1
|
Kelley M, Holmes CJ, Herbert C, Rayhan A, Joves J, Uhran M, Klaus L, Frigard R, Singh K, Limbach PA, Addepalli B, Benoit JB. Tyrosine transfer RNA levels and modifications during blood-feeding and vitellogenesis in the mosquito, Aedes aegypti. INSECT MOLECULAR BIOLOGY 2024. [PMID: 39105593 DOI: 10.1111/imb.12950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/23/2024] [Indexed: 08/07/2024]
Abstract
Mosquitoes such as Aedes aegypti must consume a blood meal for the nutrients necessary for egg production. Several transcriptome and proteome changes occur post-blood meal that likely corresponds with codon usage alterations. Transfer RNA (tRNA) is the adapter molecule that reads messenger RNA codons to add the appropriate amino acid during protein synthesis. Chemical modifications to tRNA enhance codon decoding, improving the accuracy and efficiency of protein synthesis. Here, we examined tRNA modifications and transcripts associated with the blood meal and subsequent periods of vitellogenesis in A. aegypti. More specifically, we assessed tRNA transcript abundance and modification levels in the fat body at critical times post blood-feeding. Based on a combination of alternative codon usage and identification of particular modifications, we discovered that increased transcription of tyrosine tRNAs is likely critical during the synthesis of egg yolk proteins in the fat body following a blood meal. Altogether, changes in both the abundance and modification of tRNA are essential factors in the process of vitellogenin production after blood-feeding in mosquitoes.
Collapse
Affiliation(s)
- Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Cassandra Herbert
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Asif Rayhan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Judd Joves
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Melissa Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Lucas Klaus
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Ronja Frigard
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Khwahish Singh
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA
| | | | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, USA
| |
Collapse
|
2
|
van Breugel ME, Gerber A, van Leeuwen F. The choreography of chromatin in RNA polymerase III regulation. Biochem Soc Trans 2024; 52:1173-1189. [PMID: 38666598 PMCID: PMC11346459 DOI: 10.1042/bst20230770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.
Collapse
Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam 1081HV, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
| |
Collapse
|
3
|
Stewart RK, Nguyen P, Laederach A, Volkan PC, Sawyer JK, Fox DT. Orb2 enables rare-codon-enriched mRNA expression during Drosophila neuron differentiation. Nat Commun 2024; 15:5270. [PMID: 38902233 PMCID: PMC11190236 DOI: 10.1038/s41467-024-48344-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/25/2024] [Indexed: 06/22/2024] Open
Abstract
Regulation of codon optimality is an increasingly appreciated layer of cell- and tissue-specific protein expression control. Here, we use codon-modified reporters to show that differentiation of Drosophila neural stem cells into neurons enables protein expression from rare-codon-enriched genes. From a candidate screen, we identify the cytoplasmic polyadenylation element binding (CPEB) protein Orb2 as a positive regulator of rare-codon-dependent mRNA stability in neurons. Using RNA sequencing, we reveal that Orb2-upregulated mRNAs in the brain with abundant Orb2 binding sites have a rare-codon bias. From these Orb2-regulated mRNAs, we demonstrate that rare-codon enrichment is important for mRNA stability and social behavior function of the metabotropic glutamate receptor (mGluR). Our findings reveal a molecular mechanism by which neural stem cell differentiation shifts genetic code regulation to enable critical mRNA stability and protein expression.
Collapse
Affiliation(s)
- Rebeccah K Stewart
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Patrick Nguyen
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Jessica K Sawyer
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA
- Duke Regeneration Center, Duke University, Durham, NC, USA
| | - Donald T Fox
- Department of Pharmacology & Cancer Biology, Duke University, Durham, NC, USA.
- Duke Regeneration Center, Duke University, Durham, NC, USA.
| |
Collapse
|
4
|
Aubé F, Fontrodona N, Guiguettaz L, Vallin E, Fabbri L, Lapendry A, Vagner S, Ricci EP, Auboeuf D. Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair. NAR Cancer 2024; 6:zcae019. [PMID: 38690580 PMCID: PMC11059277 DOI: 10.1093/narcan/zcae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024] Open
Abstract
Amino acid bioavailability impacts mRNA translation in a codon-dependent manner. Here, we report that the anti-cancer MAPK inhibitors (MAPKi) decrease the intracellular concentration of aspartate and glutamate in melanoma cells. This coincides with the accumulation of ribosomes on codons corresponding to these amino acids and triggers the translation-dependent degradation of mRNAs encoding aspartate- and glutamate-rich proteins, involved in DNA metabolism such as DNA replication and repair. Consequently, cells that survive MAPKi degrade aspartate and glutamate likely to generate energy, which simultaneously decreases their requirement for amino acids due to the downregulation of aspartate- and glutamate-rich proteins involved in cell proliferation. Concomitantly, the downregulation of aspartate- and glutamate-rich proteins involved in DNA repair increases DNA damage loads. Thus, DNA repair defects, and therefore mutations, are at least in part a secondary effect of the metabolic adaptation of cells exposed to MAPKi.
Collapse
Affiliation(s)
- Fabien Aubé
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Nicolas Fontrodona
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Laura Guiguettaz
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Elodie Vallin
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Lucilla Fabbri
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France
- Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
- Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Audrey Lapendry
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Stephan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France
- Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
- Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| |
Collapse
|
5
|
Huang L, Bai D, Su X. Altered expression of transfer RNAs and their possible roles in brain white matter injury. Neuroreport 2024; 35:536-541. [PMID: 38597261 DOI: 10.1097/wnr.0000000000002036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Transfer RNAs (tRNAs) can regulate cell behavior and are associated with neurological disorders. Here, we aimed to investigate the expression levels of tRNAs in oligodendrocyte precursor cells (OPCs) and their possible roles in the regulation of brain white matter injury (WMI). Newborn Sprague-Dawley rats (postnatal day 5) were used to establish a model that mimicked neonatal brain WMI. RNA-array analysis was performed to examine the expression of tRNAs in OPCs. psRNAtarget software was used to predict target mRNAs of significantly altered tRNAs. Gene ontology (GO) and KEGG were used to analyze the pathways for target mRNAs. Eighty-nine tRNAs were changed after WMI (fold change absolute ≥1.5, P < 0.01), with 31 downregulated and 58 upregulated. Among them, three significantly changed tRNAs were identified, with two being significantly increased (chr10.trna1314-ProTGG and chr2.trna2771-ProAGG) and one significantly decreased (chr10.trna11264-GlyTCC). Further, target mRNA prediction and GO/KEGG pathway analysis indicated that the target mRNAs of these tRNAs are mainly involved in G-protein coupled receptor signaling pathways and beta-alanine metabolism, which are both related to myelin formation. In summary, the expression of tRNAs in OPCs was significantly altered after brain WMI, suggesting that tRNAs may play important roles in regulating WMI. This improves the knowledge about WMI pathophysiology and may provide novel treatment targets for WMI.
Collapse
Affiliation(s)
- Lingyi Huang
- Department of Orthodontics, West China College of Stomatology/State Key Laboratory of Oral Diseases, Sichuan University
| | - Ding Bai
- Department of Orthodontics, West China College of Stomatology/State Key Laboratory of Oral Diseases, Sichuan University
| | - Xiaojuan Su
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
6
|
Kolodkin-Gal I, Dash O, Rak R. Probiotic cultivated meat: bacterial-based scaffolds and products to improve cultivated meat. Trends Biotechnol 2024; 42:269-281. [PMID: 37805297 DOI: 10.1016/j.tibtech.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/09/2023]
Abstract
Cultivated meat is emerging to replace traditional livestock industries, which have ecological costs, including land and water overuse and considerable carbon emissions. During cultivated meat production, mammalian cells can increase their numbers dramatically through self-renewal/proliferation and transform into mature cells, such as muscle or fat cells, through maturation/differentiation. Here, we address opportunities for introducing probiotic bacteria into the cultivated meat industry, including using them to produce renewable antimicrobials and scaffolding materials. We also offer solutions to challenges, including the growth of bacteria and mammalian cells, the effect of probiotic bacteria on production costs, and the effect of bacteria and their products on texture and taste. Our summary provides a promising framework for applying microbial composites in the cultivated meat industry.
Collapse
Affiliation(s)
- Ilana Kolodkin-Gal
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
| | - Orit Dash
- Department of Animal Sciences, Faculty of Agriculture and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel; Institute of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Roni Rak
- Institute of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel.
| |
Collapse
|
7
|
Padhiar NH, Katneni U, Komar AA, Motorin Y, Kimchi-Sarfaty C. Advances in methods for tRNA sequencing and quantification. Trends Genet 2024; 40:276-290. [PMID: 38123442 DOI: 10.1016/j.tig.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023]
Abstract
In the past decade tRNA sequencing (tRNA-seq) has attracted considerable attention as an important tool for the development of novel approaches to quantify highly modified tRNA species and to propel tRNA research aimed at understanding the cellular physiology and disease and development of tRNA-based therapeutics. Many methods are available to quantify tRNA abundance while accounting for modifications and tRNA charging/acylation. Advances in both library preparation methods and bioinformatic workflows have enabled developments in next-generation sequencing (NGS) workflows. Other approaches forgo NGS applications in favor of hybridization-based approaches. In this review we provide a brief comparative overview of various tRNA quantification approaches, focusing on the advantages and disadvantages of these methods, which together facilitate reliable tRNA quantification.
Collapse
Affiliation(s)
- Nigam H Padhiar
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Anton A Komar
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - Yuri Motorin
- CNRS-Université de Lorraine, UAR 2008, IBSLor UMR 7365 IMoPA, Nancy, France.
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
| |
Collapse
|
8
|
van Breugel ME, van Kruijsbergen I, Mittal C, Lieftink C, Brouwer I, van den Brand T, Kluin RJC, Hoekman L, Menezes RX, van Welsem T, Del Cortona A, Malik M, Beijersbergen RL, Lenstra TL, Verstrepen KJ, Pugh BF, van Leeuwen F. Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly. Mol Cell 2023; 83:4205-4221.e9. [PMID: 37995691 PMCID: PMC11289708 DOI: 10.1016/j.molcel.2023.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/27/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Transcription of tRNA genes by RNA polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the local chromatin proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII-regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced, and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and tuning the physiological response to changing metabolic demands.
Collapse
Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Chitvan Mittal
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ineke Brouwer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Teun van den Brand
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Renée X Menezes
- Biostatistics Centre and Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Andrea Del Cortona
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
| |
Collapse
|
9
|
Kelley M, Holmes CJ, Herbert C, Rayhan A, Joves J, Uhran M, Frigard R, Singh K, Limbach PA, Addepalli B, Benoit JB. Tyrosine transfer RNA levels and modifications during blood-feeding and vitellogenesis in the mosquito, Aedes aegypti. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569187. [PMID: 38076852 PMCID: PMC10705485 DOI: 10.1101/2023.11.29.569187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Mosquitoes such as Aedes aegypti must consume a blood meal for the nutrients necessary for egg production. Several transcriptome and proteome changes occur post blood meal that likely corresponds with codon usage alterations. Transfer RNA (tRNA) is the adapter molecule that reads messenger RNA (mRNA) codons to add the appropriate amino acid during protein synthesis. Chemical modifications to tRNA enhance codons' decoding, improving the accuracy and efficiency of protein synthesis. Here, we examined tRNA modifications and transcripts associated with the blood meal and subsequent periods of vitellogenesis in A. aegypti. More specifically, we assessed tRNA transcript abundance and modification levels in the fat body at critical times post blood-feeding. Based on a combination of alternative codon usage and identification of particular modifications, we identified that increased transcription of tyrosine tRNAs is likely critical during the synthesis of egg yolk proteins in the fat body following a blood meal. Altogether, changes in both the abundance and modification of tRNA are essential factors in the process of vitellogenin production after blood-feeding in mosquitoes.
Collapse
Affiliation(s)
- Melissa Kelley
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | | | - Cassandra Herbert
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45211
| | - Asif Rayhan
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45211
| | - Judd Joves
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Melissa Uhran
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Ronja Frigard
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | - Khwahish Singh
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| | | | | | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45211
| |
Collapse
|
10
|
Anastassiadis T, Köhrer C. Ushering in the era of tRNA medicines. J Biol Chem 2023; 299:105246. [PMID: 37703991 PMCID: PMC10583094 DOI: 10.1016/j.jbc.2023.105246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
Long viewed as an intermediary in protein translation, there is a growing awareness that tRNAs are capable of myriad other biological functions linked to human health and disease. These emerging roles could be tapped to leverage tRNAs as diagnostic biomarkers, therapeutic targets, or even as novel medicines. Furthermore, the growing array of tRNA-derived fragments, which modulate an increasingly broad spectrum of cellular pathways, is expanding this opportunity. Together, these molecules offer drug developers the chance to modulate the impact of mutations and to alter cell homeostasis. Moreover, because a single therapeutic tRNA can facilitate readthrough of a genetic mutation shared across multiple genes, such medicines afford the opportunity to define patient populations not based on their clinical presentation or mutated gene but rather on the mutation itself. This approach could potentially transform the treatment of patients with rare and ultrarare diseases. In this review, we explore the diverse biology of tRNA and its fragments, examining the past and present challenges to provide a comprehensive understanding of the molecules and their therapeutic potential.
Collapse
|
11
|
Tijaro-Bulla S, Nyandwi SP, Cui H. Physiological and engineered tRNA aminoacylation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1789. [PMID: 37042417 DOI: 10.1002/wrna.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Aminoacyl-tRNA synthetases form the protein family that controls the interpretation of the genetic code, with tRNA aminoacylation being the key chemical step during which an amino acid is assigned to a corresponding sequence of nucleic acids. In consequence, aminoacyl-tRNA synthetases have been studied in their physiological context, in disease states, and as tools for synthetic biology to enable the expansion of the genetic code. Here, we review the fundamentals of aminoacyl-tRNA synthetase biology and classification, with a focus on mammalian cytoplasmic enzymes. We compile evidence that the localization of aminoacyl-tRNA synthetases can be critical in health and disease. In addition, we discuss evidence from synthetic biology which made use of the importance of subcellular localization for efficient manipulation of the protein synthesis machinery. This article is categorized under: RNA Processing Translation > Translation Regulation RNA Processing > tRNA Processing RNA Export and Localization > RNA Localization.
Collapse
Affiliation(s)
| | | | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
12
|
Zhang D, Zhu L, Wang F, Li P, Wang Y, Gao Y. Molecular mechanisms of eukaryotic translation fidelity and their associations with diseases. Int J Biol Macromol 2023; 242:124680. [PMID: 37141965 DOI: 10.1016/j.ijbiomac.2023.124680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/27/2023] [Indexed: 05/06/2023]
Abstract
Converting genetic information into functional proteins is a complex, multi-step process, with each step being tightly regulated to ensure the accuracy of translation, which is critical to cellular health. In recent years, advances in modern biotechnology, especially the development of cryo-electron microscopy and single-molecule techniques, have enabled a clearer understanding of the mechanisms of protein translation fidelity. Although there are many studies on the regulation of protein translation in prokaryotes, and the basic elements of translation are highly conserved in prokaryotes and eukaryotes, there are still great differences in the specific regulatory mechanisms. This review describes how eukaryotic ribosomes and translation factors regulate protein translation and ensure translation accuracy. However, a certain frequency of translation errors does occur in translation, so we describe diseases that arise when the rate of translation errors reaches or exceeds a threshold of cellular tolerance.
Collapse
Affiliation(s)
- Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhu
- College of Basic Medical, Qingdao Binhai University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| | - Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| |
Collapse
|
13
|
Scheepbouwer C, Aparicio-Puerta E, Gomez-Martin C, Verschueren H, van Eijndhoven M, Wedekind LE, Giannoukakos S, Hijmering N, Gasparotto L, van der Galien HT, van Rijn RS, Aronica E, Kibbelaar R, Heine VM, Wesseling P, Noske DP, Vandertop WP, de Jong D, Pegtel DM, Hackenberg M, Wurdinger T, Gerber A, Koppers-Lalic D. ALL-tRNAseq enables robust tRNA profiling in tissue samples. Genes Dev 2023; 37:243-257. [PMID: 36810209 PMCID: PMC10111867 DOI: 10.1101/gad.350233.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/26/2023] [Indexed: 02/23/2023]
Abstract
Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. However, it remains unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research.
Collapse
Affiliation(s)
- Chantal Scheepbouwer
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands;
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | | | - Cristina Gomez-Martin
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Heleen Verschueren
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Monique van Eijndhoven
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Laurine E Wedekind
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Stavros Giannoukakos
- Genetics Department, Faculty of Science, University of Granada, 18071 Granada, Spain
| | - Nathalie Hijmering
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Lisa Gasparotto
- Department of Child and Adolescent Psychiatry, Emma Children's Hospital, Amsterdam UMC, Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Hilde T van der Galien
- Department of Hematology, Medical Center Leeuwarden, 8934 AD Leeuwarden, the Netherlands
- HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands
| | - Roos S van Rijn
- Department of Hematology, Medical Center Leeuwarden, 8934 AD Leeuwarden, the Netherlands
- HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology Amsterdam Neuroscience, Amsterdam UMC location University of Amsterdam, 1105 AZ Amsterdam, the Netherlands
| | - Robby Kibbelaar
- HemoBase Population Registry Consortium, 8934 AD Leeuwarden, the Netherlands
- Department of Pathology, Pathology Friesland, 8917 EN Leeuwarden, the Netherlands
| | - Vivi M Heine
- Department of Child and Adolescent Psychiatry, Emma Children's Hospital, Amsterdam UMC, Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Pieter Wesseling
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Laboratory for Childhood Cancer Pathology, Princess Máxima Center for Pediatric Oncology, University Medical Center Utrecht, 3584 CS Utrecht, the Netherlands
| | - David P Noske
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - W Peter Vandertop
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Daphne de Jong
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - D Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Michael Hackenberg
- Genetics Department, Faculty of Science, University of Granada, 18071 Granada, Spain
| | - Tom Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Danijela Koppers-Lalic
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands;
- Brain Tumor Center Amsterdam, Amsterdam UMC location Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
| |
Collapse
|
14
|
Benisty H, Hernandez-Alias X, Weber M, Anglada-Girotto M, Mantica F, Radusky L, Senger G, Calvet F, Weghorn D, Irimia M, Schaefer MH, Serrano L. Genes enriched in A/T-ending codons are co-regulated and conserved across mammals. Cell Syst 2023; 14:312-323.e3. [PMID: 36889307 DOI: 10.1016/j.cels.2023.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/11/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023]
Abstract
Codon usage influences gene expression distinctly depending on the cell context. Yet, the importance of codon bias in the simultaneous turnover of specific groups of protein-coding genes remains to be investigated. Here, we find that genes enriched in A/T-ending codons are expressed more coordinately in general and across tissues and development than those enriched in G/C-ending codons. tRNA abundance measurements indicate that this coordination is linked to the expression changes of tRNA isoacceptors reading A/T-ending codons. Genes with similar codon composition are more likely to be part of the same protein complex, especially for genes with A/T-ending codons. The codon preferences of genes with A/T-ending codons are conserved among mammals and other vertebrates. We suggest that this orchestration contributes to tissue-specific and ontogenetic-specific expression, which can facilitate, for instance, timely protein complex formation.
Collapse
Affiliation(s)
- Hannah Benisty
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Marc Weber
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Miquel Anglada-Girotto
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Federica Mantica
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Leandro Radusky
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Gökçe Senger
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Donate Weghorn
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, Milan 20139, Italy
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain.
| |
Collapse
|
15
|
Clusan L, Percevault F, Jullion E, Le Goff P, Tiffoche C, Fernandez-Calero T, Métivier R, Marin M, Pakdel F, Michel D, Flouriot G. Codon adaptation by synonymous mutations impacts the functional properties of the estrogen receptor-alpha protein in breast cancer cells. Mol Oncol 2023. [PMID: 36808875 DOI: 10.1002/1878-0261.13399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/30/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Oestrogen receptor-alpha (ERα) positivity is intimately associated with the development of hormone-dependent breast cancers. A major challenge in the treatment of these cancers is to understand and overcome the mechanisms of endocrine resistance. Recently, two distinct translation programmes using specific transfer RNA (tRNA) repertoires and codon usage frequencies were evidenced during cell proliferation and differentiation. Considering the phenotype switch of cancer cells to more proliferating and less-differentiated states, we can speculate that the changes in the tRNA pool and codon usage that likely occur make the ERα coding sequence no longer adapted, impacting translational rate, co-translational folding and the resulting functional properties of the protein. To verify this hypothesis, we generated an ERα synonymous coding sequence whose codon usage was optimized to the frequencies observed in genes expressed specifically in proliferating cells and then investigated the functional properties of the encoded receptor. We demonstrate that such a codon adaptation restores ERα activities to levels observed in differentiated cells, including: (a) an enhanced contribution exerted by transactivation function 1 (AF1) in ERα transcriptional activity; (b) enhanced interactions with nuclear receptor corepressor 1 and 2 [NCoR1 and NCoR2 (also known as SMRT) respectively], promoting repressive capability; and (c) reduced interactions with SRC proto-oncogene, non-receptor tyrosine kinase (Src) and phosphoinositide 3-kinase (PI3K) p85 kinases, inhibiting MAPK and AKT signalling pathway.
Collapse
Affiliation(s)
- Léa Clusan
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Frederic Percevault
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Emmanuelle Jullion
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Pascale Le Goff
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Christophe Tiffoche
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Tamara Fernandez-Calero
- Departamento de Ciencias Exactas Y Naturales, Universidad Catolica del Uruguay, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur Montevideo, Uruguay
| | - Raphaël Métivier
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Monica Marin
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Farzad Pakdel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Denis Michel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Gilles Flouriot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| |
Collapse
|
16
|
Martin S, Allan KC, Pinkard O, Sweet T, Tesar PJ, Coller J. Oligodendrocyte differentiation alters tRNA modifications and codon optimality-mediated mRNA decay. Nat Commun 2022; 13:5003. [PMID: 36008413 PMCID: PMC9411196 DOI: 10.1038/s41467-022-32766-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 08/15/2022] [Indexed: 11/08/2022] Open
Abstract
Oligodendrocytes are specialized cells that confer neuronal myelination in the central nervous system. Leukodystrophies associated with oligodendrocyte deficits and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocyte cell lineage and find that specific tRNAs are hypomodified in oligodendrocytes within or near the anticodon compared to oligodendrocyte progenitor cells (OPCs). This hypomodified state may be the result of differential expression of key modification enzymes during oligodendrocyte differentiation. Moreover, we observe a concomitant relationship between tRNA hypomodification and tRNA decoding potential; observing oligodendrocyte specific alterations in codon optimality-mediated mRNA decay and ribosome transit. Our results reveal that oligodendrocytes naturally maintain a delicate, hypersensitized tRNA/mRNA axis. We suggest this axis is a potential mediator of pathology in leukodystrophies and white matter disease when further insult to tRNA metabolism is introduced.
Collapse
Affiliation(s)
- Sophie Martin
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kevin C Allan
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Otis Pinkard
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Thomas Sweet
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jeff Coller
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| |
Collapse
|
17
|
Lee AK, Aifantis I, Thandapani P. Emerging roles for tRNAs in hematopoiesis and hematological malignancies. Trends Immunol 2022; 43:466-477. [PMID: 35490133 DOI: 10.1016/j.it.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022]
Abstract
tRNAs are central players in decoding the genetic code linking codons in mRNAs with cognate amino acids during protein synthesis. Recent discoveries have placed tRNAs as key regulators of gene expression during hematopoiesis, especially in hematopoietic stem cell (HSC) maintenance and immune development. These functions have been shown to be influenced by dynamic changes in tRNA expression, post-transcriptional base modifications, tRNA-interacting proteins, and tRNA fragmentation; these events underlie the complexity of tRNA-mediated regulatory events in hematopoiesis. In this review, we discuss these recent findings and highlight how deregulation of tRNA biogenesis can contribute to hematological malignancies.
Collapse
Affiliation(s)
- Anna K Lee
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| | - Palaniraja Thandapani
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
18
|
Kovalski JR, Kuzuoglu‐Ozturk D, Ruggero D. Protein synthesis control in cancer: selectivity and therapeutic targeting. EMBO J 2022; 41:e109823. [PMID: 35315941 PMCID: PMC9016353 DOI: 10.15252/embj.2021109823] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Translational control of mRNAs is a point of convergence for many oncogenic signals through which cancer cells tune protein expression in tumorigenesis. Cancer cells rely on translational control to appropriately adapt to limited resources while maintaining cell growth and survival, which creates a selective therapeutic window compared to non-transformed cells. In this review, we first discuss how cancer cells modulate the translational machinery to rapidly and selectively synthesize proteins in response to internal oncogenic demands and external factors in the tumor microenvironment. We highlight the clinical potential of compounds that target different translation factors as anti-cancer therapies. Next, we detail how RNA sequence and structural elements interface with the translational machinery and RNA-binding proteins to coordinate the translation of specific pro-survival and pro-growth programs. Finally, we provide an overview of the current and emerging technologies that can be used to illuminate the mechanisms of selective translational control in cancer cells as well as within the microenvironment.
Collapse
Affiliation(s)
- Joanna R Kovalski
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Duygu Kuzuoglu‐Ozturk
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Davide Ruggero
- Helen Diller Family Comprehensive Cancer CenterUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of UrologyUniversity of California, San FranciscoSan FranciscoCAUSA
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoCAUSA
| |
Collapse
|
19
|
Valine tRNA levels and availability regulate complex I assembly in leukaemia. Nature 2022; 601:428-433. [PMID: 34937946 PMCID: PMC9116157 DOI: 10.1038/s41586-021-04244-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023]
Abstract
Although deregulation of transfer RNA (tRNA) biogenesis promotes the translation of pro-tumorigenic mRNAs in cancers1,2, the mechanisms and consequences of tRNA deregulation in tumorigenesis are poorly understood. Here we use a CRISPR-Cas9 screen to focus on genes that have been implicated in tRNA biogenesis, and identify a mechanism by which altered valine tRNA biogenesis enhances mitochondrial bioenergetics in T cell acute lymphoblastic leukaemia (T-ALL). Expression of valine aminoacyl tRNA synthetase is transcriptionally upregulated by NOTCH1, a key oncogene in T-ALL, underlining a role for oncogenic transcriptional programs in coordinating tRNA supply and demand. Limiting valine bioavailability through restriction of dietary valine intake disrupted this balance in mice, resulting in decreased leukaemic burden and increased survival in vivo. Mechanistically, valine restriction reduced translation rates of mRNAs that encode subunits of mitochondrial complex I, leading to defective assembly of complex I and impaired oxidative phosphorylation. Finally, a genome-wide CRISPR-Cas9 loss-of-function screen in differential valine conditions identified several genes, including SLC7A5 and BCL2, whose genetic ablation or pharmacological inhibition synergized with valine restriction to reduce T-ALL growth. Our findings identify tRNA deregulation as a critical adaptation in the pathogenesis of T-ALL and provide a molecular basis for the use of dietary approaches to target tRNA biogenesis in blood malignancies.
Collapse
|
20
|
Shefer K, Boulos A, Gotea V, Arafat M, Ben Chaim Y, Muharram A, Isaac S, Eden A, Sperling J, Elnitski L, Sperling R. A novel role for nucleolin in splice site selection. RNA Biol 2021; 19:333-352. [PMID: 35220879 PMCID: PMC8890436 DOI: 10.1080/15476286.2021.2020455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 12/10/2021] [Indexed: 01/12/2023] Open
Abstract
Latent 5' splice sites, not normally used, are highly abundant in human introns, but are activated under stress and in cancer, generating thousands of nonsense mRNAs. A previously proposed mechanism to suppress latent splicing was shown to be independent of NMD, with a pivotal role for initiator-tRNA independent of protein translation. To further elucidate this mechanism, we searched for nuclear proteins directly bound to initiator-tRNA. Starting with UV-crosslinking, we identified nucleolin (NCL) interacting directly and specifically with initiator-tRNA in the nucleus, but not in the cytoplasm. Next, we show the association of ini-tRNA and NCL with pre-mRNA. We further show that recovery of suppression of latent splicing by initiator-tRNA complementation is NCL dependent. Finally, upon nucleolin knockdown we show activation of latent splicing in hundreds of coding transcripts having important cellular functions. We thus propose nucleolin, a component of the endogenous spliceosome, through its direct binding to initiator-tRNA and its effect on latent splicing, as the first protein of a nuclear quality control mechanism regulating splice site selection to protect cells from latent splicing that can generate defective mRNAs.
Collapse
Affiliation(s)
- Kinneret Shefer
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Ayub Boulos
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Valer Gotea
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Maram Arafat
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Yair Ben Chaim
- Department of Natural Sciences, The Open University, RaananaIsrael
| | - Aya Muharram
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Sara Isaac
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Amir Eden
- Department of Cell and Developmental Biology, The Hebrew University of Jerusalem, JerusalemIsrael
| | - Joseph Sperling
- Department of Organic Chemistry, The Weizmann Institute of Science, RehovotIsrael
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MDUSA
| | - Ruth Sperling
- Department of Genetics, The Hebrew University of Jerusalem, JerusalemIsrael
| |
Collapse
|
21
|
Gillen SL, Waldron JA, Bushell M. Codon optimality in cancer. Oncogene 2021; 40:6309-6320. [PMID: 34584217 PMCID: PMC8585667 DOI: 10.1038/s41388-021-02022-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 12/14/2022]
Abstract
A key characteristic of cancer cells is their increased proliferative capacity, which requires elevated levels of protein synthesis. The process of protein synthesis involves the translation of codons within the mRNA coding sequence into a string of amino acids to form a polypeptide chain. As most amino acids are encoded by multiple codons, the nucleotide sequence of a coding region can vary dramatically without altering the polypeptide sequence of the encoded protein. Although mutations that do not alter the final amino acid sequence are often thought of as silent/synonymous, these can still have dramatic effects on protein output. Because each codon has a distinct translation elongation rate and can differentially impact mRNA stability, each codon has a different degree of 'optimality' for protein synthesis. Recent data demonstrates that the codon preference of a transcriptome matches the abundance of tRNAs within the cell and that this supply and demand between tRNAs and mRNAs varies between different cell types. The largest observed distinction is between mRNAs encoding proteins associated with proliferation or differentiation. Nevertheless, precisely how codon optimality and tRNA expression levels regulate cell fate decisions and their role in malignancy is not fully understood. This review describes the current mechanistic understanding on codon optimality, its role in malignancy and discusses the potential to target codon optimality therapeutically in the context of cancer.
Collapse
Affiliation(s)
- Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK, G61 1QH.
| |
Collapse
|
22
|
Dynamic changes in tRNA modifications and abundance during T cell activation. Proc Natl Acad Sci U S A 2021; 118:2106556118. [PMID: 34642250 DOI: 10.1073/pnas.2106556118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2021] [Indexed: 12/13/2022] Open
Abstract
The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA (transfer RNA) supply and mRNA (messenger RNA) demand during cancerous proliferation. Yet dynamic changes may also occur during physiologically normal proliferation, and these are less well characterized. We examined the tRNA and mRNA pools of T cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observed a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool relaxed back to the basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T cell activation. These modifications occur in the anticodon loops of two tRNAs that decode "slippery codons," which are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with an HIV gag-pol frameshifting site reporter. These results may explain HIV's specific tropism toward proliferating T cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a layer of translation regulation during T cell proliferation and expose a potential tradeoff between cellular growth and translation fidelity.
Collapse
|
23
|
Sekulovski S, Devant P, Panizza S, Gogakos T, Pitiriciu A, Heitmeier K, Ramsay EP, Barth M, Schmidt C, Tuschl T, Baas F, Weitzer S, Martinez J, Trowitzsch S. Assembly defects of human tRNA splicing endonuclease contribute to impaired pre-tRNA processing in pontocerebellar hypoplasia. Nat Commun 2021; 12:5610. [PMID: 34584079 PMCID: PMC8479045 DOI: 10.1038/s41467-021-25870-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Introns of human transfer RNA precursors (pre-tRNAs) are excised by the tRNA splicing endonuclease TSEN in complex with the RNA kinase CLP1. Mutations in TSEN/CLP1 occur in patients with pontocerebellar hypoplasia (PCH), however, their role in the disease is unclear. Here, we show that intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers independently of CLP1. Splice site recognition involves the mature domain and the anticodon-intron base pair of pre-tRNAs. The 2.1-Å resolution X-ray crystal structure of a TSEN15–34 heterodimer and differential scanning fluorimetry analyses show that PCH mutations cause thermal destabilization. While endonuclease activity in recombinant mutant TSEN is unaltered, we observe assembly defects and reduced pre-tRNA cleavage activity resulting in an imbalanced pre-tRNA pool in PCH patient-derived fibroblasts. Our work defines the molecular principles of intron excision in humans and provides evidence that modulation of TSEN stability may contribute to PCH phenotypes. Mutations within subunits of the tRNA splicing endonuclease complex (TSEN) are associated with pontocerebellar hypoplasia (PCH). Here the authors show that tRNA intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers, and provide evidence that modulation of TSEN stability may contribute to PCH phenotypes.
Collapse
Affiliation(s)
- Samoil Sekulovski
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Pascal Devant
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.,Ph.D. Program in Virology, Harvard Medical School, Boston, MA, USA.,Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Silvia Panizza
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Tasos Gogakos
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Anda Pitiriciu
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | - Katharina Heitmeier
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany
| | | | - Marie Barth
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary research center HALOmem, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Frank Baas
- Department of Clinical Genetics, Leiden University, Leiden, Netherlands
| | - Stefan Weitzer
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Javier Martinez
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/Main, Germany.
| |
Collapse
|
24
|
Aharon-Hefetz N, Frumkin I, Mayshar Y, Dahan O, Pilpel Y, Rak R. Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest. eLife 2020; 9:e58461. [PMID: 33357381 PMCID: PMC7781600 DOI: 10.7554/elife.58461] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Different subsets of the tRNA pool in human cells are expressed in different cellular conditions. The 'proliferation-tRNAs' are induced upon normal and cancerous cell division, while the 'differentiation-tRNAs' are active in non-dividing, differentiated cells. Here we examine the essentiality of the various tRNAs upon cellular growth and arrest. We established a CRISPR-based editing procedure with sgRNAs that each target a tRNA family. We measured tRNA essentiality for cellular growth and found that most proliferation-tRNAs are essential compared to differentiation- tRNAs in rapidly growing cell lines. Yet in more slowly dividing lines, the differentiation-tRNAs were more essential. In addition, we measured the essentiality of each tRNA family upon response to cell cycle arresting signals. Here we detected a more complex behavior with both proliferation-tRNAs and differentiation tRNAs showing various levels of essentiality. These results provide the so-far most comprehensive functional characterization of human tRNAs with intricate roles in various cellular states.
Collapse
Affiliation(s)
- Noa Aharon-Hefetz
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Idan Frumkin
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Yoav Mayshar
- Department of Molecular Cell Biology, Weizmann Institute of ScienceRehovotIsrael
| | - Orna Dahan
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| | - Roni Rak
- Department of Molecular Genetics, Weizmann Institute of ScienceRehovotIsrael
| |
Collapse
|