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Lv X, Zhang R, Li S, Jin X. tRNA Modifications and Dysregulation: Implications for Brain Diseases. Brain Sci 2024; 14:633. [PMID: 39061374 PMCID: PMC11274612 DOI: 10.3390/brainsci14070633] [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: 04/15/2024] [Revised: 06/05/2024] [Accepted: 06/12/2024] [Indexed: 07/28/2024] Open
Abstract
Transfer RNAs (tRNAs) are well-known for their essential function in protein synthesis. Recent research has revealed a diverse range of chemical modifications that tRNAs undergo, which are crucial for various cellular processes. These modifications are necessary for the precise and efficient translation of proteins and also play important roles in gene expression regulation and cellular stress response. This review examines the role of tRNA modifications and dysregulation in the pathophysiology of various brain diseases, including epilepsy, stroke, neurodevelopmental disorders, brain tumors, Alzheimer's disease, and Parkinson's disease. Through a comprehensive analysis of existing research, our study aims to elucidate the intricate relationship between tRNA dysregulation and brain diseases. This underscores the critical need for ongoing exploration in this field and provides valuable insights that could facilitate the development of innovative diagnostic tools and therapeutic approaches, ultimately improving outcomes for individuals grappling with complex neurological conditions.
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Affiliation(s)
- Xinxin Lv
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| | - Ruorui Zhang
- Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA 90089, USA;
| | - Shanshan Li
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
| | - Xin Jin
- School of Medicine, Nankai University, Tianjin 300071, China; (X.L.); (S.L.)
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2
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Wang Y, Yang H, Geerts C, Furtos A, Waters P, Cyr D, Wang S, Mitchell GA. The multiple facets of acetyl-CoA metabolism: Energetics, biosynthesis, regulation, acylation and inborn errors. Mol Genet Metab 2023; 138:106966. [PMID: 36528988 DOI: 10.1016/j.ymgme.2022.106966] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
Acetyl-coenzyme A (Ac-CoA) is a core metabolite with essential roles throughout cell physiology. These functions can be classified into energetics, biosynthesis, regulation and acetylation of large and small molecules. Ac-CoA is essential for oxidative metabolism of glucose, fatty acids, most amino acids, ethanol, and of free acetate generated by endogenous metabolism or by gut bacteria. Ac-CoA cannot cross lipid bilayers, but acetyl groups from Ac-CoA can shuttle across membranes as part of carrier molecules like citrate or acetylcarnitine, or as free acetate or ketone bodies. Ac-CoA is the basic unit of lipid biosynthesis, providing essentially all of the carbon for the synthesis of fatty acids and of isoprenoid-derived compounds including cholesterol, coenzyme Q and dolichols. High levels of Ac-CoA in hepatocytes stimulate lipid biosynthesis, ketone body production and the diversion of pyruvate metabolism towards gluconeogenesis and away from oxidation; low levels exert opposite effects. Acetylation changes the properties of molecules. Acetylation is necessary for the synthesis of acetylcholine, acetylglutamate, acetylaspartate and N-acetyl amino sugars, and to metabolize/eliminate some xenobiotics. Acetylation is a major post-translational modification of proteins. Different types of protein acetylation occur. The most-studied form occurs at the epsilon nitrogen of lysine residues. In histones, lysine acetylation can alter gene transcription. Acetylation of other proteins has diverse, often incompletely-documented effects. Inborn errors related to Ac-CoA feature a broad spectrum of metabolic, neurological and other features. To date, a small number of studies of animals with inborn errors of CoA thioesters has included direct measurement of acyl-CoAs. These studies have shown that low levels of tissue Ac-CoA correlate with the development of clinical signs, hinting that shortage of Ac-CoA may be a recurrent theme in these conditions. Low levels of Ac-CoA could potentially disrupt any of its roles.
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Affiliation(s)
- Youlin Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Hao Yang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Chloé Geerts
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Alexandra Furtos
- Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - Paula Waters
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Québec, Canada
| | - Denis Cyr
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Québec, Canada
| | - Shupei Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Grant A Mitchell
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada.
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3
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Integrative Proteomics and Transcriptomics Profiles of the Oviduct Reveal the Prolificacy-Related Candidate Biomarkers of Goats ( Capra hircus) in Estrous Periods. Int J Mol Sci 2022; 23:ijms232314888. [PMID: 36499219 PMCID: PMC9737051 DOI: 10.3390/ijms232314888] [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: 10/20/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The oviduct is a dynamic reproductive organ for mammalian reproduction and is required for gamete storage, maturation, fertilization, and early embryonic development, and it directly affects fecundity. However, the molecular regulation of prolificacy occurring in estrous periods remain poorly understood. This study aims to gain a better understanding of the genes involved in regulating goat fecundity in the proteome and transcriptome levels of the oviducts. Twenty female Yunshang black goats (between 2 and 3 years old, weight 52.22 ± 0.43 kg) were divided into high- and low-fecundity groups in the follicular (FH and FL, five individuals per group) and luteal (LH and LL, five individuals per group) phases, respectively. The DIA-based high-resolution mass spectrometry (MS) method was used to quantify proteins in twenty oviducts. A total of 5409 proteins were quantified, and Weighted gene co-expression network analysis (WGCNA) determined that the tan module was highly associated with the high-fecundity trait in the luteal phase, and identified NUP107, ANXA11, COX2, AKP13, and ITF140 as hub proteins. Subsequently, 98 and 167 differentially abundant proteins (DAPs) were identified in the FH vs. FL and LH vs. LL comparison groups, respectively. Parallel reaction monitoring (PRM) was used to validate the results of the proteomics data, and the hub proteins were analyzed with Western blot (WB). In addition, biological adhesion and transporter activity processes were associated with oviductal function, and several proteins that play roles in oviductal communication with gametes or embryos were identified, including CAMSAP3, ITGAM, SYVN1, EMG1, ND5, RING1, CBS, PES1, ELP3, SEC24C, SPP1, and HSPA8. Correlation analysis of proteomics and transcriptomic revealed that the DAPs and differentially expressed genes (DEGs) are commonly involved in the metabolic processes at the follicular phase; they may prepare the oviductal microenvironment for gamete reception; and the MAP kinase activity, estrogen receptor binding, and angiotensin receptor binding terms were enriched in the luteal phase, which may be actively involved in reproductive processes. By generating the proteome data of the oviduct at two critical phases and integrating transcriptome analysis, we uncovered novel aspects of oviductal gene regulation of fecundity and provided a reference for other mammals.
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Funk H, DiVita DJ, Sizemore HE, Wehrle K, Miller CLW, Fraley ME, Mullins AK, Guy AR, Phizicky EM, Guy MP. Identification of a Trm732 Motif Required for 2'- O-methylation of the tRNA Anticodon Loop by Trm7. ACS OMEGA 2022; 7:13667-13675. [PMID: 35559166 PMCID: PMC9088939 DOI: 10.1021/acsomega.1c07231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Posttranscriptional tRNA modifications are essential for proper gene expression, and defects in the enzymes that perform tRNA modifications are associated with numerous human disorders. Throughout eukaryotes, 2'-O-methylation of residues 32 and 34 of the anticodon loop of tRNA is important for proper translation, and in humans, a lack of these modifications results in non-syndromic X-linked intellectual disability. In yeast, the methyltransferase Trm7 forms a complex with Trm732 to 2'-O-methylate tRNA residue 32 and with Trm734 to 2'-O-methylate tRNA residue 34. Trm732 and Trm734 are required for the methylation activity of Trm7, but the role of these auxiliary proteins is not clear. Additionally, Trm732 and Trm734 homologs are implicated in biological processes not directly related to translation, suggesting that these proteins may have additional cellular functions. To identify critical amino acids in Trm732, we generated variants and tested their ability to function in yeast cells. We identified a conserved RRSAGLP motif in the conserved DUF2428 domain of Trm732 that is required for tRNA modification activity by both yeast Trm732 and its human homolog, THADA. The identification of Trm732 variants that lack tRNA modification activity will help to determine if other biological functions ascribed to Trm732 and THADA are directly due to tRNA modification or to secondary effects due to other functions of these proteins.
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Affiliation(s)
- Holly
M. Funk
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Daisy J. DiVita
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Hannah E. Sizemore
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Kendal Wehrle
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Catherine L. W. Miller
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
| | - Morgan E. Fraley
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Alex K. Mullins
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Adrian R. Guy
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
| | - Eric M. Phizicky
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
| | - Michael P. Guy
- Department
of Chemistry & Biochemistry, Northern
Kentucky University, Highland
Heights, Kentucky 41076, United States
- Department
of Biochemistry and Biophysics, University
of Rochester School of Medicine, Rochester, New York 14642, United States
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5
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Abbassi NEH, Biela A, Glatt S, Lin TY. How Elongator Acetylates tRNA Bases. Int J Mol Sci 2020; 21:E8209. [PMID: 33152999 PMCID: PMC7663514 DOI: 10.3390/ijms21218209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 12/13/2022] Open
Abstract
Elp3, the catalytic subunit of the eukaryotic Elongator complex, is a lysine acetyltransferase that acetylates the C5 position of wobble-base uridines (U34) in transfer RNAs (tRNAs). This Elongator-dependent RNA acetylation of anticodon bases affects the ribosomal translation elongation rates and directly links acetyl-CoA metabolism to both protein synthesis rates and the proteome integrity. Of note, several human diseases, including various cancers and neurodegenerative disorders, correlate with the dysregulation of Elongator's tRNA modification activity. In this review, we focus on recent findings regarding the structure of Elp3 and the role of acetyl-CoA during its unique modification reaction.
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Affiliation(s)
- Nour-el-Hana Abbassi
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
| | - Ting-Yu Lin
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland; (N.-e.-H.A.); (A.B.)
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6
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Yoo H, Lee YJ, Park C, Son D, Choi DY, Park JH, Choi HJ, La HW, Choi YJ, Moon EH, Saur D, Chung HM, Song H, Do JT, Jang H, Lee DR, Park C, Lee OH, Cho SG, Hong SH, Kong G, Kim JH, Choi Y, Hong K. Epigenetic priming by Dot1l in lymphatic endothelial progenitors ensures normal lymphatic development and function. Cell Death Dis 2020; 11:14. [PMID: 31908356 PMCID: PMC6944698 DOI: 10.1038/s41419-019-2201-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/08/2019] [Accepted: 12/09/2019] [Indexed: 11/20/2022]
Abstract
Proper functioning of the lymphatic system is required for normal immune responses, fluid balance, and lipid reabsorption. Multiple regulatory mechanisms are employed to ensure the correct formation and function of lymphatic vessels; however, the epigenetic modulators and mechanisms involved in this process are poorly understood. Here, we assess the regulatory role of mouse Dot1l, a histone H3 lysine (K) 79 (H3K79) methyltransferase, in lymphatic formation. Genetic ablation of Dot1l in Tie2(+) endothelial cells (ECs), but not in Lyve1(+) or Prox1(+) lymphatic endothelial cells (LECs) or Vav1(+) definitive hematopoietic stem cells, leads to catastrophic lymphatic anomalies, including skin edema, blood–lymphatic mixing, and underdeveloped lymphatic valves and vessels in multiple organs. Remarkably, targeted Dot1l loss in Tie2(+) ECs leads to fully penetrant lymphatic aplasia, whereas Dot1l overexpression in the same cells results in partially hyperplastic lymphatics in the mesentery. Genetic studies reveal that Dot1l functions in c-Kit(+) hemogenic ECs during mesenteric lymphatic formation. Mechanistically, inactivation of Dot1l causes a reduction of both H3K79me2 levels and the expression of genes important for LEC development and function. Thus, our study establishes that Dot1l-mediated epigenetic priming and transcriptional regulation in LEC progenitors safeguard the proper lymphatic development and functioning of lymphatic vessels.
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Affiliation(s)
- Hyunjin Yoo
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Young Jae Lee
- Lee Gil Ya Cancer and Diabetes Institute, Korea Mouse Phenotyping Center (KMPC), Gachon University, Incheon, Yeonsu-gu, 21999, Republic of Korea
| | - Chanhyeok Park
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Dabin Son
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Dong Yoon Choi
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Ji-Hyun Park
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Hee-Jin Choi
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Hyun Woo La
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Yun-Jung Choi
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Eun-Hye Moon
- Lee Gil Ya Cancer and Diabetes Institute, Korea Mouse Phenotyping Center (KMPC), Gachon University, Incheon, Yeonsu-gu, 21999, Republic of Korea
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Baden-Württemberg, Heidelberg, 69120, Germany.,Department of Medicine II and Institute of Translational Cancer Research, Klinikum rechts der Isar, Technische Universität München, Bavaria, München, 81675, Germany
| | - Hyung Min Chung
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Hyuk Song
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Hoon Jang
- Department of Biomedical Science, CHA University, Seongnam, Bundang-gu, 13488, Republic of Korea
| | - Dong Ryul Lee
- Department of Biomedical Science, CHA University, Seongnam, Bundang-gu, 13488, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Ok-Hee Lee
- Department of Biomedical Science, CHA University, Seongnam, Bundang-gu, 13488, Republic of Korea
| | - Ssang-Goo Cho
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Gu Kong
- Department of Pathology, College of Medicine, Hanyang University, Seoul, Seongdong-gu, 04763, Republic of Korea
| | - Jin-Hoi Kim
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea
| | - Youngsok Choi
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea.
| | - Kwonho Hong
- Department of Stem Cell & Regenerative Biotechnology, Humanized Pig Research Center (SRC), Konkuk University, Seoul, Gwangjin-gu, 05029, Republic of Korea.
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7
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Thornlow BP, Armstrong J, Holmes AD, Howard JM, Corbett-Detig RB, Lowe TM. Predicting transfer RNA gene activity from sequence and genome context. Genome Res 2020; 30:85-94. [PMID: 31857444 PMCID: PMC6961574 DOI: 10.1101/gr.256164.119] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/12/2019] [Indexed: 01/25/2023]
Abstract
Transfer RNA (tRNA) genes are among the most highly transcribed genes in the genome owing to their central role in protein synthesis. However, there is evidence for a broad range of gene expression across tRNA loci. This complexity, combined with difficulty in measuring transcript abundance and high sequence identity across transcripts, has severely limited our collective understanding of tRNA gene expression regulation and evolution. We establish sequence-based correlates to tRNA gene expression and develop a tRNA gene classification method that does not require, but benefits from, comparative genomic information and achieves accuracy comparable to molecular assays. We observe that guanine + cytosine (G + C) content and CpG density surrounding tRNA loci is exceptionally well correlated with tRNA gene activity, supporting a prominent regulatory role of the local genomic context in combination with internal sequence features. We use our tRNA gene activity predictions in conjunction with a comprehensive tRNA gene ortholog set spanning 29 placental mammals to estimate the evolutionary rate of functional changes among orthologs. Our method adds a new dimension to large-scale tRNA functional prediction and will help prioritize characterization of functional tRNA variants. Its simplicity and robustness should enable development of similar approaches for other clades, as well as exploration of functional diversification of members of large gene families.
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Affiliation(s)
- Bryan P Thornlow
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Joel Armstrong
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, California 95064, USA
| | - Andrew D Holmes
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Jonathan M Howard
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, California 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, California 95064, USA
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8
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Krutyhołowa R, Hammermeister A, Zabel R, Abdel-Fattah W, Reinhardt-Tews A, Helm M, Stark MJR, Breunig KD, Schaffrath R, Glatt S. Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Nucleic Acids Res 2019; 47:4814-4830. [PMID: 30916349 PMCID: PMC6511879 DOI: 10.1093/nar/gkz190] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/14/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Posttranscriptional RNA modifications occur in all domains of life. Modifications of anticodon bases are of particular importance for ribosomal decoding and proteome homeostasis. The Elongator complex modifies uridines in the wobble position and is highly conserved in eukaryotes. Despite recent insights into Elongator's architecture, the structure and function of its regulatory factor Kti12 have remained elusive. Here, we present the crystal structure of Kti12′s nucleotide hydrolase domain trapped in a transition state of ATP hydrolysis. The structure reveals striking similarities to an O-phosphoseryl-tRNA kinase involved in the selenocysteine pathway. Both proteins employ similar mechanisms of tRNA binding and show tRNASec-dependent ATPase activity. In addition, we demonstrate that Kti12 binds directly to Elongator and that ATP hydrolysis is crucial for Elongator to maintain proper tRNA anticodon modification levels in vivo. In summary, our data reveal a hitherto uncharacterized link between two translational control pathways that regulate selenocysteine incorporation and affect ribosomal tRNA selection via specific tRNA modifications.
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Affiliation(s)
- Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Rene Zabel
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | | | - Mark Helm
- Institut für Pharmazie und Biochemie, Universität Mainz, Mainz, Germany
| | - Michael J R Stark
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, UK
| | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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9
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Forward Genetic Screen for Caenorhabditis elegans Mutants with a Shortened Locomotor Healthspan. G3-GENES GENOMES GENETICS 2019; 9:2415-2423. [PMID: 31213517 PMCID: PMC6686916 DOI: 10.1534/g3.119.400241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two people with the same lifespan do not necessarily have the same healthspan. One person may retain locomotor and cognitive abilities until the end of life, while another person may lose them during adulthood. Unbiased searches for genes that are required to maintain locomotor ability during adulthood may uncover key regulators of locomotor healthspan. Here, we take advantage of the relatively short lifespan of the nematode Caenorhabditis elegans and develop a novel screening procedure to collect mutants with locomotor deficits that become apparent in adulthood. After ethyl methanesulfonate mutagenesis, we isolated five C. elegans mutant strains that progressively lose adult locomotor ability. In one of the mutant strains, a nonsense mutation in elpc-2, which encodes Elongator Complex Protein Component 2, causes a progressive decline in locomotor ability during adulthood. Mutants and mutations identified in the present screen may provide insights into mechanisms of age-related locomotor impairment and the maintenance of locomotor healthspan.
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10
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Stafuzza NB, Silva RMDO, Fragomeni BDO, Masuda Y, Huang Y, Gray K, Lourenco DAL. A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive. BMC Genomics 2019; 20:321. [PMID: 31029102 PMCID: PMC6487013 DOI: 10.1186/s12864-019-5687-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Background In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs. Results A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained. The PennCNV algorithm identified 46,118 CNVs, which were aggregated by overlapping in 425 CNV regions (CNVRs) ranging from 2.5 Kb to 9718.4 Kb and covering 197 Mb (~ 7.01%) of the pig autosomal genome. The WssGWAS identified 16 genomic regions explaining more than 1% of the additive genetic variance for number of piglets born alive. The overlap between CNVR and WssGWAS analyses identified common regions on SSC2 (4.2–5.2 Mb), SSC3 (3.9–4.9 Mb), SSC12 (56.6–57.6 Mb), and SSC17 (17.3–18.3 Mb). Those regions are known for harboring important causative variants for pig reproductive traits based on their crucial functions in fertilization, development of gametes and embryos. Functional analysis by the Panther software identified 13 gene ontology biological processes significantly represented in this study such as reproduction, developmental process, cellular component organization or biogenesis, and immune system process, which plays relevant roles in swine reproductive traits. Conclusion Our research helps to improve the understanding of the genetic architecture of number of piglets born alive, given that the combination of GWAS and CNV analyses allows for a more efficient identification of the genomic regions and biological processes associated with this trait in Duroc pigs. Pig breeding programs could potentially benefit from a more accurate discovery of important genomic regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Department of Exact Science, School of Agricultural and Veterinarian Sciences (FCAV), Sao Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Rafael Medeiros de Oliveira Silva
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.,National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | | | - Yutaka Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Yijian Huang
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
| | - Kent Gray
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
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11
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Bento-Abreu A, Jager G, Swinnen B, Rué L, Hendrickx S, Jones A, Staats KA, Taes I, Eykens C, Nonneman A, Nuyts R, Timmers M, Silva L, Chariot A, Nguyen L, Ravits J, Lemmens R, Cabooter D, Van Den Bosch L, Van Damme P, Al-Chalabi A, Bystrom A, Robberecht W. Elongator subunit 3 (ELP3) modifies ALS through tRNA modification. Hum Mol Genet 2019; 27:1276-1289. [PMID: 29415125 PMCID: PMC6159532 DOI: 10.1093/hmg/ddy043] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal degenerative motor neuron disorder of which the progression is influenced by several disease-modifying factors. Here, we investigated ELP3, a subunit of the elongator complex that modifies tRNA wobble uridines, as one of such ALS disease modifiers. ELP3 attenuated the axonopathy of a mutant SOD1, as well as of a mutant C9orf72 ALS zebrafish model. Furthermore, the expression of ELP3 in the SOD1G93A mouse extended the survival and attenuated the denervation in this model. Depletion of ELP3 in vitro reduced the modified tRNA wobble uridine mcm5s2U and increased abundance of insoluble mutant SOD1, which was reverted by exogenous ELP3 expression. Interestingly, the expression of ELP3 in the motor cortex of ALS patients was reduced and correlated with mcm5s2U levels. Our results demonstrate that ELP3 is a modifier of ALS and suggest a link between tRNA modification and neurodegeneration.
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Affiliation(s)
- Andre Bento-Abreu
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Gunilla Jager
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Bart Swinnen
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Laura Rué
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Stijn Hendrickx
- Department of Pharmaceutical & Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ashley Jones
- Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Kim A Staats
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Ines Taes
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Caroline Eykens
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Annelies Nonneman
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Rik Nuyts
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Mieke Timmers
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Lara Silva
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Alain Chariot
- GIGA-Molecular Biology of Diseases and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), C.H.U. Sart Tilman, B-4000 Liège, Belgium
| | - Laurent Nguyen
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, B-4000 Liège, Belgium
| | - John Ravits
- Department of Neurosciences, ALS Translational Research, University of California, San Diego, La Jolla, CA, USA
| | - Robin Lemmens
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Deirdre Cabooter
- Department of Pharmaceutical & Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Ammar Al-Chalabi
- Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Anders Bystrom
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
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12
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Abstract
RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programs. They affect diverse eukaryotic biological processes, and the correct deposition of many of these modifications is required for normal development. Messenger RNA (mRNA) modifications regulate various aspects of mRNA metabolism. For example, N 6-methyladenosine (m6A) affects the translation and stability of the modified transcripts, thus providing a mechanism to coordinate the regulation of groups of transcripts during cell state maintenance and transition. Similarly, some modifications in transfer RNAs are essential for RNA structure and function. Others are deposited in response to external cues and adapt global protein synthesis and gene-specific translational accordingly and thereby facilitate proper development.
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Affiliation(s)
- Michaela Frye
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
- German Cancer Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Bryan T Harada
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Mikaela Behm
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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13
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Yu D, Tan Y, Chakraborty M, Tomchik S, Davis RL. Elongator complex is required for long-term olfactory memory formation in Drosophila. Learn Mem 2018; 25:183-196. [PMID: 29545390 PMCID: PMC5855525 DOI: 10.1101/lm.046557.117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/12/2018] [Indexed: 12/13/2022]
Abstract
The evolutionarily conserved Elongator Complex associates with RNA polymerase II for transcriptional elongation. Elp3 is the catalytic subunit, contains histone acetyltransferase activity, and is associated with neurodegeneration in humans. Elp1 is a scaffolding subunit and when mutated causes familial dysautonomia. Here, we show that elp3 and elp1 are required for aversive long-term olfactory memory in Drosophila RNAi knockdown of elp3 in adult mushroom bodies impairs long-term memory (LTM) without affecting earlier forms of memory. RNAi knockdown with coexpression of elp3 cDNA reverses the impairment. Similarly, RNAi knockdown of elp1 impairs LTM and coexpression of elp1 cDNA reverses this phenotype. The LTM deficit in elp3 and elp1 knockdown flies is accompanied by the abolishment of a LTM trace, which is registered as increased calcium influx in response to the CS+ odor in the α-branch of mushroom body neurons. Coexpression of elp1 or elp3 cDNA rescues the memory trace in parallel with LTM. These data show that the Elongator complex is required in adult mushroom body neurons for long-term behavioral memory and the associated long-term memory trace.
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Affiliation(s)
- Dinghui Yu
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Ying Tan
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Molee Chakraborty
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, Florida 33458, USA
| | - Seth Tomchik
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, Florida 33458, USA
| | - Ronald L Davis
- Department of Neuroscience, Scripps Research Institute Florida, Jupiter, Florida 33458, USA
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14
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Dauden MI, Jaciuk M, Müller CW, Glatt S. Structural asymmetry in the eukaryotic Elongator complex. FEBS Lett 2017; 592:502-515. [DOI: 10.1002/1873-3468.12865] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/08/2017] [Accepted: 09/24/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Maria I. Dauden
- Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
| | - Marcin Jaciuk
- Max Planck Research Group at the Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
| | - Christoph W. Müller
- Structural and Computational Biology Unit European Molecular Biology Laboratory Heidelberg Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
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15
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Kolaj-Robin O, Séraphin B. Structures and Activities of the Elongator Complex and Its Cofactors. RNA MODIFICATION 2017; 41:117-149. [DOI: 10.1016/bs.enz.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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