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Popper B, Bürkle M, Ciccopiedi G, Marchioretto M, Forné I, Imhof A, Straub T, Viero G, Götz M, Schieweck R. Ribosome inactivation regulates translation elongation in neurons. J Biol Chem 2024; 300:105648. [PMID: 38219816 PMCID: PMC10869266 DOI: 10.1016/j.jbc.2024.105648] [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] [Received: 10/07/2023] [Revised: 12/10/2023] [Accepted: 01/02/2024] [Indexed: 01/16/2024] Open
Abstract
Cellular plasticity is crucial for adapting to ever-changing stimuli. As a result, cells consistently reshape their translatome, and, consequently, their proteome. The control of translational activity has been thoroughly examined at the stage of translation initiation. However, the regulation of ribosome speed in cells is widely unknown. In this study, we utilized a timed ribosome runoff approach, along with proteomics and transmission electron microscopy, to investigate global translation kinetics in cells. We found that ribosome speeds vary among various cell types, such as astrocytes, induced pluripotent human stem cells, human neural stem cells, and human and rat neurons. Of all cell types studied, mature cortical neurons exhibit the highest rate of translation. This finding is particularly remarkable because mature cortical neurons express the eukaryotic elongation factor 2 (eEF2) at lower levels than other cell types. Neurons solve this conundrum by inactivating a fraction of their ribosomes. As a result, the increase in eEF2 levels leads to a reduction of inactive ribosomes and an enhancement of active ones. Processes that alter the demand for active ribosomes, like neuronal excitation, cause increased inactivation of redundant ribosomes in an eEF2-dependent manner. Our data suggest a novel regulatory mechanism in which neurons dynamically inactivate ribosomes to facilitate translational remodeling. These findings have important implications for developmental brain disorders characterized by, among other things, aberrant translation.
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Affiliation(s)
- Bastian Popper
- Core Facility Animal Models, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Martina Bürkle
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Giuliana Ciccopiedi
- Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Graduate School of Systemic Neurosciences, LMU Munich, Munich, Germany
| | - Marta Marchioretto
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Ignasi Forné
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Axel Imhof
- Protein Analysis Unit, Department for Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Tobias Straub
- Bioinformatics Core Facility, Department of Molecular Biology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Gabriella Viero
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy
| | - Magdalena Götz
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany; SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center (BMC), LMU Munich, Munich, Germany
| | - Rico Schieweck
- Department of Physiological Genomics, Biomedical Center (BMC), LMU Munich, Munich, Germany; Department for Cell Biology & Anatomy, Biomedical Center (BMC), LMU Munich, Munich, Germany; Institute of Biophysics, National Research Council (CNR) Unit at Trento, Povo, Italy.
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2
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Sun WX, Zhang KH, Zhou Q, Hu SH, Lin Y, Xu W, Zhao SM, Yuan YY. Tryptophanylation of insulin receptor by WARS attenuates insulin signaling. Cell Mol Life Sci 2024; 81:25. [PMID: 38212570 PMCID: PMC11072365 DOI: 10.1007/s00018-023-05082-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 01/13/2024]
Abstract
Increased circulating amino acid levels have been linked to insulin resistance and development of type 2 diabetes (T2D), but the underlying mechanism remains largely unknown. Herein, we show that tryptophan modifies insulin receptor (IR) to attenuate insulin signaling and impair glucose uptake. Mice fed with tryptophan-rich chow developed insulin resistance. Excessive tryptophan promoted tryptophanyl-tRNA synthetase (WARS) to tryptophanylate lysine 1209 of IR (W-K1209), which induced insulin resistance by inhibiting the insulin-stimulated phosphorylation of IR, AKT, and AS160. SIRT1, but not other sirtuins, detryptophanylated IRW-K1209 to increase the insulin sensitivity. Collectively, we unveiled the mechanisms of how tryptophan impaired insulin signaling, and our data suggested that WARS might be a target to attenuate insulin resistance in T2D patients.
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Affiliation(s)
- Wen-Xing Sun
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China
- Department of Nutrition and Food Hygiene, School of Public Health, Nantong University, Nantong, People's Republic of China
| | - Kai-Hui Zhang
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, People's Republic of China
- Children's Research Institute, Children's Hospital Affiliated to Shandong University (Jinan Children's Hospital), Jinan, People's Republic of China
| | - Qian Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China
- NHC Key Lab of Reproduction Regulation, Shanghai Key Laboratory of Metabolic Remodeling and Health, and Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Song-Hua Hu
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China
- NHC Key Lab of Reproduction Regulation, Shanghai Key Laboratory of Metabolic Remodeling and Health, and Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Yan Lin
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China
- NHC Key Lab of Reproduction Regulation, Shanghai Key Laboratory of Metabolic Remodeling and Health, and Children's Hospital of Fudan University, Shanghai, People's Republic of China
- Shanghai Fifth People's Hospital of Fudan University, Fudan University, Shanghai, People's Republic of China
| | - Wei Xu
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China
- NHC Key Lab of Reproduction Regulation, Shanghai Key Laboratory of Metabolic Remodeling and Health, and Children's Hospital of Fudan University, Shanghai, People's Republic of China
- Shanghai Fifth People's Hospital of Fudan University, Fudan University, Shanghai, People's Republic of China
| | - Shi-Min Zhao
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China.
- NHC Key Lab of Reproduction Regulation, Shanghai Key Laboratory of Metabolic Remodeling and Health, and Children's Hospital of Fudan University, Shanghai, People's Republic of China.
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, College of Pharmacy, Qinghai University for Nationalities, Xining, People's Republic of China.
| | - Yi-Yuan Yuan
- Obstetrics and Gynecology Hospital of Fudan University, Institutes of Biomedical Sciences, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, People's Republic of China.
- NHC Key Lab of Reproduction Regulation, Shanghai Key Laboratory of Metabolic Remodeling and Health, and Children's Hospital of Fudan University, Shanghai, People's Republic of China.
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3
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Mao Y, Zhang J, Zhou Q, He X, Zheng Z, Wei Y, Zhou K, Lin Y, Yu H, Zhang H, Zhou Y, Lin P, Wu B, Yuan Y, Zhao J, Xu W, Zhao S. Hypoxia induces mitochondrial protein lactylation to limit oxidative phosphorylation. Cell Res 2024; 34:13-30. [PMID: 38163844 PMCID: PMC10770133 DOI: 10.1038/s41422-023-00864-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/01/2023] [Indexed: 01/03/2024] Open
Abstract
Oxidative phosphorylation (OXPHOS) consumes oxygen to produce ATP. However, the mechanism that balances OXPHOS activity and intracellular oxygen availability remains elusive. Here, we report that mitochondrial protein lactylation is induced by intracellular hypoxia to constrain OXPHOS. We show that mitochondrial alanyl-tRNA synthetase (AARS2) is a protein lysine lactyltransferase, whose proteasomal degradation is enhanced by proline 377 hydroxylation catalyzed by the oxygen-sensing hydroxylase PHD2. Hypoxia induces AARS2 accumulation to lactylate PDHA1 lysine 336 in the pyruvate dehydrogenase complex and carnitine palmitoyltransferase 2 (CPT2) lysine 457/8, inactivating both enzymes and inhibiting OXPHOS by limiting acetyl-CoA influx from pyruvate and fatty acid oxidation, respectively. PDHA1 and CPT2 lactylation can be reversed by SIRT3 to activate OXPHOS. In mouse muscle cells, lactylation is induced by lactate oxidation-induced intracellular hypoxia during exercise to constrain high-intensity endurance running exhaustion time, which can be increased or decreased by decreasing or increasing lactylation levels, respectively. Our results reveal that mitochondrial protein lactylation integrates intracellular hypoxia and lactate signals to regulate OXPHOS.
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Affiliation(s)
- Yunzi Mao
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jiaojiao Zhang
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qian Zhou
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiadi He
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Zhifang Zheng
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yun Wei
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Kaiqiang Zhou
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yan Lin
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Shanghai, China
- Shanghai Fifth People's Hospital of Fudan University, Fudan University, Shanghai, China
| | - Haowen Yu
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Haihui Zhang
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yineng Zhou
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Pengcheng Lin
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, College of Pharmacy, Qinghai University for Nationalities, Xining, Qinghai, China
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yiyuan Yuan
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Shanghai, China
| | - Jianyuan Zhao
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Shanghai, China
| | - Wei Xu
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Shanghai, China.
- Shanghai Fifth People's Hospital of Fudan University, Fudan University, Shanghai, China.
| | - Shimin Zhao
- The Obstetrics & Gynecology Hospital of Fudan University, Shanghai Key Laboratory of Metabolic Remodeling and Health, State Key Laboratory of Genetic Engineering, School of Life Sciences, Children's Hospital of Fudan University, and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
- NHC Key Lab of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), Shanghai, China.
- Key Laboratory for Tibet Plateau Phytochemistry of Qinghai Province, College of Pharmacy, Qinghai University for Nationalities, Xining, Qinghai, China.
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4
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Flagg MP, Lam B, Lam DK, Le TM, Kao A, Slaiwa YI, Hampton RY. Exploring the "misfolding problem" by systematic discovery and analysis of functional-but-degraded proteins. Mol Biol Cell 2023; 34:ar125. [PMID: 37729018 PMCID: PMC10848938 DOI: 10.1091/mbc.e23-06-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023] Open
Abstract
In both health and disease, the ubiquitin-proteasome system (UPS) degrades point mutants that retain partial function but have decreased stability compared with their wild-type counterparts. This class of UPS substrate includes routine translational errors and numerous human disease alleles, such as the most common cause of cystic fibrosis, ΔF508-CFTR. Yet, there is no systematic way to discover novel examples of these "minimally misfolded" substrates. To address that shortcoming, we designed a genetic screen to isolate functional-but-degraded point mutants, and we used the screen to study soluble, monomeric proteins with known structures. These simple parent proteins yielded diverse substrates, allowing us to investigate the structural features, cytotoxicity, and small-molecule regulation of minimal misfolding. Our screen can support numerous lines of inquiry, and it provides broad access to a class of poorly understood but biomedically critical quality-control substrates.
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Affiliation(s)
- Matthew P. Flagg
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Breanna Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Darren K. Lam
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Tiffany M. Le
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Andy Kao
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Yousif I. Slaiwa
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Randolph Y. Hampton
- Division of Biological Sciences, the Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093
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5
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Buianova AA, Proskura MV, Cheranev VV, Belova VA, Shmitko AO, Pavlova AS, Vasiliadis IA, Suchalko ON, Rebrikov DV, Petrosyan EK, Korostin DO. Candidate Genes for IgA Nephropathy in Pediatric Patients: Exome-Wide Association Study. Int J Mol Sci 2023; 24:15984. [PMID: 37958966 PMCID: PMC10647220 DOI: 10.3390/ijms242115984] [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: 09/30/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
IgA nephropathy (IgAN) is an autoimmune disorder which is believed to be non-monogenic. We performed an exome-wide association study of 70 children with IgAN and 637 healthy donors. The HLA allele frequencies were compared between the patients and healthy donors from the bone marrow registry of the Pirogov University. We tested 78,020 gene markers for association and performed functional enrichment analysis and transcription factor binding preference detection. We identified 333 genetic variants, employing three inheritance models. The most significant association with the disorder was observed for rs143409664 (PRAG1) in the case of the additive and dominant models (PBONF = 1.808 × 10-15 and PBONF = 1.654 × 10-15, respectively), and for rs13028230 (UBR3) in the case of the recessive model (PBONF = 1.545 × 10-9). Enrichment analysis indicated the strongly overrepresented "immune system" and "kidney development" terms. The HLA-DQA1*01:01:01G allele (p = 0.0076; OR, 2.021 [95% CI, 1.322-3.048]) was significantly the most frequent among IgAN patients. Here, we characterized, for the first time, the genetic background of Russian IgAN patients, identifying the risk alleles typical of the population. The most important signals were detected in previously undescribed loci.
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Affiliation(s)
- Anastasiia A. Buianova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Mariia V. Proskura
- Nephrology Department, Russian Children’s Clinical Hospital, Leninsky Prospect 117, 119571 Moscow, Russia; (M.V.P.); (E.K.P.)
| | - Valery V. Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Vera A. Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Anna O. Shmitko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Anna S. Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Iuliia A. Vasiliadis
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Oleg N. Suchalko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Denis V. Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
| | - Edita K. Petrosyan
- Nephrology Department, Russian Children’s Clinical Hospital, Leninsky Prospect 117, 119571 Moscow, Russia; (M.V.P.); (E.K.P.)
| | - Dmitriy O. Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova Str., 1, p. 1, 117513 Moscow, Russia; (V.V.C.); (V.A.B.); (A.O.S.); (A.S.P.); (I.A.V.); (O.N.S.); (D.V.R.); (D.O.K.)
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6
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Clay KJ, Yang Y, Clark C, Petrascheck M. Proteostasis is differentially modulated by inhibition of translation initiation or elongation. eLife 2023; 12:e76465. [PMID: 37795690 PMCID: PMC10581687 DOI: 10.7554/elife.76465] [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: 12/17/2021] [Accepted: 08/29/2023] [Indexed: 10/06/2023] Open
Abstract
Recent work has revealed an increasingly important role for mRNA translation in maintaining proteostasis. Here, we use chemical inhibitors targeting discrete steps of translation to compare how lowering the concentration of all or only translation initiation-dependent proteins rescues Caenorhabditis elegans from proteotoxic stress. We systematically challenge proteostasis and show that pharmacologically inhibiting translation initiation or elongation elicits a distinct protective profile. Inhibiting elongation protects from heat and proteasome dysfunction independently from HSF-1 but does not protect from age-associated protein aggregation. Conversely, inhibition of initiation protects from heat and age-associated protein aggregation and increases lifespan, dependent on hsf-1, but does not protect from proteotoxicity caused by proteasome dysfunction. Surprisingly, we find that the ability of the translation initiation machinery to control the concentration of newly synthesized proteins depends on HSF-1. Inhibition of translation initiation in wild-type animals reduces the concentration of newly synthesized proteins but increases it in hsf-1 mutants. Our findings suggest that the HSF-1 pathway is not only a downstream target of translation but also directly cooperates with the translation initiation machinery to control the concentration of newly synthesized proteins to restore proteostasis.
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Affiliation(s)
- Khalyd J Clay
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Yongzhi Yang
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Christina Clark
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
| | - Michael Petrascheck
- Department of Molecular Medicine, Department of Neuroscience, Scripps Research InstituteLa JollaUnited States
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7
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Zheng WQ, Zhang JH, Li ZH, Liu X, Zhang Y, Huang S, Li J, Zhou B, Eriani G, Wang ED, Zhou XL. Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy. Proc Natl Acad Sci U S A 2023; 120:e2309714120. [PMID: 37669377 PMCID: PMC10500172 DOI: 10.1073/pnas.2309714120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/08/2023] [Indexed: 09/07/2023] Open
Abstract
Proofreading (editing) of mischarged tRNAs by cytoplasmic aminoacyl-tRNA synthetases (aaRSs), whose impairment causes neurodegeneration and cardiac diseases, is of high significance for protein homeostasis. However, whether mitochondrial translation needs fidelity and the significance of editing by mitochondrial aaRSs have been unclear. Here, we show that mammalian cells critically depended on the editing of mitochondrial threonyl-tRNA synthetase (mtThrRS, encoded by Tars2), disruption of which accumulated Ser-tRNAThr and generated a large abundance of Thr-to-Ser misincorporated peptides in vivo. Such infidelity impaired mitochondrial translation and oxidative phosphorylation, causing oxidative stress and cell cycle arrest in the G0/G1 phase. Notably, reactive oxygen species (ROS) scavenging by N-acetylcysteine attenuated this abnormal cell proliferation. A mouse model of heart-specific defective mtThrRS editing was established. Increased ROS levels, blocked cardiomyocyte proliferation, contractile dysfunction, dilated cardiomyopathy, and cardiac fibrosis were observed. Our results elucidate that mitochondria critically require a high level of translational accuracy at Thr codons and highlight the cellular dysfunctions and imbalance in tissue homeostasis caused by mitochondrial mistranslation.
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Affiliation(s)
- Wen-Qiang Zheng
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Jian-Hui Zhang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Zi-Han Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Xiuxiu Liu
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Yong Zhang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Shuo Huang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Jinsong Li
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Bin Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Gilbert Eriani
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg67084, France
| | - En-Duo Wang
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Xiao-Long Zhou
- Key Laboratory of RNA Science and Engineering, State Key Laboratory of Molecular Biology, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
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8
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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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9
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Kalotay E, Klugmann M, Housley GD, Fröhlich D. Recessive aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models. Front Neurosci 2023; 17:1182874. [PMID: 37274208 PMCID: PMC10234152 DOI: 10.3389/fnins.2023.1182874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Protein synthesis is a fundamental process that underpins almost every aspect of cellular functioning. Intriguingly, despite their common function, recessive mutations in aminoacyl-tRNA synthetases (ARSs), the family of enzymes that pair tRNA molecules with amino acids prior to translation on the ribosome, cause a diverse range of multi-system disorders that affect specific groups of tissues. Neurological development is impaired in most ARS-associated disorders. In addition to central nervous system defects, diseases caused by recessive mutations in cytosolic ARSs commonly affect the liver and lungs. Patients with biallelic mutations in mitochondrial ARSs often present with encephalopathies, with variable involvement of peripheral systems. Many of these disorders cause severe disability, and as understanding of their pathogenesis is currently limited, there are no effective treatments available. To address this, accurate in vivo models for most of the recessive ARS diseases are urgently needed. Here, we discuss approaches that have been taken to model recessive ARS diseases in vivo, highlighting some of the challenges that have arisen in this process, as well as key results obtained from these models. Further development and refinement of animal models is essential to facilitate a better understanding of the pathophysiology underlying recessive ARS diseases, and ultimately to enable development and testing of effective therapies.
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Affiliation(s)
- Elizabeth Kalotay
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Matthias Klugmann
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gary D. Housley
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Dominik Fröhlich
- Translational Neuroscience Facility and Department of Physiology, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
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10
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Cui H, Diedrich JK, Wu DC, Lim JJ, Nottingham RM, Moresco JJ, Yates JR, Blencowe BJ, Lambowitz AM, Schimmel P. Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2. Nat Cell Biol 2023; 25:592-603. [PMID: 37059883 DOI: 10.1038/s41556-023-01118-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 02/27/2023] [Indexed: 04/16/2023]
Abstract
Cells respond to perturbations such as inflammation by sensing changes in metabolite levels. Especially prominent is arginine, which has known connections to the inflammatory response. Aminoacyl-tRNA synthetases, enzymes that catalyse the first step of protein synthesis, can also mediate cell signalling. Here we show that depletion of arginine during inflammation decreased levels of nuclear-localized arginyl-tRNA synthetase (ArgRS). Surprisingly, we found that nuclear ArgRS interacts and co-localizes with serine/arginine repetitive matrix protein 2 (SRRM2), a spliceosomal and nuclear speckle protein, and that decreased levels of nuclear ArgRS correlated with changes in condensate-like nuclear trafficking of SRRM2 and splice-site usage in certain genes. These splice-site usage changes cumulated in the synthesis of different protein isoforms that altered cellular metabolism and peptide presentation to immune cells. Our findings uncover a mechanism whereby an aminoacyl-tRNA synthetase cognate to a key amino acid that is metabolically controlled during inflammation modulates the splicing machinery.
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Affiliation(s)
- Haissi Cui
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - Justin J Lim
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA
| | - James J Moresco
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Center for the Genetics of Host Defense, UT Southwestern Medical Center, Dallas, TX, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Benjamin J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of Texas at Austin, Austin, TX, USA.
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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11
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Two isoleucyl tRNAs that decode synonymous codons divergently regulate breast cancer metastatic growth by controlling translation of proliferation-regulating genes. NATURE CANCER 2022; 3:1484-1497. [PMID: 36510010 DOI: 10.1038/s43018-022-00469-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/19/2022] [Indexed: 12/14/2022]
Abstract
The human genome contains 61 codons encoding 20 amino acids. Synonymous codons representing a given amino acid are decoded by a set of transfer RNAs (tRNAs) called isoacceptors. We report the surprising observation that two isoacceptor tRNAs that decode synonymous codons become modulated in opposing directions during breast cancer progression. Specifically, tRNAIleUAU became upregulated, whereas tRNAIleGAU became repressed as breast cancer cells attained enhanced metastatic capacity. Functionally, tRNAIleUAU promoted and tRNAIleGAU suppressed metastatic colonization in mouse xenograft models. These tRNAs mediated opposing effects on codon-dependent translation of growth-promoting genes, consistent with genomic enrichment or depletion of their cognate codons in mitotic genes. Our findings uncover a specific isoacceptor tRNA pair that act in opposition, divergently impacting growth-regulating genes and a disease phenotype. Degeneracy of the genetic code can thus be biologically exploited by human cancer cells via tRNA isoacceptor shifts that causally facilitate the transition toward a growth-promoting state.
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12
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Jin B, Xie L, Zhan D, Zhou L, Feng Z, He J, Qin J, Zhao C, Luo L, Li L. Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised alanyl-tRNA synthetase. Development 2022; 149:276217. [DOI: 10.1242/dev.200342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/28/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders; however, its function in embryonic neurogenesis remains unclear. This study identified an aars1cq71/cq71 mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. aars1 transcripts were highly expressed in primary neural progenitor cells, and their aberration resulted in protein overloading and activated Perk. nfe2l2b, a paralog of mammalian Nfe2l2, which encodes Nrf2, is a pivotal executor of Perk signaling that regulates neuronal phenotypes in aars1cq71/cq71 mutants. Interference of nfe2l2b in nfe2l2bΔ1/Δ1 mutants did not affect global larval development. However, aars1cq71/cq71;nfe2l2bΔ1/Δ1 mutant embryos exhibited increased neuronal cell survival and neurogenesis compared with their aars1cq71/cq71 siblings. nfe2l2b was harnessed by Perk at two levels. Its transcript was regulated by Chop, an implementer of Perk. It was also phosphorylated by Perk. Both pathways synergistically assured the nuclear functions of nfe2l2b to control cell survival by targeting p53. Our study extends the understanding of tRNA synthetase in neurogenesis and implies that Nrf2 is a cue to mitigate neurodegenerative pathogenesis.
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Affiliation(s)
- Binbin Jin
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Liqin Xie
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Dan Zhan
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Luping Zhou
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Zhi Feng
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Jiangyong He
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Jie Qin
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Congjian Zhao
- Chongqing Engineering Research Center of Medical Electronics and Information Technology, School of Biomedical Engineering and informatics, Chongqing University of Posts and Telecommunications 2 , Chongqing 40065 , China
| | - Lingfei Luo
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University 1 , Chongqing 400715 , China
| | - Li Li
- Research Center of Stem Cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 3 , Chongqing 400714 , China
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13
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Zhang Z, Meng P, Zhang H, Jia Y, Wen Y, Zhang J, Chen Y, Li C, Pan C, Cheng S, Yang X, Yao Y, Liu L, Zhang F. Brain Proteome-Wide Association Study Identifies Candidate Genes that Regulate Protein Abundance Associated with Post-Traumatic Stress Disorder. Genes (Basel) 2022; 13:genes13081341. [PMID: 35893077 PMCID: PMC9332745 DOI: 10.3390/genes13081341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
Although previous genome-wide association studies (GWASs) on post-traumatic stress disorder (PTSD) have identified multiple risk loci, how these loci confer risk of PTSD remains unclear. Through the FUSION pipeline, we integrated two human brain proteome reference datasets (ROS/MAP and Banner) with the PTSD GWAS dataset, respectively, to conduct a proteome-wide association study (PWAS) analysis. Then two transcriptome reference weights (Rnaseq and Splicing) were applied to a transcriptome-wide association study (TWAS) analysis. Finally, the PWAS and TWAS results were investigated through brain imaging analysis. In the PWAS analysis, 8 and 13 candidate genes were identified in the ROS/MAP and Banner reference weight groups, respectively. Examples included ADK (pPWAS-ROS/MAP = 3.00 × 10−5) and C3orf18 (pPWAS-Banner = 7.07 × 10−31). Moreover, the TWAS also detected multiple candidate genes associated with PTSD in two different reference weight groups, including RIMS2 (pTWAS-Splicing = 3.84 × 10−2), CHMP1A (pTWAS-Rnaseq = 5.09 × 10−4), and SIRT5 (pTWAS-Splicing = 4.81 × 10−3). Further comparison of the PWAS and TWAS results in different populations detected the overlapping genes: MADD (pPWAS-Banner = 4.90 × 10−2, pTWAS-Splicing = 1.23 × 10−2) in the total population and GLO1(pPWAS-Banner = 4.89 × 10−3, pTWAS-Rnaseq = 1.41 × 10−3) in females. Brain imaging analysis revealed several different brain imaging phenotypes associated with MADD and GLO1 genes. Our study identified multiple candidate genes associated with PTSD in the proteome and transcriptome levels, which may provide new clues to the pathogenesis of PTSD.
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14
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Phenylalanine impairs insulin signaling and inhibits glucose uptake through modification of IRβ. Nat Commun 2022; 13:4291. [PMID: 35879296 PMCID: PMC9314339 DOI: 10.1038/s41467-022-32000-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/08/2022] [Indexed: 11/09/2022] Open
Abstract
Whether amino acids act on cellular insulin signaling remains unclear, given that increased circulating amino acid levels are associated with the onset of type 2 diabetes (T2D). Here, we report that phenylalanine modifies insulin receptor beta (IRβ) and inactivates insulin signaling and glucose uptake. Mice fed phenylalanine-rich chow or phenylalanine-producing aspartame or overexpressing human phenylalanyl-tRNA synthetase (hFARS) develop insulin resistance and T2D symptoms. Mechanistically, FARS phenylalanylate lysine 1057/1079 of IRβ (F-K1057/1079), inactivating IRβ and preventing insulin from promoting glucose uptake by cells. SIRT1 reverse F-K1057/1079 and counteract the insulin-inactivating effects of hFARS and phenylalanine. F-K1057/1079 and SIRT1 levels in white blood cells from T2D patients are positively and negatively correlated with T2D onset, respectively. Blocking F-K1057/1079 with phenylalaninol sensitizes insulin signaling and relieves T2D symptoms in hFARS-transgenic and db/db mice. These findings shed light on the activation of insulin signaling and T2D progression through inhibition of phenylalanylation. Whether amino acids act on cellular insulin signaling remains unclear. Here, the authors find that phenylalanine modifies insulin receptor beta (IRβ) and inactivates insulin signaling and glucose uptake and positively correlated with T2D onset.
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15
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Leucyl-tRNA synthetase is a tumour suppressor in breast cancer and regulates codon-dependent translation dynamics. Nat Cell Biol 2022; 24:307-315. [PMID: 35288656 PMCID: PMC8977047 DOI: 10.1038/s41556-022-00856-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/27/2022] [Indexed: 12/17/2022]
Abstract
Tumourigenesis and cancer progression require enhanced global protein translation1–3. Such enhanced translation is caused by oncogenic and tumour suppressive events that drive the synthesis and activity of translational machinery4,5. Here we report the surprising observation that leucyl-tRNA synthetase (LARS) becomes repressed during mammary cell transformation and in human breast cancer. Monoallelic genetic deletion of LARS in mouse mammary glands enhanced breast cancer tumour formation and proliferation. LARS repression reduced the abundance of select leucine tRNA isoacceptors, leading to impaired leucine codon-dependent translation of growth suppressive genes including epithelial membrane protein 3 (EMP3) and gamma-glutamyltransferase 5 (GGT5). Our findings uncover a tumour suppressive tRNA synthetase and reveal that dynamic repression of a specific tRNA synthetase—along with its downstream cognate tRNAs—elicits a downstream codon-biased translational gene network response that enhances breast tumour formation and growth.
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16
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Shim JA, Jo Y, Hwang H, Lee SE, Ha D, Lee JH, Kim J, Song P, Lee D, Hong C. Defects in aminoacyl-tRNA synthetase cause partial B and T cell immunodeficiency. Cell Mol Life Sci 2022; 79:87. [PMID: 35067747 PMCID: PMC11071942 DOI: 10.1007/s00018-021-04122-z] [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: 09/22/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 11/29/2022]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are emerging as important regulators in various immune diseases; however, their roles in immune cells remain unclear. In this study, using alanyl-tRNA synthetase (AARS) mutant (sti) mice with neurodegenerative disorder, we investigated the effect of translational fidelity in immune cells. Dysfunctional AARS caused disorders in immune cell responses and cellularity. The impairment was caused by dampened TCR signaling than cytokine signaling. Therefore, sti mutant inhibits TCR signaling, impeding T cell survival and responses. B cell numbers were decreased in sti mice. Despite low B cell cellularity, serum IgM, IgA, and IgE levels were higher in sti mice than in wild-type mice. Misacylation of ARS and the consequent translational infidelity induce disturbances in signaling pathways critical for immune cell survival and responses. Our findings provide a novel mechanism by which translational fidelity might play a critical role in cellular and humoral immune responses.
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Affiliation(s)
- Ju A Shim
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Yuna Jo
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Hyunju Hwang
- Asan Institute for Life Sciences and Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - So Eun Lee
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Dahyeon Ha
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Jun Hwa Lee
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Jayoung Kim
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Parkyong Song
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Dongjun Lee
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea
| | - Changwan Hong
- Department of Anatomy, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea.
- Department of Convergence Medical Science, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea.
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan, 50612, Republic of Korea.
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17
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Huang Q, Xiong H, Tao Z, Yue F, Xiao N. Clinical phenotypes and molecular findings in ten Chinese patients with Kleefstra Syndrome Type 1 due to EHMT1 defects. Eur J Med Genet 2021; 64:104289. [PMID: 34265435 DOI: 10.1016/j.ejmg.2021.104289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 07/03/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Kleefstra syndrome type 1 (KS1, OMIM#610253) is a rare autosomal-dominant Mendelian disorder due to heterozygous mutations in the EHMT1 gene or heterozygous deletion of genomic segment of 9q34.3(9qdel). Neurodevelopmental disorder (NDD), intellectual disability (ID) and childhood-onset hypotonia are the well-known phenotypes of KS1. However, these findings were all investigated based on western patients with KS1. METHODS KS1 patients were diagnosed by genetic tests. The clinical data was collected and the phenotypes were standardized by compared with patients that previously reported. In silico, conservational and protein structural analysis were performed to assessment the missense variants. RESULTS Ten patients from unrelated families were diagnosed as KS1, who all had NDD and seven of them had global developmental delay (GDD) with significant personal-social disabilities. Among the ten patients, only one (1/10) patient showed neonatal or infantile obesity. The other nine patients were heterozygous variations, including three missense mutations (p.Glu235Gly, p.Asp903Gly, and p.Leu943Pro), three frameshifting mutations (p.Asn1106Lysfs*71, p.Asn1055Tyrfs*121, and p.Lys288Argfs*20), one nonsense mutation (p.Arg246*), one slice site mutation (c.3540+2T > C) and one 9q34.3 deletion in gene of EHMT1. Furthermore, missense mutations showed potential pathogenicity analyzed by in silico. CONCLUSION We demonstrated that the clinical features in Chinese patients with KS1 were due to EHMT1 defects. We also reported seven novel variants which enriched the mutation spectrum and provided a good understanding of the pathogenesis of KS1.
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Affiliation(s)
- Qinrong Huang
- Department of Rehabilitation Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, PR China.
| | - Hui Xiong
- Department of Pediatrics, Peking University First Hospital, PR China
| | - Zhe Tao
- Department of Neurology, Dalian Children's Hospital, Dalian Medical University, Liaoning, 116012, PR China
| | - FeiFei Yue
- Department of Pediatrics, The Third Affiliated Hospital of Xinxiang Medical College, PR China
| | - Nong Xiao
- Department of Rehabilitation Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, PR China.
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18
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Wang XD, Lin ZK, Ji SX, Bi SY, Liu WX, Zhang GF, Wan FH, Lü ZC. Molecular Characterization of TRPA Subfamily Genes and Function in Temperature Preference in Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae). Int J Mol Sci 2021; 22:ijms22137157. [PMID: 34281211 PMCID: PMC8268038 DOI: 10.3390/ijms22137157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/20/2021] [Accepted: 06/29/2021] [Indexed: 02/03/2023] Open
Abstract
To reveal the mechanism of temperature preference in Tuta absoluta, one of the top 20 plant pests in the world, we cloned and identified TaTRPA1, TaPain, and TaPyx genes by RACE and bioinformatic analysis, and clarified their expression profiles during different development stages using real-time PCR, and revealed their function in preference temperature by RNAi. The full-length cDNA of TaPain was 3136 bp, with a 2865-bp open reading frame encoding a 259.89-kDa protein; and the partial length cDNA of TaPyx was 2326-bp, with a 2025-bp open reading frame encoding a 193.16-kDa protein. In addition, the expression of TaTRPA1 and TaPyx was significantly lower in larvae than other stages, and it was significantly higher in pupae and newly emerging males for TaPain. After feeding target double-stranded RNA (dsRNA), the preferred temperature decreased 2 °C more than the control group. In conclusion, the results firstly indicated the molecular characterization of TRPA subfamily genes and their key role in temperature perception in T. absoluta, and the study will help us to understand the temperature-sensing mechanism in the pest, and will provide some basis for study of other Lepidoptera insects’ temperature preference. Moreover, it is of great significance in enriching the research progress of “thermos TRP”.
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Affiliation(s)
- Xiao-Di Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
| | - Ze-Kai Lin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
| | - Shun-Xia Ji
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
| | - Si-Yan Bi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
| | - Wan-Xue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
| | - Gui-Fen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
| | - Fang-Hao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhi-Chuang Lü
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (X.-D.W.); (Z.-K.L.); (S.-X.J.); (S.-Y.B.); (W.-X.L.); (G.-F.Z.); (F.-H.W.)
- Correspondence: ; Tel.: +86-10-8210-9572
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Georgescu MM, Islam MZ, Li Y, Traylor J, Nanda A. Novel targetable FGFR2 and FGFR3 alterations in glioblastoma associate with aggressive phenotype and distinct gene expression programs. Acta Neuropathol Commun 2021; 9:69. [PMID: 33853673 PMCID: PMC8048363 DOI: 10.1186/s40478-021-01170-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/27/2021] [Indexed: 02/07/2023] Open
Abstract
Prognostic molecular subgrouping of glioblastoma is an ongoing effort and the current classification includes IDH-wild-type and IDH-mutant entities, the latter showing significantly better prognosis. We performed a comparative integrated analysis of the FGFR glioblastoma subgroup consisting of 5 cases from a prospective 101-patient-cohort. FGFR alterations included FGFR2-TACC2 and FGFR2 amplifications arising in a multifocal IDH-mutant glioblastoma with unexpected 2.5-month patient survival, novel FGFR3 carboxy-terminal duplication and FGFR3-TLN1 fusion, and two previously described FGFR3-TACC3 fusions. The FGFR2 tumors showed additional mutations in SERPINE1/PAI-1 and MMP16, as part of extensive extracellular matrix remodeling programs. Whole transcriptomic analysis revealed common proliferation but distinct morphogenetic gene expression programs that correlated with tumor histology. The kinase program revealed EPHA3, LTK and ALK receptor tyrosine kinase overexpression in individual FGFR tumors. Paradoxically, all FGFR-fused glioblastomas shared strong PI3K and MAPK pathway suppression effected by SPRY, DUSP and AKAP12 inhibitors, whereas the FGFR2-TACC2 tumor elicited also EGFR suppression by ERRFI1 upregulation. This integrated analysis outlined the proliferation and morphogenetic expression programs in FGFR glioblastoma, and identified four novel, clinically targetable FGFR2 and FGFR3 alterations that confer aggressive phenotype and trigger canonical pathway feedback inhibition, with important therapeutic implications.
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Abstract
Among the 20 cytoplasmic aminoacyl-tRNA synthetases (aaRSs), alanyl-tRNA synthetase (AlaRS) has unique features. AlaRS is the only aaRS that exclusively recognizes a single G3:U70 wobble base pair in the acceptor stem of tRNA, which serves as the identity element for both the synthetic and the proofreading activities of the synthetase. The recognition is relaxed during evolution and eukaryotic AlaRS can mis-aminoacylate noncognate tRNAs with a G4:U69 base pair seemingly as a deliberate gain of function for unknown reasons. Unlike other class II aaRSs, dimerization of AlaRS is not necessarily required for aminoacylation possibly due to functional compensations from the C-terminal domain (C-Ala). In contrast to other 19 cytoplasmic aaRSs that append additional domains or motifs to acquire new functions during evolution, the functional expansion of AlaRS is likely achieved through transformations of the existing C-Ala. Given both essential canonical and diverse non-canonical roles of AlaRS, dysfunction of AlaRS leads to neurodegenerative disorders in human and various pathological phenotypes in mouse models. In this review, the uniqueness of AlaRS in both physiological and pathological events is systematically discussed, with a particular focus on its novel functions gained in evolution.
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Affiliation(s)
- Han Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
| | - Litao Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, China
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21
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22
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Han NC, Kelly P, Ibba M. Translational quality control and reprogramming during stress adaptation. Exp Cell Res 2020; 394:112161. [PMID: 32619498 DOI: 10.1016/j.yexcr.2020.112161] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022]
Abstract
Organisms encounter stress throughout their lives, and therefore require the ability to respond rapidly to environmental changes. Although transcriptional responses are crucial for controlling changes in gene expression, regulation at the translational level often allows for a faster response at the protein levels which permits immediate adaptation. The fidelity and robustness of protein synthesis are actively regulated under stress. For example, mistranslation can be beneficial to cells upon environmental changes and also alters cellular stress responses. Additionally, stress modulates both global and selective translational regulation through mechanisms including the change of aminoacyl-tRNA activity, tRNA pool reprogramming and ribosome heterogeneity. In this review, we draw on studies from both the prokaryotic and eukaryotic systems to discuss current findings of cellular adaptation at the level of translation, specifically translational fidelity and activity changes in response to a wide array of environmental stressors including oxidative stress, nutrient depletion, temperature variation, antibiotics and host colonization.
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Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA
| | - Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA.
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23
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Abstract
The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key players in an increasing number of other cellular processes, with far-reaching consequences in health and disease. The biochemical versatility of the synthetases has also proven pivotal in efforts to expand the genetic code, further emphasizing the wide-ranging roles of the aminoacyl-tRNA synthetase family in synthetic and natural biology.
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Affiliation(s)
- Miguel Angel Rubio Gomez
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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24
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Mori N. [Brain and Neuronal Aging: Aged Brain Controls via Gene Expression Fidelity and Master Regulatory Factors]. YAKUGAKU ZASSHI 2020; 140:395-404. [PMID: 32115559 DOI: 10.1248/yakushi.19-00193-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Providing plausible strategies for brain aging protection should be a critical concern for countries with large elderly populations including Japan. Age-related cognitive impairments and movement disorders, such as Alzheimer's and Parkinson's diseases, are caused by neurodegeneration that primarily initiates in the hippocampus and the midbrain substantia nigra, respectively. Neurons are postmitotic, and therefore, the accuracy of cellular metabolism should be crucial for maintaining neural functions throughout their life. Thus accuracy of protein synthesis is a critical concern in discussing mechanisms of aging. The essence of the so-called "error catastrophe theory" of aging was on the fidelity of ribosomal translation and/or aminoacylation of tRNA. There is evidence that reduced protein synthesis accuracy results in neurodegeneration. Similarly, reduced proteostasis via autophagy and proteasomes in aging is crucial for protein quality control and well documented as a risk for aging. In both neurodegeneration and protein quality controls, various proteins are involved in their regulation, but recent evidence suggests that repressor element-1 silencing transcription factor (REST) could be a master regulatory protein that is crucial for orchestrating the neural protecting events in human brain aging. REST is induced in the aged brain, and protects neurons against oxidative stress and protein toxicity. Interestingly, REST is identical with neuron-restrictive silencer factor (NRSF), the master regulator of neural development. Thus NRSF/REST play important roles in both neurogenesis and neurodegeneration. In this review, I summarize the interesting scientific crossover, and discuss the potential use of NRSF/REST as a pharmaceutical target for controlling aging, particularly in relation to brain aging.
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Affiliation(s)
- Nozomu Mori
- Department of Anatomy and Neurobiology, Nagasaki University School of Medicine
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25
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Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for protein synthesis with evolutionarily conserved enzymatic mechanisms. Despite their similarity across organisms, scientists have been able to generate effective anti-infective agents based on the structural differences in the catalytic clefts of ARSs from pathogens and humans. However, recent genomic, proteomic and functionomic advances have unveiled unexpected disease-associated mutations and altered expression, secretion and interactions in human ARSs, revealing hidden biological functions beyond their catalytic roles in protein synthesis. These studies have also brought to light their potential as a rich and unexplored source for new therapeutic targets and agents through multiple avenues, including direct targeting of the catalytic sites, controlling disease-associated protein-protein interactions and developing novel biologics from the secreted ARS proteins or their parts. This Review addresses the emerging biology and therapeutic applications of human ARSs in diseases including autoimmune and rare diseases, and cancer.
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26
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Martin PB, Hicks AN, Holbrook SE, Cox GA. Overlapping spectrums: The clinicogenetic commonalities between Charcot-Marie-Tooth and other neurodegenerative diseases. Brain Res 2020; 1727:146532. [PMID: 31678418 PMCID: PMC6939129 DOI: 10.1016/j.brainres.2019.146532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022]
Abstract
Charcot-Marie-Tooth (CMT) disease is a progressive and heterogeneous inherited peripheral neuropathy. A myriad of genetic factors have been identified that contribute to the degeneration of motor and sensory axons in a length-dependent manner. Emerging biological themes underlying disease include defects in axonal trafficking, dysfunction in RNA metabolism and protein homeostasis, as well deficits in the cellular stress response. Moreover, genetic contributions to CMT can have overlap with other neuropathies, motor neuron diseases (MNDs) and neurodegenerative disorders. Recent progress in understanding the molecular biology of CMT and overlapping syndromes aids in the search for necessary therapeutic targets.
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Affiliation(s)
- Paige B Martin
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Amy N Hicks
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Sarah E Holbrook
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Gregory A Cox
- The Jackson Laboratory, Bar Harbor, ME 04609, USA; Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA.
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27
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Han NC, Bullwinkle TJ, Loeb KF, Faull KF, Mohler K, Rinehart J, Ibba M. The mechanism of β-N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49898-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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28
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Han NC, Bullwinkle TJ, Loeb KF, Faull KF, Mohler K, Rinehart J, Ibba M. The mechanism of β- N-methylamino-l-alanine inhibition of tRNA aminoacylation and its impact on misincorporation. J Biol Chem 2019; 295:1402-1410. [PMID: 31862734 DOI: 10.1074/jbc.ra119.011714] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/10/2019] [Indexed: 11/06/2022] Open
Abstract
β-N-methylamino-l-alanine (BMAA) is a nonproteinogenic amino acid that has been associated with neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and Alzheimer's disease (AD). BMAA has been found in human protein extracts; however, the mechanism by which it enters the proteome is still unclear. It has been suggested that BMAA is misincorporated at serine codons during protein synthesis, but direct evidence of its cotranslational incorporation is currently lacking. Here, using LC-MS-purified BMAA and several biochemical assays, we sought to determine whether any aminoacyl-tRNA synthetase (aaRS) utilizes BMAA as a substrate for aminoacylation. Despite BMAA's previously predicted misincorporation at serine codons, following a screen for amino acid activation in ATP/PPi exchange assays, we observed that BMAA is not a substrate for human seryl-tRNA synthetase (SerRS). Instead, we observed that BMAA is a substrate for human alanyl-tRNA synthetase (AlaRS) and can form BMAA-tRNAAla by escaping from the intrinsic AlaRS proofreading activity. Furthermore, we found that BMAA inhibits both the cognate amino acid activation and the editing functions of AlaRS. Our results reveal that, in addition to being misincorporated during translation, BMAA may be able to disrupt the integrity of protein synthesis through multiple different mechanisms.
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Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
| | - Tammy J Bullwinkle
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
| | - Kaeli F Loeb
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry & Biobehavioral Sciences, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California 90024-1759
| | - Kyle Mohler
- Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520.,Systems Biology Institute, Yale University, New Haven, Connecticut 06520
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology, Yale University, New Haven, Connecticut 06520.,Systems Biology Institute, Yale University, New Haven, Connecticut 06520
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43220
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Alanyl-tRNA Synthetase Quality Control Prevents Global Dysregulation of the Escherichia coli Proteome. mBio 2019; 10:mBio.02921-19. [PMID: 31848288 PMCID: PMC6918089 DOI: 10.1128/mbio.02921-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mechanisms have evolved to prevent errors in replication, transcription, and translation of genetic material, with translational errors occurring most frequently. Errors in protein synthesis can occur at two steps, during tRNA aminoacylation and ribosome decoding. Recent advances in protein mass spectrometry have indicated that previous reports of translational errors have potentially underestimated the frequency of these events, but also that the majority of translational errors occur during ribosomal decoding, suggesting that aminoacylation errors are evolutionarily less tolerated. Despite that interpretation, there is evidence that some aminoacylation errors may be regulated, and thus provide a benefit to the cell, while others are clearly detrimental. Here, we show that while it has been suggested that regulated Thr-to-Ser substitutions may be beneficial, there is a threshold beyond which these errors are detrimental. In contrast, we show that errors mediated by alanyl-tRNA synthetase (AlaRS) are not well tolerated and induce a global stress response that leads to gross perturbation of the Escherichia coli proteome, with potentially catastrophic effects on fitness and viability. Tolerance for Ala mistranslation appears to be much lower than with other translational errors, consistent with previous reports of multiple proofreading mechanisms targeting mischarged tRNAAla These results demonstrate the essential role of aminoacyl-tRNA proofreading in optimizing cellular fitness and suggest that any potentially beneficial effects of mistranslation may be confined to specific amino acid substitutions.IMPORTANCE Errors in protein synthesis have historically been assumed to be detrimental to the cell. While there are many reports that translational errors are consequential, there is a growing body of evidence that some mistranslation events may be tolerated or even beneficial. Using two models of mistranslation, we compare the direct phenotypic effects of these events in Escherichia coli This work provides insight into the threshold for tolerance of specific mistranslation events that were previously predicted to be broadly neutral to proteome integrity. Furthermore, these data reveal the effects of mistranslation beyond the general unfolded stress response, leading to global translational reprogramming.
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Park H, Kim T, Kim J, Yamamoto Y, Tanaka-Yamamoto K. Inputs from Sequentially Developed Parallel Fibers Are Required for Cerebellar Organization. Cell Rep 2019; 28:2939-2954.e5. [DOI: 10.1016/j.celrep.2019.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/10/2019] [Accepted: 07/30/2019] [Indexed: 11/15/2022] Open
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31
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Levi O, Garin S, Arava Y. RNA mimicry in post-transcriptional regulation by aminoacyl tRNA synthetases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1564. [PMID: 31414576 DOI: 10.1002/wrna.1564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/10/2019] [Accepted: 07/25/2019] [Indexed: 12/15/2022]
Abstract
Aminoacyl tRNA synthetases (aaRS) are well studied for their roles in tRNA charging with cognate amino acid. Nevertheless, numerous lines of evidence indicate that these proteins have roles other than tRNA charging. These include coordination of cellular signaling cascades, induction of cytokines outside the cell and transcription regulation. Herein, we focus on their roles in post-transcriptional regulation of mRNA expression. We describe functions that are related to antitermination of transcription, RNA splicing and mRNA translation. Cases were recognition of mRNA by the aaRS involves recognition of tRNA-like structures are described. Such recognition may be achieved by repurposing tRNA-binding domains or through domains added to the aaRS later in evolution. Furthermore, we describe cases in which binding by aaRS is implicated in autogenous regulation of expression. Overall, we propose RNA-mimicry as a common mode of interaction between aaRS and mRNA which allows efficient expression regulation. This article is categorized under: RNA Processing > tRNA Processing RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation.
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Affiliation(s)
- Ofri Levi
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Shahar Garin
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Yoav Arava
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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32
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Jakubowski H. Homocysteine Modification in Protein Structure/Function and Human Disease. Physiol Rev 2019; 99:555-604. [PMID: 30427275 DOI: 10.1152/physrev.00003.2018] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Epidemiological studies established that elevated homocysteine, an important intermediate in folate, vitamin B12, and one carbon metabolism, is associated with poor health, including heart and brain diseases. Earlier studies show that patients with severe hyperhomocysteinemia, first identified in the 1960s, exhibit neurological and cardiovascular abnormalities and premature death due to vascular complications. Although homocysteine is considered to be a nonprotein amino acid, studies over the past 2 decades have led to discoveries of protein-related homocysteine metabolism and mechanisms by which homocysteine can become a component of proteins. Homocysteine-containing proteins lose their biological function and acquire cytotoxic, proinflammatory, proatherothrombotic, and proneuropathic properties, which can account for the various disease phenotypes associated with hyperhomocysteinemia. This review describes mechanisms by which hyperhomocysteinemia affects cellular proteostasis, provides a comprehensive account of the biological chemistry of homocysteine-containing proteins, and discusses pathophysiological consequences and clinical implications of their formation.
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Affiliation(s)
- Hieronim Jakubowski
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, International Center for Public Health , Newark, New Jersey ; and Department of Biochemistry and Biotechnology, Poznań University of Life Sciences , Poznań , Poland
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33
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Cell biology in support of neurological research: 2018 highlights. Lancet Neurol 2018; 18:19-20. [PMID: 30563677 DOI: 10.1016/s1474-4422(18)30462-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 11/24/2022]
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