encoding genes. This review focuses on two such genes-DARS1 and DARS2-which encode cytosolic and mitochondrial aspartyl-tRNA synthetases, and the clinical conditions associated with mutations of these genes. We also describe attempts made at modeling these conditions in mice, which have both yielded important mechanistic insights. Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) is a disease caused by a range of mutations in the DARS2 gene, initially identified in 2003. Ten years later, hypomyelination with brainstem and spinal cord involvement and leg spasticity (HBSL), caused by mutations of cytosolic DARS1, was discovered. Multiple parallels have been drawn between the two conditions. The Magnetic Resonance Imaging (MRI) patterns are strikingly similar, but still set these two conditions apart from other leukodystrophies. Clinically, both conditions are characterized by lower limb spasticity, often associated with other pyramidal signs. However, perhaps due to earlier detection, a wider range of symptoms, including peripheral neuropathy, as well as visual and hearing changes have been described in LBSL patients. Both HBSL and LBSL are spectrum disorders lacking genotype to phenotype correlation. While the fatal phenotype of Dars1 or Dars2 single gene deletion mouse mutants revealed that the two enzymes lack functional redundancy, further pursuit of disease modeling are required to shed light onto the underlying disease mechanism, and enable examination of experimental treatments, including gene therapies.
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Affiliation(s)
| | | | | | - Dominik Fröhlich
- Translational Neuroscience Facility and Department of Physiology, School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
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7
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Fröhlich D, Mendes MI, Kueh AJ, Bongers A, Herold MJ, Salomons GS, Housley GD, Klugmann M. A Hypomorphic Dars1 D367Y Model Recapitulates Key Aspects of the Leukodystrophy HBSL. Front Cell Neurosci 2021; 14:625879. [PMID: 33551752 PMCID: PMC7855723 DOI: 10.3389/fncel.2020.625879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/21/2020] [Indexed: 01/18/2023] Open
Abstract
Hypomyelination with brain stem and spinal cord involvement and leg spasticity (HBSL) is a leukodystrophy caused by missense mutations of the aspartyl-tRNA synthetase-encoding gene DARS1. The clinical picture includes the regression of acquired motor milestones, spasticity, ataxia, seizures, nystagmus, and intellectual disabilities. Morphologically, HBSL is characterized by a distinct pattern of hypomyelination in the central nervous system including the anterior brainstem, the cerebellar peduncles and the supratentorial white matter as well as the dorsal columns and the lateral corticospinal tracts of the spinal cord. Adequate HBSL animal models are lacking. Dars1 knockout mice are embryonic lethal precluding examination of the etiology. To address this, we introduced the HBSL-causing Dars1 D367Y point mutation into the mouse genome. Surprisingly, mice carrying this mutation homozygously were phenotypically normal. As hypomorphic mutations are more severe in trans to a deletion, we crossed Dars1 D367Y/D367Y mice with Dars1-null carriers. The resulting Dars1 D367Y/- offspring displayed a strong developmental delay compared to control Dars1 D367Y/+ littermates, starting during embryogenesis. Only a small fraction of Dars1 D367Y/- mice were born, and half of these mice died with hydrocephalus during the first 3 weeks of life. Of the few Dars1 D367Y/- mice that were born at term, 25% displayed microphthalmia. Throughout postnatal life, Dars1 D367Y/- mice remained smaller and lighter than their Dars1 D367Y/+ littermates. Despite this early developmental deficit, once they made it through early adolescence Dars1 D367Y/- mice were phenotypically inconspicuous for most of their adult life, until they developed late onset motor deficits as well as vacuolization and demyelination of the spinal cord white matter. Expression levels of the major myelin proteins were reduced in Dars1 D367Y/- mice compared to controls. Taken together, Dars1 D367Y/- mice model aspects of the clinical picture of the corresponding missense mutation in HBSL. This model will enable studies of late onset deficits, which is precluded in Dars1 knockout mice, and can be leveraged to test potential HBSL therapeutics including DARS1 gene replacement therapy.
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Affiliation(s)
- Dominik Fröhlich
- Translational Neuroscience Facility & Department of Physiology, School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Marisa I. Mendes
- Metabolic Unit/Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Andrew J. Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Andre Bongers
- Biomedical Resources Imaging Laboratory, UNSW Sydney, Kensington, NSW, Australia
| | - Marco J. Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gajja S. Salomons
- Metabolic Unit/Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Gary D. Housley
- Translational Neuroscience Facility & Department of Physiology, School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Matthias Klugmann
- Translational Neuroscience Facility & Department of Physiology, School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
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8
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Khan K, Baleanu-Gogonea C, Willard B, Gogonea V, Fox PL. 3-Dimensional architecture of the human multi-tRNA synthetase complex. Nucleic Acids Res 2020; 48:8740-8754. [PMID: 32644155 PMCID: PMC7470956 DOI: 10.1093/nar/gkaa569] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/08/2020] [Accepted: 07/06/2020] [Indexed: 11/24/2022] Open
Abstract
In mammalian cells, eight cytoplasmic aminoacyl-tRNA synthetases (AARS), and three non-synthetase proteins, reside in a large multi-tRNA synthetase complex (MSC). AARSs have critical roles in interpretation of the genetic code during protein synthesis, and in non-canonical functions unrelated to translation. Nonetheless, the structure and function of the MSC remain unclear. Partial or complete crystal structures of all MSC constituents have been reported; however, the structure of the holo-MSC has not been resolved. We have taken advantage of cross-linking mass spectrometry (XL-MS) and molecular docking to interrogate the three-dimensional architecture of the MSC in human HEK293T cells. The XL-MS approach uniquely provides structural information on flexibly appended domains, characteristic of nearly all MSC constituents. Using the MS-cleavable cross-linker, disuccinimidyl sulfoxide, inter-protein cross-links spanning all MSC constituents were observed, including cross-links between eight protein pairs not previously known to interact. Intra-protein cross-links defined new structural relationships between domains in several constituents. Unexpectedly, an asymmetric AARS distribution was observed featuring a clustering of tRNA anti-codon binding domains on one MSC face. Possibly, the non-uniform localization improves efficiency of delivery of charged tRNA’s to an interacting ribosome during translation. In summary, we show a highly compact, 3D structural model of the human holo-MSC.
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Affiliation(s)
- Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | | | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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Deep Transcriptomic Analysis Reveals the Dynamic Developmental Progression during Early Development of Channel Catfish ( Ictalurus punctatus). Int J Mol Sci 2020; 21:ijms21155535. [PMID: 32748829 PMCID: PMC7432863 DOI: 10.3390/ijms21155535] [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: 05/31/2020] [Revised: 07/21/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
The transition from fertilized egg to larva in fish is accompanied with various biological processes. We selected seven early developmental stages in channel catfish, Ictalurus punctatus, for transcriptome analysis, and covered 22,635 genes with 590 million high-quality RNA-sequencing (seq) reads. Differential expression analysis between neighboring developmental timepoints revealed significantly enriched biological categories associated with growth, development and morphogenesis, which was most evident at 2 vs. 5 days post fertilization (dpf) and 5 vs. 6 dpf. A gene co-expression network was constructed using the Weighted Gene Co-expression Network Analysis (WGCNA) approach and four critical modules were identified. Among candidate hub genes, GDF10, FOXA2, HCEA and SYCE3 were involved in head formation, egg development and the transverse central element of synaptonemal complexes. CK1, OAZ2, DARS1 and UBE2V2 were mainly associated with regulation of cell cycle, growth, brain development, differentiation and proliferation of enterocytes. IFI44L and ZIP10 were critical for the regulation of immune activity and ion transport. Additionally, TCK1 and TGFB1 were related to phosphate transport and regulating cell proliferation. All these genes play vital roles in embryogenesis and regulation of early development. These results serve as a rich dataset for functional genomic studies. Our work reveals new insights of the underlying mechanisms in channel catfish early development.
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Ramakrishnan C, Nagarajan R, Sekijima M, Michael Gromiha M. Molecular dynamics simulations of cognate and non-cognate AspRS-tRNA Asp complexes. J Biomol Struct Dyn 2020; 39:493-501. [PMID: 31900102 DOI: 10.1080/07391102.2019.1711188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Aspartyl tRNA synthetase (AspRS), one of the 20 aminoacyl-tRNA synthetases, plays an important role in protein synthesis by catalyzing the aminoacylation reaction and synthesises Aspartyl-tRNA (tRNAAsp). A typical three-dimensional structure of AspRS comprises three distinct domains for the recognition of cognate tRNA and catalysis, namely, anti-codon binding domain/N-terminal domain, hinge domain and catalytic domain through their interactions with anti-codon loop, D-stem and acceptor arm of cognate tRNA, respectively. In this work, we have studied the structural characteristics of each domain of AspRS to understand the recognition mechanism of tRNAAsp using molecular dynamics simulations. The dynamics of AspRS-tRNAAsp complexes from E.coli (cognate and non-cognate), S.cerevisiae (cognate) and T.thermophilus (non-cognate) were compared to understand the differences in recognition of cognate and non-cognate tRNAs. Our results explain that the conformational changes associated with the recognition of tRNA occur only in the cognate complexes. Among the cognate complexes, the conformational changes in yeast AspRS are highly controlled during tRNAAsp recognition than that of in the E. coli AspRS. Moreover, the functional motions required for the tRNA recognition are observed only in the cognate complexes, and the conformational changes in AspRS and their recognition of tRNAAsp are organism specific.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- C Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - R Nagarajan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - M Sekijima
- Advanced Computational Drug Discovery Unit, Tokyo Institute of Technology, Yokohama, Japan
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.,Advanced Computational Drug Discovery Unit, Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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11
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Hahn H, Park SH, Kim HJ, Kim S, Han BW. The DRS-AIMP2-EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex. IUCRJ 2019; 6:958-967. [PMID: 31576228 PMCID: PMC6760448 DOI: 10.1107/s2052252519010790] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/01/2019] [Indexed: 05/16/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) play essential roles in protein biosynthesis as well as in other cellular processes, often using evolutionarily acquired domains. For possible cooperativity and synergistic effects, nine ARSs assemble into the multi-tRNA synthetase complex (MSC) with three scaffold proteins: aminoacyl-tRNA synthetase complex-interacting multifunctional proteins 1, 2 and 3 (AIMP1, AIMP2 and AIMP3). X-ray crystallographic methods were implemented in order to determine the structure of a ternary subcomplex of the MSC comprising aspartyl-tRNA synthetase (DRS) and two glutathione S-transferase (GST) domains from AIMP2 and glutamyl-prolyl-tRNA synthetase (AIMP2GST and EPRSGST, respectively). While AIMP2GST and EPRSGST interact via conventional GST heterodimerization, DRS strongly interacts with AIMP2GST via hydrogen bonds between the α7-β9 loop of DRS and the β2-α2 loop of AIMP2GST, where Ser156 of AIMP2GST is essential for the assembly. Structural analyses of DRS-AIMP2GST-EPRSGST reveal its pivotal architecture in the MSC and provide valuable insights into the overall assembly and conditionally required disassembly of the MSC.
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Affiliation(s)
- Hyunggu Hahn
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Ho Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Jin M. Unique roles of tryptophanyl-tRNA synthetase in immune control and its therapeutic implications. Exp Mol Med 2019; 51:1-10. [PMID: 30613102 PMCID: PMC6321835 DOI: 10.1038/s12276-018-0196-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 08/15/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022] Open
Abstract
Tryptophanyl tRNA synthetase (WRS) is an essential enzyme as it catalyzes the ligation of tryptophan to its cognate tRNA during translation. Interestingly, mammalian WRS has evolved to acquire domains or motifs for novel functions beyond protein synthesis; WRS can also further expand its functions via alternative splicing and proteolytic cleavage. WRS is localized not only to the nucleus but also to the extracellular space, playing a key role in innate immunity, angiogenesis, and IFN-γ signaling. In addition, the expression of WRS varies significantly in different tissues and pathological states, implying that it plays unique roles in physiological homeostasis and immune defense. This review addresses the current knowledge regarding the evolution, structural features, and context-dependent functions of WRS, particularly focusing on its roles in immune regulation. Targeting tryptophanyl tRNA synthetase (WRS), an evolutionarily conserved enzyme involved in protein synthesis, could be an effective strategy for modulating the immune system. In addition to helping translate mRNA into amino acid sequences in cytoplasm, human WRS can be secreted and activate immune responses against invading pathogens. Mirim Jin at Gachon University, Incheon, South Korea, reviews recent studies on the structure, expression pattern and functions of WRS other than protein synthesis. High levels of WRS protein have been found in patients with sepsis and autoimmune diseases suggesting that inhibiting WRS could be a potential therapeutic approach for treating these conditions. Further research into WRS will shed light not only on how it regulates the immune system, but also on how it exerts other reported effects on blood vessel formation and cell migration.
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Affiliation(s)
- Mirim Jin
- Department of Microbiology, College of Medicine, Gachon University, Incheon, Korea. .,Department of Health Science and Technology, GAIHST, Gachon University, Incheon, Korea.
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13
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Park JS, Park MC, Lee KY, Goughnour PC, Jeong SJ, Kim HS, Kim HJ, Lee BJ, Kim S, Han BW. Unique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity. Int J Biol Macromol 2018; 120:835-845. [PMID: 30171954 DOI: 10.1016/j.ijbiomac.2018.08.171] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Asparaginyl-tRNA synthetase (NRS) is not only essential in protein translation but also associated with autoimmune diseases. Particularly, patients with antibodies that recognize NRS often develop interstitial lung disease (ILD). However, the underlying mechanism of how NRS is recognized by immune cells and provokes inflammatory responses is not well-understood. Here, we found that the crystal structure of the unique N-terminal extension domain of human NRS (named as UNE-N, where -N denotes NRS) resembles that of the chemotactic N-terminal domain of NRS from a filarial nematode, Brugia malayi, which recruits and activates specific immune cells by interacting with CXC chemokine receptor 1 and 2. UNE-N induced migration of CC chemokine receptor 3 (CCR3)-expressing cells. The chemokine activity of UNE-N was significantly reduced by suppressing CCR3 expression with CCR3-targeting siRNA, and the loop3 region of UNE-N was shown to interact mainly with the extracellular domains of CCR3 in nuclear magnetic resonance perturbation experiments. Based on these results, evolutionarily acquired UNE-N elicits chemokine activities that would promote NRS-CCR3-mediated proinflammatory signaling in ILD.
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Affiliation(s)
- Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Min Chul Park
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Young Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Peter C Goughnour
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Jae Jeong
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Therapeutic Target Discovery Branch, Division of Precision Medicine and Cancer Informatics, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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Mimura I, Hirakawa Y, Kanki Y, Kushida N, Nakaki R, Suzuki Y, Tanaka T, Aburatani H, Nangaku M. Novel lnc RNA regulated by HIF-1 inhibits apoptotic cell death in the renal tubular epithelial cells under hypoxia. Physiol Rep 2018; 5:5/8/e13203. [PMID: 28420760 PMCID: PMC5408278 DOI: 10.14814/phy2.13203] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 02/15/2017] [Indexed: 12/22/2022] Open
Abstract
Chronic tubulointerstitial hypoxia plays an important role as the final common pathway to end-stage renal disease. HIF-1 (hypoxia-inducible factor-1) is a master transcriptional factor under hypoxia, regulating downstream target genes. Genome-wide analysis of HIF-1 binding sites using high-throughput sequencers has clarified various kinds of downstream targets and made it possible to demonstrate the novel roles of HIF-1. Our aim of this study is to identify novel HIF-1 downstream epigenetic targets which may play important roles in the kidney. Immortalized tubular cell lines (HK2; human kidney-2) and primary cultured cells (RPTEC; renal proximal tubular cell lines) were exposed to 1% hypoxia for 24-72 h. We performed RNA-seq to clarify the expression of mRNA and long non-coding RNA (lncRNA). We also examined ChIP-seq to identify HIF-1 binding sites under hypoxia. RNA-seq identified 44 lncRNAs which are up-regulated under hypoxic condition in both cells. ChIP-seq analysis demonstrated that HIF-1 also binds to the lncRNAs under hypoxia. The expression of novel lncRNA, DARS-AS1 (aspartyl-tRNA synthetase anti-sense 1), is up-regulated only under hypoxia and HIF-1 binds to its promoter region, which includes two hypoxia-responsive elements. Its expression is also up-regulated with cobalt chloride exposure, while it is not under hypoxia when HIF-1 is knocked down by siRNA To clarify the biological roles of DARS-AS1, we measured the activity of caspase 3/7 using anti-sense oligo of DARS-AS1. Knockdown of DARS-AS1 deteriorated apoptotic cell death. In conclusion, we identified the novel lncRNAs regulated by HIF-1 under hypoxia and clarified that DARS-AS1 plays an important role in inhibiting apoptotic cell death in renal tubular cells.
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Affiliation(s)
- Imari Mimura
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Hirakawa
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo., Tokyo, Japan
| | - Natsuki Kushida
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Nakaki
- Division of GenomeScience, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsuhiro Tanaka
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Division of GenomeScience, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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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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Cho HY, Maeng SJ, Cho HJ, Choi YS, Chung JM, Lee S, Kim HK, Kim JH, Eom CY, Kim YG, Guo M, Jung HS, Kang BS, Kim S. Assembly of Multi-tRNA Synthetase Complex via Heterotetrameric Glutathione Transferase-homology Domains. J Biol Chem 2015; 290:29313-28. [PMID: 26472928 DOI: 10.1074/jbc.m115.690867] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 01/27/2023] Open
Abstract
Many multicomponent protein complexes mediating diverse cellular processes are assembled through scaffolds with specialized protein interaction modules. The multi-tRNA synthetase complex (MSC), consisting of nine different aminoacyl-tRNA synthetases and three non-enzymatic factors (AIMP1-3), serves as a hub for many signaling pathways in addition to its role in protein synthesis. However, the assembly process and structural arrangement of the MSC components are not well understood. Here we show the heterotetrameric complex structure of the glutathione transferase (GST) domains shared among the four MSC components, methionyl-tRNA synthetase (MRS), glutaminyl-prolyl-tRNA synthetase (EPRS), AIMP2 and AIMP3. The MRS-AIMP3 and EPRS-AIMP2 using interface 1 are bridged via interface 2 of AIMP3 and EPRS to generate a unique linear complex of MRS-AIMP3:EPRS-AIMP2 at the molar ratio of (1:1):(1:1). Interestingly, the affinity at interface 2 of AIMP3:EPRS can be varied depending on the occupancy of interface 1, suggesting the dynamic nature of the linear GST tetramer. The four components are optimally arranged for maximal accommodation of additional domains and proteins. These characteristics suggest the GST tetramer as a unique and dynamic structural platform from which the MSC components are assembled. Considering prevalence of the GST-like domains, this tetramer can also provide a tool for the communication of the MSC with other GST-containing cellular factors.
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Affiliation(s)
- Ha Yeon Cho
- From the School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea
| | - Seo Jin Maeng
- From the School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea
| | - Hyo Je Cho
- From the School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea
| | - Yoon Seo Choi
- From the School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea
| | - Jeong Min Chung
- the Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Korea
| | - Sangmin Lee
- the Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Korea
| | - Hoi Kyoung Kim
- the Department of Molecular Medicine and Biopharmaceutical Sciences, Medicinal Bioconvergence Research Center, Graduate School of Convergence Technology, Seoul National University, Seoul 151-742, Korea
| | - Jong Hyun Kim
- the Department of Molecular Medicine and Biopharmaceutical Sciences, Medicinal Bioconvergence Research Center, Graduate School of Convergence Technology, Seoul National University, Seoul 151-742, Korea
| | - Chi-Yong Eom
- the NanoBio Convergence Research Team, Western Seoul Center, Korea Basic Science Institute, Seoul 120-750, Korea
| | - Yeon-Gil Kim
- the Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-834, Korea
| | - Min Guo
- the Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida 33458, and
| | - Hyun Suk Jung
- the Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Korea
| | - Beom Sik Kang
- From the School of Life Science and Biotechnology, KNU Creative BioResearch Group, Kyungpook National University, Daegu 702-701, Korea,
| | - Sunghoon Kim
- the Department of Molecular Medicine and Biopharmaceutical Sciences, Medicinal Bioconvergence Research Center, Graduate School of Convergence Technology, Seoul National University, Seoul 151-742, Korea, the The National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai 201203, China
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17
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Wolf NI, Toro C, Kister I, Latif KA, Leventer R, Pizzino A, Simons C, Abbink TEM, Taft RJ, van der Knaap MS, Vanderver A. DARS-associated leukoencephalopathy can mimic a steroid-responsive neuroinflammatory disorder. Neurology 2014; 84:226-30. [PMID: 25527264 DOI: 10.1212/wnl.0000000000001157] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To describe the expanding clinical spectrum of a recently described hereditary leukoencephalopathy, hypomyelination with brainstem and spinal cord involvement and leg spasticity, which is caused by mutations in the aspartyl tRNA-synthetase encoding gene DARS, including patients with an adolescent onset. METHODS Three patients with mutations in DARS were identified by combining MRI pattern recognition and genetic analysis. RESULTS One patient had the typical infantile presentation, but 2 patients with onset in late adolescence had a disease mimicking an acquired inflammatory CNS disorder. Adolescent-onset patients presented with subacute spastic paraplegia and had positive response to steroids. They had only minor focal supratentorial white matter abnormalities, but identical spinal cord changes involving dorsal columns and corticospinal tracts. Clinical presentation included subacute spastic paraplegia with partial improvement on steroids. CONCLUSIONS Focal T2 hyperintense white matter changes on brain MRI in combination with spinal cord signal abnormalities usually suggest acquired inflammatory conditions such as multiple sclerosis, especially in the context of relapsing course and a positive response to steroid treatment. Adolescents with mutations in DARS can present with a comparable clinical picture, broadening the clinical spectrum of hypomyelination with brainstem and spinal cord involvement and leg spasticity.
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Affiliation(s)
- Nicole I Wolf
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands.
| | - Camilo Toro
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Ilya Kister
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Kartikasalwah Abd Latif
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Richard Leventer
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Amy Pizzino
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Cas Simons
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Truus E M Abbink
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Ryan J Taft
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
| | - Adeline Vanderver
- From the Department of Child Neurology (N.I.W., T.E.M.A., M.S.v.d.K.), VU University Medical Center, Amsterdam; the Neuroscience Campus Amsterdam (N.I.W., T.E.M.A., M.S.v.d.K.), the Netherlands; the NIH Undiagnosed Diseases Program (C.T.), National Institutes of Health, Bethesda, MD; the NYU Multiple Sclerosis Center (I.K.), Department of Neurology, NYU School of Medicine, New York; the Department of Radiology (K.A.L.), Hospital Kuala Lumpur, Malaysia; the Department of Neurology (R.L.), Royal Children's Hospital; Murdoch Children's Research Institute (R.L.); the Department of Pediatrics (R.L.), University of Melbourne, Australia; the Department of Neurology (A.P., A.V.), Children's National Medical Center, Washington, DC; the Institute for Molecular Bioscience (C.S., R.J.T.), University of Queensland, St Lucia, Queensland, Australia; the Departments of Integrative Systems Biology and Pediatrics (R.J.T.), George Washington University School of Medicine, Washington, DC; Illumina Inc. (R.J.T.), San Diego, CA; and the Department of Functional Genomics (M.S.v.d.K.), Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, the Netherlands
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Dias J, Renault L, Pérez J, Mirande M. Small-angle X-ray solution scattering study of the multi-aminoacyl-tRNA synthetase complex reveals an elongated and multi-armed particle. J Biol Chem 2013; 288:23979-89. [PMID: 23836901 PMCID: PMC3745343 DOI: 10.1074/jbc.m113.489922] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/01/2013] [Indexed: 02/01/2023] Open
Abstract
In animal cells, nine aminoacyl-tRNA synthetases are associated with the three auxiliary proteins p18, p38, and p43 to form a stable and conserved large multi-aminoacyl-tRNA synthetase complex (MARS), whose molecular mass has been proposed to be between 1.0 and 1.5 MDa. The complex acts as a molecular hub for coordinating protein synthesis and diverse regulatory signal pathways. Electron microscopy studies defined its low resolution molecular envelope as an overall rather compact, asymmetric triangular shape. Here, we have analyzed the composition and homogeneity of the native mammalian MARS isolated from rabbit liver and characterized its overall internal structure, size, and shape at low resolution by hydrodynamic methods and small-angle x-ray scattering in solution. Our data reveal that the MARS exhibits a much more elongated and multi-armed shape than expected from previous reports. The hydrodynamic and structural features of the MARS are large compared with other supramolecular assemblies involved in translation, including ribosome. The large dimensions and non-compact structural organization of MARS favor a large protein surface accessibility for all its components. This may be essential to allow structural rearrangements between the catalytic and cis-acting tRNA binding domains of the synthetases required for binding the bulky tRNA substrates. This non-compact architecture may also contribute to the spatiotemporal controlled release of some of its components, which participate in non-canonical functions after dissociation from the complex.
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Affiliation(s)
- José Dias
- From the Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France and
| | - Louis Renault
- From the Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France and
| | - Javier Pérez
- SOLEIL Synchrotron, L'Orme des Merisiers Saint-Aubin, Gif-sur-Yvette, France
| | - Marc Mirande
- From the Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France and
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