251
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Huang HY, Hopper AK. Multiple Layers of Stress-Induced Regulation in tRNA Biology. Life (Basel) 2016; 6:life6020016. [PMID: 27023616 PMCID: PMC4931453 DOI: 10.3390/life6020016] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/14/2016] [Accepted: 03/17/2016] [Indexed: 01/28/2023] Open
Abstract
tRNAs are the fundamental components of the translation machinery as they deliver amino acids to the ribosomes during protein synthesis. Beyond their essential function in translation, tRNAs also function in regulating gene expression, modulating apoptosis and several other biological processes. There are multiple layers of regulatory mechanisms in each step of tRNA biogenesis. For example, tRNA 3′ trailer processing is altered upon nutrient stress; tRNA modification is reprogrammed under various stresses; nuclear accumulation of tRNAs occurs upon nutrient deprivation; tRNA halves accumulate upon oxidative stress. Here we address how environmental stresses can affect nearly every step of tRNA biology and we describe the possible regulatory mechanisms that influence the function or expression of tRNAs under stress conditions.
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Affiliation(s)
- Hsiao-Yun Huang
- Department of Biology, Indiana University, 915 E third St., Myers 300, Bloomington, IN 47405, USA.
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
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252
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Silent Polymorphisms: Can the tRNA Population Explain Changes in Protein Properties? Life (Basel) 2016; 6:life6010009. [PMID: 26901226 PMCID: PMC4810240 DOI: 10.3390/life6010009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/26/2016] [Accepted: 02/05/2016] [Indexed: 01/18/2023] Open
Abstract
Silent mutations are being intensively studied. We previously showed that the estrogen receptor alpha Ala87’s synonymous polymorphism affects its functional properties. Whereas a link has been clearly established between the effect of silent mutations, tRNA abundance and protein folding in prokaryotes, this connection remains controversial in eukaryotic systems. Although a synonymous polymorphism can affect mRNA structure or the interaction with specific ligands, it seems that the relative frequencies of isoacceptor tRNAs could play a key role in the protein-folding process, possibly through modulation of translation kinetics. Conformational changes could be subtle but enough to cause alterations in solubility, proteolysis profiles, functional parameters or intracellular targeting. Interestingly, recent advances describe dramatic changes in the tRNA population associated with proliferation, differentiation or response to chemical, physical or biological stress. In addition, several reports reveal changes in tRNAs’ posttranscriptional modifications in different physiological or pathological conditions. In consequence, since changes in the cell state imply quantitative and/or qualitative changes in the tRNA pool, they could increase the likelihood of protein conformational variants, related to a particular codon usage during translation, with consequences of diverse significance. These observations emphasize the importance of genetic code flexibility in the co-translational protein-folding process.
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253
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El-Hattab AW, Saleh MA, Hashem A, Al-Owain M, Asmari AA, Rabei H, Abdelraouf H, Hashem M, Alazami AM, Patel N, Shaheen R, Faqeih EA, Alkuraya FS. ADAT3-related intellectual disability: Further delineation of the phenotype. Am J Med Genet A 2016; 170A:1142-7. [PMID: 26842963 DOI: 10.1002/ajmg.a.37578] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/20/2016] [Indexed: 11/09/2022]
Abstract
ADAT3-related intellectual disability has been recently described in 24 individuals from eight Saudi families who had cognitive impairment and strabismus. Other common features included growth failure, microcephaly, tone abnormalities, epilepsy, and nonspecific brain abnormalities. A single homozygous founder mutation (c.382G>A:p.(V128M)) in the ADAT3 gene, which encodes a protein that functions in tRNA editing, was identified in all affected individuals. In this report, we present additional 15 individuals from 11 families (10 Saudis and 1 Emirati) who are homozygous for the same founder mutation. In addition to the universal findings of intellectual disability and strabismus, the majority exhibited microcephaly and growth failure. Additional features not reported in the original cohort include dysmorphic facial features (prominent forehead, up-slanted palpebral fissures, epicanthus, and depressed nasal bridge), behavioral problems (hyperactivity and aggressiveness), recurrent otitis media, and growth hormone deficiency. ADAT3-related intellectual disability is an important recognizable cause of intellectual disability in Arabia.
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Affiliation(s)
- Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Mohammed A Saleh
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Amal Hashem
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mohammed Al-Owain
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ali Al Asmari
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hala Rabei
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Hanem Abdelraouf
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eissa A Faqeih
- Section of Medical Genetics, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
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254
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Khan SY, Hackett SF, Riazuddin SA. Non-coding RNA profiling of the developing murine lens. Exp Eye Res 2016; 145:347-351. [PMID: 26808486 DOI: 10.1016/j.exer.2016.01.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/13/2016] [Indexed: 11/15/2022]
Abstract
Non-coding RNAs (ncRNAs) are emerging as an important player in the regulation of genome integrity and gene expression, and they have been implicated in the pathogenesis of many diseases. The aim of the present study is to identify the repertoire of ncRNAs expressed in the developing mouse lens. We previously reported the mouse lens transcriptome, including mRNA and microRNA (miRNA) profiling at two embryonic (E15 and E18) and four postnatal (P0, P3, P6, and P9) time points. We analyzed the data from small RNA-Seq and mRNA-Seq libraries to investigate the ncRNA profile. Our analysis revealed expression of 12 different classes of ncRNA in the murine lens at six developmental time points. Annotation of small RNA data showed expression of 1,756 antisense ncRNA (asncRNA) in the mouse lens transcriptome. Likewise, we identified 82 P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA), 345 transfer RNA (tRNA), 12 small nuclear RNA (snRNA), 167 small nucleolar RNA (snoRNA), 19 small Cajal body-specific RNA (scaRNA), six ribosomal RNA (rRNA), 18 tRNA-like structures, one MALAT1-associated small cytoplasmic RNA (mascRNA), one Vault RNA (vtRNA), and one Y RNA expressed in the developing mouse lens. In parallel, bioinformatic investigation of mRNA-Seq data identified expression of 1,952 long intergenic ncRNA (lincRNA) in the developing mouse lens. In conclusion, we report a comprehensive ncRNA profile in the murine lens at six developmental time points. To the best of our knowledge, this is first report investigating different classes of ncRNAs in the developing mouse lens and will be monumental in elucidating processes essential for the development of the ocular lens and the maintenance of its transparency.
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Affiliation(s)
- Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Sean F Hackett
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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255
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Abstract
tRNA molecules undergo extensive post-transcriptional processing to generate the mature functional tRNA species that are essential for translation in all organisms. These processing steps include the introduction of numerous specific chemical modifications to nucleotide bases and sugars; among these modifications, methylation reactions are by far the most abundant. The tRNA methyltransferases comprise a diverse enzyme superfamily, including members of multiple structural classes that appear to have arisen independently during evolution. Even among closely related family members, examples of unusual substrate specificity and chemistry have been observed. Here we review recent advances in tRNA methyltransferase mechanism and function with a particular emphasis on discoveries of alternative substrate specificities and chemistry associated with some methyltransferases. Although the molecular function for a specific tRNA methylation may not always be clear, mutations in tRNA methyltransferases have been increasingly associated with human disease. The impact of tRNA methylation on human biology is also discussed.
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Affiliation(s)
- William E Swinehart
- a Center for RNA Biology and Department of Chemistry and Biochemistry ; Ohio State University ; Columbus , OH USA
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256
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Post-Transcriptional Modifications of RNA: Impact on RNA Function and Human Health. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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257
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Grzybkowska A, Jędrzejczyk D, Rostkowski M, Chworos A, Dybala-Defratyka A. RNA model evaluation based on MD simulation of four tRNA analogs. RSC Adv 2016. [DOI: 10.1039/c6ra14933b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Characteristic of 3D structures of tRNA analogs generated from primary sequence, subjected to all-atom MD simulation and assessed using selected RNA model evaluation methods.
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Affiliation(s)
- Anna Grzybkowska
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Dominika Jędrzejczyk
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Michał Rostkowski
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Arkadiusz Chworos
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
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258
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Fu Y, Lee I, Lee YS, Bao X. Small Non-coding Transfer RNA-Derived RNA Fragments (tRFs): Their Biogenesis, Function and Implication in Human Diseases. Genomics Inform 2015; 13:94-101. [PMID: 26865839 PMCID: PMC4742329 DOI: 10.5808/gi.2015.13.4.94] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 12/19/2015] [Accepted: 12/21/2015] [Indexed: 02/06/2023] Open
Abstract
tRNA-derived RNA fragments (tRFs) are an emerging class of non-coding RNAs (ncRNAs). A growing number of reports have shown that tRFs are not random degradation products but are functional ncRNAs made of specific tRNA cleavage. They play regulatory roles in several biological contexts such as cancer, innate immunity, stress responses, and neurological disorders. In this review, we summarize the biogenesis and functions of tRFs.
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Affiliation(s)
- Yu Fu
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | - Yong Sun Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xiaoyong Bao
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX 77555, USA.; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.; The Institute of Translational Science, University of Texas Medical Branch, Galveston, TX 77555, USA.; The Institute for Human Infections & Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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259
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Landmarks in the Evolution of (t)-RNAs from the Origin of Life up to Their Present Role in Human Cognition. Life (Basel) 2015; 6:life6010001. [PMID: 26703740 PMCID: PMC4810232 DOI: 10.3390/life6010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
How could modern life have evolved? The answer to that question still remains unclear. However, evidence is growing that, since the origin of life, RNA could have played an important role throughout evolution, right up to the development of complex organisms and even highly sophisticated features such as human cognition. RNA mediated RNA-aminoacylation can be seen as a first landmark on the path from the RNA world to modern DNA- and protein-based life. Likewise, the generation of the RNA modifications that can be found in various RNA species today may already have started in the RNA world, where such modifications most likely entailed functional advantages. This association of modification patterns with functional features was apparently maintained throughout the further course of evolution, and particularly tRNAs can now be seen as paradigms for the developing interdependence between structure, modification and function. It is in this spirit that this review highlights important stepping stones of the development of (t)RNAs and their modifications (including aminoacylation) from the ancient RNA world up until their present role in the development and maintenance of human cognition. The latter can be seen as a high point of evolution at its present stage, and the susceptibility of cognitive features to even small alterations in the proper structure and functioning of tRNAs underscores the evolutionary relevance of this RNA species.
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260
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Hoernes TP, Clementi N, Faserl K, Glasner H, Breuker K, Lindner H, Hüttenhofer A, Erlacher MD. Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code. Nucleic Acids Res 2015; 44:852-62. [PMID: 26578598 PMCID: PMC4737146 DOI: 10.1093/nar/gkv1182] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/22/2015] [Indexed: 01/05/2023] Open
Abstract
Nucleotide modifications within RNA transcripts are found in every organism in all three domains of life. 6-methyladeonsine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) are highly abundant nucleotide modifications in coding sequences of eukaryal mRNAs, while m5C and m6A modifications have also been discovered in archaeal and bacterial mRNAs. Employing in vitro translation assays, we systematically investigated the influence of nucleotide modifications on translation. We introduced m5C, m6A, Ψ or 2′-O-methylated nucleotides at each of the three positions within a codon of the bacterial ErmCL mRNA and analyzed their influence on translation. Depending on the respective nucleotide modification, as well as its position within a codon, protein synthesis remained either unaffected or was prematurely terminated at the modification site, resulting in reduced amounts of the full-length peptide. In the latter case, toeprint analysis of ribosomal complexes was consistent with stalling of translation at the modified codon. When multiple nucleotide modifications were introduced within one codon, an additive inhibitory effect on translation was observed. We also identified the m5C modification to alter the amino acid identity of the corresponding codon, when positioned at the second codon position. Our results suggest a novel mode of gene regulation by nucleotide modifications in bacterial mRNAs.
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Affiliation(s)
- Thomas Philipp Hoernes
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Nina Clementi
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Faserl
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Heidelinde Glasner
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Matthias David Erlacher
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
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261
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Selitsky SR, Sethupathy P. tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. BMC Bioinformatics 2015; 16:354. [PMID: 26530785 PMCID: PMC4632369 DOI: 10.1186/s12859-015-0800-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/23/2015] [Indexed: 11/29/2022] Open
Abstract
Background Small RNA-sequencing has revealed the diversity and high abundance of small RNAs derived from tRNAs, referred to as tRNA-derived RNAs. However, at present, there is no standardized nomenclature and there are no methods for accurate annotation and quantification of these small RNAs. tRNA-derived RNAs have unique features that limit the utility of conventional alignment tools and quantification methods. Results We describe here the challenges of mapping, naming, and quantifying tRNA-derived RNAs and present a novel method that addresses them, called tDRmapper. We then use tDRmapper to perform a comparative analysis of tRNA-derived RNA profiles across different human cell types and diseases. We found that (1) tRNA-derived RNA profiles can differ dramatically across different cell types and disease states, (2) that positions and types of chemical modifications of tRNA-derived RNAs vary by cell type and disease, and (3) that entirely different tRNA-derived RNA species can be produced from the same parental tRNA depending on the cell type. Conclusion tDRmappernot only provides a standardized nomenclature and quantification scheme, but also includes graphical visualization that facilitates the discovery of novel tRNA and tRNA-derived RNA biology.
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Affiliation(s)
- Sara R Selitsky
- Bioinformatics and Computational Biology Curriculum, University of North Carolina, Chapel Hill, NC, USA. .,Departments of Genetics, University of North Carolina, Chapel Hill, NC, USA. .,Microbiology & Immunology, University of North Carolina, Chapel Hill, NC, USA.
| | - Praveen Sethupathy
- Bioinformatics and Computational Biology Curriculum, University of North Carolina, Chapel Hill, NC, USA. .,Departments of Genetics, University of North Carolina, Chapel Hill, NC, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
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262
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Armengod ME, Meseguer S, Villarroya M, Prado S, Moukadiri I, Ruiz-Partida R, Garzón MJ, Navarro-González C, Martínez-Zamora A. Modification of the wobble uridine in bacterial and mitochondrial tRNAs reading NNA/NNG triplets of 2-codon boxes. RNA Biol 2015; 11:1495-507. [PMID: 25607529 DOI: 10.4161/15476286.2014.992269] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Posttranscriptional modification of the uridine located at the wobble position (U34) of tRNAs is crucial for optimization of translation. Defects in the U34 modification of mitochondrial-tRNAs are associated with a group of rare diseases collectively characterized by the impairment of the oxidative phosphorylation system. Retrograde signaling pathways from mitochondria to nucleus are involved in the pathophysiology of these diseases. These pathways may be triggered by not only the disturbance of the mitochondrial (mt) translation caused by hypomodification of tRNAs, but also as a result of nonconventional roles of mt-tRNAs and mt-tRNA-modifying enzymes. The evolutionary conservation of these enzymes supports their importance for cell and organismal functions. Interestingly, bacterial and eukaryotic cells respond to stress by altering the expression or activity of these tRNA-modifying enzymes, which leads to changes in the modification status of tRNAs. This review summarizes recent findings about these enzymes and sets them within the previous data context.
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Affiliation(s)
- M Eugenia Armengod
- a Laboratory of RNA Modification and Mitochondrial Diseases ; Centro de Investigación Príncipe Felipe ; Valencia , Spain
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263
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Abstract
tRNA modifications are crucial for efficient and accurate protein translation, with defects often linked to disease. There are 7 cytoplasmic tRNA modifications in the yeast Saccharomyces cerevisiae that are formed by an enzyme consisting of a catalytic subunit and an auxiliary protein, 5 of which require only a single subunit in bacteria, and 2 of which are not found in bacteria. These enzymes include the deaminase Tad2-Tad3, and the methyltransferases Trm6-Trm61, Trm8-Trm82, Trm7-Trm732, and Trm7-Trm734, Trm9-Trm112, and Trm11-Trm112. We describe the occurrence and biological role of each modification, evidence for a required partner protein in S. cerevisiae and other eukaryotes, evidence for a single subunit in bacteria, and evidence for the role of the non-catalytic binding partner. Although it is unclear why these eukaryotic enzymes require partner proteins, studies of some 2-subunit modification enzymes suggest that the partner proteins help expand substrate range or allow integration of cellular activities.
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Affiliation(s)
- Michael P Guy
- a Department of Biochemistry and Biophysics; Center for RNA Biology ; University of Rochester School of Medicine ; Rochester , NY USA
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264
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Machnicka MA, Olchowik A, Grosjean H, Bujnicki JM. Distribution and frequencies of post-transcriptional modifications in tRNAs. RNA Biol 2015; 11:1619-29. [PMID: 25611331 DOI: 10.4161/15476286.2014.992273] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.
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265
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Karlsborn T, Tükenmez H, Mahmud AKMF, Xu F, Xu H, Byström AS. Elongator, a conserved complex required for wobble uridine modifications in eukaryotes. RNA Biol 2015; 11:1519-28. [PMID: 25607684 DOI: 10.4161/15476286.2014.992276] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Elongator is a 6 subunit protein complex highly conserved in eukaryotes. The role of this complex has been controversial as the pleiotropic phenotypes of Elongator mutants have implicated the complex in several cellular processes. However, in yeast there is convincing evidence that the primary and probably only role of this complex is in formation of the 5-methoxycarbonylmethyl (mcm(5)) and 5-carbamoylmethyl (ncm(5)) side chains on uridines at wobble position in tRNA. In this review we summarize the cellular processes that have been linked to the Elongator complex and discuss its role in tRNA modification and regulation of translation. We also describe additional gene products essential for formation of ncm(5) and mcm(5) side chains at U34 and their influence on Elongator activity.
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Affiliation(s)
- Tony Karlsborn
- a Department of Molecular Biology ; Umeå University; Umeå , Sweden
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266
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Addepalli B, Lesner NP, Limbach PA. Detection of RNA nucleoside modifications with the uridine-specific ribonuclease MC1 from Momordica charantia. RNA (NEW YORK, N.Y.) 2015; 21:1746-1756. [PMID: 26221047 PMCID: PMC4574751 DOI: 10.1261/rna.052472.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/28/2015] [Indexed: 06/06/2023]
Abstract
A codon-optimized recombinant ribonuclease, MC1 is characterized for its uridine-specific cleavage ability to map nucleoside modifications in RNA. The published MC1 amino acid sequence, as noted in a previous study, was used as a template to construct a synthetic gene with a natural codon bias favoring expression in Escherichia coli. Following optimization of various expression conditions, the active recombinant ribonuclease was successfully purified as a C-terminal His-tag fusion protein from E. coli [Rosetta 2(DE3)] cells. The isolated protein was tested for its ribonuclease activity against oligoribonucleotides and commercially available E. coli tRNA(Tyr I). Analysis of MC1 digestion products by ion-pairing reverse phase liquid-chromatography coupled with mass spectrometry (IP-RP-LC-MS) revealed enzymatic cleavage of RNA at the 5'-termini of uridine and pseudouridine, but cleavage was absent if the uridine was chemically modified or preceded by a nucleoside with a bulky modification. Furthermore, the utility of this enzyme to generate complementary digestion products to other common endonucleases, such as RNase T1, which enables the unambiguous mapping of modified residues in RNA is demonstrated.
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Affiliation(s)
- Balasubrahmanym Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
| | - Nicholas P Lesner
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA Department of Chemistry, The College of Wooster, Wooster, Ohio 44691-2393, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221-0172, USA
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267
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Filonava L, Torres AG, Ribas de Pouplana L. A novel cause for primordial dwarfism revealed: defective tRNA modification. Genome Biol 2015; 16:216. [PMID: 26429597 PMCID: PMC4591068 DOI: 10.1186/s13059-015-0786-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A mutation in the WDR4 gene, coding for a tRNA-modifying enzyme, leads to reduced levels of guanosine methylation in tRNA in patients with primordial dwarfism. See related Research article: http://www.genomebiology.com/2015/16/1/210.
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Affiliation(s)
- Liudmila Filonava
- Institute for Research in Biomedicine (IRB Barcelona), Carrer de Baldiri Reixac 10, Barcelona, 08028, Catalonia, Spain
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), Carrer de Baldiri Reixac 10, Barcelona, 08028, Catalonia, Spain
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), Carrer de Baldiri Reixac 10, Barcelona, 08028, Catalonia, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluis Companys 23, Barcelona, 08010, Catalonia, Spain.
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268
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Shaheen R, Abdel-Salam GMH, Guy MP, Alomar R, Abdel-Hamid MS, Afifi HH, Ismail SI, Emam BA, Phizicky EM, Alkuraya FS. Mutation in WDR4 impairs tRNA m(7)G46 methylation and causes a distinct form of microcephalic primordial dwarfism. Genome Biol 2015; 16:210. [PMID: 26416026 PMCID: PMC4587777 DOI: 10.1186/s13059-015-0779-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/14/2015] [Indexed: 04/13/2023] Open
Abstract
Background Primordial dwarfism is a state of extreme prenatal and postnatal growth deficiency, and is characterized by marked clinical and genetic heterogeneity. Results Two presumably unrelated consanguineous families presented with an apparently novel form of primordial dwarfism in which severe growth deficiency is accompanied by distinct facial dysmorphism, brain malformation (microcephaly, agenesis of corpus callosum, and simplified gyration), and severe encephalopathy with seizures. Combined autozygome/exome analysis revealed a novel missense mutation in WDR4 as the likely causal variant. WDR4 is the human ortholog of the yeast Trm82, an essential component of the Trm8/Trm82 holoenzyme that effects a highly conserved and specific (m7G46) methylation of tRNA. The human mutation and the corresponding yeast mutation result in a significant reduction of m7G46 methylation of specific tRNA species, which provides a potential mechanism for primordial dwarfism associated with this lesion, since reduced m7G46 modification causes a growth deficiency phenotype in yeast. Conclusion Our study expands the number of biological pathways underlying primordial dwarfism and adds to a growing list of human diseases linked to abnormal tRNA modification. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0779-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Michael P Guy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.,Current address: Department of Chemistry, Northern Kentucky University, Highland Heights, KY, USA
| | - Rana Alomar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed S Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Hanan H Afifi
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Samira I Ismail
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Bayoumi A Emam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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269
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Reverendo M, Soares AR, Pereira PM, Carreto L, Ferreira V, Gatti E, Pierre P, Moura GR, Santos MA. TRNA mutations that affect decoding fidelity deregulate development and the proteostasis network in zebrafish. RNA Biol 2015; 11:1199-213. [PMID: 25483040 DOI: 10.4161/rna.32199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Mutations in genes that encode tRNAs, aminoacyl-tRNA syntheases, tRNA modifying enzymes and other tRNA interacting partners are associated with neuropathies, cancer, type-II diabetes and hearing loss, but how these mutations cause disease is unclear. We have hypothesized that levels of tRNA decoding error (mistranslation) that do not fully impair embryonic development can accelerate cell degeneration through proteome instability and saturation of the proteostasis network. To test this hypothesis we have induced mistranslation in zebrafish embryos using mutant tRNAs that misincorporate Serine (Ser) at various non-cognate codon sites. Embryo viability was affected and malformations were observed, but a significant proportion of embryos survived by activating the unfolded protein response (UPR), the ubiquitin proteasome pathway (UPP) and downregulating protein biosynthesis. Accumulation of reactive oxygen species (ROS), mitochondrial and nuclear DNA damage and disruption of the mitochondrial network, were also observed, suggesting that mistranslation had a strong negative impact on protein synthesis rate, ER and mitochondrial homeostasis. We postulate that mistranslation promotes gradual cellular degeneration and disease through protein aggregation, mitochondrial dysfunction and genome instability.
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270
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Lu Z, Filonov GS, Noto JJ, Schmidt CA, Hatkevich TL, Wen Y, Jaffrey SR, Matera AG. Metazoan tRNA introns generate stable circular RNAs in vivo. RNA (NEW YORK, N.Y.) 2015; 21:1554-65. [PMID: 26194134 PMCID: PMC4536317 DOI: 10.1261/rna.052944.115] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 07/06/2015] [Indexed: 05/23/2023]
Abstract
We report the discovery of a class of abundant circular noncoding RNAs that are produced during metazoan tRNA splicing. These transcripts, termed tRNA intronic circular (tric)RNAs, are conserved features of animal transcriptomes. Biogenesis of tricRNAs requires anciently conserved tRNA sequence motifs and processing enzymes, and their expression is regulated in an age-dependent and tissue-specific manner. Furthermore, we exploited this biogenesis pathway to develop an in vivo expression system for generating "designer" circular RNAs in human cells. Reporter constructs expressing RNA aptamers such as Spinach and Broccoli can be used to follow the transcription and subcellular localization of tricRNAs in living cells. Owing to the superior stability of circular vs. linear RNA isoforms, this expression system has a wide range of potential applications, from basic research to pharmaceutical science.
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Affiliation(s)
- Zhipeng Lu
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Grigory S Filonov
- Department of Pharmacology, Weill Cornell Medical College, New York, New York 10065, USA
| | - John J Noto
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Casey A Schmidt
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Talia L Hatkevich
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Ying Wen
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medical College, New York, New York 10065, USA
| | - A Gregory Matera
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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271
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TRM6/61 connects PKCα with translational control through tRNAiMet stabilization: impact on tumorigenesis. Oncogene 2015; 35:1785-96. [DOI: 10.1038/onc.2015.244] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 04/29/2015] [Accepted: 05/16/2015] [Indexed: 12/17/2022]
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272
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Cao X, Limbach PA. Enhanced detection of post-transcriptional modifications using a mass-exclusion list strategy for RNA modification mapping by LC-MS/MS. Anal Chem 2015; 87:8433-40. [PMID: 26176336 PMCID: PMC4542202 DOI: 10.1021/acs.analchem.5b01826] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
There
has been a renewed appreciation for the dynamic nature of
ribonucleic acid (RNA) modifications and for the impact of modified
RNAs on organism health resulting in an increased emphasis on developing
analytical methods capable of detecting modifications within specific
RNA sequence contexts. Here we demonstrate that a DNA-based exclusion
list enhances data dependent liquid chromatography tandem mass spectrometry
(LC-MS/MS) detection of post-transcriptionally modified nucleosides
within specific RNA sequences. This approach is possible because all
post-transcriptional modifications of RNA, except pseudouridine, result
in a mass increase in the canonical nucleoside undergoing chemical
modification. Thus, DNA-based sequences reflect the state of the RNA
prior to or in the absence of modification. The utility of this exclusion
list strategy is demonstrated through the RNA modification mapping
of total tRNAs from the bacteria Escherichia coli, Lactococcus lactis, and Streptomyces griseus. Creation of a DNA-based exclusion list is shown to consistently
enhance the number of detected modified ribonuclease (RNase) digestion
products by ∼20%. All modified RNase digestion products that
were detected during standard data dependent acquisition (DDA) LC-MS/MS
were also detected when the DNA-based exclusion list was used. Consequently,
the increase in detected modified RNase digestion products is attributed
to new experimental information only obtained when using the exclusion
list. This exclusion list strategy should be broadly applicable to
any class of RNA and improves the utility of mass spectrometry approaches
for discovery-based analyses of RNA modifications, such as are required
for studies of the epitranscriptome.
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Affiliation(s)
- Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
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273
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Dégut C, Ponchon L, Folly-Klan M, Barraud P, Tisné C. The m1A(58) modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI. Biophys Chem 2015; 210:27-34. [PMID: 26189113 DOI: 10.1016/j.bpc.2015.06.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/16/2015] [Accepted: 06/27/2015] [Indexed: 01/23/2023]
Abstract
The enzymes of the TrmI family catalyze the formation of the m(1)A58 modification in tRNA. We previously solved the crystal structure of the Thermus thermophilus enzyme and conducted a biophysical study to characterize the interaction between TrmI and tRNA. TrmI enzymes are active as a tetramer and up to two tRNAs can bind to TrmI simultaneously. In this paper, we present the structures of two TrmI mutants (D170A and Y78A). These residues are conserved in the active site of TrmIs and their mutations result in a dramatic alteration of TrmI activity. Both structures of TrmI mutants revealed the flexibility of the N-terminal domain that is probably important to bind tRNA. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine. This structure reinforces the previously proposed role of Y78, i.e. stabilize the conformation of the A58 ribose needed to hold the adenosine in the active site. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site. This structure and recent data confirms the central role of D170 residue binding the amino moiety of SAM and the exocyclic amino group of adenine. Possible mechanisms for methyl transfer are then discussed.
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Affiliation(s)
- Clément Dégut
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Marcia Folly-Klan
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Pierre Barraud
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris.
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274
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Chawla M, Oliva R, Bujnicki JM, Cavallo L. An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. Nucleic Acids Res 2015; 43:6714-29. [PMID: 26117545 PMCID: PMC4538814 DOI: 10.1093/nar/gkv606] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/28/2015] [Indexed: 01/08/2023] Open
Abstract
Posttranscriptional modifications greatly enhance the chemical information of RNA molecules, contributing to explain the diversity of their structures and functions. A significant fraction of RNA experimental structures available to date present modified nucleobases, with half of them being involved in H-bonding interactions with other bases, i.e. ‘modified base pairs’. Herein we present a systematic investigation of modified base pairs, in the context of experimental RNA structures. To this end, we first compiled an atlas of experimentally observed modified base pairs, for which we recorded occurrences and structural context. Then, for each base pair, we selected a representative for subsequent quantum mechanics calculations, to find out its optimal geometry and interaction energy. Our structural analyses show that most of the modified base pairs are non Watson–Crick like and are involved in RNA tertiary structure motifs. In addition, quantum mechanics calculations quantify and provide a rationale for the impact of the different modifications on the geometry and stability of the base pairs they participate in.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia
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275
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Rojas-Benitez D, Thiaville PC, de Crécy-Lagard V, Glavic A. The Levels of a Universally Conserved tRNA Modification Regulate Cell Growth. J Biol Chem 2015; 290:18699-707. [PMID: 26063805 DOI: 10.1074/jbc.m115.665406] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 01/05/2023] Open
Abstract
N(6)-Threonylcarbamoyl-adenosine (t(6)A) is a universal modification occurring at position 37 in nearly all tRNAs that decode A-starting codons, including the eukaryotic initiator tRNA (tRNAi (Met)). Yeast lacking central components of the t(6)A synthesis machinery, such as Tcs3p (Kae1p) or Tcs5p (Bud32p), show slow-growth phenotypes. In the present work, we show that loss of the Drosophila tcs3 homolog also leads to a severe reduction in size and demonstrate, for the first time in a non-microbe, that Tcs3 is required for t(6)A synthesis. In Drosophila and in mammals, tRNAi (Met) is a limiting factor for cell and animal growth. We report that the t(6)A-modified form of tRNAi (Met) is the actual limiting factor. We show that changing the proportion of t(6)A-modified tRNAi (Met), by expression of an un-modifiable tRNAi (Met) or changing the levels of Tcs3, regulate target of rapamycin (TOR) kinase activity and influences cell and animal growth in vivo. These findings reveal an unprecedented relationship between the translation machinery and TOR, where translation efficiency, limited by the availability of t(6)A-modified tRNA, determines growth potential in eukaryotic cells.
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Affiliation(s)
- Diego Rojas-Benitez
- From the Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile 7800024 and
| | - Patrick C Thiaville
- the Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida32611-0700
| | - Valérie de Crécy-Lagard
- the Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida32611-0700
| | - Alvaro Glavic
- From the Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago, Chile 7800024 and
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276
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Nedialkova DD, Leidel SA. Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. Cell 2015; 161:1606-18. [PMID: 26052047 PMCID: PMC4503807 DOI: 10.1016/j.cell.2015.05.022] [Citation(s) in RCA: 367] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/28/2015] [Accepted: 04/10/2015] [Indexed: 01/15/2023]
Abstract
Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress, accumulate aggregates of endogenous proteins, and are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA modifications in maintaining proteome integrity. tRNA anticodon modification loss slows translation at cognate codons in vivo Codon-specific translational pausing triggers protein misfolding in yeast and worms Codon translation rates and protein homeostasis are restored by tRNA overexpression
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Affiliation(s)
- 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, 48149 Muenster, Germany
| | - Sebastian A Leidel
- 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, 48149 Muenster, Germany; Faculty of Medicine, University of Muenster, Albert-Schweitzer-Campus 1, 48149 Muenster, Germany.
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277
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Sakaguchi Y, Miyauchi K, Kang BI, Suzuki T. Nucleoside Analysis by Hydrophilic Interaction Liquid Chromatography Coupled with Mass Spectrometry. Methods Enzymol 2015; 560:19-28. [PMID: 26253964 DOI: 10.1016/bs.mie.2015.03.015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA molecules contain a wide variety of chemical modifications that cannot be deduced from the genomic sequence. RNA modifications confer a chemical diversity to simple RNA molecules, enabling a greater variety of biological functions. To detect RNA modifications, highly sensitive analytical tools are required. Liquid chromatography/mass spectrometry (LC/MS) has been playing a vital role in analyzing minor modified nucleosides in RNA specimens from various sources. Reverse-phase chromatography (RPC) has been used for LC/MS for a long time because RPC is compatible with electrospray ionization (ESI) MS. However, RPC is not always suitable for detecting hydrophilic or polar nucleosides. We here describe a different mode of LC/MS for detecting RNA modifications using hydrophilic interaction liquid chromatography (HILIC). HILIC/ESI-MS is a valuable alternative for profiling modified nucleosides.
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Affiliation(s)
- Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Byeong-il Kang
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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278
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Auger C, Appanna ND, Alhasawi A, Appanna VD. Deciphering metabolic networks by blue native polyacrylamide gel electrophoresis: A functional proteomic exploration. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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279
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Wilusz JE. Controlling translation via modulation of tRNA levels. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:453-70. [PMID: 25919480 DOI: 10.1002/wrna.1287] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 03/13/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are critical adaptor molecules that carry amino acids to a messenger RNA (mRNA) template during protein synthesis. Although tRNAs have commonly been viewed as abundant 'house-keeping' RNAs, it is becoming increasingly clear that tRNA expression is tightly regulated. Depending on a cell's proliferative status, the pool of active tRNAs is rapidly changed, enabling distinct translational programs to be expressed in differentiated versus proliferating cells. Here, I highlight several post-transcriptional regulatory mechanisms that allow the expression or functions of tRNAs to be altered. Modulating the modification status or structural stability of individual tRNAs can cause those specific tRNA transcripts to selectively accumulate or be degraded. Decay generally occurs via the rapid tRNA decay pathway or by the nuclear RNA surveillance machinery. In addition, the CCA-adding enzyme plays a critical role in determining the fate of a tRNA. The post-transcriptional addition of CCA to the 3' ends of stable tRNAs generates the amino acid attachment site, whereas addition of CCACCA to unstable tRNAs prevents aminoacylation and marks the tRNA for degradation. In response to various stresses, tRNAs can accumulate in the nucleus or be further cleaved into small RNAs, some of which inhibit translation. By implementing these various post-transcriptional control mechanisms, cells are able to fine-tune tRNA levels to regulate subsets of mRNAs as well as overall translation rates.
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Affiliation(s)
- Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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280
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Torres AG, Piñeyro D, Rodríguez-Escribà M, Camacho N, Reina O, Saint-Léger A, Filonava L, Batlle E, Ribas de Pouplana L. Inosine modifications in human tRNAs are incorporated at the precursor tRNA level. Nucleic Acids Res 2015; 43:5145-57. [PMID: 25916855 PMCID: PMC4446420 DOI: 10.1093/nar/gkv277] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/20/2015] [Indexed: 11/12/2022] Open
Abstract
Transfer RNAs (tRNAs) are key adaptor molecules of the genetic code that are heavily modified post-transcriptionally. Inosine at the first residue of the anticodon (position 34; I34) is an essential widespread tRNA modification that has been poorly studied thus far. The modification in eukaryotes results from a deamination reaction of adenine that is catalyzed by the heterodimeric enzyme adenosine deaminase acting on tRNA (hetADAT), composed of two subunits: ADAT2 and ADAT3. Using high-throughput small RNA sequencing (RNAseq), we show that this modification is incorporated to human tRNAs at the precursor tRNA level and during maturation. We also functionally validated the human genes encoding for hetADAT and show that the subunits of this enzyme co-localize in nucleus in an ADAT2-dependent manner. Finally, by knocking down HsADAT2, we demonstrate that variations in the cellular levels of hetADAT will result in changes in the levels of I34 modification in all its potential substrates. Altogether, we present RNAseq as a powerful tool to study post-transcriptional tRNA modifications at the precursor tRNA level and give the first insights on the biology of I34 tRNA modification in metazoans.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - David Piñeyro
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Marta Rodríguez-Escribà
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Noelia Camacho
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Adélaïde Saint-Léger
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Liudmila Filonava
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), P/Lluis Companys 23, Barcelona, 08010 Catalonia, Spain
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), C/Baldiri Reixac 10, Barcelona, 08028 Catalonia, Spain Catalan Institution for Research and Advanced Studies (ICREA), P/Lluis Companys 23, Barcelona, 08010 Catalonia, Spain
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281
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Abbreviated Pathway for Biosynthesis of 2-Thiouridine in Bacillus subtilis. J Bacteriol 2015; 197:1952-62. [PMID: 25825430 DOI: 10.1128/jb.02625-14] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/23/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED The 2-thiouridine (s(2)U) modification of the wobble position in glutamate, glutamine, and lysine tRNA molecules serves to stabilize the anticodon structure, improving ribosomal binding and overall efficiency of the translational process. Biosynthesis of s(2)U in Escherichia coli requires a cysteine desulfurase (IscS), a thiouridylase (MnmA), and five intermediate sulfur-relay enzymes (TusABCDE). The E. coli MnmA adenylates and subsequently thiolates tRNA to form the s(2)U modification. Bacillus subtilis lacks IscS and the intermediate sulfur relay proteins, yet its genome contains a cysteine desulfurase gene, yrvO, directly adjacent to mnmA. The genomic synteny of yrvO and mnmA combined with the absence of the Tus proteins indicated a potential functionality of these proteins in s(2)U formation. Here, we provide evidence that the B. subtilis YrvO and MnmA are sufficient for s(2)U biosynthesis. A conditional B. subtilis knockout strain showed that s(2)U abundance correlates with MnmA expression, and in vivo complementation studies in E. coli IscS- or MnmA-deficient strains revealed the competency of these proteins in s(2)U biosynthesis. In vitro experiments demonstrated s(2)U formation by YrvO and MnmA, and kinetic analysis established a partnership between the B. subtilis proteins that is contingent upon the presence of ATP. Furthermore, we observed that the slow-growth phenotype of E. coli ΔiscS and ΔmnmA strains associated with s(2)U depletion is recovered by B. subtilis yrvO and mnmA. These results support the proposal that the involvement of a devoted cysteine desulfurase, YrvO, in s(2)U synthesis bypasses the need for a complex biosynthetic pathway by direct sulfur transfer to MnmA. IMPORTANCE The 2-thiouridine (s(2)U) modification of the wobble position in glutamate, glutamine, and lysine tRNA is conserved in all three domains of life and stabilizes the anticodon structure, thus guaranteeing fidelity in translation. The biosynthesis of s(2)U in Escherichia coli requires seven proteins: the cysteine desulfurase IscS, the thiouridylase MnmA, and five intermediate sulfur-relay enzymes (TusABCDE). Bacillus subtilis and most Gram-positive bacteria lack a complete set of biosynthetic components. Interestingly, the mnmA coding sequence is located adjacent to yrvO, encoding a cysteine desulfurase. In this work, we provide evidence that the B. subtilis YrvO is able to transfer sulfur directly to MnmA. Both proteins are sufficient for s(2)U biosynthesis in a pathway independent of the one used in E. coli.
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282
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Jüdes A, Ebert F, Bär C, Thüring KL, Harrer A, Klassen R, Helm M, Stark MJ, Schaffrath R. Urmylation and tRNA thiolation functions of ubiquitin-like Uba4·Urm1 systems are conserved from yeast to man. FEBS Lett 2015; 589:904-9. [DOI: 10.1016/j.febslet.2015.02.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/11/2015] [Accepted: 02/24/2015] [Indexed: 02/07/2023]
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283
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Wei FY, Zhou B, Suzuki T, Miyata K, Ujihara Y, Horiguchi H, Takahashi N, Xie P, Michiue H, Fujimura A, Kaitsuka T, Matsui H, Koga Y, Mohri S, Suzuki T, Oike Y, Tomizawa K. Cdk5rap1-mediated 2-methylthio modification of mitochondrial tRNAs governs protein translation and contributes to myopathy in mice and humans. Cell Metab 2015; 21:428-42. [PMID: 25738458 DOI: 10.1016/j.cmet.2015.01.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/24/2014] [Accepted: 01/26/2015] [Indexed: 12/20/2022]
Abstract
Transfer RNAs (tRNAs) contain a wide variety of posttranscriptional modifications that are important for accurate decoding. Mammalian mitochondrial tRNAs (mt-tRNAs) are modified by nuclear-encoded tRNA-modifying enzymes; however, the physiological roles of these modifications remain largely unknown. In this study, we report that Cdk5 regulatory subunit-associated protein 1 (Cdk5rap1) is responsible for 2-methylthio (ms(2)) modifications of mammalian mt-tRNAs for Ser(UCN), Phe, Tyr, and Trp codons. Deficiency in ms(2) modification markedly impaired mitochondrial protein synthesis, which resulted in respiratory defects in Cdk5rap1 knockout (KO) mice. The KO mice were highly susceptive to stress-induced mitochondrial remodeling and exhibited accelerated myopathy and cardiac dysfunction under stressed conditions. Furthermore, we demonstrate that the ms(2) modifications of mt-tRNAs were sensitive to oxidative stress and were reduced in patients with mitochondrial disease. These findings highlight the fundamental role of ms(2) modifications of mt-tRNAs in mitochondrial protein synthesis and their pathological consequences in mitochondrial disease.
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Affiliation(s)
- Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Bo Zhou
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Keishi Miyata
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yoshihiro Ujihara
- First Department of Physiology, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Haruki Horiguchi
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Nozomu Takahashi
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Peiyu Xie
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hiroyuki Michiue
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Atsushi Fujimura
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Hideki Matsui
- Department of Physiology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yasutoshi Koga
- Department of Pediatrics and Child Health, Kurume University Graduate School of Medicine, Fukuoka 830-0011, Japan
| | - Satoshi Mohri
- First Department of Physiology, Kawasaki Medical School, Okayama 701-0192, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
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284
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Salinas-Giegé T, Giegé R, Giegé P. tRNA biology in mitochondria. Int J Mol Sci 2015; 16:4518-59. [PMID: 25734984 PMCID: PMC4394434 DOI: 10.3390/ijms16034518] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/23/2015] [Accepted: 01/29/2015] [Indexed: 01/23/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.
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Affiliation(s)
- Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
| | - Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
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285
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Abstract
tRNAs are widely believed to segregate into two classes, I and II. Computational analysis of eukaryotic tRNA entries in Genomic tRNA Database, however, leads to new, albeit paradoxical, presence of more than a thousand class-I tRNAs with uncharacteristic long variable arms (V-arms), like in class-II. Out of 62,202 tRNAs from 69 eukaryotes, as many as 1431 class-I tRNAs have these novel extended V-arms, and we refer to them as paradoxical tRNAs (pxtRNAs). A great majority of these 1431 pxtRNA genes are located in intergenic regions, about 18% embedded in introns of genes or ESTs, and just one in 3'UTR. A check on the conservations of 2D and 3D base pairs for each position of these pxtRNAs reveals a few variations, but they seem to have almost all the known features (already known identity and conserved elements of tRNA). Analyses of the A-Box and B-Box of these pxtRNA genes in eukaryotes display salient deviations from the previously annotated conserved features of the standard promoters, whereas the transcription termination signals are just canonical and non-canonical runs of thymidine, similar to the ones in standard tRNA genes. There is just one such pxtRNA(ProAGG) gene in the entire human genome, and the availability of data allows epigenetic analysis of this human pxtRNA(ProAGG) in three different cell lines, H1 hESC, K562, and NHEK, to assess the level of its expression. Histone acetylation and methylation of this lone pxtRNA(ProAGG) gene in human differ from that of the nine standard human tRNA(ProAGG) genes. The V-arm nucleotide sequences and their secondary structures in pxtRNA differ from that of class-II tRNA. Considering these differences, hypotheses of alternative splicing, non-canonical intron and gene transfer are examined to partially improve the Cove scores of these pxtRNAs and to critically question their antecedence and novelty.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Arpa Samadder
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India
| | - Pijush Das
- b Cancer Biology & Inflammatory Disorder Division , Indian Institute of Chemical Biology , Kolkata , India
| | - Smarajit Das
- c Department of Medical Biochemistry and Cell Biology , Institute of Biomedicine, University of Gothenburg , Gothenburg , Sweden
| | - Jayprokas Chakrabarti
- a Computational Biology Group , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700032 , India.,d Gyanxet, BF 286 Salt Lake, Kolkata , India
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286
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Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. Proc Natl Acad Sci U S A 2015; 112:2764-9. [PMID: 25675486 DOI: 10.1073/pnas.1415525112] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Familial dysautonomia (FD), a hereditary sensory and autonomic neuropathy, is caused by missplicing of exon 20, resulting from an intronic mutation in the inhibitor of kappa light polypeptide gene enhancer in B cells, kinase complex-associated protein (IKBKAP) gene encoding IKK complex-associated protein (IKAP)/elongator protein 1 (ELP1). A newly established splicing reporter assay allowed us to visualize pathogenic splicing in cells and to screen small chemicals for the ability to correct the aberrant splicing of IKBKAP. Using this splicing reporter, we screened our chemical libraries and identified a compound, rectifier of aberrant splicing (RECTAS), that rectifies the aberrant IKBKAP splicing in cells from patients with FD. Here, we found that the levels of modified uridine at the wobble position in cytoplasmic tRNAs are reduced in cells from patients with FD and that treatment with RECTAS increases the expression of IKAP and recovers the tRNA modifications. These findings suggest that the missplicing of IKBKAP results in reduced tRNA modifications in patients with FD and that RECTAS is a promising therapeutic drug candidate for FD.
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287
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Abdel-Fattah W, Jablonowski D, Di Santo R, Thüring KL, Scheidt V, Hammermeister A, ten Have S, Helm M, Schaffrath R, Stark MJR. Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast. PLoS Genet 2015; 11:e1004931. [PMID: 25569479 PMCID: PMC4287497 DOI: 10.1371/journal.pgen.1004931] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/01/2014] [Indexed: 12/26/2022] Open
Abstract
Elongator is a conserved protein complex comprising six different polypeptides that has been ascribed a wide range of functions, but which is now known to be required for modification of uridine residues in the wobble position of a subset of tRNAs in yeast, plants, worms and mammals. In previous work, we showed that Elongator's largest subunit (Elp1; also known as Iki3) was phosphorylated and implicated the yeast casein kinase I Hrr25 in Elongator function. Here we report identification of nine in vivo phosphorylation sites within Elp1 and show that four of these, clustered close to the Elp1 C-terminus and adjacent to a region that binds tRNA, are important for Elongator's tRNA modification function. Hrr25 protein kinase directly modifies Elp1 on two sites (Ser-1198 and Ser-1202) and through analyzing non-phosphorylatable (alanine) and acidic, phosphomimic substitutions at Ser-1198, Ser-1202 and Ser-1209, we provide evidence that phosphorylation plays a positive role in the tRNA modification function of Elongator and may regulate the interaction of Elongator both with its accessory protein Kti12 and with Hrr25 kinase. tRNA molecules function as adapters in protein synthesis, bringing amino acids to the ribosome and reading the genetic code through codon-anticodon base pairing. When the tRNA contains a uridine residue in the “wobble position” of its anticodon, which base-pairs with purine residues in the third position of a cognate codon, it is almost always chemically modified and modification is required for efficient decoding. In eukaryotic cells, these wobble uridine modifications require a conserved protein complex called Elongator. Our work shows that Elp1, Elongator's largest subunit, is phosphorylated on several sites. By blocking phosphorylation at these positions using mutations, we identified four phosphorylation sites that are important for Elongator's role in tRNA modification. We have also shown that Hrr25 protein kinase, a member of the casein kinase I (CKI) family, is responsible for modification of two of the sites that are important for Elongator function. Phosphorylation appears to affect interaction of the Elongator complex both with its kinase (Hrr25) and with Kti12, an accessory protein previously implicated in Elongator function. Our studies imply that Elp1 phosphorylation plays a positive role in Elongator-mediated tRNA modification and raise the possibility that wobble uridine modification may be regulated, representing a potential translational control mechanism.
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Affiliation(s)
- Wael Abdel-Fattah
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Rachael Di Santo
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Kathrin L. Thüring
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Viktor Scheidt
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
| | | | - Sara ten Have
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark Helm
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Germany
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- * E-mail: (RS); (MJRS)
| | - Michael J. R. Stark
- Centre for Gene Regulation & Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail: (RS); (MJRS)
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288
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Kirchner S, Ignatova Z. Emerging roles of tRNA in adaptive translation, signalling dynamics and disease. Nat Rev Genet 2014; 16:98-112. [DOI: 10.1038/nrg3861] [Citation(s) in RCA: 355] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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289
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Iron-sulfur proteins responsible for RNA modifications. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:1272-83. [PMID: 25533083 DOI: 10.1016/j.bbamcr.2014.12.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/08/2014] [Accepted: 12/09/2014] [Indexed: 12/22/2022]
Abstract
RNA molecules are decorated with various chemical modifications, which are introduced post-transcriptionally by RNA-modifying enzymes. These modifications are required for proper RNA function. Among more than 100 known species of RNA modifications, several modified bases in tRNAs and rRNAs are introduced by RNA-modifying enzymes containing iron-sulfur (Fe/S) clusters. Most Fe/S-containing RNA-modifying enzymes contain radical SAM domains that catalyze a variety of chemical reactions, including methylation, methylthiolation, carboxymethylation, tricyclic purine formation, and deazaguanine formation. Lack of these modifications can cause pathological consequences. Here, we review recent studies on the biogenesis and function of RNA modifications mediated by Fe/S proteins. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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290
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Anderson P, Ivanov P. tRNA fragments in human health and disease. FEBS Lett 2014; 588:4297-304. [PMID: 25220675 PMCID: PMC4339185 DOI: 10.1016/j.febslet.2014.09.001] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 01/07/2023]
Abstract
Transfer RNA (tRNA) is traditionally considered to be an adaptor molecule that helps ribosomes to decode messenger RNA (mRNA) and synthesize protein. Recent studies have demonstrated that tRNAs also serve as a major source of small non-coding RNAs that possess distinct and varied functions. These tRNA fragments are heterogeneous in size, nucleotide composition, biogenesis and function. Here we describe multiple roles that tRNA fragments play in cell physiology and discuss their relevance to human health and disease.
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Affiliation(s)
- Paul Anderson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Pavel Ivanov
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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291
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Torres AG, Piñeyro D, Filonava L, Stracker TH, Batlle E, Ribas de Pouplana L. A-to-I editing on tRNAs: biochemical, biological and evolutionary implications. FEBS Lett 2014; 588:4279-86. [PMID: 25263703 DOI: 10.1016/j.febslet.2014.09.025] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/16/2014] [Accepted: 09/16/2014] [Indexed: 12/13/2022]
Abstract
Inosine on transfer RNAs (tRNAs) are post-transcriptionally formed by a deamination mechanism of adenosines at positions 34, 37 and 57 of certain tRNAs. Despite its ubiquitous nature, the biological role of inosine in tRNAs remains poorly understood. Recent developments in the study of nucleotide modifications are beginning to indicate that the dynamics of such modifications are used in the control of specific genetic programs. Likewise, the essentiality of inosine-modified tRNAs in genome evolution and animal biology is becoming apparent. Here we review our current understanding on the role of inosine in tRNAs, the enzymes that catalyze the modification and the evolutionary link between such enzymes and other deaminases.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - David Piñeyro
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - Liudmila Filonava
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - Travis H Stracker
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), P/ Lluís Companys 23, Barcelona 08010, Catalonia, Spain
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB Barcelona), C/ Baldiri Reixac 10, Barcelona 08028, Catalonia, Spain; Catalan Institution for Research and Advanced Studies (ICREA), P/ Lluís Companys 23, Barcelona 08010, Catalonia, Spain.
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292
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Casas E, Vavouri T. Sperm epigenomics: challenges and opportunities. Front Genet 2014; 5:330. [PMID: 25278962 PMCID: PMC4166955 DOI: 10.3389/fgene.2014.00330] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/03/2014] [Indexed: 11/16/2022] Open
Abstract
Sperm is a highly differentiated cell type whose function is to deliver a haploid genome to the oocyte. The sperm “epigenomes” were traditionally considered to be insignificant – the sperm is transcriptionally inactive, its genome is packaged in sperm-specific protamine toroids instead of nucleosomes, and its DNA methylation profile is erased immediately post-fertilization. Yet, in recent years there has been an increase in the number of reported cases of apparent epigenetic inheritance through the male germline, suggesting that the sperm epigenome may transmit information between generations. At the same time, technical advances have made the genome-wide profiling of different layers of the sperm epigenome feasible. As a result, a large number of datasets have been recently generated and analyzed with the aim to better understand what non-genetic material is contained within the sperm and whether it has any function post-fertilization. Here, we provide an overview of the current knowledge of the sperm epigenomes as well as the challenges in analysing them and the opportunities in understanding the potential non-genetic carriers of information in sperm.
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Affiliation(s)
- Eduard Casas
- Institute of Predictive and Personalized Medicine of Cancer Barcelona, Spain
| | - Tanya Vavouri
- Institute of Predictive and Personalized Medicine of Cancer Barcelona, Spain
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293
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Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, Kellner S, Hölter SM, Garrett L, Wurst W, Becker L, Klopstock T, Fuchs H, Gailus-Durner V, Hrabĕ de Angelis M, Káradóttir RT, Helm M, Ule J, Gleeson JG, Odom DT, Frye M. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J 2014; 33:2020-39. [PMID: 25063673 PMCID: PMC4195770 DOI: 10.15252/embj.201489282] [Citation(s) in RCA: 404] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 06/23/2014] [Indexed: 12/16/2022] Open
Abstract
Mutations in the cytosine-5 RNA methyltransferase NSun2 cause microcephaly and other neurological abnormalities in mice and human. How post-transcriptional methylation contributes to the human disease is currently unknown. By comparing gene expression data with global cytosine-5 RNA methylomes in patient fibroblasts and NSun2-deficient mice, we find that loss of cytosine-5 RNA methylation increases the angiogenin-mediated endonucleolytic cleavage of transfer RNAs (tRNA) leading to an accumulation of 5' tRNA-derived small RNA fragments. Accumulation of 5' tRNA fragments in the absence of NSun2 reduces protein translation rates and activates stress pathways leading to reduced cell size and increased apoptosis of cortical, hippocampal and striatal neurons. Mechanistically, we demonstrate that angiogenin binds with higher affinity to tRNAs lacking site-specific NSun2-mediated methylation and that the presence of 5' tRNA fragments is sufficient and required to trigger cellular stress responses. Furthermore, the enhanced sensitivity of NSun2-deficient brains to oxidative stress can be rescued through inhibition of angiogenin during embryogenesis. In conclusion, failure in NSun2-mediated tRNA methylation contributes to human diseases via stress-induced RNA cleavage.
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Affiliation(s)
- Sandra Blanco
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Joana V Flores
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Shobbir Hussain
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Claudia Kutter
- Li Ka Shing Centre, CR-UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Peter Humphreys
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Margus Lukk
- Li Ka Shing Centre, CR-UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Patrick Lombard
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | | | - Martyna Popis
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Stefanie Kellner
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Mainz, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Lillian Garrett
- German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany German Center for Vertigo and Balance Disorders, Munich, Germany
| | - Lore Becker
- German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany Institute for Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Klopstock
- German Center for Vertigo and Balance Disorders, Munich, Germany Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany Institute for Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany Institute for Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Hrabĕ de Angelis
- German Mouse Clinic, Helmholtz Zentrum München, Neuherberg, Germany Institute for Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ragnhildur T Káradóttir
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Mark Helm
- Johannes Gutenberg University Mainz, Institute for Pharmacy and Biochemistry, Mainz, Germany
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Joseph G Gleeson
- Laboratory of Pediatric Brain Diseases, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Duncan T Odom
- Li Ka Shing Centre, CR-UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Michaela Frye
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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294
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Abbott JA, Francklyn CS, Robey-Bond SM. Transfer RNA and human disease. Front Genet 2014; 5:158. [PMID: 24917879 PMCID: PMC4042891 DOI: 10.3389/fgene.2014.00158] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/14/2014] [Indexed: 12/25/2022] Open
Abstract
Pathological mutations in tRNA genes and tRNA processing enzymes are numerous and result in very complicated clinical phenotypes. Mitochondrial tRNA (mt-tRNA) genes are “hotspots” for pathological mutations and over 200 mt-tRNA mutations have been linked to various disease states. Often these mutations prevent tRNA aminoacylation. Disrupting this primary function affects protein synthesis and the expression, folding, and function of oxidative phosphorylation enzymes. Mitochondrial tRNA mutations manifest in a wide panoply of diseases related to cellular energetics, including COX deficiency (cytochrome C oxidase), mitochondrial myopathy, MERRF (Myoclonic Epilepsy with Ragged Red Fibers), and MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). Diseases caused by mt-tRNA mutations can also affect very specific tissue types, as in the case of neurosensory non-syndromic hearing loss and pigmentary retinopathy, diabetes mellitus, and hypertrophic cardiomyopathy. Importantly, mitochondrial heteroplasmy plays a role in disease severity and age of onset as well. Not surprisingly, mutations in enzymes that modify cytoplasmic and mitochondrial tRNAs are also linked to a diverse range of clinical phenotypes. In addition to compromised aminoacylation of the tRNAs, mutated modifying enzymes can also impact tRNA expression and abundance, tRNA modifications, tRNA folding, and even tRNA maturation (e.g., splicing). Some of these pathological mutations in tRNAs and processing enzymes are likely to affect non-canonical tRNA functions, and contribute to the diseases without significantly impacting on translation. This chapter will review recent literature on the relation of mitochondrial and cytoplasmic tRNA, and enzymes that process tRNAs, to human disease. We explore the mechanisms involved in the clinical presentation of these various diseases with an emphasis on neurological disease.
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Affiliation(s)
- Jamie A Abbott
- Department of Biochemistry, College of Medicine, University of Vermont Burlington, VT, USA
| | | | - Susan M Robey-Bond
- Department of Biochemistry, College of Medicine, University of Vermont Burlington, VT, USA
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295
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Suzuki T, Suzuki T. A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs. Nucleic Acids Res 2014; 42:7346-57. [PMID: 24831542 PMCID: PMC4066797 DOI: 10.1093/nar/gku390] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In mammalian mitochondria, 22 species of tRNAs encoded in mitochondrial DNA play crucial roles in the translation of 13 essential subunits of the respiratory chain complexes involved in oxidative phosphorylation. Following transcription, mitochondrial tRNAs are modified by nuclear-encoded tRNA-modifying enzymes. These modifications are required for the proper functioning of mitochondrial tRNAs (mt tRNAs), and the absence of these modifications can cause pathological consequences. To date, however, the information available about these modifications has been incomplete. To address this issue, we isolated all 22 species of mt tRNAs from bovine liver and comprehensively determined the post-transcriptional modifications in each tRNA by mass spectrometry. Here, we describe the primary structures with post-transcriptional modifications of seven species of mt tRNAs which were previously uncharacterized, and provide revised information regarding base modifications in five other mt tRNAs. In the complete set of bovine mt tRNAs, we found 15 species of modified nucleosides at 118 positions (7.48% of total bases). This result provides insight into the molecular mechanisms underlying the decoding system in mammalian mitochondria and enables prediction of candidate tRNA-modifying enzymes responsible for each modification of mt tRNAs.
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Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
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