1
|
Kyrgiafini MA, Vasilev VV, Chatziparasidou A, Mamuris Z. ΜicroRNA (miRNA) Variants in Male Infertility: Insights from Whole-Genome Sequencing. Genes (Basel) 2024; 15:1393. [PMID: 39596593 PMCID: PMC11593656 DOI: 10.3390/genes15111393] [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: 09/08/2024] [Revised: 10/14/2024] [Accepted: 10/24/2024] [Indexed: 11/28/2024] Open
Abstract
BACKGROUND/OBJECTIVES Male infertility is a complex condition with various underlying genetic factors. microRNAs (miRNAs) play a crucial role in gene regulation, and their disruption can significantly impact fertility. This study aimed to identify variants within miRNA genes and elucidate their impact on male infertility. METHODS Whole genome sequencing was performed on blood samples from men with asthenozoospermia, oligozoospermia, and teratozoospermia, compared to normozoospermic controls. The analysis revealed a significant number of unique variants in each infertile group. We subsequently focused on variants in miRNA regions, followed by an in silico analysis to investigate the role of the identified variants and miRNAs in male infertility. RESULTS Focused analysis on miRNA genes identified 19 exclusive variants in teratozoospermic men, 24 in asthenozoospermic, and 27 in oligozoospermic, all mapping to pre-miRNAs or mature miRNAs. Functional analyses using Gene Ontology (GO) and KEGG pathways highlighted key biological processes and pathways disrupted by these variants and miRNA-mRNA interactions, including transcription regulation, signaling, and cancer-related pathways. Furthermore, six variants (rs17797090, rs1844035, rs7210937, rs451887, rs12233076, and rs6787734) were common across the infertile groups, suggesting their importance in male infertility or their potential as biomarkers. Common variants were also validated in another clinically relevant group of men. Some miRNAs with identified variants, such as hsa-miR-449b and hsa-miR-296, have been previously implicated in male infertility and exhibit differential expression between fertile and infertile men, according to the literature, too. CONCLUSION These results provide new insights into the genetic basis of male infertility and open avenues for future research and therapeutic interventions.
Collapse
Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Veselin Veselinov Vasilev
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Alexia Chatziparasidou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
- Embryolab IVF Unit, St. 173-175 Ethnikis Antistaseos, Kalamaria, 55134 Thessaloniki, Greece
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| |
Collapse
|
2
|
Chaverra M, Cheney AM, Scheel A, Miller A, George L, Schultz A, Henningsen K, Kominsky D, Walk H, Kennedy WR, Kaufmann H, Walk S, Copié V, Lefcort F. ELP1, the Gene Mutated in Familial Dysautonomia, Is Required for Normal Enteric Nervous System Development and Maintenance and for Gut Epithelium Homeostasis. J Neurosci 2024; 44:e2253232024. [PMID: 39138000 PMCID: PMC11391678 DOI: 10.1523/jneurosci.2253-23.2024] [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: 11/20/2023] [Revised: 07/31/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024] Open
Abstract
Familial dysautonomia (FD) is a rare sensory and autonomic neuropathy that results from a mutation in the ELP1 gene. Virtually all patients report gastrointestinal (GI) dysfunction and we have recently shown that FD patients have a dysbiotic gut microbiome and altered metabolome. These findings were recapitulated in an FD mouse model and moreover, the FD mice had reduced intestinal motility, as did patients. To understand the cellular basis for impaired GI function in FD, the enteric nervous system (ENS; both female and male mice) from FD mouse models was analyzed during embryonic development and adulthood. We show here that not only is Elp1 required for the normal formation of the ENS, but it is also required in adulthood for the regulation of both neuronal and non-neuronal cells and for target innervation in both the mucosa and in intestinal smooth muscle. In particular, CGRP innervation was significantly reduced as was the number of dopaminergic neurons. Examination of an FD patient's gastric biopsy also revealed reduced and disoriented axons in the mucosa. Finally, using an FD mouse model in which Elp1 was deleted exclusively from neurons, we found significant changes to the colon epithelium including reduced E-cadherin expression, perturbed mucus layer organization, and infiltration of bacteria into the mucosa. The fact that deletion of Elp1 exclusively in neurons is sufficient to alter the intestinal epithelium and perturb the intestinal epithelial barrier highlights a critical role for neurons in regulating GI epithelium homeostasis.
Collapse
Affiliation(s)
- Marta Chaverra
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Alexandra M Cheney
- Biochemistry and Chemistry, Montana State University, Bozeman, Montana 59717
| | - Alpha Scheel
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Alessa Miller
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Lynn George
- Department of Biological and Physical Sciences, Montana State University, Billings, Montana 59101
| | - Anastasia Schultz
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Katelyn Henningsen
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Douglas Kominsky
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Heather Walk
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - William R Kennedy
- Department of Neurology, University of Minnesota, Minneapolis, Minnesota 55455
| | - Horacio Kaufmann
- Department of Neurology, New York University School of Medicine, New York, New York 10016
| | - Seth Walk
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| | - Valérie Copié
- Biochemistry and Chemistry, Montana State University, Bozeman, Montana 59717
| | - Frances Lefcort
- Departments of Microbiology and Cell Biology, Montana State University, Bozeman, Montana 59717
| |
Collapse
|
3
|
Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
Collapse
Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
| |
Collapse
|
4
|
Dalwadi U, Mannar D, Zierhut F, Yip CK. Biochemical and Structural Characterization of Human Core Elongator and Its Subassemblies. ACS OMEGA 2022; 7:3424-3433. [PMID: 35128251 PMCID: PMC8811885 DOI: 10.1021/acsomega.1c05719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Conserved from yeast to humans and composed of six core subunits (Elp1-Elp6), Elongator is a multiprotein complex that catalyzes the modification of the anticodon loop of transfer RNAs (tRNAs) and in turn regulates messenger RNA decoding efficiency. Previous studies showed that yeast Elongator consists of two subassemblies (yElp1/2/3 and yElp4/5/6) and adopts an asymmetric overall architecture. Yet, much less is known about the structural properties of the orthologous human Elongator. Furthermore, the order in which the different Elongator subunits come together to form the full assembly as well as how they coordinate with one another to catalyze tRNA modification is not fully understood. Here, we purified recombinant human Elongator subunits and subassemblies and examined them by single-particle electron microscopy. We found that the human Elongator complex is assembled from two subcomplexes that share similar overall morphologies as their yeast counterparts. Complementary co-purification and pulldown assays revealed that the scaffolding subunit human ELP1 (hELP1) has stabilizing effects on the human ELP3 catalytic subunit. Furthermore, the peripheral hELP2 subunit appears to enhance the integrity and substrate-binding ability of the dimeric hELP1/2/3. Lastly, we found that hELP4/5/6 is recruited to hELP1/2/3 via hELP3. Collectively, our work generated insights into the assembly process of core human Elongator and the coordination of different subunits within this complex.
Collapse
|
5
|
WEI YS, LIN WZ, WANG TE, LEE WY, LI SH, LIN FJ, NIXON B, SIPILÄ P, TSAI PS. Polarized epithelium-sperm co-culture system reveals stimulatory factors for the secretion of mouse epididymal quiescin sulfhydryl oxidase 1. J Reprod Dev 2022; 68:198-208. [PMID: 35228412 PMCID: PMC9184822 DOI: 10.1262/jrd.2021-128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Spermatozoa acquire fertilization ability through post-translational modifications. These membrane surface alterations occur in various segments of the epididymis. Quiescin sulfhydryl
oxidases, which catalyze thiol-oxidation reactions, are involved in disulfide bond formation, which is essential for sperm maturation, upon transition and migration in the epididymis. Using
castration and azoospermia transgenic mouse models, in the present study, we showed that quiescin sulfhydryl oxidase 1 (QSOX1) protein expression and secretion are positively correlated with
the presence of testosterone and sperm cells. A two-dimensional in vitro epithelium-sperm co-culture system provided further evidence in support of the notion that both
testosterone and its dominant metabolite, 5α-dihydrotestosterone, promote epididymal QSOX1 secretion. We also demonstrated that immature caput spermatozoa, but not mature cauda sperm cells,
exhibited great potential to stimulate QSOX1 secretion in vitro, suggesting that sperm maturation is a key regulatory factor for mouse epididymal QSOX1 secretion. Proteomic
analysis identified 582 secretory proteins from the co-culture supernatant, of which 258 were sperm-specific and 154 were of epididymal epithelium-origin. Gene Ontology analysis indicated
that these secreted proteins exhibit functions known to facilitate sperm membrane organization, cellular activity, and sperm-egg recognition. Taken together, our data demonstrated that
testosterone and sperm maturation status are key regulators of mouse epididymal QSOX1 protein expression and secretion.
Collapse
Affiliation(s)
- Yu-Syuan WEI
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Wan-Zhen LIN
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Tse-En WANG
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Yun LEE
- Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Sheng-Hsiang LI
- Department of Medical Research, Mackay Memorial Hospital, Tamshui 25160, Taiwan
| | - Fu-Jung LIN
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Brett NIXON
- Priority Research Centre for Reproduction, School of Environmental and Life Sciences, Discipline of Biological Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Petra SIPILÄ
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku 20520, Finland
| | - Pei-Shiue TSAI
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
6
|
Chen WT, Tseng HY, Jiang CL, Lee CY, Chi P, Chen LY, Lo KY, Wang IC, Lin FJ. Elp1 facilitates RAD51-mediated homologous recombination repair via translational regulation. J Biomed Sci 2021; 28:81. [PMID: 34819065 PMCID: PMC8613991 DOI: 10.1186/s12929-021-00773-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022] Open
Abstract
Background RAD51-dependent homologous recombination (HR) is one of the most important pathways for repairing DNA double-strand breaks (DSBs), and its regulation is crucial to maintain genome integrity. Elp1 gene encodes IKAP/ELP1, a core subunit of the Elongator complex, which has been implicated in translational regulation. However, how ELP1 contributes to genome maintenance is unclear. Methods To investigate the function of Elp1, Elp1-deficient mouse embryonic fibroblasts (MEFs) were generated. Metaphase chromosome spreading, immunofluorescence, and comet assays were used to access chromosome abnormalities and DSB formation. Functional roles of Elp1 in MEFs were evaluated by cell viability, colony forming capacity, and apoptosis assays. HR-dependent DNA repair was assessed by reporter assay, immunofluorescence, and western blot. Polysome profiling was used to evaluate translational efficiency. Differentially expressed proteins and signaling pathways were identified using a label-free liquid chromatography–tandem mass spectrometry (LC–MS/MS) proteomics approach. Results Here, we report that Elp1 depletion enhanced genomic instability, manifested as chromosome breakage and genotoxic stress-induced genomic DNA fragmentation upon ionizing radiation (IR) exposure. Elp1-deficient cells were hypersensitive to DNA damage and exhibited impaired cell proliferation and defective HR repair. Moreover, Elp1 depletion reduced the formation of IR-induced RAD51 foci and decreased RAD51 protein levels. Polysome profiling analysis revealed that ELP1 regulated RAD51 expression by promoting its translation in response to DNA damage. Notably, the requirement for ELP1 in DSB repair could be partially rescued in Elp1-deficient cells by reintroducing RAD51, suggesting that Elp1-mediated HR-directed repair of DSBs is RAD51-dependent. Finally, using proteome analyses, we identified several proteins involved in cancer pathways and DNA damage responses as being differentially expressed upon Elp1 depletion. Conclusions Our study uncovered a molecular mechanism underlying Elp1-mediated regulation of HR activity and provides a novel link between translational regulation and genome stability. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-021-00773-z.
Collapse
Affiliation(s)
- Wei-Ting Chen
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Huan-Yi Tseng
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chung-Lin Jiang
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan
| | - Chih-Ying Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Liuh-Yow Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - I-Ching Wang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Fu-Jung Lin
- Department of Biochemical Science and Technology, National Taiwan University, No.1, Sec.4, Roosevelt Rd., Taipei, 10617, Taiwan. .,Research Center for Development Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan.
| |
Collapse
|
7
|
Genetic Association of the Functional WDR4 Gene in Male Fertility. J Pers Med 2021; 11:jpm11080760. [PMID: 34442404 PMCID: PMC8399419 DOI: 10.3390/jpm11080760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 11/19/2022] Open
Abstract
Infertility is one of the important problems in the modern world. Male infertility is characterized by several clinical manifestations, including low sperm production (oligozoospermia), reduced sperm motility (asthenozoospermia), and abnormal sperm morphology (teratozoospermia). WDR4, known as Wuho, controls fertility in Drosophila. However, it is unclear whether WDR4 is associated with clinical manifestations of male fertility in human. Here, we attempted to determine the physiological functions of WDR4 gene. Two cohorts were applied to address this question. The first cohort was the general population from Taiwan Biobank. Genomic profiles from 68,948 individuals and 87 common physiological traits were applied for phenome-wide association studies (PheWAS). The second cohort comprised patients with male infertility from Wan Fang Hospital, Taipei Medical University. In total, 81 male participants were recruited for the genetic association study. Clinical records including gender, age, total testosterone, follicle-stimulating hormone (FSH), luteinizing hormone (LH), total sperm number, sperm motility, and sperm morphology were collected. In the first cohort, results from PheWAS exhibited no associations between WDR4 genetic variants and 87 common physiological traits. In the second cohort, a total of four tagging single-nucleotide polymorphisms (tSNPs) from WDR4 gene (rs2298666, rs465663, rs2248490, and rs3746939) were selected for genotyping. We found that SNP rs465663 solely associated with asthenozoospermia. Functional annotations through the GTEx portal revealed the correlation between TT or TC genotype and low expression of WDR4. Furthermore, we used mouse embryonic fibroblasts cells from mwdr4 heterozygous (+/‒) mice for functional validation by western blotting. Indeed, low expression of WDR4 contributed to ROS-induced DNA fragmentation. In conclusion, our results suggest a critical role of WDR4 gene variant as well as protein expression in asthenozoospermia.
Collapse
|
8
|
Tao L, He XY, Wang FY, Pan LX, Wang XY, Gan SQ, Di R, Chu MX. Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep. Anim Genet 2021; 52:545-549. [PMID: 34002409 DOI: 10.1111/age.13078] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
Litter size is one of the most important reproductive traits of sheep, which has pronounced effects on the profit of husbandry enterprises and enthusiasm of breeders. Despite the importance of litter size, the underlying genetic mechanisms have not been entirely elucidated. Therefore, based on a high-density SNP chip, genome-wide comparative analysis was performed between two groups with different fecundity to reveal candidate genes linked to litter size via detection of homozygosity and selection signatures in Luzhong mutton sheep. Consequently, nine promising genes were identified from six runs of homozygosity islands, and functionally linked to reproduction (ACTL7A, ACTL7B, and ELP1), embryonic development (KLF5 and PIBF1), and cell cycle (DACH1, BORA, DIS3, and MZT1). A total of 128 genes were observed under selection, of which HECW1 and HTR1E were related to total lambs born, GABRG3, LRP1B, and MACROD2 to teat number, and AGBL1 to reproductive seasonality. Additionally, the presence of inbreeding depression implies the urgency of reasonable mating system to increase litter size in the present herd. These findings provide a comprehensive insight to the genetic makeup of litter size, and also contribute to implementation of marker-assisted selection in sheep.
Collapse
Affiliation(s)
- L Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - X Y He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - F Y Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L X Pan
- Ji'nan Laiwu Yingtai Agriculture and Animal Husbandry Technology Co., Ltd, Ji'nan, Shandong, 271114, China
| | - X Y Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - S Q Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang, 832000, China
| | - R Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - M X Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| |
Collapse
|
9
|
Chujo T, Tomizawa K. Human transfer RNA modopathies: diseases caused by aberrations in transfer RNA modifications. FEBS J 2021; 288:7096-7122. [PMID: 33513290 PMCID: PMC9255597 DOI: 10.1111/febs.15736] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/13/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
tRNA molecules are post-transcriptionally modified by tRNA modification enzymes. Although composed of different chemistries, more than 40 types of human tRNA modifications play pivotal roles in protein synthesis by regulating tRNA structure and stability as well as decoding genetic information on mRNA. Many tRNA modifications are conserved among all three kingdoms of life, and aberrations in various human tRNA modification enzymes cause life-threatening diseases. Here, we describe the class of diseases and disorders caused by aberrations in tRNA modifications as 'tRNA modopathies'. Aberrations in over 50 tRNA modification enzymes are associated with tRNA modopathies, which most frequently manifest as dysfunctions of the brain and/or kidney, mitochondrial diseases, and cancer. However, the molecular mechanisms that link aberrant tRNA modifications to human diseases are largely unknown. In this review, we provide a comprehensive compilation of human tRNA modification functions, tRNA modification enzyme genes, and tRNA modopathies, and we summarize the elucidated pathogenic mechanisms underlying several tRNA modopathies. We will also discuss important questions that need to be addressed in order to understand the molecular pathogenesis of tRNA modopathies.
Collapse
Affiliation(s)
- Takeshi Chujo
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Japan
| |
Collapse
|
10
|
Schäck MA, Jablonski KP, Gräf S, Klassen R, Schaffrath R, Kellner S, Hammann C. Eukaryotic life without tQCUG: the role of Elongator-dependent tRNA modifications in Dictyostelium discoideum. Nucleic Acids Res 2020; 48:7899-7913. [PMID: 32609816 PMCID: PMC7430636 DOI: 10.1093/nar/gkaa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022] Open
Abstract
In the Elongator-dependent modification pathway, chemical modifications are introduced at the wobble uridines at position 34 in transfer RNAs (tRNAs), which serve to optimize codon translation rates. Here, we show that this three-step modification pathway exists in Dictyostelium discoideum, model of the evolutionary superfamily Amoebozoa. Not only are previously established modifications observable by mass spectrometry in strains with the most conserved genes of each step deleted, but also additional modifications are detected, indicating a certain plasticity of the pathway in the amoeba. Unlike described for yeast, D. discoideum allows for an unconditional deletion of the single tQCUG gene, as long as the Elongator-dependent modification pathway is intact. In gene deletion strains of the modification pathway, protein amounts are significantly reduced as shown by flow cytometry and Western blotting, using strains expressing different glutamine leader constructs fused to GFP. Most dramatic are these effects, when the tQCUG gene is deleted, or Elp3, the catalytic component of the Elongator complex is missing. In addition, Elp3 is the most strongly conserved protein of the modification pathway, as our phylogenetic analysis reveals. The implications of this observation are discussed with respect to the evolutionary age of the components acting in the Elongator-dependent modification pathway.
Collapse
Affiliation(s)
- Manfred A Schäck
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Kim Philipp Jablonski
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Stefanie Kellner
- Department of Chemistry and Pharmacy, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, DE 28759 Bremen, Germany
| |
Collapse
|
11
|
Plant Elongator-Protein Complex of Diverse Activities Regulates Growth, Development, and Immune Responses. Int J Mol Sci 2020; 21:ijms21186912. [PMID: 32971769 PMCID: PMC7555253 DOI: 10.3390/ijms21186912] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/23/2022] Open
Abstract
Contrary to the conserved Elongator composition in yeast, animals, and plants, molecular functions and catalytic activities of the complex remain controversial. Elongator was identified as a component of elongating RNA polymerase II holoenzyme in yeast, animals, and plants. Furthermore, it was suggested that Elonagtor facilitates elongation of transcription via histone acetyl transferase activity. Accordingly, phenotypes of Arabidopsis elo mutants, which show development, growth, or immune response defects, correlate with transcriptional downregulation and the decreased histone acetylation in the coding regions of crucial genes. Plant Elongator was also implicated in other processes: transcription and processing of miRNA, regulation of DNA replication by histone acetylation, and acetylation of alpha-tubulin. Moreover, tRNA modification, discovered first in yeast and confirmed in plants, was claimed as the main activity of Elongator, leading to specificity in translation that might also result indirectly in a deficiency in transcription. Heterologous overexpression of individual Arabidopsis Elongator subunits and their respective phenotypes suggest that single Elongator subunits might also have another function next to being a part of the complex. In this review, we shall present the experimental evidence of all molecular mechanisms and catalytic activities performed by Elongator in nucleus and cytoplasm of plant cells, which might explain how Elongator regulates growth, development, and immune responses.
Collapse
|
12
|
Rojas-Benítez D, L. Allende M. Elongator Subunit 3 (Elp3) Is Required for Zebrafish Trunk Development. Int J Mol Sci 2020; 21:E925. [PMID: 32023806 PMCID: PMC7036906 DOI: 10.3390/ijms21030925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/02/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Transfer RNAs (tRNAs) are the most post-transcriptionally modified RNA species. Some of these modifications, especially the ones located in the anti-codon loop, are required for decoding capabilities of tRNAs. Such is the case for 5-methoxy-carbonyl-methyl-2-thio-uridine (mcm5s2U), synthetized by the Elongator complex. Mutants for its sub-units display pleiotropic phenotypes. In this paper, we analyze the role of elp3 (Elongator catalytic sub-unit) in zebrafish development. We found that it is required for trunk development; elp3 knock-down animals presented diminished levels of mcm5s2U and sonic hedgehog (Shh) signaling activity. Activation of this pathway was sufficient to revert the phenotype caused by elp3 knockdown, indicating a functional relationship between Elongator and Shh through a yet unknown molecular mechanism.
Collapse
Affiliation(s)
- Diego Rojas-Benítez
- FONDAP Center for Genome Regulation (CGR), Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | | |
Collapse
|
13
|
Yang KT, Inoue A, Lee YJ, Jiang CL, Lin FJ. Loss of Ikbkap/Elp1 in mouse oocytes causes spindle disorganization, developmental defects in preimplantation embryos and impaired female fertility. Sci Rep 2019; 9:18875. [PMID: 31827135 PMCID: PMC6906334 DOI: 10.1038/s41598-019-55090-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/23/2019] [Indexed: 01/08/2023] Open
Abstract
Elongator complexes are well known to be involved in a wide variety of cellular processes; however, their functions in mammalian oocytes have not been characterized. Here, we demonstrated in mice that specific deletion of one of the core subunits, Ikbkap/Elp1, in oocytes resulted in spindle defects and chromosome disorganization without affecting folliculogenesis. In accordance with these findings, we observed that Ikbkap mutant female mice are subfertile. Further analyses uncovered that kinetochore–microtubule attachments are severely compromised in Ikbkap-deficient oocytes. Moreover, we revealed that Ikbkap modulates the acetylation status of α-tubulin in oocytes, which may at least in part mediate the meiotic phenotypes described above by affecting microtubule dynamics and kinetochore function. Finally, we showed that embryos derived from Ikbkap-deficient oocytes exhibit an increased frequency of aneuploidy, digyny, progressive delays in preimplantation development, and severe degeneration before reaching the blastocyst stage. In summary, we identify Ikbkap as an important player in regulating oocyte meiosis by modulating tubulin acetylation for chromosome/spindle organization.
Collapse
Affiliation(s)
- Kuo-Tai Yang
- Department of Animal Science, National Pingtung University of Science and Technology, 91201, Pingtung, Taiwan
| | - Azusa Inoue
- Howard Hughes Medical Institute, Harvard Medical School, 02115, Boston, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, 02115, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.,RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yi-Jing Lee
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chung-Lin Jiang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Fu-Jung Lin
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan. .,Research Center for Development Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan.
| |
Collapse
|
14
|
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: 7.7] [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.
Collapse
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
| |
Collapse
|
15
|
Roles of Elongator Dependent tRNA Modification Pathways in Neurodegeneration and Cancer. Genes (Basel) 2018; 10:genes10010019. [PMID: 30597914 PMCID: PMC6356722 DOI: 10.3390/genes10010019] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 02/07/2023] Open
Abstract
Transfer RNA (tRNA) is subject to a multitude of posttranscriptional modifications which can profoundly impact its functionality as the essential adaptor molecule in messenger RNA (mRNA) translation. Therefore, dynamic regulation of tRNA modification in response to environmental changes can tune the efficiency of gene expression in concert with the emerging epitranscriptomic mRNA regulators. Several of the tRNA modifications are required to prevent human diseases and are particularly important for proper development and generation of neurons. In addition to the positive role of different tRNA modifications in prevention of neurodegeneration, certain cancer types upregulate tRNA modification genes to sustain cancer cell gene expression and metastasis. Multiple associations of defects in genes encoding subunits of the tRNA modifier complex Elongator with human disease highlight the importance of proper anticodon wobble uridine modifications (xm⁵U34) for health. Elongator functionality requires communication with accessory proteins and dynamic phosphorylation, providing regulatory control of its function. Here, we summarized recent insights into molecular functions of the complex and the role of Elongator dependent tRNA modification in human disease.
Collapse
|
16
|
Impact of tRNA Modifications and tRNA-Modifying Enzymes on Proteostasis and Human Disease. Int J Mol Sci 2018; 19:ijms19123738. [PMID: 30477220 PMCID: PMC6321623 DOI: 10.3390/ijms19123738] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/17/2018] [Accepted: 11/20/2018] [Indexed: 12/14/2022] Open
Abstract
Transfer RNAs (tRNAs) are key players of protein synthesis, as they decode the genetic information organized in mRNA codons, translating them into the code of 20 amino acids. To be fully active, tRNAs undergo extensive post-transcriptional modifications, catalyzed by different tRNA-modifying enzymes. Lack of these modifications increases the level of missense errors and affects codon decoding rate, contributing to protein aggregation with deleterious consequences to the cell. Recent works show that tRNA hypomodification and tRNA-modifying-enzyme deregulation occur in several diseases where proteostasis is affected, namely, neurodegenerative and metabolic diseases. In this review, we discuss the recent findings that correlate aberrant tRNA modification with proteostasis imbalances, in particular in neurological and metabolic disorders, and highlight the association between tRNAs, their modifying enzymes, translational decoding, and disease onset.
Collapse
|
17
|
Dalwadi U, Yip CK. Structural insights into the function of Elongator. Cell Mol Life Sci 2018; 75:1613-1622. [PMID: 29332244 PMCID: PMC11105301 DOI: 10.1007/s00018-018-2747-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/09/2017] [Accepted: 01/08/2018] [Indexed: 12/13/2022]
Abstract
Conserved from yeast to humans, Elongator is a protein complex implicated in multiple processes including transcription regulation, α-tubulin acetylation, and tRNA modification, and its defects have been shown to cause human diseases such as familial dysautonomia. Elongator consists of two copies of six core subunits (Elp1, Elp2, Elp3, Elp4, Elp5, and Elp6) that are organized into two subcomplexes: Elp1/2/3 and Elp4/5/6 and form a stable assembly of ~ 850 kDa in size. Although the catalytic subunit of Elongator is Elp3, which contains a radical S-adenosyl-L-methionine (SAM) domain and a putative histone acetyltransferase domain, the Elp4/5/6 subcomplex also possesses ATP-modulated tRNA binding activity. How at the molecular level, Elongator performs its multiple functions and how the different subunits regulate Elongator's activities remains poorly understood. Here, we provide an overview of the proposed functions of Elongator and describe how recent structural studies provide new insights into the mechanism of action of this multifunctional complex.
Collapse
Affiliation(s)
- Udit Dalwadi
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
| |
Collapse
|
18
|
Lentini JM, Ramos J, Fu D. Monitoring the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification in eukaryotic tRNAs via the γ-toxin endonuclease. RNA (NEW YORK, N.Y.) 2018; 24:749-758. [PMID: 29440318 PMCID: PMC5900570 DOI: 10.1261/rna.065581.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
The post-transcriptional modification of tRNA at the wobble position is a universal process occurring in all domains of life. In eukaryotes, the wobble uridine of particular tRNAs is transformed to the 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) modification which is critical for proper mRNA decoding and protein translation. However, current methods to detect mcm5s2U are technically challenging and/or require specialized instrumental expertise. Here, we show that γ-toxin endonuclease from the yeast Kluyveromyces lactis can be used as a probe for assaying mcm5s2U status in the tRNA of diverse eukaryotic organisms ranging from protozoans to mammalian cells. The assay couples the mcm5s2U-dependent cleavage of tRNA by γ-toxin with standard molecular biology techniques such as northern blot analysis or quantitative PCR to monitor mcm5s2U levels in multiple tRNA isoacceptors. The results gained from the γ-toxin assay reveals the evolutionary conservation of the mcm5s2U modification across eukaryotic species. Moreover, we have used the γ-toxin assay to verify uncharacterized eukaryotic Trm9 and Trm112 homologs that catalyze the formation of mcm5s2U. These findings demonstrate the use of γ-toxin as a detection method to monitor mcm5s2U status in diverse eukaryotic cell types for cellular, genetic, and biochemical studies.
Collapse
Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Jillian Ramos
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York 14627, USA
| |
Collapse
|
19
|
Goffena J, Lefcort F, Zhang Y, Lehrmann E, Chaverra M, Felig J, Walters J, Buksch R, Becker KG, George L. Elongator and codon bias regulate protein levels in mammalian peripheral neurons. Nat Commun 2018; 9:889. [PMID: 29497044 PMCID: PMC5832791 DOI: 10.1038/s41467-018-03221-z] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Familial dysautonomia (FD) results from mutation in IKBKAP/ELP1, a gene encoding the scaffolding protein for the Elongator complex. This highly conserved complex is required for the translation of codon-biased genes in lower organisms. Here we investigate whether Elongator serves a similar function in mammalian peripheral neurons, the population devastated in FD. Using codon-biased eGFP sensors, and multiplexing of codon usage with transcriptome and proteome analyses of over 6,000 genes, we identify two categories of genes, as well as specific gene identities that depend on Elongator for normal expression. Moreover, we show that multiple genes in the DNA damage repair pathway are codon-biased, and that with Elongator loss, their misregulation is correlated with elevated levels of DNA damage. These findings link Elongator's function in the translation of codon-biased genes with both the developmental and neurodegenerative phenotypes of FD, and also clarify the increased risk of cancer associated with the disease.
Collapse
Affiliation(s)
- Joy Goffena
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Frances Lefcort
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Yongqing Zhang
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Elin Lehrmann
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Marta Chaverra
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, 59717, USA
| | - Jehremy Felig
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Joseph Walters
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Richard Buksch
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA
| | - Kevin G Becker
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Lynn George
- Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT, 59101, USA.
| |
Collapse
|
20
|
Rubin BY, Anderson SL. IKBKAP/ELP1 gene mutations: mechanisms of familial dysautonomia and gene-targeting therapies. APPLICATION OF CLINICAL GENETICS 2017; 10:95-103. [PMID: 29290691 PMCID: PMC5735983 DOI: 10.2147/tacg.s129638] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The successful completion of the Human Genome Project led to the discovery of the molecular basis of thousands of genetic disorders. The identification of the mutations that cause familial dysautonomia (FD), an autosomal recessive disorder that impacts sensory and autonomic neurons, was aided by the release of the human DNA sequence. The identification and characterization of the genetic cause of FD have changed the natural history of this disease. Genetic testing programs, which were established shortly after the disease-causing mutations were identified, have almost completely eliminated the birth of children with this disorder. Characterization of the principal disease-causing mutation has led to the development of therapeutic modalities that ameliorate its effect, while the development of mouse models that recapitulate the impact of the mutation has allowed for the in-depth characterization of its impact on neuronal development and survival. The intense research focus on this disorder, while clearly benefiting the FD patient population, also serves as a model for the positive impact focused research efforts can have on the future of other genetic diseases. Here, we present the research advances and scientific breakthroughs that have changed and will continue to change the natural history of this centuries-old genetic disease.
Collapse
Affiliation(s)
- Berish Y Rubin
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - Sylvia L Anderson
- Department of Biological Sciences, Fordham University, Bronx, NY, USA
| |
Collapse
|
21
|
Johansson MJO, Xu F, Byström AS. Elongator-a tRNA modifying complex that promotes efficient translational decoding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:401-408. [PMID: 29170010 DOI: 10.1016/j.bbagrm.2017.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/19/2017] [Indexed: 12/22/2022]
Abstract
Naturally occurring modifications of the nucleosides in the anticodon region of tRNAs influence their translational decoding properties. Uridines present at the wobble position in eukaryotic cytoplasmic tRNAs often contain a 5-carbamoylmethyl (ncm(5)) or 5-methoxycarbonylmethyl (mcm(5)) side-chain and sometimes also a 2-thio or 2'-O-methyl group. The first step in the formation of the ncm(5) and mcm(5) side-chains requires the conserved six-subunit Elongator complex. Although Elongator has been implicated in several different cellular processes, accumulating evidence suggests that its primary, and possibly only, cellular function is to promote modification of tRNAs. In this review, we discuss the biosynthesis and function of modified wobble uridines in eukaryotic cytoplasmic tRNAs, focusing on the in vivo role of Elongator-dependent modifications in Saccharomyces cerevisiae. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.
Collapse
Affiliation(s)
| | - Fu Xu
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Anders S Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden.
| |
Collapse
|
22
|
Animal and cellular models of familial dysautonomia. Clin Auton Res 2017; 27:235-243. [PMID: 28667575 DOI: 10.1007/s10286-017-0438-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/15/2017] [Indexed: 12/11/2022]
Abstract
Since Riley and Day first described the clinical phenotype of patients with familial dysautonomia (FD) over 60 years ago, the field has made considerable progress clinically, scientifically, and translationally in treating and understanding the etiology of FD. FD is classified as a hereditary sensory and autonomic neuropathy (HSAN type III) and is both a developmental and a progressive neurodegenerative condition that results from an autosomal recessive mutation in the gene IKBKAP, also known as ELP1. FD primarily impacts the peripheral nervous system but also manifests in central nervous system disruption, especially in the retina and optic nerve. While the disease is rare, the rapid progress being made in elucidating the molecular and cellular mechanisms mediating the demise of neurons in FD should provide insight into degenerative pathways common to many neurological disorders. Interestingly, the protein encoded by IKBKAP/ELP1, IKAP or ELP1, is a key scaffolding subunit of the six-subunit Elongator complex, and variants in other Elongator genes are associated with amyotrophic lateral sclerosis (ALS), intellectual disability, and Rolandic epilepsy. Here we review the recent model systems that are revealing the molecular and cellular pathophysiological mechanisms mediating FD. These powerful model systems can now be used to test targeted therapeutics for mitigating neuronal loss in FD and potentially other disorders.
Collapse
|
23
|
Chaverra M, George L, Mergy M, Waller H, Kujawa K, Murnion C, Sharples E, Thorne J, Podgajny N, Grindeland A, Ueki Y, Eiger S, Cusick C, Babcock AM, Carlson GA, Lefcort F. The familial dysautonomia disease gene IKBKAP is required in the developing and adult mouse central nervous system. Dis Model Mech 2017; 10:605-618. [PMID: 28167615 PMCID: PMC5451171 DOI: 10.1242/dmm.028258] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/23/2017] [Indexed: 02/06/2023] Open
Abstract
Hereditary sensory and autonomic neuropathies (HSANs) are a genetically and clinically diverse group of disorders defined by peripheral nervous system (PNS) dysfunction. HSAN type III, known as familial dysautonomia (FD), results from a single base mutation in the gene IKBKAP that encodes a scaffolding unit (ELP1) for a multi-subunit complex known as Elongator. Since mutations in other Elongator subunits (ELP2 to ELP4) are associated with central nervous system (CNS) disorders, the goal of this study was to investigate a potential requirement for Ikbkap in the CNS of mice. The sensory and autonomic pathophysiology of FD is fatal, with the majority of patients dying by age 40. While signs and pathology of FD have been noted in the CNS, the clinical and research focus has been on the sensory and autonomic dysfunction, and no genetic model studies have investigated the requirement for Ikbkap in the CNS. Here, we report, using a novel mouse line in which Ikbkap is deleted solely in the nervous system, that not only is Ikbkap widely expressed in the embryonic and adult CNS, but its deletion perturbs both the development of cortical neurons and their survival in adulthood. Primary cilia in embryonic cortical apical progenitors and motile cilia in adult ependymal cells are reduced in number and disorganized. Furthermore, we report that, in the adult CNS, both autonomic and non-autonomic neuronal populations require Ikbkap for survival, including spinal motor and cortical neurons. In addition, the mice developed kyphoscoliosis, an FD hallmark, indicating its neuropathic etiology. Ultimately, these perturbations manifest in a developmental and progressive neurodegenerative condition that includes impairments in learning and memory. Collectively, these data reveal an essential function for Ikbkap that extends beyond the peripheral nervous system to CNS development and function. With the identification of discrete CNS cell types and structures that depend on Ikbkap, novel strategies to thwart the progressive demise of CNS neurons in FD can be developed. Summary:Ikbkap is essential for normal CNS development, neuronal survival and behavior, adding to our understanding of the role of the Elongator complex in the mammalian CNS.
Collapse
Affiliation(s)
- Marta Chaverra
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Lynn George
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA.,Department of Biological and Physical Sciences, Montana State University Billings, Billings, MT 59101, USA
| | - Marc Mergy
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Hannah Waller
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Katharine Kujawa
- Department of Psychology, Montana State University, Bozeman, MT 59717, USA
| | - Connor Murnion
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Ezekiel Sharples
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Julian Thorne
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA.,University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Nathaniel Podgajny
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | | | - Yumi Ueki
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Steven Eiger
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Cassie Cusick
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - A Michael Babcock
- Department of Psychology, Montana State University, Bozeman, MT 59717, USA
| | | | - Frances Lefcort
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| |
Collapse
|
24
|
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: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
25
|
Delaunay S, Rapino F, Tharun L, Zhou Z, Heukamp L, Termathe M, Shostak K, Klevernic I, Florin A, Desmecht H, Desmet CJ, Nguyen L, Leidel SA, Willis AE, Büttner R, Chariot A, Close P. Elp3 links tRNA modification to IRES-dependent translation of LEF1 to sustain metastasis in breast cancer. J Exp Med 2016; 213:2503-2523. [PMID: 27811057 PMCID: PMC5068235 DOI: 10.1084/jem.20160397] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 09/02/2016] [Indexed: 12/18/2022] Open
Abstract
Quantitative and qualitative changes in mRNA translation occur in tumor cells and support cancer progression and metastasis. Posttranscriptional modifications of transfer RNAs (tRNAs) at the wobble uridine 34 (U34) base are highly conserved and contribute to translation fidelity. Here, we show that ELP3 and CTU1/2, partner enzymes in U34 mcm5s2-tRNA modification, are up-regulated in human breast cancers and sustain metastasis. Elp3 genetic ablation strongly impaired invasion and metastasis formation in the PyMT model of invasive breast cancer. Mechanistically, ELP3 and CTU1/2 support cellular invasion through the translation of the oncoprotein DEK. As a result, DEK promotes the IRES-dependent translation of the proinvasive transcription factor LEF1. Consistently, a DEK mutant, whose codon composition is independent of U34 mcm5s2-tRNA modification, escapes the ELP3- and CTU1-dependent regulation and restores the IRES-dependent LEF1 expression. Our results demonstrate that the key role of U34 tRNA modification is to support specific translation during breast cancer progression and highlight a functional link between tRNA modification- and IRES-dependent translation during tumor cell invasion and metastasis.
Collapse
Affiliation(s)
- Sylvain Delaunay
- Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Francesca Rapino
- Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Lars Tharun
- Institute for Pathology, University Hospital Cologne, 50937 Cologne, Germany
| | - Zhaoli Zhou
- Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Lukas Heukamp
- Institute for Pathology, University Hospital Cologne, 50937 Cologne, Germany
| | - Martin Termathe
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster
- Faculty of Medicine, University of Muenster, 48129 Muenster, Germany
| | - Kateryna Shostak
- Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Iva Klevernic
- Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Alexandra Florin
- Institute for Pathology, University Hospital Cologne, 50937 Cologne, Germany
| | - Hadrien Desmecht
- Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Christophe J Desmet
- GIGA-Infection, Immunity and Inflammation, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Laurent Nguyen
- GIGA-Neurosiences, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster
- Faculty of Medicine, University of Muenster, 48129 Muenster, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, 48129 Muenster, Germany
| | - Anne E Willis
- Medical Research Council Toxicology Unit, Leicester LE1 9HN, England, UK
| | - Reinhard Büttner
- Institute for Pathology, University Hospital Cologne, 50937 Cologne, Germany
| | - Alain Chariot
- Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
- Walloon Excellence in Life Sciences and Biotechnology (WELBIO), 1300 Wavre, Belgium
| | - Pierre Close
- Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium
- GIGA-Molecular Biology of Diseases, University of Liège, 4000 Liège, Belgium
- GIGA-Research, University of Liège, 4000 Liège, Belgium
| |
Collapse
|
26
|
Li B, Luo H, Weng Q, Wang S, Pan Z, Xie Z, Wu W, Liu H, Li Q. Differential DNA methylation of the meiosis-specific geneFKBP6in testes of yak and cattle-yak hybrids. Reprod Domest Anim 2016; 51:1030-1038. [DOI: 10.1111/rda.12794] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/17/2016] [Indexed: 12/15/2022]
Affiliation(s)
- B Li
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - H Luo
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Q Weng
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - S Wang
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Z Pan
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Z Xie
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - W Wu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - H Liu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| | - Q Li
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing China
| |
Collapse
|
27
|
Dietrich P, Dragatsis I. Familial Dysautonomia: Mechanisms and Models. Genet Mol Biol 2016; 39:497-514. [PMID: 27561110 PMCID: PMC5127153 DOI: 10.1590/1678-4685-gmb-2015-0335] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/16/2016] [Indexed: 11/22/2022] Open
Abstract
Hereditary Sensory and Autonomic Neuropathies (HSANs) compose a heterogeneous group of genetic disorders characterized by sensory and autonomic dysfunctions. Familial Dysautonomia (FD), also known as HSAN III, is an autosomal recessive disorder that affects 1/3,600 live births in the Ashkenazi Jewish population. The major features of the disease are already present at birth and are attributed to abnormal development and progressive degeneration of the sensory and autonomic nervous systems. Despite clinical interventions, the disease is inevitably fatal. FD is caused by a point mutation in intron 20 of the IKBKAP gene that results in severe reduction in expression of IKAP, its encoded protein. In vitro and in vivo studies have shown that IKAP is involved in multiple intracellular processes, and suggest that failed target innervation and/or impaired neurotrophic retrograde transport are the primary causes of neuronal cell death in FD. However, FD is far more complex, and appears to affect several other organs and systems in addition to the peripheral nervous system. With the recent generation of mouse models that recapitulate the molecular and pathological features of the disease, it is now possible to further investigate the mechanisms underlying different aspects of the disorder, and to test novel therapeutic strategies.
Collapse
Affiliation(s)
- Paula Dietrich
- Department of Physiology, The University of Tennessee, Memphis, TN, USA
| | - Ioannis Dragatsis
- Department of Physiology, The University of Tennessee, Memphis, TN, USA
| |
Collapse
|
28
|
Yoo H, Son D, Jang YJ, Hong K. Indispensable role for mouse ELP3 in embryonic stem cell maintenance and early development. Biochem Biophys Res Commun 2016; 478:631-6. [PMID: 27476491 DOI: 10.1016/j.bbrc.2016.07.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/28/2016] [Indexed: 11/17/2022]
Abstract
ELP3, a core component of Elongator, has been implicated in translational regulation via modification of tRNA at the wobble position. However, the precise biological function of ELP3 in early mouse development has not yet been defined. We here provide evidence that ELP3 plays crucial roles in mouse embryonic stem cell (ESC) maintenance and early development. ELP3 was detected ubiquitously in blastocysts and E10.5 embryos and shown to be increased during ESC differentiation. Depletion of ELP3 in ESC led to aberrant cell cycle progression, along with reduced expression of genes for pluripotency. Interestingly, our analyses revealed that, although the mRNA levels of the genes related to cell cycle were increased, protein levels were diminished in knockdown (KD) ESCs. The data, therefore, suggest that ELP3 function is critical for translational efficiency of the genes. Consistent with a proliferation defect in KD cells, Elp3 knockout (KO) embryos suffered from severe growth retardation and failed to develop beyond E12.5. In conclusion, we have demonstrated that ELP3 plays an indispensable role in ESC survival, differentiation and embryonic development in mouse.
Collapse
Affiliation(s)
- Hyunjin Yoo
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea
| | - Dabin Son
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea
| | - Young-Joo Jang
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea
| | - Kwonho Hong
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 330-714, Republic of Korea.
| |
Collapse
|
29
|
Cdk2 catalytic activity is essential for meiotic cell division in vivo. Biochem J 2016; 473:2783-98. [PMID: 27371320 DOI: 10.1042/bcj20160607] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/29/2016] [Indexed: 01/18/2023]
Abstract
Cyclin-dependent kinases (Cdks) control the eukaryotic cell cycle by phosphorylating serine and threonine residues in key regulatory proteins, but some Cdk family members may exert kinase-independent functions that cannot easily be assessed using gene knockout approaches. While Cdk2-deficient mice display near-normal mitotic cell proliferation due to the compensatory activities of Cdk1 and Cdk4, they are unable to undergo meiotic generation of gametes and are consequently sterile. To investigate whether Cdk2 regulates meiosis via protein phosphorylation or by alternative kinase-independent mechanisms, we generated two different knockin mouse strains in which Cdk2 point mutations ablated enzyme activity without altering protein expression levels. Mice homozygous for the mutations Cdk2(D145N/D145N) or Cdk2(T160A/T160A) expressed only 'kinase-dead' variants of Cdk2 under the control of the endogenous promoter, and despite exhibiting normal expression of cell cycle regulatory proteins and complexes, both mutations rendered mice sterile. Mouse cells that expressed only 'kinase-dead' variants of Cdk2 displayed normal mitotic cell cycle progression and proliferation both in vitro and in vivo, indicating that loss of Cdk2 kinase activity exerted little effect on this mode of cell division. In contrast, the reproductive organs of Cdk2 mutant mice exhibited abnormal morphology and impaired function associated with defective meiotic cell division and inability to produce gametes. Cdk2 mutant animals were therefore comparable to gene knockout mice, which completely lack the Cdk2 protein. Together, our data indicate that the essential meiotic functions of Cdk2 depend on its kinase activity, without which the generation of haploid cells is disrupted, resulting in sterility of otherwise healthy animals.
Collapse
|
30
|
Hervé M, Ibrahim EC. MicroRNA screening identifies a link between NOVA1 expression and a low level of IKAP in familial dysautonomia. Dis Model Mech 2016; 9:899-909. [PMID: 27483351 PMCID: PMC5007982 DOI: 10.1242/dmm.025841] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/22/2016] [Indexed: 12/20/2022] Open
Abstract
Familial dysautonomia (FD) is a rare neurodegenerative disease caused by a mutation in intron 20 of the IKBKAP gene (c.2204+6T>C), leading to tissue-specific skipping of exon 20 and a decrease in the synthesis of the encoded protein IKAP (also known as ELP1). Small non-coding RNAs known as microRNAs (miRNAs) are important post-transcriptional regulators of gene expression and play an essential role in the nervous system development and function. To better understand the neuronal specificity of IKAP loss, we examined expression of miRNAs in human olfactory ecto-mesenchymal stem cells (hOE-MSCs) from five control individuals and five FD patients. We profiled the expression of 373 miRNAs using microfluidics and reverse transcription coupled to quantitative PCR (RT-qPCR) on two biological replicate series of hOE-MSC cultures from healthy controls and FD patients. This led to the total identification of 26 dysregulated miRNAs in FD, validating the existence of a miRNA signature in FD. We then selected the nine most discriminant miRNAs for further analysis. The signaling pathways affected by these dysregulated miRNAs were largely within the nervous system. In addition, many targets of these dysregulated miRNAs had been previously demonstrated to be affected in FD models. Moreover, we found that four of our nine candidate miRNAs target the neuron-specific splicing factor NOVA1. We demonstrated that overexpression of miR-203a-3p leads to a decrease of NOVA1, counter-balanced by an increase of IKAP, supporting a potential interaction between NOVA1 and IKAP. Taken together, these results reinforce the choice of miRNAs as potential therapeutic targets and suggest that NOVA1 could be a regulator of FD pathophysiology. Summary: A miRNA screening conducted in olfactory stem cells from patients links the neuron-specific splicing factor NOVA1 to neurodegeneration in familial dysautonomia.
Collapse
Affiliation(s)
- Mylène Hervé
- CRN2M-UMR7286, Aix-Marseille Université, CNRS, Faculté de Médecine Nord, Marseille 13344, Cedex 15, France
| | - El Chérif Ibrahim
- CRN2M-UMR7286, Aix-Marseille Université, CNRS, Faculté de Médecine Nord, Marseille 13344, Cedex 15, France
| |
Collapse
|
31
|
Zhang C, Wu J. Production of offspring from a germline stem cell line derived from prepubertal ovaries of germline reporter mice. Mol Hum Reprod 2016; 22:457-64. [PMID: 27141102 DOI: 10.1093/molehr/gaw030] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 04/22/2016] [Indexed: 01/01/2023] Open
Abstract
STUDY HYPOTHESIS We investigated whether DEAD-box polypeptide 4 (DDX4) positive cells from post-natal ovaries of germline lineage reporter mice can be isolated based on endogenously expressed fluorescent proteins and used to establish a cell line for producing offspring. STUDY FINDING DDX4-positive cells from post-natal ovaries of germline lineage reporter mice can be isolated and used to establish a cell line for producing offspring. WHAT IS KNOWN ALREADY In recent years, female germline stem cells (FGSCs) have been isolated from the ovaries of post-natal mice by magnetic-activated cell sorting or fluorescence-activated cell sorting (FACS) relying on an antibody against DDX4. However, whether DDX4-positive cells from post-natal ovaries of germline lineage reporter mice can be established without using an antibody, as well as a cell line established for producing offspring, remains unknown. STUDY DESIGN, SAMPLES/MATERIALS, METHODS To obtain the expected offspring (Ddx4-Cre;mT/mG mice), Ddx4-Cre mice were crossed with mT/mG mice. In the ovaries of Ddx4-Cre;mT/mG mice, germ cells were destined to express enhanced green fluorescent protein (EGFP) while somatic cells still express tandem dimer Tomato (tdTomato). Therefore, the germ cells could be clearly distinguished from somatic cells by fluorescent proteins. Then, we investigated the pattern of fluorescent cells in the ovaries of 21-day-old Ddx4-Cre;mT/mG mice under a fluorescent microscope. Germ cells were sorted by FACS without using antibody and used to establish a FGSC line. The FGSC line was analyzed by DDX4 immunostaining, Edu (5-ethynyl-2'-deoxyuridine) labeling, and RT-PCR for germ cell markers. Finally, the physiological function of the FGSC line was examined by transplanting FGSCs into the ovaries of sterilized recipients and subsequent mating. MAIN RESULTS AND THE ROLE OF CHANCE Firstly, we have successfully isolated FGSCs from the ovaries of 21-day-old Ddx4-Cre;mT/mG mice based on endogenously expressed fluorescent proteins. FACS was used to separate the cells and 2.3% of all viable cells was EGFP-positive germ cells. Subsequently, a FGSC line was established that was doubly positive for DDX4 immunostaining and Edu labeling. The mRNA expression of several germ cell markers in this cell line, such as Ddx4, Deleted in azoospermia-like (Dazl), B lymphocyte-induced maturation protein-1 (Blimp1), Stella and Fragilis, was detected. Lastly, the FGSC line was proven to be functional under physiological conditions, as offspring were produced after transplanting FGSCs into ovaries of sterilized recipients and a subsequent mating. LIMITATIONS, REASONS FOR CAUTION The molecular mechanisms of proliferation and differentiation of FGSCs in vivo and in vitro still need to be elucidated. WIDER IMPLICATIONS OF THE FINDINGS Our results confirm that DDX4-positive cells can be separated from post-natal mouse ovaries and used to establish cell lines that are functional in producing offspring, and provide further evidence for the existence of post-natal FGSCs in mammals. The Ddx4-Cre;mT/mG mouse strain is an ideal model for the isolation, characterization and propagation of FGSCs and is a useful tool for fully elucidating the molecular mechanisms of proliferation and differentiation of FGSCs in vivo and in vitro. LARGE SCALE DATA none. STUDY FUNDING AND COMPETING INTERESTS This work was supported by National Basic Research Program of China (2013CB967401) and the National Nature Science Foundation of China (81370675, 81200472 and 81421061). The authors declare no competing interests.
Collapse
Affiliation(s)
- Chen Zhang
- Renji Hospital Shanghai Jiaotong University School of Medicine, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ji Wu
- Renji Hospital Shanghai Jiaotong University School of Medicine, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, Ningxia Medical University, Yinchuan 750004, China Shanghai Key Laboratory of Reproductive Medicine, Shanghai 200025, China
| |
Collapse
|
32
|
Laguesse S, Creppe C, Nedialkova DD, Prévot PP, Borgs L, Huysseune S, Franco B, Duysens G, Krusy N, Lee G, Thelen N, Thiry M, Close P, Chariot A, Malgrange B, Leidel SA, Godin JD, Nguyen L. A Dynamic Unfolded Protein Response Contributes to the Control of Cortical Neurogenesis. Dev Cell 2016; 35:553-567. [PMID: 26651292 DOI: 10.1016/j.devcel.2015.11.005] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 10/07/2015] [Accepted: 11/09/2015] [Indexed: 12/21/2022]
Abstract
The cerebral cortex contains layers of neurons sequentially generated by distinct lineage-related progenitors. At the onset of corticogenesis, the first-born progenitors are apical progenitors (APs), whose asymmetric division gives birth directly to neurons. Later, they switch to indirect neurogenesis by generating intermediate progenitors (IPs), which give rise to projection neurons of all cortical layers. While a direct lineage relationship between APs and IPs has been established, the molecular mechanism that controls their transition remains elusive. Here we show that interfering with codon translation speed triggers ER stress and the unfolded protein response (UPR), further impairing the generation of IPs and leading to microcephaly. Moreover, we demonstrate that a progressive downregulation of UPR in cortical progenitors acts as a physiological signal to amplify IPs and promotes indirect neurogenesis. Thus, our findings reveal a contribution of UPR to cell fate acquisition during mammalian brain development.
Collapse
Affiliation(s)
- Sophie Laguesse
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Catherine Creppe
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Danny D Nedialkova
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, Albert-Schweitzer-Campus 1, 48129 Muenster, Germany
| | - Pierre-Paul Prévot
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Laurence Borgs
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Sandra Huysseune
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Bénédicte Franco
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Guérin Duysens
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Nathalie Krusy
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Gabsang Lee
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicolas Thelen
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Marc Thiry
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Pierre Close
- GIGA-Signal Transduction, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Alain Chariot
- GIGA-Signal Transduction, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Brigitte Malgrange
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Strasse 54, 48149 Muenster, Germany; Faculty of Medicine, University of Muenster, 48129 Muenster, Germany; Cells-in-Motion Cluster of Excellence, University of Muenster, Albert-Schweitzer-Campus 1, 48129 Muenster, Germany
| | - Juliette D Godin
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium.
| | - Laurent Nguyen
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Interdisciplinary Cluster for Applied Genoproteomics (GIGA-R), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), University of Liège, C.H.U. Sart Tilman, Liège 4000, Belgium.
| |
Collapse
|
33
|
Karlsborn T, Mahmud AKMF, Tükenmez H, Byström AS. Loss of ncm 5 and mcm 5 wobble uridine side chains results in an altered metabolic profile. Metabolomics 2016; 12:177. [PMID: 27738410 PMCID: PMC5037161 DOI: 10.1007/s11306-016-1120-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/14/2016] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The Elongator complex, comprising six subunits (Elp1p-Elp6p), is required for formation of 5-carbamoylmethyl (ncm5) and 5-methoxycarbonylmethyl (mcm5) side chains on wobble uridines in 11 out of 42 tRNA species in Saccharomyces cerevisiae. Loss of these side chains reduces the efficiency of tRNA decoding during translation, resulting in pleiotropic phenotypes. Overexpression of hypomodified [Formula: see text], which in wild-type strains are modified with mcm5s2U, partially suppress phenotypes of an elp3Δ strain. OBJECTIVES To identify metabolic alterations in an elp3Δ strain and elucidate whether these metabolic alterations are suppressed by overexpression of hypomodified [Formula: see text]. METHOD Metabolic profiles were obtained using untargeted GC-TOF-MS of a temperature-sensitive elp3Δ strain carrying either an empty low-copy vector, an empty high-copy vector, a low-copy vector harboring the wild-type ELP3 gene, or a high-copy vector overexpressing [Formula: see text]. The temperature sensitive elp3Δ strain derivatives were cultivated at permissive (30 °C) or semi-permissive (34 °C) growth conditions. RESULTS Culturing an elp3Δ strain at 30 or 34 °C resulted in altered metabolism of 36 and 46 %, respectively, of all metabolites detected when compared to an elp3Δ strain carrying the wild-type ELP3 gene. Overexpression of hypomodified [Formula: see text] suppressed a subset of the metabolic alterations observed in the elp3Δ strain. CONCLUSION Our results suggest that the presence of ncm5- and mcm5-side chains on wobble uridines in tRNA are important for metabolic homeostasis.
Collapse
Affiliation(s)
- Tony Karlsborn
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | | | - Hasan Tükenmez
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Anders S. Byström
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| |
Collapse
|
34
|
Molla-Herman A, Vallés AM, Ganem-Elbaz C, Antoniewski C, Huynh JR. tRNA processing defects induce replication stress and Chk2-dependent disruption of piRNA transcription. EMBO J 2015; 34:3009-27. [PMID: 26471728 PMCID: PMC4687792 DOI: 10.15252/embj.201591006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 09/01/2015] [Accepted: 09/04/2015] [Indexed: 02/01/2023] Open
Abstract
RNase P is a conserved endonuclease that processes the 5' trailer of tRNA precursors. We have isolated mutations in Rpp30, a subunit of RNase P, and find that these induce complete sterility in Drosophila females. Here, we show that sterility is not due to a shortage of mature tRNAs, but that atrophied ovaries result from the activation of several DNA damage checkpoint proteins, including p53, Claspin, and Chk2. Indeed, we find that tRNA processing defects lead to increased replication stress and de-repression of transposable elements in mutant ovaries. We also report that transcription of major piRNA sources collapse in mutant germ cells and that this correlates with a decrease in heterochromatic H3K9me3 marks on the corresponding piRNA-producing loci. Our data thus link tRNA processing, DNA replication, and genome defense by small RNAs. This unexpected connection reveals constraints that could shape genome organization during evolution.
Collapse
Affiliation(s)
- Anahi Molla-Herman
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Ana Maria Vallés
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Carine Ganem-Elbaz
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| | - Christophe Antoniewski
- GED, UPMC, CNRS UMR 7622, IBPS, Developmental Biology Laboratory (IBPS-LBD), Paris, France
| | - Jean-René Huynh
- Department of Genetics and Developmental Biology, Institut Curie, Paris, France CNRS UMR3215, Inserm U934, Paris, France
| |
Collapse
|
35
|
Ladang A, Rapino F, Heukamp LC, Tharun L, Shostak K, Hermand D, Delaunay S, Klevernic I, Jiang Z, Jacques N, Jamart D, Migeot V, Florin A, Göktuna S, Malgrange B, Sansom OJ, Nguyen L, Büttner R, Close P, Chariot A. Elp3 drives Wnt-dependent tumor initiation and regeneration in the intestine. J Exp Med 2015; 212:2057-75. [PMID: 26527802 PMCID: PMC4647259 DOI: 10.1084/jem.20142288] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 09/30/2015] [Indexed: 01/04/2023] Open
Abstract
Ladang et al. report that Elp3, a subunit of the Elongator complex, is induced by Wnt signaling and is required to initiate colon cancer development through the regulation of Sox9 translation. They also show that this mechanism is relevant in radiation-induced intestinal regeneration. Tumor initiation in the intestine can rapidly occur from Lgr5+ crypt columnar stem cells. Dclk1 is a marker of differentiated Tuft cells and, when coexpressed with Lgr5, also marks intestinal cancer stem cells. Here, we show that Elp3, the catalytic subunit of the Elongator complex, is required for Wnt-driven intestinal tumor initiation and radiation-induced regeneration by maintaining a subpool of Lgr5+/Dclk1+/Sox9+ cells. Elp3 deficiency dramatically delayed tumor appearance in Apc-mutated intestinal epithelia and greatly prolonged mice survival without affecting the normal epithelium. Specific ablation of Elp3 in Lgr5+ cells resulted in marked reduction of polyp formation upon Apc inactivation, in part due to a decreased number of Lgr5+/Dclk1+/Sox9+ cells. Mechanistically, Elp3 is induced by Wnt signaling and promotes Sox9 translation, which is needed to maintain the subpool of Lgr5+/Dclk1+ cancer stem cells. Consequently, Elp3 or Sox9 depletion led to similar defects in Dclk1+ cancer stem cells in ex vivo organoids. Finally, Elp3 deficiency strongly impaired radiation-induced intestinal regeneration, in part because of decreased Sox9 protein levels. Together, our data demonstrate the crucial role of Elp3 in maintaining a subpopulation of Lgr5-derived and Sox9-expressing cells needed to trigger Wnt-driven tumor initiation in the intestine.
Collapse
Affiliation(s)
- Aurélie Ladang
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Francesca Rapino
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Lukas C Heukamp
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Lars Tharun
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Kateryna Shostak
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Damien Hermand
- Unité de Recherche en Physiologie Moléculaire-Laboratoire de Génétique Moléculaire, University of Namur, 5000 Namur, Belgium
| | - Sylvain Delaunay
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Iva Klevernic
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Zheshen Jiang
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Nicolas Jacques
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Diane Jamart
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Valérie Migeot
- Unité de Recherche en Physiologie Moléculaire-Laboratoire de Génétique Moléculaire, University of Namur, 5000 Namur, Belgium
| | - Alexandra Florin
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Serkan Göktuna
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Brigitte Malgrange
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium GIGA Neurosciences, University of Liège, 4000 Liège, Belgium
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, Scotland, UK
| | - Laurent Nguyen
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium GIGA Neurosciences, University of Liège, 4000 Liège, Belgium Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavre, Belgium
| | - Reinhard Büttner
- Institut für Pathologie, University Hospital Cologne, 50937 Cologne, Germany
| | - Pierre Close
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Cancer Signaling, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium
| | - Alain Chariot
- Interdisciplinary Cluster for Applied Genoproteomics, University of Liège, 4000 Liège, Belgium Laboratory of Medical Chemistry, University of Liège, 4000 Liège, Belgium GIGA-Signal Transduction, University of Liège, 4000 Liège, Belgium Walloon Excellence in Life Sciences and Biotechnology, 1300 Wavre, Belgium
| |
Collapse
|
36
|
Karlsborn T, Tükenmez H, Mahmud AKMF, Xu F, Xu H, Byström AS. Elongator, a conserved complex required for wobble uridine modifications in eukaryotes. RNA Biol 2015; 11:1519-28. [PMID: 25607684 DOI: 10.4161/15476286.2014.992276] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U34 and their influence on Elongator activity.
Collapse
Affiliation(s)
- Tony Karlsborn
- a Department of Molecular Biology ; Umeå University; Umeå , Sweden
| | | | | | | | | | | |
Collapse
|
37
|
Lefler S, Cohen MA, Kantor G, Cheishvili D, Even A, Birger A, Turetsky T, Gil Y, Even-Ram S, Aizenman E, Bashir N, Maayan C, Razin A, Reubinoff BE, Weil M. Familial Dysautonomia (FD) Human Embryonic Stem Cell Derived PNS Neurons Reveal that Synaptic Vesicular and Neuronal Transport Genes Are Directly or Indirectly Affected by IKBKAP Downregulation. PLoS One 2015; 10:e0138807. [PMID: 26437462 PMCID: PMC4593545 DOI: 10.1371/journal.pone.0138807] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 09/03/2015] [Indexed: 12/21/2022] Open
Abstract
A splicing mutation in the IKBKAP gene causes Familial Dysautonomia (FD), affecting the IKAP protein expression levels and proper development and function of the peripheral nervous system (PNS). Here we found new molecular insights for the IKAP role and the impact of the FD mutation in the human PNS lineage by using a novel and unique human embryonic stem cell (hESC) line homozygous to the FD mutation originated by pre implantation genetic diagnosis (PGD) analysis. We found that IKBKAP downregulation during PNS differentiation affects normal migration in FD-hESC derived neural crest cells (NCC) while at later stages the PNS neurons show reduced intracellular colocalization between vesicular proteins and IKAP. Comparative wide transcriptome analysis of FD and WT hESC-derived neurons together with the analysis of human brains from FD and WT 12 weeks old embryos and experimental validation of the results confirmed that synaptic vesicular and neuronal transport genes are directly or indirectly affected by IKBKAP downregulation in FD neurons. Moreover we show that kinetin (a drug that corrects IKBKAP alternative splicing) promotes the recovery of IKAP expression and these IKAP functional associated genes identified in the study. Altogether, these results support the view that IKAP might be a vesicular like protein that might be involved in neuronal transport in hESC derived PNS neurons. This function seems to be mostly affected in FD-hESC derived PNS neurons probably reflecting some PNS neuronal dysfunction observed in FD.
Collapse
Affiliation(s)
- Sharon Lefler
- Laboratory for Neurodegenerative Diseases and Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, The Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Malkiel A Cohen
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Gal Kantor
- Laboratory for Neurodegenerative Diseases and Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, The Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - David Cheishvili
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Aviel Even
- Laboratory for Neurodegenerative Diseases and Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, The Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| | - Anastasya Birger
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Tikva Turetsky
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Yaniv Gil
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Sharona Even-Ram
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Einat Aizenman
- Department of Obstetrics and Gynecology, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Nibal Bashir
- Department of Obstetric and Gynecology, Hadassah Hospital Mount Scopus, Hebrew University Medical School, Jerusalem, Israel
| | - Channa Maayan
- Department of Pediatrics, Hadassah Hospital Mount Scopus, Hebrew University Medical School, Jerusalem, Israel
| | - Aharon Razin
- Department of Developmental Biology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Benjamim E Reubinoff
- The Hadassah Human Embryonic Stem Cell Research Center, The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel; Department of Obstetrics and Gynecology, Hadassah Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Miguel Weil
- Laboratory for Neurodegenerative Diseases and Personalized Medicine, Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, The Sagol School of Neurosciences, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
38
|
Dimerization of elongator protein 1 is essential for Elongator complex assembly. Proc Natl Acad Sci U S A 2015; 112:10697-702. [PMID: 26261306 DOI: 10.1073/pnas.1502597112] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The evolutionarily conserved Elongator complex, which is composed of six subunits elongator protein 1 (Elp1 to -6), plays vital roles in gene regulation. The molecular hallmark of familial dysautonomia (FD) is the splicing mutation of Elp1 [also known as IκB kinase complex-associated protein (IKAP)] in the nervous system that is believed to be the primary cause of the devastating symptoms of this disease. Here, we demonstrate that disease-related mutations in Elp1 affect Elongator assembly, and we have determined the structure of the C-terminal portion of human Elp1 (Elp1-CT), which is sufficient for full-length Elp1 dimerization, as well as the structure of the cognate dimerization domain of yeast Elp1 (yElp1-DD). Our study reveals that the formation of the Elp1 dimer contributes to its stability in vitro and in vivo and is required for the assembly of both the human and yeast Elongator complexes. Functional studies suggest that Elp1 dimerization is essential for yeast viability. Collectively, our results identify the evolutionarily conserved dimerization domain of Elp1 and suggest that the pathological mechanisms underlying the onset and progression of Elp1 mutation-related disease may result from impaired Elongator activities.
Collapse
|
39
|
The Elp2 subunit is essential for elongator complex assembly and functional regulation. Structure 2015; 23:1078-86. [PMID: 25960406 DOI: 10.1016/j.str.2015.03.018] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Revised: 03/20/2015] [Accepted: 03/25/2015] [Indexed: 01/24/2023]
Abstract
Elongator is a highly conserved multiprotein complex composed of six subunits (Elp1-6). Elongator has been associated with various cellular activities and has attracted clinical attention because of its role in certain neurodegenerative diseases. Here, we present the crystal structure of the Elp2 subunit revealing two seven-bladed WD40 β propellers, and show by structure-guided mutational analyses that the WD40 fold integrity of Elp2 is necessary for its binding to Elp1 and Elp3 subunits in multiple species. The detailed biochemical experiments indicate that Elp2 binds microtubules through its conserved alkaline residues in vitro and in vivo. We find that both the mutually independent Elp2-mediated Elongator assembly and the cytoskeleton association are important for yeast viability. In addition, mutation of Elp2 greatly affects the histone H3 acetylation activity of Elongator in vivo. Our results indicate that Elp2 is a necessary component for functional Elongator and acts as a hub in the formation of various complexes.
Collapse
|
40
|
Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. Proc Natl Acad Sci U S A 2015; 112:2764-9. [PMID: 25675486 DOI: 10.1073/pnas.1415525112] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by missplicing of exon 20, resulting from an intronic mutation in the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene encoding IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1). A newly established splicing reporter assay allowed us to visualize pathogenic splicing in cells and to screen small chemicals for the ability to correct the aberrant splicing of IKBKAP. Using this splicing reporter, we screened our chemical libraries and identified a compound, rectifier of aberrant splicing (RECTAS), that rectifies the aberrant IKBKAP splicing in cells from patients with FD. Here, we found that the levels of modified uridine at the wobble position in cytoplasmic tRNAs are reduced in cells from patients with FD and that treatment with RECTAS increases the expression of IKAP and recovers the tRNA modifications. These findings suggest that the missplicing of IKBKAP results in reduced tRNA modifications in patients with FD and that RECTAS is a promising therapeutic drug candidate for FD.
Collapse
|
41
|
Kolaj-Robin O, McEwen AG, Cavarelli J, Séraphin B. Structure of the Elongator cofactor complex Kti11/Kti13 provides insight into the role of Kti13 in Elongator-dependent tRNA modification. FEBS J 2015; 282:819-33. [PMID: 25604895 DOI: 10.1111/febs.13199] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/12/2015] [Accepted: 01/14/2015] [Indexed: 12/26/2022]
Abstract
UNLABELLED Modification of wobble uridines of many eukaryotic tRNAs requires the Elongator complex, a highly conserved six-subunit eukaryotic protein assembly, as well as the Killer toxin-insensitive (Kti) proteins 11-14. Kti11 was additionally shown to be implicated in the biosynthesis of diphthamide, a post-translationally modified histidine of translation elongation factor 2. Recent data indicate that iron-bearing Kti11 functions as an electron donor to the [4Fe-4S] cluster of radical S-Adenosylmethionine enzymes, triggering the subsequent radical reaction. We show here that recombinant yeast Kti11 forms a stable 1 : 1 complex with Kti13. To obtain insights into the function of this heterodimer, the Kti11/Kti13 complex was purified to homogeneity, crystallized, and its structure determined at 1.45 Å resolution. The importance of several residues mediating complex formation was confirmed by mutagenesis. Kti13 adopts a fold characteristic of RCC1-like proteins. The seven-bladed β-propeller consists of a unique mixture of four- and three-stranded blades. In the complex, Kti13 orients Kti11 and restricts access to its electron-carrying iron atom, constraining the electron transfer capacity of Kti11. Based on these findings, we propose a role for Kti13, and discuss the possible functional implications of complex formation. DATABASE Structural data have been submitted to the Protein Data Bank under accession number 4X33.
Collapse
Affiliation(s)
- Olga Kolaj-Robin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de Recherche Scientifique UMR 7104/Institut National de Santé et de Recherche Médicale U964/Université de Strasbourg, Illkirch, France
| | | | | | | |
Collapse
|
42
|
Abdel-Fattah W, Jablonowski D, Di Santo R, Thüring KL, Scheidt V, Hammermeister A, ten Have S, Helm M, Schaffrath R, Stark MJR. Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast. PLoS Genet 2015; 11:e1004931. [PMID: 25569479 PMCID: PMC4287497 DOI: 10.1371/journal.pgen.1004931] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/01/2014] [Indexed: 12/26/2022] Open
Abstract
Elongator is a conserved protein complex comprising six different polypeptides that has been ascribed a wide range of functions, but which is now known to be required for modification of uridine residues in the wobble position of a subset of tRNAs in yeast, plants, worms and mammals. In previous work, we showed that Elongator's largest subunit (Elp1; also known as Iki3) was phosphorylated and implicated the yeast casein kinase I Hrr25 in Elongator function. Here we report identification of nine in vivo phosphorylation sites within Elp1 and show that four of these, clustered close to the Elp1 C-terminus and adjacent to a region that binds tRNA, are important for Elongator's tRNA modification function. Hrr25 protein kinase directly modifies Elp1 on two sites (Ser-1198 and Ser-1202) and through analyzing non-phosphorylatable (alanine) and acidic, phosphomimic substitutions at Ser-1198, Ser-1202 and Ser-1209, we provide evidence that phosphorylation plays a positive role in the tRNA modification function of Elongator and may regulate the interaction of Elongator both with its accessory protein Kti12 and with Hrr25 kinase. tRNA molecules function as adapters in protein synthesis, bringing amino acids to the ribosome and reading the genetic code through codon-anticodon base pairing. When the tRNA contains a uridine residue in the “wobble position” of its anticodon, which base-pairs with purine residues in the third position of a cognate codon, it is almost always chemically modified and modification is required for efficient decoding. In eukaryotic cells, these wobble uridine modifications require a conserved protein complex called Elongator. Our work shows that Elp1, Elongator's largest subunit, is phosphorylated on several sites. By blocking phosphorylation at these positions using mutations, we identified four phosphorylation sites that are important for Elongator's role in tRNA modification. We have also shown that Hrr25 protein kinase, a member of the casein kinase I (CKI) family, is responsible for modification of two of the sites that are important for Elongator function. Phosphorylation appears to affect interaction of the Elongator complex both with its kinase (Hrr25) and with Kti12, an accessory protein previously implicated in Elongator function. Our studies imply that Elp1 phosphorylation plays a positive role in Elongator-mediated tRNA modification and raise the possibility that wobble uridine modification may be regulated, representing a potential translational control mechanism.
Collapse
Affiliation(s)
- Wael Abdel-Fattah
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Rachael Di Santo
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kathrin L. Thüring
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Viktor Scheidt
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Sara ten Have
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail: (RS); (MJRS)
| | - Michael J. R. Stark
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail: (RS); (MJRS)
| |
Collapse
|
43
|
Karlsborn T, Tükenmez H, Chen C, Byström AS. Familial dysautonomia (FD) patients have reduced levels of the modified wobble nucleoside mcm5s2U in tRNA. Biochem Biophys Res Commun 2014; 454:441-5. [DOI: 10.1016/j.bbrc.2014.10.116] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/21/2014] [Indexed: 12/30/2022]
|
44
|
Di Santo R, Bandau S, Stark MJR. A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex. Mol Microbiol 2014; 92:1227-42. [PMID: 24750273 PMCID: PMC4150532 DOI: 10.1111/mmi.12624] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2014] [Indexed: 12/25/2022]
Abstract
Elongator is a conserved, multi-protein complex discovered in Saccharomyces cerevisiae, loss of which confers a range of pleiotropic phenotypes. Elongator in higher eukaryotes is required for normal growth and development and a mutation in the largest subunit of human Elongator (Elp1) causes familial dysautonomia, a severe recessive neuropathy. Elongator promotes addition of mcm(5) and ncm(5) modifications to uridine in the tRNA anticodon 'wobble' position in both yeast and higher eukaryotes. Since these modifications are required for the tRNAs to function efficiently, a translation defect caused by hypomodified tRNAs may therefore underlie the variety of phenotypes associated with Elongator dysfunction. The Elp1 carboxy-terminal domain contains a highly conserved arginine/lysine-rich region that resembles a nuclear localization sequence (NLS). Using alanine substitution mutagenesis, we show that this region is essential for Elongator's function in tRNA wobble uridine modification. However, rather than acting to determine the nucleo-cytoplasmic distribution of Elongator, we find that the basic region plays a critical role in a novel interaction between tRNA and the Elp1 carboxy-terminal domain. Thus the conserved basic region in Elp1 may be essential for tRNA wobble uridine modification by acting as tRNA binding motif.
Collapse
Affiliation(s)
- Rachael Di Santo
- Centre for Gene Regulation & Expression, College of Life Sciences, MSI/WTB Complex, University of DundeeDundee, DD1 5EH, Scotland, UK
| | | | - Michael J R Stark
- Centre for Gene Regulation & Expression, College of Life Sciences, MSI/WTB Complex, University of DundeeDundee, DD1 5EH, Scotland, UK
| |
Collapse
|
45
|
Sarin LP, Leidel SA. Modify or die?--RNA modification defects in metazoans. RNA Biol 2014; 11:1555-67. [PMID: 25692999 PMCID: PMC4615230 DOI: 10.4161/15476286.2014.992279] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 12/21/2022] Open
Abstract
Chemical RNA modifications are present in all kingdoms of life and many of these post-transcriptional modifications are conserved throughout evolution. However, most of the research has been performed on single cell organisms, whereas little is known about how RNA modifications contribute to the development of metazoans. In recent years, the identification of RNA modification genes in genome wide association studies (GWAS) has sparked new interest in previously neglected genes. In this review, we summarize recent findings that connect RNA modification defects and phenotypes in higher eukaryotes. Furthermore, we discuss the implications of aberrant tRNA modification in various human diseases including metabolic defects, mitochondrial dysfunctions, neurological disorders, and cancer. As the molecular mechanisms of these diseases are being elucidated, we will gain first insights into the functions of RNA modifications in higher eukaryotes and finally understand their roles during development.
Collapse
MESH Headings
- Amyotrophic Lateral Sclerosis/genetics
- Amyotrophic Lateral Sclerosis/metabolism
- Amyotrophic Lateral Sclerosis/pathology
- Animals
- Dysautonomia, Familial/genetics
- Dysautonomia, Familial/metabolism
- Dysautonomia, Familial/pathology
- Epilepsy, Rolandic/genetics
- Epilepsy, Rolandic/metabolism
- Epilepsy, Rolandic/pathology
- Genome-Wide Association Study
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Mutation
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Nucleic Acid Conformation
- Phenotype
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
Collapse
Affiliation(s)
- L Peter Sarin
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
- Faculty of Medicine; University of Münster; Münster, Germany
| |
Collapse
|