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Khan D, Ramachandiran I, Vasu K, China A, Khan K, Cumbo F, Halawani D, Terenzi F, Zin I, Long B, Costain G, Blaser S, Carnevale A, Gogonea V, Dutta R, Blankenberg D, Yoon G, Fox PL. Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6A site accessibility. Nat Commun 2024; 15:4284. [PMID: 38769304 PMCID: PMC11106242 DOI: 10.1038/s41467-024-48549-x] [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: 10/15/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is an autosomal recessive disorder characterized by defective central nervous system myelination. Exome sequencing of two siblings with severe cognitive and motor impairment and progressive hypomyelination characteristic of HLD revealed homozygosity for a missense single-nucleotide variant (SNV) in EPRS1 (c.4444 C > A; p.Pro1482Thr), encoding glutamyl-prolyl-tRNA synthetase, consistent with HLD15. Patient lymphoblastoid cell lines express markedly reduced EPRS1 protein due to dual defects in nuclear export and cytoplasmic translation of variant EPRS1 mRNA. Variant mRNA exhibits reduced METTL3 methyltransferase-mediated writing of N6-methyladenosine (m6A) and reduced reading by YTHDC1 and YTHDF1/3 required for efficient mRNA nuclear export and translation, respectively. In contrast to current models, the variant does not alter the sequence of m6A target sites, but instead reduces their accessibility for modification. The defect was rescued by antisense morpholinos predicted to expose m6A sites on target EPRS1 mRNA, or by m6A modification of the mRNA by METTL3-dCas13b, a targeted RNA methylation editor. Our bioinformatic analysis predicts widespread occurrence of SNVs associated with human health and disease that similarly alter accessibility of distal mRNA m6A sites. These results reveal a new RNA-dependent etiologic mechanism by which SNVs can influence gene expression and disease, consequently generating opportunities for personalized, RNA-based therapeutics targeting these disorders.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fabio Cumbo
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Dalia Halawani
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Isaac Zin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Briana Long
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Amanda Carnevale
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Grace Yoon
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Department of Paediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA.
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Wang W, Ma C, Zhang Q, Jiang Y. TMT-labeled quantitative malonylome analysis on the longissimus dorsi muscle of Laiwu pigs reveals the role of ACOT7 in fat deposition. J Proteomics 2024; 298:105129. [PMID: 38395145 DOI: 10.1016/j.jprot.2024.105129] [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: 11/29/2023] [Revised: 01/29/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by an extremely high level of intramuscular fat (IMF) content (9% ∼ 12%), but the regulatory mechanism underlying intramuscular fat deposition in skeletal muscle is still unknown. In this study, the TMT-labeled quantitative malonylome of the longissimus dorsi muscle in Laiwu pigs at the fastest IMF deposition stage (240 d vs 120 d) was compared to analyze the molecular mechanism of IMF variation in pigs. In Laiwu pigs aged 240 days/120 days, we identified 291 malonylated lysine sites across 188 proteins in the longissimus dorsi muscle. Among these, 38 sites across 31 proteins exhibited differential malonylation. Annotation analysis and enrichment analysis were performed for differentially malonylated proteins (DMPs). These DMPs were mainly clustered into 12 GO functional categories accounting for 5 biological processes, 4 cellular components and 3 molecular functions, and 2 signaling pathways by KEGG enrichment analysis. The function of differentially malonylated protein ACOT7 in the process of fat deposition was further investigated during the differentiation of 3 T3-L1 cells. The results showed that the protein level of ACOT7 in 3 T3-L1 cells decreased but the malonylated level of ACOT7 increased significantly. The malonyl-CoA that is synthesized by ACSF3 affected the malonylation level of ACOT7 in 3 T3-L1 cells. SIGNIFICANCE: The intramuscular fat (IMF) content, by affecting sensory quality traits of meat, such as tenderness, flavor and juiciness, plays an important role in meat quality. Using TMT-based quantitative malonylated proteome analysis, we identified malonylated proteins in LD muscle samples in two stages (120 d and 240 d) of development and further identified differentially malonylated proteins, such as SLC25A4, ANXA5, TPM3 and ACOT7, that are associated with intramuscular fat deposition and fat metabolism in pigs. These differentially malonylated proteins could serve as candidates for elucidating the molecular mechanism of IMF deposition in pigs. In addition, we found that the malonyl-CoA in 3 T3-L1 cells is mainly synthesized by ACSF3, affecting the malonylated level of ACOT7. The study provides some data concerning the role of protein malonylation in regulating the variation in porcine IMF content.
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Affiliation(s)
- Wenlei Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Taian 271018, PR China.
| | - Cai Ma
- Department of Medical Genetics and Cell Biology, Binzhou Medical University, No. 346 Guanhai Road, Yantai 264003, PR China.
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Taian 271018, PR China.
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61 Daizong Street, Taian 271018, PR China.
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3
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Zhang P, Catterson JH, Grönke S, Partridge L. Inhibition of S6K lowers age-related inflammation and increases lifespan through the endolysosomal system. NATURE AGING 2024; 4:491-509. [PMID: 38413780 PMCID: PMC11031405 DOI: 10.1038/s43587-024-00578-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Suppression of target of rapamycin complex 1 (TORC1) by rapamycin ameliorates aging in diverse species. S6 kinase (S6K) is an essential mediator, but the mechanisms involved are unclear. Here we show that activation of S6K specifically in Drosophila fat-body blocked extension of lifespan by rapamycin, induced accumulation of multilamellar lysosomes and blocked age-associated hyperactivation of the NF-κB-like immune deficiency (IMD) pathway, indicative of reduced inflammaging. Syntaxin 13 mediated the effects of TORC1-S6K signaling on lysosome morphology and inflammaging, suggesting they may be linked. Inflammaging depended on the IMD receptor regulatory isoform PGRP-LC, and repression of the IMD pathway from midlife extended lifespan. Age-related inflammaging was higher in females than in males and was not lowered in males by rapamycin treatment or lowered S6K. Rapamycin treatment also elevated Syntaxin 12/13 levels in mouse liver and prevented age-related increase in noncanonical NF-κB signaling, suggesting that the effect of TORC1 on inflammaging is conserved from flies to mammals.
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Affiliation(s)
- Pingze Zhang
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - James H Catterson
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK
- Centre for Discovery Brain Sciences, UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | | | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, UK.
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4
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Ipas H, Gouws EB, Abell NS, Chiou PC, Devanathan SK, Hervé S, Lee S, Mercado M, Reinsborough C, Halabelian L, Arrowsmith CH, Xhemalçe B. ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation. EMBO Rep 2024; 25:1570-1588. [PMID: 38263329 PMCID: PMC10933402 DOI: 10.1038/s44319-024-00059-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: 11/27/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
5'-end modifications play key roles in determining RNA fates. Phospho-methylation is a noncanonical cap occurring on either 5'-PPP or 5'-P ends. We used ChemRAP, in which affinity purification of cellular proteins with chemically synthesized modified RNAs is coupled to quantitative proteomics, to identify 5'-Pme "readers". We show that 5'-Pme is directly recognized by EPRS, the central subunit of the multisynthetase complex (MSC), through its linker domain, which has previously been involved in key noncanonical EPRS and MSC functions. We further determine that the 5'-Pme writer BCDIN3D regulates the binding of EPRS to specific mRNAs, either at coding regions rich in MSC codons, or around start codons. In the case of LRPPRC (leucine-rich pentatricopeptide repeat containing), a nuclear-encoded mitochondrial protein associated with the French Canadian Leigh syndrome, BCDIN3D deficiency abolishes binding of EPRS around its mRNA start codon, increases its translation but ultimately results in LRPPRC mislocalization. Overall, our results suggest that BCDIN3D may regulate the translation of specific mRNA via RNA-5'-Pme.
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Affiliation(s)
- Hélène Ipas
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Ellen B Gouws
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Nathan S Abell
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Po-Chin Chiou
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Sravan K Devanathan
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Solène Hervé
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Sidae Lee
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Marvin Mercado
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Calder Reinsborough
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA
| | - Levon Halabelian
- Structural Genomics Consortium, and Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, and Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Blerta Xhemalçe
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, 78712, Austin, TX, USA.
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5
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Yoon I, Kim U, Choi J, Kim S. Disease association and therapeutic routes of aminoacyl-tRNA synthetases. Trends Mol Med 2024; 30:89-105. [PMID: 37949787 DOI: 10.1016/j.molmed.2023.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are enzymes that catalyze the ligation of amino acids to tRNAs for translation. Beyond their traditional role in translation, ARSs have acquired regulatory functions in various biological processes (epi-translational functions). With their dual-edged activities, aberrant expression, secretion, and mutations of ARSs are associated with human diseases, including cancer, autoimmune diseases, and neurological diseases. The increasing numbers of newly unveiled activities and disease associations of ARSs have spurred interest in novel drug development, targeting disease-related catalytic and noncatalytic activities of ARSs as well as harnessing ARSs as sources for biological therapeutics. This review speculates how the translational and epi-translational activities of ARSs can be related and describes how their activities can be linked to diseases and drug discovery.
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Affiliation(s)
- Ina Yoon
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Uijoo Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Jaeyoung Choi
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea
| | - Sunghoon Kim
- Institute for Artificial Intelligence and Biomedical Research, Medicinal Bioconvergence Research Center, College of Pharmacy, Yonsei University, Incheon 21983, Republic of Korea; College of Medicine, Gangnam Severance Hospital, Yonsei University, Seoul 06273, Republic of Korea; Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Incheon 21983, Republic of Korea.
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6
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Wu J, Hollinger J, Bonanno E, Jiang F, Yao P. Cardiomyocyte-Specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy. Cells 2023; 13:35. [PMID: 38201239 PMCID: PMC10778562 DOI: 10.3390/cells13010035] [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: 09/17/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Glutamyl-prolyl-tRNA synthetase (EPRS1), an aminoacyl-tRNA synthetase (ARS) ligating glutamic acid and proline to their corresponding tRNAs, plays an essential role in decoding proline codons during translation elongation. The physiological function of EPRS1 in cardiomyocytes (CMs) and the potential effects of the CM-specific loss of Eprs1 remain unknown. Here, we found that heterozygous Eprs1 knockout in CMs does not cause any significant changes in CM hypertrophy induced by pressure overload, while homozygous knockout leads to dilated cardiomyopathy, heart failure, and lethality at around 1 month after Eprs1 deletion. The transcriptomic profiling of early-stage Eprs1 knockout hearts suggests a significantly decreased expression of multiple ion channel genes and an increased gene expression in proapoptotic pathways and integrated stress response. Proteomic analysis shows decreased protein expression in multi-aminoacyl-tRNA synthetase complex components, fatty acids, and branched-chain amino acid metabolic enzymes, as well as a compensatory increase in cytosolic translation machine-related proteins. Immunoblot analysis indicates that multiple proline-rich proteins were reduced at the early stage, which might contribute to the cardiac dysfunction of Eprs1 knockout mice. Taken together, this study demonstrates the physiological and molecular outcomes of loss-of-function of Eprs1 in vivo and provides valuable insights into the potential side effects on CMs, resulting from the EPRS1-targeting therapeutic approach.
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Affiliation(s)
- Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA; (J.W.); (J.H.)
| | - Jared Hollinger
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA; (J.W.); (J.H.)
| | - Emily Bonanno
- Undergraduate Program in Biology and Medicine, Department of Biological Sciences: Biochemistry, University of Rochester, Rochester, NY 14620, USA;
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA; (J.W.); (J.H.)
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA; (J.W.); (J.H.)
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
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7
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Wang Y, Wang G, Hu S, Yin C, Zhao P, Zhou X, Shao S, Liu R, Hu W, Liu GL, Ke W, Song Z. FARSB Facilitates Hepatocellular Carcinoma Progression by Activating the mTORC1 Signaling Pathway. Int J Mol Sci 2023; 24:16709. [PMID: 38069034 PMCID: PMC10706030 DOI: 10.3390/ijms242316709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignant tumor with high mortality. Human phenylalanine tRNA synthetase (PheRS) comprises two α catalytic subunits encoded by the FARSA gene and two β regulatory subunits encoded by the FARSB gene. FARSB is a potential oncogene, but no experimental data show the relationship between FARSB and HCC progression. We found that the high expression of FARSB in liver cancer is closely related to patients' low survival and poor prognosis. In liver cancer cells, the mRNA and protein expression levels of FARSB are increased and promote cell proliferation and migration. Mechanistically, FARSB activates the mTOR complex 1 (mTORC1) signaling pathway by binding to the component Raptor of the mTORC1 complex to play a role in promoting cancer. In addition, we found that FARSB can inhibit erastin-induced ferroptosis by regulating the mTOR signaling pathway, which may be another mechanism by which FARSB promotes HCC progression. In summary, FARSB promotes HCC progression and is associated with the poor prognosis of patients. FARSB is expected to be a biomarker for early screening and treatment of HCC.
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Affiliation(s)
- Yaofeng Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Gengqiao Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Shaobo Hu
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Chuanzheng Yin
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Peng Zhao
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Xing Zhou
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Shuyu Shao
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Ran Liu
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Wenjun Hu
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.H.); (G.L.L.)
| | - Gang Logan Liu
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.H.); (G.L.L.)
| | - Wenbo Ke
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
| | - Zifang Song
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (Y.W.); (G.W.); (S.H.); (C.Y.); (P.Z.); (X.Z.); (S.S.); (R.L.)
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8
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Lee EY, Hwang J, Kim MH. Phosphocode-dependent glutamyl-prolyl-tRNA synthetase 1 signaling in immunity, metabolism, and disease. Exp Mol Med 2023; 55:2116-2126. [PMID: 37779151 PMCID: PMC10618286 DOI: 10.1038/s12276-023-01094-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 10/03/2023] Open
Abstract
Ubiquitously expressed aminoacyl-tRNA synthetases play essential roles in decoding genetic information required for protein synthesis in every living species. Growing evidence suggests that they also function as crossover mediators of multiple biological processes required for homeostasis. In humans, eight cytoplasmic tRNA synthetases form a central machinery called the multi-tRNA synthetase complex (MSC). The formation of MSCs appears to be essential for life, although the role of MSCs remains unclear. Glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is the most evolutionarily derived component within the MSC that plays a critical role in immunity and metabolism (beyond its catalytic role in translation) via stimulus-dependent phosphorylation events. This review focuses on the role of EPRS1 signaling in inflammation resolution and metabolic modulation. The involvement of EPRS1 in diseases such as cancer is also discussed.
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Affiliation(s)
- Eun-Young Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Jungwon Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
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Wu J, Hollinger J, Bonanno E, Jiang F, Yao P. Cardiomyocyte-specific Loss of Glutamyl-prolyl-tRNA Synthetase Leads to Disturbed Protein Homeostasis and Dilated Cardiomyopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.19.558539. [PMID: 37790482 PMCID: PMC10542137 DOI: 10.1101/2023.09.19.558539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Glutamyl-prolyl-tRNA synthetase (EPRS1), an aminoacyl-tRNA synthetase (ARS) ligating glutamic acid and proline to their corresponding tRNAs, plays an essential role in decoding proline codons during translation elongation. The physiological function of EPRS1 in cardiomyocytes (CMs) and the potential effects of CM-specific loss of EPRS1 remain unknown. Here, we found that heterozygous Eprs1 knockout in CMs does not cause any significant changes in CM hypertrophy induced by pressure overload, while homozygous knockout leads to dilated cardiomyopathy, heart failure, and lethality at around 1 month after Eprs1 deletion. Transcriptomic profiling of early-stage Eprs1 knockout hearts suggests a significantly decreased expression of multiple ion channel genes and an increased gene expression in proapoptotic pathways and integrated stress response. Proteomic analysis shows decreased protein expression of multi-aminoacyl-tRNA synthetase complex components, fatty acid, and branched-chain amino acid metabolic enzymes, as well as a compensatory increase in cytosolic translation machine-related proteins. Immunoblot analysis indicated that multiple proline-rich proteins were reduced at the early stage, which might contribute to cardiac dysfunction of Eprs1 knockout mice. Taken together, this study demonstrates the physiological and molecular outcome of loss-of-function of EPRS1 in vivo and provides valuable insights into the potential side effects on CMs resulting from the EPRS1-targeting therapeutic approach.
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Affiliation(s)
- Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
| | - Jared Hollinger
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
| | - Emily Bonanno
- Undergraduate Program in Biology and Medicine, Department of Biological Sciences: Biochemistry, University of Rochester, Rochester, New York 14620 USA
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
- Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
- The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
- The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, New York 14642 USA
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10
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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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11
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Wang C, Jiang S, Cheng J, Wang C, Guo M. Deciphering the difference of casein fraction in human milk associated with infant gender using quantitative proteomics. Int J Biol Macromol 2023; 247:125796. [PMID: 37442503 DOI: 10.1016/j.ijbiomac.2023.125796] [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: 04/18/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
Human milk is an ideal natural food for infants, and the infant's gender may have impact on protein composition of breast milk. In this study, we used 4D label-free quantitative proteomics techniques to identify and quantitatively analyze casein fraction in breast milk secreted for male and female infants. The results showed that a total of 2064 proteins were identified in human milk, and 95 of them were differentially abundant proteins. Compared to breast milk secreted by mothers of female infants, 21 proteins were up-regulated, and 59 proteins were down-regulated in breast milk secreted by mothers of male infants. The most abundant domain among the differentially abundant proteins was the immunoglobulin V-set domain, which may be involved in immune regulation. Gene Ontology functional analysis revealed that, the main biological processes, molecular functions, and cellular components corresponded to cellular process, binding, and cell part, respectively. The Kyoto Encyclopedia of Genes and Genomes pathways were mainly associated with human diseases and metabolism, with biosynthesis of cofactors being the most involved pathway. The results contribute to our understanding of the composition of casein in breast milk, and may provide information about the nutritional differences in breast milk from mothers of newborns of different genders.
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Affiliation(s)
- Ce Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China; Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Shilong Jiang
- R&D Center, Heilongjiang Feihe Dairy Co., Ltd, Beijing, China
| | - Jianjun Cheng
- Dairy Science Laboratory, Northeast Agricultural University, Harbin 150030, China
| | - Cuina Wang
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Mingruo Guo
- Dairy Science Laboratory, Northeast Agricultural University, Harbin 150030, China; Department of Nutrition and Food Sciences, College of Agriculture and Life Sciences, University of Vermont, Burlington, VT 05405, USA.
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12
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Glassman I, Le N, Asif A, Goulding A, Alcantara CA, Vu A, Chorbajian A, Mirhosseini M, Singh M, Venketaraman V. The Role of Obesity in Breast Cancer Pathogenesis. Cells 2023; 12:2061. [PMID: 37626871 PMCID: PMC10453206 DOI: 10.3390/cells12162061] [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: 05/22/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Research has shown that obesity increases the risk for type 2 diabetes mellitus (Type 2 DM) by promoting insulin resistance, increases serum estrogen levels by the upregulation of aromatase, and promotes the release of reactive oxygen species (ROS) by macrophages. Increased circulating glucose has been shown to activate mammalian target of rapamycin (mTOR), a significant signaling pathway in breast cancer pathogenesis. Estrogen plays an instrumental role in estrogen-receptor-positive breast cancers. The role of ROS in breast cancer warrants continued investigation, in relation to both pathogenesis and treatment of breast cancer. We aim to review the role of obesity in breast cancer pathogenesis and novel therapies mediating obesity-associated breast cancer development. We explore the association between body mass index (BMI) and breast cancer incidence and the mechanisms by which oxidative stress modulates breast cancer pathogenesis. We discuss the role of glutathione, a ubiquitous antioxidant, in breast cancer therapy. Lastly, we review breast cancer therapies targeting mTOR signaling, leptin signaling, blood sugar reduction, and novel immunotherapy targets.
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Affiliation(s)
- Ira Glassman
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Nghia Le
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Aamna Asif
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Anabel Goulding
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Cheldon Ann Alcantara
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Annie Vu
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Abraham Chorbajian
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Mercedeh Mirhosseini
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
| | - Manpreet Singh
- Corona Regional Medical Center, Department of Emergency Medicine, Corona, CA 92882, USA
| | - Vishwanath Venketaraman
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA (N.L.); (A.A.); (C.A.A.); (M.M.)
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13
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Desai H, Ofori S, Boatner L, Yu F, Villanueva M, Ung N, Nesvizhskii AI, Backus K. Multi-omic stratification of the missense variant cysteinome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.12.553095. [PMID: 37645963 PMCID: PMC10461992 DOI: 10.1101/2023.08.12.553095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Cancer genomes are rife with genetic variants; one key outcome of this variation is gain-ofcysteine, which is the most frequently acquired amino acid due to missense variants in COSMIC. Acquired cysteines are both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain uncharacterized. Here, we pair cysteine chemoproteomics-a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues-with genomics to reveal the hidden landscape of cysteine acquisition. For both cancer and healthy genomes, we find that cysteine acquisition is a ubiquitous consequence of genetic variation that is further elevated in the context of decreased DNA repair. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNA-seq data, with a customized 2-stage false discovery rate (FDR) error controlled proteomic search, further enhanced with a user-friendly FragPipe interface. Integration of CADD predictions of deleteriousness revealed marked enrichment for likely damaging variants that result in acquisition of cysteine. By deploying chemoproteogenomics across eleven cell lines, we identify 116 gain-of-cysteines, of which 10 were liganded by electrophilic druglike molecules. Reference cysteines proximal to missense variants were also found to be pervasive, 791 in total, supporting heretofore untapped opportunities for proteoform-specific chemical probe development campaigns. As chemoproteogenomics is further distinguished by sample-matched combinatorial variant databases and compatible with redox proteomics and small molecule screening, we expect widespread utility in guiding proteoform-specific biology and therapeutic discovery.
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Affiliation(s)
- Heta Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Samuel Ofori
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Nicholas Ung
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Keriann Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
- DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
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14
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Merat R. The human antigen R as an actionable super-hub within the network of cancer cell persistency and plasticity. Transl Oncol 2023; 35:101722. [PMID: 37352624 DOI: 10.1016/j.tranon.2023.101722] [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: 04/07/2023] [Revised: 05/30/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023] Open
Abstract
In this perspective article, a clinically inspired phenotype-driven experimental approach is put forward to address the challenge of the adaptive response of solid cancers to small-molecule targeted therapies. A list of conditions is derived, including an experimental quantitative assessment of cell plasticity and an information theory-based detection of in vivo dependencies, for the discovery of post-transcriptional druggable mechanisms capable of preventing at multiple levels the emergence of plastic dedifferentiated slow-proliferating cells. The approach is illustrated by the author's own work in the example case of the adaptive response of BRAFV600-melanoma to BRAF inhibition. A bench-to-bedside and back to bench effort leads to a therapeutic strategy in which the inhibition of the baseline activity of the interferon-γ-activated inhibitor of translation (GAIT) complex, incriminated in the expression insufficiency of the RNA-binding protein HuR in a minority of cells, results in the suppression of the plastic, intermittently slow-proliferating cells involved in the adaptive response. A similar approach is recommended for the validation of other classes of mechanisms that we seek to modulate to overcome this complex challenge of modern cancer therapy.
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Affiliation(s)
- Rastine Merat
- Dermato-Oncology Unit, Division of Dermatology, Geneva University Hospitals, Switzerland; Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Switzerland.
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15
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Khan D, Terenzi F, Liu G, Ghosh PK, Ye F, Nguyen K, China A, Ramachandiran I, Chakraborty S, Stefan J, Khan K, Vasu K, Dong F, Willard B, Karn J, Gack MU, Fox PL. A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon. Nat Commun 2023; 14:3385. [PMID: 37296097 PMCID: PMC10250186 DOI: 10.1038/s41467-023-39091-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, generates multiple protein-coding, subgenomic RNAs (sgRNAs) from a longer genomic RNA, all bearing identical termini with poorly understood roles in regulating viral gene expression. Insulin and interferon-gamma, two host-derived, stress-related agents, and virus spike protein, induce binding of glutamyl-prolyl-tRNA synthetase (EPRS1), within an unconventional, tetra-aminoacyl-tRNA synthetase complex, to the sgRNA 3'-end thereby enhancing sgRNA expression. We identify an EPRS1-binding sarbecoviral pan-end activating RNA (SPEAR) element in the 3'-end of viral RNAs driving agonist-induction. Translation of another co-terminal 3'-end feature, ORF10, is necessary for SPEAR-mediated induction, independent of Orf10 protein expression. The SPEAR element enhances viral programmed ribosomal frameshifting, thereby expanding its functionality. By co-opting noncanonical activities of a family of essential host proteins, the virus establishes a post-transcriptional regulon stimulating global viral RNA translation. A SPEAR-targeting strategy markedly reduces SARS-CoV-2 titer, suggesting a pan-sarbecoviral therapeutic modality.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - GuanQun Liu
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Prabar K Ghosh
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Fengchun Ye
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Kien Nguyen
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Shruti Chakraborty
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jennifer Stefan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Franklin Dong
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Belinda Willard
- Lerner Research Institute Proteomics and Metabolomics Core, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Michaela U Gack
- Florida Research and Innovation Center, Cleveland Clinic Foundation, Port St. Lucie, FL, 34987, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
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16
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Mannick JB, Lamming DW. Targeting the biology of aging with mTOR inhibitors. NATURE AGING 2023; 3:642-660. [PMID: 37142830 PMCID: PMC10330278 DOI: 10.1038/s43587-023-00416-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/07/2023] [Indexed: 05/06/2023]
Abstract
Inhibition of the protein kinase mechanistic target of rapamycin (mTOR) with the Food and Drug Administration (FDA)-approved therapeutic rapamycin promotes health and longevity in diverse model organisms. More recently, specific inhibition of mTORC1 to treat aging-related conditions has become the goal of basic and translational scientists, clinicians and biotechnology companies. Here, we review the effects of rapamycin on the longevity and survival of both wild-type mice and mouse models of human diseases. We discuss recent clinical trials that have explored whether existing mTOR inhibitors can safely prevent, delay or treat multiple diseases of aging. Finally, we discuss how new molecules may provide routes to the safer and more selective inhibition of mTOR complex 1 (mTORC1) in the decade ahead. We conclude by discussing what work remains to be done and the questions that will need to be addressed to make mTOR inhibitors part of the standard of care for diseases of aging.
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Affiliation(s)
| | - Dudley W Lamming
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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17
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Kalotay E, Klugmann M, Housley GD, Fröhlich D. Dominant aminoacyl-tRNA synthetase disorders: lessons learned from in vivo disease models. Front Neurosci 2023; 17:1182845. [PMID: 37274211 PMCID: PMC10234151 DOI: 10.3389/fnins.2023.1182845] [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: 04/05/2023] [Indexed: 06/06/2023] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) play an essential role in protein synthesis, being responsible for ligating tRNA molecules to their corresponding amino acids in a reaction known as 'tRNA aminoacylation'. Separate ARSs carry out the aminoacylation reaction in the cytosol and in mitochondria, and mutations in almost all ARS genes cause pathophysiology most evident in the nervous system. Dominant mutations in multiple cytosolic ARSs have been linked to forms of peripheral neuropathy including Charcot-Marie-Tooth disease, distal hereditary motor neuropathy, and spinal muscular atrophy. This review provides an overview of approaches that have been employed to model each of these diseases in vivo, followed by a discussion of the existing animal models of dominant ARS disorders and key mechanistic insights that they have provided. In summary, ARS disease models have demonstrated that loss of canonical ARS function alone cannot fully account for the observed disease phenotypes, and that pathogenic ARS variants cause developmental defects within the peripheral nervous system, despite a typically later onset of disease in humans. In addition, aberrant interactions between mutant ARSs and other proteins have been shown to contribute to the disease phenotypes. These findings provide a strong foundation for future research into this group of diseases, providing methodological guidance for studies on ARS disorders that currently lack in vivo models, as well as identifying candidate therapeutic targets.
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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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18
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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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19
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Liu Y, Xing K, Ao H, Zhang F, Zhao X, Liu H, Shi Y, Yu Y, Wang C. Competing endogenous RNA network construction based on long non-coding RNAs, microRNAs, and mRNAs related to fat deposition in Songliao black swine. Anim Genet 2023; 54:132-143. [PMID: 36596449 DOI: 10.1111/age.13283] [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: 07/18/2021] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 01/05/2023]
Abstract
China has a long history of pig breeding and a number of local breeds. The Songliao Black pig, bred in China in 2009, shows high variation in backfat thickness and therefore is well-suited to fat deposition research. Fat deposition is a complex trait, and the underlying regulatory factors are not fully characterized. In this study, the molecular basis of fat deposition traits was evaluated by comparisons between three individuals with extremely high-backfat thickness and three with extremely low-backfat thickness selected from 53 gilts. Subcutaneous adipose tissues of the back were collected for strand-specific library RNA sequencing (RNA-seq) and small RNA-seq. We identified 13 184 mRNAs, 2046 long non-coding (lnc)RNAs, and 494 micro (mi)RNAs by high-throughput sequencing. Furthermore, we detected 150 differentially expressed mRNAs, 66 differentially expressed lncRNAs, and eight differentially expressed miRNAs. A functional enrichment analysis indicated that these genes are involved in multiple fat metabolism-related pathways, including positive regulation of fat cell differentiation, and fat digestion and absorption. We used various algorithms (miRanda, TargetScan, and RNAhybrid) to predict targeting relationships and constructed a competing endogenous RNA network containing seven lncRNAs, three miRNAs, and six mRNAs. All these genes were differentially expressed between the extremely high and low backfat thickness groups or enriched in pathways related to fat metabolism. Our results provide insight into the regulatory mechanisms by which non-coding RNAs and their target genes influence backfat deposition in pigs. Furthermore, our newly constructed competing endogenous RNA (lncRNA-miRNA-mRNA) network provides a basis for further exploration of fat deposition traits and non-coding RNA functions.
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Affiliation(s)
- Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Hong Ao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xitong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huatao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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20
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Shirokova O, Zaborskaya O, Pchelin P, Kozliaeva E, Pershin V, Mukhina I. Genetic and Epigenetic Sexual Dimorphism of Brain Cells during Aging. Brain Sci 2023; 13:brainsci13020195. [PMID: 36831738 PMCID: PMC9954625 DOI: 10.3390/brainsci13020195] [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: 12/22/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
In recent years, much of the attention paid to theoretical and applied biomedicine, as well as neurobiology, has been drawn to various aspects of sexual dimorphism due to the differences that male and female brain cells demonstrate during aging: (a) a dimorphic pattern of response to therapy for neurodegenerative disorders, (b) different age of onset and different degrees of the prevalence of such disorders, and (c) differences in their symptomatic manifestations in men and women. The purpose of this review is to outline the genetic and epigenetic differences in brain cells during aging in males and females. As a result, we hereby show that the presence of brain aging patterns in males and females is due to a complex of factors associated with the effects of sex chromosomes, which subsequently entails a change in signal cascades in somatic cells.
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Affiliation(s)
- Olesya Shirokova
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Correspondence:
| | - Olga Zaborskaya
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Pavel Pchelin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Elizaveta Kozliaeva
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
| | - Vladimir Pershin
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
| | - Irina Mukhina
- Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod 603950, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Avenue, Nizhny Novgorod 603002, Russia
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21
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Chang R, Zhang Y, Sun J, Xu K, Li C, Zhang J, Mei W, Zhang H, Zhang J. Maternal pre-pregnancy body mass index and offspring with overweight/obesity at preschool age: The possible role of epigenome-wide DNA methylation changes in cord blood. Pediatr Obes 2023; 18:e12969. [PMID: 36102013 DOI: 10.1111/ijpo.12969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Epigenome-wide association studies have identified some DNA methylation sites associated with body mass index (BMI) or obesity. Studies in the Asian population are lacking. OBJECTIVE To examine the association of cord blood genome-wide DNA methylation (GWDm) changes with maternal pre-pregnancy BMI and children's BMI-z score at preschool age. Additionally, we also explored the genome-wide differentially methylated regions and differentially methylated probes between preschoolers with overweight/obesity and normal-weight counterparts. METHODS This two-stage study design included (1) a GWDm analysis of 30 mother-child pairs from 633 participants of the Zhuhai birth cohort with data on newborn cord blood, maternal pre-pregnancy BMI, and children's BMI at 3 years of age; and (2) a targeted validation analysis of the cord blood of ten children with overweight/obesity and ten matched controls to validate the CpG sites. RESULTS In the first stage, no significant CpG sites were found to be associated with children's BMI-z score at preschool age after FDR correction with the p-values of the CpG sites in FOXN3 (cg23501836) and ZNF264 (cg27437574) being close to 1 × 10-6 . In the second stage, a significant difference of CpG sites in AHRR (chr5:355067-355068) and FOXN3 (chr14: 89630264-89630272 and chr14: 89630387-89630388) was found between the ten children with overweight/obesity and ten controls (p < 0.05). The CpG sites in FOXN3 (chr14:89630264-89630272 and chr14:89630295-89630296) and ZNF264 (chr19: 57703104-57703107 and chr19: 57703301-57703307) were associated with children's BMI-z score; and the CpG sites in FOXN3 (chr14: 89630264-89630272 and chr14: 89630387-89630388) were associated with maternal pre-pregnancy BMI. CONCLUSIONS DNA methylation in FOXN3 and AHRR is associated with overweight/obesity in preschool-aged children, and the methylation in FOXN3 and ZNF264 might be associated with children's BMI-z score. FOXN3 methylation may be associated with maternal pre-pregnancy BMI, suggesting its potential role in the children's BMI-z score or overweight/obesity. Our results provide novel insights into the mechanisms of children's obesity.
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Affiliation(s)
- Ruixia Chang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuanyuan Zhang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Sun
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Xu
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chunan Li
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingli Zhang
- Traditional Chinese Medicine Hospital, Zhuhai, Guangdong, China
| | - Wenhua Mei
- Zhuhai Center for Disease Control and Prevention, Zhuhai, Guangdong, China
| | - Hongzhong Zhang
- Zhuhai Women and Children's Hospital, Zhuhai, Guangdong, China
| | - Jianduan Zhang
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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22
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Vasu K, Ramachandiran I, Chechi A, Khan K, Khan D, Kaufman R, Fox PL. Translational control of murine adiponectin expression by an upstream open reading frame element. RNA Biol 2023; 20:737-749. [PMID: 37702393 PMCID: PMC10501164 DOI: 10.1080/15476286.2023.2256094] [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] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023] Open
Abstract
Adiponectin, an adipocyte-specific secretory protein encoded by the ADIPOQ gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse Adipoq mRNA 5'-leader identified an inhibitory cis-regulatory sequence. The 5'-leader harbours two potential upstream open reading frames (uORFs) overlapping the principal downstream ORF. Mutation of the uORF ATGs increased reporter translation ~3-fold, indicative of a functional uORF. uORFs are common in mammalian mRNAs; however, only a select group resist translational repression by the integrated stress response (ISR). Thapsigargin (TG), which induces endoplasmic reticulum (ER) stress and the ISR, enhanced expression of a reporter bearing the Adipoq 5'-leader; polysome profiling verified translation-stimulation. TG-stimulated translation was absent in cells defective in Ser51 phosphorylation of eukaryotic initiation factor 2α (eIF2α), required for the ISR. To determine its role in expression and function of endogenous adiponectin, the upstream uORF was disrupted by CRISPR-Cas9-mediated mutagenesis of differentiated mouse 3T3-L1 adipocytes. uORF disruption in adipocytes increased adiponectin expression, triacylglycerol accumulation, and glucose uptake, and inhibited paracrine muscle and liver cell expression of gluconeogenic enzymes, establishing an important role of the uORF in adiponectin-mediated responses to stress.
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Affiliation(s)
- Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Aayushi Chechi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Randall Kaufman
- Degenerative Diseases Program, Center for Genetic Disorders and Aging Research, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paul L. Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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23
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Islam T, Albracht-Schulte K, Ramalingam L, Schlabritz-Lutsevich N, Park OH, Zabet-Moghaddam M, Kalupahana NS, Moustaid-Moussa N. Anti-inflammatory mechanisms of polyphenols in adipose tissue: role of gut microbiota, intestinal barrier integrity and zinc homeostasis. J Nutr Biochem 2022; 115:109242. [PMID: 36442715 DOI: 10.1016/j.jnutbio.2022.109242] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 09/18/2022] [Accepted: 10/14/2022] [Indexed: 11/27/2022]
Abstract
Obesity is associated with an imbalance of micro-and macro-nutrients, gut dysbiosis, and a "leaky" gut phenomenon. Polyphenols, such as curcumin, resveratrol, and anthocyanins may alleviate the systemic effects of obesity, potentially by improving gut microbiota, intestinal barrier integrity (IBI), and zinc homeostasis. The essential micronutrient zinc plays a crucial role in the regulation of enzymatic processes, including inflammation, maintenance of the microbial ecology, and intestinal barrier integrity. In this review, we focus on IBI- which prevents intestinal lipopolysaccharide (LPS) leakage - as a critical player in polyphenol-mediated protective effects against obesity-associated white adipose tissue (WAT) inflammation. This occurs through mechanisms that block the movement of the bacterial endotoxin LPS across the gut barrier. Available research suggests that polyphenols reduce WAT and systemic inflammation via crosstalk with inflammatory NF-κB, the mammalian target of rapamycin (mTOR) signaling and zinc homeostasis.
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Affiliation(s)
- Tariful Islam
- Department of Nutritional Sciences, Texas Tech University, Lubbock, Texas, USA; Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA
| | - Kembra Albracht-Schulte
- Department of Nutritional Sciences, Texas Tech University, Lubbock, Texas, USA; Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA
| | - Latha Ramalingam
- Department of Nutritional Sciences, Texas Tech University, Lubbock, Texas, USA; Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA
| | - Natalia Schlabritz-Lutsevich
- Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA; Advanced Fertility Center, Odessa, Texas, USA
| | - Oak-Hee Park
- Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA; College of Human Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Masoud Zabet-Moghaddam
- Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA; Center for Biotechnology and Genomics, Texas Tech University, Lubbock, Texas, USA
| | - Nishan S Kalupahana
- Department of Nutritional Sciences, Texas Tech University, Lubbock, Texas, USA; Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA; Department of Physiology, University of Peradeniya, Peradeniya, Sri Lanka
| | - Naima Moustaid-Moussa
- Department of Nutritional Sciences, Texas Tech University, Lubbock, Texas, USA; Obesity Research Institute, Texas Tech University, Lubbock, Texas, USA.
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24
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Li Q, Spalding KL. The regulation of adipocyte growth in white adipose tissue. Front Cell Dev Biol 2022; 10:1003219. [PMID: 36483678 PMCID: PMC9723158 DOI: 10.3389/fcell.2022.1003219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/03/2022] [Indexed: 10/25/2023] Open
Abstract
Adipocytes can increase in volume up to a thousand-fold, storing excess calories as triacylglycerol in large lipid droplets. The dramatic morphological changes required of adipocytes demands extensive cytoskeletal remodeling, including lipid droplet and plasma membrane expansion. Cell growth-related signalling pathways are activated, stimulating the production of sufficient amino acids, functional lipids and nucleotides to meet the increasing cellular needs of lipid storage, metabolic activity and adipokine secretion. Continued expansion gives rise to enlarged (hypertrophic) adipocytes. This can result in a failure to maintain growth-related homeostasis and an inability to cope with excess nutrition or respond to stimuli efficiently, ultimately leading to metabolic dysfunction. We summarize recent studies which investigate the functional and cellular structure remodeling of hypertrophic adipocytes. How adipocytes adapt to an enlarged cell size and how this relates to cellular dysfunction are discussed. Understanding the healthy and pathological processes involved in adipocyte hypertrophy may shed light on new strategies for promoting healthy adipose tissue expansion.
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Affiliation(s)
- Qian Li
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Kirsty L. Spalding
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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25
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Regulation of BRCA1 stability through the tandem UBX domains of isoleucyl-tRNA synthetase 1. Nat Commun 2022; 13:6732. [PMID: 36347866 PMCID: PMC9643514 DOI: 10.1038/s41467-022-34612-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) have evolved to acquire various additional domains. These domains allow ARSs to communicate with other cellular proteins in order to promote non-translational functions. Vertebrate cytoplasmic isoleucyl-tRNA synthetases (IARS1s) have an uncharacterized unique domain, UNE-I. Here, we present the crystal structure of the chicken IARS1 UNE-I complexed with glutamyl-tRNA synthetase 1 (EARS1). UNE-I consists of tandem ubiquitin regulatory X (UBX) domains that interact with a distinct hairpin loop on EARS1 and protect its neighboring proteins in the multi-synthetase complex from degradation. Phosphomimetic mutation of the two serine residues in the hairpin loop releases IARS1 from the complex. IARS1 interacts with BRCA1 in the nucleus, regulates its stability by inhibiting ubiquitylation via the UBX domains, and controls DNA repair function.
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26
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Adjuvants in fungicide formulations can be skin sensitizers and cause different types of cell stress responses. Toxicol Rep 2022; 9:2030-2041. [DOI: 10.1016/j.toxrep.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
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27
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Lee EY, Kim SM, Hwang JH, Jang SY, Park S, Choi S, Lee GS, Hwang J, Moon JH, Fox PL, Kim S, Lee CH, Kim MH. Glutamyl-prolyl-tRNA synthetase 1 coordinates early endosomal anti-inflammatory AKT signaling. Nat Commun 2022; 13:6455. [PMID: 36309524 PMCID: PMC9617928 DOI: 10.1038/s41467-022-34226-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/12/2022] [Indexed: 12/25/2022] Open
Abstract
The AKT signaling pathway plays critical roles in the resolution of inflammation. However, the underlying mechanisms of anti-inflammatory regulation and signal coordination remain unclear. Here, we report that anti-inflammatory AKT signaling is coordinated by glutamyl-prolyl-tRNA synthetase 1 (EPRS1). Upon inflammatory activation, AKT specifically phosphorylates Ser999 of EPRS1 in the cytoplasmic multi-tRNA synthetase complex, inducing release of EPRS1. EPRS1 compartmentalizes AKT to early endosomes via selective binding to the endosomal membrane lipid phosphatidylinositol 3-phosphate and assembles an AKT signaling complex specific for anti-inflammatory activity. These events promote AKT activation-mediated GSK3β phosphorylation, which increase anti-inflammatory cytokine production. EPRS1-deficient macrophages do not assemble the early endosomal complex and consequently exacerbate inflammation, decreasing the survival of EPRS1-deficient mice undergoing septic shock and ulcerative colitis. Collectively, our findings show that the housekeeping protein EPRS1 acts as a mediator of inflammatory homeostasis by coordinating compartment-specific AKT signaling.
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Affiliation(s)
- Eun-Young Lee
- grid.249967.70000 0004 0636 3099Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea
| | - Su-Man Kim
- grid.249967.70000 0004 0636 3099Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea
| | - Jung Hwan Hwang
- grid.249967.70000 0004 0636 3099Laboratory Animal Resource Center, KRIBB, Daejeon, 34141 Korea
| | - Song Yee Jang
- grid.249967.70000 0004 0636 3099Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea ,grid.249967.70000 0004 0636 3099Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141 Korea
| | - Shinhye Park
- grid.249967.70000 0004 0636 3099Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea
| | - Sanghyeon Choi
- grid.249967.70000 0004 0636 3099Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea
| | - Ga Seul Lee
- grid.249967.70000 0004 0636 3099Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141 Korea
| | - Jungwon Hwang
- grid.249967.70000 0004 0636 3099Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea
| | - Jeong Hee Moon
- grid.249967.70000 0004 0636 3099Core Research Facility & Analysis Center, KRIBB, Daejeon, 34141 Korea
| | - Paul L. Fox
- grid.239578.20000 0001 0675 4725Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195 USA
| | - Sunghoon Kim
- grid.15444.300000 0004 0470 5454Medicinal Bioconvergence Research Center, College of Pharmacy and College of Medicine, Gangnam Severance Hospital, Yonsei University, Incheon, 21983 Korea
| | - Chul-Ho Lee
- grid.249967.70000 0004 0636 3099Laboratory Animal Resource Center, KRIBB, Daejeon, 34141 Korea
| | - Myung Hee Kim
- grid.249967.70000 0004 0636 3099Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Korea
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28
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Multimodal cotranslational interactions direct assembly of the human multi-tRNA synthetase complex. Proc Natl Acad Sci U S A 2022; 119:e2205669119. [PMID: 36037331 PMCID: PMC9457175 DOI: 10.1073/pnas.2205669119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amino acid ligation to cognate transfer RNAs (tRNAs) is catalyzed by aminoacyl-tRNA synthetases (aaRSs)-essential interpreters of the genetic code during translation. Mammalian cells harbor 20 cytoplasmic aaRSs, out of which 9 (in 8 proteins), with 3 non-aaRS proteins, AIMPs 1 to 3, form the ∼1.25-MDa multi-tRNA synthetase complex (MSC). The function of MSC remains uncertain, as does its mechanism of assembly. Constituents of multiprotein complexes encounter obstacles during assembly, including inappropriate interactions, topological constraints, premature degradation of unassembled subunits, and suboptimal stoichiometry. To facilitate orderly and efficient complex formation, some complexes are assembled cotranslationally by a mechanism in which a fully formed, mature protein binds a nascent partner as it emerges from the translating ribosome. Here, we show out of the 121 possible interaction events between the 11 MSC constituents, 15 are cotranslational. AIMPs are involved in the majority of these cotranslational interactions, suggesting they are not only critical for MSC structure but also for assembly. Unexpectedly, several cotranslational events involve more than the usual dyad of interacting proteins. We show two modes of cotranslational interaction, namely a "multisite" mechanism in which two or more mature proteins bind the same nascent peptide at distinct sites and a second "piggy-back" mechanism in which a mature protein carries a second fully formed protein and binds to a single site on an emerging peptide. Multimodal mechanisms of cotranslational interaction offer a diversity of pathways for ordered, piecewise assembly of small subcomplexes into larger heteromultimeric complexes such as the mammalian MSC.
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29
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Chen YF, Lee CW, Wu HH, Lin WT, Lee OK. Immunometabolism of macrophages regulates skeletal muscle regeneration. Front Cell Dev Biol 2022; 10:948819. [PMID: 36147742 PMCID: PMC9485946 DOI: 10.3389/fcell.2022.948819] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Sarcopenia is an age-related progressive loss of skeletal muscle mass, quality, and strength disease. In addition, sarcopenia is tightly correlated with age-associated pathologies, such as sarcopenic obesity and osteoporosis. Further understanding of disease mechanisms and the therapeutic strategies in muscle regeneration requires a deeper knowledge of the interaction of skeletal muscle and other cells in the muscle tissue. Skeletal muscle regeneration is a complex process that requires a series of highly coordinated events involving communication between muscle stem cells and niche cells, such as muscle fibro/adipogenic progenitors and macrophages. Macrophages play a critical role in tissue regeneration and the maintenance of muscle homeostasis by producing growth factors and cytokines that regulate muscle stem cells and myofibroblast activation. Furthermore, the aging-related immune dysregulation associated with the release of trophic factors and the polarization in macrophages transiently affect the inflammatory phase and impair muscle regeneration. In this review, we focus on the role and regulation of macrophages in skeletal muscle regeneration and homeostasis. The aim of this review is to highlight the important roles of macrophages as a therapeutic target in age-related sarcopenia and the increasing understanding of how macrophages are regulated will help to advance skeletal muscle regeneration.
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Affiliation(s)
- Yu-Fan Chen
- Center for Translational Genomics Research, China Medical University Hospital, Taichung, Taiwan
| | - Chien-Wei Lee
- Center for Translational Genomics Research, China Medical University Hospital, Taichung, Taiwan
| | - Hao-Hsiang Wu
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Stem Cell Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wei-Ting Lin
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, Taiwan
| | - Oscar K. Lee
- Center for Translational Genomics Research, China Medical University Hospital, Taichung, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Stem Cell Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Orthopedics, China Medical University Hospital, Taichung, Taiwan
- *Correspondence: Oscar K. Lee,
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30
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Fumagalli S, Pende M. S6 kinase 1 at the central node of cell size and ageing. Front Cell Dev Biol 2022; 10:949196. [PMID: 36036012 PMCID: PMC9417411 DOI: 10.3389/fcell.2022.949196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Genetic evidence in living organisms from yeast to plants and animals, including humans, unquestionably identifies the Target Of Rapamycin kinase (TOR or mTOR for mammalian/mechanistic) signal transduction pathway as a master regulator of growth through the control of cell size and cell number. Among the mTOR targets, the activation of p70 S6 kinase 1 (S6K1) is exquisitely sensitive to nutrient availability and rapamycin inhibition. Of note, in vivo analysis of mutant flies and mice reveals that S6K1 predominantly regulates cell size versus cell proliferation. Here we review the putative mechanisms of S6K1 action on cell size by considering the main functional categories of S6K1 targets: substrates involved in nucleic acid and protein synthesis, fat mass accumulation, retrograde control of insulin action, senescence program and cytoskeleton organization. We discuss how S6K1 may be involved in the observed interconnection between cell size, regenerative and ageing responses.
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Affiliation(s)
| | - Mario Pende
- *Correspondence: Stefano Fumagalli, ; Mario Pende,
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31
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Inhibition of the DAPKs-L13a axis prevents a GAIT-like motif-mediated HuR insufficiency in melanoma cells. Biochem Biophys Res Commun 2022; 626:21-29. [DOI: 10.1016/j.bbrc.2022.07.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 07/17/2022] [Accepted: 07/21/2022] [Indexed: 11/20/2022]
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32
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Wang G, Chen L, Qin S, Zhang T, Yao J, Yi Y, Deng L. Mechanistic Target of Rapamycin Complex 1: From a Nutrient Sensor to a Key Regulator of Metabolism and Health. Adv Nutr 2022; 13:1882-1900. [PMID: 35561748 PMCID: PMC9526850 DOI: 10.1093/advances/nmac055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 01/28/2023] Open
Abstract
Mechanistic target of rapamycin complex 1 (mTORC1) is a multi-protein complex widely found in eukaryotes. It serves as a central signaling node to coordinate cell growth and metabolism by sensing diverse extracellular and intracellular inputs, including amino acid-, growth factor-, glucose-, and nucleotide-related signals. It is well documented that mTORC1 is recruited to the lysosomal surface, where it is activated and, accordingly, modulates downstream effectors involved in regulating protein, lipid, and glucose metabolism. mTORC1 is thus the central node for coordinating the storage and mobilization of nutrients and energy across various tissues. However, emerging evidence indicated that the overactivation of mTORC1 induced by nutritional disorders leads to the occurrence of a variety of metabolic diseases, including obesity and type 2 diabetes, as well as cancer, neurodegenerative disorders, and aging. That the mTORC1 pathway plays a crucial role in regulating the occurrence of metabolic diseases renders it a prime target for the development of effective therapeutic strategies. Here, we focus on recent advances in our understanding of the regulatory mechanisms underlying how mTORC1 integrates metabolic inputs as well as the role of mTORC1 in the regulation of nutritional and metabolic diseases.
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Affiliation(s)
- Guoyan Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Chen
- Division of Laboratory Safety and Services, Northwest A&F University, Yangling Shaanxi, China
| | - Senlin Qin
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tingting Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Junhu Yao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yanglei Yi
- Address correspondence to YLY (e-mail: )
| | - Lu Deng
- Address correspondence to LD (e-mail: )
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33
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Functional and pathologic association of aminoacyl-tRNA synthetases with cancer. Exp Mol Med 2022; 54:553-566. [PMID: 35501376 PMCID: PMC9166799 DOI: 10.1038/s12276-022-00765-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 11/26/2022] Open
Abstract
Although key tumorigenic and tumor-suppressive factors have been unveiled over the last several decades, cancer remains the most life-threatening disease. Multiomic analyses of patient samples and an in-depth understanding of tumorigenic processes have rapidly revealed unexpected pathologic associations of new cellular factors previously overlooked in cancer biology. In this regard, the newly discovered activities of human aminoacyl-tRNA synthases (ARSs) deserve attention not only for their pathological significance in tumorigenesis but also regarding diagnostic and therapeutic implications. ARSs are not only essential enzymes covalently linking substrate amino acids to cognate tRNAs for protein synthesis but also function as regulators of cellular processes by sensing different cellular conditions. With their catalytic role in protein synthesis and their regulatory role in homeostasis, functional alterations or dysregulation of ARSs might be pathologically associated with tumorigenesis. This review focuses on the potential implications of ARS genes and proteins in different aspects of cancer based on various bioinformatic analyses and experimental data. We also review their diverse activities involving extracellular secretion, protein–protein interactions, and amino acid sensing, which are related to cancers. The newly discovered cancer-related activities of ARSs are expected to provide new opportunities for detecting, preventing and curing cancers. Enzymes called aminoacyl-tRNA synthetases (ARSs), which play a central role in all life, are becoming implicated in several aspects of cancer in ways that may lead to new approaches for prevention, detection and treatment. ARS enzymes catalyse the ligation of amino acids to transfer RNA molecules to allow amino acids to combine in the correct sequences to form proteins. Jung Min Han, Sunghoon Kim and colleagues at Yonsei University, Incheon, South Korea, review researches implicating ARS enzymes and the genes that code for them in a variety of cancers. The behavior of ARS enzymes and their genes are found to be altered in several types of cancer cells in ways that may either initiate or support the onset and development of the disease, through which they could be suggested as targets for novel anti-cancer drugs.
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34
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Simcox J, Lamming DW. The central moTOR of metabolism. Dev Cell 2022; 57:691-706. [PMID: 35316619 PMCID: PMC9004513 DOI: 10.1016/j.devcel.2022.02.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/20/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022]
Abstract
The protein kinase mechanistic target of rapamycin (mTOR) functions as a central regulator of metabolism, integrating diverse nutritional and hormonal cues to control anabolic processes, organismal physiology, and even aging. This review discusses the current state of knowledge regarding the regulation of mTOR signaling and the metabolic regulation of the four macromolecular building blocks of the cell: carbohydrate, nucleic acid, lipid, and protein by mTOR. We review the role of mTOR in the control of organismal physiology and aging through its action in key tissues and discuss the potential for clinical translation of mTOR inhibition for the treatment and prevention of diseases of aging.
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Affiliation(s)
- Judith Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Dudley W Lamming
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA; Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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35
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Khan K, Gogonea V, Fox PL. Aminoacyl-tRNA synthetases of the multi-tRNA synthetase complex and their role in tumorigenesis. Transl Oncol 2022; 19:101392. [PMID: 35278792 PMCID: PMC8914993 DOI: 10.1016/j.tranon.2022.101392] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/27/2022] [Accepted: 02/28/2022] [Indexed: 12/16/2022] Open
Abstract
In mammalian cells, 20 aminoacyl-tRNA synthetases (AARS) catalyze the ligation of amino acids to their cognate tRNAs to generate aminoacylated-tRNAs. In higher eukaryotes, 9 of the 20 AARSs, along with 3 auxiliary proteins, join to form the cytoplasmic multi-tRNA synthetase complex (MSC). The complex is absent in prokaryotes, but evolutionary expansion of MSC constituents, primarily by addition of novel interacting domains, facilitates formation of subcomplexes that join to establish the holo-MSC. In some cases, environmental cues direct the release of constituents from the MSC which enables the execution of non-canonical, i.e., "moonlighting", functions distinct from their essential activities in protein translation. These activities are generally beneficial, but can also be deleterious to the cell. Elucidation of the non-canonical activities of several AARSs residing in the MSC suggest they are potential therapeutic targets for cancer, as well as metabolic and neurologic diseases. Here, we describe the role of MSC-resident AARSs in cancer progression, and the factors that regulate their release from the MSC. Also, we highlight recent developments in therapeutic modalities that target MSC AARSs for cancer prevention and treatment.
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Affiliation(s)
- Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States of America.
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, United States of America
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, United States of America.
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36
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Chen R, Skutella T. Synergistic Anti-Ageing through Senescent Cells Specific Reprogramming. Cells 2022; 11:cells11050830. [PMID: 35269453 PMCID: PMC8909644 DOI: 10.3390/cells11050830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/13/2022] [Accepted: 02/24/2022] [Indexed: 01/02/2023] Open
Abstract
In this review, we seek a novel strategy for establishing a rejuvenating microenvironment through senescent cells specific reprogramming. We suggest that partial reprogramming can produce a secretory phenotype that facilitates cellular rejuvenation. This strategy is desired for specific partial reprogramming under control to avoid tumour risk and organ failure due to loss of cellular identity. It also alleviates the chronic inflammatory state associated with ageing and secondary senescence in adjacent cells by improving the senescence-associated secretory phenotype. This manuscript also hopes to explore whether intervening in cellular senescence can improve ageing and promote damage repair, in general, to increase people’s healthy lifespan and reduce frailty. Feasible and safe clinical translational protocols are critical in rejuvenation by controlled reprogramming advances. This review discusses the limitations and controversies of these advances’ application (while organizing the manuscript according to potential clinical translation schemes) to explore directions and hypotheses that have translational value for subsequent research.
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37
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Yang L, Zhang Z, Wang D, Jiang Y, Liu Y. Targeting mTOR Signaling in Type 2 Diabetes Mellitus and Diabetes Complications. Curr Drug Targets 2022; 23:692-710. [PMID: 35021971 DOI: 10.2174/1389450123666220111115528] [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: 08/03/2021] [Revised: 10/21/2021] [Accepted: 12/01/2021] [Indexed: 11/22/2022]
Abstract
The mechanistic target of rapamycin (mTOR) is a pivotal regulator of cell metabolism and growth. In the form of two different multi-protein complexes, mTORC1 and mTORC2, mTOR integrates cellular energy, nutrient and hormonal signals to regulate cellular metabolic homeostasis. In type 2 diabetes mellitus (T2DM) aberrant mTOR signaling underlies its pathological conditions and end-organ complications. Substantial evidence suggests that two mTOR-mediated signaling schemes, mTORC1-p70S6 kinase 1 (S6K1) and mTORC2-protein kinase B (AKT), play a critical role in insulin sensitivity and that their dysfunction contributes to development of T2DM. This review summaries our current understanding of the role of mTOR signaling in T2DM and its associated complications, as well as the potential use of mTOR inhibitors in treatment of T2DM.
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Affiliation(s)
- Lin Yang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Zhixin Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Doudou Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China
| | - Yu Jiang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Ying Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 102488, China
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38
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Giska I, Pimenta J, Farelo L, Boursot P, Hackländer K, Jenny H, Reid N, Montgomery WI, Prodöhl PA, Alves PC, Melo-Ferreira J. The evolutionary pathways for local adaptation in mountain hares. Mol Ecol 2022; 31:1487-1503. [PMID: 34995383 PMCID: PMC9303332 DOI: 10.1111/mec.16338] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022]
Abstract
Understanding the evolution of local adaptations is a central aim of evolutionary biology and key for the identification of unique populations and lineages of conservation relevance. By combining RAD sequencing and whole‐genome sequencing, we identify genetic signatures of local adaptation in mountain hares (Lepus timidus) from isolated and distinctive habitats of its wide distribution: Ireland, the Alps and Fennoscandia. Demographic modelling suggested that the split of these mountain hares occurred around 20 thousand years ago, providing the opportunity to study adaptive evolution over a short timescale. Using genome‐wide scans, we identified signatures of extreme differentiation among hares from distinct geographic areas that overlap with area‐specific selective sweeps, suggesting targets for local adaptation. Several identified candidate genes are associated with traits related to the uniqueness of the different environments inhabited by the three groups of mountain hares, including coat colour, ability to live at high altitudes and variation in body size. In Irish mountain hares, a variant of ASIP, a gene previously implicated in introgression‐driven winter coat colour variation in mountain and snowshoe hares (L. americanus), may underlie brown winter coats, reinforcing the repeated nature of evolution at ASIP moulding adaptive seasonal colouration. Comparative genomic analyses across several hare species suggested that mountain hares’ adaptive variants appear predominantly species‐specific. However, using coalescent simulations, we also show instances where the candidate adaptive variants have been introduced via introgressive hybridization. Our study shows that standing adaptive variation, including that introgressed from other species, was a crucial component of the post‐glacial dynamics of species.
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Affiliation(s)
- Iwona Giska
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - João Pimenta
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre Boursot
- Institut des Sciences de l'Évolution Montpellier (ISEM), Université Montpellier, CNRS, IRD, Montpellier, France
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, Vienna, Austria.,Deutsche Wildtier Stiftung (German Wildlife Foundation), Hamburg, Germany
| | - Hannes Jenny
- Department of Wildlife and Fishery Service Grison, Chur, Switzerland
| | - Neil Reid
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - W Ian Montgomery
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Paulo A Prodöhl
- Institute of Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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39
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Kim MH, Kang BS. Structure and Dynamics of the Human Multi-tRNA Synthetase Complex. Subcell Biochem 2022; 99:199-233. [PMID: 36151377 DOI: 10.1007/978-3-031-00793-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential enzymes that ligate amino acids to their cognate tRNAs during protein synthesis. A growing body of scientific evidence acknowledges that ubiquitously expressed ARSs act as crossover mediators of biological processes, such as immunity and metabolism, beyond translation. In particular, a cytoplasmic multi-tRNA synthetase complex (MSC), which consists of eight ARSs and three ARS-interacting multifunctional proteins in humans, is recognized to be a central player that controls the complexity of biological systems. Although the role of the MSC in biological processes including protein synthesis is still unclear, maintaining the structural integrity of MSC is essential for life. This chapter deals with current knowledge on the structural aspects of the human MSC and its protein components. The main focus is on the regulatory functions of MSC beyond its catalytic activity.
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Affiliation(s)
- Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea.
| | - Beom Sik Kang
- School of Life Sciences, Kyungpook National University, Daegu, South Korea.
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40
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Li X, Ge J, Li Y, Cai Y, Zheng Q, Huang N, Gu Y, Han Q, Li Y, Sun R, Liu R. Integrative lipidomic and transcriptomic study unravels the therapeutic effects of saikosaponins A and D on non-alcoholic fatty liver disease. Acta Pharm Sin B 2021; 11:3527-3541. [PMID: 34900534 PMCID: PMC8642447 DOI: 10.1016/j.apsb.2021.03.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become one of the most prominent causes of chronic liver diseases and malignancies. However, few therapy has been approved. Radix Bupleuri (RB) is the most frequently used herbal medicine for the treatment of liver diseases. In the current study, we aim to systemically evaluate the therapeutic effects of saikosaponin A (SSa) and saikosaponin D (SSd), the major bioactive monomers in RB, against NAFLD and to investigate the underlying mechanisms. Our results demonstrated that both SSa and SSd improved diet-induced NAFLD. Integrative lipidomic and transcriptomic analysis revealed that SSa and SSd modulated glycerolipid metabolism by regulating related genes, like Lipe and Lipg. SSd profoundly suppressed the fatty acid biosynthesis by downregulating Fasn and Acaca expression and promoted fatty acid degradation by inducing Acox1 and Cpt1a expression. Bioinformatic analysis further predicted the implication of master transcription factors, including peroxisome proliferator-activated receptor alpha (PPARα), in the protective effects of SSa and SSd. These results were further confirmed in vitro in mouse primary hepatocytes. In summary, our study uncoded the complicated mechanisms underlying the promising anti-steatosis activities of saikosaponins (SSs), and provided critical evidence inspiring the discovery of innovative therapies based on SSa and SSd for the treatment of NAFLD and related complications.
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41
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Zhong FY, Li J, Wang YM, Chen Y, Song J, Yang Z, Zhang L, Tian T, Hu YF, Qin ZY. MicroRNA-506 modulates insulin resistance in human adipocytes by targeting S6K1 and altering the IRS1/PI3K/AKT insulin signaling pathway. J Bioenerg Biomembr 2021; 53:679-692. [PMID: 34718921 PMCID: PMC8595185 DOI: 10.1007/s10863-021-09923-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022]
Abstract
The incidence of obesity has increased rapidly, becoming a worldwide public health issue that involves insulin resistance. A growing number of recent studies have demonstrated that microRNAs play a significant role in controlling the insulin signaling network. For example, miR-506-3p expression has been demonstrated to correlate with insulin sensitivity; however, the underlying mechanism remains unknown. In this study, we found that miR-506-3p enhanced glucose uptake by 2-deoxy-D-glucose uptake assays and regulated the protein expression of key genes involved in the PI3K/AKT insulin signaling pathway including IRS1, PI3K, AKT, and GlUT4. We next predicted ribosomal protein S6 kinase B1 (S6K1) to be a candidate target of miR-506-3p by bioinformatics analysis and confirmed using dual-luciferase assays that miR-506-3p regulated S6K1 expression by binding to its 3'-UTR. Moreover, modulating S6K1 expression counteracted the effects of miR-506-3p on glucose uptake and PI3K/AKT pathway activation. In conclusion, miR-506-3p altered IR in adipocytes by regulating S6K1-mediated PI3K/AKT pathway activation. Taken together, these findings provide novel insights and potential targets for IR therapy.
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Affiliation(s)
- Feng-Yu Zhong
- The First Clinical Medical College of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Jing Li
- Department of Children's Health Care, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Maternal and Child Health Care Hospital, Nanjing, 210036, Jiangsu, China
| | - Yu-Mei Wang
- Department of Screening for Neonatal Diseases, Huai'an Maternity and Child Health Care Hospital Affiliated to Yangzhou University Medical College, Huaian, 223002, Jiangsu, China
| | - Yao Chen
- The First Clinical Medical College of Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Jia Song
- Department of Children's Health Care, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Maternal and Child Health Care Hospital, Nanjing, 210036, Jiangsu, China
| | - Zi Yang
- Department of Children's Health Care, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Maternal and Child Health Care Hospital, Nanjing, 210036, Jiangsu, China
| | - Lin Zhang
- Department of Children's Health Care, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Maternal and Child Health Care Hospital, Nanjing, 210036, Jiangsu, China
| | - Tian Tian
- Department of Children's Health Care, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Maternal and Child Health Care Hospital, Nanjing, 210036, Jiangsu, China
| | - You-Fang Hu
- Department of Children's Health Care, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Maternal and Child Health Care Hospital, Nanjing, 210036, Jiangsu, China.
| | - Zhen-Ying Qin
- Department of Children's Health Care, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Maternal and Child Health Care Hospital, Nanjing, 210036, Jiangsu, China.
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Widjaja AA, Viswanathan S, Jinrui D, Singh BK, Tan J, Wei Ting JG, Lamb D, Shekeran SG, George BL, Schafer S, Carling D, Adami E, Cook SA. Molecular Dissection of Pro-Fibrotic IL11 Signaling in Cardiac and Pulmonary Fibroblasts. Front Mol Biosci 2021; 8:740650. [PMID: 34651016 PMCID: PMC8505966 DOI: 10.3389/fmolb.2021.740650] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
In fibroblasts, TGFβ1 stimulates IL11 upregulation that leads to an autocrine loop of IL11-dependent pro-fibrotic protein translation. The signaling pathways downstream of IL11, which acts via IL6ST, are contentious with both STAT3 and ERK implicated. Here we dissect IL11 signaling in fibroblasts and study IL11-dependent protein synthesis pathways in the context of approved anti-fibrotic drug mechanisms of action. We show that IL11-induced ERK activation drives fibrogenesis and while STAT3 phosphorylation (pSTAT3) is also seen, this appears unrelated to fibroblast activation. Ironically, recombinant human IL11, which has been used extensively in mouse experiments to infer STAT3 activity downstream of IL11, increases pSTAT3 in Il11ra1 null mouse fibroblasts. Unexpectedly, inhibition of STAT3 was found to induce severe proteotoxic ER stress, generalized fibroblast dysfunction and cell death. In contrast, inhibition of ERK prevented fibroblast activation in the absence of ER stress. IL11 stimulated an axis of ERK/mTOR/P70RSK protein translation and its selectivity for Collagen 1 synthesis was ascribed to an EPRS-regulated, ribosome stalling mechanism. Surprisingly, the anti-fibrotic drug nintedanib caused dose-dependent ER stress and lesser pSTAT3 expression. Pirfenidone had no effect on ER stress whereas anti-IL11 specifically inhibited the ERK/mTOR axis while reducing ER stress. These studies define the translation-specific signaling pathways downstream of IL11, intersect immune and metabolic signaling and reveal unappreciated effects of nintedanib.
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Affiliation(s)
- Anissa A Widjaja
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Sivakumar Viswanathan
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Dong Jinrui
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Brijesh K Singh
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Jessie Tan
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Joyce Goh Wei Ting
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - David Lamb
- Boehringer Ingelheim, Immunology and Respiratory, Ingelheim am Rhein, Germany
| | - Shamini G Shekeran
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Benjamin L George
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Sebastian Schafer
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - David Carling
- MRC-London Institute of Medical Sciences, London, United Kingdom
| | - Eleonora Adami
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Stuart A Cook
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore, Singapore.,National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore.,MRC-London Institute of Medical Sciences, London, United Kingdom
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Dunislawska A, Herosimczyk A, Ozgo M, Lepczynski A, Ciechanowicz AK, Bednarczyk M, Siwek M. Proteome changes upon in ovo stimulation with Lactobacillus synbiotic in chicken liver. Poult Sci 2021; 100:101449. [PMID: 34601437 PMCID: PMC8531852 DOI: 10.1016/j.psj.2021.101449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/18/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
The liver, as the main metabolic organ, plays a key role in many vital processes, including nutrient metabolism, fat digestion, blood protein synthesis, and endocrine management. As one of the immune organs, it has a remarkable ability to adequately activate the immune cells in response to metabolic signals. The anatomy of the liver ensures its close interaction with the gut so that nutrients and gut microbiota contribute to normal metabolism. In chickens, the intestinal microbiota plays an important role in supporting health and improving production parameters. The most effective method of stimulating the microbiota is to administer an appropriate bioactive compound during embryonic development. In ovo stimulation on d 12 of egg incubation involves the delivery of the substance into the air chamber. The aim of the study was to analyze the changes at the protein level after in ovo administration of the synbiotic on d 12 of egg incubation. Our study is the first to conduct a proteome analysis in liver after the administration of a Lactobacillus synbiotic in ovo. Eggs of broiler chickens were injected with a synbiotic—Lactobacillus plantarum with raffinose family oligosaccharides (RFO). On d 21 posthatching liver was collected. We performed analyses based on two-dimensional electrophoresis, matrix-assisted laser desorption/ionization (MALDI) time-of-flight, and MALDI Fourier-transform ion cyclotron resonance to obtain a global view of the hepatic proteome changes in response to in ovo injection. A representative pattern of significantly altered liver proteins was observed after stimulation with the synbiotic. A total of 16 protein spots were differentially expressed, with 5 downregulated and 11 upregulated spots. We conclude that the in ovo synbiotic treatment had the potential to accelerate the major energy-yielding metabolic pathways in the liver of adult broilers.
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Affiliation(s)
- Aleksandra Dunislawska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka 28, Bydgoszcz 85-084, Poland.
| | - Agnieszka Herosimczyk
- Department of Physiology, Cytobiology and Proteomics, West Pomeraninan University of Technology, Janickiego 29, Szczecin 71-270, Poland
| | - Malgorzata Ozgo
- Department of Physiology, Cytobiology and Proteomics, West Pomeraninan University of Technology, Janickiego 29, Szczecin 71-270, Poland
| | - Adam Lepczynski
- Department of Physiology, Cytobiology and Proteomics, West Pomeraninan University of Technology, Janickiego 29, Szczecin 71-270, Poland
| | - Andrzej Krzysztof Ciechanowicz
- Department of Regenerative Medicine, Centre for Preclinical Research and Technology, Medical University of Warsaw, Zwirki and Wigury 61, Warsaw 02-091, Poland
| | - Marek Bednarczyk
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka 28, Bydgoszcz 85-084, Poland
| | - Maria Siwek
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka 28, Bydgoszcz 85-084, Poland
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44
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Dai C, Reyes-Ordoñez A, You JS, Chen J. A non-translational role of threonyl-tRNA synthetase in regulating JNK signaling during myogenic differentiation. FASEB J 2021; 35:e21948. [PMID: 34569098 DOI: 10.1096/fj.202101094r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/30/2021] [Accepted: 09/08/2021] [Indexed: 11/11/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are house-keeping enzymes that are essential for protein synthesis. However, it has become increasingly evident that some aaRSs also have non-translational functions. Here we report the identification of a non-translational function of threonyl-tRNA synthetase (ThrRS) in myogenic differentiation. We find that ThrRS negatively regulates myoblast differentiation in vitro and injury-induced skeletal muscle regeneration in vivo. This function is independent of amino acid binding or aminoacylation activity of ThrRS, and knockdown of ThrRS leads to enhanced differentiation without affecting the global protein synthesis rate. Furthermore, we show that the non-catalytic new domains (UNE-T and TGS) of ThrRS are both necessary and sufficient for the myogenic function. In searching for a molecular mechanism of this new function, we find the kinase JNK to be a downstream target of ThrRS. Our data further reveal MEKK4 and MKK4 as upstream regulators of JNK in myogenesis and the MEKK4-MKK4-JNK pathway to be a mediator of the myogenic function of ThrRS. Finally, we show that ThrRS physically interacts with Axin1, disrupts Axin1-MEKK4 interaction and consequently inhibits JNK signaling. In conclusion, we uncover a non-translational function for ThrRS in the maintenance of homeostasis of skeletal myogenesis and identify the Axin1-MEKK4-MKK4-JNK signaling axis to be an immediate target of ThrRS action.
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Affiliation(s)
- Chong Dai
- Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Adriana Reyes-Ordoñez
- Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jae-Sung You
- Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jie Chen
- Department of Cell & Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Liu X, Li S, Wang L, Zhang W, Wang Y, Gui L, Zan L, Zhao C. The Effect of FATP1 on Adipocyte Differentiation in Qinchuan Beef Cattle. Animals (Basel) 2021; 11:ani11102789. [PMID: 34679811 PMCID: PMC8532991 DOI: 10.3390/ani11102789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Previous research found that FATP1 plays an important role in the regulation of fatty acid metabolism and lipid accumulation in pig and chicken, but its function has not been explored in bovine adipocyte yet. In this study, we investigated the effect of FATP1 expression on preadipocyte differentiation in Qinchuan cattle using overexpression and interference assays. Our results reveal that FATP1 overexpression promoted preadipocyte differentiation, lipid droplet formation, and the expression of LPL and PPARγ, while FATP1 interference had the opposite effects on adipocyte differentiation and fat deposition. Following FATP1 overexpression and FATP1 interference in adipocytes, RNA-seq analysis identified that SLPI, STC1, SEMA6A, TNFRSF19, SLN, PTGS2, ADCYP1, FADS2, and SCD genes were differentially expressed. Pathway analysis revealed that the PPAR signaling pathway, AMPK signal pathway, and Insulin signaling pathway were enriched with differentially expressed genes. We propose that the FATP1 gene may affect the beef quality by involving adipocyte differentiation and lipid deposition, and may shed new light on the formation mechanisms of adipose tissues. Abstract FATP1 plays an important role in the regulation of fatty acid metabolism and lipid accumulation. In this study, we investigated the patterns of FATP1 expression in various tissues obtained from calf and adult Qinchuan cattle, and in differentiating adipocytes. Next, we investigated the effect of FATP1 expression on preadipocyte differentiation in Qinchuan cattle using overexpression and interference assays. We also identified the differentially expressed genes (DEGs) and pathways associated with FATP1 overexpression/interference. Our results reveal that FATP1 was broadly expressed in heart, kidney, muscle, small intestine, large intestine, and perirenal fat tissues. While FATP1 overexpression promoted preadipocyte differentiation, fat deposition, and the expression of several genes involved in fat metabolism, FATP1 interference had the opposite effects on adipocyte differentiation. Following FATP1 overexpression and FATP1 interference in adipocytes, RNA-seq analysis was performed to identify DEGs related to fat metabolism. The DEGs identified include SLPI, STC1, SEMA6A, TNFRSF19, SLN, PTGS2, ADCYP1, FADS2, and SCD. Pathway analysis revealed that the DEGs were enriched in the PPAR signaling pathway, AMPK signal pathway, and Insulin signaling pathway. Our results provide an in-depth understanding of the function and regulation mechanism of FAPT1 in fat metabolism.
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Affiliation(s)
- Xuchun Liu
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China; (X.L.); (S.L.); (L.W.); (W.Z.); (Y.W.); (L.Z.)
| | - Shijun Li
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China; (X.L.); (S.L.); (L.W.); (W.Z.); (Y.W.); (L.Z.)
| | - Liyun Wang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China; (X.L.); (S.L.); (L.W.); (W.Z.); (Y.W.); (L.Z.)
| | - Weiyi Zhang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China; (X.L.); (S.L.); (L.W.); (W.Z.); (Y.W.); (L.Z.)
| | - Yujuan Wang
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China; (X.L.); (S.L.); (L.W.); (W.Z.); (Y.W.); (L.Z.)
| | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China;
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China; (X.L.); (S.L.); (L.W.); (W.Z.); (Y.W.); (L.Z.)
| | - Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, China; (X.L.); (S.L.); (L.W.); (W.Z.); (Y.W.); (L.Z.)
- Correspondence: ; Tel.: +86-29-8709-1247; Fax: +86-29-8709-1148
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EPRS/GluRS promotes gastric cancer development via WNT/GSK-3β/β-catenin signaling pathway. Gastric Cancer 2021; 24:1021-1036. [PMID: 33740160 DOI: 10.1007/s10120-021-01180-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Glutamyl-prolyl-tRNA synthetase (EPRS/GluRS) is primarily part of the multi-synthetase complex that may play a key role in cancer development. However, the biological function, molecular mechanism, and inhibitor of EPRS have not been investigated in gastric cancer (GC). METHODS Immunohistochemistry was performed to detect the expression of EPRS in human gastric tumor tissues. Knocking down of EPRS, cell-derived xenograft mouse model, and patient-derived xenograft mouse model was used to identify the biological function of EPRS. Immunoprecipitation was applied to elucidate the interaction between EPRS and SCYL2. Computer docking model and multiple in vitro and in vivo experiments were conducted to discover EPRS inhibitors. RESULTS Here, we report that EPRS is frequently overexpressed in GC tissues compared to that adjacent controls and its overexpression predicts poor prognosis in GC patients. Functionally, high expression of EPRS positively co-relates with GC development both in vitro and in vivo. Mechanistically, EPRS directly binds with SCYL2 to enhance the activation of WNT/GSK-3β/β-catenin signaling pathway and the accumulation of β-catenin in the nuclear, leading to GC cell proliferation and tumor growth. Moreover, we identified that xanthoangelol (XA) and 4-hydroxyderricin (4-HD) can directly bind to EPRS to block WNT/GSK-3β/β-catenin signaling pathway. More importantly, XA and 4-HD restrain gastric cancer patient-derived xenograft tumor growth and Helicobacter pylori combined with alcohol-induced atrophic gastritis and gastric tumorigenesis. CONCLUSION These findings unveil a promising strategy for GC prevention and therapy by targeting EPRS-mediated WNT/GSK-3β/β-catenin cascades. Moreover, XA and 4-HD may be effective reagents used for GC prevention and therapy.
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Adams RA, Fernandes-Cerqueira C, Notarnicola A, Mertsching E, Xu Z, Lo WS, Ogilvie K, Chiang KP, Ampudia J, Rosengren S, Cubitt A, King DJ, Mendlein JD, Yang XL, Nangle LA, Lundberg IE, Jakobsson PJ, Schimmel P. Serum-circulating His-tRNA synthetase inhibits organ-targeted immune responses. Cell Mol Immunol 2021; 18:1463-1475. [PMID: 31797905 PMCID: PMC8166958 DOI: 10.1038/s41423-019-0331-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 10/29/2019] [Indexed: 12/13/2022] Open
Abstract
His-tRNA synthetase (HARS) is targeted by autoantibodies in chronic and acute inflammatory anti-Jo-1-positive antisynthetase syndrome. The extensive activation and migration of immune cells into lung and muscle are associated with interstitial lung disease, myositis, and morbidity. It is unknown whether the sequestration of HARS is an epiphenomenon or plays a causal role in the disease. Here, we show that HARS circulates in healthy individuals, but it is largely undetectable in the serum of anti-Jo-1-positive antisynthetase syndrome patients. In cultured primary human skeletal muscle myoblasts (HSkMC), HARS is released in increasing amounts during their differentiation into myotubes. We further show that HARS regulates immune cell engagement and inhibits CD4+ and CD8+ T-cell activation. In mouse and rodent models of acute inflammatory diseases, HARS administration downregulates immune activation. In contrast, neutralization of extracellular HARS by high-titer antibody responses during tissue injury increases susceptibility to immune attack, similar to what is seen in humans with anti-Jo-1-positive disease. Collectively, these data suggest that extracellular HARS is homeostatic in normal subjects, and its sequestration contributes to the morbidity of the anti-Jo-1-positive antisynthetase syndrome.
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Affiliation(s)
- Ryan A Adams
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - Cátia Fernandes-Cerqueira
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Antonella Notarnicola
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | | | - Zhiwen Xu
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
- IAS HKUST- Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, and Pangu Biopharma, Hong Kong, China
| | - Wing-Sze Lo
- IAS HKUST- Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, and Pangu Biopharma, Hong Kong, China
| | - Kathleen Ogilvie
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - Kyle P Chiang
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - Jeanette Ampudia
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - Sanna Rosengren
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - Andrea Cubitt
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - David J King
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - John D Mendlein
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - Xiang-Lei Yang
- The Scripps Laboratories for tRNA Synthetase Research, 10650 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Leslie A Nangle
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA, 92121, USA
| | - Ingrid E Lundberg
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Per-Johan Jakobsson
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Paul Schimmel
- The Scripps Laboratories for tRNA Synthetase Research, 10650 North Torrey Pines Road, La Jolla, CA, 92037, USA.
- The Scripps Laboratories for tRNA Synthetase Research, Scripps Florida, 130 Scripps Way, Jupiter, FL, 33458, USA.
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Roles of tRNA metabolism in aging and lifespan. Cell Death Dis 2021; 12:548. [PMID: 34039958 PMCID: PMC8154886 DOI: 10.1038/s41419-021-03838-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/17/2022]
Abstract
Transfer RNAs (tRNAs) mainly function as adapter molecules that decode messenger RNAs (mRNAs) during protein translation by delivering amino acids to the ribosome. Traditionally, tRNAs are considered as housekeepers without additional functions. Nevertheless, it has become apparent from biological research that tRNAs are involved in various physiological and pathological processes. Aging is a form of gradual decline in physiological function that ultimately leads to increased vulnerability to multiple chronic diseases and death. Interestingly, tRNA metabolism is closely associated with aging and lifespan. In this review, we summarize the emerging roles of tRNA-associated metabolism, such as tRNA transcription, tRNA molecules, tRNA modifications, tRNA aminoacylation, and tRNA derivatives, in aging and lifespan, aiming to provide new ideas for developing therapeutics and ultimately extending lifespan in humans.
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Abstract
The need to describe and understand signaling pathways in live cell is seen as a primary route to identifying and developing targeted medicines. Signaling cascade is also seen as a complex communication and involves interactions between multiple interconnecting proteins. Where subcellularly and how different proteins interact need to be preserved during investigation. Furthermore, these complex events occurring simultaneously may lead to a single or multiple end point or cell function such as protein synthesis, cell cytoskeleton formation, DNA damage repair, or autophagy. There is therefore a need of real-time noninvasive methods for protein assays to enable direct visualization of the interactions in their natural environment and hence overcome the limitations of methods that rely on invasive cell disruption techniques. Förster resonance energy transfer (FRET) coupled with fluorescence lifetime imaging microscopy (FLIM) is an advanced imaging method to observe protein-protein interactions at nanometer scale inside single living cells in real-time. Here we describe the development and use of two-channel pulsed interleave excitation (PIE) for multiple protein interactions in the mTORC1 pathway. The proteins were first tagged with multiple color fluorescent protein derivatives. The FRET-FLIM combination means that the information gained from using standard steady-state FRET between interacting proteins is considerably improved by monitoring changes in the excited-state lifetime of the donor fluorophore where its quenching in the presence of the acceptor is evidence for a direct physical interaction.
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Vasu K, Ramachandiran I, Terenzi F, Khan D, China A, Khan K, Chechi A, Baleanu-Gogonea C, Gogonea V, Fox PL. The zinc-binding domain of mammalian prolyl-tRNA synthetase is indispensable for catalytic activity and organism viability. iScience 2021; 24:102215. [PMID: 33748704 PMCID: PMC7960942 DOI: 10.1016/j.isci.2021.102215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/26/2021] [Accepted: 02/17/2021] [Indexed: 01/10/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AARS) participate in decoding the genome by catalyzing conjugation of amino acids to their cognate tRNAs. During evolution, biochemical and environmental conditions markedly influenced the sequence and structure of the 20 AARSs, revealing adaptations dictating canonical and orthogonal activities. Here, we investigate the function of the appended Zn2+-binding domain (ZBD) in the bifunctional AARS, glutamyl-prolyl-tRNA synthetase (GluProRS). We developed GluProRS mutant mice by CRISPR-Cas9 with a deletion of 29 C-terminal amino acids, including two of four Zn2+-coordinating cysteines. Homozygous ZBD mutant mice die before embryonic day 12.5, but heterozygous mice are healthy. ZBD disruption profoundly reduces GluProRS canonical function by dual mechanisms: it induces rapid proteasomal degradation of the protein and inhibits ProRS aminoacylation activity, likely by sub-optimal positioning of ATP in the spatially adjacent catalytic domain. Collectively, our studies reveal the ZBD as a critical determinant of ProRS activity and GluProRS stability in vitro and in vivo. Conserved zinc-binding domain (ZBD) of GluProRS is required for Pro-tRNA charging ZBD stabilizes GluProRS and positions C-terminal carboxylate in the catalytic site Embryonic lethality in mice with defective GluProRS ZBD reveals in vivo essentiality Locked nucleic acid qPCR assay for CRISPR-mediated screening of chimeric mutant mice
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Affiliation(s)
- Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Aayushi Chechi
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | - Valentin Gogonea
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.,Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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