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Eck RJ, Stair JG, Kraemer BC, Liachko NF. Simple models to understand complex disease: 10 years of progress from Caenorhabditis elegans models of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Front Neurosci 2024; 17:1300705. [PMID: 38239833 PMCID: PMC10794587 DOI: 10.3389/fnins.2023.1300705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
The nematode Caenorhabditis elegans are a powerful model system to study human disease, with numerous experimental advantages including significant genetic and cellular homology to vertebrate animals, a short lifespan, and tractable behavioral, molecular biology and imaging assays. Beginning with the identification of SOD1 as a genetic cause of amyotrophic lateral sclerosis (ALS), C. elegans have contributed to a deeper understanding of the mechanistic underpinnings of this devastating neurodegenerative disease. More recently this work has expanded to encompass models of other types of ALS and the related disease frontotemporal lobar degeneration (FTLD-TDP), including those characterized by mutation or accumulation of the proteins TDP-43, C9orf72, FUS, HnRNPA2B1, ALS2, DCTN1, CHCHD10, ELP3, TUBA4A, CAV1, UBQLN2, ATXN3, TIA1, KIF5A, VAPB, GRN, and RAB38. In this review we summarize these models and the progress and insights from the last ten years of using C. elegans to study the neurodegenerative diseases ALS and FTLD-TDP.
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Affiliation(s)
- Randall J. Eck
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, United States
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jade G. Stair
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
| | - Brian C. Kraemer
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Nicole F. Liachko
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, United States
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States
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2
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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.
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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
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3
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Huang G, Zhang F, Xie D, Ma Y, Wang P, Cao G, Chen L, Lin S, Zhao Z, Cai Z. High-throughput profiling of RNA modifications by ultra-performance liquid chromatography coupled to complementary mass spectrometry: Methods, quality control, and applications. Talanta 2023; 263:124697. [PMID: 37262985 DOI: 10.1016/j.talanta.2023.124697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/03/2023]
Abstract
Although next-generation sequencing technology has been used to delineate RNA modifications in recent years, the paucity of appropriate converting reactions or specific antibodies impedes the accurate characterization and quantification of numerous RNA modifications, especially when these modifications demonstrate wide variations across developmental stages and cell types. In this study, we developed a high-throughput analytical platform coupling ultra-performance liquid chromatograph (UPLC) with complementary mass spectrometry (MS) to identify and quantify RNA modifications in both synthetic and biological samples. Sixty-four types of RNA modifications, including positional isomers and hypermodified ribonucleosides, were successfully monitored within a 16-min single run of UPLC-MS. Two independent methods to cross-validate the purity of RNA extracted from Caenorhabditis elegans (C. elegans) were developed using the coexisting C. elegans and Escherichia coli (E. coli) as a surveillance system. To test the validity of the method, we investigated the RNA modification landscape of three model organisms, C. elegans, E. coli, and Arabidopsis thaliana (A. thaliana). Both the identity and molarity of modified ribonucleosides markedly varied among the species. Moreover, our platform is not only useful for exploring the dynamics of RNA modifications in response to environmental cues (e.g., cold shock) but can also help with the identification of RNA-modifying enzymes in genetic studies. Cumulatively, our method presents a novel platform for the comprehensive analysis of RNA modifications, which will be of benefit to both analytical chemists involved in biomarker discovery and biologists conducting functional studies of RNA modifications.
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Affiliation(s)
- Gefei Huang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Feng Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Pengxi Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Guodong Cao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Leijian Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Siyi Lin
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China.
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4
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Elongator stabilizes microtubules to control central spindle asymmetry and polarized trafficking of cell fate determinants. Nat Cell Biol 2022; 24:1606-1616. [PMID: 36302967 PMCID: PMC7613801 DOI: 10.1038/s41556-022-01020-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/19/2022] [Indexed: 01/18/2023]
Abstract
Asymmetric cell division gives rise to two daughter cells that inherit different determinants, thereby acquiring different fates. Polarized trafficking of endosomes containing fate determinants recently emerged as an evolutionarily conserved feature of asymmetric cell division to enhance the robustness of asymmetric cell fate determination in flies, fish and mammals. In particular, polarized sorting of signalling endosomes by an asymmetric central spindle contributes to asymmetric cell division in Drosophila melanogaster. However, how central spindle asymmetry arises remains elusive. Here we identify a moonlighting function of the Elongator complex-an established protein acetylase and tRNA methylase involved in the fidelity of protein translation-as a key factor for central spindle asymmetry. Elongator controls spindle asymmetry by stabilizing microtubules differentially on the anterior side of the central spindle. Accordingly, lowering the activity of Elongator on the anterior side using nanobodies mistargets endosomes to the wrong cell. Molecularly, Elongator regulates microtubule dynamics independently of its acetylation and methylation enzymatic activities. Instead, Elongator directly binds to microtubules and increases their polymerization speed while decreasing their catastrophe frequency. Our data establish a non-canonical role of Elongator at the core of cytoskeleton polarity and asymmetric signalling.
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5
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Sulfur Availability Impacts Accumulation of the 2-Thiouridine tRNA Modification in Bacillus subtilis. J Bacteriol 2022; 204:e0000922. [PMID: 35467390 DOI: 10.1128/jb.00009-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Posttranscriptional modifications to tRNA are critical elements for the folding and functionality of these adaptor molecules. Sulfur modifications in tRNA are installed by specialized enzymes that act on cognate tRNA substrates at specific locations. Most studied organisms contain a general cysteine desulfurase to mobilize sulfur for the synthesis of S-tRNA and other thio-cofactors. Bacillus subtilis and other Gram-positive bacteria encode multiple cysteine desulfurases that partner with specific sulfur acceptors in the biosynthesis of thio-cofactors. This metabolic layout suggests an alternate mode of regulation in these biosynthetic pathways. In this study, tRNA modifications were exploited as a readout for the functionality of pathways involving cysteine desulfurases. These analyses showed that the relative abundance of 2-thiouridine-modified tRNA (s2U) responds to sulfur availability in the growth medium in a dose-dependent manner. This study found that low sulfur concentrations lead to decreased levels of the s2U cysteine desulfurase YrvO and thiouridylase MnmA, without altering the levels of other cysteine desulfurases, SufS, NifS, and NifZ. Analysis of pathway metabolites that depend on the activity of cysteine desulfurases indicates that sulfur nutrient availability specifically impacts s2U accumulation while having no effect on the levels of other S-modified tRNA or activity levels of Fe-S enzymes. Collectively, these results support a model in which s2U tRNA serves as a marker for sulfur availability in B. subtilis. IMPORTANCE The 2-thiouridine (s2U) tRNA modification is found ubiquitously across all domains of life. YrvO and MnmA, the enzymes involved in this modification, are essential in B. subtilis, confirming the well-established role of s2U in maintaining translational efficiency and, consequently, cellular viability. Herein, we show that in the model Gram-positive organism Bacillus subtilis, the levels of s2U are responsive to sulfur availability. Downregulation of the s2U biosynthetic components leads to lower s2U levels, which may serve as a signal for the slowing of the translational apparatus during cellular nutrient insufficiency. Our findings provide the basis for the identification of a potential bacterial mode of regulation during S-metabolite depletion that may use s2U as a marker of suboptimal metabolic status.
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Leonard CE, Quiros J, Lefcort F, Taneyhill LA. Loss of Elp1 disrupts trigeminal ganglion neurodevelopment in a model of familial dysautonomia. eLife 2022; 11:71455. [PMID: 35713404 PMCID: PMC9273214 DOI: 10.7554/elife.71455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 06/17/2022] [Indexed: 01/28/2023] Open
Abstract
Familial dysautonomia (FD) is a sensory and autonomic neuropathy caused by mutations in elongator complex protein 1 (ELP1). FD patients have small trigeminal nerves and impaired facial pain and temperature perception. These signals are relayed by nociceptive neurons in the trigeminal ganglion, a structure that is composed of both neural crest- and placode-derived cells. Mice lacking Elp1 in neural crest derivatives ('Elp1 CKO') are born with small trigeminal ganglia, suggesting Elp1 is important for trigeminal ganglion development, yet the function of Elp1 in this context is unknown. We demonstrate that Elp1, expressed in both neural crest- and placode-derived neurons, is not required for initial trigeminal ganglion formation. However, Elp1 CKO trigeminal neurons exhibit abnormal axon outgrowth and deficient target innervation. Developing nociceptors expressing the receptor TrkA undergo early apoptosis in Elp1 CKO, while TrkB- and TrkC-expressing neurons are spared, indicating Elp1 supports the target innervation and survival of trigeminal nociceptors. Furthermore, we demonstrate that specific TrkA deficits in the Elp1 CKO trigeminal ganglion reflect the neural crest lineage of most TrkA neurons versus the placodal lineage of most TrkB and TrkC neurons. Altogether, these findings explain defects in cranial gangliogenesis that may lead to loss of facial pain and temperature sensation in FD.
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Affiliation(s)
- Carrie E Leonard
- Department of Avian and Animal Sciences, University of Maryland, College ParkCollege ParkUnited States
| | - Jolie Quiros
- Department of Avian and Animal Sciences, University of Maryland, College ParkCollege ParkUnited States
| | - Frances Lefcort
- Department of Microbiology and Cell Biology, Montana State UniversityBozemanUnited States
| | - Lisa A Taneyhill
- Department of Avian and Animal Sciences, University of Maryland, College ParkCollege ParkUnited States
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7
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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: 2.0] [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.
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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.
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8
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Dannfald A, Favory JJ, Deragon JM. Variations in transfer and ribosomal RNA epitranscriptomic status can adapt eukaryote translation to changing physiological and environmental conditions. RNA Biol 2021; 18:4-18. [PMID: 34159889 PMCID: PMC8677040 DOI: 10.1080/15476286.2021.1931756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 01/27/2023] Open
Abstract
The timely reprogramming of gene expression in response to internal and external cues is essential to eukaryote development and acclimation to changing environments. Chemically modifying molecular receptors and transducers of these signals is one way to efficiently induce proper physiological responses. Post-translation modifications, regulating protein biological activities, are central to many well-known signal-responding pathways. Recently, messenger RNA (mRNA) chemical (i.e. epitranscriptomic) modifications were also shown to play a key role in these processes. In contrast, transfer RNA (tRNA) and ribosomal RNA (rRNA) chemical modifications, although critical for optimal function of the translation apparatus, and much more diverse and quantitatively important compared to mRNA modifications, were until recently considered as mainly static chemical decorations. We present here recent observations that are challenging this view and supporting the hypothesis that tRNA and rRNA modifications dynamically respond to various cell and environmental conditions and contribute to adapt translation to these conditions.
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Affiliation(s)
- Arnaud Dannfald
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Jacques Favory
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
| | - Jean-Marc Deragon
- CNRS LGDP-UMR5096, Pepignan, France
- Université de Perpignan via Domitia, Perpignan, France
- Institut Universitaire de France, Paris, France
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9
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Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L. Regulation of gene expression via translational buffering. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119140. [PMID: 34599983 DOI: 10.1016/j.bbamcr.2021.119140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]
Abstract
Translation of an mRNA represents a critical step during the expression of protein-coding genes. As mechanisms governing post-transcriptional regulation of gene expression are progressively unveiled, it is becoming apparent that transcriptional programs are not fully reflected in the proteome. Herein, we highlight a previously underappreciated post-transcriptional mode of regulation of gene expression termed translational buffering. In principle, translational buffering opposes the impact of alterations in mRNA levels on the proteome. We further describe three types of translational buffering: compensation, which maintains protein levels e.g. across species or individuals; equilibration, which retains pathway stoichiometry; and offsetting, which acts as a reversible mechanism that maintains the levels of selected subsets of proteins constant despite genetic alteration and/or stress-induced changes in corresponding mRNA levels. While mechanisms underlying compensation and equilibration have been reviewed elsewhere, the principal focus of this review is on the less-well understood mechanism of translational offsetting. Finally, we discuss potential roles of translational buffering in homeostasis and disease.
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Affiliation(s)
- Eric P Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clelia Timpone
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
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10
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Clark K, Lee C, Gillette R, Sweedler JV. Characterization of Neuronal RNA Modifications during Non-associative Learning in Aplysia Reveals Key Roles for tRNAs in Behavioral Sensitization. ACS CENTRAL SCIENCE 2021; 7:1183-1190. [PMID: 34345669 PMCID: PMC8323240 DOI: 10.1021/acscentsci.1c00351] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 05/12/2023]
Abstract
Subtle changes in the landscape of post-transcriptional modifications have emerged as putative regulators of central nervous system plasticity and activity-induced protein synthesis. However, simultaneous characterization of multiple RNA modifications and their covariation during learning and memory paradigms has been impeded by the complexity of animal models and lack of untargeted approaches for identifying pathway-relevant RNA modifications in small-volume samples. Here, we used mass spectrometry to profile spatiotemporal changes in dozens of neuronal RNA modifications in Aplysia californica during behavioral sensitization of a simple defensive reflex. Unique RNA modification patterns were observed in the major ganglia of trained and naı̇ve animals, with two tRNA modifications, namely, 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) and 1-methyladenosine (m1A), at significantly higher levels in trained subjects. We report that tRNAs, and their modifications, correlate with increased polyglutamine synthesis and excitability in neurons, characterizing the first link between noncoding RNA modifications and non-associative learning.
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Affiliation(s)
- Kevin
D. Clark
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Colin Lee
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Rhanor Gillette
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
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11
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Tavares JF, Davis NK, Poim A, Reis A, Kellner S, Sousa I, Soares AR, Moura GMR, Dedon PC, Santos M. tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast. RNA Biol 2021; 18:563-575. [PMID: 32893724 PMCID: PMC7971265 DOI: 10.1080/15476286.2020.1819671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/28/2023] Open
Abstract
Protein synthesis rate and accuracy are tightly controlled by the cell and are essential for proteome homoeostasis (proteostasis); however, the full picture of how mRNA translational factors maintain protein synthesis accuracy and co-translational protein folding are far from being fully understood. To address this question, we evaluated the role of 70 yeast tRNA-modifying enzyme genes on protein aggregation and used mass spectrometry to identify the aggregated proteins. We show that modification of uridine at anticodon position 34 (U34) by the tRNA-modifying enzymes Elp1, Elp3, Sml3 and Trm9 is critical for proteostasis, the mitochondrial tRNA-modifying enzyme Slm3 plays a fundamental role in general proteostasis and that stress response proteins whose genes are enriched in codons decoded by tRNAs lacking mcm5U34, mcm5s2U34, ncm5U34, ncm5Um34, modifications are overrepresented in protein aggregates of the ELP1, SLM3 and TRM9 KO strains. Increased rates of amino acid misincorporation were also detected in these strains at protein sites that specifically mapped to the codons sites that are decoded by the hypomodified tRNAs, demonstrating that U34 tRNA modifications safeguard the proteome from translational errors, protein misfolding and proteotoxic stress.
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Affiliation(s)
- Joana F Tavares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Nick K. Davis
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Ana Poim
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Andreia Reis
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
| | - Inês Sousa
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana R. Soares
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Gabriela M R Moura
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology – MIT, Cambridge, US
- Singapore-MIT Alliance for Research and Technology, Campus for Research Excellence and Technical Enterprise – CREATE, Singapore
| | - Manuel Santos
- Department of Medical Sciences, Institute of Biomedicine – iBiMED, University of Aveiro, Aveiro, Portugal
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12
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Li L, Gruner K, Tourtellotte WG. Retrograde nerve growth factor signaling abnormalities in familial dysautonomia. J Clin Invest 2021; 130:2478-2487. [PMID: 32281946 DOI: 10.1172/jci130401] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 01/23/2020] [Indexed: 12/11/2022] Open
Abstract
Familial dysautonomia (FD) is the most prevalent form of hereditary sensory and autonomic neuropathy (HSAN). In FD, a germline mutation in the Elp1 gene leads to Elp1 protein decrease that causes sympathetic neuron death and sympathetic nervous system dysfunction (dysautonomia). Elp1 is best known as a scaffolding protein within the nuclear hetero-hexameric transcriptional Elongator protein complex, but how it functions in sympathetic neuron survival is very poorly understood. Here, we identified a cytoplasmic function for Elp1 in sympathetic neurons that was essential for retrograde nerve growth factor (NGF) signaling and neuron target tissue innervation and survival. Elp1 was found to bind to internalized TrkA receptors in an NGF-dependent manner, where it was essential for maintaining TrkA receptor phosphorylation (activation) by regulating PTPN6 (Shp1) phosphatase activity within the signaling complex. In the absence of Elp1, Shp1 was hyperactivated, leading to premature TrkA receptor dephosphorylation, which resulted in retrograde signaling failure and neuron death. Inhibiting Shp1 phosphatase activity in the absence of Elp1 rescued NGF-dependent retrograde signaling, and in an animal model of FD it rescued abnormal sympathetic target tissue innervation. These results suggest that regulation of retrograde NGF signaling in sympathetic neurons by Elp1 may explain sympathetic neuron loss and physiologic dysautonomia in patients with FD.
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Affiliation(s)
- Lin Li
- Department of Pathology and Laboratory Medicine
| | | | - Warren G Tourtellotte
- Department of Pathology and Laboratory Medicine.,Department of Neurology.,Department of Neurosurgery, and.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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13
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Lentini JM, Fu D. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease. Methods Mol Biol 2021; 2298:197-216. [PMID: 34085247 DOI: 10.1007/978-1-0716-1374-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The post-transcriptional modification of tRNAs at the wobble position plays a critical role in proper mRNA decoding and efficient protein synthesis. In particular, certain wobble uridines in eukaryotes are converted to 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The mcm5s2U modification modulates decoding during translation by increasing the stringency of the wobble uridine to base pair with its canonical nucleotide partner, thereby restricting decoding to its cognate codon. Here, we outline a technique to monitor wobble uridine status in mcm5s2U-containing tRNAs using the gamma-toxin endonuclease from the yeast Kluyveromyces lactis that naturally cleaves tRNAs containing the mcm5s2U modification. This technique is coupled to Northern blotting or reverse transcription-PCR to enable rapid and sensitive detection of changes in mcm5s2U modification state.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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14
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Fernandes De Abreu DA, Salinas-Giegé T, Drouard L, Remy JJ. Alanine tRNAs Translate Environment Into Behavior in Caenorhabditis elegans. Front Cell Dev Biol 2020; 8:571359. [PMID: 33195203 PMCID: PMC7662486 DOI: 10.3389/fcell.2020.571359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/12/2020] [Indexed: 12/16/2022] Open
Abstract
Caenorhabditis elegans nematodes produce and maintain imprints of attractive chemosensory cues to which they are exposed early in life. Early odor-exposure increases adult chemo-attraction to the same cues. Imprinting is transiently or stably inherited, depending on the number of exposed generations. We show here that the Alanine tRNA (UGC) plays a central role in regulating C. elegans chemo-attraction. Naive worms fed on tRNAAla (UGC) purified from odor-experienced worms, acquire odor-specific imprints. Chemo-attractive responses require the tRNA-modifying Elongator complex sub-units 1 (elpc-1) and 3 (elpc-3) genes. elpc-3 deletions impair chemo-attraction, which is fully restored by wild-type tRNAAla (UGC) feeding. A stably inherited decrease of odor-specific responses ensues from early odor-exposition of elpc-1 deletion mutants. tRNAAla (UGC) may adopt various chemical forms to mediate the cross-talk between innately-programmed and environment-directed chemo-attractive behavior.
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Affiliation(s)
- Diana Andrea Fernandes De Abreu
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
| | - Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Laurence Drouard
- Institut de Biologie Moléculaire des Plantes-CNRS, Université de Strasbourg, Strasbourg, France
| | - Jean-Jacques Remy
- Genes, Environment, Plasticity, Institut Sophia Agrobiotech ISA UMR CNRS 7254, INRAE 1355, Université Nice Côte d’Azur, Sophia-Antipolis, France
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15
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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: 0.5] [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.
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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
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16
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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: 1.3] [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.
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17
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Liu H, Ren D, Jiang L, Li X, Yao Y, Mi L, Chen W, Mo A, Jiang N, Yang J, Chen P, Ma H, Luo X, Lu P. A Natural Variation in PLEIOTROPIC DEVELOPMENTAL DEFECTS Uncovers a Crucial Role for Chloroplast tRNA Modification in Translation and Plant Development. THE PLANT CELL 2020; 32:2345-2366. [PMID: 32327539 PMCID: PMC7346568 DOI: 10.1105/tpc.19.00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 03/30/2020] [Accepted: 04/15/2020] [Indexed: 05/28/2023]
Abstract
The modification of tRNA is important for accurate, efficient protein translation. A number of tRNA-modifying enzymes were found to influence various developmental processes in distinct organisms. However, few genetic or molecular studies have focused on genes encoding tRNA-modifying enzymes in green plant organelles. Here, we discovered that PDD OL , a natural variation allele of PLEIOTROPIC DEVELOPMENTAL DEFECTS (PDD), leads to pleiotropic developmental defects in a near-isogenic line (NIL) generated by introgressing the wild rice Oryza longistaminata into the rice (Oryza sativa) cv 187R. Map-based cloning revealed that PDD encodes an evolutionarily conserved tRNA-modifying GTPase belonging to the tRNA modification E family. The function of PDD was further confirmed by genetic complementation experiments and mutant analysis. PDD mRNA is primarily expressed in leaves, and PDD is localized to chloroplasts. Biochemical analyses indicated that PDD187R forms homodimers and has strong GTPase activity, whereas PDDOL fails to form homodimers and has weak GTPase activity. Liquid chromatography-coupled tandem quadrupole mass spectrometry revealed that PDD is associated with the 5-methylaminomethyl-2-thiouridine modification of chloroplast tRNA. Furthermore, compared to 187R, NIL-PDD OL has severely reduced levels of proteins involved in photosynthesis and ribosome biogenesis but increased levels of plastid-encoded RNA polymerase subunits. Finally, we demonstrate that the defect due to PDD OL alters chloroplast gene expression, thereby affecting communication between the chloroplast and the nucleus.
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Affiliation(s)
- Hui Liu
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ding Ren
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Ling Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaojing Li
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yuan Yao
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Limin Mi
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Wanli Chen
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ning Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinshui Yang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Xiaojin Luo
- School of Life Sciences, Fudan University, Shanghai 200433, China
- MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai 200433, China
| | - Pingli Lu
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
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18
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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: 0.3] [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.
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Affiliation(s)
- Diego Rojas-Benítez
- FONDAP Center for Genome Regulation (CGR), Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
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19
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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: 1.2] [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.
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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.
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20
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Krutyhołowa R, Hammermeister A, Zabel R, Abdel-Fattah W, Reinhardt-Tews A, Helm M, Stark MJR, Breunig KD, Schaffrath R, Glatt S. Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Nucleic Acids Res 2019; 47:4814-4830. [PMID: 30916349 PMCID: PMC6511879 DOI: 10.1093/nar/gkz190] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/14/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Posttranscriptional RNA modifications occur in all domains of life. Modifications of anticodon bases are of particular importance for ribosomal decoding and proteome homeostasis. The Elongator complex modifies uridines in the wobble position and is highly conserved in eukaryotes. Despite recent insights into Elongator's architecture, the structure and function of its regulatory factor Kti12 have remained elusive. Here, we present the crystal structure of Kti12′s nucleotide hydrolase domain trapped in a transition state of ATP hydrolysis. The structure reveals striking similarities to an O-phosphoseryl-tRNA kinase involved in the selenocysteine pathway. Both proteins employ similar mechanisms of tRNA binding and show tRNASec-dependent ATPase activity. In addition, we demonstrate that Kti12 binds directly to Elongator and that ATP hydrolysis is crucial for Elongator to maintain proper tRNA anticodon modification levels in vivo. In summary, our data reveal a hitherto uncharacterized link between two translational control pathways that regulate selenocysteine incorporation and affect ribosomal tRNA selection via specific tRNA modifications.
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Affiliation(s)
- Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Rene Zabel
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | | | - Mark Helm
- Institut für Pharmazie und Biochemie, Universität Mainz, Mainz, Germany
| | - Michael J R Stark
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, UK
| | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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21
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Forward Genetic Screen for Caenorhabditis elegans Mutants with a Shortened Locomotor Healthspan. G3-GENES GENOMES GENETICS 2019; 9:2415-2423. [PMID: 31213517 PMCID: PMC6686916 DOI: 10.1534/g3.119.400241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two people with the same lifespan do not necessarily have the same healthspan. One person may retain locomotor and cognitive abilities until the end of life, while another person may lose them during adulthood. Unbiased searches for genes that are required to maintain locomotor ability during adulthood may uncover key regulators of locomotor healthspan. Here, we take advantage of the relatively short lifespan of the nematode Caenorhabditis elegans and develop a novel screening procedure to collect mutants with locomotor deficits that become apparent in adulthood. After ethyl methanesulfonate mutagenesis, we isolated five C. elegans mutant strains that progressively lose adult locomotor ability. In one of the mutant strains, a nonsense mutation in elpc-2, which encodes Elongator Complex Protein Component 2, causes a progressive decline in locomotor ability during adulthood. Mutants and mutations identified in the present screen may provide insights into mechanisms of age-related locomotor impairment and the maintenance of locomotor healthspan.
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22
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Bento-Abreu A, Jager G, Swinnen B, Rué L, Hendrickx S, Jones A, Staats KA, Taes I, Eykens C, Nonneman A, Nuyts R, Timmers M, Silva L, Chariot A, Nguyen L, Ravits J, Lemmens R, Cabooter D, Van Den Bosch L, Van Damme P, Al-Chalabi A, Bystrom A, Robberecht W. Elongator subunit 3 (ELP3) modifies ALS through tRNA modification. Hum Mol Genet 2019; 27:1276-1289. [PMID: 29415125 PMCID: PMC6159532 DOI: 10.1093/hmg/ddy043] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/30/2018] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal degenerative motor neuron disorder of which the progression is influenced by several disease-modifying factors. Here, we investigated ELP3, a subunit of the elongator complex that modifies tRNA wobble uridines, as one of such ALS disease modifiers. ELP3 attenuated the axonopathy of a mutant SOD1, as well as of a mutant C9orf72 ALS zebrafish model. Furthermore, the expression of ELP3 in the SOD1G93A mouse extended the survival and attenuated the denervation in this model. Depletion of ELP3 in vitro reduced the modified tRNA wobble uridine mcm5s2U and increased abundance of insoluble mutant SOD1, which was reverted by exogenous ELP3 expression. Interestingly, the expression of ELP3 in the motor cortex of ALS patients was reduced and correlated with mcm5s2U levels. Our results demonstrate that ELP3 is a modifier of ALS and suggest a link between tRNA modification and neurodegeneration.
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Affiliation(s)
- Andre Bento-Abreu
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Gunilla Jager
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Bart Swinnen
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Laura Rué
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Stijn Hendrickx
- Department of Pharmaceutical & Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ashley Jones
- Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Kim A Staats
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Ines Taes
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Caroline Eykens
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Annelies Nonneman
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Rik Nuyts
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Mieke Timmers
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Lara Silva
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Alain Chariot
- GIGA-Molecular Biology of Diseases and Walloon Excellence in Life Sciences and Biotechnology (WELBIO), C.H.U. Sart Tilman, B-4000 Liège, Belgium
| | - Laurent Nguyen
- GIGA-Neurosciences, University of Liège, C.H.U. Sart Tilman, B-4000 Liège, Belgium
| | - John Ravits
- Department of Neurosciences, ALS Translational Research, University of California, San Diego, La Jolla, CA, USA
| | - Robin Lemmens
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Deirdre Cabooter
- Department of Pharmaceutical & Pharmacological Sciences, Pharmaceutical Analysis, B-3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Neurobiology, VIB-Center for Brain & Disease Research, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Ammar Al-Chalabi
- Department of Clinical Neuroscience, Institute of Psychiatry, King's College London, London SE5 8AF, UK
| | - Anders Bystrom
- Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven-University of Leuven, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
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23
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The emerging impact of tRNA modifications in the brain and nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:412-428. [PMID: 30529455 DOI: 10.1016/j.bbagrm.2018.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Deciphering the Role of the Non-Coding Genome in Regulating Gene-Diet Interactions. Nutrients 2018; 10:nu10121831. [PMID: 30486341 PMCID: PMC6316136 DOI: 10.3390/nu10121831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 01/01/2023] Open
Abstract
Protein encoding genes constitute a small fraction of mammalian genomes. In addition to the protein coding genes, there are other functional units within the genome that are transcribed, but not translated into protein, the so called non-coding RNAs. There are many types of non-coding RNAs that have been identified and shown to have important roles in regulating gene expression either at the transcriptional or post-transcriptional level. A number of recent studies have highlighted that dietary manipulation in mammals can influence the expression or function of a number of classes of non-coding RNAs that contribute to the protein translation machinery. The identification of protein translation as a common target for nutritional regulation underscores the need to investigate how this may mechanistically contribute to phenotypes and diseases that are modified by nutritional intervention. Finally, we describe the state of the art and the application of emerging ‘-omics’ technologies to address the regulation of protein translation in response to diet.
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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: 76] [Impact Index Per Article: 12.7] [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.
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Sarin LP, Kienast SD, Leufken J, Ross RL, Dziergowska A, Debiec K, Sochacka E, Limbach PA, Fufezan C, Drexler HCA, Leidel SA. Nano LC-MS using capillary columns enables accurate quantification of modified ribonucleosides at low femtomol levels. RNA (NEW YORK, N.Y.) 2018; 24:1403-1417. [PMID: 30012570 PMCID: PMC6140458 DOI: 10.1261/rna.065482.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 07/11/2018] [Indexed: 05/14/2023]
Abstract
Post-transcriptional chemical modifications of (t)RNA molecules are crucial in fundamental biological processes, such as translation. Despite their biological importance and accumulating evidence linking them to various human diseases, technical challenges have limited their detection and accurate quantification. Here, we present a sensitive capillary nanoflow liquid chromatography mass spectrometry (nLC-MS) pipeline for quantitative high-resolution analysis of ribonucleoside modifications from complex biological samples. We evaluated two porous graphitic carbon (PGC) materials and one end-capped C18 reference material as stationary phases for reversed-phase separation. We found that these matrices have complementing retention and separation characteristics, including the capability to separate structural isomers. PGC and C18 matrices yielded excellent signal-to-noise ratios in nLC-MS while differing in the separation capability and sensitivity for various nucleosides. This emphasizes the need for tailored LC-MS setups for optimally detecting as many nucleoside modifications as possible. Detection ranges spanning up to six orders of magnitude enable the analysis of individual ribonucleosides down to femtomol concentrations. Furthermore, normalizing the obtained signal intensities to a stable isotope labeled spike-in enabled direct comparison of ribonucleoside levels between different samples. In conclusion, capillary columns coupled to nLC-MS constitute a powerful and sensitive tool for quantitative analysis of modified ribonucleosides in complex biological samples. This setup will be invaluable for further unraveling the intriguing and multifaceted biological roles of RNA modifications.
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Affiliation(s)
- L Peter Sarin
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Sandra D Kienast
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Johannes Leufken
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Agnieszka Dziergowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Katarzyna Debiec
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Christian Fufezan
- Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, 48143, Germany
| | - Hannes C A Drexler
- Bioanalytical Mass Spectrometry Unit, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, Muenster, 48149, Germany
- Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, 48149, Germany
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Ueki Y, Shchepetkina V, Lefcort F. Retina-specific loss of Ikbkap/Elp1 causes mitochondrial dysfunction that leads to selective retinal ganglion cell degeneration in a mouse model of familial dysautonomia. Dis Model Mech 2018; 11:dmm.033746. [PMID: 29929962 PMCID: PMC6078410 DOI: 10.1242/dmm.033746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/12/2018] [Indexed: 12/26/2022] Open
Abstract
Familial dysautonomia (FD) is an autosomal recessive disorder marked by developmental and progressive neuropathies. It is caused by an intronic point-mutation in the IKBKAP/ELP1 gene, which encodes the inhibitor of κB kinase complex-associated protein (IKAP, also called ELP1), a component of the elongator complex. Owing to variation in tissue-specific splicing, the mutation primarily affects the nervous system. One of the most debilitating hallmarks of FD that affects patients' quality of life is progressive blindness. To determine the pathophysiological mechanisms that are triggered by the absence of IKAP in the retina, we generated retina-specific Ikbkap conditional knockout (CKO) mice using Pax6-Cre, which abolished Ikbkap expression in all cell types of the retina. Although sensory and autonomic neuropathies in FD are known to be developmental in origin, the loss of IKAP in the retina did not affect its development, demonstrating that IKAP is not required for retinal development. The loss of IKAP caused progressive degeneration of retinal ganglion cells (RGCs) by 1 month of age. Mitochondrial membrane integrity was breached in RGCs, and later in other retinal neurons. In Ikbkap CKO retinas, mitochondria were depolarized, and complex I function and ATP were significantly reduced. Although mitochondrial impairment was detected in all Ikbkap-deficient retinal neurons, RGCs were the only cell type to degenerate; the survival of other retinal neurons was unaffected. This retina-specific FD model is a useful in vivo model for testing potential therapeutics for mitigating blindness in FD. Moreover, our data indicate that RGCs and mitochondria are promising targets. Summary: The elongator subunit IKBKAP/ELP1 is not required for development, but is essential for maintaining mitochondrial function and retina morphology. Loss of this subunit causes progressive, selective degeneration of retinal ganglion cells.
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Affiliation(s)
- Yumi Ueki
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Veronika Shchepetkina
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
| | - Frances Lefcort
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT 59717, USA
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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: 3.3] [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.
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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.
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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: 1.8] [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.
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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
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30
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Han L, Guy MP, Kon Y, Phizicky EM. Lack of 2'-O-methylation in the tRNA anticodon loop of two phylogenetically distant yeast species activates the general amino acid control pathway. PLoS Genet 2018; 14:e1007288. [PMID: 29596413 PMCID: PMC5892943 DOI: 10.1371/journal.pgen.1007288] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 04/10/2018] [Accepted: 03/05/2018] [Indexed: 01/03/2023] Open
Abstract
Modification defects in the tRNA anticodon loop often impair yeast growth and cause human disease. In the budding yeast Saccharomyces cerevisiae and the phylogenetically distant fission yeast Schizosaccharomyces pombe, trm7Δ mutants grow poorly due to lack of 2'-O-methylation of C32 and G34 in the tRNAPhe anticodon loop, and lesions in the human TRM7 homolog FTSJ1 cause non-syndromic X-linked intellectual disability (NSXLID). However, it is unclear why trm7Δ mutants grow poorly. We show here that despite the fact that S. cerevisiae trm7Δ mutants had no detectable tRNAPhe charging defect in rich media, the cells constitutively activated a robust general amino acid control (GAAC) response, acting through Gcn2, which senses uncharged tRNA. Consistent with reduced available charged tRNAPhe, the trm7Δ growth defect was suppressed by spontaneous mutations in phenylalanyl-tRNA synthetase (PheRS) or in the pol III negative regulator MAF1, and by overexpression of tRNAPhe, PheRS, or EF-1A; all of these also reduced GAAC activation. Genetic analysis also demonstrated that the trm7Δ growth defect was due to the constitutive robust GAAC activation as well as to the reduced available charged tRNAPhe. Robust GAAC activation was not observed with several other anticodon loop modification mutants. Analysis of S. pombe trm7 mutants led to similar observations. S. pombe Trm7 depletion also resulted in no observable tRNAPhe charging defect and a robust GAAC response, and suppressors mapped to PheRS and reduced GAAC activation. We speculate that GAAC activation is widely conserved in trm7 mutants in eukaryotes, including metazoans, and might play a role in FTSJ1-mediated NSXLID. The ubiquitous tRNA anticodon loop modifications have important but poorly understood functions in decoding mRNAs in the ribosome to ensure accurate and efficient protein synthesis, and their lack often impairs yeast growth and causes human disease. Here we investigate why ribose methylation of residues 32 and 34 in the anticodon loop is important. Mutations in the corresponding methyltransferase Trm7/FTSJ1 cause poor growth in the budding yeast Saccharomyces cerevisiae and near lethality in the evolutionarily distant fission yeast Schizosaccharomyces pombe, each due to reduced functional tRNAPhe. We previously showed that tRNAPhe anticodon loop modification in yeast and humans required two evolutionarily conserved Trm7 interacting proteins for Cm32 and Gm34 modification, which then stimulated G37 modification. We show here that both S. cerevisiae and S. pombe trm7Δ mutants have apparently normal tRNAPhe charging, but constitutively activate a robust general amino acid control (GAAC) response, acting through Gcn2, which senses uncharged tRNA. We also show that S. cerevisiae trm7Δ mutants grow poorly due in part to constitutive GAAC activation as well as to the uncharged tRNAPhe. We propose that TRM7 is important to prevent constitutive GAAC activation throughout eukaryotes, including metazoans, which may explain non-syndromic X-linked intellectual disability associated with human FTSJ1 mutations.
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Affiliation(s)
- Lu Han
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
| | - Michael P. Guy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
- Department of Chemistry and Biochemistry, Northern Kentucky University, Highland Heights, KY, United States of America
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
| | - Eric M. Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, NY, United States of America
- * E-mail:
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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: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [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. Familial dysautonomia is linked to mutations in IKBKAP, a scaffolding protein for the Elongator complex, which regulates codon-biased gene translation in yeast. Here the authors show in mammalian neurons that IKBKAP loss alters expression of codon-biased genes, including some involved in DNA damage.
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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.
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Wang Y, Pang C, Li X, Hu Z, Lv Z, Zheng B, Chen P. Identification of tRNA nucleoside modification genes critical for stress response and development in rice and Arabidopsis. BMC PLANT BIOLOGY 2017; 17:261. [PMID: 29268705 PMCID: PMC5740945 DOI: 10.1186/s12870-017-1206-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/06/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Modification of nucleosides on transfer RNA (tRNA) is important either for correct mRNA decoding process or for tRNA structural stabilization. Nucleoside methylations catalyzed by MTase (methyltransferase) are the most common type among all tRNA nucleoside modifications. Although tRNA modified nucleosides and modification enzymes have been extensively studied in prokaryotic systems, similar research remains preliminary in higher plants, especially in crop species, such as rice (Oryza sativa). Rice is a monocot model plant as well as an important cereal crop, and stress tolerance and yield are of great importance for rice breeding. RESULTS In this study, we investigated how the composition and abundance of tRNA modified nucleosides could change in response to drought, salt and cold stress, as well as in different tissues during the whole growth season in two model plants-O. sativa and Arabidopsis thaliana. Twenty two and 20 MTase candidate genes were identified in rice and Arabidopsis, respectively, by protein sequence homology and conserved domain analysis. Four methylated nucleosides, Am, Cm, m1A and m7G, were found to be very important in stress response both in rice and Arabidopsis. Additionally, three nucleosides,Gm, m5U and m5C, were involved in plant development. Hierarchical clustering analysis revealed consistency on Am, Cm, m1A and m7G MTase candidate genes, and the abundance of the corresponding nucleoside under stress conditions. The same is true for Gm, m5U and m5C modifications and corresponding methylation genes in different tissues during different developmental stages. CONCLUSIONS We identified candidate genes for various tRNA modified nucleosides in rice and Arabidopsis, especially on MTases for methylated nucleosides. Based on bioinformatics analysis, nucleoside abundance assessments and gene expression profiling, we propose four methylated nucleosides (Am, Cm, m1A and m7G) that are critical for stress response in rice and Arabidopsis, and three methylated nucleosides (Gm, m5U and m5C) that might be important during development.
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Affiliation(s)
- Youmei Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chaoqun Pang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xukai Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi Province 030801 China
| | - Zhen Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhengyi Lv
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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Sokołowski M, Klassen R, Bruch A, Schaffrath R, Glatt S. Cooperativity between different tRNA modifications and their modification pathways. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:409-418. [PMID: 29222069 DOI: 10.1016/j.bbagrm.2017.12.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/30/2017] [Accepted: 12/03/2017] [Indexed: 12/11/2022]
Abstract
Ribonucleotide modifications perform a wide variety of roles in synthesis, turnover and functionality of tRNA molecules. The presence of particular chemical moieties can refine the internal interaction network within a tRNA molecule, influence its thermodynamic stability, contribute novel chemical properties and affect its decoding behavior during mRNA translation. As the lack of specific modifications in the anticodon stem and loop causes disrupted proteome homeostasis, diminished response to stress conditions, and the onset of human diseases, the underlying modification cascades have recently gained particular scientific and clinical interest. Nowadays, a complicated but conclusive image of the interconnectivity between different enzymatic modification cascades and their resulting tRNA modifications emerges. Here we summarize the current knowledge in the field, focusing on the known instances of cross talk among the enzymatic tRNA modification pathways and the consequences on the dynamic regulation of the tRNA modificome by various factors. 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.
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Affiliation(s)
- Mikołaj Sokołowski
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Alexander Bruch
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Kassel, Germany.
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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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: 18] [Impact Index Per Article: 2.6] [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.
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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.
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36
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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: 3.4] [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.
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van Delft P, Akay A, Huber SM, Bueschl C, Rudolph KLM, Di Domenico T, Schuhmacher R, Miska EA, Balasubramanian S. The Profile and Dynamics of RNA Modifications in Animals. Chembiochem 2017; 18:979-984. [PMID: 28449301 PMCID: PMC5784800 DOI: 10.1002/cbic.201700093] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 12/28/2022]
Abstract
More than a hundred distinct modified nucleosides have been identified in RNA, but little is known about their distribution across different organisms, their dynamic nature and their response to cellular and environmental stress. Mass-spectrometry-based methods have been at the forefront of identifying and quantifying modified nucleosides. However, they often require synthetic reference standards, which do not exist in the case of many modified nucleosides, and this therefore impedes their analysis. Here we use a metabolic labelling approach to achieve rapid generation of bio-isotopologues of the complete Caenorhabditis elegans transcriptome and its modifications and use them as reference standards to characterise the RNA modification profile in this multicellular organism through an untargeted liquid-chromatography tandem high-resolution mass spectrometry (LC-HRMS) approach. We furthermore show that several of these RNA modifications have a dynamic response to environmental stress and that, in particular, changes in the tRNA wobble base modification 5-methoxycarbonylmethyl-2-thiouridine (mcm5 s2 U) lead to codon-biased gene-expression changes in starved animals.
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Affiliation(s)
- Pieter van Delft
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Alper Akay
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
| | - Sabrina M. Huber
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Christoph Bueschl
- Center for Analytical ChemistryDepartment of AgrobiotechnologyUniversity of Natural Resources and Life SciencesViennaKonrad-Lorenz-Strasse 203430Tulln an der DonauAustria
| | - Konrad L. M. Rudolph
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Tomás Di Domenico
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Rainer Schuhmacher
- Center for Analytical ChemistryDepartment of AgrobiotechnologyUniversity of Natural Resources and Life SciencesViennaKonrad-Lorenz-Strasse 203430Tulln an der DonauAustria
| | - Eric A. Miska
- Gurdon InstituteUniversity of CambridgeTennis Court RoadCambridgeCB2 1QNUK
- Department of GeneticsUniversity of CambridgeDowning StreetCambridgeCB2 3EHUK
- Wellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeCB10 1SAUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeRobinson WayCambridgeCB2 0REUK
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38
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Bednářová A, Hanna M, Durham I, VanCleave T, England A, Chaudhuri A, Krishnan N. Lost in Translation: Defects in Transfer RNA Modifications and Neurological Disorders. Front Mol Neurosci 2017; 10:135. [PMID: 28536502 PMCID: PMC5422465 DOI: 10.3389/fnmol.2017.00135] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/20/2017] [Indexed: 11/13/2022] Open
Abstract
Transfer RNAs (tRNAs) are key molecules participating in protein synthesis. To augment their functionality they undergo extensive post-transcriptional modifications and, as such, are subject to regulation at multiple levels including transcription, transcript processing, localization and ribonucleoside base modification. Post-transcriptional enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and influences specific anticodon-codon interactions and regulates translation, its efficiency and fidelity. This phenomenon of nucleoside modification is most remarkable and results in a rich structural diversity of tRNA of which over 100 modified nucleosides have been characterized. Most often these hypermodified nucleosides are found in the wobble position of tRNAs, where they play a direct role in codon recognition as well as in maintaining translational efficiency and fidelity, etc. Several recent studies have pointed to a link between defects in tRNA modifications and human diseases including neurological disorders. Therefore, defects in tRNA modifications in humans need intensive characterization at the enzymatic and mechanistic level in order to pave the way to understand how lack of such modifications are associated with neurological disorders with the ultimate goal of gaining insights into therapeutic interventions.
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Affiliation(s)
- Andrea Bednářová
- Department of Biochemistry and Physiology, Institute of Entomology, Biology Centre, Academy of SciencesČeské Budějovice, Czechia.,Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Marley Hanna
- Molecular Biosciences Program, Arkansas State UniversityJonesboro, AR, USA
| | - Isabella Durham
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State UniversityMississippi State, MS, USA
| | - Tara VanCleave
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | - Alexis England
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
| | | | - Natraj Krishnan
- Laboratory of Molecular Biology and Biochemistry, Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State UniversityMississippi State, MS, USA
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39
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Agris PF, Narendran A, Sarachan K, Väre VYP, Eruysal E. The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity. Enzymes 2017; 41:1-50. [PMID: 28601219 DOI: 10.1016/bs.enz.2017.03.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The posttranscriptional modifications of tRNA's anticodon stem and loop (ASL) domain represent a third level, a third code, to the accuracy and efficiency of translating mRNA codons into the correct amino acid sequence of proteins. Modifications of tRNA's ASL domain are enzymatically synthesized and site specifically located at the anticodon wobble position-34 and 3'-adjacent to the anticodon at position-37. Degeneracy of the 64 Universal Genetic Codes and the limitation in the number of tRNA species require some tRNAs to decode more than one codon. The specific modification chemistries and their impact on the tRNA's ASL structure and dynamics enable one tRNA to decode cognate and "wobble codons" or to expand recognition to synonymous codons, all the while maintaining the translational reading frame. Some modified nucleosides' chemistries prestructure tRNA to read the two codons of a specific amino acid that shares a twofold degenerate codon box, and other chemistries allow a different tRNA to respond to all four codons of a fourfold degenerate codon box. Thus, tRNA ASL modifications are critical and mutations in genes for the modification enzymes and tRNA, the consequences of which is a lack of modification, lead to mistranslation and human disease. By optimizing tRNA anticodon chemistries, structure, and dynamics in all organisms, modifications ensure translational fidelity of mRNA transcripts.
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Affiliation(s)
- Paul F Agris
- The RNA Institute, State University of New York, Albany, NY, United States.
| | - Amithi Narendran
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Kathryn Sarachan
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Ville Y P Väre
- The RNA Institute, State University of New York, Albany, NY, United States
| | - Emily Eruysal
- The RNA Institute, State University of New York, Albany, NY, United States
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40
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Ranjan N, Rodnina MV. Thio-Modification of tRNA at the Wobble Position as Regulator of the Kinetics of Decoding and Translocation on the Ribosome. J Am Chem Soc 2017; 139:5857-5864. [PMID: 28368583 DOI: 10.1021/jacs.7b00727] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Uridine 34 (U34) at the wobble position of the tRNA anticodon is post-transcriptionally modified, usually to mcm5s2, mcm5, or mnm5. The lack of the mcm5 or s2 modification at U34 of tRNALys, tRNAGlu, and tRNAGln causes ribosome pausing at the respective codons in yeast. The pauses occur during the elongation step, but the mechanism that triggers ribosome pausing is not known. Here, we show how the s2 modification in yeast tRNALys affects mRNA decoding and tRNA-mRNA translocation. Using real-time kinetic analysis we show that mcm5-modified tRNALys lacking the s2 group has a lower affinity of binding to the cognate codon and is more efficiently rejected than the fully modified tRNALys. The lack of the s2 modification also slows down the rearrangements in the ribosome-EF-Tu-GDP-Pi-Lys-tRNALys complex following GTP hydrolysis by EF-Tu. Finally, tRNA-mRNA translocation is slower with the s2-deficient tRNALys. These observations explain the observed ribosome pausing at AAA codons during translation and demonstrate how the s2 modification helps to ensure the optimal translation rates that maintain proteome homeostasis of the cell.
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Affiliation(s)
- Namit Ranjan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Goettingen, Germany
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41
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Zheng C, Black KA, Dos Santos PC. Diverse Mechanisms of Sulfur Decoration in Bacterial tRNA and Their Cellular Functions. Biomolecules 2017; 7:biom7010033. [PMID: 28327539 PMCID: PMC5372745 DOI: 10.3390/biom7010033] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/10/2017] [Accepted: 03/16/2017] [Indexed: 01/01/2023] Open
Abstract
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species. Interestingly, a novel proposal has been given for interplay among thionucleosides and the biosynthesis of other thiocofactors, through participation of shared-enzyme intermediates, the functions of which are impacted by the availability of substrate as well as metabolic demand of thiocofactors. This review describes the occurrence of thio-modifications in bacterial tRNA and current methods for detection of these modifications that have enabled studies on the biosynthesis and functions of S-containing tRNA across bacteria. It provides insight into potential modes of regulation and potential evolutionary events responsible for divergence in sulfur metabolism among prokaryotes.
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Affiliation(s)
- Chenkang Zheng
- Department of Chemistry, Wake Forest University, Winston-Salem, NC 27101, USA.
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42
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Abstract
Wobble uridines (U34) are generally modified in all species. U34 modifications can be essential in metazoans but are not required for viability in fungi. In this review, we provide an overview on the types of modifications and how they affect the physico-chemical properties of wobble uridines. We describe the molecular machinery required to introduce these modifications into tRNA posttranscriptionally and discuss how posttranslational regulation may affect the activity of the modifying enzymes. We highlight the activity of anticodon specific RNases that target U34 containing tRNA. Finally, we discuss how defects in wobble uridine modifications lead to phenotypes in different species. Importantly, this review will mainly focus on the cytoplasmic tRNAs of eukaryotes. A recent review has extensively covered their bacterial and mitochondrial counterparts.1
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Affiliation(s)
- Raffael Schaffrath
- a Institut für Biologie, FG Mikrobiologie , Universität Kassel , Germany
| | - Sebastian A Leidel
- b Max Planck Institute for Molecular Biomedicine , Germany.,c Cells-in-Motion Cluster of Excellence , University of Münster , Münster , Germany.,d Medical Faculty , University of Münster , Albert-Schweitzer-Campus 1, Münster , Germany
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43
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Kolaj-Robin O, Séraphin B. Structures and Activities of the Elongator Complex and Its Cofactors. RNA MODIFICATION 2017; 41:117-149. [DOI: 10.1016/bs.enz.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Dauden MI, Kosinski J, Kolaj-Robin O, Desfosses A, Ori A, Faux C, Hoffmann NA, Onuma OF, Breunig KD, Beck M, Sachse C, Séraphin B, Glatt S, Müller CW. Architecture of the yeast Elongator complex. EMBO Rep 2016; 18:264-279. [PMID: 27974378 PMCID: PMC5286394 DOI: 10.15252/embr.201643353] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 11/08/2016] [Indexed: 11/09/2022] Open
Abstract
The highly conserved eukaryotic Elongator complex performs specific chemical modifications on wobble base uridines of tRNAs, which are essential for proteome stability and homeostasis. The complex is formed by six individual subunits (Elp1-6) that are all equally important for its tRNA modification activity. However, its overall architecture and the detailed reaction mechanism remain elusive. Here, we report the structures of the fully assembled yeast Elongator and the Elp123 sub-complex solved by an integrative structure determination approach showing that two copies of the Elp1, Elp2, and Elp3 subunits form a two-lobed scaffold, which binds Elp456 asymmetrically. Our topological models are consistent with previous studies on individual subunits and further validated by complementary biochemical analyses. Our study provides a structural framework on how the tRNA modification activity is carried out by Elongator.
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Affiliation(s)
- Maria I Dauden
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Olga Kolaj-Robin
- Université de Strasbourg, IGBMC, Illkirch, France.,CNRS, IGBMC UMR 7104, Illkirch, France.,Inserm, IGBMC U964, Illkirch, France
| | - Ambroise Desfosses
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Celine Faux
- Université de Strasbourg, IGBMC, Illkirch, France.,CNRS, IGBMC UMR 7104, Illkirch, France.,Inserm, IGBMC U964, Illkirch, France
| | - Niklas A Hoffmann
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Osita F Onuma
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Karin D Breunig
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Bertrand Séraphin
- Université de Strasbourg, IGBMC, Illkirch, France.,CNRS, IGBMC UMR 7104, Illkirch, France.,Inserm, IGBMC U964, Illkirch, France
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Christoph W Müller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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45
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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: 121] [Impact Index Per Article: 15.1] [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.
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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
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46
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Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi. Nat Struct Mol Biol 2016; 23:794-802. [PMID: 27455459 PMCID: PMC5018218 DOI: 10.1038/nsmb.3265] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022]
Abstract
During translation elongation decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons have recently received increasing attention. The conserved eukaryotic Elongator complex specifically modifies uridines located in the wobble base position of tRNAs. Here, we present the crystal structure of Dehalococcoides mccartyi Elp3 (DmcElp3) at 2.15 Å resolution. Our results reveal the unexpected arrangement of Elp3 lysine acetyl transferase (KAT) and radical S-adenosyl-methionine (SAM) domains that share a large interface to form a composite active site and tRNA binding pocket with an iron sulfur cluster located in the dimerization interface of two DmcElp3 molecules. Structure-guided mutagenesis studies of yeast Elp3 confirm the relevance of our findings for eukaryotic Elp3s and for understanding Elongator’s role in the onset of various neurodegenerative diseases and cancer in humans.
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47
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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: 146] [Impact Index Per Article: 18.3] [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.
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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.
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Pain D, Dancis A. Roles of Fe-S proteins: from cofactor synthesis to iron homeostasis to protein synthesis. Curr Opin Genet Dev 2016; 38:45-51. [PMID: 27061491 DOI: 10.1016/j.gde.2016.03.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 02/27/2016] [Accepted: 03/09/2016] [Indexed: 12/28/2022]
Abstract
Fe-S cluster assembly is an essential process for all cells. Impairment of Fe-S cluster assembly creates diseases in diverse and surprising ways. In one scenario, the loss of function of lipoic acid synthase, an enzyme with Fe-S cluster cofactor in mitochondria, impairs activity of various lipoamide-dependent enzymes with drastic consequences for metabolism. In a second scenario, the heme biosynthetic pathway in red cell precursors is specifically targeted, and iron homeostasis is perturbed, but lipoic acid synthesis is unaffected. In a third scenario, tRNA modifications arising from action of the cysteine desulfurase and/or Fe-S cluster proteins are lost, which may lead to impaired protein synthesis. These defects can then result in cancer, neurologic dysfunction or type 2 diabetes.
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Affiliation(s)
- Debkumar Pain
- Department of Pharmacology, Physiology, and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07101, USA
| | - Andrew Dancis
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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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: 1.0] [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.
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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
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50
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Deng W, Babu IR, Su D, Yin S, Begley TJ, Dedon PC. Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation. PLoS Genet 2015; 11:e1005706. [PMID: 26670883 PMCID: PMC4689569 DOI: 10.1371/journal.pgen.1005706] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/06/2015] [Indexed: 12/30/2022] Open
Abstract
Post-transcriptional modifications of transfer RNAs (tRNAs) have long been recognized to play crucial roles in regulating the rate and fidelity of translation. However, the extent to which they determine global protein production remains poorly understood. Here we use quantitative proteomics to show a direct link between wobble uridine 5-methoxycarbonylmethyl (mcm5) and 5-methoxy-carbonyl-methyl-2-thio (mcm5s2) modifications catalyzed by tRNA methyltransferase 9 (Trm9) in tRNAArg(UCU) and tRNAGlu(UUC) and selective translation of proteins from genes enriched with their cognate codons. Controlling for bias in protein expression and alternations in mRNA expression, we find that loss of Trm9 selectively impairs expression of proteins from genes enriched with AGA and GAA codons under both normal and stress conditions. Moreover, we show that AGA and GAA codons occur with high frequency in clusters along the transcripts, which may play a role in modulating translation. Consistent with these results, proteins subject to enhanced ribosome pausing in yeast lacking mcm5U and mcm5s2U are more likely to be down-regulated and contain a larger number of AGA/GAA clusters. Together, these results suggest that Trm9-catalyzed tRNA modifications play a significant role in regulating protein expression within the cell. Here we present evidence for a more complicated role for transfer RNAs (tRNAs) than as mere adapters that link the genetic code in messenger RNA (mRNA) to the amino acid sequence of a protein during translation. tRNAs have long been known to be modified with dozens of different chemical structures other than the 4 canonical ribonucleosides, though the role of these modifications in controlling translation is poorly understood. By quantifying the expression of thousands of proteins in the yeast S. cerevisiae, we identified a mechanistic link between modified ribonucleosides located at the wobble position of two tRNAs, tRNAArg(UCU) and tRNAGlu(UUC), and the translation of proteins derived from genes enriched with codons read by these tRNAs: AGA and GAA. In cells lacking the enzyme that inserts these modifications, tRNA methyltransferase 9 (Trm9), we found a significant reduction in proteins from genes enriched with AGA and GAA codons and with runs of these codons. Also, mRNAs enriched with runs of AGA and GAA codons are subject to stalled translation on ribosomes in yeast lacking mcm5U and mcm5s2U. Together, these results reveal a distinct role for Trm9-catalyzed tRNA modifications in selectively regulating the expression of proteins enriched with AGA and GAA codons.
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Affiliation(s)
- Wenjun Deng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - I. Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dan Su
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas J. Begley
- SUNY College of Nanoscale Science and Engineering, Albany, New York, United States of America
- RNA Institute and Cancer Research Center, University at Albany, State University of New York, Albany, New York, United States of America
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Singapore-MIT Alliance for Research and Technology, Singapore
- * E-mail:
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